Project description:Evaluation of short-read-only, long-read-only, and hybrid assembly approaches on metagenomic samples demonstrating how they affect gene and protein prediction which is relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic, and metaproteomic data to evaluate the metagenomic-based protein predictions.
Project description:Differentially expressed genes may provide insight into the underlying mechanisms of Gulf War Illness involved in neurodegeneration.
Project description:This pilot study enrolled 9 GWI (Gulf War Illness) cases identified from the Department of Veterans Affairs GWI registry, and 11 sedentary control veterans who had not been deployed to the Persian Gulf and were matched to cases by sex, body mass index (BMI) and age.<br>We exposed GWI patients and matched controls to an exercise challenge to explore differences in immune cell function measured by classic immune assays and gene expression profiling.
Project description:Combat veterans from the Persian Gulf War have unexplained yet persistent impairment in colonic motility due to combat-related toxic exposures. Central to Gulf War-related toxic exposures was the unmitigated ingestion of Pyridostigmine bromide (PB). We previously developed a Gulf War Illness (GWI) mouse model, where acute PB exposure led to immediate disruptions in colonic motility. Here, we explore mechanisms by which acute enteric neuroinflammation produces peristent impairment in colonic motility. GWI mice were exposed to PB transiently, and allowed to recover with no exposures for 1 month. GWI mice had significantly increased amplitudes of colonic contraction and diminished nerve-stimulated colonic relaxation, compared to naive controls. Immunohistological characterization demonstrated persistent chronic damage in enteric neuronal network integrity, accompanied by a significant imbalance in excitatory and inhibitory motor neuronal populations. Inflammatory CD40+ tissue- resident macrophages were identified with enteric neural stem cells in GWI colons, with an increase in secreted inflammatory cytokines. Unbiased transcriptomic analysis corroborated peristent low grade enteric neuroinflammation, overall resulting in impaired repair and regeneration of neural circuity in GWI. Our learnings can be leveraged to design new regenerative therapies for Gulf War veterans, and broadly impact our understanding of severeal inflammatory disorders of the gut.
Project description:Ammonia-oxidizing archaeal (AOA) amoA diversity and relative abundance in Gulf of Mexico sediments (0-2 cm) were investigated using a functional gene microarray; a two color array with a universal internal standard
