Mixed carbon substrates: a necessary nuisance or a missed opportunity?

Although fermentation with single carbon sources is the preferred mode of operation in current industrial biotechnology, the use of multiple substrates has been continuously investigated throughout the years. Generally, microbial metabolism varies significantly when cells are presented with mixed carbon substrates compared to a single carbon-energy source, as different nutrients interact in complex ways within the metabolic network. By exploiting these distinct modes of interaction, researchers have identified unique opportunities to optimize metabolism using mixed carbon sources. Here we review situations where process yield and productivity are markedly improved through the judicious introduction of substrate mixtures. Our goal is to illustrate that with proper design of the choice of substrates and the way they are introduced to cultures, metabolic optimization with mixed substrates can be a unique strategy that complements genetic engineering techniques to enhance cell performance beyond what is accomplished in single substrate fermentations.

General information

Publication status: Published
MoE publication type: A2 Review article in a scientific journal
Organisations: Materials Science and Environmental Engineering, Massachusetts Institute of Technology, Department of Chemical Engineering
Contributors: Liu, N., Santala, S., Stephanopoulos, G.
Number of pages: 7
Pages: 15-21
Publication date: 1 Apr 2020
Peer-reviewed: Yes

Publication information

Journal: CURRENT OPINION IN BIOTECHNOLOGY
Volume: 62
ISSN (Print): 0958-1669
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Biomedical Engineering
Source: Scopus
Source ID: 85071874245

Research output: Contribution to journalReview ArticleScientificpeer-review

Co-culture of human induced pluripotent stem cell-derived retinal pigment epithelial cells and endothelial cells on double collagen-coated honeycomb films

In vitro cell culture models representing the physiological and pathological features of the outer retina are urgently needed. Artificial tissue replacements for patients suffering from degenerative retinal diseases are similarly in great demand. Here, we developed a co-culture system based solely on the use of human induced pluripotent stem cell (hiPSC)-derived cells. For the first time, hiPSC-derived retinal pigment epithelium (RPE) and endothelial cells (EC) were cultured on opposite sides of porous polylactide substrates prepared by breath figures (BF), where both surfaces had been collagen-coated by Langmuir–Schaefer (LS) technology. Small modifications of casting conditions during material preparation allowed the production of free-standing materials with distinct porosity, wettability and ion diffusion capacity. Complete pore coverage was achieved by the collagen coating procedure, resulting in a detectable nanoscale topography. Primary retinal endothelial cells (ACBRI181) and umbilical cord vein endothelial cells (hUVEC) were utilised as EC references. Mono-cultures of all ECs were prepared for comparison. All tested materials supported cell attachment and growth. In mono-culture, properties of the materials had a major effect on the growth of all ECs. In co-culture, the presence of hiPSC-RPE affected the primary ECs more significantly than hiPSC-EC. In consistency, hiPSC-RPE were also less affected by hiPSC-EC than by the primary ECs. Finally, our results show that the modulation of the porosity of the materials can promote or prevent EC migration. In short, we showed that the behaviour of the cells is highly dependent on the three main variables of the study: the presence of a second cell type in co-culture, the source of endothelial cells and the biomaterial properties. The combination of BF and LS methodologies is a powerful strategy to develop thin but stable materials enabling cell growth and modulation of cell-cell contact. Statement of significance: Artificial blood-retinal barriers (BRB), mimicking the interface at the back of the eye, are urgently needed as physiological and disease models, and for tissue transplantation targeting patients suffering from degenerative retinal diseases. Here, we developed a new co-culture model based on thin, biodegradable porous films, coated on both sides with collagen, one of the main components of the natural BRB, and cultivated endothelial and retinal pigment epithelial cells on opposite sides of the films, forming a three-layer structure. Importantly, our hiPSC-EC and hiPSC-RPE co-culture model is the first to exclusively use human induced pluripotent stem cells as cell source, which have been widely regarded as an practical candidate for therapeutic applications in regenerative medicine.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Materials Science and Environmental Engineering, BioMediTech, Research group: Biomaterials and Tissue Engineering Group, Tampere University, Tampere University Hospital
Contributors: Calejo, M. T., Saari, J., Vuorenpää, H., Vuorimaa-Laukkanen, E., Kallio, P., Aalto-Setälä, K., Miettinen, S., Skottman, H., Kellomäki, M., Juuti-Uusitalo, K.
Number of pages: 17
Pages: 327-343
Publication date: 2020
Peer-reviewed: Yes
Early online date: 2019

Publication information

Journal: Acta Biomaterialia
Volume: 101
ISSN (Print): 1742-7061
Original language: English
ASJC Scopus subject areas: Biotechnology, Biomaterials, Biochemistry, Biomedical Engineering, Molecular Biology
Keywords: Breath figures, Co-culture, hiPSC-endothelial cells, hiPSC-RPE, Polylactide
Electronic versions: 
Source: Scopus
Source ID: 85075520020

Research output: Contribution to journalArticleScientificpeer-review

Transcription closed and open complex formation coordinate expression of genes with a shared promoter region

Many genes are spaced closely, allowing coordination without explicit control through shared regulatory elements and molecular interactions. We study the dynamics of a stochastic model of a gene-pair in a head-to-head configuration, sharing promoter elements, which accounts for the rate-limiting steps in transcription initiation. We find that only in specific regions of the parameter space of the rate-limiting steps is orderly coexpression exhibited, suggesting that successful cooperation between closely spaced genes requires the coevolution of compatible rate-limiting step configuration. The model predictions are validated using in vivo single-cell, single-RNA measurements of the dynamics of pairs of genes sharing promoter elements. Our results suggest that, in E. coli, the kinetics of the rate-limiting steps in active transcription can play a central role in shaping the dynamics of gene-pairs sharing promoter elements.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: BioMediTech, Research group: Laboratory of Biosystem Dynamics-LBD
Contributors: Häkkinen, A., Oliveira, S. M., Neeli-Venkata, R., Ribeiro, A. S.
Number of pages: 11
Publication date: 1 Dec 2019
Peer-reviewed: Yes

Publication information

Journal: Journal of the Royal Society Interface
Volume: 16
Issue number: 161
Article number: 20190507
ISSN (Print): 1742-5689
Original language: English
ASJC Scopus subject areas: Biotechnology, Biophysics, Bioengineering, Biomaterials, Biochemistry, Biomedical Engineering
Keywords: Bidirectional promoter, Gene expression noise, Transcription
Source: Scopus
Source ID: 85076351347

Research output: Contribution to journalArticleScientificpeer-review

Effects of elevated pressures on the activity of acidophilic bioleaching microorganisms

This study reports effects of elevated pressures on the oxidation of a soluble ferrous iron and low-grade sulphidic ore as little is known about biological iron and sulphur oxidation under these conditions. Pressure effects were studied in a pressurised batch-operated stirred tank reactor using acidophilic enrichment cultures. The oxidation of soluble Fe2+ by enrichment culture dominated by Leptospirillum ferriphilum, Sulfobacillus sp. and Ferrimicrobium acidiphilum increased with increasing pressure induced by technical air to up to +3 bar (0.63 bar PO2) and was inhibited at +7 bar (1.47 bar PO2). Elevated pressures induced by nitrogen (low oxygen partial pressure) were tolerated up to +40 bar. Another enrichment culture dominated by Acidithiobacillus ferrivorans, Sulfobacillus sp. and F. acidiphilum partially oxidised the ore at pressures up to +20 bar induced with air (4.2 bar PO2). This is the first study reporting activity of acidophiles under pressurised conditions in a stirred tank reactor.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Materials Science and Environmental Engineering
Contributors: Hajdu-Rahkama, R., Ahoranta, S., Lakaniemi, A., Puhakka, J. A.
Publication date: 15 Oct 2019
Peer-reviewed: Yes

Publication information

Journal: Biochemical Engineering Journal
Volume: 150
Article number: 107286
ISSN (Print): 1369-703X
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Environmental Engineering, Biomedical Engineering
Keywords: Acidophiles, Biooxidation, Iron oxidation, Pressure tolerance, Pressurised stirred tank reactor
Source: Scopus
Source ID: 85070494949

Research output: Contribution to journalArticleScientificpeer-review

An efficient auxin-inducible degron system with low basal degradation in human cells

Auxin-inducible degron technology allows rapid and controlled protein depletion. However, basal degradation without auxin and inefficient auxin-inducible depletion have limited its utility. We have identified a potent auxin-inducible degron system composed of auxin receptor F-box protein AtAFB2 and short degron miniIAA7. The system showed minimal basal degradation and enabled rapid auxin-inducible depletion of endogenous human transmembrane, cytoplasmic and nuclear proteins in 1 h with robust functional phenotypes.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Physics, University of Helsinki Faculty of Medicine, Minerva Foundation Institute for Medical Research Helsinki, University of Helsinki, Computational Physics Laboratory
Contributors: Li, S., Prasanna, X., Salo, V. T., Vattulainen, I., Ikonen, E.
Number of pages: 4
Pages: 866-869
Publication date: 1 Sep 2019
Peer-reviewed: Yes

Publication information

Journal: Nature Methods
Volume: 16
Issue number: 9
ISSN (Print): 1548-7091
Original language: English
ASJC Scopus subject areas: Biotechnology, Biochemistry, Molecular Biology, Cell Biology
Source: Scopus
Source ID: 85071234380

Research output: Contribution to journalArticleScientificpeer-review

Pneumatic unidirectional cell stretching device for mechanobiological studies of cardiomyocytes

In this paper, we present a transparent mechanical stimulation device capable of uniaxial stimulation, which is compatible with standard bioanalytical methods used in cellular mechanobiology. We validate the functionality of the uniaxial stimulation system using human-induced pluripotent stem cells-derived cardiomyocytes (hiPSC-CMs). The pneumatically controlled device is fabricated from polydimethylsiloxane (PDMS) and provides uniaxial strain and superior optical performance compatible with standard inverted microscopy techniques used for bioanalytics (e.g., fluorescence microscopy and calcium imaging). Therefore, it allows for a continuous investigation of the cell state during stretching experiments. The paper introduces design and fabrication of the device, characterizes the mechanical performance of the device and demonstrates the compatibility with standard bioanalytical analysis tools. Imaging modalities, such as high-resolution live cell phase contrast imaging and video recordings, fluorescent imaging and calcium imaging are possible to perform in the device. Utilizing the different imaging modalities and proposed stretching device, we demonstrate the capability of the device for extensive further studies of hiPSC-CMs. We also demonstrate that sarcomere structures of hiPSC-CMs organize and orient perpendicular to uniaxial strain axis and thus express more maturated nature of cardiomyocytes.

General information

Publication status: E-pub ahead of print
MoE publication type: A1 Journal article-refereed
Organisations: Research group: Micro and Nanosystems Research Group, BioMediTech, Risø Campus, Tampere University of Applied Sciences, Eindhoven University of Technology, Tampere University Hospital
Contributors: Kreutzer, J., Viehrig, M., Pölönen, R. P., Zhao, F., Ojala, M., Aalto-Setälä, K., Kallio, P.
Publication date: 23 Aug 2019
Peer-reviewed: Yes

Publication information

Journal: BIOMECHANICS AND MODELING IN MECHANOBIOLOGY
ISSN (Print): 1617-7959
Original language: English
ASJC Scopus subject areas: Biotechnology, Modelling and Simulation, Mechanical Engineering
Keywords: Cardiomyocytes, hiPSC, Mechanical stimulation, PDMS

Bibliographical note

EXT="Zhao, Feihu"

Source: Scopus
Source ID: 85070939275

Research output: Contribution to journalArticleScientificpeer-review

Sodium channels enable fast electrical signaling and regulate phagocytosis in the retinal pigment epithelium

Background: Voltage-gated sodium (Nav) channels have traditionally been considered a trademark of excitable cells. However, recent studies have shown the presence of Nav channels in several non-excitable cells, such as astrocytes and macrophages, demonstrating that the roles of these channels are more diverse than was previously thought. Despite the earlier discoveries, the presence of Nav channel-mediated currents in the cells of retinal pigment epithelium (RPE) has been dismissed as a cell culture artifact. We challenge this notion by investigating the presence and possible role of Nav channels in RPE both ex vivo and in vitro. Results: Our work demonstrates that several subtypes of Nav channels are found in human embryonic stem cell (hESC)-derived and mouse RPE, most prominently subtypes Nav1.4, Nav1.6, and Nav1.8. Whole cell patch clamp recordings from the hESC-derived RPE monolayers showed that the current was inhibited by TTX and QX-314 and was sensitive to the selective blockers of the main Nav subtypes. Importantly, we show that the Nav channels are involved in photoreceptor outer segment phagocytosis since blocking their activity significantly reduces the efficiency of particle internalization. Consistent with this role, our electron microscopy results and immunocytochemical analysis show that Nav1.4 and Nav1.8 accumulate on phagosomes and that pharmacological inhibition of Nav channels as well as silencing the expression of Nav1.4 with shRNA impairs the phagocytosis process. Conclusions: Taken together, our study shows that Nav channels are present in RPE, giving this tissue the capacity of fast electrical signaling. The channels are critical for the physiology of RPE with an important role in photoreceptor outer segment phagocytosis.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: BioMediTech, Tampere University, University of Jyvaskyla, Tampere University Hospital
Contributors: Johansson, J. K., Karema-Jokinen, V. I., Hakanen, S., Jylhä, A., Uusitalo, H., Vihinen-Ranta, M., Skottman, H., Ihalainen, T. O., Nymark, S.
Publication date: 15 Aug 2019
Peer-reviewed: Yes

Publication information

Journal: BMC BIOLOGY
Volume: 17
Issue number: 1
Article number: 63
ISSN (Print): 1741-7007
Original language: English
ASJC Scopus subject areas: Biotechnology, Structural Biology, Ecology, Evolution, Behavior and Systematics, Physiology, Biochemistry, Genetics and Molecular Biology(all), Agricultural and Biological Sciences(all), Plant Science, Developmental Biology, Cell Biology
Keywords: Ion channels, Na, Patch clamp, Phagocytosis, Photoreceptors, Retina, RPE
Electronic versions: 
Source: Scopus
Source ID: 85071165212

Research output: Contribution to journalArticleScientificpeer-review

Alkane and wax ester production from lignin-related aromatic compounds

Lignin has potential as a sustainable feedstock for microbial production of industrially relevant molecules. However, the required lignin depolymerization yields a heterogenic mixture of aromatic monomers that are challenging substrates for the microorganisms commonly used in the industry. Here, we investigated the properties of lignin-related aromatic compounds (LRAs), namely coumarate, ferulate, and caffeate, in the synthesis of biomass and products in an LRA-utilizing bacterial host Acinetobacter baylyi ADP1. The biosynthesis products, wax esters, and alkanes are relevant compounds for the chemical and fuel industries. Here, wax esters were produced by a native pathway of ADP1, whereas alkanes were produced by a synthetic pathway introduced to the host. Using individual LRAs as substrates, the growth and product formation were monitored with internal biosensors and off-line analytics. Of the tested LRAs, coumarate was the most propitious in terms of product synthesis. Wax esters were produced from coumarate with yield and titer of 37 mg/gcoumarate and 202 mg/L, whereas alkanes were produced with a yield of 62.3 µg /gcoumarate and titer of 152 µg/L. This study demonstrates the microbial preference for certain LRAs and highlights the potential of A. baylyi ADP1 as a host for LRA upgrading to value-added products.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Materials Science and Environmental Engineering, Research group: Bio- and Circular Economy
Contributors: Salmela, M., Lehtinen, T., Efimova, E., Santala, S., Santala, V.
Number of pages: 12
Pages: 1934-1945
Publication date: 1 Aug 2019
Peer-reviewed: Yes

Publication information

Journal: Biotechnology and Bioengineering
Volume: 116
Issue number: 8
ISSN (Print): 0006-3592
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Applied Microbiology and Biotechnology
Keywords: Acinetobacter baylyi ADP1, alkane, lignin, wax ester
Source: Scopus
Source ID: 85070728183

Research output: Contribution to journalArticleScientificpeer-review

An architectural understanding of natural sway frequencies in trees

The relationship between form and function in trees is the subject of a longstanding debate in forest ecology and provides the basis for theories concerning forest ecosystem structure and metabolism. Trees interact with the wind in a dynamic manner and exhibit natural sway frequencies and damping processes that are important in understanding wind damage. Tree-wind dynamics are related to tree architecture, but this relationship is not well understood. We present a comprehensive view of natural sway frequencies in trees by compiling a dataset of field measurement spanning conifers and broadleaves, tropical and temperate forests. The field data show that a cantilever beam approximation adequately predicts the fundamental frequency of conifers, but not that of broadleaf trees. We also use structurally detailed tree dynamics simulations to test fundamental assumptions underpinning models of natural frequencies in trees. We model the dynamic properties of greater than 1000 trees using a finite-element approach based on accurate three-dimensional model trees derived from terrestrial laser scanning data. We show that (1) residual variation, the variation not explained by the cantilever beam approximation, in fundamental frequencies of broadleaf trees is driven by their architecture; (2) slender trees behave like a simple pendulum, with a single natural frequency dominating their motion, which makes them vulnerable to wind damage and (3) the presence of leaves decreases both the fundamental frequency and the damping ratio. These findings demonstrate the value of new three-dimensional measurements for understanding wind impacts on trees and suggest new directions for improving our understanding of tree dynamics from conifer plantations to natural forests.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computing Sciences, University of Oxford, SCION, University of Connecticut, Delft University of Technology, Wageningen University and Research Centre, University of Massachusetts Amherst, National Parks Board, University of Melbourne, Oregon State University, Universiteit Gent, National Physical Laboratory, University College London, NERC National Centre for Earth Observation (NCEO), 16 Center for International Forestry Research (CIFOR), Swedish University of Agricultural Sciences, INRA
Contributors: Jackson, T., Shenkin, A., Moore, J., Bunce, A., van Emmerik, T., Kane, B., Burcham, D., James, K., Selker, J., Calders, K., Origo, N., Disney, M., Burt, A., Wilkes, P., Raumonen, P., Gonzalez de Tanago Menaca, J., Lau, A., Herold, M., Goodman, R. C., Fourcaud, T., Malhi, Y.
Number of pages: 1
Publication date: 28 Jun 2019
Peer-reviewed: Yes

Publication information

Journal: Journal of the Royal Society. Interface
Volume: 16
Issue number: 155
ISSN (Print): 1742-5689
Original language: English
ASJC Scopus subject areas: Biotechnology, Biophysics, Bioengineering, Biomaterials, Biochemistry, Biomedical Engineering
Keywords: finite-element analysis, fundamental frequency, natural frequencies, terrestrial laser scanning, tree architecture, wind damage
Source: Scopus
Source ID: 85067464325

Research output: Contribution to journalArticleScientificpeer-review

The Role of Temperature and Lipid Charge on Intake/Uptake of Cationic Gold Nanoparticles into Lipid Bilayers

Understanding the molecular mechanisms governing nanoparticle–membrane interactions is of prime importance for drug delivery and biomedical applications. Neutron reflectometry (NR) experiments are combined with atomistic and coarse-grained molecular dynamics (MD) simulations to study the interaction between cationic gold nanoparticles (AuNPs) and model lipid membranes composed of a mixture of zwitterionic di-stearoyl-phosphatidylcholine (DSPC) and anionic di-stearoyl-phosphatidylglycerol (DSPG). MD simulations show that the interaction between AuNPs and a pure DSPC lipid bilayer is modulated by a free energy barrier. This can be overcome by increasing temperature, which promotes an irreversible AuNP incorporation into the lipid bilayer. NR experiments confirm the encapsulation of the AuNPs within the lipid bilayer at temperatures around 55 °C. In contrast, the AuNP adsorption is weak and impaired by heating for a DSPC–DSPG (3:1) lipid bilayer. These results demonstrate that both the lipid charge and the temperature play pivotal roles in AuNP–membrane interactions. Furthermore, NR experiments indicate that the (negative) DSPG lipids are associated with lipid extraction upon AuNP adsorption, which is confirmed by coarse-grained MD simulations as a lipid-crawling effect driving further AuNP aggregation. Overall, the obtained detailed molecular view of the interaction mechanisms sheds light on AuNP incorporation and membrane destabilization.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Research group: Biological Physics and Soft Matter, Research area: Computational Physics, Physics, Computational Physics Laboratory, University of Helsinki, Politecnico di Milano, Institut Laue-Langevin, Max Planck Institute of Colloids and Interfaces, MEMPHYS−Center for Biomembrane Physics, Norwegian Univ. of Sci. and Technol., G2Elab/Institut Néel
Contributors: Lolicato, F., Joly, L., Martinez-Seara, H., Fragneto, G., Scoppola, E., Baldelli Bombelli, F., Vattulainen, I., Akola, J., Maccarini, M.
Publication date: 7 Jun 2019
Peer-reviewed: Yes

Publication information

Journal: Small
Volume: 15
Issue number: 23
Article number: 1805046
ISSN (Print): 1613-6810
Original language: English
ASJC Scopus subject areas: Biotechnology, Biomaterials, Chemistry(all), Materials Science(all)
Keywords: gold nanoparticles, lipid membranes, molecular dynamics simulations, nanotoxicity, neutron reflectometry
Electronic versions: 

Bibliographical note

EXT="Martinez-Seara, Hector"

Source: Scopus
Source ID: 85064688737

Research output: Contribution to journalArticleScientificpeer-review

Connection of Collimation, Asymmetric Beaming, and Independent Transmission-Reflection Processes in Concentric-Groove Gratings Supporting Spoof Surface Plasmons

Transmission through subwavelength apertures enables separation of the incidence half-space and the exit half-space, which leads to that the spatial distribution of the field in the latter is not affected by the distribution in the former. The distribution in the exit half-space is mainly determined by the properties of surface plasmons (SPs) at the exit-side interface. In this paper, for the microwave structures with one-side concentric corrugations around a single annular hole, we demonstrate the possible connections between asymmetric transmission in the beaming regime and collimation of the waves incident at different angles, which can be considered as two sides of the same phenomenon occurring due to the common effect of such a separation and the radiation shaping effect being possible due to the spoof SPs at the corrugated exit interface. Collimation manifests itself in that the waves incident at different angles from a wide range contribute to the single outgoing beam so that a far-zone observer cannot distinguish between the contributions of different angles of arrival. Asymmetry in transmission manifests itself in that the spatial shaping of radiation (beaming) in the exit half-space appears only for one of the two opposite incidence directions. Moreover, even in the structures with the same corrugations on both sides, i.e., without asymmetric transmission, spatial separation of two wave processes, e.g., two symmetric or asymmetric collimation processes, can be obtained for a wide range of nonzero angles of incidence.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Photonics, Bilkent University, KU Leuven, Adam Mickiewicz University
Contributors: Habib, M., Serebryannikov, A. E., Caglayan, H., Vandenbosch, G. A., Ozbay, E.
Number of pages: 9
Pages: 721-729
Publication date: Jun 2019
Peer-reviewed: Yes
Early online date: 2018

Publication information

Journal: Plasmonics
Volume: 14
Issue number: 3
ISSN (Print): 1557-1955
Original language: English
ASJC Scopus subject areas: Biotechnology, Biophysics, Biochemistry
Keywords: Asymmetric transmission, Beaming, Collimation, Spoof plasmon
Source: Scopus
Source ID: 85053476979

Research output: Contribution to journalArticleScientificpeer-review

Effects of percutaneous transluminal angioplasty of superficial femoral artery on photoplethysmographic pulse transit times

We analyze the changes in upper and lower limb pulse transit times (PTT) caused by peripheral artery disease (PAD) and its treatment with percutaneous transluminal angioplasty (PTA) of the superficial femoral artery. PTTs were extracted from the photoplethysmograms (PPG) recorded from an index finger and 2nd toes. PTTs were defined between the R-peaks of the ECG and different reference points of the (PPG): foot and peak points, maxima of 1st and 2nd derivative, and by means of intersecting tangents method. Also the PTTs between the toe and finger pulses were analyzed. Our sample consists of 24 subjects examined before and after the PTA and in 1-month follow-up visit. Also 28 older than 65 years controls having normal ankle-to-brachial pressure index (ABI) and no history in cardiovascular diseases as well as 21 younger subjects were examined. The differences between the groups and pre- and post-treatment phases were analyzed by means of non-parametric statistical tests. The changes in the PTTs of upper limb and non-treated lower limb were negligible. The agreement with the reference values, ABI and toe pressures, was studied by kappa-analysis, resulting in kappa-values of 0.33<formula><tex>$\times$</tex></formula>0.91. Differences in PTTs were found between pre-treatment state of the treated limb, post-treatment state and the follow-up visit, as well as between the pre-treatment state and controls. If patients' age and systolic blood pressure were taken into consideration, the method of lower limb PTT calculation from the peak point turns out feasible in finding the markers of PAD and monitoring post- treatment vascular remodellation.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Faculty of Biomedical Sciences and Engineering, Research group: Sensor Technology and Biomeasurements (STB), Division of Vascular Surgery, Division of Interventional Radiology, Oulu University Hospital, Tampere University Hospital
Contributors: Peltokangas, M., Suominen, V., Vakhitov, D., Korhonen, J., Verho, J., Mattila, V. M., Romsi, P., Lekkala, J., Vehkaoja, A., Oksala, N.
Pages: 1058-1065
Publication date: May 2019
Peer-reviewed: Yes
Early online date: 27 Jun 2018

