Research and Testing Laboratory LLC

Lubbock, TX, United States

Research and Testing Laboratory LLC

Lubbock, TX, United States
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Moore-Kucera J.,Texas Tech University | Cox S.B.,Research and Testing Laboratory LLC | Peyron M.,Western Washington University | Bailes G.,Western Washington University | And 5 more authors.
Applied Microbiology and Biotechnology | Year: 2014

Plastics are used widely as agricultural mulches to suppress weeds and retain soil moisture. Disposal of conventional plastic mulches requires physical removal for disposal in a landfill or incineration. Biodegradable plastic mulches that could be tilled into the soil at the end of a growing season represent an attractive alternative to conventional plastic mulches. In this study, three commercially available mulches labeled as "biodegradable" and one experimental, potentially biodegradable mulch were used during a tomato growing season, and then buried in field soil at three locations for approximately 6 months, as would occur typically in an agricultural setting. Degradation after 6 months in soil was minimal for all but the cellulosic mulch. After removal of mulches from soil, fungi were isolated from the mulch surfaces and tested for their ability to colonize and degrade the same mulches in pure culture. The majority of culturable soil fungi that colonized biodegradable mulches were within the family Trichocomaceae (which includes beneficial, pathogenic, and mycotoxigenic species of Aspergillus and Penicillium). These isolates were phylogenetically similar to fungi previously reported to degrade both conventional and biodegradable plastics. Under pure culture conditions, only a subset of fungal isolates achieved detectable mulch degradation. No isolate substantially degraded any mulch. Additionally, DNA was extracted from bulk soil surrounding buried mulches and ribosomal DNA was used to assess the soil microbial community. Soil microbial community structure was significantly affected by geographical location, but not by mulch treatments. © 2014 Springer-Verlag.

Erickson R.A.,Texas Tech University | Erickson R.A.,U.S. Geological Survey | Cox S.B.,Texas Tech University | Cox S.B.,Research and Testing Laboratory LLC | And 5 more authors.
Ecological Modelling | Year: 2014

Population models have emerged as a powerful tool to better understand the ecological effects of toxicant exposure. Currently, most ecotoxicology population models are deterministic and fail to account for natural variability in biological processes and uncertainty in parameter estimates. We developed, parameterized, and analyzed a Daphnia population model with three different levels of demographic stochasticity to examine how a pesticide, pendimethalin, affects population dynamics. We conducted laboratory studies to generate the data used for the modeling process. The simplest model only included parameter uncertainty and variability. The second model included daily stochastic fecundities. The third model included stochastic fecundities and stochastic mortalities. Of the three models, the second model with stochastic fecundity best described our laboratory test system. All three models were used to test hypotheses about how pesticides would affect population dynamics. We found that pendimethalin either decreased the baseline juvenile survivorship rate or the carrying capacity. We could differentiate the two test effects with our system. Our findings demonstrate how stochastic population models may provide insight into pesticide exposure. © 2013 Elsevier B.V.

Mutlu E.A.,Rush University Medical Center | Keshavarzian A.,Rush University Medical Center | Keshavarzian A.,Rush University | Keshavarzian A.,University Utrecht | And 17 more authors.
PLoS Pathogens | Year: 2014

HIV progression is characterized by immune activation and microbial translocation. One factor that may be contributing to HIV progression could be a dysbiotic microbiome. We therefore hypothesized that the GI mucosal microbiome is altered in HIV patients and this alteration correlates with immune activation in HIV. 121 specimens were collected from 21 HIV positive and 22 control human subjects during colonoscopy. The composition of the lower gastrointestinal tract mucosal and luminal bacterial microbiome was characterized using 16S rDNA pyrosequencing and was correlated to clinical parameters as well as immune activation and circulating bacterial products in HIV patients on ART. The composition of the HIV microbiome was significantly different than that of controls; it was less diverse in the right colon and terminal ileum, and was characterized by loss of bacterial taxa that are typically considered commensals. In HIV samples, there was a gain of some pathogenic bacterial taxa. This is the first report characterizing the terminal ileal and colonic mucosal microbiome in HIV patients with next generation sequencing. Limitations include use of HIV-infected subjects on HAART therapy. © 2014 Mutlu et al.

