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

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

Elowitz

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

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

LabWatch september 21

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