Life Sciences Commons^™

Deep Learning Architectures For Multi-Label Classification Of Intelligent Health Risk Prediction, Andrew Maxwell, Runzhi Li, Bei Yang, Heng Weng, Aihua Ou, Huixiao Hong, Zhaoxian Zhou, Ping Gong, Chaoyang Zhang

Faculty Publications

No abstract provided.

Deep Experimental Profiling Of Microrna Diversity, Deployment, And Evolution Across The Drosophila Genus, Jaaven Mohammed, Alex S. Flynt, Alexandra M. Panzarino, Md Mosharrof Hossain Mondal, Matthew Decruz, Adam Siepel, Eric C. Lai

Faculty Publications

To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5′ end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs. Within the bulk collection of species-restricted miRNAs, two notable subpopulations are splicing-derived mirtrons and testes-restricted, recently evolved, clustered (TRC) canonical miRNAs. We quantified miRNA birth and death …

Homogenization Techniques For Population Dynamics In Strongly Heterogeneous Landscapes, Brian P. Yurk, Christina A. Cobbold

Faculty Publications

An important problem in spatial ecology is to understand how population-scale patterns emerge from individual-level birth, death, and movement processes. These processes, which depend on local landscape characteristics, vary spatially and may exhibit sharp transitions through behavioural responses to habitat edges, leading to discontinuous population densities. Such systems can be modelled using reaction–diffusion equations with interface conditions that capture local behaviour at patch boundaries. In this work we develop a novel homogenization technique to approximate the large-scale dynamics of the system. We illustrate our approach, which also generalizes to multiple species, with an example of logistic growth within a periodic …

Genome Sequences Of Mycobacteriophages Amgine, Amohnition, Bella96, Cain, Darthp, Hammy, Krueger, Lasthope, Peanam, Phelpsodu, Phrank, Sirphilip, Slimphazie, And Unicorn, Kirk R. Anders, Nazir Barekzi, Aaron A. Best, Gregory D. Frederick, Dmitri V. Mavrodi, Edwin Vasquez, Sea-Phages, Nana Yaa A. Amoh, Frederick N. Baliraine, William J. Buchser, Thomas P. Cast, Carmen E. Chamberlain, Hui-Min Chung, William A. D'Angelo, Christian T. Farris, Mariceli Fernandez-Martinez, Haley D. Fischman, Mark H. Forsyth, Anna G. Fortier, Kara F. Gallo, Greta J. Held, Miguel A. Lomas, Natalia Y. Maldonado-Vasquez, Claudia H. Moonsammy, Peace Namboote, Sudip Paudel, Sarah-Elizabeth Polley, Gabriella Reyes, Michael R. Rubin, Margaret S. Saha, Joseph Stukey, Tristan D. Tobias, Rebecca A. Garlena, Ty H. Stoner, Steven G. Cresawn, Deborah Jacobs-Sera, Welkin H. Pope, Daniel A. Russell, Graham F. Hatfull

Faculty Publications

We report the genome sequences of 14 cluster K mycobacteriophages isolated using Mycobacterium smegmatis mc²155 as host. Four are closely related to subcluster K1 phages, and 10 are members of subcluster K6. The phage genomes span considerable sequence diversity, including multiple types of integrases and integration sites.

Colorful Seashells: Identification Of Haem Pathway Genes Associated With The Synthesis Of Porphyrin Shell Color In Marine Snails, Suzanne T. Williams, Anne E. Lockyer, Patricia Dyal, Tomoyuki Nakano, Celia K. C. Churchill, Daniel Isaac Speiser

Faculty Publications

Very little is known about the evolution of molluskan shell pigments, although Mollusca is a highly diverse, species rich, and ecologically important group of animals comprised of many brightly colored taxa. The marine snail genus Clanculus was chosen as an exceptional model for studying the evolution of shell color, first, because in Clanculus margaritarius and Clanculus pharaonius both shell and foot share similar colors and patterns; and second, because recent studies have identified the pigments, trochopuniceus (pink-red), and trochoxouthos (yellow-brown), both comprised of uroporphyrin I and uroporphyrin III, in both shell and colored foot tissue of these species. These unusual …