Publication information

Journal: IEEE Journal of Biomedical and Health Informatics
Volume: 23
Issue number: 3
ISSN (Print): 2168-2194
Original language: English
ASJC Scopus subject areas: Biotechnology, Computer Science Applications, Electrical and Electronic Engineering, Health Information Management
Keywords: Atherosclerosis, Peripheral artery disease, Photoplethysmography, Pulse wave measurements
Additional files: 
Source: Scopus
Source ID: 85049142393

Research output: Contribution to journalArticleScientificpeer-review

Synthetic metabolic pathway for the production of 1-alkenes from lignin-derived molecules

Background: Integration of synthetic metabolic pathways to catabolically diverse chassis provides new opportunities for sustainable production. One attractive scenario is the use of abundant waste material to produce a readily collectable product, which can reduce the production costs. Towards that end, we established a cellular platform for the production of semivolatile medium-chain α-olefins from lignin-derived molecules: we constructed 1-undecene synthesis pathway in Acinetobacter baylyi ADP1 using ferulate, a lignin-derived model compound, as the sole carbon source for both cell growth and product synthesis. Results: In order to overcome the toxicity of ferulate, we first applied adaptive laboratory evolution to A. baylyi ADP1, resulting in a highly ferulate-tolerant strain. The adapted strain exhibited robust growth in 100 mM ferulate while the growth of the wild type strain was completely inhibited. Next, we expressed two heterologous enzymes in the wild type strain to confer 1-undecene production from glucose: a fatty acid decarboxylase UndA from Pseudomonas putida, and a thioesterase 'TesA from Escherichia coli. Finally, we constructed the 1-undecene synthesis pathway in the ferulate-tolerant strain. The engineered cells were able to produce biomass and 1-undecene solely from ferulate, and excreted the product directly to the culture headspace. Conclusions: In this study, we employed a bacterium Acinetobacter baylyi ADP1 to integrate a natural aromatics degrading pathway to a synthetic production route, allowing the upgradation of lignin derived molecules to value-added products. We developed a highly ferulate-tolerant strain and established the biosynthesis of an industrially relevant chemical, 1-undecene, solely from the lignin-derived model compound. This study reports the production of alkenes from lignin derived molecules for the first time and demonstrates the potential of lignin as a sustainable resource in the bio-based synthesis of valuable products.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Materials Science and Environmental Engineering, Research group: Bio- and Circular Economy
Contributors: Luo, J., Lehtinen, T., Efimova, E., Santala, V., Santala, S.
Number of pages: 13
Publication date: 11 Mar 2019
Peer-reviewed: Yes

Publication information

Journal: Microbial Cell Factories
Volume: 18
Issue number: 1
Article number: 48
ISSN (Print): 1475-2859
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Applied Microbiology and Biotechnology
Keywords: 1-Alkenes, Acinetobacter baylyi, Adaptive laboratory evolution, Ferulate, Lignin
Source: Scopus
Source ID: 85062867820

Research output: Contribution to journalArticleScientificpeer-review

Mechanical impact stimulation platform tailored for high-resolution light microscopy

High frequency (HF) mechanical vibration has been used in vitro to study the cellular response to mechanical stimulation and induce stem cell differentiation. However, detailed understanding of the effect of the mechanical cues on cellular physiology is lacking. To meet this limitation, we have designed a system, which enables monitoring of living cells by high-resolution light microscopy during mechanical stimulation by HF vibration or mechanical impacts. The system consists of a commercial speaker, and a 3D printed sample vehicle and frame. The speaker moves the sample in the horizontal plane, allowing simultaneous microscopy. The HF vibration (30–200 Hz) performances of two vehicles made of polymer and aluminum were characterized with accelerometer. The mechanical impacts were characterized by measuring the acceleration of the aluminum vehicle and by time lapse imaging. The lighter polymer vehicle produced higher HF vibration magnitudes at 30–50 Hz frequencies than the aluminum vehicle. However, the aluminum vehicle performed better at higher frequencies (60–70 Hz, 90–100 Hz, 150 Hz). Compatibility of the system in live cell experiments was investigated with epithelial cells (MDCKII, expressing Emerald-Occludin) and HF (0.56 Gpeak, 30 Hz and 60 Hz) vibration. Our findings indicated that our system is compatible with high-resolution live cell microscopy. Furthermore, the epithelial cells were remarkable stable under mechanical vibration stimulation. To conclude, we have designed an inexpensive tool for the studies of cellular biophysics, which combines versatile in vivo like mechanical stimuli with live cell imaging, showing a great potential for several cellular applications.

General information

Publication status: E-pub ahead of print
MoE publication type: A1 Journal article-refereed
Organisations: BioMediTech, Research group: Computational Biophysics and Imaging Group
Contributors: Halonen, H. T., Hyttinen, J. A., Ihalainen, T. O.
Publication date: 2019
Peer-reviewed: Yes

Publication information

Journal: HEALTH AND TECHNOLOGY
ISSN (Print): 2190-7188
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Applied Microbiology and Biotechnology, Biomedical Engineering
Keywords: HF vibration, In vitro mechanical stimulation, Live cell imaging, Mechanical impacts, Mechanobiology, Real-time imaging
Source: Scopus
Source ID: 85074696220

Research output: Contribution to journalArticleScientificpeer-review

Optical wireless cochlear implants

In the present contribution, we introduce a wireless optical communication-based system architecture which is shown to significantly improve the reliability and the spectral and power efficiency of the transcutaneous link in cochlear implants (CIs). We refer to the proposed system as optical wireless cochlear implant (OWCI). In order to provide a quantified understanding of its design parameters, we establish a theoretical framework that takes into account the channel particularities, the integration area of the internal unit, the transceivers misalignment, and the characteristics of the optical units. To this end, we derive explicit expressions for the corresponding average signal-to-noise-ratio, outage probability, ergodic spectral efficiency and capacity of the transcutaneous optical link (TOL). These expressions are subsequently used to assess the dependence of the TOL’s communication quality on the transceivers design parameters and the corresponding channels characteristics. The offered analytic results are corroborated with respective results from Monte Carlo simulations. Our findings reveal that OWCI is a particularly promising architecture that drastically increases the reliability and effectiveness of the CI TOL, whilst it requires considerably lower transmit power compared to the corresponding widely-used radio frequency (RF) solution.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Research group: Wireless Communications and Positioning, Electrical Engineering, Aristotle University of Thessaloniki, Khalifa University, University of Piraeus, Department of Electrical and Computer Engineering
Contributors: Trevlakis, S. E., Boulogeorgos, A. A. A., Sofotasios, P. C., Muhaidat, S., Karagiannidis, G. K.
Number of pages: 24
Pages: 707-730
Publication date: 2019
Peer-reviewed: Yes

Publication information

Journal: Biomedical Optics Express
Volume: 10
Issue number: 2
ISSN (Print): 2156-7085
Original language: English
ASJC Scopus subject areas: Biotechnology, Atomic and Molecular Physics, and Optics
Source: Scopus
Source ID: 85061526751

Research output: Contribution to journalArticleScientificpeer-review

O2-requiring molecular reporters of gene expression for anaerobic microorganisms

Many genetic reporter systems require molecular oxygen; therefore, the use of reporter genes to study molecular mechanisms in anaerobic microorganisms has been hampered by the lack of convenient reporting systems. We describe reporter gene whole cell-based biosensor systems based on luciferase genes and the associated oxygen-requiring enzymes. By using two different oxygen-dependent reporters, insect and bacterial luciferases, and two bacterial hosts, Gram (+) Bifidobacterium longum and Gram (-) Escherichia coli, we show that the enzymes can be used in gene expression studies of anaerobic bacteria. E. coli, a facultative anaerobe, was grown both in aerobic and anaerobic conditions with an arabinose-inducible expression system. We show that a short treatment time of few minutes in ambient atmosphere is sufficient to detect light emission from living cells that is directly proportional to the number of cells and to the inducer concentration. The induction levels were the same in both the aerobically and anaerobically cultured cells. Similar results were obtained in the case of B. longum cultured in anaerobic conditions.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chemistry and Bioengineering, Research group: Bio- and Circular Economy, Università degli Studi di Milano
Contributors: Guglielmetti, S., Santala, V., Mangayil, R., Ciranna, A., Karp, M. T.
Number of pages: 6
Pages: 1-6
Publication date: 2019
Peer-reviewed: Yes
Early online date: 20 Sep 2018

Publication information

Journal: Biosensors and Bioelectronics
Volume: 123
ISSN (Print): 0956-5663
Original language: English
ASJC Scopus subject areas: Biotechnology, Biophysics, Biomedical Engineering, Electrochemistry
Keywords: Bioluminescence, Gram (+), Gram (-), Luciferase, Arabinose induction
Electronic versions: 
Source: Scopus
Source ID: 85053858794

Research output: Contribution to journalArticleScientificpeer-review

Quality and Capacity Analysis of Molecular Communications in Bacterial Synthetic Logic Circuits

Synthetic logic circuits have been proposed as potential solutions for theranostics of biotechnological problems. One proposed model is the engineering of bacteria cells to create logic gates, and the communication between the bacteria populations will enable the circuit operation. In this paper, we analyse the quality of bacteria-based synthetic logic circuit through molecular communications that represent communication along a bus between three gates. In the bacteria-based synthetic logic circuit, the system receives environmental signals as molecular inputs and will process this information through a cascade of synthetic logic gates and free diffusion channels. We analyse the performance of this circuit by evaluating its quality and its relationship to the channel capacity of the molecular communications links that interconnect the bacteria populations. Our results show the effect of the molecular environmental delay and molecular amplitude differences over both the channel capacity and circuit quality. Furthermore, based on these metrics we also obtain an optimum region for the circuit operation resulting in an accuracy of 80&#x0025; for specific conditions. These results show that the performance of synthetic biology circuits can be evaluated through molecular communications, and lays the groundwork for combined systems that can contribute to future biomedical and biotechnology applications.

General information

Publication status: Accepted/In press
MoE publication type: A1 Journal article-refereed
Organisations: Electrical Engineering, Waterford Institute of Technology
Contributors: Martins, D. P., Barros, M. T., Balasubramaniam, S.
Publication date: 2019
Peer-reviewed: Yes

Publication information

Journal: IEEE Transactions on Nanobioscience
ISSN (Print): 1536-1241
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Medicine (miscellaneous), Biomedical Engineering, Pharmaceutical Science, Computer Science Applications, Electrical and Electronic Engineering
Keywords: Engineered bacteria, Logic circuits, Logic gates, Microorganisms, Molecular communication (telecommunication), Molecular communications, Sensors, Sociology, Statistics, Synthetic logic circuits
Source: Scopus
Source ID: 85070392121

Research output: Contribution to journalArticleScientificpeer-review

Robocasting of Bioactive SiO2-P2O5-CaO-MgO-Na2O-K2O Glass Scaffolds

Bioactive silicate glass scaffolds were fabricated by a robocasting process in which all the movements of the printing head were programmed by compiling a script (text file). A printable ink made of glass powder and Pluronic F-127, acting as a binder, was extruded to obtain macroporous scaffolds with a grid-like three-dimensional structure. The scaffold architecture was investigated by scanning electron microscopy and microtomographic analysis, which allowed quantifying the microstructural parameters (pore size 150-180 μm and strut diameter 300 μm). In vitro tests in simulated body fluid (SBF) confirmed the apatite-forming ability (i.e., bioactivity) of the scaffolds. The compressive strength (around 10 MPa for as-produced scaffolds) progressively decreased during immersion in SBF (3.3 MPa after 4 weeks) but remains acceptable for bone repair applications. Taken together, these results (adequate porosity and mechanical strength as well as bioactivity) support the potential suitability of the prepared scaffolds for bone substitution.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: BioMediTech, Politecnico di Torino, Innovation Center Iceland (ICI)
Contributors: Baino, F., Barberi, J., Fiume, E., Orlygsson, G., Massera, J., Verné, E.
Publication date: 2019
Peer-reviewed: Yes

Publication information

Journal: Journal of Healthcare Engineering
Volume: 2019
Article number: 5153136
ISSN (Print): 2040-2295
Original language: English
ASJC Scopus subject areas: Biotechnology, Surgery, Biomedical Engineering, Health Informatics
Electronic versions: 
Source: Scopus
Source ID: 85065603850

Research output: Contribution to journalArticleScientificpeer-review

Dynamic decoupling of biomass and wax ester biosynthesis in Acinetobacter baylyi by an autonomously regulated switch

For improving the microbial production of fuels and chemicals, gene knock-outs and overexpression are routinely applied to intensify the carbon flow from substrate to product. However, their possibilities in dynamic control of the flux between the biomass and product synthesis are limited, whereas dynamic metabolic switches can be used for optimizing the distribution of carbon and resources. The production of single cell oils is especially challenging, as the synthesis is strictly regulated, competes directly with biomass, and requires defined conditions, such as nitrogen limitation. Here, we engineered a metabolic switch for redirecting carbon flow from biomass to wax ester production in Acinetobacter baylyi ADP1 using acetate as a carbon source. Isocitrate lyase, an essential enzyme for growth on acetate, was expressed under an arabinose inducible promoter. The autonomous downregulation of the expression is based on the gradual oxidation of the arabinose inducer by a glucose dehydrogenase gcd. The depletion of the inducer, occurring simultaneously to acetate consumption, switches the cells from a biomass mode to a lipid synthesis mode, enabling the efficient channelling of carbon to wax esters in a simple batch culture. In the engineered strain, the yield and titer of wax esters were improved by 3.8 and 3.1 folds, respectively, over the control strain. In addition, the engineered strain accumulated wax esters 19% of cell dry weight, being the highest reported among microbes. The study provides important insights into the dynamic engineering of the biomass-dependent synthesis pathways for the improved production of biocompounds from low-cost and sustainable substrates.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chemistry and Bioengineering, Research group: Bio- and Circular Economy
Contributors: Santala, S., Efimova, E., Santala, V.
Publication date: 1 Dec 2018
Peer-reviewed: Yes

Publication information

Journal: Metabolic Engineering Communications
Volume: 7
Article number: e00078
ISSN (Print): 2214-0301
Ratings: 
  • Scopus rating (2018): CiteScore 5.05 SJR 1.699 SNIP 1.112
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering
Keywords: Acetate, Autonomous circuit, Decoupling, Dynamic control, Lipid biosynthesis, Wax esters
Electronic versions: 
Source: Scopus
Source ID: 85053844687

Research output: Contribution to journalArticleScientificpeer-review

The importance of controlled mismatch of biomechanical compliances of implantable scaffolds and native tissue for articular cartilage regeneration

Scaffolds for articular cartilage repair have to be optimally biodegradable with simultaneous promotion of hyaline cartilage formation under rather complex biomechanical and physiological conditions. It has been generally accepted that scaffold structure and composition would be the best when it mimics the structure of native cartilage. However, a reparative construct mimicking the mature native tissue in a healing tissue site presents a biological mismatch of reparative stimuli. In this work, we studied a new recombinant human type III collagen-polylactide (rhCol-PLA) scaffolds. The rhCol-PLA scaffolds were assessed for their relative performance in simulated synovial fluids of 1 and 4 mg/mL sodium hyaluronate with application of model-free analysis with Biomaterials Enhanced Simulation Test (BEST). Pure PLA scaffold was used as a control. The BEST results were compared to the results of a prior in vivo study with rhCol-PLA. Collectively the data indicated that a successful articular cartilage repair require lower stiffness of the scaffold compared to surrounding cartilage yet matching the strain compliance both in static and dynamic conditions. This ensures an optimal combination of load transfer and effective oscillatory nutrients supply to the cells. The results encourage further development of intelligent scaffold structures for optimal articular cartilage repair rather than simply trying to imitate the respective original tissue.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Faculty of Biomedical Sciences and Engineering, Aalto University, Seqvera Ltd., University of Helsinki
Contributors: Gasik, M., Zühlke, A., Haaparanta, A., Muhonen, V., Laine, K., Bilotsky, Y., Kellomäki, M., Kiviranta, I.
Publication date: 30 Nov 2018
Peer-reviewed: Yes

Publication information

Journal: Frontiers in Bioengineering and Biotechnology
Volume: 6
Issue number: NOV
Article number: 187
ISSN (Print): 2296-4185
Ratings: 
  • Scopus rating (2018): CiteScore 4.04 SJR 1.248 SNIP 1.319
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Histology, Biomedical Engineering
Keywords: Articular cartilage, Biomechanics, Collagen, PLA, Scaffold, Synovial fluid, Testing
Electronic versions: 
Source: Scopus
Source ID: 85058709882

Research output: Contribution to journalArticleScientificpeer-review

Super-resolution microscopy for biological specimens: Lensless phase retrieval in noisy conditions

The paper is devoted to a computational super-resolution microscopy. A complex-valued wavefront of a transparent biological cellular specimen is restored from multiple intensity diffraction patterns registered with noise. For this problem, the recently developed lensless super-resolution phase retrieval algorithm [Optica, 4(7), 786 (2017)] is modified and tuned. This algorithm is based on a random phase coding of the wavefront and on a sparse complex-domain approximation of the specimen. It is demonstrated in experiments, that the reliable phase and amplitude imaging of the specimen is achieved for the low signal-to-noise ratio provided a low dynamic range of observations. The filterings in the observation domain and specimen variables are specific features of the applied algorithm. If these filterings are omitted the algorithm becomes a super-resolution version of the standard iterative phase retrieval algorithms. In comparison with this simplified algorithm with no filterings, our algorithm shows a valuable improvement in imaging with much smaller number of observations and shorter exposure time. In this way, presented algorithm demonstrates ability to work in a low radiation photon-limited mode.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Signal Processing, Research group: Computational Imaging-CI, ITMO University
Contributors: Shevkunov, I., Katkovnik, V., Petrov, N. V., Egiazarian, K.
Number of pages: 13
Pages: 5511-5523
Publication date: 1 Nov 2018
Peer-reviewed: Yes

Publication information

Journal: Biomedical Optics Express
Volume: 9
Issue number: 11
Article number: #340805
ISSN (Print): 2156-7085
Ratings: 
  • Scopus rating (2018): CiteScore 4.1 SJR 1.516 SNIP 1.565
Original language: English
ASJC Scopus subject areas: Biotechnology, Atomic and Molecular Physics, and Optics
Electronic versions: 
Source: Scopus
Source ID: 85056609807

Research output: Contribution to journalArticleScientificpeer-review

Molecular Communications Pulse-based Jamming Model for Bacterial Biofilm Suppression

Studies have recently shown that the bacteria survivability within biofilms is responsible for the emergence of superbugs. The combat of bacterial infections, without enhancing its resistance to antibiotics, includes the use of nanoparticles to quench the quorum sensing of these biofilm-forming bacteria. Several sequential and parallel multi-stage communication processes are involved in the formation of biofilms. In this paper, we use proteomic data from a wet lab experiment to identify the communication channels that are vital to these processes.We also identified the main proteins from each channel and propose the use of jamming signals from synthetically engineered bacteria to suppress the production of those proteins. This biocompatible technique is based on synthetic biology and enables the inhibition of biofilm formation. We analyse the communications performance of the jamming process, by evaluating the path loss for a number of conditions that include different engineered bacterial population sizes, distances between the populations and molecular signal power. Our results show that sufficient molecular pulsebased jamming signals are able to prevent the biofilm formation by creating lossy communications channels (almost -3 dB for certain scenarios). From these results, we define the main design parameters to develop a fully operational bacteria-based jamming system.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Electronics and Communications Engineering, Research group: Emerging Technologies for Nano-Bio-Info-Cogno, Waterford Institute of Technology, Kasetsart University
Contributors: Martins, D. P., Leetanasaksakul, K., Barros, M. T., Thamchaipenet, A., Donnelly, W., Balasubramaniam, S.
Number of pages: 12
Pages: 533-542
Publication date: Oct 2018
Peer-reviewed: Yes
Early online date: 19 Sep 2018

Publication information

Journal: IEEE Transactions on Nanobioscience
Volume: 17
Issue number: 4
ISSN (Print): 1536-1241
Ratings: 
  • Scopus rating (2018): CiteScore 2.23 SJR 0.541 SNIP 0.741
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Medicine (miscellaneous), Biomedical Engineering, Pharmaceutical Science, Computer Science Applications, Electrical and Electronic Engineering
Keywords: Biofilm suppression, Communications systems, Jamming, Synthetic logic circuits
Source: Scopus
Source ID: 85053611196

Research output: Contribution to journalArticleScientificpeer-review

Temperature control as key factor for optimal biohydrogen production from thermomechanical pulping wastewater

This study evaluates the use of non-pretreated thermo-mechanical pulping (TMP) wastewater as a potential substrate for hydrogen production by dark fermentation. Batch incubations were conducted in a temperature gradient incubator at temperatures ranging from 37 to 80 °C, using an inoculum from a thermophilic, xylose-fed, hydrogen-producing fluidised bed reactor. The aim was to assess the short-term response of the microbial communities to the different temperatures with respect to both hydrogen yield and composition of the active microbial community. High throughput sequencing (MiSeq) of the reversely transcribed 16S rRNA showed that Thermoanaerobacterium sp. dominated the active microbial community at 70 °C, resulting in the highest hydrogen yield of 3.6 (±0.1) mmol H2 g−1 CODtot supplied. Lower hydrogen yields were obtained at the temperature range from 37 to 65 °C, likely due to consumption of the produced hydrogen by homoacetogenesis. No hydrogen production was detected at temperatures above 70 °C. Thermomechanical pulping wastewaters are released at high temperatures (50–80 °C), and thus dark fermentation at 70 °C could be sustained using the heat produced by the pulp and paper plant itself without any requirement for external heating.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chemistry and Bioengineering, Research group: Bio- and Circular Economy, Research group: Industrial Bioengineering and Applied Organic Chemistry, Natl. University of Ireland, Galway, Institute for Water Education, UNESCO–IHE
Contributors: Dessì, P., Porca, E., Lakaniemi, A., Collins, G., Lens, P. N.
Number of pages: 8
Pages: 214-221
Publication date: 15 Sep 2018
Peer-reviewed: Yes

Publication information

Journal: Biochemical Engineering Journal
Volume: 137
ISSN (Print): 1369-703X
Ratings: 
  • Scopus rating (2018): CiteScore 3.61 SJR 0.904 SNIP 1.147
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Environmental Engineering, Biomedical Engineering
Keywords: Dark fermentation, MiSeq, Pulp and paper mill wastewater, Thermoanaerobacterium, Thermomechanical pulping, Thermophilic
Electronic versions: 
Source: Scopus
Source ID: 85048157059

Research output: Contribution to journalArticleScientificpeer-review

Nocturnal Heart Rate Variability Spectrum Characterization in Preschool Children with Asthmatic Symptoms

Asthma is a chronic lung disease that usually develops during chilhood. Despite that symptoms can almost be controlled with medication, early diagnosis is desirable in order to reduce permanent airway obstruction risk. It has been suggested that abnormal parasympathetic nervous system (PSNS) activity might be closely related with the pathogenesis of asthma, and that this PSNS activity could be reflected in cardiac vagal control. In this work, an index to measure the spectral regularity of the high frequency (HF) component of heart rate variability (HRV) spectrum, named peakness (P), is proposed. Three different implementations of P, based on electrocardiogram (ECG) recordings, impedance pneumography (IP) recordings and a combination of both, were employed in the characterization of a group of pre-school children classified attending to their risk of developing asthma. Peakier componentswere observed in the HF band of those children classified as high-risk (p &lt; 0.005), who also presented reduced sympathvoagal balance. Results suggest that high-risk of developing asthma might be related with a lack of adaptability of PSNS.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Faculty of Biomedical Sciences and Engineering, Research group: Physiological Measurement Systems and Methods Group, University of Zaragoza, KU Leuven, University of Helsinki
Contributors: Milagro, J., Gil, E., Lazaro, J., Seppae, V. P., Malmberg, L. P., Pelkonen, A. S., Kotaniemi-Syrjanen, A., Makela, M., Viik, J., Bailon, R.
Pages: 1332-1340
Publication date: Sep 2018
Peer-reviewed: Yes
Early online date: 16 Nov 2017

Publication information

Journal: IEEE Journal of Biomedical and Health Informatics
Volume: 22
Issue number: 5
ISSN (Print): 2168-2194
Ratings: 
  • Scopus rating (2018): CiteScore 5.67 SJR 1.122 SNIP 2.4
Original language: English
ASJC Scopus subject areas: Biotechnology, Computer Science Applications, Electrical and Electronic Engineering, Health Information Management
Keywords: asthma, children, Electrocardiography, Heart rate variability, heart rate variability, Informatics, parasympathetic nervous system, peakness, Pediatrics, Pregnancy, Respiratory system, Signal to noise ratio
Source: Scopus
Source ID: 85035749268

