UA Biophysics:SysBio Meeting:Journal Watch: Difference between revisions
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==eLIFE== | ==eLIFE== | ||
''' | '''29 September 2015''' | ||
'''August 2015''' | |||
• [http:// | • [http://elifesciences.org/content/4/e07935 Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network] | ||
'''Search: Computational and Systems Biology''' | '''Search: Computational and Systems Biology''' | ||
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• [http://dx.doi.org/10.7554/eLife.06559 Limits on information transduction through amplitude and frequency regulation of transcription factor activity] | • [http://dx.doi.org/10.7554/eLife.06559 Limits on information transduction through amplitude and frequency regulation of transcription factor activity] | ||
==Nature Reviews of Microbiology== | ==Nature Reviews of Microbiology== | ||
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==Physical Review Letters== | ==Physical Review Letters== | ||
'''Journal Watch Agosto 17 2016''' | |||
• [http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.058101 Constraints on Fluctuations in Sparsely Characterized Biological Systems] | |||
De Paulsson, Limites en el ruido desde lo general usando propiedades matemáticas. | |||
• [http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.238101 From Quasiperiodic Partial Synchronization to Collective Chaos in Populations of Inhibitory Neurons with Delay] | |||
De redes neuronales y termodinámica. Caos. | |||
• [http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.258104 Cooperativity of Negative Autoregulation Confers Increased Mutational Robustness] | |||
Estudio del feedback negativo. | |||
• [http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.117.018102 Heterodimer Autorepression Loop: A Robust and Flexible Pulse-Generating Genetic Module] | |||
Un motif parecido a lo que se quiere para sistemas TA. | |||
• [http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.117.038001 Single-File Escape of Colloidal Particles from Microfluidic Channels] | |||
De microfluidos. | |||
• [http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.098101 Emergent Collective Chemotaxis without Single-Cell Gradient Sensing] | |||
• [http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.238701 Information Flows? A Critique of Transfer Entropies] | |||
Informacion, entropia y sistemas complejos. | |||
'''Volume 115, Issue 14, 2 Octuber 2015 (Partial)''' | |||
'''Volume 115, Issue 11, 11 September 2015''' | |||
• [http://dx.doi.org.ezproxy.uniandes.edu.co:8080/10.1103/PhysRevLett.115.118102 Free Energy Cost of Reducing Noise while Maintaining a High Sensitivity] | |||
'''Volume 115, Issue 12, 18 September 2015''' | |||
• [http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.115.128101 Subdominant Dense Clusters Allow for Simple Learning and High Computational Performance in Neural Networks with Discrete Synapses] | |||
'''Volume 115, Issue 8, 21 August 2015''' | '''Volume 115, Issue 8, 21 August 2015''' | ||
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• [http://dx.doi.org.ezproxy.uniandes.edu.co:8080/10.1103/PhysRevLett.115.050602 Multidimensional Langevin Modeling of Nonoverdamped Dynamics] | • [http://dx.doi.org.ezproxy.uniandes.edu.co:8080/10.1103/PhysRevLett.115.050602 Multidimensional Langevin Modeling of Nonoverdamped Dynamics] | ||
'''Volume 115, Issue 3, 17 July 2015''' | '''Volume 115, Issue 3, 17 July 2015''' | ||
• [http://dx.doi.org.ezproxy.uniandes.edu.co:8080/10.1103/PhysRevLett.115.038102 Physical Limit to Concentration Sensing Amid Spurious Ligands] | • [http://dx.doi.org.ezproxy.uniandes.edu.co:8080/10.1103/PhysRevLett.115.038102 Physical Limit to Concentration Sensing Amid Spurious Ligands] | ||
'''Volume 114, Issue 24, 19 June 2015''' | '''Volume 114, Issue 24, 19 June 2015''' | ||
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• [http://stm.sciencemag.org.ezproxy.uniandes.edu.co:8080/content/7/297/297ra114.abstract?sid=1fd9e158-2701-4841-a7cc-20f5b218f209 Fitness cost of antibiotic susceptibility during bacterial infection] | • [http://stm.sciencemag.org.ezproxy.uniandes.edu.co:8080/content/7/297/297ra114.abstract?sid=1fd9e158-2701-4841-a7cc-20f5b218f209 Fitness cost of antibiotic susceptibility during bacterial infection] | ||
• [http://stke.sciencemag.org.ezproxy.uniandes.edu.co:8080/content/8/386/ec200.abstract?sid=e4290fbd-9e68-4a0b-bc1d-0e45f9b5d1a4 Biochemical basis of a 24-hour clock] | |||
