UA Biophysics:SysBio Meeting:2016-II Meetings:Lab Watch September 21 2016

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Uri Alon and Terrence Hwa

21 September 2016

Alon Lab

Hwa Lab

Marx Lab & Lenski Lab

Marx Lab

Regulatory revolution: Evolving the "Anti-LacI" Repressor

Fast Growth Increases the Selective Advantage of a Mutation Arising Recurrently during Evolution under Metal Limitation

Evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild type physiology

Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous variants in a key enzyme.

Multiple long-term, experimentally-evolved populations of Escherichia coli acquire dependence upon citrate as an iron chelator for optimal growth on glucose.

Lenski Lab

Games Microbes Play

Developmental cheating in the social bacterium Myxococcus xanthus

Loss of social behaviours in Myxococcus xantus during evolution in an unstructured habitat

Coevolution drives the emergence of complex traits and promotes evolvability

Repeatability and contingency in the evolution of a key innovation in phage Lambda

Linking genetic change to community evolution: insights from studies of bacteria and bacteriophage.

Tradeoff between horizontal and vertical modes of transmission in bacterial plasmids

Effect of resource enrichment on a chemostat community of bacteria and bacteriophage

Kim Lewis and Kenn Gerdes

Kim Lewis

HipBA–promoter structures reveal the basis of heritable multidrug tolerance

Persister formation in Staphylococcus aureus is associated with ATP depletion

Kenn Gerdes Lab

Pumping persisters

Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Module-Encoded mRNases

Remarkable Functional Convergence: Alarmone ppGpp Mediates Persistence by Activating Type I and II Toxin-Antitoxins

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

J Paulsson

• 2016 Noise-proofing the repressilator: synchronous long-term oscillations in a synthetic gene circuit.

• 2016 Mechanical slowing-down of cytoplasmic diffusion allows in vivo counting of proteins in individual cells.

• 2016 Constraints on Fluctuations in Sparsely Characterized Biological Systems.

• 2016 Visualization of Periplasmic and Cytoplasmic Proteins with a Self-Labeling Protein Tag.

• 2016 Exploiting Natural Fluctuations to Identify Kinetic Mechanisms in Sparsely Characterized Systems.

M Dunlop

• 2016 Phenotypic Diversity Using Bimodal and Unimodal Expression of Stress Response Proteins

• 2016 Stochastic expression of a multiple antibiotic resistance activator confers transient resistance in single cells

• 2016 Performing selections under dynamic conditions for synthetic biology applications

• 2015 Noise and Low-Level Dynamics Can Coordinate Multicomponent Bet Hedging Mechanisms[ ]

N Balaban

• 2016 Quantitative Measurements of Type I and Type II Persisters Using ScanLag

• 2015 Lineage correlations of single cell division time as a probe of cell-cycle dynamics


An excitable gene regulatory circuit induces transient cellular differentiation

Dynamics of epigenetic regulation at the single-cell level

van Oudenaarden

Studying Lineage Decision-Making In Vitro: Emerging Concepts and Novel Tools

MicroRNA control of protein expression noise


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


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


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


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

LabWatch september 21

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