A5012114342- CRISPR and Genetic Engineering
- Gene Regulatory Network Analysis
- Evolution and Genetic Dynamics
- RNA and protein synthesis mechanisms
- Evolutionary Game Theory and Cooperation
- RNA Research and Splicing
- Bacterial Genetics and Biotechnology
- Advanced Optical Network Technologies
- Advanced Photonic Communication Systems
- Microbial Community Ecology and Physiology
- Micro and Nano Robotics
- Microtubule and mitosis dynamics
- Algal biology and biofuel production
- Cancer Cells and Metastasis
- Circadian rhythm and melatonin
- Innovative Microfluidic and Catalytic Techniques Innovation
- Cellular Mechanics and Interactions
- 3D Printing in Biomedical Research
- Congenital heart defects research
- Plant and Biological Electrophysiology Studies
- Mathematical Biology Tumor Growth
- Light effects on plants
- Cancer Mechanisms and Therapy
- Slime Mold and Myxomycetes Research
- Modular Robots and Swarm Intelligence
Cornell University
2016-2022
Laboratoire des Biomolécules
2021
University of Chicago
2013-2021
Orange (France)
2018-2020
Université Paris-Saclay
2018
Inserm
2008-2018
Université d'Évry Val-d'Essonne
2018
Institut de Biologie de l'École Normale Supérieure
2011-2017
Centre National de la Recherche Scientifique
2000-2017
Harvard University
2016
The emergence of bacterial antibiotic resistance is a growing problem, yet the variables that influence rate are not well understood. In microfluidic device designed to mimic naturally occurring niches, Escherichia coli ciprofloxacin developed within 10 hours. Resistance emerged with as few 100 bacteria in initial inoculation. Whole-genome sequencing resistant organisms revealed four functional single-nucleotide polymorphisms attained fixation. Knowledge about rapid heterogeneous conditions...
Bacteria prudently regulate their metabolic phenotypes by sensing the availability of specific nutrients, expressing required genes for metabolism, and repressing them after metabolites are depleted. It is unclear, however, how genetic networks maintain transmit phenotypic states between generations under rapidly fluctuating environments. By subjecting bacteria to carbon sources (glucose lactose) using microfluidics, we discover two types non-genetic memory in Escherichia coli analyze...
Abstract Plasmids are one of the most commonly used platforms for genetic engineering and recombinant gene expression in bacteria. The range available copy numbers cloning vectors is largely restricted to handful Origins Replication (ORIs) that have been isolated from plasmids found nature. Here, we introduce two systems allow continuous, finely-tuned control plasmid number between 1 800 copies per cell: a with an anhydrotetracycline-controlled number, parallelized assay generate continuous...
In Arabidopsis, the basic leucine zipper transcription factor ABI5 activates several late embryogenesis–abundant genes, including AtEm1 and AtEm6. However, expression of many other seed maturation genes is independent ABI5. We investigated possibility that homologs also participate in regulation gene during maturation. identified 13 ABI5-related Arabidopsis genomic sequence. RNA gel blot analysis showed seven these are active they display distinct kinetics. isolated characterized two mutant...
To investigate the transition from non-cancerous to metastatic a physical sciences perspective, Physical Sciences-Oncology Centers (PS-OC) Network performed molecular and biophysical comparative studies of non-tumorigenic MCF-10A MDA-MB-231 breast epithelial cell lines, commonly used as models cancer metastasis. Experiments were in 20 laboratories 12 PS-OCs. Each laboratory was supplied with identical aliquots common reagents culture protocols. Analyses these measurements revealed dramatic...
β-Lactam antibiotics disrupt the assembly of peptidoglycan (PG) within bacterial cell wall by inhibiting enzymatic activity penicillin-binding proteins (PBPs). It was recently shown that β-lactam treatment initializes a futile cycle PG synthesis and degradation, highlighting major gaps in our understanding lethal effects PBP inhibition antibiotics. Here, we assess downstream metabolic consequences Escherichia coli with mecillinam show lethality from PBP2 is specific consequence toxic shifts...
The Arabidopsis abscisic acid (ABA) insensitive (ABI)5 transcription factor participates in the ABA‐dependent induction of late embryogenesis abundant (LEA) genes final stages seed development. We tested whether VP16 transcriptional activation domain is sufficient to provide ABI5 with ability activate AtEm LEA vegetative tissues. took advantage a new transgenic selection assay based on green fluorescent protein (GFP) fluorescence and found that VP16‐ABI5 triggered growth retardation...
We report on the emergence of spontaneously forming migrating bands E. coli bacteria inside a microchannel containing microstructured ratchets. show that collection is able to migrate against funnel-shaped barriers by creating and maintaining chemoattractant gradient. A transition between pure rectification chemotaxis-driven collective motion predicted from theoretical models, observed experimentally as initial inoculation density varied.
The emergence of resistance to chemotherapy by cancer cells, when combined with metastasis, is the primary driver mortality in and has proven be refractory many efforts. Theory computer modeling suggest that rate driven strong selective pressure mutagenic enhanced motility mutant cells a gradient areas higher drug concentration lower population competition. To test these models, we constructed synthetic microecology which superposed doxorubicin across motile, metastatic breast (MDA-MB-231)....
