Department of Biological Sciences

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    2008-09 Annual Report Department of Biological Sciences
    (Virginia Tech, 2009-08-19)
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    2009-10 Annual Report Department of Biological Sciences
    (Virginia Tech, 2010-08-11)
  • A modular curriculum to teach undergraduates ecological forecasting improves student and instructor confidence in their data science skills
    Lofton, Mary E.; Moore, Tadhg N.; Woelmer, Whitney M.; Thomas, R. Quinn; Carey, Cayelan C. (Oxford University Press, 2024-10-10)
    Data science skills (e.g., analyzing, modeling, and visualizing large data sets) are increasingly needed by undergraduates in the life sciences. However, a lack of both student and instructor confidence in data science skills presents a barrier to their inclusion in undergraduate curricula. To reduce this barrier, we developed four teaching modules in the Macrosystems EDDIE (for environmental data-driven inquiry and exploration) program to introduce undergraduate students and instructors to ecological forecasting, an emerging subdiscipline that integrates multiple data science skills. Ecological forecasting aims to improve natural resource management by providing future predictions of ecosystems with uncertainty. We assessed module efficacy with 596 students and 26 instructors over 3 years and found that module completion increased students’ confidence in their understanding of ecological forecasting and instructors’ likelihood to work with long-term, high-frequency sensor network data. Our modules constitute one of the first formalized data science curricula on ecological forecasting for undergraduates.
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    A naturally derived biomaterial formulation for improved menstrual care
    Bataglioli, Rogerio Aparecido; Kaur, Harsimran; Muller, John; Geddes, Elizabeth; Champine, Carrie; Hsu, Bryan B. (Cell Press, 2024-07-10)
    Adequately managing menstruation is an important factor in the overall quality of life for women. With a growing discussion of the global need for its improvement, it is clear that better management of menstruation can positively influence social, educational, and professional outcomes. Herein, we describe a biopolymer-based formulation that gels blood in a mechanism alternative to coagulation. We first tested several biopolymer mixtures with blood and quantified increases in viscosity, finding that high-molecular-weight alginate in combination with glycerol could rapidly absorb and gel blood. We then demonstrated that this powder could be deployed both as a traditional menstrual pad filler and as an additive to menstrual cups to reduce leakage and spillage, respectively. Finally, we include an antimicrobial polymer to impair the growth of Staphylococcus aureus, a bacterium associated with toxic shock syndrome. Collectively, our work describes a biodegradable formulation derived from renewable resources that can improve menstrual care.
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    Aberrant early growth of individual trigeminal sensory and motor axons in a series of mouse genetic models of 22q11.2 deletion syndrome
    Motahari, Zahra; Maynard, Thomas M.; Popratiloff, Anastas; Moody, Sally A.; LaMantia, Anthony-Samuel (2020-09-15)
    We identified divergent modes of initial axon growth that prefigure disrupted differentiation of the trigeminal nerve (CN V), a cranial nerve essential for suckling, feeding and swallowing (S/F/S), a key innate behavior compromised in multiple genetic developmental disorders including DiGeorge/22q11.2 Deletion Syndrome (22q11.2 DS). We combined rapid in vivo labeling of single CN V axons in LgDel(+/-) mouse embryos, a genomically accurate 22q11.2DS model, and 3D imaging to identify and quantify phenotypes that could not be resolved using existing methods. We assessed these phenotypes in three 22q11.2-related genotypes to determine whether individual CN V motor and sensory axons wander, branch and sprout aberrantly in register with altered anterior-posterior hindbrain patterning and gross morphological disruption of CN V seen in LgDel(+/-). In the additional 22q11.2-related genotypes: Tbx1(+/-), Ranbp1(+/-), Ranbp1(+/-) and LgDel(+/-):Raldh2(+/-); axon phenotypes are seen when hindbrain patterning and CN V gross morphology is altered, but not when it is normal or restored toward WT. This disordered growth of CN V sensory and motor axons, whose appropriate targeting is critical for optimal S/F/S, may be an early, critical determinant of imprecise innervation leading to inefficient oropharyngeal function associated with 22q11.2 deletion from birth onward.
