A5023992004- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Lipid Membrane Structure and Behavior
- Bacterial biofilms and quorum sensing
- Gene Regulatory Network Analysis
- Gut microbiota and health
- Bacteriophages and microbial interactions
- Force Microscopy Techniques and Applications
- Escherichia coli research studies
- Antibiotic Resistance in Bacteria
- CRISPR and Genetic Engineering
- Pickering emulsions and particle stabilization
- Vibrio bacteria research studies
- Protein Structure and Dynamics
- Dendrimers and Hyperbranched Polymers
- Algebraic structures and combinatorial models
- Probiotics and Fermented Foods
- Black Holes and Theoretical Physics
- Evolution and Genetic Dynamics
- Advanced Fluorescence Microscopy Techniques
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Clostridium difficile and Clostridium perfringens research
- Microbial Community Ecology and Physiology
- Blood disorders and treatments
California University of Pennsylvania
2014-2025
University of Pennsylvania
2015-2024
University of the Sciences
2023-2024
Philadelphia University
2014-2015
Argonne National Laboratory
2005
Rockefeller University
1996-2000
ExxonMobil (United States)
1995-1996
University of California, Santa Barbara
1991-1994
Harvard University
1965-1990
Massachusetts General Hospital
1965
Summary Quantitative spatial distributions of ribosomes (S2‐YFP) and RNA polymerase (RNAP; β′‐yGFP) in live Escherichia coli are measured by superresolution fluorescence microscopy. In moderate growth conditions, nucleoid–ribosome segregation is strong, RNAP localizes to the nucleoid lobes. The mean copy numbers per cell 4600 RNAPs 55 000 ribosomes. Only 10–15% lie within densest part lobes, at most 4% two ribosome‐rich endcaps. predominant observed diffusion coefficient D ribo = 0.04 µm 2 s...
Significance It is generally thought that the gut microbes consume oxygen and maintain lumen in a deeply anaerobic state. However, we found of germ-free mice also anaerobic, suggesting there exist other mechanisms responsible for consumption addition to microbes’ respiration. These comprise oxidative reactions, such as oxidation lipids organic substrates. Both microbiota chemistry regulate luminal levels turn influence composition microbial communities throughout intestinal tract.
Abstract Run-and-tumble motility is widely used by swimming microorganisms including numerous prokaryotic and eukaryotic organisms. Here, we experimentally investigate the run-and-tumble dynamics of bacterium E. coli in polymeric solutions. We find that even small amounts polymer solution can drastically change dynamics: cells tumble less their velocity increases, leading to an enhancement cell translational diffusion a sharp decline rotational diffusion. show suppression tumbling due fluid...
Bacterial urease activity of the gut microbiota alters nitrogen flux, leading to dysbiosis and worsening colitis in mice.
We find a new long-range interaction between foreign inclusions (e.g. mobile proteins) in fluid membrane which is mediated by the itself. The falls off as 1/R4, can be attractive or repulsive depending on temperature and elastic properties of inclusion membrane, for large distances compared with electrostatic, van der Waals, other lipid-mediated forces.
The material properties of lipid bilayers can affect membrane protein function whenever conformational changes in the membrane-spanning proteins perturb structure surrounding bilayer. This coupling between and bilayer arises from hydrophobic interactions We analyze free energy cost associated with a mismatch, i.e., difference length protein's exterior surface average thickness bilayer's core, using (liquid-crystal) elastic model deformations. deformation is described as sum three...
We present experiments in which single proteins were imaged and tracked within mammalian cells. Single of R-phycoerythrin (RPE) by epifluorescence microscopy the nucleoplasm cytoplasm at 71 frames/s. acquired two-dimensional trajectories (corresponding to projection three-dimensional onto plane focus) for an average 17 frames 16 nucleus. Diffusion constants determined from linear fits mean square displacement squared per frame. find that distribution diffusion RPE cells is broader than...
We show that after integrating over the zero mode in Liouville correlation functions, remaining functional integral resembles a free theory and may be evaluated by formally continuing central charge. apply this technique to unitary minimal models coupled gravity on sphere, computing number of three-point functions. After taking into account normalizations operators integral, we find exact agreement between functions results from matrix models.
