A5017809118- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Bacterial Genetics and Biotechnology
- Plant Virus Research Studies
- Evolution and Genetic Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Cancer Genomics and Diagnostics
- Microbial Community Ecology and Physiology
- Insect and Pesticide Research
- Lung Cancer Treatments and Mutations
- Photosynthetic Processes and Mechanisms
- Acute Myeloid Leukemia Research
- SARS-CoV-2 and COVID-19 Research
- Genomics and Rare Diseases
- Lung Cancer Research Studies
- Myeloproliferative Neoplasms: Diagnosis and Treatment
- Bacterial biofilms and quorum sensing
- Mycobacterium research and diagnosis
- CRISPR and Genetic Engineering
- Insect and Arachnid Ecology and Behavior
- Zoonotic diseases and public health
- RNA modifications and cancer
- Career Development and Diversity
- SARS-CoV-2 detection and testing
- Reproductive tract infections research
University of Canterbury
2023-2025
Massey University
2012-2025
Methodist Hospital
2017-2024
Houston Methodist
2013-2020
Methodist Hospital
2013-2020
Cornell University
2017-2020
University of Pittsburgh
2003-2018
Baylor College of Medicine
2013
South Texas Veterans Health Care System
2013
The University of Texas Health Science Center at San Antonio
2013
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.
There is concern about second and subsequent waves of COVID-19 caused by the SARS-CoV-2 coronavirus occurring in communities globally that had an initial disease wave. Metropolitan Houston, TX, with a population 7 million, experiencing massive wave began late May 2020. To understand molecular genomic architecture evolution relationship between virus genotypes patient features, we sequenced genomes 5,085 strains from these two waves. Our report provides first characterization causing distinct
When a particular lac mutant of Escherichia coli starves in the presence lactose, nongrowing cells appear to direct mutations preferentially sites that allow growth (adaptive mutation). This observation suggested limitation stimulates mutability. Evidence is provided here this behavior actually caused by standard Darwinian process which natural selection acts three sequential steps. First, favors subpopulation with an amplification gene; next, it + revertant allele within amplified array....
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...
Summary In bacteria, Ter sites bound to Tus/Rtp proteins halt replication forks moving only in one direction, providing a convenient mechanism terminate them once the chromosome had been replicated. Considering importance of termination and its position as checkpoint cell division, accumulated knowledge on these systems has not dispelled fundamental questions regarding role biology: why are there so many copies Ter, they distributed over such large portion chromosome, is tus gene conserved...
ABSTRACT We sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. The were from viruses recovered earliest recognized phase pandemic and ongoing massive second wave infections. virus was originally introduced into Houston many times independently. Virtually all have a Gly614 amino acid replacement spike protein, polymorphism that has been linked to increased transmission...
Background: Bacteriophages are becoming increasingly important in the race to find alternatives antibiotics. Unfortunately, bacteriophages that might otherwise be useful sometimes discarded due low titers making them unsuitable for downstream applications. Methods: Here, we present two distinct approaches used experimentally evolve novel New Zealand Paenibacillus larvae bacteriophages. The first approach uses traditional agar-overlay method, whereas other was a 96-well plate liquid infection...
Maintenance of rod-shape in bacterial cells depends on the actin-like protein MreB. Deletion mreB from Pseudomonas fluorescens SBW25 results viable spherical variable volume and reduced fitness. Using a combination time-resolved microscopy biochemical assay peptidoglycan synthesis, we show that fitness is consequence perturbed cell size homeostasis arises primarily differential growth daughter cells. A 1000-generation selection experiment resulted rapid restoration with derived retaining...
A report on research that explicates three models of pedagogical practice underpin and characterize inquiry instruction in a course-based experience.
The bacterium Paenibacillus larvae is responsible for the devastating honey bee (Apis mellifera) disease American Foulbrood. Research into bacteriophages that infect P. growing rapidly due to increasing antibiotic resistance and restrictions on use in beehives some countries. In this study, we present sequenced annotated genomes of 26 novel phages recently isolated New Zealand, which brings total number 96. belong pre-existing Vegas or Harrison clusters. We performed a comprehensive genomic...
Maintenance of rod-shape in bacterial cells depends on the actin-like protein MreB. Deletion mreB from Pseudomonas fluorescens SBW25 results viable spherical variable volume and reduced fitness. Using a combination time-resolved microscopy biochemical assay peptidoglycan synthesis, we show that fitness is consequence perturbed cell size homeostasis arises primarily differential growth daughter cells. A 1,000-generation selection experiment resulted rapid restoration with derived retaining...
Abstract Eleven laboratories participated in a collaborative study to compare the dry rehydratable film (Petrifilm® SM and Petrifilm® VRB) methods, respectively, standard plate count (SPC) violet red bile agar (VRBA) methods for estimation of total bacteria coliform counts raw homogenized pasteurized milk. Each laboratory analyzed 16 samples (8 different blind duplicate) by both SPC Petrifilm methods. A second set was VRBA VRB The repeatability deviations (the square root between-replicates...
Escherichia coli is a single species with numerous recognized roles, from lab workhorse to beneficial intestinal commensal or deadly pathogen. The extant strains have disparate lifestyles as result of differential niche expansion since their divergence 25–40 million years ago, ten times longer than the estimated between chimpanzees and humans [1,2]. Not only do these roles vary by strain (variant) species, but recognition strain’s role in one context does not exclude radically different...
- Thyroid nodules have a prevalence of approximately 70% in adults. Fine-needle aspiration (FNA) is minimally invasive, cost-effective, standard method to collect tissue from thyroid for cytologic examination. However, 15% FNA specimens cannot be unambiguously diagnosed as benign or malignant.- To investigate whether clinically actionable data can obtained using next-generation sequencing residual needle rinse material.- A total 24 with malignant (n = 6), indeterminate 9), 9) diagnoses were...
A considerable number of patients with high-grade cervical lesions have undergone preceding human papillomavirus (HPV) tests negative results. In the present study, we attempted to elucidate factors potentially contributing findings by testing biopsied samples from these patients.Of 1654 women HPV and follow-up cervicovaginal biopsies March 1, 2013 June 30, 2014, 21 252 (8.3%) biopsy-confirmed squamous intraepithelial lesion (HSIL) or worse had results high-risk (hr)HPV tests. The...
Bacteriophage ϕPsa21 is a potential biocontrol agent that infects the kiwifruit phytopathogen Pseudomonas syringae pv. actinidiae. "jumbo" phage with genome of ∼305 kb. Here, we present sequence and discuss genes indicative formation nucleoid structures during viral replication.
Abstract We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. These were viruses causing infections earliest recognized phase pandemic affecting Houston. Substantial viral genomic diversity was identified, which we interpret to mean that virus introduced into Houston many times independently by individuals who had traveled different parts country and world. The majority are...
Despite significant frequencies of lateral gene transfer between species, higher taxonomic groups bacteria show ecological and phenotypic cohesion. This suggests that barriers prevent panmictic dissemination genes via transfer. We have proposed most bacterial genomes a functional architecture imposed by Architecture IMparting Sequences (AIMS). AIMS are defined as 8 base pair sequences preferentially abundant on leading strands, whose abundance strand-bias positively correlated with proximity...