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    Above-ground tree carbon storage in response to nitrogen deposition in the US is heterogeneous and may have weakened
    Clark, Christopher M.; Thomas, R. Quinn; Horn, Kevin J. (Springer Nature, 2023-02-14)
    Long-term nitrogen deposition may not provide sustained stimulation of tree carbon storage, suggest analyses of a tree inventory and growth for the contiguous US between 2000 and 2016, compared to data for the 1980s and 1990s. Changes in nitrogen (N) availability affect the ability for forest ecosystems to store carbon (C). Here we extend an analysis of the growth and survival of 94 tree species and 1.2 million trees, to estimate the incremental effects of N deposition on changes in aboveground C (dC/dN) across the contiguous U.S. (CONUS). We find that although the average effect of N deposition on aboveground C is positive for the CONUS (dC/dN = +9 kg C per kg N), there is wide variation among species and regions. Furthermore, in the Northeastern U.S. where we may compare responses from 2000-2016 with those from the 1980s-90s, we find the recent estimate of dC/dN is weaker than from the 1980s-90s due to species-level changes in responses to N deposition. This suggests that the U.S. forest C-sink varies widely across forests and may be weakening overall, possibly necessitating more aggressive climate policies than originally thought.
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    Absence of Mycobacterium intracellulare and Presence of Mycobacterium chimaera in Household Water and Biofilm Samples of Patients in the United States with Mycobacterium avium Complex Respiratory Disease
    Wallace, Richard J. Jr.; Iakhiaeva, Elena; Williams, Myra D.; Brown-Elliott, Barbara A.; Vasireddy, Sruthi; Vasireddy, Ravikiran; Lande, Leah; Peterson, Donald D.; Sawicki, Janet; Kwait, Rebecca; Tichenor, Wellington S.; Turenne, Christine; Falkinham, Joseph O. III (American Society for Microbiology, 2013-03-27)
    Recent studies have shown that respiratory isolates from pulmonary disease patients and household water/biofilm isolates of Mycobacterium avium could be matched by DNA fingerprinting. To determine if this is true for Mycobacterium intracellulare, household water sources for 36 patients with Mycobacterium avium complex (MAC) lung disease were evaluated. MAC household water isolates from three published studies that included 37 additional MAC respiratory disease patients were also evaluated. Species identification was done initially using nonsequencing methods with confirmation by internal transcribed spacer (ITS) and/or partial 16S rRNA gene sequencing. M. intracellulare was identified by nonsequencing methods in 54 respiratory cultures and 41 household water/biofilm samples. By ITS sequencing, 49 (90.7%) respiratory isolates were M. intracellulare and 4 (7.4%) were Mycobacterium chimaera. In contrast, 30 (73%) household water samples were M. chimaera, 8 (20%) were other MAC X species (i.e., isolates positive with a MAC probe but negative with species-specific M. avium and M. intracellulare probes), and 3 (7%) were M. avium; none were M. intracellulare. In comparison, M. avium was recovered from 141 water/biofilm samples. These results indicate that M. intracellulare lung disease in the United States is acquired from environmental sources other than household water. Nonsequencing methods for identification of nontuberculous mycobacteria (including those of the MAC) might fail to distinguish closely related species (such as M. intracellulare and M. chimaera). This is the first report of M. chimaera recovery from household water. The study underscores the importance of taxonomy and distinguishing the many species and subspecies of the MAC.
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    Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental Aspects
    Cornish-Bowden, Athel; Rasnick, David; Heng, Henry H.; Horne, Steven; Abdallah, Batoul; Liu, Guo; Ye, Christine J.; Bloomfield, Mathew; Vincent, Mark D.; Aldaz, C. M.; Karlsson, Jenny; Valind, Anders; Jansson, Caroline; Gisselsson, David; Graves, Jennifer A. M.; Stepanenko, Aleksei A.; Andreieva, Svitlana V.; Korets, Kateryna V.; Mykytenko, Dmytro O.; Huleyuk, Nataliya L.; Baklaushev, Vladimir P.; Kovaleva, Oksana A.; Chekhonin, Vladimir P.; Vassetzky, Yegor S.; Avdieiev, Stanislav S.; Bakker, Bjorn; Taudt, Aaron S.; Belderbos, Mirjam E.; Porubsky, David; Spierings, Diana C. J.; de Jong, Tristan V.; Halsema, Nancy; Kazemier, Hinke G.; Hoekstra-Wakker, Karina; Bradley, Allan; de Bont, Eveline S. J. M.; van den Berg, Anke; Guryev, Victor; Lansdorp, Peter M.; Tatché, Maria C.; Foijer, Floris; Liehr, Thomas; Baudoin, Nicolaas