• [http://www.sciencemag.org.ezproxy.uniandes.edu.co:8080/content/349/6245/324.abstract?sid=e4290fbd-9e68-4a0b-bc1d-0e45f9b5d1a4 A protein fold switch joins the circadian oscillator to clock output in cyanobacteria] | |||
• [http://stke.sciencemag.org.ezproxy.uniandes.edu.co:8080/content/8/383/ra66.abstract?sid=aab4e605-aa84-4a29-8f0c-015e6c134350 Simple synthetic protein scaffolds can create adjustable artificial MAPK circuits in yeast and mammalian cells] | |||
• [http://www.sciencemag.org.ezproxy.uniandes.edu.co:8080/content/348/6242/1407.summary?sid=586da687-d294-4364-9525-6521de712405 An enhanced view of gene control] | |||
==PLOS Biology== | ==PLOS Biology== | ||
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• [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002042 Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts] | • [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002042 Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts] | ||
'''Journal Watch Agosto 17 2016''' | |||
• [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001549 Cooperation and the Fate of Microbial Societies] | |||
• [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0040299 Cooperation among Microorganisms] | |||
• [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0030194 The Evolution of Norms] | |||
• [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060130 Sperm Sociality: Cooperation, Altruism, and Spite] | |||
• [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060014 The Evolution of Quorum Sensing in Bacterial Biofilms] | |||
==Journal of Mathematical Biology== | ==Journal of Mathematical Biology== | ||
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• [http://www.cell.com/trends/microbiology/abstract/S0966-842X(15)00150-X Entry and exit of bacterial outer membrane proteins] | • [http://www.cell.com/trends/microbiology/abstract/S0966-842X(15)00150-X Entry and exit of bacterial outer membrane proteins] | ||
==PNAS== | |||
'''Adaptación de microorganismos frente a ambientes cambiantes''' | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/110/50/20338.abstract?sid=cf25ffcb-d89e-499a-8a8b-f2680a9e98b8 Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments] | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/110/34/14006.abstract?sid=cf25ffcb-d89e-499a-8a8b-f2680a9e98b8 Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population] | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/108/17/7271.abstract?sid=96988b2f-b5ef-466c-b8b4-16373f4538c1 A mathematical model for adaptive prediction of environmental changes by microorganisms] | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/107/41/17845.abstract?sid=3b92b6aa-e3a1-4f55-8fe4-f13fea6b7eec Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis] | |||
'''Adaptación de levaduras frente a ambientes nutricionales diferentes''' | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/112/5/1636.abstract?sid=cf25ffcb-d89e-499a-8a8b-f2680a9e98b8 Galactose metabolic genes in yeast respond to a ratio of galactose and glucose] | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/108/29/12179.abstract?sid=82de435a-857e-4619-9d8a-6b02d595b710 Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis] | |||
'''Sistemas toxina-antitoxina y persistencia''' | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/110/27/E2528.abstract?sid=cf25ffcb-d89e-499a-8a8b-f2680a9e98b8 Molecular mechanisms of multiple toxin–antitoxin systems are coordinated to govern the persister phenotype] | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/109/31/12740.abstract?sid=77352602-0afc-46a9-94e1-54e6726b70f9 Large mutational target size for rapid emergence of bacterial persistence] | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/112/16/5171.abstract?sid=bd6d3a74-098b-4d60-aa00-65de7cc903c7 Stochastic induction of persister cells by HipA through (p)ppGpp-mediated activation of mRNA endonucleases] | |||
'''Teoría de juegos, redes genéticas''' | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/107/4/1391.abstract?sid=50416c56-f25d-4403-9527-183679641bdf Bacterial strategies for chemotaxis response] | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/111/19/6994.abstract?sid=53d85262-84f1-4f62-a4c1-b971ff6a4a3f Phenotypic switching in gene regulatory networks] | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/98/15/8614.abstract?sid=53d85262-84f1-4f62-a4c1-b971ff6a4a3f Intrinsic noise in gene regulatory networks] | |||
'''Microfluidos''' | |||
• [http://www.pnas.org.ezproxy.uniandes.edu.co:8080/content/106/36/15225.abstract?sid=344a7baa-cfa3-4c77-93b5-be0e51f9198b High-sensitivity microfluidic calorimeters for biological and chemical applications] | |||