Research output: Contribution to journalArticleScientificpeer-review

Production of alkanes from CO2 by engineered bacteria

Background: Microbial biosynthesis of alkanes is considered a promising method for the sustainable production of drop-in fuels and chemicals. Carbon dioxide would be an ideal carbon source for these production systems, but efficient production of long carbon chains from CO2 is difficult to achieve in a single organism. A potential solution is to employ acetogenic bacteria for the reduction of CO2 to acetate, and engineer a second organism to convert the acetate into long-chain hydrocarbons. Results: In this study, we demonstrate alkane production from CO2 by a system combining the acetogen Acetobacterium woodii and a non-native alkane producer Acinetobacter baylyi ADP1 engineered for alkane production. Nine synthetic two-step alkane biosynthesis pathways consisting of different aldehyde- and alkane-producing enzymes were combinatorically constructed and expressed in A. baylyi. The aldehyde-producing enzymes studied were AAR from Synechococcus elongatus, Acr1 from A. baylyi, and a putative dehydrogenase from Nevskia ramosa. The alkane-producing enzymes were ADOs from S. elongatus and Nostoc punctiforme, and CER1 from Arabidopsis thaliana. The performance of the pathways was evaluated with a twin-layer biosensor, which allowed the monitoring of both the intermediate (fatty aldehyde), and end product (alkane) formation. The highest alkane production, as indicated by the biosensor, was achieved with a pathway consisting of AAR and ADO from S. elongatus. The performance of this pathway was further improved by balancing the relative expression levels of the enzymes to limit the accumulation of the intermediate fatty aldehyde. Finally, the acetogen A. woodii was used to produce acetate from CO2 and H2, and the acetate was used for alkane production by the engineered A. baylyi, thereby leading to the net production of long-chain alkanes from CO2. Conclusions: A modular system for the production of drop-in liquid fuels from CO2 was demonstrated. Among the studied synthetic pathways, the combination of ADO and AAR from S. elongatus was found to be the most efficient in heterologous alkane production in A. baylyi. Furthermore, limiting the accumulation of the fatty aldehyde intermediate was found to be beneficial for the alkane production. Nevertheless, the alkane productivity of the system remained low, representing a major challenge for future research.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chemistry and Bioengineering, Research group: Bio- and Circular Economy
Contributors: Lehtinen, T., Virtanen, H., Santala, S., Santala, V.
Publication date: 21 Aug 2018
Peer-reviewed: Yes

Publication information

Journal: Biotechnology for Biofuels
Volume: 11
Article number: 228
ISSN (Print): 1754-6834
Ratings: 
  • Scopus rating (2018): CiteScore 5.84 SJR 1.762 SNIP 1.451
Original language: English
ASJC Scopus subject areas: Biotechnology, Applied Microbiology and Biotechnology, Renewable Energy, Sustainability and the Environment, Energy(all), Management, Monitoring, Policy and Law
Keywords: Acetate, Acetogen, Acinetobacter baylyi ADP1, Aldehyde, Alkane, Biofuel, Biosensor, Carbon dioxide, CO, Drop in

Bibliographical note

INT=keb,"Virtanen, Henri"

Source: Scopus
Source ID: 85052519319

Research output: Contribution to journalArticleScientificpeer-review

Selenate removal in biofilm systems: Effect of nitrate and sulfate on selenium removal efficiency, biofilm structure and microbial community

BACKGROUND: Selenium (Se) discharged into natural waterbodies can accumulate over time and have negative impacts on the environment. Se-laden wastewater streams can be treated using biological processes. However, the presence of other electron acceptors in wastewater, such as nitrate (NO3 -) and sulfate (SO4 2-), can influence selenate (SeO4 2-) reduction and impact the efficiency of biological treatment systems. RESULTS: SeO4 2- removal by biofilms formed from an anaerobic sludge inoculum was investigated in the presence of NO3 - and SO4 2- using drip flow reactors operated continuously for 10days at pH7.0 and 30°C. The highest total Se (∼60%) and SeO4 2- (∼80%) removal efficiencies were observed when the artificial wastewater contained SO4 2-. A maximum amount of 68μmol Se cm-2 was recovered from the biofilm matrix in SO4 2-+SeO4 2- exposed biofilms and biofilm mass was 2.7-fold increased for biofilms grown in the presence of SO4 2-. When SeO4 2- was the only electron acceptor, biofilms were thin and compact. In the simultaneous presence of NO3 - or SO4 2-, biofilms were thicker (> 0.6mm), less compact and exhibited gas pockets. CONCLUSION: The presence of SO4 2- had a beneficial effect on biofilm growth and the SeO4 2- removal efficiency, while the presence of NO3 - did not have a significant effect on SeO4 2- removal by the biofilms.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chemistry and Bioengineering, Hydraulic and Environmental Engineering (IHE) Inst. for Water Education, Montana State University (MSU), Bhabha Atomic Research Centre, UPEM
Contributors: Tan, L. C., Espinosa-Ortiz, E. J., Nancharaiah, Y. V., van Hullebusch, E. D., Gerlach, R., Lens, P. N.
Pages: 2380-2389
Publication date: Aug 2018
Peer-reviewed: Yes
Early online date: 1 Jan 2018

Publication information

Journal: Journal of Chemical Technology and Biotechnology
Volume: 93
Issue number: 8
ISSN (Print): 0268-2575
Ratings: 
  • Scopus rating (2018): CiteScore 2.88 SJR 0.715 SNIP 0.883
Original language: English
ASJC Scopus subject areas: Biotechnology, Chemical Engineering(all), Renewable Energy, Sustainability and the Environment, Fuel Technology, Waste Management and Disposal, Pollution, Organic Chemistry, Inorganic Chemistry
Keywords: Biofilm, Biofilm characterization, Co-electron acceptors, Nitrate, Selenate, Selenium removal, Sulfate
Source: Scopus
Source ID: 85043713774

Research output: Contribution to journalArticleScientificpeer-review

Metabolic pairing of aerobic and anaerobic production in a one-pot batch cultivation

Background: The versatility of microbial metabolic pathways enables their utilization in vast number of applications. However, the electron and carbon recovery rates, essentially constrained by limitations of cell energetics, are often too low in terms of process feasibility. Cocultivation of divergent microbial species in a single process broadens the metabolic landscape, and thus, the possibilities for more complete carbon and energy utilization. Results: In this study, we integrated the metabolisms of two bacteria, an obligate anaerobe Clostridium butyricum and an obligate aerobe Acinetobacter baylyi ADP1. In the process, a glucose-negative mutant of A. baylyi ADP1 first deoxidized the culture allowing C. butyricum to grow and produce hydrogen from glucose. In the next phase, ADP1 produced long chain alkyl esters (wax esters) utilizing the by-products of C. butyricum, namely acetate and butyrate. The coculture produced 24.5 ± 0.8 mmol/l hydrogen (1.7 ± 0.1 mol/mol glucose) and 28 mg/l wax esters (10.8 mg/g glucose). Conclusions: The cocultivation of strictly anaerobic and aerobic bacteria allowed the production of both hydrogen gas and long-chain alkyl esters in a simple one-pot batch process. The study demonstrates the potential of 'metabolic pairing' using designed microbial consortia for more optimal electron and carbon recovery.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chemistry and Bioengineering
Contributors: Salmela, M., Lehtinen, T., Efimova, E., Santala, S., Mangayil, R.
Publication date: 3 Jul 2018
Peer-reviewed: Yes

Publication information

Journal: Biotechnology for Biofuels
Volume: 11
Issue number: 1
Article number: 187
ISSN (Print): 1754-6834
Ratings: 
  • Scopus rating (2018): CiteScore 5.84 SJR 1.762 SNIP 1.451
Original language: English
ASJC Scopus subject areas: Biotechnology, Applied Microbiology and Biotechnology, Renewable Energy, Sustainability and the Environment, Energy(all), Management, Monitoring, Policy and Law
Keywords: Hydrogen production, Integrated metabolism, Metabolic pairing, Synthetic microbial consortia, Wax esters
Electronic versions: 
Source: Scopus
Source ID: 85049884043

Research output: Contribution to journalArticleScientificpeer-review

Pectin and Mucin Enhance the Bioadhesion of Drug Loaded Nanofibrillated Cellulose Films

Purpose: Bioadhesion is an important property of biological membranes, that can be utilized in pharmaceutical and biomedical applications. In this study, we have fabricated mucoadhesive drug releasing films with bio-based, non-toxic and biodegradable polymers that do not require chemical modifications. Methods: Nanofibrillar cellulose and anionic type nanofibrillar cellulose were used as film forming materials with known mucoadhesive components mucin, pectin and chitosan as functional bioadhesion enhancers. Different polymer combinations were investigated to study the adhesiveness, solid state characteristics, film morphology, swelling, mechanical properties, drug release with the model compound metronidazole and in vitro cytotoxicity using TR146 cells to model buccal epithelium. Results: SEM revealed lamellar structures within the films, which had a thickness ranging 40–240 μm depending on the film polymer composition. All bioadhesive components were non-toxic and showed high adhesiveness. Rapid drug release was observed, as 60–80% of the total amount of metronidazole was released in 30 min depending on the film formulation. Conclusions: The liquid molding used was a straightforward and simple method to produce drug releasing highly mucoadhesive films, which could be utilized in treating local oral diseases, such as periodontitis. All materials used were natural biodegradable polymers from renewable sources, which are generally regarded as safe.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chemistry and Bioengineering, Research group: Chemistry & Advanced Materials, Aalto University, Universita degli Studi di Padova, Italy, University of Helsinki, University of Helsinki
Contributors: Laurén, P., Paukkonen, H., Lipiäinen, T., Dong, Y., Oksanen, T., Räikkönen, H., Ehlers, H., Laaksonen, P., Yliperttula, M., Laaksonen, T.
Publication date: 1 Jul 2018
Peer-reviewed: Yes

Publication information

Journal: Pharmaceutical Research
Volume: 35
Issue number: 7
Article number: 145
ISSN (Print): 0724-8741
Ratings: 
  • Scopus rating (2018): CiteScore 3.89 SJR 1.093 SNIP 1.108
Original language: English
ASJC Scopus subject areas: Biotechnology, Molecular Medicine, Pharmacology, Pharmaceutical Science, Organic Chemistry, Pharmacology (medical)
Keywords: bioadhesion, drug release, mucoadhesion, nanofibrillar cellulose, TR146
Electronic versions: 
URLs: 
Source: Scopus
Source ID: 85047448577

Research output: Contribution to journalArticleScientificpeer-review

Segmentation of vessel structures from photoacoustic images with reliability assessment

Photoacoustic imaging enables the imaging of soft biological tissue with combined optical contrast and ultrasound resolution. One of the targets of interest is tissue vasculature. However, the photoacoustic images may not directly provide the information on, for example, vasculature structure. Therefore, the images are improved by reducing noise and artefacts, and processed for better visualisation of the target of interest. In this work, we present a new segmentation method of photoacoustic images that also straightforwardly produces assessments of its reliability. The segmentation depends on parameters which have a natural tendency to increase the reliability as the parameter values monotonically change. The reliability is assessed by counting classifications of image voxels with different parameter values. The resulting segmentation with reliability offers new ways and tools to analyse photoacoustic images and new possibilities for utilising them as anatomical priors in further computations. Our MATLAB implementation of the method is available as an open-source software package [P. Raumonen, Matlab, 2018].

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Mathematics, University of Eastern Finland, University College London
Contributors: Raumonen, P., Tarvainen, T.
Number of pages: 18
Pages: 2887-2904
Publication date: 1 Jul 2018
Peer-reviewed: Yes

Publication information

Journal: Biomedical Optics Express
Volume: 9
Issue number: 7
ISSN (Print): 2156-7085
Ratings: 
  • Scopus rating (2018): CiteScore 4.1 SJR 1.516 SNIP 1.565
Original language: English
ASJC Scopus subject areas: Biotechnology, Atomic and Molecular Physics, and Optics
Source: Scopus
Source ID: 85049377889

Research output: Contribution to journalArticleScientificpeer-review

Switchable light reflectance in dilute magneto-optical colloids based on nickel ferrite nanowires

Optical properties of diluted narrow band gap magnetic semiconductor nanowire colloids are controlled by modest magnetic fields under 100 Oe. High aspect ratio NiFe2O4 nanowires are used to achieve responsiveness to magnetic field, light absorption and -scattering. Visible light reflectance of the diluted colloids can be either increased or decreased depending on the nanowire alignment relative to the direction of the light propagation. The prepared colloids can be applied as magneto-optical switches or as smart window devices.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Photonics, Institute of Physics, University of Tartu, Riga Technical University, CRPP, University of Latvia
Contributors: Sutka, A., Timusk, M., Joost, U., Ignatans, R., Maiorov, M.
Number of pages: 3
Pages: 119-121
Publication date: 2 May 2018
Peer-reviewed: Yes

Publication information

Journal: e-Journal of Surface Science and Nanotechnology
Volume: 16
ISSN (Print): 1348-0391
Ratings: 
  • Scopus rating (2018): CiteScore 0.58 SJR 0.216 SNIP 0.337
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Condensed Matter Physics, Mechanics of Materials, Surfaces and Interfaces, Surfaces, Coatings and Films
Keywords: Colloid, Ferrimagnetic, Magneto-optical, Nanowire, NiFe2O4

Bibliographical note

INT=fot,"Joost, Urmas"

Source: Scopus
Source ID: 85047369076

Research output: Contribution to journalArticleScientificpeer-review

Non-intersecting leaf insertion algorithm for tree structure models

We present an algorithm and an implementation to insert broadleaves or needleleaves into a quantitative structure model according to an arbitrary distribution, and a data structure to store the required information efficiently. A structure model contains the geometry and branching structure of a tree. The purpose of this work is to offer a tool for making more realistic simulations of tree models with leaves, particularly for tree models developed from terrestrial laser scanning (TLS) measurements. We demonstrate leaf insertion using cylinder-based structure models, but the associated software implementation is written in a way that enables the easy use of other types of structure models. Distributions controlling leaf location, size and angles as well as the shape of individual leaves are user definable, allowing any type of distribution. The leaf generation process consist of two stages, the first of which generates individual leaf geometry following the input distributions, while in the other stage intersections are prevented by carrying out transformations when required. Initial testing was carried out on English oak trees to demonstrate the approach and to assess the required computational resources. Depending on the size and complexity of the tree, leaf generation takes between 6 and 18 min. Various leaf area density distributions were defined, and the resulting leaf covers were compared with manual leaf harvesting measurements. The results are not conclusive, but they show great potential for the method. In the future, if our method is demonstrated to work well for TLS data from multiple tree types, the approach is likely to be very useful for three-dimensional structure and radiative transfer simulation applications, including remote sensing, ecology and forestry, among others.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Mathematics, Forest Research, Department of Applied Health Research, NERC National Centre for Earth Observation (NCEO), University of Salford, Newcastle University, United Kingdom, York St John University
Contributors: Åkerblom, M., Raumonen, P., Casella, E., Disney, M. I., Danson, F. M., Gaulton, R., Schofield, L. A., Kaasalainen, M.
Publication date: 6 Apr 2018
Peer-reviewed: Yes

Publication information

Journal: Interface Focus
Volume: 8
Issue number: 2
Article number: 20170045
ISSN (Print): 2042-8898
Ratings: 
  • Scopus rating (2018): CiteScore 2.97 SJR 1.138 SNIP 0.939
Original language: English
ASJC Scopus subject areas: Biotechnology, Biophysics, Bioengineering, Biochemistry, Biomaterials, Biomedical Engineering
Keywords: Laser scanning, Leaf distribution, Leaf insertion, Quantitative structure model, Tree reconstruction
Electronic versions: 
Source: Scopus
Source ID: 85043466694

Research output: Contribution to journalArticleScientificpeer-review

Uncertainty in multispectral lidar signals caused by incidence angle effects

Multispectral terrestrial laser scanning (TLS) is an emerging technology. Several manufacturers already offer commercial dual or three wavelength airborne laser scanners, while multispectral TLS is still carried out mainly with research instruments. Many of these research efforts have focused on the study of vegetation. The aim of this paper is to study the uncertainty of the measurement of spectral indices of vegetation with multispectral lidar. Using two spectral indices as examples, we find that the uncertainty is due to systematic errors caused by the wavelength dependency of laser incidence angle effects. This finding is empirical, and the error cannot be removed by modelling or instrument modification. The discovery and study of these effects has been enabled by hyperspectral and multispectral TLS, and it has become a subject of active research within the past few years. We summarize the most recent studies on multi-wavelength incidence angle effects and present new results on the effect of specular reflection from the leaf surface, and the surface structure, which have been suggested to play a key role. We also discuss the consequences to the measurement of spectral indices with multispectral TLS, and a possible correction scheme using a synthetic laser footprint.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Mathematics, Department of Navigation and Positioning, FGI
Contributors: Kaasalainen, S., Åkerblom, M., Nevalainen, O., Hakala, T., Kaasalainen, M.
Publication date: 6 Apr 2018
Peer-reviewed: Yes

Publication information

Journal: Interface Focus
Volume: 8
Issue number: 2
Article number: 20170033
ISSN (Print): 2042-8898
Ratings: 
  • Scopus rating (2018): CiteScore 2.97 SJR 1.138 SNIP 0.939
Original language: English
ASJC Scopus subject areas: Biotechnology, Biophysics, Bioengineering, Biochemistry, Biomaterials, Biomedical Engineering
Keywords: Hyperspectral, Incidence angle, Laser scanning, Vegetation
Electronic versions: 
Source: Scopus
Source ID: 85043458754

Research output: Contribution to journalArticleScientificpeer-review

Weighing trees with lasers: Advances, challenges and opportunities

Terrestrial laser scanning (TLS) is providing exciting new ways to quantify tree and forest structure, particularly above-ground biomass (AGB). We show how TLS can address some of the key uncertainties and limitations of current approaches to estimating AGB based on empirical allometric scaling equations (ASEs) that underpin all large-scale estimates of AGB. TLS provides extremely detailed non-destructive measurements of tree form independent of tree size and shape. We show examples of three-dimensional (3D) TLS measurements from various tropical and temperate forests and describe how the resulting TLS point clouds can be used to produce quantitative 3D models of branch and trunk size, shape and distribution. These models can drastically improve estimates of AGB, provide new, improved large-scale ASEs, and deliver insights into a range of fundamental tree properties related to structure. Large quantities of detailed measurements of individual 3D tree structure also have the potential to open new and exciting avenues of research in areas where difficulties of measurement have until now prevented statistical approaches to detecting and understanding underlying patterns of scaling, form and function. We discuss these opportunities and some of the challenges that remain to be overcome to enable wider adoption of TLS methods.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Mathematics, Department of Applied Health Research, NERC National Centre for Earth Observation (NCEO), National Physical Laboratory, Universiteit Gent, School of Geography, University of Leeds
Contributors: Disney, M. I., Boni Vicari, M., Burt, A., Calders, K., Lewis, S. L., Raumonen, P., Wilkes, P.
Publication date: 6 Apr 2018
Peer-reviewed: Yes

Publication information

Journal: Interface Focus
Volume: 8
Issue number: 2
Article number: 20170048
ISSN (Print): 2042-8898
Ratings: 
  • Scopus rating (2018): CiteScore 2.97 SJR 1.138 SNIP 0.939
Original language: English
ASJC Scopus subject areas: Biotechnology, Biophysics, Bioengineering, Biochemistry, Biomaterials, Biomedical Engineering
Keywords: Above-ground biomass, Buttress, Canopy, Lidar, Structure, Terrestrial laser scanning
Electronic versions: 

Bibliographical note

EXT="Lewis, S. L."

Source: Scopus
Source ID: 85043466280

Research output: Contribution to journalArticleScientificpeer-review

Improved fatty aldehyde and wax ester production by overexpression of fatty acyl-CoA reductases

Background: Fatty aldehydes are industrially relevant compounds, which also represent a common metabolic intermediate in the microbial synthesis of various oleochemicals, including alkanes, fatty alcohols and wax esters. The key enzymes in biological fatty aldehyde production are the fatty acyl-CoA/ACP reductases (FARs) which reduce the activated acyl molecules to fatty aldehydes. Due to the disparity of FARs, identification and in vivo characterization of reductases with different properties are needed for the construction of tailored synthetic pathways for the production of various compounds. Results: Fatty aldehyde production in Acinetobacter baylyi ADP1 was increased by the overexpression of three different FARs: a native A. baylyi FAR Acr1, a cyanobacterial Aar, and a putative, previously uncharacterized dehydrogenase (Ramo) from Nevskia ramosa. The fatty aldehyde production was followed in real-time inside the cells with a luminescence-based tool, and the highest aldehyde production was achieved with Aar. The fate of the overproduced fatty aldehydes was studied by measuring the production of wax esters by a native downstream pathway of A. baylyi, for which fatty aldehyde is a specific intermediate. The wax ester production was improved with the overexpression of Acr1 or Ramo compared to the wild type A. baylyi by more than two-fold, whereas the expression of Aar led to only subtle wax ester production. The overexpression of FARs did not affect the length of the acyl chains of the wax esters. Conclusions: The fatty aldehyde production, as well as the wax ester production of A. baylyi, was improved with the overexpression of a key enzyme in the pathway. The wax ester titer (0.45 g/l) achieved with the overexpression of Acr1 is the highest reported without hydrocarbon supplementation to the culture. The contrasting behavior of the different reductases highlight the significance of in vivo characterization of enzymes and emphasizes the possibilities provided by the diversity of FARs for pathway and product modulation.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chemistry and Bioengineering, Research group: Bio- and Circular Economy
Contributors: Lehtinen, T., Efimova, E., Santala, S., Santala, V.
Publication date: 8 Feb 2018
Peer-reviewed: Yes

Publication information

Journal: Microbial Cell Factories
Volume: 17
Issue number: 1
Article number: 19
ISSN (Print): 1475-2859
Ratings: 
  • Scopus rating (2018): CiteScore 4.43 SJR 1.407 SNIP 1.232
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Applied Microbiology and Biotechnology
Keywords: Acinetobacter baylyi ADP1, FAR, Fatty acyl-CoA reductase, Fatty aldehyde, Wax ester
Electronic versions: 
Source: Scopus
Source ID: 85041848256

Research output: Contribution to journalArticleScientificpeer-review

Azopolymer photopatterning for directional control of angiogenesis

Understanding cellular behavior in response to microenvironmental stimuli is central to tissue engineering. An increasing number of reports emphasize the high sensitivity of cells to the physical characteristics of the surrounding milieu and in particular, topographical cues. In this work, we investigated the influence of dynamic topographic signal presentation on sprout formation and the possibility to obtain a space–time control over sprouting directionality without growth factors, in order to investigate the contribution of just topography in the angiogenic process. To test our hypothesis, we employed a 3D angiogenesis assay based on the use of spheroids derived from human umbilical vein endothelial cells (HUVECs). We then modulated the in situ presentation of topographical cues during early-stage angiogenesis through real-time photopatterning of an azobenzene-containing polymer, poly (Disperse Red 1 methacrylate) (pDR1m). Pattern inscription on the polymer surface was made using the focused laser of a confocal microscope. We demonstrate that during early-stage angiogenesis, sprouts followed the pattern direction, while spheroid cores acquired a polarized shape. These findings confirmed that sprout directionality was influenced by the photo-inscribed pattern, probably through contact guidance of leader cells, thus validating the proposed platform as a valuable tool for understanding complex processes involved in cell-topography interactions in multicellular systems. Statement of Significance The complex relationship between endothelial cells and the surrounding environment that leads to formation of a newly formed vascular network during tissue repair is currently unknown. We have developed an innovative in vitro platform to study these mechanisms in a space and time controlled fashion simulating what happens during regeneration. In particular, we combine a “smart” surface, namely a polymer film, with a three-dimensional living cell aggregate. The polymer is activated by light through which we can design a path to guide cells toward the formation of a new vessel. Our work lies at the intersection of stimuli-responsive biointerfaces and cell biology and may be particularly inspiring for those interested in designing biomaterial surface related to angiogenesis.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Chemistry and Bioengineering, Center for Advanced Biomaterials for Healthcare, Italian Institute of Technology, Dipartimento di Ingegneria Chimica dei Materiali e della Produzione Industriale, ENEA/CREATE/Università Degli Studi Napoli Federico II, Laboratory of Chemistry and Bioengineering
Contributors: Fedele, C., De Gregorio, M., Netti, P. A., Cavalli, S., Attanasio, C.
Number of pages: 9
Pages: 317-325
Publication date: 1 Nov 2017
Peer-reviewed: Yes

Publication information

Journal: Acta Biomaterialia
Volume: 63
ISSN (Print): 1742-7061
Ratings: 
  • Scopus rating (2017): CiteScore 6.97 SJR 1.967 SNIP 1.815
Original language: English
ASJC Scopus subject areas: Biotechnology, Biomaterials, Biochemistry, Biomedical Engineering, Molecular Biology
Keywords: Angiogenesis, Azopolymers, Directional sprouting, Photopatterning, Topographical cues
Source: Scopus
Source ID: 85029628146

Research output: Contribution to journalArticleScientificpeer-review

Elucidation of Compression-Induced Surface Crystallization in Amorphous Tablets Using Sum Frequency Generation (SFG) Microscopy

Purpose: To investigate the effect of compression on the crystallization behavior in amorphous tablets using sum frequency generation (SFG) microscopy imaging and more established analytical methods. Method: Tablets containing neat amorphous griseofulvin with/without excipients (silica, hydroxypropyl methylcellulose acetate succinate (HPMCAS), microcrystalline cellulose (MCC) and polyethylene glycol (PEG)) were prepared. They were analyzed upon preparation and storage using attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy, scanning electron microscopy (SEM) and SFG microscopy. Results: Compression-induced crystallization occurred predominantly on the surface of the neat amorphous griseofulvin tablets, with minimal crystallinity being detected in the core of the tablets. The presence of various types of excipients was not able to mitigate the compression-induced surface crystallization of the amorphous griseofulvin tablets. However, the excipients affected the crystallization rate of amorphous griseofulvin in the core of the tablet upon compression and storage. Conclusions: SFG microscopy can be used in combination with ATR-FTIR spectroscopy and SEM to understand the crystallization behaviour of amorphous tablets upon compression and storage. When selecting excipients for amorphous formulations, it is important to consider the effect of the excipients on the physical stability of the amorphous formulations.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, University of Helsinki, Division of Biopharmaceutical Sciences, Biomedicum Imaging Unit, FIN-00014 University of Helsinki
Contributors: Mah, P. T., Novakovic, D., Saarinen, J., van Landeghem, S., Peltonen, L., Laaksonen, T., Isomäki, A., Strachan, C. J.
Number of pages: 14
Pages: 957-970
Publication date: May 2017
Peer-reviewed: Yes
Early online date: 13 Oct 2016

Publication information

Journal: Pharmaceutical Research
Volume: 34
Issue number: 5
ISSN (Print): 0724-8741
Ratings: 
  • Scopus rating (2017): CiteScore 3.3 SJR 1.077 SNIP 1.054
Original language: English
ASJC Scopus subject areas: Biotechnology, Molecular Medicine, Pharmacology, Pharmaceutical Science, Organic Chemistry, Pharmacology (medical)
Source: Scopus
Source ID: 84991051806

Research output: Contribution to journalArticleScientificpeer-review

Tunable Plasmonic Silver Nanodomes for Surface-Enhanced Raman Scattering

Surface-enhanced Raman scattering (SERS) is an emerging analytical method used in biological and non-biological structure characterization. Since the nanostructure plasmonic properties is a significant factor for SERS performance, nanostructure fabrication with tunable plasmonic properties are crucial in SERS studies. In this study, a novel method for fabrication of tunable plasmonic silver nanodomes (AgNDs) is presented. The convective-assembly method is preferred for the deposition of latex particles uniformly on a regular glass slide and used as a template for polydimethylsiloxane (PDMS) to prepare nanovoids on a PDMS surface. The obtained nanovoids on the PDMS are used as a mold for AgNDs fabrication. The nanovoids are filled with Ag deposition by the electrochemical method to obtain metallic AgNDs. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) are used for characterization of the structural properties of all fabricated AgNDs. The optical properties of AgNDs are characterized with the evaluation of SERS activity of 4-aminothiphonel and rhodamine 6G. In addition to experimental characterizations, the finite difference time domain (FDTD) method is used for the theoretical plasmonic properties calculation of the AgNDs. The experimental and theoretical results show that the SERS performance of AgNDs is strongly dependent on the heights and diameters of the AgNDs.

