A5082427689- Bacterial biofilms and quorum sensing
- Micro and Nano Robotics
- Lipid Membrane Structure and Behavior
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Microbial Natural Products and Biosynthesis
- Slime Mold and Myxomycetes Research
- Microfluidic and Bio-sensing Technologies
- Bacterial Genetics and Biotechnology
- Cell Image Analysis Techniques
- Metabolomics and Mass Spectrometry Studies
- Gene Regulatory Network Analysis
- Semantic Web and Ontologies
- Gut microbiota and health
- Plant and Biological Electrophysiology Studies
- Neutrophil, Myeloperoxidase and Oxidative Mechanisms
- Escherichia coli research studies
- Geographic Information Systems Studies
- Clostridium difficile and Clostridium perfringens research
- Legionella and Acanthamoeba research
- Metal-Catalyzed Oxygenation Mechanisms
Dartmouth College
2016-2024
ScienceSouth
2021
Abstract Background The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation protein function. Results Here, we report on results third CAFA challenge, CAFA3, that featured expanded analysis over previous rounds, both in terms volume data analyzed types performed. In a novel major new development, predictions assessment goals drove some experimental assays, resulting functional annotations for...
Cross-experiment comparisons in public data compendia are challenged by unmatched conditions and technical noise. The ADAGE method, which performs unsupervised integration with denoising autoencoder neural networks, can identify biological patterns, but because models, like many over-parameterized, different models perform equally well. To enhance model robustness better build signatures consistent pathways, we developed an ensemble (eADAGE) that integrated stable across models. We applied...
What are bacteria doing during "reversible attachment," the period of transient surface attachment when they initially engage a surface, besides attaching themselves to surface? Can an cell help any other attach? If so, does it all cells or employ more selective strategy either nearby (spatial neighbors) its progeny (temporal neighbors)? Using community tracking methods at single-cell resolution, we suggest answers these questions based on how reversible progresses sensing for Pseudomonas...
Pseudomonas aeruginosa is the most prevalent opportunistic pathogen in airways of cystic fibrosis (CF) patients. The pulmonary disorder characterized by recurrent microbial infections and an exaggerated host inflammatory immune response led primarily influx neutrophils. Under these conditions, chronic colonization with P. associated diminished function increased morbidity mortality. has a wide array genetic mechanisms that facilitate its persistent airway despite extensive innate responses....
ABSTRACT Swarming is a macroscopic phenomenon in which surface bacteria organize into motile population. The flagellar motor that drives swarming Pseudomonas aeruginosa powered by stators MotAB and MotCD. Deletion of the MotCD stator eliminates swarming, whereas deletion enhances swarming. Interestingly, we measured strongly asymmetric availability wild-type (WT) strain, with produced at an approximately 40-fold higher level than stators. However, utilization free swimming cells requires...
Abstract The Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation protein function. Here we report on results third CAFA challenge, CAFA3, that featured expanded analysis over previous rounds, both in terms volume data analyzed types performed. In a novel major new development, predictions assessment goals drove some experimental assays, resulting functional annotations for more than 1000...
Pseudomonas aeruginosa frequently encounters microbes that produce ethanol. Low concentrations of ethanol reduced P. swim zone area by up to 45% in soft agar. The reduction swimming required the flagellar motor proteins MotAB and two PilZ domain (FlgZ PilZ). PilY1 type 4 pilus alignment complex (comprising PilMNOP) were previously implicated regulation surface-associated cells for ethanol-dependent motility repression. As FlgZ requires second messenger bis-(3'-5')-cyclic dimeric GMP...
The downregulation of Pseudomonas aeruginosa flagellar motility is a key event in biofilm formation, host colonization, and the formation microbial communities, but external factors that repress are not well understood. Here, we report on soft agar, swarming can be repressed by cells nonmotile due to absence flagellum or rotation. Mutants lack either biosynthesis rotation, when present at as little 5% total population, suppressed wild-type cells. Non-swarming required functional type IV pili...
Abstract Cross experiment comparisons in public data compendia are challenged by unmatched conditions and technical noise. The ADAGE method, which performs unsupervised integration with neural networks, can effectively identify biological patterns, but because models, like many over-parameterized, different models perform equally well. To enhance model robustness better build signatures consistent pathways, we developed an ensemble (eADAGE) that integrated stable across models. We applied...
Swarming is a macroscopic phenomenon in which surface bacteria organize into motile population. The flagellar motor that drives swarming
Abstract Pseudomonas aeruginosa frequently encounters microbes that produce bioactive metabolites including ethanol. At concentrations do not affect growth, we found ethanol reduces P. motility by 30% in a swim agar assay and this decrease is accompanied 2.5-fold increase levels of cyclic diguanylate (c-di-GMP), second messenger represses motility, planktonic cells. A screen mutants lacking genes involved c-di-GMP metabolism identified SadC GcbA as cyclases zone reduction ethanol-induced...
Abstract Despite possessing the machinery to sense, adhere to, and proliferate on surfaces, it is commonly observed that bacteria initially have a difficult time attaching surface. Before forming bacterial biofilm, planktonic exhibit random period of transient surface attachment known as “reversible attachment” which poorly understood. Using community tracking methods at single-cell resolution, we examine how reversible progresses during initial stages sensing. Pseudomonas aeruginosa strains...
Abstract The downregulation of Pseudomonas aeruginosa flagellar motility is a key event in biofilm formation, host-colonization, and the formation microbial communities, but external factors that repress are not well understood. Here, we report under swarming conditions, can be repressed by cells non-motile due to absence flagellum or rotation. Non-swarming cells, mutations prevent either biosynthesis rotation, present at 5% total population suppressed wild-type conditions tested this study....