==Molecular Microbiology== | |||
• [http://onlinelibrary.wiley.com/doi/10.1111/mmi.13147/abstract Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations] | |||
• [http://onlinelibrary.wiley.com/doi/10.1111/mmi.12884/abstract Escherichia coli persister cells suppress translation by selectively disassembling and degrading their ribosomes] | |||
• [http://onlinelibrary.wiley.com/doi/10.1111/mmi.13082/abstract A novel pathway for outer membrane protein biogenesis in Gram-negative bacteria] | |||
• [http://onlinelibrary.wiley.com/doi/10.1111/mmi.12757/abstract Perturbation of the interaction between Gal4p and Gal80p of the Saccharomyces cerevisiae GAL switch results in altered responses to galactose and glucose] | |||
==Cell== | |||
• [http://www.cell.com/cell/abstract/S0092-8674(15)00828-4Wireless Optofluidic Systems for Programmable In Vivo Pharmacology and Optogenetics] | |||
==Biophysical Journal== | |||
•[http://www.cell.com/biophysj/abstract/S0006-3495(15)00617-7 Isocost Lines Describe the Cellular Economy of Genetic Circuits] | |||
•[http://www.cell.com/biophysj/abstract/S0006-3495(14)01273-9 Understanding Gene Expression Heterogeneity in Living Cells with Single-Molecule Fluorescence Microscopy] | |||
•[http://www.cell.com/biophysj/abstract/S0006-3495(13)03394-8 Sensitivity Analysis and Model Reduction Applied to Adapting Biological Systems] | |||
•[http://www.cell.com/biophysj/abstract/S0006-3495(13)05603-8 Information Transmission through Pancreatic Beta Cell Signaling Pathways] | |||
•[http://www.cell.com/biophysj/abstract/S0006-3495(14)01128-X Systems Mechanobiology: Tension-Inhibited Protein Turnover Is Sufficient to Physically Control Gene Circuits] | |||
•[http://www.cell.com/biophysj/abstract/S0006-3495(14)03742-4 Stochastic Control of Intracellular Latency and Transactivation in Human Immunodeficiency Virus Type 1 (HIV-1)] | |||
•[http://www.cell.com/biophysj/abstract/S0006-3495(11)02938-9 Irreversible Thermodynamics of Transcriptional Regulation] | |||
•[http://www.cell.com/biophysj/abstract/S0006-3495(14)01482-9 The Engineering of Artificial Cellular Systems using Synthetic Biology Approaches] | |||
•[http://www.cell.com/biophysj/abstract/S0006-3495(12)04019-2 Microfluidics Assisted Cell Screening] | |||
==Plasmid== | |||
• [http://www.sciencedirect.com/science/article/pii/S0147619X14000882 Plasmids in the driving seat: The regulatory RNA Rcd gives plasmid ColE1 control over division and growth of its E. coli host] | |||
• [http://www.sciencedirect.com/science/article/pii/S0147619X15300044 Transformation of Shewanella baltica with ColE1-like and P1 plasmids and their maintenance during bacterial growth in cultures] | |||
• [http://www.sciencedirect.com/science/article/pii/S0147619X14000559 Mechanisms of plasmid segregation: Have multicopy plasmids been overlooked?] | |||
• [http://www.sciencedirect.com/science/article/pii/S0147619X14000031 Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains] | |||
• [http://www.sciencedirect.com/science/article/pii/S0147619X13000954 New quantitative methods for measuring plasmid loss rates reveal unexpected stability] | |||
• [http://www.sciencedirect.com/science/article/pii/S0147619X1200008X Evaluating quantitative methods for measuring plasmid copy numbers in single cells] | |||
[[UA Biophysics:SysBio Meeting|Return to | [[UA Biophysics:SysBio Meeting:2015-II Meetings|Return to 2015-II Meetings]]<br> |
Latest revision as of 06:00, 30 August 2016
eLIFE
29 September 2015
August 2015
Search: Computational and Systems Biology
• Expression noise facilitates the evolution of gene regulation
Nature Reviews of Microbiology
September 2015 Issue 9 Vol 13
• Review Highlights: Biofilms: Oscillations relieve the siege
• Article Series: Bacterial protein networks: properties and functions
• Reviews: The yin and yang of hepatitis C: synthesis and decay of hepatitis C virus RNA
• Genome Watch: Looking at Beijing’s skyline
• HipBA–promoter structures reveal the basis of heritable multidrug tolerance
August 2015 Issue 8 Vol 13
• Research Highlights: Obg controls bacterial persistence
July 2015 Issue 7 Vol 13
May 2015 Issue 6 Vol 13
• Research Highlights: Metalloregulatory riboswitches
Physical Review Letters
Journal Watch Agosto 17 2016
• Constraints on Fluctuations in Sparsely Characterized Biological Systems De Paulsson, Limites en el ruido desde lo general usando propiedades matemáticas.
• From Quasiperiodic Partial Synchronization to Collective Chaos in Populations of Inhibitory Neurons with Delay De redes neuronales y termodinámica. Caos.