Organisms use a variety of strategies to adapt their environments and maximize long-term growth potential, but quantitative characterization the benefits conferred by such strategies, as well impact on whole population's rate growth, remains challenging. Here, we path-integral framework that describes how selection acts lineages—i.e., life histories individuals ancestors—to demonstrate lineage-based measurements can be used quantify selective pressures acting population. We apply this...
Circadian clocks are oscillatory systems that allow organisms to anticipate rhythmic changes in the environment. Several studies have shown circadian connected metabolism, but it is not generally clear whether metabolic signaling one voice among many influence clock or cycling major synchronizer. To address this question cyanobacteria, we used a synthetic biology approach make normally autotrophic cells capable of growth on exogenous sugar. This allowed us manipulate metabolism independently...
We use a microfabricated ecology with doxorubicin gradient and population fragmentation to produce strong Darwinian selective pressure that drives forward the rapid emergence of resistance in multiple myeloma (MM) cancer cells. RNA sequencing resistant cells was used examine (i) genes high de novo substitution densities (i.e., hot genes) (ii) never substituted cold genes). The set genes, which were 21% sequenced, further winnowed down by examining excess expression levels. Both most highly...
The structural rearrangements accompanying mRNA during translation in mammalian cells remain poorly understood. Here, we discovered that YB-1 (YBX1), a major partner of mRNAs the cytoplasm, forms linear nucleoprotein filament with mRNA, when part unstructured C-terminus has been truncated. possesses cold-shock domain (CSD), remnant bacterial cold shock proteins have ability to stimulate under low temperatures through an RNA chaperone activity. structure indicates CSD preserved its activity...
CRISPR (clustered regularly interspaced short palindromic repeats) utility relies on a stable Cas effector complex binding to its target site. However, bound DNA may be removed by motor proteins carrying out host processes and the mechanism governing this removal remains unclear. Intriguingly, during interference, RNA polymerase (RNAP) progression is only fully blocked endonuclease-deficient (dCas) from protospacer adjacent motif (PAM)-proximal side. By mapping dCas-DNA interactions at high...
ABSTRACT The operon encoding the general stress transcription factor ς B and two proteins of its regulatory network, RsbV RsbW, was cloned from gram-positive bacterium Bacillus anthracis by PCR amplification chromosomal DNA with degenerate primers, inverse PCR, direct cloning. gene cluster very similar to subtilis sigB both in primary sequences products order three genes. However, deduced upstream downstream this showed no similarity other encoded B. operon. Therefore, contains genes rather...
Competing populations in shared spaces with nonrenewable resources do not necessarily wage a battle for dominance at the cost of extinction less-fit strain if there are fitness advantages to presence other strain. We report on use nanofabricated habitat landscapes study population dynamics competing wild type and growth advantage stationary phase (GASP) mutant strains Escherichia coli sealed heterogeneous nutrient environment. Although GASP mutants competitors wild-type bacteria, we find...
Historically, reconfigurable optical add/drop multiplexers (ROADMs) have been proprietary with respect to their data and control planes. There has a growing desire among network operators move away from such elements. Together other industry partners, we created the OpenROADM multi-source agreement published interoperability specifications as well YANG models for OpenROADM-compliant hardware software. This paper provides an overview of initiative, its current status, results tests. It also...
The versatility of CRISPR-Cas endonucleases as a tool for biomedical research has led to diverse applications in gene editing, programmable transcriptional control, and nucleic acid detection. Most systems, however, suffer from off-target effects unpredictable nonspecific binding that negatively impact their reliability broader applicability. To better evaluate the mismatches on DNA target recognition binding, we develop massively parallel CRISPR interference (CRISPRi) assay measure energy...
We demonstrate a novel and robust microfluidic chip with combined functions of continuous culture output PC-3 prostate cancer cells. With digital controls, polydimethylsiloxane (PDMS) flexible diaphragms are able to apply hydrodynamic shear forces on cultures, detaching fraction attached cells from the surface for while leaving others reuse in subsequent cultures. The fractions detached remaining can be precisely controlled. system has not only advantages small size, high cell efficiency,...
The development of the different muscles within somite is a complex process that involves Hedgehog (Hh) signaling pathway. To specify proper number muscle cells and organize them spatially temporally, Hh pathway needs to be precisely regulated at levels, but only few factors external have been described. Here, we report for first time role STAR family RNA-binding protein Quaking A (QkA) in development. We show zebrafish loss QkA function affects fast fiber maturation as well Hh-induced...
One of the physiological responses bacteria to external stress is assemble into a biofilm. The formation biofilm greatly increases bacterial population's resistance hostile environment by shielding cells, for example, from antibiotics. In this paper, we describe conditions necessary emergence biofilms in natural environments and relate them inside microfluidic devices. We show that competing species Escherichia coli form spatially segregate themselves response starvation stress, use situ...