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Biologistics—Diffusion coefficients for complete proteome of Escherichia coli
2012
Computer applications in the biosciences : CABIOS
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contain the complete information about the diffusion coefficients of proteins in a given cell type. ...
We exemplify the method with the database of in vivo DC for all proteins (4,302 records) from the proteome of K12 strain of E. coli, together with examples of DC of amino acids, sugars, RNA and DNA. ...
Marcin Fialkowski for inspiring discussions. ...
doi:10.1093/bioinformatics/bts537
pmid:22942021
pmcid:PMC3496334
fatcat:f7zl5oyx4zcfndq2miqnouknyy
Mathematical modeling of gene expression: a guide for the perplexed biologist
2011
Critical reviews in biochemistry and molecular biology
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for quantitative understanding of biological systems. ...
For those interested in beginning a transcriptional mathematical modeling project, we provide here an overview of major types of models and their applications to transcriptional networks. ...
Declaration of interest The authors declare to have no conflict of interest. The authors alone are responsible for the content and the writing of the manuscript. ...
doi:10.3109/10409238.2011.556597
pmid:21417596
pmcid:PMC3086598
fatcat:uei7p4jtbnfoxfpm67va4ucwrq
Computational and experimental approaches to chart theEscherichia colicell-envelope-associated proteome and interactome
2009
FEMS Microbiology Reviews
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In this review, we summarize the state of the art of computational and proteomic approaches for determining the components of the E. coli cell-envelope proteome, as well as exploring the physical and functional ...
Strikingly, however, only half of the c. 1200 putative cell-envelope-related proteins of E. coli currently have experimentally attributed functions, indicating an opportunity for discovery. ...
Acknowledgements The authors wish to thank Sadhna Phanse, and the anonymous reviewers for their motivating comments during the preparation of this manuscript. ...
doi:10.1111/j.1574-6976.2008.00141.x
pmid:19054114
pmcid:PMC2704936
fatcat:mohn3yvjangdzest5i7z3f2dgm
Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?
2003
Biotechnology and Bioengineering
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This review considers constraints in terms of environmental, physicochemical, and self-imposed regulatory and evolutionary constraints with the purpose of refining current constraintbased models of cell ...
Cells must abide by a number of constraints. The environmental constraints of cellular behavior and physicochemical limitations affect cellular processes. ...
The authors thank Markus Herrgard and Jason Papin for helpful discussions and reviews. ...
doi:10.1002/bit.10849
pmid:14708117
fatcat:zhsoh3jbonaivbdzwv7euujvke
Is the intrinsic disorder of proteins the cause of the scale-free architecture of protein–protein interaction networks?
2007
Proteomics
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In this paper, we investigate the role of protein disorder in the network topology. We find that the disorder of a protein (or of its neighbors) is independent of its number of PPIs. ...
This result suggests that protein disorder does not play a role in the scale-free architecture of protein networks. ...
We started downloading the PPI networks for Homo sapiens (human), S. cerevisiae (yeast), Drosophila melanogaster (fly), Caenorhabditis elegans (worm), and Escherichia coli (bacterium) from the Biomolecular ...
doi:10.1002/pmic.200600455
pmid:17285562
fatcat:ezeofyhi7negpdebvp7hmuxrhq
Isolation and purification ofThermus thermophilusHpaB by a crystallization approach
2010
Acta Crystallographica. Section F : Structural Biology and Crystallization Communications
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The oxygenase HpaB is a component of the 4-hydroxyphenylacetate 3-monooxygenase enzyme that is responsible for the hydroxylation of 4-hydroxyphenylacetate. ...
While isolating integral membrane respiratory complexes from Thermus thermophilus, microcrystals of HpaB were formed. Further purification of the enzyme was achieved by repetitive crystallization. ...
Based on these observations, two groups, with the Acinetobacter baumannii and Escherichia coli enzymes as representatives, can be identified. ...
doi:10.1107/s1744309110003714
pmid:20208179
pmcid:PMC2833055
fatcat:rdegp6dz7zcglbyjknyft7b2ku
Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study
2011
PLoS Computational Biology
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We analyze and compare the behavior of the inducible lac genetic switch using well-stirred and spatially resolved simulations for Escherichia coli cells modeled under fast and slow-growth conditions. ...
Using cryoelectron tomography of an E. coli cell and data from proteomics studies, we construct spatial in vivo models of cells and quantify the noise contributions and effects on repressor rebinding due ...
Acknowledgments The authors would like to acknowledge John Stone for helpful discussions on implementation of the code on the GPU.
Author Contributions ...
doi:10.1371/journal.pcbi.1002010
pmid:21423716
pmcid:PMC3053318
fatcat:zyiwxi4vlbdolefsgrvormgr2m
Heparin-Binding Protein: A Novel Biomarker Linking Four Different Cardiovascular Diseases
2020
Cardiology Research and Practice
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Clustering coefficients were calculated using Cytoscape, and MCODE was used for subnet analysis. ...