General information

Publication status: Accepted/In press
MoE publication type: A1 Journal article-refereed
Organisations: Gaziantep University, Bingöl University, Bilkent University
Contributors: Kahraman, M., Ozbay, A., Yuksel, H., Solmaz, R., Demir, B., Caglayan, H.
Number of pages: 11
Pages: 1-11
Publication date: 5 Apr 2017
Peer-reviewed: Yes

Publication information

Journal: Plasmonics
ISSN (Print): 1557-1955
Ratings: 
  • Scopus rating (2017): CiteScore 2.13 SJR 0.679 SNIP 0.805
Original language: English
ASJC Scopus subject areas: Biotechnology, Biophysics, Biochemistry
Keywords: Electrochemical deposition, FDTD method, Plasmonic, SERS, Silver Nanodomes, Tunable

Bibliographical note

EXT="Caglayan, Humeyra"

Source: Scopus
Source ID: 85017133474

Research output: Contribution to journalArticleScientificpeer-review

Multivariate statistical analysis for the identification of potential seafood spoilage indicators

Volatile organic compounds (VOCs) characterize the spoilage of seafood packaged under modified atmospheres (MAs) and could thus be used for quality monitoring. However, the VOC profile typically contains numerous multicollinear compounds and depends on the product and storage conditions. Identification of potential spoilage indicators thus calls for multivariate statistics. The aim of the present study was to define suitable statistical methods for this purpose (exploratory analysis) and to consequently characterize the spoilage of brown shrimp (Crangon crangon) and Atlantic cod (Gadus morhua) stored under different conditions (selective analysis). Hierarchical cluster analysis (HCA), principal components analysis (PCA) and partial least squares regression analysis (PLS) were applied as exploratory techniques (brown shrimp, 4 °C, 50%CO2/50%N2) and PLS was further selected for spoilage marker identification. Evolution of acetic acid, 2,3-butanediol, isobutyl alcohol, 3-methyl-1-butanol, dimethyl sulfide, ethyl acetate and trimethylamine was frequently in correspondence with changes in the microbiological quality or sensory rejection. Analysis of these VOCs could thus enhance the detection of seafood spoilage and the development of intelligent packaging technologies.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Materials Science, Laboratory of Food Microbiology and Food Preservation, Universiteit Gent, Paper Converting and Packaging Technology
Contributors: Kuuliala, L., Abatih, E., Ioannidis, A. G., Vanderroost, M., De Meulenaer, B., Ragaert, P., Devlieghere, F.
Number of pages: 12
Pages: 49-60
Publication date: 1 Feb 2017
Peer-reviewed: Yes

Publication information

Journal: Food Control
Volume: 84
ISSN (Print): 0956-7135
Ratings: 
  • Scopus rating (2017): CiteScore 4.06 SJR 1.502 SNIP 1.728
Original language: English
ASJC Scopus subject areas: Biotechnology, Food Science
Keywords: Hierarchical cluster analysis, Intelligent packaging, Partial least squares regression analysis, Principal components analysis, Selected-ion flow-tube mass spectrometry
Electronic versions: 
URLs: 
Source: Scopus
Source ID: 85026361014

Research output: Contribution to journalArticleScientificpeer-review

Aligned Poly(ε-caprolactone) Nanofibers Guide the Orientation and Migration of Human Pluripotent Stem Cell-Derived Neurons, Astrocytes, and Oligodendrocyte Precursor Cells In Vitro

Stem cell transplantations for spinal cord injury (SCI) have been studied extensively for the past decade in order to replace the damaged tissue with human pluripotent stem cell (hPSC)-derived neural cells. Transplanted cells may, however, benefit from supporting and guiding structures or scaffolds in order to remain viable and integrate into the host tissue. Biomaterials can be used as supporting scaffolds, as they mimic the characteristics of the natural cellular environment. In this study, hPSC-derived neurons, astrocytes, and oligodendrocyte precursor cells (OPCs) are cultured on aligned poly(ε-caprolactone) nanofiber platforms, which guide cell orientation to resemble that of spinal cord in vivo. All cell types are shown to efficiently spread over the nanofiber platform and orient according to the fiber alignment. Human neurons and astrocytes require extracellular matrix molecule coating for the nanofibers, but OPCs grow on nanofibers without additional treatment. Furthermore, the nanofiber platform is combined with a 3D hydrogel scaffold with controlled thickness, and nanofiber-mediated orientation of hPSC-derived neurons is also demonstrated in a 3D environment. In this work, clinically relevant materials and substrates for nanofibers, fiber coatings, and hydrogel scaffolds are used and combined with cells suitable for developing functional cell grafts for SCI repair.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Materials Science, Research group: Materials Characterization
Contributors: Hyysalo, A., Ristola, M., Joki, T., Honkanen, M., Vippola, M., Narkilahti, S.
Publication date: 2017
Peer-reviewed: Yes
Early online date: 2017

Publication information

Journal: MACROMOLECULAR BIOSCIENCE
Volume: 17
Issue number: 7
Article number: 1600517
ISSN (Print): 1616-5187
Ratings: 
  • Scopus rating (2017): CiteScore 3.24 SJR 1.017 SNIP 0.776
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Biomaterials, Polymers and Plastics, Materials Chemistry
Keywords: 3D environment, Differentiated neural cell, Human pluripotent stem cell, Nanofiber, Orientation
Source: Scopus
Source ID: 85017192272

Research output: Contribution to journalArticleScientificpeer-review

Electrical Contacts in SOI MEMS Using Aerosol Jet Printing

In this study, an additive method to make electrical contacts in SOI MEMS devices with aerosol jet printing is introduced. Small grooves were etched to the frame of MEMS accelerometer in the same step with the active structure release. Aluminum ink was jetted to the trenches in wafer-level to bridge the device layer to the handle wafer with the minimum amount of material. After subsequent annealing ohmic contacts between p-type device layer and p-type handle silicon were verified by I-V measurements. The via resistance less than 4 Y per via is measured. The method demonstrated in this work provides simple and low-cost approach for SOI handle contact where additional packaging of wafer process steps can be avoided.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Electronics and Communications Engineering, Research group: Laboratory for Future Electronics, Murata Electronics Oy
Contributors: Khorramdel, B., Torkkeli, A., Mäntysalo, M.
Pages: 34-40
Publication date: 2017
Peer-reviewed: Yes
Early online date: 19 Oct 2017

Publication information

Journal: IEEE Journal of the Electron Devices Society
Volume: 6
ISSN (Print): 2168-6734
Ratings: 
  • Scopus rating (2017): CiteScore 3.37 SJR 1.016 SNIP 1.462
Original language: English
ASJC Scopus subject areas: Biotechnology, Electronic, Optical and Magnetic Materials, Electrical and Electronic Engineering
Keywords: additive manufacturing., aerosol jet printing, Aerosols, Cavity resonators, Electrical resistance measurement, Ink, inkjet printing, microelectromechanical systems (MEMS), Micromechanical devices, Printing, silicon on insulator (SOI), Silicon-on-insulator
Source: Scopus
Source ID: 85032682442

Research output: Contribution to journalArticleScientificpeer-review

Abstract: Direction as a vibration loading parameter in bone tissue engineering

General information

Publication status: Published
Organisations: Department of Electronics and Communications Engineering, Research group: Computational Biophysics and Imaging Group, BioMediTech, National Center of Science and Technology, Ministry of Education and Science, Republic of Kazakhstan, Tampere University Hospital, Adult Stem Cell Research Group, The National Science Centre, Poland, Regenerative Medicine, Adult Stem Cell Group, Univ Tampere, University of Tampere, Inst Biosci & Med Technol BioMediTech
Contributors: Halonen, H., Kyllönen, L., Ihalainen, T. O., Miettinen, S., Hyttinen, J.
Publication date: 25 Nov 2016
Peer-reviewed: Unknown
Event: Paper presented at BioMediTech Research Day 2016, Tampere, Finland.
ASJC Scopus subject areas: Biotechnology, Cell Biology, Biomedical Engineering
Keywords: HMHF vibration loading, Adipose stem cells, Osteogenic differentiation

Research output: Other conference contributionPaper, poster or abstractScientific

Selenium: environmental significance, pollution, and biological treatment technologies

Selenium is an essential trace element needed for all living organisms. Despite its essentiality, selenium is a potential toxic element to natural ecosystems due to its bioaccumulation potential. Though selenium is found naturally in the earth's crust, especially in carbonate rocks and volcanic and sedimentary soils, about 40% of the selenium emissions to atmospheric and aquatic environments are caused by various industrial activities such as mining-related operations. In recent years, advances in water quality and pollution monitoring have shown that selenium is a contaminant of potential environmental concern. This has practical implications on industry to achieve the stringent selenium regulatory discharge limit of 5 μg Se L− 1 for selenium containing wastewaters set by the United States Environmental Protection Agency. Over the last few decades, various technologies have been developed for the treatment of selenium-containing wastewaters. Biological selenium reduction has emerged as the leading technology for removing selenium from wastewaters since it offers a cheaper alternative compared to physico-chemical treatments and is suitable for treating dilute and variable selenium-laden wastewaters. Moreover, biological treatment has the advantage of forming elemental selenium nanospheres which exhibit unique optical and spectral properties for various industrial applications, i.e. medical, electrical, and manufacturing processes. However, despite the advances in biotechnology employing selenium reduction, there are still several challenges, particularly in achieving stringent discharge limits, the long-term stability of biogenic selenium and predicting the fate of bioreduced selenium in the environment. This review highlights the significance of selenium in the environment, health, and industry and biotechnological advances made in the treatment of selenium contaminated wastewaters. The challenges and future perspectives are overviewed considering recent biotechnological advances in the management of these selenium-laden wastewaters.

General information

Publication status: Published
MoE publication type: A2 Review article in a scientific journal
Organisations: Department of Chemistry and Bioengineering, UNESCO-IHE Institute for Water Education, Bhabha Atomic Research Centre, UPEM
Contributors: Tan, L. C., Nancharaiah, Y. V., van Hullebusch, E. D., Lens, P. N. L.
Number of pages: 22
Pages: 886-907
Publication date: 1 Sep 2016
Peer-reviewed: Yes

Publication information

Journal: Biotechnology Advances
Volume: 34
Issue number: 5
ISSN (Print): 0734-9750
Ratings: 
  • Scopus rating (2016): CiteScore 11.05 SJR 2.747 SNIP 3.195
Original language: English
ASJC Scopus subject areas: Biotechnology
Keywords: Bioreactors, Bioremediation, Selenium bioreduction, Selenium environmental impact, Selenium nanoparticles, Selenium pollution, Selenium recovery, Selenium wastewaters
Source: Scopus
Source ID: 84992046700

Research output: Contribution to journalReview ArticleScientificpeer-review

Abstract: Direction as a vibration loading parameter in osteogenic differentiation of adipose stem cells

General information

Publication status: Published
Organisations: Department of Electronics and Communications Engineering, Research group: Computational Biophysics and Imaging Group, BioMediTech
Contributors: Halonen, H., Kyllönen, L., Ihalainen, T. O., Miettinen, S., Hyttinen, J.
Number of pages: 1
Publication date: 10 Jul 2016
Peer-reviewed: Unknown
Event: Paper presented at Congress of the European Society of biomechanics ESB2016, Lyon, France.
ASJC Scopus subject areas: Biotechnology, Cell Biology, Biomedical Engineering
Keywords: HMHF vibration loading, Adipose stem cells, Osteogenic differentiation

Research output: Other conference contributionPaper, poster or abstractScientific

Biological and Bioelectrochemical Recovery of Critical and Scarce Metals

Metal-bearing solid and liquid wastes are increasingly considered as secondary sources of critical and scarce metals. Undoubtedly, microorganisms are a cost-effective resource for extracting and concentrating diffuse elements from secondary sources. Microbial biotechnology for extracting base metals from ores and treatment of metal-laden wastewaters has already been applied at full scale. By contrast, microbe-metal interactions in the recovery of scarce metals and a few critical metals have received attention, whereas the recovery of many others has been barely explored. Therefore, this article explores and details the potential application of microbial biotechnologies in the recovery of critical and scarce metals. In the past decade bioelectrochemical systems have emerged as a new technology platform for metal recovery coupled to the removal of organic matter. Overview of potential applications of microorganisms in critical metal recovery.Engineering of microbe-metal interactions for recovering rare earth elements and platinum group metals.Reductive mineral dissolution is a new dimension to biomining.Bioelectrochemical systems offer a new technology platform in metal recovery.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Industrial Bioengineering and Applied Organic Chemistry, Biofouling and Biofilm Processes Section, Bhabha Atomic Research Centre, Council of Scientific and Industrial Research India, Hydraulic and Environmental Engineering (IHE) Inst. for Water Education
Contributors: Nancharaiah, Y. V., Mohan, S. V., Lens, P. N. L.
Number of pages: 19
Pages: 137-155
Publication date: 2016
Peer-reviewed: Yes

Publication information

Journal: Trends in Biotechnology
Volume: 34
Issue number: 2
ISSN (Print): 0167-7799
Ratings: 
  • Scopus rating (2016): CiteScore 9.97 SJR 4.203 SNIP 3.177
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering
Keywords: Bioelectrochemical systems, Biomining, Bioprecipitation, Biorecovery, Critical metals, Microbial fuel cells, Platinum group metals, Rare earth elements
Source: Scopus
Source ID: 84961085643

Research output: Contribution to journalArticleScientificpeer-review

Improved properties for packaging materials by nanoscale surface modification and ALD barrier coating

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Materials Science, Research group: Paper Converting and Packaging, Metsä Board, Bemis, LUT Energy, Masaryk University
Contributors: Lahti, J., Lavonen, J., Lahtinen, K., Johansson, P., Seppänen, T., Cameron, D. C.
Number of pages: 23
Pages: 684-706
Publication date: 2016

Host publication information

Title of host publication: TAPPI International Conference on Nanotechnology for Renewable Materials 2016
Volume: 2
Publisher: TAPPI Press
ISBN (Electronic): 9781510828001
ASJC Scopus subject areas: Biotechnology, Biomaterials, Materials Chemistry, Surfaces, Coatings and Films
Source: Scopus
Source ID: 84992694476

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Roll-to-roll application of photocatalytic TiO2 nanoparticles for printed functionality

In this work ultraviolet A (UVA) light controlled photocatalytic activity of TiO2 nanoparticles is utilized on paper, paperboard, and plastic films for controlled wetting and oxygen sensors for modified atmosphere packages (MAPs). A liquid flame spray (LFS) process is used for a large-area TiO2 nanoparticle deposition on natural fibre based substrates such as paperboard that results in a superhydrophobic surface. Controlled wettability is achieved using an UVA light activation that converts the surface to hydrophilic whereas an oven heat treatment recovers the initial superhydrophobicity. On the other hand, a TiO2 nanoparticles with methylene blue (MB) dye is used to detect the presence of oxygen in modified atmosphere packages. We believe that photocatalytically active surfaces with tailorable properties will find many applications in the near future, for example, with printed functional devices.

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Physics, Research area: Aerosol Physics, Research group: Aerosol Synthesis, Center for Functional Materials at Biological Interfaces (FUNMAT), Abo Akad Univ, Abo Akademi University, Dept Phys, Omya International AG, AGH University of Science and Technology, Aerosol Physics Laboratory
Contributors: Saarinen, J. J., Valtakari, D., Bollström, R., Stepien, M., Haapanen, J., Mäkelä, J. M., Toivakka, M.
Number of pages: 4
Pages: 47-50
Publication date: 2016

Host publication information

Title of host publication: Advanced Manufacturing, Electronics and Microsystems : TechConnect Briefs 2016
Volume: 4
Publisher: TechConnect
ISBN (Electronic): 9780997511734
ASJC Scopus subject areas: Fluid Flow and Transfer Processes, Biotechnology, Surfaces, Coatings and Films, Fuel Technology
Keywords: Controlled wetting, Nanoparticles, O sensor, Photocatalysis, TiO
Source: Scopus
Source ID: 84988974879

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Gene expression analysis upon lncRNA DDSR1 knockdown in human fibroblasts

Long non-coding RNAs (lncRNAs) play important roles in regulating diverse biological processes including DNA damage and repair. We have recently reported that the DNA damage inducible lncRNA DNA damage-sensitive RNA1 (DDSR1) regulates DNA repair by homologous recombination (HR). Since lncRNAs also modulate gene expression, we identified gene expression changes upon DDSR1 knockdown in human fibroblast cells. Gene expression analysis after RNAi treatment targeted against DDSR1 revealed 119 genes that show differential expression. Here we provide a detailed description of the microarray data (NCBI GEO accession number GSE67048) and the data analysis procedure associated with the publication by Sharma et al., 2015 in EMBO Reports [1].

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Science X (CompX), National Cancer Institute, Frederick National Laboratory for Cancer Research
Contributors: Jia, L., Sun, Z., Wu, X., Misteli, T., Sharma, V.
Number of pages: 3
Pages: 277-279
Publication date: 1 Dec 2015
Peer-reviewed: Yes

Publication information

Journal: Genomics Data
Volume: 6
ISSN (Print): 2213-5960
Ratings: 
  • Scopus rating (2015): CiteScore 0.42 SJR 0.227 SNIP 0.088
Original language: English
ASJC Scopus subject areas: Molecular Medicine, Biochemistry, Biotechnology, Genetics
Keywords: DDSR1, LncRNA
Source: Scopus
Source ID: 84945932080

Research output: Contribution to journalArticleScientificpeer-review

Metabolic engineering of Acinetobacter baylyi ADP1 for removal of Clostridium butyricum growth inhibitors produced from lignocellulosic hydrolysates

Background: Pretreatment of lignocellulosic biomass can produce inhibitory compounds that are harmful for microorganisms used in the production of biofuels and other chemicals from lignocellulosic sugars. Selective inhibitor removal can be achieved with biodetoxification where microorganisms catabolize the inhibitors without consuming the sugars. We engineered the strictly aerobic Acinetobacter baylyi ADP1 for detoxification of lignocellulosic hydrolysates by removing the gene for glucose dehydrogenase, gcd, which catalyzes the first step in its glucose catabolism. Results: The engineered A. baylyi ADP1 strain was shown to be incapable of consuming the main sugar components of lignocellulosic hydrolysates, i.e., glucose, xylose, and arabinose, but rapidly utilized acetate and formate. Formate was consumed during growth on acetate and by stationary phase cells, and this was enhanced in the presence of a common aromatic inhibitor of lignocellulosic hydrolysates, 4-hydroxybenzoate. The engineered strain tolerated glucose well up to 70 g/l, and the consumption of glucose, xylose, or arabinose was not observed in prolonged cultivations. The engineered strain was applied in removal of oxygen, a gaseous inhibitor of anaerobic fermentations. Co-cultivation with the A. baylyi ADP1 gcd knockout strain under initially aerobic conditions allowed the strictly anaerobic Clostridium butyricum to grow and produce hydrogen (H2) from sugars of the enzymatic rice straw hydrolysate. Conclusions: We demonstrated that the model organism of bacterial genetics and metabolism, A. baylyi ADP1, could be engineered to be an efficient biodetoxification strain of lignocellulosic hydrolysates. Only one gene knockout was required to completely eliminate sugar consumption and the strain could be used in production of anaerobic conditions for the strictly anaerobic hydrogen producer, C. butyricum. Because of these encouraging results, we believe that A. baylyi ADP1 is a promising candidate for the detoxification of lignocellulosic hydrolysates for bioprocesses.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Industrial Bioengineering and Applied Organic Chemistry, Urban circular bioeconomy (UrCirBio), Rhodes University
Contributors: Kannisto, M. S., Mangayil, R. K., Shrivastava-Bhattacharya, A., Pletschke, B. I., Karp, M. T., Santala, V. P.
Publication date: 1 Dec 2015
Peer-reviewed: Yes

Publication information

Journal: Biotechnology for Biofuels
Volume: 8
Issue number: 1
Article number: 198
ISSN (Print): 1754-6834
Ratings: 
  • Scopus rating (2015): CiteScore 6.79 SJR 2.487 SNIP 1.957
Original language: English
ASJC Scopus subject areas: Energy(all), Management, Monitoring, Policy and Law, Biotechnology, Applied Microbiology and Biotechnology, Renewable Energy, Sustainability and the Environment
Keywords: Acinetobacter baylyi, Biodetoxification, Biohydrogen, Clostridium butyricum, Metabolic engineering, Rice straw hydrolysate
Source: Scopus
Source ID: 84956930091

Research output: Contribution to journalArticleScientificpeer-review

Tuning the Plasmonic Extinction Resonances of Hexagonal Arrays of Ag Nanoparticles

Plasmonically enhanced effects on a self-assembled, hexagonal array layer of ~4-nm silver nanoparticles are analyzed using three-dimensional finite-difference time-domain (3D FDTD) simulations and compared against experimentally measured extinction spectra. The effect of particle size, lattice spacing, and lack of monodispersity of the hexagonal array of silver nanoparticles on the extinction resonance was investigated to help determine optimal design specifications for efficient organic solar power harvesting.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Augmented Human Activities (AHA), Ohio State University, Department of Electrical and Computer Engineering
Contributors: Ravi, A., Luthra, A., Teixeira, F. L., Berger, P. R., Coe, J. V.
Number of pages: 8
Pages: 1505-1512
Publication date: 1 Dec 2015
Peer-reviewed: Yes

