A5067393767- Forest Ecology and Biodiversity Studies
- Bacillus and Francisella bacterial research
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Forest Insect Ecology and Management
- Aquaculture disease management and microbiota
- Vibrio bacteria research studies
- Yeasts and Rust Fungi Studies
- Yersinia bacterium, plague, ectoparasites research
- Identification and Quantification in Food
- Plant Pathogens and Fungal Diseases
- Insect Resistance and Genetics
- Microbial infections and disease research
- Salmonella and Campylobacter epidemiology
- Mycorrhizal Fungi and Plant Interactions
- Neuroinflammation and Neurodegeneration Mechanisms
- Bacterial Genetics and Biotechnology
- Cellular Mechanics and Interactions
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Chromatin Dynamics
- Biofuel production and bioconversion
- Axon Guidance and Neuronal Signaling
- Proteoglycans and glycosaminoglycans research
- Nerve injury and regeneration
University of California, San Diego
2021-2024
Colorado State University
2020-2022
Los Alamos National Laboratory
2010-2019
Joint Genome Institute
2006-2014
National Institute of Cholera and Enteric Diseases
2010
Florida State University
1995-1997
University of Minnesota
1996-1997
The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members Proteobacteria, Cyanobacteria, and Fungi. appear to be versatile heterotrophs. Genomic culture indicate use carbon sources that span simple sugars more complex substrates such hemicellulose, cellulose, chitin. encode low-specificity major facilitator superfamily transporters high-affinity ABC for sugars, suggesting...
Abstract Background Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey plant pathogen, providing strategy for biological control of pests protection. Probably, most studied biocontrol agents are species genus Hypocrea / Trichoderma . Results Here we report an analysis genome sequences two atroviride (teleomorph atroviridis ) and virens (formerly Gliocladium , teleomorph ), comparison with reesei jecorina ). These three display...
Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and also largely responsible for the destructive decay wooden structures. Rapid depolymerization cellulose is a distinguishing feature brown-rot, but biochemical mechanisms underlying genetics poorly understood. Systematic examination P. genome, transcriptome, secretome revealed unique extracellular enzyme systems, including an unusual repertoire glycoside hydrolases. Genes encoding exocellobiohydrolases...
Vibrio cholerae, the causative agent of cholera, is a bacterium autochthonous to aquatic environment, and serious public health threat. V. cholerae serogroup O1 responsible for previous two cholera pandemics, in which classical El Tor biotypes were dominant sixth current seventh respectively. Cholera researchers continually face newly emerging reemerging pathogenic clones carrying diverse combinations phenotypic genotypic properties, significantly hampered control disease. To elucidate...
Abstract Background The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. important drivers carbon nitrogen cycling ecosystems. These play roles soil stability, plant biomass decomposition, endophytic interactions with plants. They may also form symbiotic associations biocrust components or be latent saprotrophs pathogens that live on tissues. However, their functional potential soils, where organic matter, nutrients water very low only periodically...
Bacillus anthracis, cereus, and thuringiensis are closely related gram-positive, spore-forming bacteria of the B. cereus sensu lato group. While independently derived strains anthracis reveal conspicuous sequence homogeneity, environmental isolates exhibit extensive genetic diversity. Here we report sequencing comparative analysis genomes two members group, 97-27 subsp. konkukian serotype H34, isolated from a necrotic human wound, E33L, which was swab zebra carcass in Namibia. These strains,...
The complete DNA sequence of the aerobic cellulolytic soil bacterium Cytophaga hutchinsonii, which belongs to phylum Bacteroidetes, is presented. genome consists a single, circular, 4.43-Mb chromosome containing 3,790 open reading frames, 1,986 have been assigned tentative function. Two most striking characteristics C. hutchinsonii are its rapid gliding motility over surfaces and contact-dependent digestion crystalline cellulose. mechanism not known, but contains homologs for each gld genes...
Growth cone turning is an important mechanism for changing the direction of neurite elongation during development nervous system. Our previous study indicated that actin filament bundles at leading margin direct distal microtubular cytoskeleton as growth cones turn to avoid substratum-bound chondroitin sulfate proteoglycan. Here, we investigated role microtubule dynamics in by using low doses vinblastine and taxol, treatments reduce dynamic shrinkage ends. We used time-lapse phase-contrast...
We present here the complete 2.4-Mb genome of cellulolytic actinobacterial thermophile Acidothermus cellulolyticus 11B. New secreted glycoside hydrolases and carbohydrate esterases were identified in genome, revealing a diverse biomass-degrading enzyme repertoire far greater than previously characterized elevating industrial value this organism. A sizable fraction these hydrolytic enzymes break down plant cell walls, remaining either degrade components fungal walls or metabolize storage...
Abstract Background Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be fermentatively at price competitive with that of anhydride, though, it replace as the precursor many bulk chemicals, transforming multi-billion dollar petrochemical market into one based on renewable resources. Actinobacillus succinogenes naturally converts sugars and CO 2 high concentrations succinic acid part mixed-acid fermentation. Efforts...