Hydrogen-Bonding-Directed Ordered Assembly Of Carboxylated Poly(3-Alkylthiophene)S, David W. Bilger, Jose A. Figueroa, Neil D. Redeker, Amrita Sarkar, Morgan Stefik, Shanjuu Zhang

Faculty Publications

Hydrogen-bonding-induced ordered assembly of poly(3-alkylthiophene)s derivatives bearing carboxylic acid groups has been investigated from diluted and concentrated solutions to solid films using ultraviolet–visible absorption spectroscopy, polarized optical microscopy, and four-point probe conductivity measurements. In dilute solutions, the polymer undergoes a spontaneous structural transition from disordered coil-like to ordered rodlike conformations, which is evidenced by time-dependent chromism. Many factors such as alkyl-chain length, types of solvents, and temperature are studied to understand the assembly behavior. Transition kinetics of the assembly process reveals a universal second-order rate law, indicating an intermolecular origin due to hydrogen bonding. When more concentrated, hydrogen bonding drives …

Brachylicoa Lui, A New Species Of Parapseudid Tanaidacean (Crustacea: Peracarida: Apseudomorpha), From The Hawaiian Islands, With A Taxonomic Key, Andrés G. Morales-Núñez, Sterling Ulrich, Richard W. Heard

Faculty Publications

Brachylicoa lui sp. n. is described from the coastal waters of the Hawaiian island of O‘ahu. It is distinguished from the other four nominal members of Brachylicoa by a combination of characters including (1) an incised margin between base of rostrum and carapace, (2) mandible palp article-1 with cluster of 20–25 simple setae, (3) maxillule biarticulate palp ending in eight “cleaning’ setae, (4) maxilliped inner sub-distal margin with two stout spiniform seta, and (5) pereopod-6 with carpus having three plumose setae on mid-dorsal margin. Brachylicoa (=Apseudes) babelmandebensis sensu Guţu is tentatively transferred to the genus Saltipedis Guţu sensu …

Msaabcr Operon Is Involved In Persister Cell Formation In Staphylococcus Aureus, Gyan S. Sahukhal, Shanti Pandey, Mohamed O. Elasri

Faculty Publications

Background

Persister cells comprise a phenotypic variant that shows extreme antibiotic tolerance resulting in treatment failures of bacterial infections. While this phenomenon has posed a great threat in public health, mechanisms underlying their formation in Staphylococcus aureus remain largely unknown. Increasing evidences of the presence of persister cells in recalcitrant infections underscores the great urgency to unravel the mechanism by which these cells develop. Previously, we characterized msaABCR operon that plays roles in regulation of virulence, biofilm development and antibiotic resistance. We also characterized the function of MsaB protein and showed that MsaB is a putative transcription factor that binds …

Multiple Species Of Cuckoos Are Superior Predictors Of Bird Species Richness In Asia, Anders Pape Møller, Federico Morelli, Yanina Benedetti, Timothy Mousseau, Tongping Su, Bo Zhou, Piotr Tryjanowski, Wei Liang

Faculty Publications

The abundance and the presence of common cuckoos Cuculus canorus have been shown to predict species richness of birds across Europe, while there are no such analyses available for other continents where species richness of parasitic cuckoos is larger. Here, we tested whether species richness of birds increased with the number of cuckoo species in two study areas in China and one in Japan. We also tested whether species richness of birds can be predicted by the number of cuckoo individuals. Furthermore, we compared the strength of association between overall bird species richness and species richness of cuckoos, Paridae, Corvidae, …

Blockade Of Cb1 Cannabinoid Receptor Alters Gut Microbiota And Attenuates Inflammation And Diet-Induced Obesity, Pegah Mehrpouya-Bahrami, Kumaraswamy Naidu Chitrala, Mitra S. Ganewatta, Chuanbing Tang, E Angela Murphy, Reilly Enos, Kandy T. Velazquez, Jamie Mccellan, Mitzi Nagarkatti, Prakash Nagarkatti