Publication information

Journal: Plasmonics
Volume: 10
Issue number: 6
ISSN (Print): 1557-1955
Ratings: 
  • Scopus rating (2015): CiteScore 2.07 SJR 0.755 SNIP 0.834
Original language: English
ASJC Scopus subject areas: Biochemistry, Biophysics, Biotechnology
Keywords: Active plasmonics, Metamaterials, Nanoparticles, Organic solar panels, Plasmon resonance
Source: Scopus
Source ID: 84947019436

Research output: Contribution to journalArticleScientificpeer-review

Simultaneous nutrient removal and lipid production with Chlorella vulgaris on sterilized and non-sterilized anaerobically pretreated piggery wastewater

Piggery wastewater is a potent nutrient source for microalgal lipid production. Wastewater has been usually sterilized when used for microalgal cultivation. This is uneconomical in large-scale applications. Therefore, lipid productivity of Chlorella vulgaris CY5 using sterilized and non-sterilized diluted anaerobically pretreated piggery wastewater was studied in batch reactors. The maximum average lipid productivity was obtained after 12 days of incubation and it was higher with the sterilized wastewater than with the non-sterilized one (117g/L/d vs. 91.3g/L/d), due to the higher biomass concentration. Because of the unexpected increase of dissolved organic carbon (DOC) in the cultures, second experiment was conducted to characterize the composition of produced DOC in non-sterilized wastewater. Carbohydrate content increased in the liquid phase but decreased in the biomass after nitrogen had been exhausted. After 12 days of incubation, soluble chemical oxygen demand (COD<inf>s</inf>) was 414±56mg/L, biomass production was 2.8±0.15g/L, and lipid content was 30.3±1.2wt%. Average lipid productivity from day zero to day 12 was 70.5±1.1g/L/d. C. vulgaris removed nutrients from the non-sterilized wastewater and produced oleaginous biomass, although the lipid productivity was higher with sterilized wastewater.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Industrial Bioengineering and Applied Organic Chemistry, Urban circular bioeconomy (UrCirBio), Center of Bioscience and Biotechnology, Research Center for Energy Technology and Strategy, National Cheng Kung University, Department of Environmental Engineering, Department of Chemical Engineering
Contributors: Marjakangas, J. M., Chen, C. Y., Lakaniemi, A. M., Puhakka, J. A., Whang, L. M., Chang, J. S.
Number of pages: 8
Pages: 177-184
Publication date: 5 Nov 2015
Peer-reviewed: Yes
Early online date: 23 Jul 2015

Publication information

Journal: Biochemical Engineering Journal
Volume: 103
ISSN (Print): 1369-703X
Ratings: 
  • Scopus rating (2015): CiteScore 2.75 SJR 0.952 SNIP 1.075
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Biomedical Engineering, Environmental Engineering
Keywords: Aerobic process, Lipid production, Microalgae, Piggery wastewater, Sterilization, Wastewater treatment
Source: Scopus
Source ID: 84939202209

Research output: Contribution to journalArticleScientificpeer-review

Comparison of different cationized proteins as biomaterials for nanoparticle-based ocular gene delivery

Cationized polymers have been proposed as transfection agents for gene therapy. The present work aims to improve the understanding of the potential use of different cationized proteins (atelocollagen, albumin and gelatin) as nanoparticle components and to investigate the possibility of modulating the physicochemical properties of the resulting nanoparticle carriers by selecting specific protein characteristics in an attempt to improve current ocular gene-delivery approaches. The toxicity profiles, as well as internalization and transfection efficiency, of the developed nanoparticles can be modulated by modifying the molecular weight of the selected protein and the amine used for cationization. The most promising systems are nanoparticles based on intermediate molecular weight gelatin cationized with the endogenous amine spermine, which exhibit an adequate toxicological profile, as well as effective association and protection of pDNA or siRNA molecules, thereby resulting in higher transfection efficiency and gene silencing than the other studied formulations.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Federal University of Rio Grande do Sul, University of Santiago de Compostela (USC), University Clinical Hospital of Santiago de Compostela (IDIS)
Contributors: Zorzi, G. K., Párraga, J. E., Seijo, B., Sanchez, A.
Number of pages: 9
Pages: 533-541
Publication date: 1 Nov 2015
Peer-reviewed: Yes

Publication information

Journal: Colloids and Surfaces B: Biointerfaces
Volume: 135
ISSN (Print): 0927-7765
Ratings: 
  • Scopus rating (2015): CiteScore 4.26 SJR 1.085 SNIP 1.232
Original language: English
ASJC Scopus subject areas: Biotechnology, Surfaces and Interfaces, Physical and Theoretical Chemistry, Colloid and Surface Chemistry
Keywords: Cationized proteins, Gene therapy, Nanoparticles, pDNA, siRNA
Source: Scopus
Source ID: 84939622417

Research output: Contribution to journalArticleScientificpeer-review

ESD qualification data used as the basis for building electrostatic discharge protected areas

ESD control programs that are based on the standards IEC61340-5-1 and ANSI/ESD S20.20 are targeted to provide safer handling of electronic parts now susceptible to damage by electrostatic discharge. However, ESD failures have occurred in EPA even when all standard control methods are met. To further improve EPAs, ESD control programs should be updated to cover all known common discharge scenarios, and multiple parallel ESD source parameters should be used to assess the level of ESD risks. In addition, a reliable ESD risk assessment should be based on discharge source circuit analysis and product sensitivity tests using the real discharge waveforms found in EPA.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Electronics and Communications Engineering, Research group: Wireless Identification and Sensing Systems Research Group, Sensing Systems for Wireless Medicine (MediSense), Cascade Metrology
Contributors: Tamminen, P., Viheriäkoski, T., Sydänheimo, L., Ukkonen, L.
Number of pages: 8
Pages: 174-181
Publication date: 1 Oct 2015
Peer-reviewed: Yes

Publication information

Journal: Journal of Electrostatics
Volume: 77
Article number: 3024
ISSN (Print): 0304-3886
Ratings: 
  • Scopus rating (2015): CiteScore 1.49 SJR 0.48 SNIP 1.183
Original language: English
ASJC Scopus subject areas: Electrical and Electronic Engineering, Electronic, Optical and Magnetic Materials, Surfaces, Coatings and Films, Condensed Matter Physics, Biotechnology
Keywords: CDM, Control program, EPA, ESD, HBM, Standards
Source: Scopus
Source ID: 84940760492

Research output: Contribution to journalArticleScientificpeer-review

Effects of anode potentials on bioelectrogenic conversion of xylose and microbial community compositions

The results on the effects of different anode potentials on current densities, coulombic efficiencies and microbial communities are contradictory and have not been studied with xylose, an important constituent of lignocellulosic materials. In this study, the effects of different anode potentials (+0.2, 0 and -0.2V vs. Ag/AgCl) on current generation, xylose degradation and microbial communities were examined with an exoelectrogenic enrichment culture originating from anaerobic sludge. Anode potential of +0.2V (vs. Ag/AgCl) resulted in the highest current density and coulombic efficiency of 1.5±0.2A/m<sup>2</sup> and 62±11%, respectively, and there was no accumulation of soluble metabolites. With anode potentials of 0 and -0.2V the current densities remained low and acetate, butyrate and propionate were detected in the end of batch runs. Different anode potentials resulted in substantial differences in the anodic bacterial species. At more positive anode potentials, Ochrobactrum intermedium reported to be capable of direct electron transfer dominated. At more negative anode potentials, a known mediator-producer, Alcaligenes faecalis, and Desulfitobacterium hafnience, that has been reported to use mediated electron transfer, were detected. This study shows that the anode potential has a substantial effect on microbial communities and on xylose metabolism.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Industrial Bioengineering and Applied Organic Chemistry, Urban circular bioeconomy (UrCirBio)
Contributors: Kokko, M. E., Mäkinen, A. E., Sulonen, M. L. K., Puhakka, J. A.
Number of pages: 5
Pages: 248-252
Publication date: 5 Sep 2015
Peer-reviewed: Yes
Early online date: 24 Jun 2015

Publication information

Journal: Biochemical Engineering Journal
Volume: 101
ISSN (Print): 1369-703X
Ratings: 
  • Scopus rating (2015): CiteScore 2.75 SJR 0.952 SNIP 1.075
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Biomedical Engineering, Environmental Engineering
Keywords: Anaerobic processes, Anode potential, Batch processing, Biocatalysis, Bioconversion, Microbial fuel cell
Source: Scopus
Source ID: 84936752873

Research output: Contribution to journalArticleScientificpeer-review

His-tagged norovirus-like particles: A versatile platform for cellular delivery and surface display

In addition to vaccines, noninfectious virus-like particles (VLPs) that mimic the viral capsid show an attractive possibility of presenting immunogenic epitopes or targeting molecules on their surface. Here, functionalization of norovirus-derived VLPs by simple non-covalent conjugation of various molecules is shown. By using the affinity between a surface-exposed polyhistidine-tag and multivalent tris-nitrilotriacetic acid (trisNTA), fluorescent dye molecules and streptavidin-biotin conjugated to trisNTA are displayed on the VLPs to demonstrate the use of these VLPs as easily modifiable nanocarriers as well as a versatile vaccine platform. The VLPs are able to enter and deliver surface-displayed fluorescent dye into HEK293T cells via a surface-attached cell internalization peptide (VSV-G). The ease of manufacturing, the robust structure of these VLPs, and the straightforward conjugation provide a technology, which can be adapted to various applications in biomedicine.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: BioMediTech, Integrated Technologies for Tissue Engineering Research (ITTE), Multi-scaled biodata analysis and modelling (MultiBAM), Environmental Science/Nanoscience Center, University of Tampere, Medical School, Goethe-University Frankfurt, Fimlab Laboratories Ltd
Contributors: Koho, T., Ihalainen, T. O., Stark, M., Uusi-Kerttula, H., Wieneke, R., Rahikainen, R., Blazevic, V., Marjomäki, V., Tampé, R., Kulomaa, M. S., Hytönen, V. P.
Number of pages: 10
Pages: 22-31
Publication date: 21 Jul 2015
Peer-reviewed: Yes

Publication information

Journal: European Journal of Pharmaceutics and Biopharmaceutics
Volume: 96
ISSN (Print): 0939-6411
Ratings: 
  • Scopus rating (2015): CiteScore 4.37 SJR 1.437 SNIP 1.458
Original language: English
ASJC Scopus subject areas: Biotechnology, Pharmaceutical Science
Keywords: Bioconjugation, Cell entry peptide, Drug delivery, Molecular display, Targeting, Virus-like particle (VLP)
Source: Scopus
Source ID: 84937598228

Research output: Contribution to journalArticleScientificpeer-review

Kinetics of the cellular intake of a gene expression inducer at high concentrations

From in vivo single-event measurements of the transient and steady-state transcription activity of a single-copy lac-ara-1 promoter in Escherichia coli, we characterize the intake kinetics of its inducer (IPTG) from the media. We show that the empirical data are well-fit by a model of intake assuming a bilayer membrane, with the passage through the second layer being rate-limiting, coupled to a stochastic, sub-Poissonian, multi-step transcription process. Using this model, we show that for a wide range of extracellular inducer levels (up to 1.25 mM) the intake process is diffusive-like, suggesting unsaturated membrane permeability. Inducer molecules travel from the periplasm to the cytoplasm in, on average, 31.7 minutes, strongly affecting cells' response time. The novel methodology followed here should aid the study of cellular intake mechanisms at the single-event level.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Signal Processing, Research group: Laboratory of Biosystem Dynamics-LBD, Multi-scaled biodata analysis and modelling (MultiBAM)
Contributors: Tran, H., Oliveira, S. M. D., Goncalves, N., Ribeiro, A. S.
Number of pages: 9
Pages: 2579-2587
Publication date: 20 Jul 2015
Peer-reviewed: Yes

Publication information

Journal: Molecular Biosystems
Volume: 11
Issue number: 9
ISSN (Print): 1742-206X
Ratings: 
  • Scopus rating (2015): CiteScore 3.04 SJR 1.26 SNIP 0.84
Original language: English
ASJC Scopus subject areas: Biotechnology, Molecular Biology
Source: Scopus
Source ID: 84938937101

Research output: Contribution to journalArticleScientificpeer-review

Bioactive glass ions as strong enhancers of osteogenic differentiation in human adipose stem cells

Bioactive glasses are known for their ability to induce osteogenic differentiation of stem cells. To elucidate the mechanism of the osteoinductivity in more detail, we studied whether ionic extracts prepared from a commercial glass S53P4 and from three experimental glasses (2-06, 1-06 and 3-06) are alone sufficient to induce osteogenic differentiation of human adipose stem cells. Cells were cultured using basic medium or osteogenic medium as extract basis. Our results indicate that cells stay viable in all the glass extracts for the whole culturing period, 14 days. At 14 days the mineralization in osteogenic medium extracts was excessive compared to the control. Parallel to the increased mineralization we observed a decrease in the cell amount. Raman and Laser Induced Breakdown Spectroscopy analyses confirmed that the mineral consisted of calcium phosphates. Consistently, the osteogenic medium extracts also increased osteocalcin production and collagen Type-I accumulation in the extracellular matrix at 13 days. Of the four osteogenic medium extracts, 2-06 and 3-06 induced the best responses of osteogenesis. However, regardless of the enhanced mineral formation, alkaline phosphatase activity was not promoted by the extracts. The osteogenic medium extracts could potentially provide a fast and effective way to differentiate human adipose stem cells in vitro.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Electronics and Communications Engineering, Research group: Biomaterials and Tissue Engineering Group, BioMediTech, Integrated Technologies for Tissue Engineering Research (ITTE), Tampere University Hospital, BioMediTech, University of Jyväskylä, Pirkanmaa Hospital District and School of Health Sciences, Adult Stem Cell Research Group, Regenerative Medicine, Adult Stem Cell Group, Johan Gadolin Process Chemistry Centre, Åbo Akademi University, National Center for Nanoscience and Technology (NCNST), Peking, China
Contributors: Ojansivu, M., Vanhatupa, S., Björkvik, L., Häkkänen, H., Kellomäki, M., Autio, R., Ihalainen, J. A., Hupa, L., Miettinen, S.
Number of pages: 14
Pages: 190-203
Publication date: 15 Jul 2015
Peer-reviewed: Yes

Publication information

Journal: Acta Biomaterialia
Volume: 21
ISSN (Print): 1742-7061
Ratings: 
  • Scopus rating (2015): CiteScore 6.58 SJR 2.02 SNIP 1.951
Original language: English
ASJC Scopus subject areas: Biomaterials, Biomedical Engineering, Biotechnology, Biochemistry, Molecular Biology
Keywords: Bioactive glass, Bone tissue engineering, Mesenchymal stem cell, Mineralization, Osteogenic differentiation

Bibliographical note

EXT="Autio, Reija"

Source: Scopus
Source ID: 84929951673

Research output: Contribution to journalArticleScientificpeer-review

Lipid production by eukaryotic microorganisms isolated from palm oil mill effluent

Microbial oil production combined with wastewater management is one option for a more sustainable future. Micrographs of microbial cultures enriched from palm oil mill effluent (POME) showed lipid inclusion in the eukaryotic cells, indicating the cells can accumulate lipids. However, enriching the culture did not increase the total lipids. Therefore, eukaryotic microorganisms were isolated from POME to investigate whether these microorganisms are potential lipid producers. Four strains were isolated, and their lipid synthesis capabilities were compared with known oleaginous yeasts in a synthetic oil-free medium. Two strains (identified as Galactomyces geotrichum and Graphium penicillioides) had the potential to accumulate lipid accumulation based on the increase in triacylglycerol content. G. penicillioides was the most promising strain for lipid production as this strain accumulated more lipids than the well-known oleaginous yeast Cryptococcus curvatus (29.1 ± 3.0. wt% vs. 20.2 ± 2.9. wt%). To our knowledge, oil synthesis and accumulation by G. penicillioides have not previously been reported.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Industrial Bioengineering and Applied Organic Chemistry, Urban circular bioeconomy (UrCirBio), National Cheng Kung University, Center of Bioscience and Biotechnology, Research Center for Energy Technology and Strategy, Neste Oil Oyj
Contributors: Marjakangas, J. M., Lakaniemi, A. M., Koskinen, P. E. P., Chang, J. S., Puhakka, J. A.
Number of pages: 7
Pages: 48-54
Publication date: 5 Jul 2015
Peer-reviewed: Yes

Publication information

Journal: Biochemical Engineering Journal
Volume: 99
ISSN (Print): 1369-703X
Ratings: 
  • Scopus rating (2015): CiteScore 2.75 SJR 0.952 SNIP 1.075
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Biomedical Engineering, Environmental Engineering
Keywords: Filamentous fungi, Lipid accumulation, Microbial growth, Palm oil mill effluent, Physiology, Yeast

Bibliographical note

EXT="Koskinen, Perttu E. P."

Source: Scopus
Source ID: 84924943977

Research output: Contribution to journalArticleScientificpeer-review

Bioluminescent whole-cell reporter gene assays as screening tools in the identification of antimicrobial natural product extracts

We describe novel tools, bioluminescent whole-cell reporter gene assays, for facilitating the use of natural products in antimicrobial drug discovery. As proof-of-concept, a plant extract library was screened and follow-up experiments were carried out. Primary results can be obtained in 2-4. h with high sensitivity, leading to significant improvements of the process.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Industrial Bioengineering and Applied Organic Chemistry, Centre for Drug Research, Helsinki University, Division of Pharmaceutical Biosciences
Contributors: Nybond, S., Karp, M., Yrjönen, T., Tammela, P.
Number of pages: 3
Pages: 54-56
Publication date: 1 Jul 2015
Peer-reviewed: Yes

Publication information

Journal: Journal of Microbiological Methods
Volume: 114
ISSN (Print): 0167-7012
Ratings: 
  • Scopus rating (2015): CiteScore 2.04 SJR 0.819 SNIP 0.849
Original language: English
ASJC Scopus subject areas: Microbiology, Molecular Biology, Microbiology (medical), Biotechnology
Keywords: Antibacterial, Bioluminescence, Cell-based assay, Escherichia coli, Natural products, Screening
Source: Scopus
Source ID: 84928920094

Research output: Contribution to journalArticleScientificpeer-review

Single-cell kinetics of a repressilator when implemented in a single-copy plasmid

Synthetic genetic clocks, such as the Elowitz-Leibler repressilator, will be key regulatory components of future synthetic circuits. We constructed a single-copy repressilator (SCR) by implementing the original repressilator circuit on a single-copy F-plasmid. After verifying its functionality, we studied its behaviour as a function of temperature and compared it with that of the original low-copy-number repressilator (LCR). Namely, we compared the period of oscillations, functionality (the fraction of cells exhibiting oscillations) and robustness to internal fluctuations (the fraction of expected oscillations that would occur). We found that, under optimal temperature conditions, the dynamics of the two systems differs significantly, although qualitatively they respond similarly to temperature changes. Exception to this is in the functionality, in which the SCR is higher at lower temperatures but lower at higher temperatures. Next, by adding IPTG to the medium at low and high concentrations during microscopy sessions, we showed that the functionality of the SCR is more robust to external perturbations, which indicates that the oscillatory behaviour of the LCR can be disrupted by affecting only a few of the copies in a cell. We conclude that the SCR, the first functional, synthetic, single-copy, ring-type genetic clock, is more robust to lower temperatures and to external perturbations than the original LCR. The SCR will be of use in future synthetic circuits, since it complements the array of tasks that the LCR can perform.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Research group: Laboratory of Biosystem Dynamics-LBD, Research group: Computational Systems Biology, Department of Signal Processing, Multi-scaled biodata analysis and modelling (MultiBAM), Prostate cancer research center (PCRC)
Contributors: Oliveira, S. M. D., Chandraseelan, J. G., Häkkinen, A., Goncalves, N. S. M., Yli-Harja, O., Startceva, S., S. Ribeiro, A.
Number of pages: 7
Pages: 1939-1945
Publication date: 1 Jul 2015
Peer-reviewed: Yes

Publication information

Journal: Molecular Biosystems
Volume: 11
Issue number: 7
ISSN (Print): 1742-206X
Ratings: 
  • Scopus rating (2015): CiteScore 3.04 SJR 1.26 SNIP 0.84
Original language: English
ASJC Scopus subject areas: Biotechnology, Molecular Biology
Source: Scopus
Source ID: 84934904914

Research output: Contribution to journalArticleScientificpeer-review

Using shRNA experiments to validate gene regulatory networks

Quantitative validation of gene regulatory networks (GRNs) inferred from observational expression data is a difficult task usually involving time intensive and costly laboratory experiments. We were able to show that gene knock-down experiments can be used to quantitatively assess the quality of large-scale GRNs via a purely data-driven approach (Olsen et al. 2014). Our new validation framework also enables the statistical comparison of multiple network inference techniques, which was a long-standing challenge in the field.In this Data in Brief we detail the contents and quality controls for the gene expression data (available from NCBI Gene Expression Omnibus repository with accession number GSE53091) associated with our study published in Genomics (Olsen et al. 2014). We also provide R code to access the data and reproduce the analysis presented in this article.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Signal Processing, BioMediTech, Research Community on Data-to-Decision (D2D), BioMediTech - Institute of Biosciences and Medical Technology, University of Toronto, Canada, Machine Learning Group, Interuniversity Institute of Bioinformatics in Brussels (IB), Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard School of Public Health, Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Centre, University Health Network University of Toronto, Department of Medical Biophysics, University of Toronto, Embedded Electronics research unit of the Bio Electro and Mechanical Systems (BEAMS) department of the Université Libre de Bruxelles
Contributors: Olsen, C., Fleming, K., Prendergast, N., Rubio, R., Emmert-Streib, F., Bontempi, G., Quackenbush, J., Haibe-Kains, B.
Number of pages: 4
Pages: 123-126
Publication date: 1 Jun 2015
Peer-reviewed: Yes

Publication information

Journal: Genomics Data
Volume: 4
ISSN (Print): 2213-5960
Ratings: 
  • Scopus rating (2015): CiteScore 0.42 SJR 0.227 SNIP 0.088
Original language: English
ASJC Scopus subject areas: Molecular Medicine, Biochemistry, Biotechnology, Genetics
Keywords: Colon cancer, Gene expression, Knock-down, Microarray, ShRNA
Source: Scopus
Source ID: 84929412251

Research output: Contribution to journalArticleScientificpeer-review

O-glycan repertoires on a mucin-type reporter protein expressed in CHO cell pools transiently transfected with O-glycan core enzyme cDNAs

Glyco-engineering of host cells is used to increase efficacy, decrease immunogenicity and increase circulatory half-lives of protein biopharmaceuticals. The effect of transiently expressed O-glycan core chain glycosyltransferases on O-glycan biosynthesis pathways in CHO cells is reported. Liquid chromatography-mass spectrometry and Western blotting were used to map the O-glycome of a mucin-type fusion protein transiently co-transfected with β1,3-. N-acetylglucosaminyltransferase 3 (extended C1 β3GnT3), core 2 β1,6-. N-acetylglucosaminyltransferase I (C2 β3GnT1) or core 3 β1,3-. N-acetylglucosaminyltransferase 6 (C3 β3GnT6) in CHO cells. Extended core 1 (GlcNAcβ1,3Galβ1,3GalNAc) and core 3 (GlcNAcβ1,3GalNAc), and increased expression of core 2 [Galβ1,3(GlcNAcβ1,6)GalNAc], O-glycans were generated on P-selectin glycoprotein ligand-1/mouse IgG2b (PSGL1/mIgG2b). Endogenous poly-. N-acetyllactosamine (poly-LacNAc) synthase elongated extended core 1 and core 3 generating O-glycans with up to five LacNAc repeats. Low amounts of core 3 O-glycans appeared upon extended C1 β3GnT3 expression. The α2,6-sialylated type 2 chain was detected upon co-transfection with the β-galactoside α2,6-sialyltransferase I. N-acetylglucosamine-6-. O-sulfotransferase 2 transferred sulfate to carbon 6 of GlcNAc in poly-LacNAc sequences. CHO cells with its known O-glycan repertoire can be used to express recombinant mucin-type proteins together with selected glycosyltransferases in order to recreate carbohydrate determinants on defined O-glycan chains. They will become important tools for assessing the core chain-dependent binding activity of carbohydrate-binding proteins.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Sahlgrenska Academy
Contributors: Liu, J., Jin, C., Cherian, R. M., Karlsson, N. G., Holgersson, J.
Number of pages: 13
Pages: 77-89
Publication date: 1 Apr 2015
Peer-reviewed: Yes

Publication information

Journal: Journal of Biotechnology
Volume: 199
ISSN (Print): 0168-1656
Ratings: 
  • Scopus rating (2015): CiteScore 2.87 SJR 1.068 SNIP 0.988
Original language: English
ASJC Scopus subject areas: Biotechnology, Applied Microbiology and Biotechnology, Medicine(all)
Keywords: CHO, Core structure, Glycosyltransferase, Mucin, O-glycans
Source: Scopus
Source ID: 84924081123

Research output: Contribution to journalArticleScientificpeer-review

Ageing-associated changes in the human DNA methylome: Genomic locations and effects on gene expression

