Biomedical subjects

Ian Hewson

Publications and source records attributed to Ian Hewson.

7 recordsLinked to original sources

PubMed2024

Diverse RNA viruses discovered in multiple seagrass species.

Seagrasses are marine angiosperms that form highly productive and diverse ecosystems. These ecosystems, however, are declining worldwide. Plant-associated microbes affect critical functions like nutrient uptake and pathogen resistance, which has led to an interest in the seagrass microbiome. However, despite their significant role in plant ecology, viruses have only recently garnered attention in seagrass species. In this study, we produced original data and mined publicly available transcriptomes to advance our understanding of RNA viral diversity in Zostera marina, Zostera muelleri, Zostera japonica, and Cymodocea nodosa. In Z. marina, we present evidence for additional Zostera marina amalgavirus 1 and 2 genotypes, and a complete genome for an alphaendornavirus previously evidenced by an RNA-dependent RNA polymerase gene fragment. In Z. muelleri, we present evidence for a second complete alphaendornavirus and near complete furovirus. Both are novel, and, to the best of our knowledge, this marks the first report of a furovirus infection naturally occurring outside of cereal grasses. In Z. japonica, we discovered genome fragments that belong to a novel strain of cucumber mosaic virus, a prolific pathogen that depends largely on aphid vectoring for host-to-host transmission. Lastly, in C. nodosa, we discovered two contigs that belong to a novel virus in the family Betaflexiviridae. These findings expand our knowledge of viral diversity in seagrasses and provide insight into seagrass viral ecology.

RNA Viruses↗

PubMed2006

Annually reoccurring bacterial communities are predictable from ocean conditions.

Factors influencing patterns in the distribution and abundance of plant and animal taxa modulate ecosystem function and ecosystem response to environmental change, which is often taken to infer low functional redundancy among such species, but such relationships are poorly known for microbial communities. Using high-resolution molecular fingerprinting, we demonstrate the existence of extraordinarily repeatable temporal patterns in the community composition of 171 operational taxonomic units of marine bacterioplankton over 4.5 years at our Microbial Observatory site, 20 km off the southern California coast. These patterns in distribution and abundance of microbial taxa were highly predictable and significantly influenced by a broad range of both abiotic and biotic factors. These findings provide statistically robust demonstration of temporal patterning in marine bacterial distribution and abundance, which suggests that the distribution and abundance of bacterial taxa may modulate ecosystem function and response and that a significant subset of the bacteria exhibit low levels of functional redundancy as documented for many plant and animal communities.

Bacteria↗

PubMed2006

New thoughts on the pathobiology of regimen-related mucosal injury.

BACKGROUND: Our understanding of the biological basis for mucosal barrier injury (mucositis) induced by cancer therapy with radiation or drugs continues to evolve. A patient's mucosal response to cancer therapy appears to be controlled by both global (i.e. gender, underlying systemic disease, race) and tissue specific (i.e. epithelial type, intrinsic endocrine system, local microbial environment, function) factors. CONCLUSION: Interactions of these elements, coupled with underlying genetic influences, most likely govern the risk, course and severity of regimen-related mucosal injury.

Antineoplastic Agents↗

PubMed2006

Improved strategy for comparing microbial assemblage fingerprints.

Microbial fingerprinting techniques permit the rapid visualization of entire assemblages in single assays, allowing direct comparison of communities in different samples, where the null hypothesis of such analyses is that all samples are the same. The comparison of fingerprints relies upon the precise estimation of all amplified DNA fragment lengths, which correspond to operational taxonomic units (OTU; analogous, but not equal to, a taxon in macroorganism studies). However, computer interpolation of size standards (and consequently OTU size calling) can be imprecise between gel runs, which can lead to imprecise calculation of similarity indices between multiple assemblages. To account for OTU size calling imprecision, all fragments within a range of sizes (a window) can be combined (i.e., "binned") where the window is as wide as the imprecision of OTU size calling. However, artifacts may occur upon binning samples that may cause samples to appear less similar to each other, caused by splitting of OTU between adjacent bin windows. In this work we present an improved binning technique that accounts for OTU size calling imprecision in the comparison of multiple fingerprints. This technique comprises binning all pairwise comparisons in multiple bin window frames, where the starting size of the window (i.e., frame) is shifted by +1 bp for a total of x frames, where x bp is the width of the maximum bin window size in any binning scheme. Pairwise similarity indices between different community fingerprints are calculated for each of the x frames. To best address the null hypothesis of the community comparison, the maximum similarity value of all x frames is then used in downstream analyses to compare the communities. We believe this binning technique provides the most accurate and least biased comparison between different microbial fingerprints.