The EnvZ/OmpR system in Escherichia coli , which regulates the expression of porins OmpF and OmpC, is one simplest best-characterized examples two-component signaling. Like many other histidine kinases, EnvZ bifunctional; it phosphorylates dephosphorylates response regulator OmpR. We have analyzed a mathematical model EnvZ-mediated cycle OmpR phosphorylation dephosphorylation. predicts that when much less abundant than OmpR, as case E. steady-state level phosphorylated (OmpR-P) insensitive...
The PhoQ/PhoP signaling system responds to low magnesium and the presence of certain cationic antimicrobial peptides. It regulates genes important for growth under these conditions, as well additional virulence in many gram-negative pathogens. PhoQ is a sensor kinase that phosphorylates activates transcription factor PhoP. Since feedback inhibition common theme stress-response circuits, we hypothesized some members PhoP regulon may play such role pathway. We therefore screened PhoP-regulated...
ABSTRACT Staphylococcus aureus frequently colonizes the airways of patients with compromised airway defenses (e.g., cystic fibrosis [CF] patients) for extended periods. Persistent and relapsing infections may be related to live S. bacteria actively residing inside epithelial cells. In this study, we infected a respiratory cell line, which was derived from CF patient, RN6390. Internalization found time dose dependent could blocked by cytochalasin D. Transmission electron microscopy revealed...
To successfully infect a host and cause the diarrheal disease cholera, Vibrio cholerae must penetrate intestinal mucosal layer express virulence genes. Previous studies have demonstrated that transcriptional regulator HapR, which is part of quorum sensing network in V. , represses expression Here, we show hapR also modulated by regulatory governs flagellar assembly. Specifically, FliA, alternative σ-factor (σ 28 ) activates late-class flagellin genes expression. In addition, mucin...
The modular synthesis of a library containing seven self-assembling amphiphilic Janus dendrimers is reported. Three these molecules contain environmentally friendly chiral-racemic fluorinated dendrons in their hydrophobic part (RF), one contains achiral hydrogenated (RH), while denoted hybrid dendrimer, combination and (RHF) its part. Two either green fluorescent dye conjugated to hydrophilic (RF-NBD) or red (RH-RhB). These RF, RH, RHF self-assembled into unilamellar onion-like soft...
The bacterial SOS response is a DNA damage repair network that strongly implicated in both survival and acquired drug resistance under antimicrobial stress. two regulators, LexA RecA, have therefore emerged as potential targets for adjuvant therapies aimed at combating resistance, although many open questions remain. For example, it not well understood whether hyperactivation viable therapeutic approach or RecA better target. Furthermore, important to determine which antimicrobials could...
Bacterial translocation from the gut microbiota is a source of sepsis in susceptible patients. Previous work suggests that overgrowth pathobionts, including Klebsiella pneumoniae, increases risk disseminated infection. Our data human dietary intervention study found that, absence fiber, K. pneumoniae bloomed during recovery antibiotic treatment. We thus hypothesized nutrients directly support or suppress colonization this pathobiont microbiota. Consistent with our humans, complex...
Total internal reflection fluorescence microscopy has been applied to image the final stage of constitutive exocytosis, which is fusion single post-Golgi carriers with plasma membrane. The use a membrane protein tagged green fluorescent allowed kinetics be followed time resolution 30 frames/s. Quantitative analysis undergoing easily distinguished from moving perpendicularly flattening into seen as simultaneous rise in total, peak, and width intensity. duration this process depends on size...
We performed transposon mutagenesis of a two-color fluorescent reporter strain to identify new regulators the porin genes ompF and ompC in Escherichia coli. Screening colonies by fluorescence microscopy revealed numerous mutants that exhibited interesting patterns expression. One mutant harbored an insertion gene encoding histidine kinase CpxA, sensor for two-component signaling system responds envelope stress. The cpxA increased transcription very strong decrease under conditions which...
We probe nonequilibrium properties of an active bacterial bath through measurements correlations passive tracer particles and the response function a driven, optically trapped tracer. These demonstrate violation fluctuation-dissipation theorem enable us to extract power spectrum stress fluctuations. In some cases, we observe 1/sqrt[omega] scaling in noise which show can be derived from theoretical model incorporating coupled stress, orientation, concentration fluctuations bacteria.