Background: Changes in DNA methylation are among the mechanisms contributing to the ageing process. We sought to identify ageing-associated DNA methylation changes at single-CpG-site resolution in blood leukocytes and to ensure that the observed changes were not due to differences in the proportions of leukocytes. The association between DNA methylation changes and gene expression levels was also investigated in the same individuals. Results: We identified 8540 high-confidence ageing-associated CpG sites, 46% of which were hypermethylated in nonagenarians. The hypermethylation-associated genes belonged to a common category: they were predicted to be regulated by a common group of transcription factors and were enriched in a related set of GO terms and canonical pathways. Conversely, for the hypomethylation-associated genes only a limited set of GO terms and canonical pathways were identified. Among the 8540 CpG sites associated with ageing, methylation level of 377 sites was also associated with gene expression levels. These genes were enriched in GO terms and canonical pathways associated with immune system functions, particularly phagocytosis. Conclusions: We find that certain ageing-associated immune-system impairments may be mediated via changes in DNA methylation. The results also imply that ageing-associated hypo- and hypermethylation are distinct processes: hypermethylation could be caused by programmed changes, whereas hypomethylation could be the result of environmental and stochastic processes.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Gerontology Research Center, School of Management (JKK), Fimlab Laboratories Ltd
Contributors: Marttila, S., Kananen, L., Häyrynen, S., Jylhävä, J., Nevalainen, T., Hervonen, A., Jylhä, M., Nykter, M., Hurme, M.
Publication date: 14 Mar 2015
Peer-reviewed: Yes

Publication information

Journal: BMC Genomics
Volume: 16
Issue number: 1
Article number: 179
ISSN (Print): 1471-2164
Ratings: 
  • Scopus rating (2015): CiteScore 4.3 SJR 2.348 SNIP 1.159
Original language: English
ASJC Scopus subject areas: Biotechnology, Genetics
Keywords: Ageing, DNA methylation, Epigenetics, Gene expression, Hypermethylation, Hypomethylation, Methylome, Molecular ageing, PBMCs
Source: Scopus
Source ID: 84928012878

Research output: Contribution to journalArticleScientificpeer-review

Multi-stable dynamics of the non-adiabatic repressilator

The assumption of the fast binding of transcription factors (TFs) to promoters is a typical point in studies of synthetic genetic circuits functioning in bacteria. Although the assumption is effective for simplifying the models, it becomes questionable in the light of in vivo measurements of the times TF spends searching for its cognate DNA sites. We investigated the dynamics of the full idealized model of the paradigmatic genetic oscillator, the repressilator, using deterministic mathematical modelling and stochastic simulations. We found (using experimentally approved parameter values) that decreases in the TF binding rate changes the type of transition between steady state and oscillation. As a result, this gives rise to the hysteresis region in the parameter space, where both the steady state and the oscillation coexist. We further show that the hysteresis is persistent over a considerable range of the parameter values, but the presence of the oscillations is limited by the low rate of TF dimer degradation. Finally, the stochastic simulation of the model confirms the hysteresis with switching between the two attractors, resulting in highly skewed period distributions. Moreover, intrinsic noise stipulates trains of large-amplitude modulations around the stable steady state outside the hysteresis region, which makes the period distributions bimodal.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Mathematics, Research group: MAT Inverse Problems, Mathematical modelling with wide societal impact (MathImpact), Department of Theoretical Physics, Lebedev Physical Institution
Contributors: Potapov, I., Zhurov, B., Volkov, E.
Publication date: 6 Mar 2015
Peer-reviewed: Yes

Publication information

Journal: Journal of the Royal Society. Interface
Volume: 12
Issue number: 104
Article number: 20141315
ISSN (Print): 1742-5689
Ratings: 
  • Scopus rating (2015): CiteScore 3.5 SJR 1.823 SNIP 1.537
Original language: English
ASJC Scopus subject areas: Biophysics, Biotechnology, Bioengineering, Biomedical Engineering, Biomaterials, Biochemistry
Keywords: Adiabatic, Bimodality, Genetic oscillator, Hysteresis, Multi-stability
Source: Scopus
Source ID: 84923240824

Research output: Contribution to journalArticleScientificpeer-review

Efficient preparation of shuffled DNA libraries through recombination (Gateway) cloning

Efficient and robust subcloning is essential for the construction of high-diversity DNA libraries in the field of directed evolution. We have developed a more efficient method for the subcloning of DNAshuffled libraries by employing recombination cloning (Gateway). The Gateway cloning procedure was performed directly after the gene reassembly reaction, without additional purification and amplification steps, thus simplifying the conventional DNA shuffling protocols. Recombination-based cloning, directly from the heterologous reassembly reaction, conserved the high quality of the library and reduced the time required for the library construction. The described method is generally compatible for the construction of DNA-shuffled gene libraries.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Fimlab Laboratories Ltd, Next Biomed Technologies NBT Oy, Karolinska University Hospital, Tampere University Hospital
Contributors: Lehtonen, S. I., Taskinen, B., Ojala, E., Kukkurainen, S., Rahikainen, R., Riihimäki, T. A., Laitinen, O. H., Kulomaa, M. S., Hytönen, V. P.
Number of pages: 6
Pages: 23-28
Publication date: 2015
Peer-reviewed: Yes

Publication information

Journal: Protein Engineering Design and Selection
Volume: 28
Issue number: 1
ISSN (Print): 1741-0126
Ratings: 
  • Scopus rating (2015): CiteScore 2.46 SJR 1.301 SNIP 0.798
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Medicine(all), Biochemistry, Molecular Biology
Keywords: Directed evolution, DNA library, DNA shuffling, Phage display recombination cloning
Source: Scopus
Source ID: 84983121996

Research output: Contribution to journalArticleScientificpeer-review

Interaction with serum albumin as a factor of the photodynamic efficacy of novel bacteriopurpurinimide derivatives

Optimization of the chemical structure of antitumor photosensitizers (PSs) is aimed at increasing their affinity to a transport protein, albumin and irreversible light-induced tumor cell damage. Bacteriopurpurinimide derivatives are promising PSs thanks to their ability to absorb light in the near infrared spectral region. Using spectrophotometry, we show that two new bacteriopurpurinimide derivatives with different substituents at the N atoms of the imide exocycle and the pyrrole ring A are capable of forming non-covalent complexes with human serum albumin (HSA). The association constant (calculated with the Benesi-Hildebrand equation) for N-ethoxybacteriopurpurinimide ethyloxime (compound 1) is higher than that for the methyl ether of methoxybacteriopurpurinimide (compound 2) (1.18×105 M-1 vs. 1.26×104 M-1, respectively). Molecular modeling provides details of the atomic interactions between 1 and 2 and amino acid residues in the FA1 binding site of HSA. The ethoxy group stabilizes the position of 1 within this site due to hydrophobic interaction with the protein. The higher affinity of 1 for HSA makes this compound more potent than 2 in photodynamic therapy for cultured human colon carcinoma cells. Photoactivation of 1 and 2 in cells induces rapid (within a few minutes of irradiation) necrosis. This mechanism of cell death may be efficient for eliminating tumors resistant to other therapies.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Emanuel’ Institute of Biochemical Physics, Russian Academy of Sciences, St. Petersburg State Polytechnical University, M.V. Lomonosov Moscow State University of Fine Chemical Technologies, N.N. Blokhin Russian Cancer Research Center, Russian Academy of Medical Sciences, Georgian Technical University
Contributors: Akimova, A. V., Rychkov, G. N., Grin, M. A., Filippova, N. A., Golovina, G. V., Durandin, N. A., Vinogradov, A. M., Kokrashvili, T. A., Mironov, A. F., Shtil, A. A., Kuzmin, V. A.
Number of pages: 8
Pages: 109-116
Publication date: 2015
Peer-reviewed: Yes

Publication information

Journal: ACTA NATURAE
Volume: 7
Issue number: 1
ISSN (Print): 2075-8251
Ratings: 
  • Scopus rating (2015): CiteScore 1.79 SJR 0.658 SNIP 0.887
Original language: English
ASJC Scopus subject areas: Biotechnology, Biochemistry, Molecular Medicine, Molecular Biology
Keywords: Albumin, Association constant, Cancer, Necrosis, Photodynamic therapy, Photosensitizers
Source: Scopus
Source ID: 84929151488

Research output: Contribution to journalArticleScientificpeer-review

Switchavidin: Reversible biotin-avidin-biotin bridges with high affinity and specificity

Switchavidin is a chicken avidin mutant displaying reversible binding to biotin, an improved binding affinity toward conjugated biotin, and low nonspecific binding due to reduced surface charge. These properties make switchavidin an optimal tool in biosensor applications for the reversible immobilization of biotinylated proteins on biotinylated sensor surfaces. Furthermore, switchavidin opens novel possibilities for patterning, purification, and labeling. (Graph Presented).

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), Multi-scaled biodata analysis and modelling (MultiBAM), Fimlab Laboratories Ltd, Johannes Kepler University, Tampere University Hospital
Contributors: Taskinen, B., Zauner, D., Lehtonen, S. I., Koskinen, M., Thomson, C., Kähkönen, N., Kukkurainen, S., Määttä, J. A. E., Ihalainen, T. O., Kulomaa, M. S., Gruber, H. J., Hytönen, V. P.
Number of pages: 11
Pages: 2233-2243
Publication date: 17 Dec 2014
Peer-reviewed: Yes

Publication information

Journal: Bioconjugate Chemistry
Volume: 25
Issue number: 12
ISSN (Print): 1043-1802
Ratings: 
  • Scopus rating (2014): CiteScore 4.85 SJR 1.711 SNIP 1.164
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Organic Chemistry, Pharmaceutical Science, Biomedical Engineering, Pharmacology, Medicine(all)
Source: Scopus
Source ID: 84918539954

Research output: Contribution to journalArticleScientificpeer-review

The talin-integrin interface under mechanical stress

The major mechanical function of talin is to couple the β-integrin cytoplasmic tails to actin filaments. A variety of β-integrin tails contain conserved binding motifs for talin, and recent research shows that β-integrins differ both in affinity to talin and preferences for other cytoplasmic adaptor proteins. While talin predominantly links β3 integrins to actin filaments within the peripheral cell adhesion sites, talin can become replaced by other integrin adaptor proteins through their overlapping binding sites on integrin tails. Although the NPxY motif in the β-integrin tail is important for talin recognition, our simulations suggest considerably smaller contribution of the NPxY motif in the force resistance of the talin-integrin complex than for the residues upstream of the NPxY. It might thus be possible for the NPxY motif to detach from talin and interact with other integrin binding proteins while the β-integrin still remains bound to talin. The epithelial integrin β6 reportedly activates latent TGFβ1, and we propose that its function may involve direct interaction with talin.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Fimlab Laboratories Ltd, HCI e 486.1, School of Management (JKK)
Contributors: Kukkurainen, S., Määttä, J. A., Saeger, J., Valjakka, J., Vogel, V., Hytönen, V. P.
Number of pages: 12
Pages: 3217-3228
Publication date: 1 Dec 2014
Peer-reviewed: Yes

Publication information

Journal: Molecular Biosystems
Volume: 10
Issue number: 12
ISSN (Print): 1742-206X
Ratings: 
  • Scopus rating (2014): CiteScore 3.06 SJR 1.348 SNIP 0.832
Original language: English
ASJC Scopus subject areas: Biotechnology, Molecular Biology, Medicine(all)
Source: Scopus
Source ID: 84908447927

Research output: Contribution to journalArticleScientificpeer-review

Rapid, Brushless Self-assembly of a PS-b-PDMS Block Copolymer for Nanolithography

Block copolymers (BCP) are highly promising self-assembling precursors for scalable nanolithography. Very regular BCP nanopatterns can be used as on-chip etch masks. The first step in the processing of BCP thin films is usually the chemical modification of the substrate surface, typically by grafting of a brush layer that renders the surface energy neutral relative to the constituent blocks. We provide here a first study on rapid, low temperature self-assembly of PS-. b-PDMS (polystyrene-. block-polydimethylsiloxane) on silicon substrates without a brush layer. We show that it forms line and antidot patterns after short solvo-thermal annealing. Unlike previous reports on this system, low temperature and short annealing time provide self-assembly in homogeneous thin films covering large substrate areas. This on-chip mask was then used for pattern transfer to the underlying silicon substrate. SEM (scanning electron microscope) images reveal silicon nanowires relative to the PDMS patterns of the BCP mask.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Frontier Photonics, Department of Micro and Nanotechnology, Danmarks Tekniske Universitet, DTU Informatik, Center for Nanostructured Graphene, Trinity College Dublin
Contributors: Rasappa, S., Schulte, L., Borah, D., Morris, M. A., Ndoni, S.
Number of pages: 5
Pages: 1-5
Publication date: 1 Oct 2014
Peer-reviewed: Yes

Publication information

Journal: Colloids and Interface Science Communications
Volume: 2
ISSN (Print): 2215-0382
Original language: English
ASJC Scopus subject areas: Biotechnology, Colloid and Surface Chemistry, Physical and Theoretical Chemistry, Materials Chemistry, Surfaces, Coatings and Films
Keywords: Aspect ratio, Brushless, Dry etching, Lines and antidots, Pattern transfer, PS-b-PDMS, Self-assembly, Silicon nanostructures, Soft mask template, Solvo-thermal annealing
Source: Scopus
Source ID: 84919650698

Research output: Contribution to journalArticleScientificpeer-review

Mixotrophic cultivation of oleaginous Chlorella sp. KR-1 mediated by actual coal-fired flue gas for biodiesel production

Flue gases mainly consist of CO<inf>2</inf> that can be utilized to facilitate microalgal culture for bioenergy production. In the present study, to evaluate the feasibility of the utilization of flue gas from a coal-burning power plant, an indigenous and high-CO<inf>2</inf>-tolerant oleaginous microalga, Chlorella sp. KR-1, was cultivated under mixotrophic conditions, and the results were evaluated. When the culture was mediated by flue gas, highest biomass (0.8 g cells/L·d) and FAME (fatty acid methyl esters) productivity (121 mg/L·d) were achieved in the mixotrophic mode with 5 g/L glucose, 5 mM nitrate, and a flow rate of 0.2 vvm. By contrast, the photoautotrophic cultivation resulted in a lower biomass (0.45 g cells/L·d) and a lower FAME productivity (60.2 mg/L·d). In general, the fatty acid profiles of Chlorella sp. KR-1 revealed meaningful contents (>40 % of saturated and mono-unsaturated fatty acids) under the mixotrophic condition, which enables the obtainment of a better quality of biodiesel than is possible under the autotrophic condition. Conclusively then, it was established that a microalgal culture mediated by flue gas can be improved by adoption of mixotrophic cultivation systems.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Urban circular bioeconomy (UrCirBio), Korea Institute of Energy Research, Pusan National University, Gachon University, Korea Basic Science Institute
Contributors: Praveenkumar, R., Kim, B., Choi, E., Lee, K., Cho, S., Hyun, J. S., Park, J. Y., Lee, Y. C., Lee, H. U., Lee, J. S., Oh, Y. K.
Number of pages: 12
Pages: 2083-2094
Publication date: 12 Sep 2014
Peer-reviewed: Yes

Publication information

Journal: Bioprocess and Biosystems Engineering
Volume: 37
Issue number: 10
ISSN (Print): 1615-7591
Ratings: 
  • Scopus rating (2014): CiteScore 1.95 SJR 0.699 SNIP 0.964
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Medicine(all)
Keywords: Biodiesel, Chlorella sp. KR-1, Coal-fired flue gas, Mixotrophic culture
Source: Scopus
Source ID: 84924759723

Research output: Contribution to journalArticleScientificpeer-review

Molecular engineering of avidin and hydrophobin for functional self-assembling interfaces

Control over the functionality of interfaces through biomolecular engineering is a central tool for nanoscale technology as well as many current applications of biology. In this work we designed fusion proteins that combined the surface adhesion and interfacial activity of a hydrophobin-protein together with the high affinity biotin-binding capability of an avidin-protein. We found that an overall architecture that was based on a circularly permuted version of avidin, dual-chain avidin, and hydrophobin gave a highly functional combination. The protein was produced in the filamentous fungus Trichoderma reesei and was efficiently purified using an aqueous two-phase partitioning procedure. The surface adhesive properties were widely different compared to wild-type avidin. Functional characterization showed that the protein assembled on hydrophobic surfaces as a thin layer even at very low concentrations and efficiently bound a biotinylated compound. The work shows how the challenge of creating a fusion protein with proteins that form multimers can be solved by structural design and how protein self-assembly can be used to efficiently functionalize interfaces.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), VTT Technical Research Centre of Finland, Fimlab Laboratories Ltd, Tampere University Hospital, Aalto University
Contributors: Kurppa, K., Hytönen, V. P., Nakari-Setälä, T., Kulomaa, M. S., Linder, M. B.
Number of pages: 8
Pages: 102-109
Publication date: 1 Aug 2014
Peer-reviewed: Yes

Publication information

Journal: Colloids and Surfaces B: Biointerfaces
Volume: 120
ISSN (Print): 0927-7765
Ratings: 
  • Scopus rating (2014): CiteScore 4.53 SJR 1.21 SNIP 1.56
Original language: English
ASJC Scopus subject areas: Surfaces and Interfaces, Biotechnology, Colloid and Surface Chemistry, Physical and Theoretical Chemistry, Medicine(all)
Keywords: Avidin, Biofunctional surface, Hydrophobin, Nanomaterial, Protein engineering
Source: Scopus
Source ID: 84901790623

Research output: Contribution to journalArticleScientificpeer-review

Assessment of metabolic flux distribution in the thermophilic hydrogen producer Caloramator celer as affected by external pH and hydrogen partial pressure

Background: Caloramator celer is a strict anaerobic, alkalitolerant, thermophilic bacterium capable of converting glucose to hydrogen (H2), carbon dioxide, acetate, ethanol and formate by a mixed acid fermentation. Depending on the growth conditions C. celer can produce H2 at high yields. For a biotechnological exploitation of this bacterium for H2 production it is crucial to understand the factors that regulate carbon and electron fluxes and therefore the final distribution of metabolites to channel the metabolic flux towards the desired product.Results: Combining experimental results from batch fermentations with genome analysis, reconstruction of central carbon metabolism and metabolic flux analysis (MFA), this study shed light on glucose catabolism of the thermophilic alkalitolerant bacterium C. celer. Two innate factors pertaining to culture conditions have been identified to significantly affect the metabolic flux distribution: culture pH and partial pressures of H2 (PH2). Overall, at alkaline to neutral pH the rate of biomass synthesis was maximized, whereas at acidic pH the lower growth rate and the less efficient biomass formation are accompanied with more efficient energy recovery from the substrate indicating high cell maintenance possibly to sustain intracellular pH homeostasis. Higher H2 yields were associated with fermentation at acidic pH as a consequence of the lower synthesis of other reduced by-products such as formate and ethanol. In contrast, PH2 did not affect the growth of C. celer on glucose. At high PH2 the cellular redox state was balanced by rerouting the flow of carbon and electrons to ethanol and formate production allowing unaltered glycolytic flux and growth rate, but resulting in a decreased H2 synthesis.Conclusion: C. celer possesses a flexible fermentative metabolism that allows redistribution of fluxes at key metabolic nodes to simultaneously control redox state and efficiently harvest energy from substrate even under unfavorable conditions (i.e. low pH and high PH2). With the H2 production in mind, acidic pH and low PH2 should be preferred for a high yield-oriented process, while a high productivity-oriented process can be achieved at alkaline pH and high PH2. © 2014 Ciranna et al.; licensee BioMed Central Ltd.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Industrial Bioengineering and Applied Organic Chemistry, Tampere University of Technology, Urban circular bioeconomy (UrCirBio), Lunds Universitet / Lunds Tekniska Högskola, Lund Univ, Lund University, Department of Applied Microbiology
Contributors: Ciranna, A., Pawar, S. S., Santala, V., Karp, M., van Niel, E. W. J.
Publication date: 28 Mar 2014
Peer-reviewed: Yes

Publication information

Journal: Microbial Cell Factories
Volume: 13
Issue number: 1
Article number: 48
ISSN (Print): 1475-2859
Ratings: 
  • Scopus rating (2014): CiteScore 4.25 SJR 1.757 SNIP 1.501
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Applied Microbiology and Biotechnology
Keywords: Biohydrogen production, Caloramator, Ethanol, Fermentation, Formate, Hydrogen tolerance, Metabolic flux analysis, Metabolic shift, Pyruvate node, Redox state

Bibliographical note

Contribution: organisation=keb,FACT1=1<br/>Portfolio EDEND: 2014-04-29<br/>Publisher name: BioMed Central Ltd.

Source: researchoutputwizard
Source ID: 236

Research output: Contribution to journalArticleScientificpeer-review

Metabolic engineering of Acinetobacter baylyi ADP1 for improved growth on gluconate and glucose

A high growth rate in bacterial cultures is usually achieved by optimizing growth conditions, but metabolism of the bacterium limits the maximal growth rate attainable on the carbon source used. This limitation can be circumvented by engineering the metabolism of the bacterium. Acinetobacter baylyi has become a model organism for studies of bacterial metabolism and metabolic engineering due to its wide substrate spectrum and easy-to-engineer genome. It produces naturally storage lipids, such as wax esters, and has a unique gluconate catabolism as it lacks a gene for pyruvate kinase. We engineered the central metabolism of A. baylyi ADP1 more favorable for gluconate catabolism by expressing the pyruvate kinase gene (pykF) of Escherichia coli. This modification increased growth rate when cultivated on gluconate or glucose as a sole carbon source in a batch cultivation. The engineered cells reached stationary phase on these carbon sources approximately twice as fast as control cells carrying an empty plasmid and produced similar amount of biomass. Furthermore, when grown on either gluconate or glucose, pykF expression did not lead to significant accumulation of overflow metabolites and consumption of the substrate remained unaltered. Increased growth rate on glucose was not accompanied with decreased wax ester production, and the pykF-expressing cells accumulated significantly more of these storage lipids with respect to cultivation time.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Industrial Bioengineering and Applied Organic Chemistry, Tampere University of Technology, Urban circular bioeconomy (UrCirBio)
Contributors: Kannisto, M., Aho, T., Karp, M., Santala, V.
Number of pages: 7
Pages: 7021-7027
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Applied and Environmental Microbiology
Volume: 80
Issue number: 22
ISSN (Print): 0099-2240
Ratings: 
  • Scopus rating (2014): CiteScore 4.02 SJR 1.872 SNIP 1.394
Original language: English
ASJC Scopus subject areas: Applied Microbiology and Biotechnology, Food Science, Biotechnology, Ecology, Medicine(all)

Bibliographical note

Contribution: organisation=keb,FACT1=1<br/>Portfolio EDEND: 2014-11-20<br/>Publisher name: American Society for Microbiology

Source: researchoutputwizard
Source ID: 650

Research output: Contribution to journalArticleScientificpeer-review

Murein lytic enzyme TgaA of Bifidobacterium bifidum MIMBb75 modulates dendritic cell maturation through its cysteine- and histidine-dependent amidohydrolase/peptidase (CHAP) amidase domain

Bifidobacteria are Gram-positive inhabitants of the human gastrointestinal tract that have evolved close interaction with their host and especially with the host's immune system. The molecular mechanisms underlying such interactions, however, are largely unidentified. In this study, we investigated the immunomodulatory potential of Bifidobacterium bifidum MIMBb75, a bacterium of human intestinal origin commercially used as a probiotic. Particularly, we focused our attention on TgaA, a protein expressed on the outer surface of MIMBb75's cells and homologous to other known bacterial immunoactive proteins. TgaA is a peptidoglycan lytic enzyme containing two active domains: lytic murein transglycosylase (LT) and cysteine- and histidine-dependent amidohydrolase/peptidase (CHAP). We ran immunological experiments stimulating dendritic cells (DCs) with the B. bifidum MIMBb75 and TgaA, with the result that both the bacterium and the protein activated DCs and triggered interleukin-2 (IL-2) production. In addition, we observed that the heterologous expression of TgaA in Bifidobacterium longum transferred to the bacterium the ability to induce IL-2. Subsequently, immunological experiments performed using two purified recombinant proteins corresponding to the single domains LT and CHAP demonstrated that the CHAP domain is the immune-reactive region of TgaA. Finally, we also showed that TgaA-dependent activation of DCs requires the protein CD14, marginally involves TRIF, and is independent of Toll-like receptor 4 (TLR4) and MyD88. In conclusion, our study suggests that the bacterial CHAP domain is a novel microbe-associated molecular pattern actively participating in the cross talk mechanisms between bifidobacteria and the host's immune system. © 2014, American Society for Microbiology.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Research group: Industrial Bioengineering and Applied Organic Chemistry, Tampere University of Technology, Urban circular bioeconomy (UrCirBio), Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, Department of Biotechnology and Biosciences, University of Milano-Bicocca
Contributors: Guglielmetti, S., Zanoni, I., Balzaretti, S., Miriani, M., Taverniti, V., de Noni, I., Presti, I., Stuknyte, M., Scarafoni, A., Arioli, S., Iametti, S., Bonomi, F., Mora, D., Karp, M., Granucci, F.
Number of pages: 8
Pages: 5170-5177
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Applied and Environmental Microbiology
Volume: 80
Issue number: 17
ISSN (Print): 0099-2240
Ratings: 
  • Scopus rating (2014): CiteScore 4.02 SJR 1.872 SNIP 1.394
Original language: English
ASJC Scopus subject areas: Applied Microbiology and Biotechnology, Food Science, Biotechnology, Ecology