Faculty Publications

Obesity is characterized by chronic low-grade, systemic inflammation, altered gut microbiota, and gut barrier disruption. Additionally, obesity is associated with increased activity of endocannabinoid system (eCB). However, the clear connection between gut microbiota and the eCB system in the regulation of energy homeostasis and adipose tissue inflammation and metabolism, remains to be established. We investigated the effect of treatment of mice with a cannabinoid receptor 1 (CB1) antagonist on Diet-Induced Obesity (DIO), specifically whether such a treatment that blocks endocannabinoid activity can induce changes in gut microbiota and anti-inflammatory state in adipose tissue. Blockade of CB1 attenuated DIO, inflammatory cytokines …

An Undergraduate Laboratory Manual For Analyzing A Crispr Mutant With A Predicted Role In Regeneration, Susan Walsh, Ashley Becker, Paxton S. Sickler, Damian G. Clarke, Erin Jimenez

Faculty Publications

Exposing students to undergraduate research has reportedly improved students’ development of knowledge and skills in the laboratory, self-efficacy, satisfaction with their research, retention, and perseverance when faced with obstacles. Furthermore, utilizing authentic course-based undergraduate research experiences (CUREs) includes all students enrolled in the class, giving those who may not otherwise have access to an independent undergraduate research project an opportunity to engage in the scientific process in context of an original, unanswered question. In the fall of 2016, second semester introductory biology students conducted a semester-long research project on the transcription factor Lin28a to determine the effect of Lin28a on …

Does Any Good Come From A Coach That Yells? Reflective Experiences From Former Athletes, David C. Barney, Alema Tauiliili

Faculty Publications

Yelling in society is a common occurrence. Parents yell at their children, bosses yell at their employees and coaches yell at their athletes. Yet, in many cases the yelling coach exhibits unkind, loud in nature, and very personal statements. The purpose of this study was to better understand former athlete’s perspectives regarding their thoughts and experiences of their coaches yelling at them. For this study yelling will imply saying loud, unkind, personal comments towards the athlete. For this study 124 former athletes were surveyed regarding their experiences with a yelling coach. Generally, it was found that the former athletes did …

Why Does It Take Two To Tango? Lifetime Fitness Consequences Of Parental Care In A Burying Beetle, Ashlee N. Smith, J. Curtis Creighton, Mark C. Belk

Faculty Publications

In species that require parental care, each parent can either care for their offspring or leave them in the care of the other parent. For each parent this creates three possible parental care strategies: biparental care, uniparental (male or female) care, and uniparental desertion by either the male or female. The burying beetle, Nicrophorus orbicollis, typically exhibits biparental care of offspring, and thus provides a unique system that allows us to compare the fitness benefits of these parental care strategies in an unconfounded way. In this study, we assess the lifetime fitness of biparental care, uniparental care, and uniparental …

Swainson's Thrushes Do Not Show Strong Wing Selectivity Prior To Crossing The Gulf Of Mexico, Rachel T. Bolus, Robert H. Diehl, Frank R. Moore, Jill L. Deppe, Michael P. Ward, Jaclyn Smolinsky, Theodore J. Zenzal Jr.

Faculty Publications

During long-distance fall migrations, nocturnally migrating Swainson’s Thrushes often stop on the northern Gulf of Mexico coast before flying across the Gulf. To minimize energetic costs, trans-Gulf migrants should stop over when they encounter crosswinds or headwinds, and depart with supportive tailwinds. However, time constrained migrants should be less selective, balancing costs of headwinds with benefits of continuing their migrations. To test the hypotheses that birds select supportive winds and that selectivity is mediated by seasonal time constraints, we examined whether local winds affected Swainson’s Thrushes’ arrival and departure at Ft. Morgan, Alabama, USA at annual, seasonal, and nightly time …

Exopolysaccharides Regulate Calcium Flow In Cariogenic Biofilms, Monika Astasov-Frauenhoffer, Muth M. Varenganayil, Alan W. Decho, Tuomas Waltimo, Olivier Braissant

Faculty Publications

Caries-associated biofilms induce loss of calcium from tooth surfaces in the presence of dietary carbohydrates. Exopolysaccharides (EPS) provide a matrix scaffold and an abundance of primary binding sites within biofilms. The role of EPS in binding calcium in cariogenic biofilms is only partially understood. Thus, the aim of the present study is to investigate the relationship between the calcium dissolution rates and calcium tolerance of caries-associated bacteria and yeast as well as to examine the properties of EPS to quantify its binding affinity for dissolved calcium. Calcium dissolution was measured by dissolution zones on Pikovskaya’s agar. Calcium tolerance was assessed …

Wyoming Producer Priorities And Perceptions Of Alfalfa Insect Pests, Randa Jabbour, Shiri Noy

Faculty Publications

No abstract provided.