C.; Nicholson, Joshua M.; Soto, Kimberly; Quintanilla, Isabel; Camps, Jordi; Cimini, Daniela; Dürrbaum, M.; Donnelly, N.; Passerini, V.; Kruse, C.; Habermann, B.; Storchová, Z.; Mandrioli, Daniele; Belpoggi, Fiorella; Silbergeld, Ellen K.; Perry, Melissa J.; Skotheim, Rolf I.; Løvf, Marthe; Johannessen, Bjarne; Hoff, Andreas M.; Zhao, Sen; SveeStrømme, Jonas M.; Sveen, Anita; Lothe, Ragnhild A.; Hehlmann, R.; Voskanyan, A.; Fabarius, A.; Böcking, Alfred; Biesterfeld, Stefan; Berynskyy, Leonid; Börgermann, Christof; Engers, Rainer; Dietz, Josef; Fritz, A.; Sehgal, N.; Vecerova, J.; Stojkovicz, B.; Ding, H.; Page, N.; Tye, C.; Bhattacharya, S.; Xu, J.; Stein, G.; Stein, J.; Berezney, R.; Gong, Xue; Grasedieck, Sarah; Swoboda, Julian; Rücker, Frank G.; Bullinger, Lars; Pollack, Jonathan R.; Roumelioti, Fani-Marlen; Chiourea, Maria; Raftopoulou, Christina; Gagos, Sarantis; Duesberg, Peter; Bloomfield, Mathew; Hwang, Sunyoung; Gustafsson, Hans T.; O’Sullivan, Ciara; Acevedo-Colina, Aracelli; Huang, Xinhe; Klose, Christian; Schevchenko, Andrej; Dickson, Robert C.; Cavaliere, Paola; Dephoure, Noah; Torres, Eduardo M.; Stampfer, Martha R.; Vrba, Lukas; LaBarge, Mark A.; Futscher, Bernard; Garbe, James C.; Trinh, Andrew L.; Zhou, Yi-Hong; Digman, Michelle (2017-06-22)
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    Abundance and Size Distribution of Particulate Matter Fractions Near a Caribbean Bank Barrier Reef
    Simmons, George M. Jr. (Inter-Research, 1979)
    Recent research indicates that corals have the ability to occupy several trophic levels and that particulate matter (PM) appears to play a major role in meeting their daily energy requirements. A study was undertaken to determine the amount and size distribution of PM near a bank barrier reef off the West Indies Laboratory on St. Croix, U.S.V.I. Size distributions were determined by filtration through selected sieves and filters ranging between 250 and 0.45 μm. Results showed that PM was greater in back-reef than fore-reef areas and greater during day than night hours. The PM collected on the smallest filters (0.45μm) remained constant during both sampling periods and could potentially supply 60 % of the daily energy requirements for corals. Inclusion of the PM on the next size filter (8.0 μm) would more than account for their daily energy requirements. The mean PM abundance found in this study (1.1 mg 1^-1) is the same as that reported at another Caribbean laboratory in the West Indies.
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    Accumulation and depuration of microplastic fibers, fragments, and tire particles in the eastern oyster, Crassostrea virginica: A toxicokinetic approach
    Weinstein, John E.; Ertel, Bonnie M.; Gray, Austin D. (Elsevier, 2022-09-01)
    Along the South Carolina coast (U.S.) where the ecologically and economically important eastern oyster (Crassostrea virginica) forms extensive intertidal reefs, recent surface water surveys found that fibers, fragments, and microscopic tire particles represented 43.6%, 30.9%, and 17.7% of the total microplastics, respectively. The aim of this study was to characterize accumulation and depuration of these particles in eastern oysters. Oysters were exposed to purple polyethylene fibers, green nylon fragments, or micronized crumb rubber at a concentration of 5000 microplastics/L, and sacrificed after 0, 24, 48, and 96 h to characterize uptake. Following 96 h, remaining oysters were transferred to microplastic-free brackish water and sacrificed at 24, 48, and 96 h to characterize depuration. For fibers and fragments, levels increased in a nonlinear fashion reaching 1.61 ± 0.6 particles/g w. w. (mean ± SE) and 0.46 ± 0.1 particles/g w. w. after 96 h, respectively. Conditional uptake clearance rate constants (ku) were estimated to be 0.0084 and 0.0025 mL/g*h for fibers and fragments, respectively. For crumb rubber, levels increased in a linear fashion reaching 3.62 ± 0.8 particles/g w. w. after 96 h, and the ku value was estimated to be 0.0077 mL/g*h. Depuration was best described using a two-compartment (double exponential) model suggesting the presence of fast and slow compartments. Conditional depuration rate constants (kd) for the slow compartments were 0.0084, 0.0205, and 0.0048/h for fibers, fragments, and crumb rubber, respectively. These results demonstrate accumulation and depuration of microplastics in eastern oysters is size-and shape-dependent. Depuration, which is a common practice for shellfish safety, is an effective way to reduce microplastic loads in eastern oysters, but the minimum recommended time of 44 h would only reduce loads of these particles by 55.5–67.6%.
