A5057475967- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Evolution and Genetic Dynamics
- CRISPR and Genetic Engineering
- Particle Dynamics in Fluid Flows
- RNA and protein synthesis mechanisms
- Fluid Dynamics and Turbulent Flows
- Gene Regulatory Network Analysis
- Monoclonal and Polyclonal Antibodies Research
- Aeolian processes and effects
- Granular flow and fluidized beds
- RNA regulation and disease
- Genomics and Phylogenetic Studies
- Antibiotic Resistance in Bacteria
- Microbial Community Ecology and Physiology
- Epigenetics and DNA Methylation
- Viral Infections and Outbreaks Research
- Trypanosoma species research and implications
- Rheology and Fluid Dynamics Studies
- Plant Virus Research Studies
- Diffusion and Search Dynamics
- Mycobacterium research and diagnosis
- Advanced Biosensing Techniques and Applications
- Dielectric materials and actuators
- Innovation and Socioeconomic Development
Texas A&M University
2015-2025
University of Illinois Urbana-Champaign
2005-2018
South China University of Technology
2018
University of Florida
2009
Argonne National Laboratory
2009
We perform direct numerical simulations of a rigid sphere translating parallel to flat wall in an otherwise quiescent ambient fluid. A spectral element method is employed the with high accuracy. For above about 100. Detailed analysis flow field around suggests that this increase due imperfect bifurcation resulting formation double-threaded wake vortical structure. In addition non-rotating sphere, we also simulate freely rotating order assess importance free rotation on translational motion...
To understand and better model the hydrodynamic force acting on a finite-sized particle moving in wall-bounded linear shear flow, here we consider two limiting cases of (a) rigid stationary spherical flow (b) rectilinear motion parallel to wall quiescent ambient flow. In present computations, Reynolds number ranges from 2 250 at separation distances nearly sitting far away wall. First characterize structure wake for compare with those [see L. Zeng, S. Balachandar, P. Fischer, J. Fluid Mech....
Prokaryotes evolved numerous systems that defend against predation by bacteriophages. In addition to well-known restriction-modification and CRISPR-Cas immunity systems, many poorly characterized exist. One class of such named BREX, consists a putative phosphatase, methyltransferase four other proteins. A Bacillus cereus BREX system provides resistance several unrelated phages leads modification specific motif in host DNA. Here, we study the action from natural Escherichia coli isolate. We...
The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen Pseudomonas aeruginosa . single-stranded RNA (ssRNA) phage PP7 binds to T4P and brought cell surface through retraction. Using fluorescence microscopy, we discovered that detaches T4P, which impairs motility restricts pathogen’s virulence. cryo–electron mutagenesis, optical trapping, Langevin dynamics simulation, resolved structure PP7, PP7/T4P complex showed detachment driven by affinity...
Bacteria form groups composed of cells and a secreted polymeric matrix that controls their spatial organization. These groups—termed biofilms—can act as refuges from environmental disturbances biotic threats, including phages. Despite the ubiquity temperate phages bacterial biofilms, live propagation within biofilms has not been characterized on cellular scales. Here, we leverage several approaches to track distinguish between lytic lysogenic host infections. We determine lysogeny...
Abstract The system of the bacterium Escherichia coli and its virus, bacteriophage lambda, is paradigmatic for gene regulation in cell-fate development, yet insight about mechanisms complexities are limited due to insufficient resolution study. Here we develop a 4-colour fluorescence reporter at single-virus level, combined with computational models unravel both interactions between phages how individual determine cellular fates. We find that cooperate during lysogenization, compete among...
Reliable information on forces a finite-sized particle in turbulent boundary layer is lacking, so workers continue to use standard drag and lift correlations developed for laminar flow predict forces. Here we consider direct numerical simulations of channel over an isolated finite size. The size the its location within are systematically varied. All relevant length time scales turbulence, attached layers particle, wake faithfully resolved, thus fully resolved simulations. results from...
Although the F-specific ssRNA phage MS2 has long had paradigm status, little is known about penetration of genomic RNA (gRNA) into cell. The initially binds to F-pilus using its maturation protein (Mat), and then Mat-bound gRNA released from viral capsid somehow crosses bacterial envelope cytoplasm. To address mechanics this process, we fluorescently labeled track dynamics during infection. We discovered that infection triggers release F-pili host cells, higher multiplicity (MOI) correlates...
F plasmids circulate widely among the Enterobacteriaceae through encoded type IV secretion systems (T4SSF s). Assembly of T4SSF s and associated pili requires 10 VirB/VirD4-like Tra subunits eight or more F-specific subunits. Recently, we presented evidence using in situ cryoelectron tomography (cryoET) that undergo structural transitions when activated for pilus production, assembled are deposited onto alternative basal platforms at cell surface. Here, deleted conserved genes from MOBF12C...
U-insertion/deletion (U-indel) RNA editing in trypanosome mitochondria is directed by guide RNAs (gRNAs). This may developmentally control respiration bloodstream forms (BSF) and insect procyclic (PCF). Holo-editosomes include the accessory Editing Substrate Binding Complex (RESC) Helicase 2 (REH2C), but specific proteins controlling differential remain unknown. Also, appears highly error prone because most U-indels do not match canonical pattern. However, despite extensive non-canonical of...
Acinetobacters pose a significant threat to human health, especially those with weakened immune systems. Type IV pili of acinetobacters play crucial roles in virulence and antibiotic resistance. Single-stranded RNA bacteriophages target the bacterial retractile pili, including type IV. Our study delves into interaction between Acinetobacter phage AP205 pili. Using cryo-electron microscopy, we solve structures virion an asymmetric dimer maturation proteins, native bearing distinct...
Caulobacter crescentus Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other pilins, pilins lack typical globular β sheet domain responsible pilus assembly phage binding. The mechanisms its interaction with ΦCb5 have been elusive. Using cryo–electron microscopy, we unveiled mechanism, featuring a unique network hydrogen bonds at core. We then identified binding...
The infection of Escherichia coli cells by bacteriophage lambda results in bifurcated means propagation, where the phage decides between lytic and lysogenic pathways. Although traditionally thought to be mutually exclusive, increasing evidence suggests that this lysis-lysogeny decision is more complex than once believed, but exploring its intricacies requires an improved resolution study. Here, with a newly developed fluorescent reporter system labeling single E. DNAs, these two distinct...
Spatial organization of biological processes allows for variability in molecular outcomes and coordinated development. Here, we investigate how underpins phage lambda development decision-making by characterizing viral components subcellular space. We use live-cell situ fluorescence imaging at the single-molecule level to examine DNA replication, transcription, virion assembly, resource recruitment single-cell infections, uniting key infection cycle into a coherent model encompassing space...
Cellular decision-making arises from the expression of genes along a regulatory cascade, which leads to choice between distinct phenotypic states. DNA dosage variations, often introduced by replication, can significantly affect gene ultimately bias decision outcomes. The bacteriophage lambda system has long served as paradigm for cell-fate determination, yet effect replication remains largely unknown. Here, through single-cell studies and mathematical modeling we show that drastically boosts...
Bacteriophage P1 is the premier transducing phage of E. coli. Despite its prominence in advancing coli genetics, modern molecular techniques have not been applied to thoroughly understand structure. Here, we report proteome virion as determined by liquid chromatography tandem mass-spectrometry. Additionally, a library single-gene knockouts identified following five previously unknown essential genes: pmgA, pmgB, pmgC, pmgG, and pmgR. In addition, proteolytic processing major capsid protein...