ABSTRACT The genomes of V ibrio cholerae O1 Matlab variant MJ-1236, Mozambique El Tor B33, and altered CIRS101 were sequenced. All three strains found to belong the phylocore group 1 clade V. , which includes 7th-pandemic serogroup O139 isolates, despite displaying certain characteristics classical biotype. harbor a hybrid CTXΦ an integrative conjugative element (ICE), leading their establishment as successful clinical clones displacement prototypical Tor. absence strain- group-specific...
Vibrio species are both ubiquitous and abundant in marine coastal waters, estuaries, ocean sediment, aquaculture settings worldwide. We report here the isolation, characterization, genome sequence of a novel species, antiquarius, isolated from mesophilic bacterial community associated with hydrothermal vents located along East Pacific Rise, near southwest coast Mexico. Genomic phenotypic analysis revealed V. antiquarius is closely related to pathogenic namely alginolyticus, parahaemolyticus,...
Microglia phenotypes are highly regulated by the brain environment, but transcriptional networks that specify maturation of human microglia poorly understood. Here, we characterized stage-specific transcriptomes and epigenetic landscapes fetal postnatal acquired corresponding data in induced pluripotent stem cell (iPSC)-derived microglia, cerebral organoids, following engraftment into humanized mice. Parallel development computational approaches considered transcription factor (TF)...
The presence of HIV in sequestered reservoirs is a central impediment to functional cure, allowing persist despite life-long antiretroviral therapy (ART), and driving variety comorbid conditions. Our understanding the latent reservoir nervous system incomplete, because difficulties accessing human tissues. Microglia contribute reservoirs, but molecular phenotype HIV-infected microglia poorly understood. We leveraged unique "Last Gift" rapid autopsy program, which people with are closely...
The extracellular matrix through which growth cones navigate contains molecules, such as chondroitin sulfate proteoglycan, that can inhibit cone advance and induce branching turning. Growth turning is accompanied by rearrangement of the cytoskeleton. To identify changes in organization actin filaments microtubules occur turn, we used time-lapse phase contrast videomicroscopy to observe embryonic chick dorsal root ganglion neuronal at a substratum border between fibronectin presence absence...
Bacillus thuringiensis is an insect pathogen that widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, Baum, Feitelson, R. Zeigler, and H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. Al Hakam, which was collected in Iraq by United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, Jackson, L. Ticknor, Keim, G. Andersen, Appl. Environ. 69:2755-2764, 2003).
Halophilic archaea accumulate molar concentrations of KCl in their cytoplasm as an osmoprotectant and have evolved highly acidic proteomes that function only at high salinity. We examined osmoprotection the photosynthetic Proteobacteria Halorhodospira halophila halochloris. Genome sequencing isoelectric focusing gel electrophoresis showed proteome H. is acidic. In line with this finding, accumulated when grown salt medium detected by x-ray microanalysis plasma emission spectrometry. This...
Members of the bacterial phylum Acidobacteria are widespread in soils and sediments worldwide, abundant many soils. challenging to culture vitro, basic features their biology functional roles soil have not been determined. Candidatus Solibacter usitatus strain Ellin6076 has a 9.9 Mb genome that is approximately 2–5 times as large other sequenced genomes. Bacterial sizes typically range from 0.5 10 influenced by gene duplication, horizontal transfer, loss evolutionary processes. Our...
Francisella tularensis is a highly virulent zoonotic pathogen that causes tularemia and, because of weaponization efforts in past world wars, considered tier 1 biothreat agent. Detection and surveillance F. may be confounded by the presence uncharacterized, closely related organisms. Through DNA-based diagnostics environmental surveys, novel clinical isolates have been obtained recent years. Here we present 7 new genomes comparison their characteristics to each other 24 publicly available as...
Several plant viruses modulate vector fitness and behavior in ways that may enhance virus transmission. Previous studies have documented indirect, plant-mediated effects of tomato spotted wilt (TSWV) infection on the fecundity, growth survival its principal thrips vector, Frankliniella occidentalis , western flower thrips. We conducted performance preference experiments combined with gene expression, phytohormone total free amino acid analyses to determine if systemically-infected plants...
Abstract Background In recent years genome sequencing has been used to characterize new bacterial species, a method of analysis available as result improved methodology and reduced cost. Included in constantly expanding list Vibrio species are several that have reclassified novel members the Vibrionaceae . The description two putative sp. RC341 RC586 for which we propose names V. metecus parilis , respectively, previously characterized non-toxigenic environmental variants cholerae is...
Dehalogenimonas lykanthroporepellens is the type species of genus Dehalogenimonas, which belongs to a deeply branching lineage within phylum Chloroflexi. This strictly anaerobic, mesophilic, non spore-forming, Gram-negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at Superfund site located near Baton Rouge, Louisiana, USA. D. interest for genome sequencing two reasons: (a) an unusual ability couple growth with reductive dechlorination...