Bibliographical note

Contribution: organisation=keb,FACT1=1<br/>Portfolio EDEND: 2014-05-19<br/>Publisher name: American Society for Microbiology

Source: researchoutputwizard
Source ID: 374

Research output: Contribution to journalArticleScientificpeer-review

Report from the 2nd Summer School in Computational Biology organized by the Queen's University of Belfast

In this paper, we present a meeting report for the 2nd Summer School in Computational Biology organized by the Queen's University of Belfast. We describe the organization of the summer school, its underlying concept and student feedback we received after the completion of the summer school.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Research Community on Data-to-Decision (D2D), Computational Biology and Machine Learning, Queen's University, Belfast, Northern Ireland
Contributors: Emmert-Streib, F., Zhang, S. D., Hamilton, P.
Number of pages: 3
Pages: 37-39
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Genomics Data
Volume: 2
ISSN (Print): 2213-5960
Ratings: 
  • Scopus rating (2014): CiteScore 0.33 SJR 0.238 SNIP 0.111
Original language: English
ASJC Scopus subject areas: Molecular Medicine, Biochemistry, Biotechnology, Genetics
Keywords: Computational biology, Genomics data, High-throughput data
Source: Scopus
Source ID: 84920678698

Research output: Contribution to journalArticleScientificpeer-review

TgaA, a VirB1-like component belonging to a putative type IV secretion system of Bifidobacterium bifidum MIMBb75

Bifidobacterium bifidum MIMBb75 is a human intestinal isolate demonstrated to be interactive with the host and efficacious as a probiotic. However, the molecular biology of this microorganism is yet largely unknown. For this reason, we undertook wholegenome sequencing of B. bifidum MIMBb75 to identify potential genetic factors that would explain the metabolic and probiotic attributes of this bacterium. Comparative genomic analysis revealed a 45-kb chromosomal region that comprises 19 putative genes coding for a potential type IV secretion system (T4SS). Thus, we undertook the initial characterization of this genetic region by studying the putative virB1-like gene, named tgaA. Gene tgaA encodes a peptidoglycan lytic enzyme containing two active domains: lytic murein transglycosylase (LT, cd00254.3) and cysteine- and histidine-dependent amidohydrolase/peptidase (CHAP, pfam05257.4). By means of several in vitro assays, we experimentally confirmed that protein TgaA, consistent with its computationally assigned role, has peptidoglycan lytic activity, which is principally associated to the LT domain. Furthermore, immunofluorescence and immunogold labeling showed that the protein TgaA is abundantly expressed on the cell surface of B. bifidum MIMBb75. According to the literature, the T4SSs, which have not been characterized before in bifidobacteria, can have important implications for bacterial cell-to-cell communication as well as cross talk with host cells, justifying the interest for further studies aimed at the investigation of this genetic region. © 2014, American Society for Microbiology.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Department of Chemistry and Bioengineering, Urban circular bioeconomy (UrCirBio)
Contributors: Guglielmetti, S., Balzaretti, S., Taverniti, V., Miriani, M., Milani, C., Scarafoni, A., Corona, S., Ciranna, A., Arioli, S., Santala, V., Iametti, S., Bonomi, F., Ventura, M., Mora, D., Karp, M.
Number of pages: 9
Pages: 5161-5169
Publication date: 2014
Peer-reviewed: Yes

Publication information

Journal: Applied and Environmental Microbiology
Volume: 80
Issue number: 17
ISSN (Print): 0099-2240
Ratings: 
  • Scopus rating (2014): CiteScore 4.02 SJR 1.872 SNIP 1.394
Original language: English
ASJC Scopus subject areas: Applied Microbiology and Biotechnology, Food Science, Biotechnology, Ecology

Bibliographical note

Contribution: organisation=keb,FACT1=1<br/>Portfolio EDEND: 2014-09-12<br/>Publisher name: American Society for Microbiology

Source: researchoutputwizard
Source ID: 373

Research output: Contribution to journalArticleScientificpeer-review

Reversible biofunctionalization of surfaces with a switchable mutant of avidin

Label-free biosensors detect binding of prey molecules (″ analytes″) to immobile bait molecules on the sensing surface. Numerous methods are available for immobilization of bait molecules. A convenient option is binding of biotinylated bait molecules to streptavidin-functionalized surfaces, or to biotinylated surfaces via biotin-avidin-biotin bridges. The goal of this study was to find a rapid method for reversible immobilization of biotinylated bait molecules on biotinylated sensor chips. The task was to establish a biotin-avidin-biotin bridge which was easily cleaved when desired, yet perfectly stable under a wide range of measurement conditions. The problem was solved with the avidin mutant M96H which contains extra histidine residues at the subunit-subunit interfaces. This mutant was bound to a mixed self-assembled monolayer (SAM) containing biotin residues on 20% of the oligo(ethylene glycol)-terminated SAM components. Various biotinylated bait molecules were bound on top of the immobilized avidin mutant. The biotin-avidin-biotin bridge was stable at pH ≥3, and it was insensitive to sodium dodecyl sulfate (SDS) at neutral pH. Only the combination of citric acid (2.5%, pH 2) and SDS (0.25%) caused instantaneous cleavage of the biotin-avidin-biotin bridge. As a consequence, the biotinylated bait molecules could be immobilized and removed as often as desired, the only limit being the time span for reproducible chip function when kept in buffer (2-3 weeks at 25 C). As expected, the high isolectric pH (pI) of the avidin mutant caused nonspecific adsorption of proteins. This problem was solved by acetylation of avidin (to pI <5), or by optimization of SAM formation and passivation with biotin-BSA and BSA.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Johannes Kepler University, Fimlab Laboratories Ltd, University of Salzburg, University of Basel, University of South Bohemia, Goethe-University Frankfurt
Contributors: Pollheimer, P., Taskinen, B., Scherfler, A., Gusenkov, S., Creus, M., Wiesauer, P., Zauner, D., Schöfberger, W., Schwarzinger, C., Ebner, A., Tampé, R., Stutz, H., Hytönen, V. P., Gruber, H. J.
Number of pages: 13
Pages: 1656-1668
Publication date: 16 Oct 2013
Peer-reviewed: Yes

Publication information

Journal: Bioconjugate Chemistry
Volume: 24
Issue number: 10
ISSN (Print): 1043-1802
Ratings: 
  • Scopus rating (2013): CiteScore 5.12 SJR 2.02 SNIP 1.201
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Organic Chemistry, Pharmaceutical Science, Biomedical Engineering, Pharmacology
Source: Scopus
Source ID: 84886070072

Research output: Contribution to journalArticleScientificpeer-review

Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information

Background: In recent years, various types of cellular networks have penetrated biology and are nowadays used omnipresently for studying eukaryote and prokaryote organisms. Still, the relation and the biological overlap among phenomenological and inferential gene networks, e.g., between the protein interaction network and the gene regulatory network inferred from large-scale transcriptomic data, is largely unexplored.Results: We provide in this study an in-depth analysis of the structural, functional and chromosomal relationship between a protein-protein network, a transcriptional regulatory network and an inferred gene regulatory network, for S. cerevisiae and E. coli. Further, we study global and local aspects of these networks and their biological information overlap by comparing, e.g., the functional co-occurrence of Gene Ontology terms by exploiting the available interaction structure among the genes.Conclusions: Although the individual networks represent different levels of cellular interactions with global structural and functional dissimilarities, we observe crucial functions of their network interfaces for the assembly of protein complexes, proteolysis, transcription, translation, metabolic and regulatory interactions. Overall, our results shed light on the integrability of these networks and their interfacing biological processes.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Research Community on Data-to-Decision (D2D), Queen's University, Belfast, Northern Ireland, Institute for Bioinformatics and Translational Research, Comp. Biol. and Machine Learn. Lab. Center for Cancer Research and Cell Biol. School of Medic.
Contributors: Matos Simoes, R. D., Dehmer, M., Emmert-Streib, F.
Publication date: 11 May 2013
Peer-reviewed: Yes

Publication information

Journal: BMC Genomics
Volume: 14
Issue number: 1
Article number: 324
ISSN (Print): 1471-2164
Ratings: 
  • Scopus rating (2013): CiteScore 4.39 SJR 2.195 SNIP 1.188
Original language: English
ASJC Scopus subject areas: Biotechnology, Genetics
Source: Scopus
Source ID: 84877302557

Research output: Contribution to journalArticleScientificpeer-review

Hollow fibers of poly(lactide-co-glycolide) and poly(ε-caprolactone) blends for vascular tissue engineering applications

At present the manufacture of small-diameter blood vessels is one of the main challenges in the field of vascular tissue engineering. Currently available vascular grafts rapidly fail due to development of intimal hyperplasia and thrombus formation. Poly(lactic-co-glycolic acid) (PLGA) hollow fiber (HF) membranes have previously been proposed for this application, but as we show in the present work, they have an inhibiting effect on cell proliferation and rather poor mechanical properties. To overcome this we prepared HF membranes via phase inversion using blends of PLGA with poly(ε-caprolactone) (PCL). The influence of polymer composition on the HF physicochemical properties (topography, water transport and mechanical properties) and cell attachment and proliferation were studied. Our results show that only the ratio PCL/PLGA of 85/15 (PCL/PLGA85/15) yielded a miscible blend after processing. A higher PLGA concentration in the blend led to immiscible PCL/PLGA phase-separated HFs with an inhomogeneous morphology and variation in the cell culture results. In fact, the PCL/PLGA85/15 blend, which had the most homogeneous morphology and suitable pore structure, showed better human adipose stem cell (hASC) attachment and proliferation compared with the homopolymers. This, combined with the good mechanical and transport properties, makes them potentially useful for the development of small-caliber vascular grafts.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), University of Cantabria, University of Twente, BioMediTech, University of Groningen
Contributors: Diban, N., Haimi, S., Bolhuis-Versteeg, L., Teixeira, S., Miettinen, S., Poot, A., Grijpma, D., Stamatialis, D.
Number of pages: 9
Pages: 6450-6458
Publication date: 2013
Peer-reviewed: Yes

Publication information

Journal: Acta Biomaterialia
Volume: 9
Issue number: 5
ISSN (Print): 1742-7061
Ratings: 
  • Scopus rating (2013): CiteScore 6.41 SJR 1.988 SNIP 2.225
Original language: English
ASJC Scopus subject areas: Biomaterials, Biomedical Engineering, Biotechnology, Biochemistry, Molecular Biology
Keywords: Blends, Hollow fibers, Poly(ε-caprolactone), Poly(lactide-co-glycolide), Vascular tissue engineering
Source: Scopus
Source ID: 84879884261

Research output: Contribution to journalArticleScientificpeer-review

Molecular modeling of the PEGylated bilayer as a model for the PEGylated liposome surface in the bloodstream

The criteria for effectiveness of drug delivery liposomes (DDLs) are structural stability, site specific targeting, and lifetime in the bloodstream. Often to increase the lifetime in bloodstream DDL is coated with poly ethylene glycol (PEG). Although it helps to improve the lifetime, there exists plenty of room for improvement in bloodstream lifetime efficacy. The search for an alternative to PEG is a very active field of research, but to apply rational design to this, a knowledge of the mechanism through which PEG functions in a superior fashion to other superficially similar polymers must be determined, and currently our understanding of this is incomplete. We have used molecular dynamics simulation of a set of PEGylated membranes in varying conditions to gain insight into this. We have also performed MD simulation with the Cholesterol as a formulation component of DDL at its effect on stability of PEGylated DDL. Lastly we looked at the factors in the targeted delivery of the novel targeting moiety identified with phage display experiments. The moiety couldn't increase the efficacy of DDL when tested invitro and invivo. By MD we could identify the factors responsible for this by investigating surface structure of DDL.

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Physics, Physics, Computational Science X (CompX), University of Helsinki, Aalto University
Contributors: Magarkar, A., Stepniewski, M., Karakas, E., Rog, T., Yliperttula, M., Urtti, A., Bunker, A.
Number of pages: 3
Pages: 576-578
Publication date: 2013

Host publication information

Title of host publication: Technical Proceedings of the 2013 NSTI Nanotechnology Conference and Expo, NSTI-Nanotech 2013
Volume: 2
ISBN (Print): 9781482205848
ASJC Scopus subject areas: Biotechnology
Keywords: Drug delivery liposome, Molecular dynamics simulation, PEGylated liposome
Source: Scopus
Source ID: 84881089910

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Person identification from actions based on Artificial Neural Networks

In this paper, we propose a person identification method exploiting human motion information. A Self Organizing Neural Network is employed in order to determine a topographic map of representative human body poses. Fuzzy Vector Quantization is applied to the human body poses appearing in a video in order to obtain a compact video representation, that will be used for person identification and action recognition. Two feedforward Artificial Neural Networks are trained to recognize the person ID and action class labels of a given test action video. Network outputs combination, based on another feedforward network, is performed in the case of multiple cameras used in the training and identification phases. Experimental results on two publicly available databases evaluate the performance of the proposed person identification approach.

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Research Community on Data-to-Decision (D2D), Aristotle University of Thessaloniki, Department of Informatics
Contributors: Iosifidis, A., Tefas, A., Pitas, I.
Number of pages: 7
Pages: 7-13
Publication date: 2013

Host publication information

Title of host publication: IEEE Workshop on Computational Intelligence in Biometrics and Identity Management, CIBIM
ISBN (Print): 9781467358798
ASJC Scopus subject areas: Biotechnology, Artificial Intelligence, Computational Theory and Mathematics
Source: Scopus
Source ID: 84891547766

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Person identification from actions based on dynemes and discriminant learning

In this paper we present a view-independent person identification method exploiting motion information. A multi-camera setup is used in order to capture the human body during action execution from different viewing angles. The method is able to incorporate several everyday actions in person identification. A comparative study of the discriminative ability of different actions for person identification is provided, denoting that several actions, except walk, can be exploited for person identification.

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Research Community on Data-to-Decision (D2D), Aristotle University of Thessaloniki, Department of Informatics
Contributors: Iosifidis, A., Tefas, A., Pitas, I.
Publication date: 2013

Host publication information

Title of host publication: 2013 International Workshop on Biometrics and Forensics, IWBF 2013
ISBN (Print): 9781467349895
ASJC Scopus subject areas: Biotechnology, Computer Science Applications
Keywords: Action-based person identification, Classification results fusion, Discriminant learning, Dyneme video representation
Source: Scopus
Source ID: 84881350564

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Roll-to-roll atomic layer deposition for flexible substrates

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Materials Science, Engineering materials science and solutions (EMASS), Lappeenranta University of Technology
Contributors: Lahtinen, K., Maydannik, P., Kääriäinen, T., Seppänen, T., Cameron, D. C., Johansson, P., Kraft, M., Kuusipalo, J.
Number of pages: 14
Pages: 726-739
Publication date: 2013

Host publication information

Title of host publication: TAPPI International Conference on Nanotechnology 2013
Publisher: TAPPI Press
ISBN (Electronic): 9781510815681
ASJC Scopus subject areas: Biomaterials, Biotechnology, Renewable Energy, Sustainability and the Environment
Source: Scopus
Source ID: 84966539214

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Undercut edges for robust capillary self-alignment in hybrid microassembly

In this paper, we report capillary self-alignment of 200 μm × 200 μm square parts on matching patterns with undercut edges. The undercut edge structure is a purely topographical feature that provides ultimate pinning for liquids of any surface tension without chemical treatment. We show contact angles close to 180° for low surface tension liquids, and capillary self-alignment using thermally curable adhesive. Sub-micron alignment accuracy after adhesive curing is verified in a scanning electron microscope (SEM).

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Faculty of Biomedical Sciences and Engineering, Research area: Microsystems, Institute of Automation and Control, Integrated Technologies for Tissue Engineering Research (ITTE), Aalto University
Contributors: Liimatainen, V., Sariola, V., Zhou, Q.
Number of pages: 4
Pages: 1088-1091
Publication date: 2013

Host publication information

Title of host publication: 8th Annual IEEE International Conference on Nano/Micro Engineered and Molecular Systems, IEEE NEMS 2013
Article number: 6559911
ISBN (Print): 9781467363525
ASJC Scopus subject areas: Biochemistry, Genetics and Molecular Biology (miscellaneous), Biotechnology
Keywords: microassembly, microfabrication, self-alignment, surface tension, wetting
Source: Scopus
Source ID: 84883063217

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Wear resistance of nanoparticle coatings on paperboard

• LFS-deposited TiO2 and SiO2 nanoparticles create superhydro-phobic and hydrophilic paper surface, • Abrasive damage of surface structure influences only slightly the wettability of superhydrophobic TiO2 and hydrophilic SiO2 coatings, • A more severe abrasive action will remove some of the nanoparticle coating, but the hydrophobic/hydrophilic properties of the surface are maintained, • SiO2 nanoparticle coated surface is more resistant to abrasion than the TiO2 coating, which indicates a stronger inter-particle and particle to surface adhesion of the former, • Investigation of nanoparticle loss from the paper surface is challenging, due to the small total mass of nanoparticles in the coating, mixed together with pigment particles and fiber debris removed during abrasion experiment.

General information

Publication status: Published
MoE publication type: A4 Article in a conference publication
Organisations: Department of Materials Science, Department of Physics, Engineering materials science and solutions (EMASS), Abo Akad Univ, Abo Akademi University, Dept Phys, Paper and Fibre Research Institute (PFI), Paper Converting and Packaging Technology, Division of Chemistry and Chemical Engineering, California Institute of Technology, Aerosol Physics Laboratory
Contributors: Stepien, M., Chinga-Carrasco, G., Saarinen, J. J., Teisala, H., Tuominen, M., Aromaa, M., Haapanen, J., Kuusipalo, J., Mäkelä, J. M., Toivakka, M.
Number of pages: 9
Pages: 821-829
Publication date: 2013

Host publication information

Title of host publication: TAPPI International Conference on Nanotechnology 2013
Publisher: TAPPI Press
ISBN (Electronic): 9781510815681
ASJC Scopus subject areas: Biomaterials, Biotechnology, Renewable Energy, Sustainability and the Environment
Source: Scopus
Source ID: 84966648395

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Oxidative stress response and fatty acid changes associated with bioaccumulation of chromium [Cr(VI)] by a fresh water cyanobacterium Chroococcus sp.

Cr(VI) at 2. 5, 5, 7. 5 and 10mg/l was removed over 1-5 days by a freshwater cyanobacterium, Chroococcus sp. 2. 5mg Cr(VI)/l gave the optimum rate. With 5mg Cr(VI)/l, activities of superoxide dismutase and catalase were increased. Amounts of palmitic (16:0), stearic (18:0) and oleic acid (18:1) in the cell also increased after exposure to Cr(VI).

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Urban circular bioeconomy (UrCirBio), Bharathidasan University
Contributors: Kumar, M. S., Praveenkumar, R., Ilavarasi, A., Rajeshwari, K., Thajuddin, N.
Number of pages: 5
Pages: 247-251
Publication date: Feb 2012
Peer-reviewed: Yes

Publication information

Journal: Biotechnology Letters
Volume: 34
Issue number: 2
ISSN (Print): 0141-5492
Ratings: 
  • Scopus rating (2012): CiteScore 2.03 SJR 0.748 SNIP 0.949
Original language: English
ASJC Scopus subject areas: Biotechnology
Keywords: Catalase, Chroococcus sp., Fatty acid changes, Oxidative stress, Superoxide dismutase
Source: Scopus
Source ID: 84856214551

Research output: Contribution to journalArticleScientificpeer-review

Production of l-xylose from l-xylulose using Escherichia coli l-fucose isomerase

l-Xylulose was used as a raw material for the production of l-xylose with a recombinantly produced Escherichia coli l-fucose isomerase as the catalyst. The enzyme had a very alkaline pH optimum (over 10.5) and displayed Michaelis-Menten kinetics for l-xylulose with a K m of 41mM and a V max of 0.23μmol/(mgmin). The half-lives determined for the enzyme at 35°C and at 45°C were 6h 50min and 1h 31min, respectively. The reaction equilibrium between l-xylulose and l-xylose was 15:85 at 35°C and thus favored the formation of l-xylose. Contrary to the l-rhamnose isomerase catalyzed reaction described previously [14] l-lyxose was not detected in the reaction mixture with l-fucose isomerase. Although xylitol acted as an inhibitor of the reaction, even at a high ratio of xylitol to l-xylulose the inhibition did not reach 50%.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Aalto University, VTT Technical Research Centre of Finland
Contributors: Usvalampi, A., Turunen, O., Valjakka, J., Pastinen, O., Leisola, M., Nyyssölä, A.
Number of pages: 6
Pages: 71-76
Publication date: 5 Jan 2012
Peer-reviewed: Yes

Publication information

Journal: ENZYME AND MICROBIAL TECHNOLOGY
Volume: 50
Issue number: 1
ISSN (Print): 0141-0229
Ratings: 
  • Scopus rating (2012): CiteScore 2.78 SJR 1.166 SNIP 1.261
Original language: English
ASJC Scopus subject areas: Biotechnology, Biochemistry, Applied Microbiology and Biotechnology
Keywords: Isomerization, L-Fucose isomerase, L-Xylose, L-Xylulose, Rare sugars
Source: Scopus
Source ID: 82455188020

Research output: Contribution to journalArticleScientificpeer-review

DNA family shuffling within the chicken avidin protein family - A shortcut to more powerful protein tools

Avidins represent an interesting group of proteins showing high structural similarity and ligand-binding properties but low similarity in primary structure. In this study, we show that it is possible to create functional chimeric proteins from the avidin protein family when applying DNA family shuffling to the genes of the avidin protein family: avidin, avidin related gene 2 and biotin-binding protein A. The novel chimeric proteins were selected by phage display biopanning against biotin, and the selected enriched proteins were characterized, displaying diverse features distinct from the parental genes, including binding to cysteine.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), BioMediTech, Tampere University Hospital, Ita-Suomen yliopisto
Contributors: Niederhauser, B., Siivonen, J., Määttä, J. A., Jänis, J., Kulomaa, M. S., Hytönen, V. P.
Number of pages: 12
Pages: 38-49
Publication date: Jan 2012
Peer-reviewed: Yes

Publication information

Journal: Journal of Biotechnology
Volume: 157
Issue number: 1
ISSN (Print): 0168-1656
Ratings: 
  • Scopus rating (2012): CiteScore 3.4 SJR 1.238 SNIP 1.312
Original language: English
ASJC Scopus subject areas: Biotechnology, Applied Microbiology and Biotechnology
Keywords: Avidin, Biotin, Directed evolution, DNA shuffling
Source: Scopus
Source ID: 84855228410

Research output: Contribution to journalArticleScientificpeer-review

Identification of proprotein convertase substrates using genome-wide expression correlation analysis

Background: Subtilisin/kexin-like proprotein convertase (PCSK) enzymes have important regulatory function in a wide variety of biological processes. PCSKs proteolytically process at a target sequence that contains basic amino acids arginine and lysine, which results in functional maturation of the target protein. In vitro assays have showed significant biochemical redundancy between the seven family members, but the phenotypes of PCSK deficient mice and patients carrying an inactive PCSK allele argue for a specific biological function. Modeling the structures of individual PCSK enzymes has offered little insights into the specificity determinants. However, previous studies have shown that there can be a coordinated expression between a PCSK and its target molecule. Here, we have surveyed the putative PCSK target proteins using genome-wide expression correlation analysis and cleavage site prediction algorithms.Results: We first performed a gene expression correlation analysis over the whole genome for all PCSK enzymes. PCSKs were found to cluster differently based on the strength of correlations. The screen for putative PCSK target proteins showed a significant enrichment (p-values from 1.2e-4 to <1.0e-10) of putative targets among the most positively correlating genes for most PCSKs. Interestingly, there was no enrichment in putative targets among the genes that correlated positively with the biologically redundant PCSK7, whereas PCSK5 showed an inverse correlation. PCSKs also showed a highly variable degree of shared target genes that were identified by expression correlation and cleavage site prediction. Multiple alignments were used to evaluate the putative targets to pinpoint the important residues for the substrate recognition. Finally, we validated our approach and identified biochemically PAPPA1 and ADAMTS6 as novel targets for FURIN proteolytic activity.Conclusions: Most PCSK enzymes display strong positive expression correlation with predicted target proteins in our genome-wide analysis. We also show that expression correlation screen combined with a cleavage site-prediction analysis can be used to identify novel bona fide target molecules for PCSKs. Exploring the positively correlating genes can thus offer additional insights into the biology of proprotein convertases.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), BioMediTech, School of Management (JKK), University of Helsinki, Tampere University Hospital
Contributors: Turpeinen, H., Kukkurainen, S., Pulkkinen, K., Kauppila, T., Ojala, K., Hytönen, V. P., Pesu, M.
Publication date: 20 Dec 2011
Peer-reviewed: Yes