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    Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles
    Highnam, Gareth; Franck, Christopher T.; Martin, Andy; Stephens, Calvin; Puthige, Ashwin; Mittelman, David (Oxford University Press, 2013-01)
    Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping microsatellite repeats called RepeatSeq, which uses Bayesian model selection guided by an empirically derived error model that incorporates sequence and read properties. Next, we apply RepeatSeq to high-coverage genomes from the 1000 Genomes Project to evaluate performance and accuracy. The software uses common formats, such as VCF, for compatibility with existing genome analysis pipelines. Source code and binaries are available at http://github.com/adaptivegenome/repeatseq.
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    Actin Filament Attachments for Sustained Motility In Vitro Are Maintained by Filament Bundling
    Hu, Xiaohua; Kuhn, Jeffrey R. (PLOS, 2012-02-16)
    We reconstructed cellular motility in vitro from individual proteins to investigate how actin filaments are organized at the leading edge. Using total internal reflection fluorescence microscopy of actin filaments, we tested how profilin, Arp2/3, and capping protein (CP) function together to propel thin glass nanofibers or beads coated with N-WASP WCA domains. Thin nanofibers produced wide comet tails that showed more structural variation in actin filament organization than did bead substrates. During sustained motility, physiological concentrations of Mg2+ generated actin filament bundles that processively attached to the nanofiber. Reduction of total Mg2+ abolished particle motility and actin attachment to the particle surface without affecting actin polymerization, Arp2/3 nucleation, or filament capping. Analysis of similar motility of microspheres showed that loss of filament bundling did not affect actin shell formation or symmetry breaking but eliminated sustained attachments between the comet tail and the particle surface. Addition of Mg2+, Lys-Lys2+, or fascin restored both comet tail attachment and sustained particle motility in low Mg2+ buffers. TIRF microscopic analysis of filaments captured by WCA-coated beads in the absence of Arp2/3, profilin, and CP showed that filament bundling by polycation or fascin addition increased barbed end capture by WCA domains. We propose a model in which CP directs barbed ends toward the leading edge and polycation-induced filament bundling sustains processive barbed end attachment to the leading edge.
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    Activity of bacteria isolated from bats against Pseudogymnoascus destructans in China
    Li, Zhongle; Li, Aoqiang; Hoyt, Joseph R.; Dai, Wentao; Leng, Haixia; Li, Yanfei; Li, Wei; Liu, Sen; Jin, Longru; Sun, Keping; Feng, Jiang (2021-02)
    White-nose syndrome, a disease that is caused by the psychrophilic fungus Pseudogymnoascus destructans, has threatened several North America bat species with extinction. Recent studies have shown that East Asian bats are infected with P. destructans but show greatly reduced infections. While several factors have been found to contribute to these reduced infections, the role of specific microbes in limiting P. destructans growth remains unexplored. We isolated three bacterial strains with the ability to inhibit P. destructans, namely, Pseudomonas yamanorum GZD14026, Pseudomonas brenneri XRD11711 and Pseudomonas fragi GZD14479, from bats in China. Pseudomonas yamanorum, with the highest inhibition score, was selected to extract antifungal active substance. Combining mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy analyses, we identified the active compound inhibiting P. destructans as phenazine-1-carboxylic acid (PCA), and the minimal inhibitory concentration (MIC) was 50.12 mu g ml(-1). Whole genome sequencing also revealed the existence of PCA biosynthesis gene clusters. Gas chromatography-mass spectrometry (GC-MS) analysis identified volatile organic compounds. The results indicated that 10 ppm octanoic acid, 100 ppm 3-tert-butyl-4-hydroxyanisole (isoprenol) and 100 ppm 3-methyl-3-buten-1-ol (BHA) inhibited the growth of P. destructans. These results support that bacteria may play a role in limiting the growth of P. destructans on bats.
