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Biology subjects

Nash, B.

Publications and source records attributed to Nash, B..

5 recordsLinked to original sources

Investigating Bacterial Contributions to Thermal Tolerance in Three Intertidal Marine Snail Tegula species

In this era of climate change there is an urgent need to better understand the mechanisms that allow organisms to thrive vs. fail in thermally stressful environments. In particular, there is growing evidence that the "holobiont" (host animal + microbiome community of bacteria, fungi, and archaea that live in an organism) affects how organisms respond to environmental stressors such as temperature and thus should be studied further. Rocky intertidal species such as Tegula snails are ideal organisms for these types of studies because closely related species exhibit variability in heat tolerance. Here, we assess potential microbiome bacterial contributions to thermal tolerance in Tegula eiseni, Tegula funebralis, and Tegula gallina that co-occur in southern California but occupy different intertidal heights that vary in thermal stress exposure. 16S sequencing of the V4 region of individuals of each species exposed to control or 5.5-hour heat stress conditions (maximum temperature = 34 {degrees}C) revealed distinct bacterial communities across species and temperature treatments. Moreover, unique bacteria of the microbiome were significantly enriched in each Tegula species. For example, Lutimonas, Polaribacter, and the exopolysaccharide (EPS)-producing bacteria Pelagicoccus was most abundant in T. gallina, the species that occupies the highest intertidal heights and thus experiences heat stress most frequently. These results suggest that microbiome-derived metabolites such as EPS could be contributing to the higher thermal tolerance of T. gallina. Overall, this study demonstrates that the bacterial microbiome should be considered when examining mechanisms of thermal tolerance in marine invertebrates.

microbiology↗

PHEIGES, all-cell-free phage synthesis and selection from engineered genomes

Bacteriophages constitute an invaluable biological reservoir for biotechnology and medicine. The ability to exploit such vast resources is hampered by the lack of methods to rapidly engineer, assemble, package genomes, and select phages. Cell-free transcription-translation (TXTL) offers experimental settings to address such a limitation. Here, we describe PHage Engineering by In vitro Gene Expression and Selection (PHEIGES) using T7 phage genome and Escherichia coli TXTL. Phage genomes are assembled in vitro from PCR-amplified fragments and directly expressed in batch TXTL reactions to produce up to 1011 PFU/ml engineered phages within one day. We further demonstrate a significant genotype-phenotype linkage of phage assembly in bulk TXTL. This enables rapid selection of phages with altered rough lipopolysaccharides specificity from phage genomes incorporating tail fiber mutant libraries. We establish the scalability of PHEIGES by one pot assembly of such mutants with fluorescent gene integration and 10% length-reduced genome.

synthetic biology↗

Assessing Microbial Diversity in Soil Samples Along the Potomac River: Implications for Environmental Health

In this study, we investigated the microbial diversity and community composition of soil samples collected from various sites along the Potomac River within an urbanized region. Our findings revealed the presence of both typical marine soil bacteria and bacterial taxa indicative of urbanization and waste runoff. We observed significant variations in microbial community structure and diversity across different sampling sites, highlighting the influence of environmental factors on microbial abundance and diversity. Through taxon set analysis, we identified shared taxa strongly associated with agricultural pollution, organochlorine pesticide contamination, and bromochloromethane pollution. Additionally, the study revealed potential disparities in human impact, water retention, and tidal/current effects among the soil samples. These insights carry significant implications for understanding the consequences of urbanization on soil microbial communities along the Potomac River and can inform strategies for managing and preserving these ecosystems. Further research is warranted to elucidate the effects of soil health and microbial diversity in this region.

microbiology↗

Large-scale proteomic analysis of T. spiralis muscle-stage ESPs identifies a novel upstream motif for in silico prediction of secreted products

The Trichinella genus contains parasitic nematodes capable of infecting a wide range of hosts including mammals, birds and reptiles. Like other helminths, T. spiralis secretes a complex mixture of bioactive molecules capable of modulating its immediate surroundings and creating a hospitable environment for growth, survival and ultimately transmission. The constitution of these excretory-secretory products (ESPs) changes depending on the tissue niche and the specific stage of parasite development. Unique to T. spiralis is a true intracellular stage wherein larvae develop inside striated myotubes. Remarkably, the parasite larvae do not destroy the host cell but rather reprogram it to support their presence and growth. This transformation is largely mediated through stage-specific secretions released into the host cell cytoplasm. In this study, we apply state of the art proteomics and computational approaches to elucidate the composition and functions of muscle-stage T. spiralis ESPs. Moreover, we define a commonly-occurring, upstream motif that we believe is associated with the stichosome, the main secretory organ of this worm, and can thus be used to predict secreted proteins across experimentally less tractable T. spiralis life cycle stages. Author SummaryTrichinella spiralis is the only helminth parasite with a true intracellular stage. Newborn larvae penetrate the intestinal wall of the host, enter the circulation and preferentially infect muscle cells. Remarkably, they do not destroy the host cell but rather initiate a series of modulatory events that transform it into a nurse cell complex, a collagenated cyst that can persist for years. Each stage of T. spiralis development is guided by host-targeted secretions released by the worm directly into its immediate environment, mediating events such as immunoregulation, cell cycle control and angiogenesis. As such, these worm effectors hold therapeutic potential for chronic and autoimmune diseases. The composition of excretory-secretory products (ESPs) changes according to what the worm needs to accomplish and what tissue niche it is occupying at the time, with many deriving from the stichosome, the worms dedicated secretory organ. In this study, we characterise ESPs of muscle-stage T. spiralis larvae using proteomic and bioinformatic approaches and we define a regulatory motif associated with stichosome-derived proteins.

cell biology↗

The Microbes Found in the Honey of New York City Beehives

Bees are incredibly important to the Earths ecosystem and provide humans with a variety of fruits and vegetables; however, due to Colony Collapse Disorder, hives are dying at an alarming rate. Colony Collapse Disorder is caused by a number of factors such as pesticides and bacteria that kill the bees. With the increase of urban beekeeping created in an effort to replenish the bee population, little is known about the microbes the bees are interacting with in New York City. This research looked at what microbes the bees came in contact with to use as a resource in identifying the differences between the neighborhoods. Two methods were used to extract the DNA, one looking at gram-positive and gram-negative bacteria and the other looking at only gram-positive. The samples were taken from around New York City, Westchester County and Pennsylvania. The Pennsylvania sample was collected from a container of honey bought from Trader Joes. The reason both urban and rural samples were used was to see if there is an obvious difference in the microbes found between them.

microbiology↗