• Cooperativity of Negative Autoregulation Confers Increased Mutational Robustness Estudio del feedback negativo.
• Heterodimer Autorepression Loop: A Robust and Flexible Pulse-Generating Genetic Module Un motif parecido a lo que se quiere para sistemas TA.
• Single-File Escape of Colloidal Particles from Microfluidic Channels De microfluidos.
• Emergent Collective Chemotaxis without Single-Cell Gradient Sensing
• Information Flows? A Critique of Transfer Entropies Informacion, entropia y sistemas complejos.
Volume 115, Issue 14, 2 Octuber 2015 (Partial)
Volume 115, Issue 11, 11 September 2015
• Free Energy Cost of Reducing Noise while Maintaining a High Sensitivity
Volume 115, Issue 12, 18 September 2015
Volume 115, Issue 8, 21 August 2015
• Generalized Communities in Networks
• Aging Wiener-Khinchin Theorem
• Wiener-Khinchin Theorem for Nonstationary Scale-Invariant Processes
Volume 115, Issue 7, 14 August 2015
• Generalization of Pairwise Models to non-Markovian Epidemics on Networks
Volume 115, Issue 5, 31 July 2015
• Multidimensional Langevin Modeling of Nonoverdamped Dynamics
Volume 115, Issue 3, 17 July 2015
• Physical Limit to Concentration Sensing Amid Spurious Ligands
Volume 114, Issue 24, 19 June 2015
• Identification of Patient Zero in Static and Temporal Networks: Robustness and Limitations
SCIENCE
• Membrane potential regulates growth
• Structure of a yeast spliceosome at 3.6-angstrom resolution
• Modified yeast produce opiates from sugar
• Complete biosynthesis of opioids in yeast
• Extended-resolution structured illumination imaging of endocytic and cytoskeletal dynamics
• Emergent genetic oscillations in a synthetic microbial consortium
• Synthetic communities, the sum of parts
• Engineering cell population behavior
• Allosteric transcriptional regulation via changes in the overall topology of the core promoter
• Differentiating between nutrient sources
• Fitness cost of antibiotic susceptibility during bacterial infection
• Biochemical basis of a 24-hour clock
• A protein fold switch joins the circadian oscillator to clock output in cyanobacteria
• An enhanced view of gene control
PLOS Biology
• Biofilm Formation As a Response to Ecological Competition
Journal Watch Agosto 17 2016
• Cooperation and the Fate of Microbial Societies
• Cooperation among Microorganisms
• Sperm Sociality: Cooperation, Altruism, and Spite
• The Evolution of Quorum Sensing in Bacterial Biofilms
Journal of Mathematical Biology
• Theory of a microfluidic serial dilution bioreactor for growth of planktonic and biofilm populations
Microbiology and Molecular Biology Reviews
• Yeast Prions: Structure, Biology, and Prion-Handling Systems
Trends in Microbiology
• Collateral sensitivity of antibiotic-resistant microbes
• Entry and exit of bacterial outer membrane proteins
PNAS
Adaptación de microorganismos frente a ambientes cambiantes
• A mathematical model for adaptive prediction of environmental changes by microorganisms
Adaptación de levaduras frente a ambientes nutricionales diferentes
• Galactose metabolic genes in yeast respond to a ratio of galactose and glucose
Sistemas toxina-antitoxina y persistencia
• Large mutational target size for rapid emergence of bacterial persistence
Teoría de juegos, redes genéticas
• Bacterial strategies for chemotaxis response
• Phenotypic switching in gene regulatory networks
• Intrinsic noise in gene regulatory networks
Microfluidos
• High-sensitivity microfluidic calorimeters for biological and chemical applications
Molecular Microbiology
• Live cell imaging of SOS and prophage dynamics in isogenic bacterial populations
• A novel pathway for outer membrane protein biogenesis in Gram-negative bacteria
Cell
• Optofluidic Systems for Programmable In Vivo Pharmacology and Optogenetics
Biophysical Journal
•Isocost Lines Describe the Cellular Economy of Genetic Circuits
•Sensitivity Analysis and Model Reduction Applied to Adapting Biological Systems
•Information Transmission through Pancreatic Beta Cell Signaling Pathways
•Irreversible Thermodynamics of Transcriptional Regulation
•The Engineering of Artificial Cellular Systems using Synthetic Biology Approaches
•Microfluidics Assisted Cell Screening
Plasmid
• Mechanisms of plasmid segregation: Have multicopy plasmids been overlooked?
• New quantitative methods for measuring plasmid loss rates reveal unexpected stability
• Evaluating quantitative methods for measuring plasmid copy numbers in single cells