UA Biophysics:SysBio Meeting:Journal Watch

eLIFE

29 September 2015

August 2015

• Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network

Search: Computational and Systems Biology

• Expression noise facilitates the evolution of gene regulation

• Limits on information transduction through amplitude and frequency regulation of transcription factor activity

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

• Redirected from Nature Research Highlights: Metabolic dependencies drive species co-occurrence in diverse microbial communities

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

• Subdominant Dense Clusters Allow for Simple Learning and High Computational Performance in Neural Networks with Discrete Synapses

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

• The rhodopsin–guanylyl cyclase of the aquatic fungus Blastocladiella emersonii enables fast optical control of cGMP signaling

• 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

• Simple synthetic protein scaffolds can create adjustable artificial MAPK circuits in yeast and mammalian cells

• An enhanced view of gene control

PLOS Biology

• Biofilm Formation As a Response to Ecological Competition

• Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts

Journal Watch Agosto 17 2016

• Cooperation and the Fate of Microbial Societies

• Cooperation among Microorganisms

• The Evolution of Norms

• 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

• Acylation of Biomolecules in Prokaryotes: a Widespread Strategy for the Control of Biological Function and Metabolic Stress

• 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

• Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

• Heterogeneity in protein expression induces metabolic variability in a modeled Escherichia coli population

• A mathematical model for adaptive prediction of environmental changes by microorganisms

• Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis

Adaptación de levaduras frente a ambientes nutricionales diferentes

• Galactose metabolic genes in yeast respond to a ratio of galactose and glucose

• Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis

Sistemas toxina-antitoxina y persistencia

• Molecular mechanisms of multiple toxin–antitoxin systems are coordinated to govern the persister phenotype

• Large mutational target size for rapid emergence of bacterial persistence

• Stochastic induction of persister cells by HipA through (p)ppGpp-mediated activation of mRNA endonucleases

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

• Escherichia coli persister cells suppress translation by selectively disassembling and degrading their ribosomes

• A novel pathway for outer membrane protein biogenesis in Gram-negative bacteria

• Perturbation of the interaction between Gal4p and Gal80p of the Saccharomyces cerevisiae GAL switch results in altered responses to galactose and glucose

Cell

• Optofluidic Systems for Programmable In Vivo Pharmacology and Optogenetics

Biophysical Journal

•Isocost Lines Describe the Cellular Economy of Genetic Circuits

•Understanding Gene Expression Heterogeneity in Living Cells with Single-Molecule Fluorescence Microscopy

•Sensitivity Analysis and Model Reduction Applied to Adapting Biological Systems

•Information Transmission through Pancreatic Beta Cell Signaling Pathways

•Systems Mechanobiology: Tension-Inhibited Protein Turnover Is Sufficient to Physically Control Gene Circuits

•Stochastic Control of Intracellular Latency and Transactivation in Human Immunodeficiency Virus Type 1 (HIV-1)

•Irreversible Thermodynamics of Transcriptional Regulation

•The Engineering of Artificial Cellular Systems using Synthetic Biology Approaches

•Microfluidics Assisted Cell Screening

Plasmid

• Plasmids in the driving seat: The regulatory RNA Rcd gives plasmid ColE1 control over division and growth of its E. coli host

• Transformation of Shewanella baltica with ColE1-like and P1 plasmids and their maintenance during bacterial growth in cultures

• Mechanisms of plasmid segregation: Have multicopy plasmids been overlooked?

• Effect of growth rate and selection pressure on rates of transfer of an antibiotic resistance plasmid between E. coli strains

• New quantitative methods for measuring plasmid loss rates reveal unexpected stability

• Evaluating quantitative methods for measuring plasmid copy numbers in single cells

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