Moreover, a large number of important HBPs were identified that may be significant for the treatment of these diseases. ...
: lists of clustering coefficients of Ec_hepint, Ec_not hepint, and Ec_hepint_random. ...
doi:10.1155/2020/9575373
pmid:32612856
pmcid:PMC7312699
fatcat:jmjg5g446fbkbkss3r5uu2qkua
Systematic functional analysis of the yeast genome
1998
Trends in Biotechnology
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The genome sequence of the yeast Saccharomyces cerevisiae has provided the first complete inventory of the working parts of a eukaryotic cell. ...
Systematic and comprehensive approaches to the elucidation of yeast gene function are discussed and the prospects for the functional genomics of eukaryotic organisms evaluated. ...
FB is grateful to Pfizer Central Research for the provision of a postgraduate research studentship. ...
doi:10.1016/s0167-7799(98)01214-1
pmid:9744112
fatcat:bngyipmjprfmhclvt65d5z466e
Does cell biology need physicists?
2011
Physics
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Allured by the chic perception and higher funding levels of disease-oriented research, many physicists have migrated to cell biology. ...
Moraru for useful discussions. ...
Motivated by their work, Howard Berg was one of the pioneers of quantitative biophysical investigations of the swimming of bacteria and showed that Escherichia coli swims by a series of runs and tumbles ...
doi:10.1103/physics.4.4
fatcat:xqcsxe67mnaonlpw73uyoy7d64
Integrated In Silico Analysis of Pathway Designs for Synthetic Photo-Electro-Autotrophy
2016
PLoS ONE
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We integrated Flux Balance Analysis of the heterotrophic chassis Escherichia coli with kinetic pathway analysis and thermodynamic pathway analysis (Max-min Driving Force). ...
photosystems and the high ATP maintenance of E. coli. ...
Major advances in synthetic biology start to allow engineering of complex features related to autotrophy into heterotrophic chassis microorganisms, such as Escherichia coli. ...
doi:10.1371/journal.pone.0157851
pmid:27336167
pmcid:PMC4919048
fatcat:cvyhpvaw3fcijlp65233xrbsna
AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis
2009
Plant Physiology
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AraGEM is a viable framework for in silico functional analysis and can be used to derive new, nontrivial hypotheses for exploring plant metabolism. ...
AraGEM is a comprehensive literature-based, genome-scale metabolic reconstruction that accounts for the functions of 1,419 unique open reading frames, 1,748 metabolites, 5,253 gene-enzyme reaction-association ...
ACKNOWLEDGMENTS We thank Simon Boyes for complementing data curation analysis in AraGEM. We also acknowledge our partners, BSES Ltd. and Metabolix, Inc. ...
doi:10.1104/pp.109.148817
pmid:20044452
pmcid:PMC2815881
fatcat:nz3nso2h2rddnnqdlh4y6b6usi
The Impact of Mistranslation on Phenotypic Variability and Fitness
2021
Evolution
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For instance, translation errors result in about 10% of cellular proteins carrying altered sequences. ...
Thus, proteome diversification arising from translation errors can potentially generate phenotypic variability, in turn increasing variability in the fate of cells or of populations. ...
ACKNOWLEDGMENTS We thank Vidyanand Nanjundiah and members of the Agashe lab for discussion and critical comments on the manuscript, and Debshankar Banerjee for the MATLAB code used for analysing the single ...
doi:10.1111/evo.14179
pmid:33491193
fatcat:63l6ddonbnb7znfpgxxd2pytpa
Biomicrofluidics: Recent trends and future challenges
2009
Sadhana (Bangalore)
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Particular emphasis is given on the microfluidics-based handling of DNA, cells, and proteins, as well as fundamental microfluidic considerations for design of biomedical microdevices. ...
Biomicrofluidics is an active area of research at present, exploring the synergy of microfluidics with cellular and molecular biology, biotechnology, and biomedical engineering. ...
(Baeumner et al 2001) , Dengue virus (Zaytseva et al 2004) and Escherichia coli (Baeumner et al 2003) . ...
doi:10.1007/s12046-009-0035-8
fatcat:7nbvjoc45bfovk7fwommwyxs7a
The Functional Network of the Arabidopsis Plastoglobule Proteome Based on Quantitative Proteomics and Genome-Wide Coexpression Analysis
2012
Plant Physiology
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An integrated view of the role of the PG is lacking. Here, we better define the PG proteome and provide a conceptual framework for further studies. ...
The PG proteome from Arabidopsis (Arabidopsis thaliana) leaf chloroplasts was determined by mass spectrometry of isolated PGs and quantitative comparison with the proteomes of unfractionated leaves, thylakoids ...
ACKNOWLEDGMENTS We thank Carole Daugherty (Cornell Center for Material Research) for critical assistance with the SEM analysis of PG preparations, Richard Medville of Electron Microscopy Sciences for the ...
doi:10.1104/pp.111.193144
pmid:22274653
pmcid:PMC3291262
fatcat:hdkvtstvzjf4xoedwzk77y2gbm
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