Bottom-Up Control Of Parasites, David S. Johnson, Richard W. Heard

Faculty Publications

Parasitism is a fundamental ecological interaction. Yet we understand relatively little about the ecological role of parasites compared to the role of free-living organisms. Bottom-up theory predicts that resource enhancement will increase the abundance and biomass of free-living organisms. Similarly, parasite abundance and biomass should increase in an ecosystem with resource enhancement. We tested this hypothesis in a landscape-level experiment in which salt marshes (60,000 m2 each) received elevated nutrient concentrations via flooding tidal waters for 11 yr to mimic eutrophication. Nutrient enrichment elevated the densities of the talitrid amphipod, Orchestia grillus, and the density and biomass of its trematode …

Hmgb1-Rage Pathway Drives Peroxynitrite Signaling-Induced Ibd-Like Inflammation In Murine Nonalcoholic Fatty Liver Disease, Varun Chandrashekaran, Ratanesh K. Seth, Diptadip Dattaroy, Firas Alhasson, Jacek Ziolenka, James Carson, Franklin G. Berger, Balaraman Kalyanaraman, Anna Mae Diehl, Saurabh Chatterjee

Faculty Publications

Recent clinical studies found a strong association of colonic inflammation and Inflammatory bowel disease (IBD)-like phenotype with NonAlcoholic Fatty liver Disease (NAFLD) yet the mechanisms remain unknown. The present study identifies high mobility group box 1 (HMGB1) as a key mediator of intestinal inflammation in NAFLD and outlines a detailed redox signaling mechanism for such a pathway. NAFLD mice showed liver damage and release of elevated HMGB1 in systemic circulation and increased intestinal tyrosine nitration that was dependent on NADPH oxidase. Intestines from NAFLD mice showed higher Toll like receptor 4 (TLR4) activation and proinflammatory cytokine release, an outcome strongly …

The Parasite Extinction Assessment & Red List: An Open-Source, Online Biodiversity Database For Neglected Symbionts, Colin J. Carlson, Oliver C. Muellerklein, Anna J. Phillips, Kevin R. Burgio, Giovanni Castaldo, Carrie A. Cizauskas, Graeme S. Cumming, Tad Dallas, Jorge Doña, Nyeema Harris, Roger Jovani, Zhongqi Miao, Heather Proctor, Hyun Seok Yoon, Wayne M. Getz

Faculty Publications

Parasite conservation is a rapidly growing field at the intersection of ecology, epidemiology, parasitology, and public health. The overwhelming diversity of parasitic life on earth, and recent work showing that parasites and other symbionts face severe extinction risk, necessitates infrastructure for parasite conservation assessments. Here, we describe the release of the Parasite Extinction Assessment & Red List (PEARL) version 1.0, an open-access database of conservation assessments and distributional data for almost 500 macroparasitic invertebrates. The current approach to vulnerability assessment is based on range shifts and loss from climate change, and will be expanded as additional data (e.g., host-parasite associations …

Open Accessarticle Food Shopping And Acquisition Behaviors In Relation To Bmi Among Residents Of Low-Income Communities In South Carolina, Angela D. Liese, Xiaonan Ma, Brett Hutto, Patrica A. Sharpe, Bethany A. Bell, Sarah Wilcox

Faculty Publications

Low-income areas in which residents have poor access to healthy foods have been referred to as “food deserts.” It is thought that improving food access may help curb the obesity epidemic. Little is known about where residents of food deserts shop and if shopping habits are associated with body mass index (BMI). We evaluated the association of food shopping and acquisition (e.g., obtaining food from church, food pantries, etc.) with BMI among 459 residents of low-income communities from two South Carolina counties, 81% of whom lived in United States Department of Agriculture-designated food deserts. Participants were interviewed about food shopping …

Initial Development Of Surface Fuel Models For The Netherlands, Brian P. Oswald, Nienke Brouwer, Ester Willemsen

