A5023676008- Bacteriophages and microbial interactions
- Mycobacterium research and diagnosis
- Genomics and Phylogenetic Studies
- Microbial infections and disease research
- RNA and protein synthesis mechanisms
- Plant Virus Research Studies
- Actinomycetales infections and treatment
- Monoclonal and Polyclonal Antibodies Research
- Plant Disease Resistance and Genetics
- Career Development and Diversity
- Tuberculosis Research and Epidemiology
- Infectious Diseases and Mycology
- Virology and Viral Diseases
- Viral gastroenteritis research and epidemiology
- Phytoplasmas and Hemiptera pathogens
- Biomedical and Engineering Education
- Higher Education Research Studies
- Interdisciplinary Research and Collaboration
- Evaluation of Teaching Practices
- Genetics, Bioinformatics, and Biomedical Research
- Microbial Community Ecology and Physiology
- SARS-CoV-2 and COVID-19 Research
- Protist diversity and phylogeny
- Plant and Fungal Interactions Research
- Innovative Teaching Methods
University of Pittsburgh
2016-2025
ABSTRACT Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model which faculty and teaching assistants from diverse academic institutions are trained teach research course for first-year undergraduate students focused on bacteriophage genomics. The situated within broader context aimed at understanding viral diversity, such that collaborators with established researchers the field. Howard Hughes...
Abstract Background Nontuberculous Mycobacterium infections, particularly abscessus, are increasingly common among patients with cystic fibrosis and chronic bronchiectatic lung diseases. Treatment is challenging due to intrinsic antibiotic resistance. Bacteriophage therapy represents a potentially novel approach. Relatively few active lytic phages available there great variation in phage susceptibilities M. abscessus isolates, requiring personalized identification. Methods isolates from 200...
Significance The Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary program is an inclusive Research Community with centralized programmatic scientific support, in which broad student engagement authentic science linked to increased accessibility research experiences for students; persistence of these students science, technology, engineering, mathematics; productivity faculty alike.
ABSTRACT The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 infecting Mycobacterium smegmatis reveals the diversity a common bacterial host, their relationships to phylogenetically proximal hosts not known. Comparative sequence analysis 79 isolated on Gordonia shows also be that can grouped into 14 clusters related genomes,...
Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and tuberculosis. All mycobacteriophages characterized to date dsDNA tailed phages, have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, although sixty-two genomes been sequenced comparatively analyzed, these likely represent only a small portion of the mycobacteriophage population at large. Here we report isolation, sequencing comparative genomic...
ABSTRACT Investigation of the human microbiome has revealed diverse and complex microbial communities at distinct anatomic sites. The sebaceous follicle provides a tractable model in which to study its dominant bacterial inhabitant, Propionibacterium acnes , is thought contribute pathogenesis disease acne. To explore diversity bacteriophages that infect P. 11 phages were isolated from follicles donors with healthy skin or acne their genomes sequenced. Comparative genomic analysis phage...
Genome modifications are central components of the continuous arms race between viruses and their hosts. The archaeosine base (G+), which was thought to be found only in archaeal tRNAs, recently detected genomic DNA Enterobacteria phage 9g proposed protect from a wide variety restriction enzymes. In this study, we identify three additional 2'-deoxy-7-deazaguanine modifications, all intermediates same pathway, viruses: 2'-deoxy-7-amido-7-deazaguanine (dADG), 2'-deoxy-7-cyano-7-deazaguanine...
Viral infection is an ongoing challenge to bacterial survival, and there strong selection for development or acquisition of defense systems that promote survival when bacteria are attacked by bacteriophages. Temperate phages play central roles in these dynamics through lysogenic expression genes defend against phage attack, including those unrelated the prophage. Few prophage-mediated viral have been characterized, but they likely widespread both genomes prophages integrated chromosomes.
Mycobacterium abscessus infections in cystic fibrosis patients are challenging to treat due widespread antibiotic resistance. The therapeutic use of lytic bacteriophages presents a new potential strategy, but the great variation among clinical M. isolates demands determination phage susceptibility prior therapy.
Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution aminoadenine for adenine, thereby forming three hydrogen bonds with thymine violating Watson-Crick pairing rules. Aminoadenine-encoded polymerases, homologous to Klenow fragment bacterial polymerase I includes 3'-exonuclease but lacks 5'-exonuclease, were found...
It has been proposed that viruses can be divided into a small number of structure-based viral lineages. One these lineages is exemplified by bacterial virus Hong Kong 97 (HK97), which represents the head-tailed dsDNA bacteriophages. Seemingly similar also infect archaea. Here we demonstrate using genomic analysis, electron cryomicroscopy, and image reconstruction major coat protein fold newly isolated archaeal Haloarcula sinaiiensis tailed 1 canonical HK97. Although it anticipated...
The bacteriophage population is vast, dynamic, old, and genetically diverse. genomics of phages that infect bacterial hosts in the phylum Actinobacteria show them to not only be diverse but also pervasively mosaic, replete with genes unknown function. To further explore this broad group bacteriophages, we describe here isolation genomic characterization 116 Microbacterium spp. Most are lytic, can grouped into twelve clusters according their overall relatedness; seven singletons no close...
Mycobacterium abscessus is an important emerging pathogen that challenging to treat with current antibiotic regimens. There substantial genomic variation in M. clinical isolates, but little known about how this influences pathogenicity and vivo growth.
Mycobacteriophage Tweety is a newly isolated phage of Mycobacterium smegmatis. It has viral morphology with an isometric head and long flexible tail, forms turbid plaques from which stable lysogens can be isolated. The genome 58 692 bp in length, contains 109 protein-coding genes, shows significant but interrupted nucleotide sequence similarity the previously described mycobacteriophages Llij, PMC Che8. However, overall possesses mosaic architecture, gene products being related to other such...
ABSTRACT A characteristic feature of bacteriophage genomes is that they are architecturally mosaic, with each individual genome representing a unique assemblage exchangeable modules. Plausible mechanisms for generating mosaicism include homologous recombination at shared boundary sequences module junctions, illegitimate in non-sequence-directed process, and site-specific recombination. Analysis the novel mycobacteriophage Giles not only extends our current perspective on genetic diversity,...
Five newly isolated mycobacteriophages--Angelica, CrimD, Adephagia, Anaya, and Pixie--have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision three subclusters: K1, K2, K3. Although the overall genome of phages are similar, TM4 appears have lost at least two segments its genome, central region containing integration...
Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells susceptible to viral infections, date, about 100 viruses have been described. Among them, there extraordinary virion morphologies as well the common head-tailed viruses. Although approximately half of isolated belong latter group, no three-dimensional structures these available. Thus, rigorous comparisons with...
The complete genome sequences of archaeal tailed viruses are currently highly underrepresented in sequence databases. Here, we report the genomic 10 new infecting different haloarchaeal hosts. Among these, only two viral genomes closely related to each other and previously described haloviruses HF1 HF2. approximately 760 kb total shows no matches CRISPR/Cas spacer host genomes. Despite their high divergence, were able identify virion structural assembly genes as well coding for DNA RNA...
Modern agriculture is expected to face an increasing global demand for food while also needing comply with higher sustainability standards. Therefore, control of crop pathogens requires new, green alternatives current methods. Potatoes are susceptible several bacterial diseases, infections by soft rot Enterobacteriaceae (SRE) being a significant contributor the major annual losses. As there currently no efficient ways combating SRE, we sought develop approach that could easily be...
Temperate phages play important roles in the physiology of their bacterial hosts and establish a lysogenic relationship with host through which prophage-expressed genes confer new phenotypes. A key phenotype is prophage-mediated defense against heterotypic viral attack, temperate collude to prevent other from attacking, sometimes exquisite specificity. Such systems have been described Pseudomonas Mycobacterium but are likely widespread throughout microbial community. Here, we describe novel...