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Destination Areas provide faculty and students with new tools to identify and solve complex, 21st-century problems in which Virginia Tech already has significant strengths and can take a global leadership role. The initiative represents the next step in the evolution of the land-grant university to meet economic and societal needs of the world.
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Browsing Destination Areas (DAs) by Subject "06 Biological Sciences"
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- Fecal Indicator Bacteria and Antibiotic Resistance Genes in Storm Runoff from Dairy Manure and Compost-Amended Vegetable PlotsJacobs, Kyle; Wind, Lauren L.; Krometis, Leigh-Anne H.; Hession, W. Cully; Pruden, Amy (American Society for Agronomy, 2019-07-01)Given the presence of antibiotics and resistant bacteria in livestock manures, it is important to identify the key pathways by which land-applied manure-derived soil amendments potentially spread resistance. The goal of this field-scale study was to identify the effects of different types of soil amendments (raw manure from cows treated with cephapirin and pirlimycin, compost from antibiotic-treated or antibiotic-free cows, or chemical fertilizer only) and crop type (lettuce [Lactuca sativa L.] or radish [Raphanus sativus L.]) on the transport of two antibiotic resistance genes (ARGs; sul1 and ermB) via storm runoff from six naturally occurring storms. Concurrent quantification of sediment and fecal indicator bacteria (FIB; Escherichia coli and enterococci) in runoff permitted comparison to traditional agricultural water quality targets that may be driving factors of ARG presence. Storm characteristics (total rainfall volume, storm duration, etc.) significantly influenced FIB concentration (two-way ANOVA, p < 0.05), although both effects from individual storm events (Kruskal-Wallis, p < 0.05) and vegetative cover influenced sediment levels. Composted and raw manure-amended plots both yielded significantly higher sul1 and ermB levels in runoff for early storms, at least 8 wk following initial planting, relative to fertilizer-only or unamended barren plots. There was no significant difference between sul1 or ermB levels in runoff from plots treated with compost derived from antibiotic-treated versus antibiotic-free dairy cattle. Our findings indicate that agricultural fields receiving manure-derived amendments release higher quantities of these two “indicator” ARGs in runoff, particularly during the early stages of the growing season, and that composting did not reduce effects of ARG loading in runoff.
- Improved plaque assay for human coronaviruses 229E and OC43Bracci, Nicole R.; Pan, Han-Chi; Lehman, Caitlin W.; Kehn-Hall, Kylene; Lin, Shih-Chao (PeerJ, 2020-12-21)In light of the COVID-19 pandemic, studies that work to understand SARS-CoV-2 are urgently needed. In turn, the less severe human coronaviruses such as HCoV-229E and OC43 are drawing newfound attention. These less severe coronaviruses can be used as a model to facilitate our understanding of the host immune response to coronavirus infection. SARS-CoV-2 must be handled under biosafety level 3 (BSL-3) conditions. Therefore, HCoV-229E and OC43, which can be handled at BSL-2 provide an alternative to SARS-CoV-2 for preclinical screening and designing of antivirals. However, to date, there is no published effective and efficient method to titrate HCoVs other than expensive indirect immunostaining. Here we present an improved approach using an agarose-based conventional plaque assay to titrate HCoV 229E and OC43 with mink lung epithelial cells, Mv1Lu. Our results indicate that titration of HCoV 229E and OC43 with Mv1Lu is consistent and reproducible. The titers produced are also comparable to those produced using human rhabdomyosarcoma (RD) cells. More importantly, Mv1Lu cells display a higher tolerance for cell-cell contact stress, decreased temperature sensitivity, and a faster growth rate. We believe that our improved low-cost plaque assay can serve as an easy tool for researchers conducting HCoV research.
- In vitro and in vivo activities of the carbonic anhydrase inhibitor, dorzolamide, against vancomycin-resistant enterococciAbutaleb, Nader S.; Elhassanny, Ahmed E. M.; Flaherty, Daniel P.; Seleem, Mohamed N. (PeerJ, 2021-03-30)Vancomycin-resistant enterococci (VRE) are a serious public health threat and a leading cause of healthcare-associated infections. Bacterial resistance to antibiotics recommended for the treatment of enterococcal infections complicates the management of these infections. Hence, there is a critical need for the discovery of new anti-VRE agents. We previously reported carbonic anhydrase inhibitors (CAIs) as new potent VRE inhibitors. In the present study, the activity of the CAI, dorzolamide was evaluated against VRE both in vitro and in vivo. Dorzolamide exhibited potent activity against a panel of clinical VRE isolates, with minimum inhibitory concentration (MIC) values ranging from 1 µg/mL to 8 µg/mL. A killing kinetics experiment determined that dorzolamide exhibited a bacteriostatic effect against VRE, which was similar to the drug of choice (linezolid). Dorzolamide interacted synergistically with gentamicin against four strains of VRE, and exhibited an additive interaction with gentamicin against six VRE strains, reducing gentamicin’s MIC by several folds. Moreover, dorzolamide outperformed linezolid in an in vivo VRE colonization reduction mouse model. Dorzolamide significantly reduced the VRE burden in fecal samples of mice by 2.9-log10 (99.9%) and 3.86-log10 (99.99%) after 3 and 5 days of treatment, respectively. Furthermore, dorzolamide reduced the VRE count in the cecal (1.74-log10 (98.2%) reduction) and ileal contents (1.5-log10 (96.3%)) of mice, which was superior to linezolid. Collectively, these results indicate that dorzolamide represents a promising treatment option that warrants consideration as a supplement to current therapeutics used for VRE infections.