Artifacts↗

PubMed2005

Coupling 16S-ITS rDNA clone libraries and automated ribosomal intergenic spacer analysis to show marine microbial diversity: development and application to a time series.

We outline an approach to simultaneously assess multilevel microbial diversity patterns utilizing 16S-ITS rDNA clone libraries coupled with automated ribosomal intergenic spacer analysis (ARISA). Sequence data from 512 clones allowed estimation of ARISA fragment lengths associated with bacteria in a coastal marine environment. We matched 92% of ARISA peaks (each comprising >1% total amplified product) with corresponding lengths from clone libraries. These peaks with putative identification accounted for an average of 83% of total amplified community DNA. At 16S rDNA similarities <98%, most taxa displayed differences in ARISA fragment lengths >10 bp, readily detectable and suggesting ARISA resolution is near the 'species' level. Prochlorococcus abundance profiles from ARISA were strongly correlated (r2=0.86) to Prochlorococcus cell counts, indicating ARISA data are roughly proportional to actual cell abundance within a defined taxon. Analysis of ARISA profiles for 42 months elucidated patterns of microbial presence and abundance providing insights into community shifts and ecological niches for specific organisms, including a coupling of ecological patterns for taxa within the Prochlorococcus, the Gamma Proteobacteria and Actinobacteria. Clade-specific ARISA protocols were developed for the SAR11 and marine cyanobacteria to resolve ambiguous identifications and to perform focused studies. 16S-ITS data allowed high-resolution identification of organisms by ITS sequence analysis, and examination of microdiversity.

Automation↗

PubMed2004

Richness and diversity of bacterioplankton species along an estuarine gradient in Moreton Bay, Australia.

Bacterioplankton community diversity was investigated in the subtropical Brisbane River-Moreton Bay estuary, Australia (27 degrees 25 minutes S, 153 degrees 5 minutes E). Bacterial communities were studied using automated rRNA intergenic spacer analysis (ARISA), which amplifies 16S-23S ribosomal DNA internally transcribed spacer regions from mixed-community DNA and detects the separated products on a fragment analyzer. Samples were collected from eight sites throughout the estuary and east to the East Australian Current (Coral Sea). Bacterioplankton communities had the highest operational taxonomic unit (OTU) richness, as measured by ARISA at eastern bay stations (S [total richness] = 84 to 85 OTU) and the lowest richness in the Coral Sea (S = 39 to 59 OTU). Richness correlated positively with bacterial abundance; however, there were no strong correlations between diversity and salinity, NO(3)(-) and PO(4)(3-) concentrations, or chlorophyll a concentration. Bacterioplankton communities at the riverine stations were different from communities in the bay or Coral Sea. The main differences in OTU richness between stations were in taxa that each represented 0.1% (the detection limit) to 0.5% of the total amplified DNA, i.e., the "tail" of the distribution. We found that some bacterioplankton taxa are specific to distinct environments while others have a ubiquitous distribution from river to sea. Bacterioplankton richness and diversity patterns in the estuary are potentially a consequence of greater niche availability, mixing of local and adjacent environment communities, or intermediate disturbance. Furthermore, these results contrast with previous reports of spatially homogeneous bacterioplankton communities in other coastal waters.

Animals↗

PubMed2003

Metagenomic analyses of an uncultured viral community from human feces.

Here we present the first metagenomic analyses of an uncultured viral community from human feces, using partial shotgun sequencing. Most of the sequences were unrelated to anything previously reported. The recognizable viruses were mostly siphophages, and the community contained an estimated 1,200 viral genotypes.

Bacteriophages↗