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    Acyl-Homoserine Lactone Recognition and Response Hindering the Quorum-Sensing Regulator EsaR
    Schu, Daniel J.; Scruggs, Jessica M.; Geissenger, Jared S.; Michel, Katherine G.; Stevens, Ann M. (Public Library of Science, 2014-09-19)
    During quorum sensing in the plant pathogen Pantoea stewartii subsp. stewartii, EsaI, an acyl-homoserine lactone (AHL) synthase, and the transcription factor EsaR coordinately control capsular polysaccharide production. The capsule is expressed only at high cell density when AHL levels are high, leading to inactivation of EsaR. In lieu of detailed structural information, the precise mechanism whereby EsaR recognizes AHL and is hindered by it, in a response opposite to that of most other LuxR homologues, remains unresolved. Hence, a random mutagenesis genetic approach was designed to isolate EsaR* variants that are immune to the effects of AHL. Error-prone PCR was used to generate the desired mutants, which were subsequently screened for their ability to repress transcription in the presence of AHL. Following sequencing, site-directed mutagenesis was used to generate all possible mutations of interest as single, rather than multiple amino acid substitutions. Eight individual amino acids playing a critical role in the AHL-insensitive phenotype have been identified. The ability of EsaR* variants to bind AHL and the effect of individual substitutions on the overall conformation of the protein were examined through in vitro assays. Six EsaR* variants had a decreased ability to bind AHL. Fluorescence anisotropy was used to examine the relative DNA binding affinity of the final two EsaR* variants, which retained some AHL binding capability but remained unresponsive to it, perhaps due to an inability of the N-terminal domain to transduce information to the C-terminal domain.
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    Adapting to Symptoms of Global Warming Rather Than Addressing the Cause
    Cairns, John Jr. (Virginia Tech, 2006)
    In recent years, global warming has been ignored and scientists producing evidence supporting this hypothesis have been denigrated and even investigated. However, as irrefutable evidence showing that global warming was a reality mounted, the message shifted to global warming may be occurring, but it is not caused by human activity. Now the message is shifting again, and humankind I been told to adapt to global warming instead of making an effort to reverse it.
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    Adaptive radiation along a deeply conserved genetic line of least resistance in Anolis lizards
    McGlothlin, Joel W.; Kobiela, Megan E.; Wright, Helen V.; Mahler, Luke D.; Kolbe, Jason K.; Losos, Jonathan B.; Brodie, Edmund D. III (Wiley, 2018)
    On microevolutionary timescales, adaptive evolution depends upon both natural selection and the underlying genetic architecture of traits under selection, which may constrain evolutionary outcomes. Whether such genetic constraints shape phenotypic diversity over macroevolutionary timescales is more controversial, however. One key prediction is that genetic constraints should bias the early stages of species divergence along “genetic lines of least resistance” defined by the genetic (co)variance matrix, G. This bias is expected to erode over time as species means and G matrices diverge, allowing phenotypes to evolve away from the major axis of variation. We tested for evidence of this signal in West Indian Anolis lizards, an iconic example of adaptive radiation. We found that the major axis of morphological evolution was well aligned with a major axis of genetic variance shared by all species despite separation times of 20–40 million years, suggesting that divergence occurred along a conserved genetic line of least resistance. Further, this signal persisted even as G itself evolved, apparently because the largest evolutionary changes in G were themselves aligned with the line of genetic least resistance. Our results demonstrate that the signature of genetic constraint may persist over much longer timescales than previously appreciated, even in the presence of evolving genetic architecture. This pattern may have arisen either because pervasive constraints have biased the course of adaptive evolution or because the G matrix itself has been shaped by selection to conform to the adaptive landscape.
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    Adenovirus transduction to express human ACE2 causes obesity-specific morbidity in mice, impeding studies on the effect of host nutritional status on SARS-CoV-2 pathogenesis
    Rai, Pallavi; Chuong, Christina; LeRoith, Tanya; Smyth, James W.; Panov, Julia; Levi, Moshe; Kehn-Hall, Kylene; Duggal, Nisha K.; Weger-Lucarelli, James (Elsevier, 2021-11-01)
    The COVID-19 pandemic has paralyzed the global economy and resulted in millions of deaths globally. People with co-morbidities like obesity, diabetes and hypertension are at an increased risk for severe COVID-19 illness. This is of overwhelming concern because 42% of Americans are obese, 30% are pre-diabetic and 9.4% have clinical diabetes. Here, we investigated the effect of obesity on disease severity following SARS-CoV-2 infection using a well-established mouse model of diet-induced obesity. Diet-induced obese and lean control C57BL/6 N mice, transduced for ACE2 expression using replication-defective adenovirus, were infected with SARS-CoV-2, and monitored for lung pathology, viral titers, and cytokine expression. No significant differences in tissue pathology or viral replication was observed between AdV transduced lean and obese groups, infected with SARS-CoV-2, but certain cytokines were expressed more significantly in infected obese mice compared to the lean ones. Notably, significant weight loss was observed in obese mice treated with the adenovirus vector, independent of SARS-CoV-2 infection, suggesting an obesity-dependent morbidity induced by the vector. These data indicate that the adenovirus-transduced mouse model of SARS-CoV-2 infection, as described here and elsewhere, may be inappropriate for nutrition studies.