Faculty Publications

Estimating the spread of wildland fire is growing concern in the Netherlands, where fire events at the wildland urban interface is a growing concern with a changing climate. A multi-year project was initiated in 2012 to obtain field-based fuel measurements to be used to estimate wildland fire spread for surface fire. The overall objective was to develop either custom fuel models or utilize existing Northern American fuel models to fuel conditions in some of the hazardous vegetation in the Netherlands. Over a four-year period, 96 plots were established, a wide variety of fuel parameters measured, and ANOVA (p ≤ 0.1) …

Biomass Estimations Of Invasives Yaupon, Chinese Privet And Chinese Tallow In East Texas Hardwood And Pine Ecosystems, Mike Tiller, Brian P. Oswald, Alyx Frantzen, Warren Conway, I-Kuai Hung

Faculty Publications

Forest understory fuels can have profound effects on fire behavior and crown fire initiation. Accurate fire behavior prediction in understory fuels is an essential component for estimating fire intensity and severity during wildfire and prescribed fire events. This study focused on estimating temporal and seasonal changes in fuel loading parameters associated with the expansion of invasive yaupon (Ilex vomitoria), Chinese privet (Ligustrum sinense), and Chinese tallow (Triadica sebifera) in East Texas pine and hardwood ecosystems. Fuel loading data of invasive species infested sites indicated significant increases in understory biomass when compared to 1988 estimates, suggesting a clear need to revise …

Parasite Biodiversity Faces Extinction And Redistribution In A Changing Climate, Colin J. Carlson, Kevin R. Burgio, Eric R. Dougherty, Anna J. Phillips, Veronica M. Bueno, Christopher F. Clements, Giovanni Castaldo, Tad Dallas, Carrie A. Cizauskas, Graeme S. Cumming, Jorge Doña, Nyeema C. Harris, Roger Jovani, Sergey Mironov, Oliver C. Muellerklein, Heather C. Proctor, Wayne M. Getz

Faculty Publications

Climate change is a well-documented driver of both wildlife extinction and disease emergence, but the negative impacts of climate change on parasite diversity are undocumented. We compiled the most comprehensive spatially explicit data set available for parasites, projected range shifts in a changing climate, and estimated extinction rates for eight major parasite clades. On the basis of 53,133 occurrences capturing the geographic ranges of 457 parasite species, conservative model projections suggest that 5 to 10% of these species are committed to extinction by 2070 from climate-driven habitat loss alone. We find no evidence that parasites with zoonotic potential have a …

Effects Of Tectonics And Large Scale Climatic Changes On The Evolutionary History Of Hyalomma Ticks, Arthur F. Sands, Dmitry A. Apanaskevich, Sonja Matthee, Ivan G. Horak, Alan Harrison, Shahid Karim, Mohammad K. Mohammad, Kosta Y. Mumcuoglu, Rupika S. Rajakaruna, Maria M. Santos-Silva, Joshua Kamani, Conrad A. Matthee

Faculty Publications

Hyalomma Koch, 1844 are ixodid ticks that infest mammals, birds and reptiles, to which 27 recognized species occur across the Afrotropical, Palearctic and Oriental regions. Despite their medical and veterinary importance, the evolutionary history of the group is enigmatic. To investigate various taxonomic hypotheses based on morphology, and also some of the mechanisms involved in the diversification of the genus, we sequenced and analysed data derived from two mtDNA fragments, three nuclear DNA genes and 47 morphological characters. Bayesian and Parsimony analyses based on the combined data (2242 characters for 84 taxa) provided maximum resolution and strongly supported the monophyly …

Connecting The Dots: Stopover Strategies Of An Intercontinental Migratory Songbird In The Context Of The Annual Cycle, Kristina Paxton, Frank R. Moore

Faculty Publications

The phases of the annual cycle for migratory species are inextricably linked. Yet, less than five percent of ecological studies examine seasonal interactions. In this study, we utilized stable hydrogen isotopes to geographically link individual black-and-white warblers (Mniotilta varia) captured during spring migration with breeding destinations to understand a migrant's stopover strategy in the context of other phases of the annual cycle. We found that stopover strategy is not only a function of a bird's current energetic state, but also the distance remaining to breeding destination and a bird's time-schedule, which has previously been linked to habitat conditions experienced …

