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Schwabe A.,VU University Amsterdam | Maarleveld T.R.,VU University Amsterdam | Maarleveld T.R.,Center for Mathematics and Computer Science | Maarleveld T.R.,BioSolar | And 2 more authors.
FEBS Letters

Single enzyme molecules display inevitable, stochastic fluctuations in their catalytic activity. In metabolism, for instance, the stochastic activity of individual enzymes is averaged out due to their high copy numbers per single cell. However, many processes inside cells rely on single enzyme activity, such as transcription, replication, translation, and histone modifications. Here we introduce the main theoretical concepts of stochastic single-enzyme activity starting from the Michaelis-Menten enzyme mechanism. Next, we discuss stochasticity of multi-substrate enzymes, of enzymes and receptors with multiple conformational states and finally, how fluctuations in receptor activity arise from fluctuations in signal concentration. This paper aims to introduce the exciting field of single-molecule enzyme kinetics and stochasticity to a wider audience of biochemists and systems biologists. © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. Source

Maarleveld T.R.,Life science | Maarleveld T.R.,BioSolar | Maarleveld T.R.,VU University Amsterdam | Boele J.,VU University Amsterdam | And 4 more authors.
Plant Physiology

Data integration is a central activity in systems biology. The integration of genomic, transcript, protein, metabolite, flux, and computational data yields unprecedented information about the system level functioning of organisms. Often, data integration is done purely computationally, leaving the user with little insight in addition to statistical information. In this article, we present a visualization tool for the metabolic network of Synechocystis sp. PCC 6803, an important model cyanobacterium for sustainable biofuel production. We illustrate how this metabolic map can be used to integrate experimental and computational data for Synechocystis sp. PCC 6803 systems biology and metabolic engineering studies. Additionally, we discuss how this map, and the software infrastructure that we supply with it, can be used in the development of other organism-specific metabolic network visualizations. In addition to the Python console package VoNDA (http://vonda.sf.net), we provide a working demonstration of the interactive metabolic map and the associated Synechocystis sp. PCC 6803 genome-scale stoichiometric model, as well as various ready-to-visualize microarray data sets, at http://f-a-m-e.org/synechocytis. © 2014 American Society of Plant Biologists. All rights reserved. Source

Maarleveld T.R.,VU University Amsterdam | Maarleveld T.R.,BioSolar | Olivier B.G.,VU University Amsterdam | Bruggeman F.J.,VU University Amsterdam | Bruggeman F.J.,Kluyver Center for Genomics of Industrial Fermentation

Single-cell and single-molecule measurements indicate the importance of stochastic phenomena in cell biology. Stochasticity creates spontaneous differences in the copy numbers of key macromolecules and the timing of reaction events between genetically-identical cells. Mathematical models are indispensable for the study of phenotypic stochasticity in cellular decision-making and cell survival. There is a demand for versatile, stochastic modeling environments with extensive, preprogrammed statistics functions and plotting capabilities that hide the mathematics from the novice users and offers low-level programming access to the experienced user. Here we present StochPy (Stochastic modeling in Python), which is a flexible software tool for stochastic simulation in cell biology. It provides various stochastic simulation algorithms, SBML support, analyses of the probability distributions of molecule copy numbers and event waiting times, analyses of stochastic time series, and a range of additional statistical functions and plotting facilities for stochastic simulations. We illustrate the functionality of StochPy with stochastic models of gene expression, cell division, and single-molecule enzyme kinetics. StochPy has been successfully tested against the SBML stochastic test suite, passing all tests. StochPy is a comprehensive software package for stochastic simulation of the molecular control networks of living cells. It allows novice and experienced users to study stochastic phenomena in cell biology. The integration with other Python software makes StochPy both a user-friendly and easily extendible simulation tool. © 2013 Maarleveld et al. Source

BioSolar, a small public company (OTCBB: BSRC.OB) that makes solar backsheets — a component of the equipment used to hold solar photovoltaic modules in place within frames and racks, and to protect the modules from weather and other damage — attained safety certifications from Underwriter Laboratories this week. The UL-certification enables BioSolar to sell its backsheets to a variety of North American solar panel manufacturers and solar developers who seek to integrate them into products they ship. BioSolar’s BioBacksheets are made of fully recyclable and biodegradable materials derived from a non-food, renewable crop, castor beans (image, below). Other industry standard backsheets are made of polyvinyl fluoride, polyester or laminated film— materials that may be UV- and weather-resistant, but are made from petroleum, and are not biodegradable or recyclable. They can even be toxic. In an interview with TechCrunch before the company attained its certifications, BioSolar chief executive David Lee said: “The solar industry has been growing by leaps and bounds in the last 20 years. Its about time for us to look at the impact of what we are doing as the solar industry to the environment. Are we sustainable as an industry? [We] want to make solar a truly green source of energy. I remember 20-30 years ago, when silicon kicked off technology development, we had this boom in the economy. Later, the big tech manufacturers realized we’ve created a pollution issue from the materials. The solar industry should do a more responsible thing, from harvesting materials to manufacture and recycling of all the components. With Biosolar, we want to make sure we are environmentally friendly and at the same time that our green technologies are cost-effective.” The company is focused on selling within North America for now, but Lee said BioSolar will seek international certifications akin to the UL mark to expand sales globally in the future. BioSolar faces competition from incumbents like DUNMORE and DuPont that supply backsheets to massive solar panel makers, already.

Chukhutsina V.U.,Wageningen University | Chukhutsina V.U.,BioSolar | Buchel C.,Goethe University Frankfurt | Van Amerongen H.,Wageningen University | Van Amerongen H.,BioSolar
Biochimica et Biophysica Acta - Bioenergetics

Diatoms, which are primary producers in the oceans, can rapidly switch on/off efficient photoprotection to respond to fast light-intensity changes in moving waters. The corresponding thermal dissipation of excess-absorbed-light energy can be observed as non-photochemical quenching (NPQ) of chlorophyll a fluorescence. Fluorescence-induction measurements on Cyclotella meneghiniana diatoms show two NPQ processes: qE1 relaxes rapidly in the dark while qE2 remains present upon switching to darkness and is related to the presence of the xanthophyll-cycle pigment diatoxanthin (Dtx). We performed picosecond fluorescence measurements on cells locked in different (quenching) states, revealing the following sequence of events during full development of NPQ. At first, trimers of light-harvesting complexes (fucoxanthin-chlorophyll a/c proteins), or FCPa, become quenched, while being part of photosystem II (PSII), due to the induced pH gradient across the thylakoid membrane. This is followed by (partial) detachment of FCPa from PSII after which quenching persists. The pH gradient also causes the formation of Dtx which leads to further quenching of isolated PSII cores and some aggregated FCPa. In subsequent darkness, the pH gradient disappears but Dtx remains present and quenching partly pertains. Only in the presence of some light the system completely recovers to the unquenched state. © 2014 Elsevier B.V. Source

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