Publication information

Journal: BMC Genomics
Volume: 12
Article number: 618
ISSN (Print): 1471-2164
Ratings: 
  • Scopus rating (2011): CiteScore 4.38 SJR 2.307 SNIP 1.191
Original language: English
ASJC Scopus subject areas: Biotechnology, Genetics
Source: Scopus
Source ID: 83655183285

Research output: Contribution to journalArticleScientificpeer-review

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

The International Stem Cell Initiative analyzed 125 human embryonic stem (ES) cell lines and 11 induced pluripotent stem (iPS) cell lines, from 38 laboratories worldwide, for genetic changes occurring during culture. Most lines were analyzed at an early and late passage. Single-nucleotide polymorphism (SNP) analysis revealed that they included representatives of most major ethnic groups. Most lines remained karyotypically normal, but there was a progressive tendency to acquire changes on prolonged culture, commonly affecting chromosomes 1, 12, 17 and 20. DNA methylation patterns changed haphazardly with no link to time in culture. Structural variants, determined from the SNP arrays, also appeared sporadically. No common variants related to culture were observed on chromosomes 1, 12 and 17, but a minimal amplicon in chromosome 20q11.21, including three genes expressed in human ES cells, ID1, BCL2L1 and HM13, occurred in >20% of the lines. Of these genes, BCL2L1 is a strong candidate for driving culture adaptation of ES cells.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), University of Sheffield, International Centre for Life, A-STAR, Immunos, Royan Institute, mediaX and H*STAR Stanford University Stanford, Sheffield Children's NHS Trust, University of Nottingham, Keck School of Medicine of USC, Hebrew University of Jerusalem, Tel Aviv University, Sackler Faculty of Medicine, Cedars-Sinai Medical Institute, University of Geneva, Manchester Academic Health Sciences Centre, Cellartis AB, University of Manchester, Genome Institute of Singapore, Hoffmann-LaRoche, Seoul National University College of Medicine, Bioprocessing Technology Institute, Roslin Cells Ltd., University of Melbourne, Harvard Stem Cell Institute, University of Edinburgh, Masaryk University, WiCell Research Institute, Hopital Cantonal Fribourgois, Department of Applied Physics, Lis Maternity Hospital Israel, Central South University China, Hadassah University Medical Center, Institute of Experimental Botany of the Academy of Sciences of the Czech Republic, University College London, National Institute for Biological Standards and Control, Karolinska University Hospital, Jawaharlal Nehru Centre for Advanced Scientific Research, NYU Langone Medical Center, Shanghai Jiaotong University, Vavilov Institute of General Genetics, Reproductive Genetics Institute, Monash University, CHA University, Vrije Universiteit Brussel, Mount Sinai Hospital, GE Healthcare, UK, Kyoto Women's University, Leiden University Medical Center - LUMC, University of Helsinki, Yale School of Medicine, Viacyte, Hospital for Sick Children University of Toronto, University of New South Wales (UNSW) Australia, Gladstone Institute of Cardiovascular Disease, CSIRO Energy Centre
Contributors: Amps, K., Andrews, P. W., Anyfantis, G., Armstrong, L., Avery, S., Baharvand, H., Baker, J., Baker, D., Munoz, M. B., Beil, S., Benvenisty, N., Ben-Yosef, D., Biancotti, J. C., Bosman, A., Brena, R. M., Brison, D., Caisander, G., Camarasa, M. V., Chen, J., Chiao, E., Choi, Y. M., Choo, A. B. H., Collins, D., Colman, A., Crook, J. M., Daley, G. Q., Dalton, A., De Sousa, P. A., Denning, C., Downie, J., Dvorak, P., Montgomery, K. D., Feki, A., Ford, A., Fox, V., Fraga, A. M., Frumkin, T., Ge, L., Gokhale, P. J., Golan-Lev, T., Gourabi, H., Gropp, M., Guangxiu, L., Hampl, A., Harron, K., Healy, L., Herath, W., Holm, F., Hovatta, O., Hyllner, J., Inamdar, M. S., Irwanto, A. K., Ishii, T., Jaconi, M., Jin, Y., Kimber, S., Kiselev, S., Knowles, B. B., Kopper, O., Kukharenko, V., Kuliev, A., Lagarkova, M. A., Laird, P. W., Lako, M., Laslett, A. L., Lavon, N., Lee, D. R., Lee, J. E., Li, C., Lim, L. S., Ludwig, T. E., Ma, Y., Maltby, E., Mateizel, I., Mayshar, Y., Mileikovsky, M., Minger, S. L., Miyazaki, T., Moon, S. Y., Moore, H., Mummery, C., Nagy, A., Nakatsuji, N., Narwani, K., Oh, S. K. W., Oh, S. K., Olson, C., Otonkoski, T., Pan, F., Park, I. H., Pells, S., Pera, M. F., Pereira, L. V., Qi, O., Raj, G. S., Reubinoff, B., Robins, A., Robson, P., Rossant, J., Salekdeh, G. H., Schulz, T. C., Sermon, K., Mohamed, J. S., Shen, H., Sherrer, E., Sidhu, K., Sivarajah, S., Skottman, H., Spits, C., Stacey, G. N., Strehl, R., Strelchenko, N., Suemori, H., Sun, B., Suuronen, R., Takahashi, K., Tuuri, T., Venu, P., Verlinsky, Y., Oostwaard, D. W. V., Weisenberger, D. J., Wu, Y., Yamanaka, S., Young, L., Zhou, Q.
Number of pages: 13
Pages: 1132-1144
Publication date: Dec 2011
Peer-reviewed: Yes

Publication information

Journal: Nature Biotechnology
Volume: 29
Issue number: 12
ISSN (Print): 1087-0156
Ratings: 
  • Scopus rating (2011): CiteScore 8.21 SJR 11.749 SNIP 6.173
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Medicine(all), Molecular Medicine, Biomedical Engineering, Applied Microbiology and Biotechnology
Source: Scopus
Source ID: 83255189758

Research output: Contribution to journalArticleScientificpeer-review

Versatile bio-ink for covalent immobilization of chimeric avidin on sol-gel substrates

A bio-ink for covalent deposition of thermostable, high affinity biotin-binding chimeric avidin onto sol-gel substrates was developed. The bio-ink was prepared from heterobifunctional crosslinker 6-maleimidohexanoic acid N-hydroxysuccinimide which was first reacted either with 3-aminopropyltriethoxysilane or 3-aminopropyldimethylethoxysilane to form silane linkers 6-maleimide- N-(3-(triethoxysilyl)propyl)hexanamide or -(ethoxydimethylsilyl)propyl)-hexanamide. C-terminal cysteine genetically engineered to chimeric avidin was reacted with the maleimide group of silane linker in methanol/PBS solution to form a suspension, which was printed on sol-gel modified PMMA film. Different concentrations of chimeric avidin and ratios between silane linkers were tested to find the best properties for the bio-ink to enable gravure or inkjet printing. Bio-ink prepared from 3-aminopropyltriethoxysilane was found to provide the highest amount of active immobilized chimeric avidin. The developed bio-ink was shown to be valuable for automated fabrication of avidin-functionalized polymer films.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Univ of Oulu, VTT Technical Research Centre of Finland, Tampere University Hospital
Contributors: Heikkinen, J. J., Kivimäki, L., Määttä, J. A. E., Mäkelä, I., Hakalahti, L., Takkinen, K., Kulomaa, M. S., Hytönen, V. P., Hormi, O. E. O.
Number of pages: 6
Pages: 409-414
Publication date: 15 Oct 2011
Peer-reviewed: Yes

Publication information

Journal: Colloids and Surfaces B: Biointerfaces
Volume: 87
Issue number: 2
ISSN (Print): 0927-7765
Ratings: 
  • Scopus rating (2011): CiteScore 3.49 SJR 1.051 SNIP 1.27
Original language: English
ASJC Scopus subject areas: Biotechnology, Colloid and Surface Chemistry, Physical and Theoretical Chemistry, Surfaces and Interfaces
Keywords: Avidin-biotin technology, Biomolecule immobilization, Biosensing, Chimeric avidin, Maleimide, Printing, Sol-gel
Source: Scopus
Source ID: 79960384544

Research output: Contribution to journalArticleScientificpeer-review

Hybrid nanoparticle design based on cationized gelatin and the polyanions dextran sulfate and chondroitin sulfate for ocular gene therapy

We describe the development of hybrid nanoparticles composed of cationized gelatin and the polyanions CS and DS for gene therapy in the ocular surface. The physicochemical properties of the nanoparticles that impact their bioperformance, such as average size and zeta potential, can be conveniently modulated by changing the ratio of polymers and the crosslinker. These systems associate plasmid DNA and are able to protect it from DNase I degradation. We corroborate that the introduction of CS or DS in the formulation decreases the in vitro toxicity of the nanoparticles to human corneal cells without compromising the transfection efficiency. These nanoparticles are potential candidates for the development of safer and more effective nanomedicines for ocular therapy. New hybrid nanoparticles composed of cationized gelatin and natural polyanions are developed and characterized. The incorporation of chondroitin sulfate or dextran sulfate in cationized gelatin nanoparticles decreases their toxicity while preserving their transfection efficiency in human corneal cells. These nanoparticles are potential candidates for the development of safer and more effective nanomedicines for ocular therapy.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Integrated Technologies for Tissue Engineering Research (ITTE), University of Santiago de Compostela (USC)
Contributors: Zorzi, G. K., Párraga, J. E., Seijo, B., Sánchez, A.
Number of pages: 9
Pages: 905-913
Publication date: 7 Jul 2011
Peer-reviewed: Yes

Publication information

Journal: MACROMOLECULAR BIOSCIENCE
Volume: 11
Issue number: 7
ISSN (Print): 1616-5187
Ratings: 
  • Scopus rating (2011): CiteScore 3.69 SJR 1.408 SNIP 1.105
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Biomaterials, Polymers and Plastics, Materials Chemistry
Keywords: Drug delivery systems, Gelation, Nanoparticles, Nanotechnology
Source: Scopus
Source ID: 79959848036

Research output: Contribution to journalArticleScientificpeer-review

Modification of the loops in the ligand-binding site turns avidin into a steroid-binding protein

Background: Engineered proteins, with non-immunoglobulin scaffolds, have become an important alternative to antibodies in many biotechnical and therapeutic applications. When compared to antibodies, tailored proteins may provide advantageous properties such as a smaller size or a more stable structure.Results: Avidin is a widely used protein in biomedicine and biotechnology. To tailor the binding properties of avidin, we have designed a sequence-randomized avidin library with mutagenesis focused at the loop area of the binding site. Selection from the generated library led to the isolation of a steroid-binding avidin mutant (sbAvd-1) showing micromolar affinity towards testosterone (Kd ~ 9 μM). Furthermore, a gene library based on the sbAvd-1 gene was created by randomizing the loop area between β-strands 3 and 4. Phage display selection from this library led to the isolation of a steroid-binding protein with significantly decreased biotin binding affinity compared to sbAvd-1. Importantly, differential scanning calorimetry and analytical gel-filtration revealed that the high stability and the tetrameric structure were preserved in these engineered avidins.Conclusions: The high stability and structural properties of avidin make it an attractive molecule for the engineering of novel receptors. This methodology may allow the use of avidin as a universal scaffold in the development of novel receptors for small molecules.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), Tampere University Hospital, Johannes Kepler University, VTT Technical Research Centre of Finland
Contributors: Riihimäki, T. A., Hiltunen, S., Rangl, M., Nordlund, H. R., Määttä, J. A., Ebner, A., Hinterdorfer, P., Kulomaa, M. S., Takkinen, K., Hytönen, V. P.
Publication date: 9 Jun 2011
Peer-reviewed: Yes

Publication information

Journal: BMC BIOTECHNOLOGY
Volume: 11
Article number: 64
Original language: English
ASJC Scopus subject areas: Biotechnology
Keywords: Avidin scaffold, Phage display, Protein engineering, Steroid hormone, Testosterone
Source: Scopus
Source ID: 79958022709

Research output: Contribution to journalArticleScientificpeer-review

Networks for systems biology: Conceptual connection of data and function

The purpose of this study is to survey the use of networks and network-based methods in systems biology. This study starts with an introduction to graph theory and basic measures allowing to quantify structural properties of networks. Then, the authors present important network classes and gene networks as well as methods for their analysis. In the last part of this study, the authors review approaches that aim at analysing the functional organisation of gene networks and the use of networks in medicine. In addition to this, the authors advocate networks as a systematic approach to general problems in systems biology, because networks are capable of assuming multiple roles that are very beneficial connecting experimental data with a functional interpretation in biological terms.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Research Community on Data-to-Decision (D2D), Computational Biology and Machine Learning Lab., Faculty of Medicine, Health and Life Sciences, Queen's University, Belfast, Northern Ireland, Institute for Bioinformatics and Translational Research
Contributors: Emmert-Streib, F., Dehmer, M.
Number of pages: 23
Pages: 185-207
Publication date: May 2011
Peer-reviewed: Yes

Publication information

Journal: IET Systems Biology
Volume: 5
Issue number: 3
ISSN (Print): 1751-8849
Ratings: 
  • Scopus rating (2011): CiteScore 1.65 SJR 0.745 SNIP 0.664
Original language: English
ASJC Scopus subject areas: Biotechnology, Cell Biology, Genetics, Molecular Biology, Modelling and Simulation
Source: Scopus
Source ID: 79960325408

Research output: Contribution to journalArticleScientificpeer-review

Chimeric avidin shows stability against harsh chemical conditions-biochemical analysis and 3D structure

Avidin and its bacterial analog streptavidin have been widely used in applications in life sciences. Recently, we described a highly thermostable engineered avidin, called chimeric avidin, which is a hybrid of avidin and avidin-related protein 4. Here, we report a protocol for pilot-scale production in E. coli and the X-ray structure of chimeric avidin. The ligand-binding properties of chimeric avidin were explored with isothermal titration calorimetry. We found chimeric avidin to be more stable against various harsh organic solvents at elevated temperatures compared to avidin and streptavidin. The properties of chimeric avidin make it a potential tool for new applications in biotechnology. Biotechnol. Bioeng. 2011; 108:481-490.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Multi-scaled biodata analysis and modelling (MultiBAM), University of Tampere Institute of Medical Technology, Hebrew University of Jerusalem
Contributors: Määttä, J. A., Eisenberg-Domovich, Y., Nordlund, H. R., Hayouka, R., Kulomaa, M. S., Livnah, O., Hytönen, V. P.
Number of pages: 10
Pages: 481-490
Publication date: Mar 2011
Peer-reviewed: Yes

Publication information

Journal: Biotechnology and Bioengineering
Volume: 108
Issue number: 3
ISSN (Print): 0006-3592
Ratings: 
  • Scopus rating (2011): CiteScore 4.08 SJR 1.668 SNIP 1.489
Original language: English
ASJC Scopus subject areas: Biotechnology, Bioengineering, Applied Microbiology and Biotechnology
Keywords: Avidin-biotin, Nanobiotechnology, Protein engineering, Thermodynamics, X-ray structure
Source: Scopus
Source ID: 78751523876

Research output: Contribution to journalArticleScientificpeer-review

Local network-based measures to assess the inferability of different regulatory networks

The purpose of this study is to compare the inferability of various synthetic as well as real biological regulatory networks. In order to assess differences we apply local network-based measures. That means, instead of applying global measures, we investigate and assess an inference algorithm locally, on the level of individual edges and subnetworks. We demonstrate the behaviour of our local network-based measures with respect to different regulatory networks by conducting large-scale simulations. As inference algorithm we use exemplarily ARACNE. The results from our exploratory analysis allow us not only to gain new insights into the strength and weakness of an inference algorithm with respect to characteristics of different regulatory networks, but also to obtain information that could be used to design novel problem-specific statistical estimators. [Includes supplementary material]

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Computational Biology and Machine Learning Lab., Faculty of Medicine, Health and Life Sciences, Queen's University, Belfast, Northern Ireland
Contributors: Emmert-Streib, F., Altay, G.
Number of pages: 12
Pages: 277-288
Publication date: Jul 2010
Peer-reviewed: Yes

Publication information

Journal: IET Systems Biology
Volume: 4
Issue number: 4
Article number: ISBEAT000004000004000277000001
ISSN (Print): 1751-8849
Ratings: 
  • Scopus rating (2010): SJR 0.773 SNIP 0.791
Original language: English
ASJC Scopus subject areas: Biotechnology, Cell Biology, Genetics, Molecular Biology, Modelling and Simulation, Medicine(all)
Source: Scopus
Source ID: 77954479475

Research output: Contribution to journalArticleScientificpeer-review

Photostable second-harmonic generation from a single KTiOPO4 nanocrystal for nonlinear microscopy

A study was conducted to report the observation and the characterization of nanometric-sized crystals extracted by centrifugation from KTP (potassium titanyl phosphate) powder. In situ atomic force microscopy (AFM) analysis of its size and analysis of its second-harmonic emission properties were performed for a well-isolated single nanocrystal. The highly efficient nonlinear response leads to the emission of several SHG photons and in a photostable and blinking-free manner due to non-resonant coherent interaction. The study retrieved the in situ three-dimensional crystal orientation by recovering the radiation pattern from the recorded defocused images. Solution-based chemical synthesis of KTP nanocrystals with a monodisperse size controlled by capping agents should lead to optimized KTP nanocrystallites and to a more accurate estimate of the size-detection threshold. Fully characterized nano-KTPs are also attractive for the development of novel schemes of nonlinear microscopy.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Laboratoire de Photonique Quantique et Moléculaire-ENS Cachan, UMR CNRS 8537, Laboratoire de Physique de la Matière Condensée-Ecole Polytechnique-CNRS, Ecole Polytechnique, Cristal Laser S.A.
Contributors: Le Xuan, L., Zhou, C., Slablab, A., Chauvat, D., Tard, C., Perruchas, S., Gacoin, T., Villeval, P., Roch, J.
Number of pages: 5
Pages: 1332-1336
Publication date: Sep 2008
Peer-reviewed: Yes

Publication information

Journal: Small
Volume: 4
Issue number: 9
ISSN (Print): 1613-6810
Ratings: 
  • Scopus rating (2008): SJR 3.884 SNIP 1.517
Original language: English
ASJC Scopus subject areas: Biomaterials, Engineering (miscellaneous), Biotechnology, Medicine(all)
Keywords: Nanocrystals, Nanoparticles, Nonlinear microscopy, Second-harmonic generation
Source: Scopus
Source ID: 52649175511

Research output: Contribution to journalArticleScientificpeer-review

Modeling of anaerobic degradation of solid slaughterhouse waste: Inhibition effects of long-chain fatty acids or ammonia

The anaerobic bioconversion of solid poultry slaughterhouse wastes was kinetically investigated. The modified version of <METHANE> simulation model was applied for description of experimental data in mesophilic laboratory digester and assays. Additionally, stages of formation and consumption of long chain fatty acids (LCFA) were included in the model. Batch data on volatile solids, ammonium, acetate, butyrate, propionate, LCFA concentrations, pH level, cumulative volume, and methane partial pressure were used for model calibration. As a reference, the model was used to describe digestion of solid sorted household waste. Simulation results showed that an inhibition of polymer hydrolysis by volatile fatty acids and acetogenesis by NH3 or LCFA could be responsible for the complex system dynamics during degradation of lipid- and protein-rich wastes.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Russian Academy of Sciences, University of Jyväskylä, Jyväskylän yliopisto
Contributors: Lokshina, L. Y., Vavilin, V. A., Salminen, E., Rintala, J.
Number of pages: 18
Pages: 15-32
Publication date: Apr 2003
Peer-reviewed: Yes

Publication information

Journal: Applied Biochemistry and Biotechnology
Volume: 109
Issue number: 1-3
ISSN (Print): 0273-2289
Ratings: 
  • Scopus rating (2003): SJR 0.444 SNIP 0.694
Original language: English
ASJC Scopus subject areas: Biochemistry, Genetics and Molecular Biology(all), Biochemistry, Biotechnology, Bioengineering
Keywords: Ammonia, Anaerobic digestion, Inhibition, Long-chain fatty acids, Model, Poultry slaughterhouse waste, Sorted solid household waste
Source: Scopus
Source ID: 0038459271

Research output: Contribution to journalArticleScientificpeer-review

Start-up and Operation of Laboratory-Scale Thermophilic Upflow Anaerobic Sludge Blanket Reactors Treating Vegetable Processing Wastewaters

Thermophilic anaerobic treatment of hot vegetable processing wastewaters was studied in laboratory-scale UASB reactors at 55°C. The high-strength wastewater streams, deriving from steam peeling and blanching of carrot, potato and swede were used. The reactors were inoculated with mesophilic granular sludge. Stable thermophilic methanogenesis with about 60% COD removal was reached within 28 days. During the 134 day study period the loading rate was increased up to 24 kg COD m-3 day-1. High treatment efficiency of more than 90% COD removal and concomitant methane production of 7.3 m3 CH4 m-3 day-1 were achieved. The anaerobic process performance was not affected by the changes in the wastewater due to the different processed vegetables. The results demonstrated the feasibility of thermophilic anaerobic treatment of vegetable processing wastewaters in UASB reactors.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: Faculty of Science and Environmental Engineering, Tampere University of Technology, University of Jyväskylä, Jyväskylän yliopisto, Aalto University
Contributors: Lepistö, S. S., Rintala, J. A.
Number of pages: 9
Pages: 331-339
Publication date: Mar 1997
Peer-reviewed: Yes

Publication information

Journal: Journal of Chemical Technology and Biotechnology
Volume: 68
Issue number: 3
ISSN (Print): 0268-2575
Original language: English
ASJC Scopus subject areas: Biotechnology, Chemical Engineering(all), Bioengineering, Chemistry(all)
Keywords: Anaerobic treatment, Food industry, Granular sludge, Start-up, Thermophilic, Vegetable processing wastewater

Bibliographical note

Contribution: organisation=bio,FACT1=1

Source: researchoutputwizard
Source ID: 30520

Research output: Contribution to journalArticleScientificpeer-review

A two-stage thermophilic anaerobic process for the treatment of source sorted household solid waste

Hydrolysis and acidification of source sorted household solid waste (SSHSW) at 70°C was studied using continuous stirred tank reactor (CSTR). The soluble COD/total initial COD-ratio of the SSHSW increased from 25 to 35% during the CSTR treatment. A thermophilic (55°C) upflow anaerobic sludge blanket (UASB) reactor removed up to 80% of the COD in the liquid fraction of the SSHSW treated at 70°C.

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: The Anaerobic Microbiology/Biotechnology Group, Department of Environmental Science and Engineering, Danmarks Tekniske Universitet, DTU Informatik
Contributors: Rintala, J. A., Ahring, B. K.
Number of pages: 6
Pages: 1097-1102
Publication date: Oct 1994
Peer-reviewed: Yes

Publication information

Journal: Biotechnology Letters
Volume: 16
Issue number: 10
ISSN (Print): 0141-5492
Original language: English
ASJC Scopus subject areas: Microbiology, Applied Microbiology and Biotechnology, Bioengineering, Biotechnology
Source: Scopus
Source ID: 0028036651

Research output: Contribution to journalArticleScientificpeer-review

Thermophilic anaerobic digestion of source-sorted household solid waste: the effects of enzyme additions

Thermophilic (55° C) methanation of source-sorted household solid waste (HSW) was studied in batch and in continuous experiments. Furthermore, the effects of additions of xylanase, lipase, protease and a mixture of these on the methanation were tested. In the batch studies, comparative assays with active and inactive enzymes were used to elucidate the role of the added enzymes. The results showed that the HSW was readily digestible, up to 400-590 mlCH4·g-1 volatile solids (VS) was produced. Only with protease added, at a concentration of 1.1 Anson protease units·kg-1 VS was a higher specific methanogenic activity found with active enzymes compared to inactive (autoclaved) enzymes or without enzyme addition. The methane yield by conversion of the HSW in the batch assays and in the reactor studies was not increased by enzyme additions (enzyme mixture).

General information

Publication status: Published
MoE publication type: A1 Journal article-refereed
Organisations: The Anaerobic Microbiology/Biotechnology Group, Department of Biotechnology, Danmarks Tekniske Universitet, DTU Informatik
Contributors: Rintala, J. A., Ahring, B. K.
Number of pages: 4
Pages: 916-919
Publication date: Feb 1994
Peer-reviewed: Yes

Publication information

Journal: Applied Microbiology and Biotechnology
Volume: 40
Issue number: 6
ISSN (Print): 0175-7598
Original language: English
ASJC Scopus subject areas: Microbiology (medical), Microbiology, Bioengineering, Biotechnology
Source: Scopus
Source ID: 0028258804

Research output: Contribution to journalArticleScientificpeer-review