Ethanol-Induced Stress Response Of Staphylococcus Aureus, Jasmine M. Pando, Richard F. Pfeltz, Jesus A. Cuaron, Vijayaraj Nagarajan, Mukti N. Mishra, Nathaniel J. Torres, Mohamed O. Elasri, Brian J. Wilkinson, John E. Gustafson

Faculty Publications

Transcriptional profiles of 2 unrelated clinical methicillin-resistant Staphylococcus aureus (MRSA) isolates were analyzed following 10% (v/v) ethanol challenge (15 min), which arrested growth but did not reduce viability. Ethanol-induced stress (EIS) resulted in differential gene expression of 1091 genes, 600 common to both strains, of which 291 were upregulated. With the exception of the downregulation of genes involved with osmotic stress functions, EIS resulted in the upregulation of genes that contribute to stress response networks, notably those altered by oxidative stress, protein quality control in general, and heat shock in particular. In addition, genes involved with …

Amblyomma Maculatum Secis Binding Protein 2 And Putative Selenoprotein P Are Indispensable For Pathogen Replication And Tick Fecundity, Khemraj Budachetri, Gary Crispell, Shahid Karim

Faculty Publications

Selenium, a vital trace element, is incorporated into selenoproteins to produce selenocysteine. Our previous studies have revealed an adaptive co-evolutionary process that has enabled the spotted fever-causing tick-borne pathogen Rickettsia parkeri to survive by manipulating an antioxidant defense system associated with selenium, which includes a full set of selenoproteins and other antioxidants in ticks. Here, we conducted a systemic investigation of SECIS binding protein 2 (SBP2) and putative selenoprotein P (SELENOP) by transcript silencing in adult female Gulf-coast ticks (Amblyomma maculatum). Knockdown of the SBP2 and SELENOP genes depleted the respective transcript levels of these tick selenogenes, and …

Assessing The Vegetative Diversity Of An East Texas Golf Course Using Principles Of Landscape Ecology, Brian P. Oswald, Penny G. Lanham, Hans M. Williams, David Kulhavy

Faculty Publications

The objectives of this study was to determine the vegetative diversity and the effects of the edge between fairways (introduced patches) and out-of-bounds areas (remnant patches) to determine if such management activities influence plant diversity. This study was conducted at the Pineywoods Country Club in the Pineywoods Region of East Texas near Nacogdoches, TX, USA by assessing the spatial distribution of these matrices and patches and their influence on edge effect composition and structure in the matrix; and, if species diversity and composition differed between these edges and interior of the matrices. Nested plots were placed along transects and canopy …

Reconstruction Of Piñon-Juniper Forest Structure To Examine Historic Wildlife Habitat Characteristics In The Davis Mountains, Usa, Brian P. Oswald, John R. Lanham, James C. Kroll, Mohammed M. Bataineh, Yanli Zhang

Faculty Publications

Changes in piñon-juniper (Pinus spp., Juniperus spp.) communities across the southwestern United States have often decreased ecological diversity of the understory and increases of exotic species. Reconstructing age and establishment patterns provides essential understanding to guide treatments and management for anthropogenically-altered forests. The goal of this study was to determine how patterns of piñon and juniper growth in the Davis Mountains, Texas, varied over time and how this pattern influenced wildlife habitat of several indicator species. Establishment patterns and basal area growth progression were identified, canopy cover estimates regressed from pre-developed canopy regression equations to re-construct historic forest stand …

In Vivo Cloning Of Up To 16 Kb Plasmids In E. Coli Is As Simple As Pcr, Faqing Huang, Joseph Rankin Spengler, Allen Yang Huang

Faculty Publications

The precise assembly of defined DNA sequences into plasmids is an essential task in bioscience research. While a number of molecular cloning techniques have been developed, many methods require specialized expensive reagents or laborious experimental procedure. Not surprisingly, conventional cloning techniques based on restriction digestion and ligation are still commonly used in routine DNA cloning. Here, we describe a simple, fast, and economical cloning method based on RecA- and RecET-independent in vivo recombination of DNA fragments with overlapping ends using E. coli. All DNA fragments were prepared by a 2-consecutive PCR procedure with Q5 DNA polymerase and used …