Erickson R.A.,Texas Tech University | Hayhoe K.,Texas Tech University | Presley S.M.,Texas Tech University | Allen L.J.S.,Texas Tech University | And 3 more authors.
Environmental Research Letters | Year: 2012

Shifts in temperature and precipitation patterns caused by global climate change may have profound impacts on the ecology of certain infectious diseases. We examine the potential impacts of climate change on the transmission and maintenance dynamics of dengue, a resurging mosquito-vectored infectious disease. In particular, we project changes in dengue season length for three cities: Atlanta, GA; Chicago, IL and Lubbock, TX. These cities are located on the edges of the range of the Asian tiger mosquito within the United States of America and were chosen as test cases. We use a disease model that explicitly incorporates mosquito population dynamics and high-resolution climate projections. Based on projected changes under the Special Report on Emissions Scenarios (SRES) A1fi (higher) and B1 (lower) emission scenarios as simulated by four global climate models, we found that the projected warming shortened mosquito lifespan, which in turn decreased the potential dengue season. These results illustrate the difficulty in predicting how climate change may alter complex systems. © 2012 IOP Publishing Ltd.

PubMed | Rush University Medical Center and Research and Testing Laboratory LLC
Type: | Journal: Clinical and translational gastroenterology | Year: 2016

Bowel preparations (BPs) taken before colonoscopy may introduce a confounding effect on the results of gastrointestinal microbiota studies. This study aimed to determine the effect of bowel preparation on the mucosa-associated and luminal colonic microbiota in healthy subjects (HC) and inflammatory bowel disease (IBD) patients.Biopsy samples (n=36) and fecal samples (n=30) were collected from 10 HC and 8 IBD subjects pre- and post-BP. 16S rRNA gene was pyrosequenced using 454 Titanium protocols. We compared the differences between the pre- and post-BP samples (i.e., comparisons-across-bowel-prep); we examined the effect of BP on the expected separation of the mucosal vs. the luminal compartments (i.e., comparisons-across-compartments). Last, we compared the baseline differences between the HC vs. IBD groups (a secondary analysis), and examined whether the differences between the HC vs. IBD changed after BP.In comparisons-across-bowel-prep, the Shannons index (SI) decreased only in the biopsy samples of IBD subjects post-BP (P=0.025) and phylogenetic diversity-whole tree (PD-WT) metric decreased in biopsy samples of HC subjects post-BP (P=0.021). In secondary comparisons, the subtle differences between the fecal samples of the HC vs. IBD groups, in terms of evenness and the SI, were not apparent post-BP. In terms of -diversity, in comparisons-across-bowel-prep, the proportion of shared operational taxonomic units (OTUs) in pre- and post-BP samples was low (~30%) and unweighted Unifrac distances between pre- and post-BP specimens ranged from 0.52 to 0.66. HC biopsies were affected more than IBD biopsies with BP (P=0.004). In comparisons-across-compartments, the proportion of shared OTUs between biopsy and fecal samples increased and Unifrac distances decreased post-BP in IBD subjects, reducing the differences between the mucosal and luminal compartments of the gut microbiota. Interindividual differences in Unifrac distances were preserved even with BP effects, although the effects were greater on weighted Unifrac distances. Bacteroidetes and its subtypes increased post-BP in both the luminal and mucosal compartments.Bowel preparations affect the composition and diversity of the fecal and luminal microbiota in the short term, introducing potential bias into experiments examining the gut microbiota. The magnitude of the effect of BP is not greater than that of interindividual variation. Both the luminal and mucosal compartments of the gut microbiota get affected, and samples from controls and IBD subjects may get affected differently. Studies of the colonic microbiota should take into account the direction and the magnitude of the change introduced by BP during the design stage of the experiments, and consider sample sizes so that potential bias is minimized.

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