- Plant essential oils synergize various pyrethroid insecticides and antagonize malathion in Aedes aegyptiNorris, Edmund J.; Gross, Aaron D.; Bartholomay, Lyric C.; Coats, J. R. (Wiley, 2019-12-01)Pyrethroid resistance is a significant threat to agricultural, urban and public health pest control activities. Because economic incentives for the production of novel active ingredients for the control of public health pests are lacking, this field is particularly affected by the potential failure of pyrethroid-based insecticides brought about by increasing pyrethroid resistance. As a result, innovative approaches are desperately needed to overcome insecticide resistance, particularly in mosquitoes that transmit deadly and debilitating pathogens. Numerous studies have demonstrated the potential of plant essential oils to enhance the efficacy of pyrethroids. The toxicity of pyrethroids combined with plant oils is significantly greater than the baseline toxicity of either oils or pyrethroids applied alone, which suggests there are synergistic interactions between components of these mixtures. The present study examined the potential of eight plant essential oils applied in one of two concentrations (1% and 5%) to enhance the toxicity of various pyrethroids (permethrin, natural pyrethrins, deltamethrin and β-cyfluthrin). The various plant essential oils enhanced the pyrethroids to differing degrees. The levels of enhancement provided by combinations of plant essential oils and pyrethroids in comparison with pyrethroids alone were calculated and synergistic outcomes characterized. Numerous plant essential oils significantly synergized a variety of pyrethroids; type I pyrethroids were synergized to a greater degree than type II pyrethroids. Eight plant essential oils significantly enhanced 24-h mortality rates provided by permethrin and six plant essential oils enhanced 24-h mortality rates obtained with natural pyrethrins. By contrast, only three plant essential plants significantly enhanced the toxicity of deltamethrin and β-cyfluthrin. Of the plant essential oils that enhanced the toxicity of these pyrethroids, some produced varying levels of synergism and antagonism. Geranium, patchouli and Texas cedarwood oils produced the highest levels of synergism, displaying co-toxicity factors of > 100 in some combinations. To assess the levels of enhancement and synergism of other classes of insecticide, malathion was also applied in combination with the plant oils. Significant antagonism was provided by a majority of the plant essential oils applied in combination with this insecticide, which suggests that plant essential oils may act to inhibit the oxidative activation processes within exposed adult mosquitoes.
- Prediction of condition-specific regulatory genes using machine learningSong, Qi; Lee, Jiyoung; Akter, Shamima; Rogers, Matthew; Grene, Ruth; Li, Song (Oxford University Press, 2020-06-19)Recent advances in genomic technologies have generated data on large-scale protein–DNA interactions and open chromatin regions for many eukaryotic species. How to identify condition-specific functions of transcription factors using these data has become a major challenge in genomic research. To solve this problem, we have developed a method called ConSReg, which provides a novel approach to integrate regulatory genomic data into predictive machine learning models of key regulatory genes. Using Arabidopsis as a model system, we tested our approach to identify regulatory genes in data sets from single cell gene expression and from abiotic stress treatments. Our results showed that ConSReg accurately predicted transcription factors that regulate differentially expressed genes with an average auROC of 0.84, which is 23.5–25% better than enrichment-based approaches. To further validate the performance of ConSReg, we analyzed an independent data set related to plant nitrogen responses. ConSReg provided better rankings of the correct transcription factors in 61.7% of cases, which is three times better than other plant tools. We applied ConSReg to Arabidopsis single cell RNA-seq data, successfully identifying candidate regulatory genes that control cell wall formation. Our methods provide a new approach to define candidate regulatory genes using integrated genomic data in plants.
- A selective sweep in the Spike gene has driven SARS-CoV-2 human adaptationKang, Lin; He, Guijuan; Sharp, Amanda K.; Wang, Xiaofeng; Brown, Anne M.; Michalak, Pawel; Weger-Lucarelli, James (Cell Press, 2021-08-19)The coronavirus disease 2019 (COVID-19) pandemic underscores the need to better understand animal-to-human transmission of coronaviruses and adaptive evolution within new hosts. We scanned more than 182,000 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes for selective sweep signatures and found a distinct footprint of positive selection located around a non-synonymous change (A1114G; T372A) within the spike protein receptor-binding domain (RBD), predicted to remove glycosylation and increase binding to human ACE2 (hACE2), the cellular receptor. This change is present in all human SARS-CoV-2 sequences but not in closely related viruses from bats and pangolins. As predicted, T372A RBD bound hACE2 with higher affinity in experimental binding assays. We engineered the reversion mutant (A372T) and found that A372 (wild-type [WT]-SARS-CoV-2) enhanced replication in human lung cells relative to its putative ancestral variant (T372), an effect that was 20 times greater than the well-known D614G mutation. Our findings suggest that this mutation likely contributed to SARS-CoV-2 emergence from animal reservoirs or enabled sustained human-to-human transmission.