Life Sciences Commons^™

Structure–Activity Relationship-Based Chemical Classification Of Highly Imbalanced Tox21 Datasets, Gabriel Idakwo, Sundar Thangapandian, Joseph Luttrell, Yan Li, Nan Wang, Zhaoxian Zhou, Huixiao Hong, Bei Yang, Chaoyang Zhang, Ping Gong

Faculty Publications

The specificity of toxicant-target biomolecule interactions lends to the very imbalanced nature of many toxicity datasets, causing poor performance in Structure–Activity Relationship (SAR)-based chemical classification. Undersampling and oversampling are representative techniques for handling such an imbalance challenge. However, removing inactive chemical compound instances from the majority class using an undersampling technique can result in information loss, whereas increasing active toxicant instances in the minority class by interpolation tends to introduce artificial minority instances that often cross into the majority class space, giving rise to class overlapping and a higher false prediction rate. In this study, in order to improve the …

Dystonia 16 (Dyt16) Mutations In Pact Cause Dysregulated Pkr Activation And Eif2Α Signaling Leading To A Compromised Stress Response, Samuel B. Burnett, Lauren S. Vaughn, Nutan Sharma, Ronit Kulkarni, Rekha C. Patel

Faculty Publications

Dystonia 16 (DYT16) is caused by mutations in PACT, the protein activator of interferon-induced double-stranded RNA-activated protein kinase (PKR). PKR regulates the integrated stress response (ISR) via phosphorylation of the translation initiation factor eIF2α. This post-translational modification attenuates general protein synthesis while concomitantly triggering enhanced translation of a few specific transcripts leading either to recovery and homeostasis or cellular apoptosis depending on the intensity and duration of stress signals. PKR plays a regulatory role in determining the cellular response to viral infections, oxidative stress, endoplasmic reticulum (ER) stress, and growth factor deprivation. In the absence of stress, both PACT and …

Biochemical And Genetic Analysis Of Ecm14, A Conserved Fungal Pseudopeptidase, R. Christian Mcdonald, Matthew James Schott, Temitope A. Idowu, Peter J. Lyons

Faculty Publications

© 2020, The Author(s). Background: Like most major enzyme families, the M14 family of metallocarboxypeptidases (MCPs) contains a number of pseudoenzymes predicted to lack enzyme activity and with poorly characterized molecular function. The genome of the yeast Saccharomyces cerevisiae encodes one member of the M14 MCP family, a pseudoenzyme named Ecm14 proposed to function in the extracellular matrix. In order to better understand the function of such pseudoenzymes, we studied the structure and function of Ecm14 in S. cerevisiae. Results: A phylogenetic analysis of Ecm14 in fungi found it to be conserved throughout the ascomycete phylum, with a group of …

Chloramination Of Iopamidol- And Bromide-Spiked Waters Containing Natural Organic Matter, Nana Osei B Ackerson, Hannah K. Liberatore, Susan D. Richardson, Micheal J. Plewa, Thomas A. Ternes, Stephen E. Duirk

Faculty Publications

Iopamidol (an iodinated X-ray contrast medium) and bromide are precursors in the formation of halogenated disinfection byproducts (DBPs). The interactions of these precursors are vital to elucidate the formation of halogenated DBPs during chloramination. This work investigated the formation of total organic halogen and select individual DBPs in two laboratory-chloraminated source waters containing iopamidol and bromide. Experiments were carried out in batch reactors containing Barberton source water (BSW) and Cleveland BSW (CSW), spiked with iopamidol (5 mu M), bromide (15 mu M), and 100 mu M monochloramine. Total organic iodine concentrations were approximately equal regardless of source water since they …

Rumen And Serum Metabolomes In Response To Endophyte-Infected Tall Fescue Seed And Isoflavone Supplementation In Beef Steers, Taylor B. Ault-Seay, Emily A. Melchior-Tiffany, Brooke A. Clemmons

Faculty Publications

Fescue toxicosis impacts beef cattle production via reductions in weight gain and muscle development. Isoflavone supplementation has displayed potential for mitigating these e ects. The objective of the current study was to evaluate isoflavone supplementation with fescue seed consumption on rumen and serum metabolomes. Angus steers (n = 36) were allocated randomly in a 2 2factorial arrangement of treatments including endophyte-infected (E+) or endophyte-free (E ) tall fescue seed, with (P+) or without (P ) isoflavones. Steers were provided a basal diet with fescue seed for 21 days, while isoflavones were orally administered daily. Following the trial, blood and rumen …

Transport Of N-Cd And Pre-Sorbed Pb In Saturated Porous Media, Salahaddin Kamrani, Vahab Amiri, Mosleh Kamrani, Mohammed Baalousha

Faculty Publications

Carbon dots (CDs) are a new type of nanomaterials of the carbon family with unique characteristics, such as their small size (e.g., <10 nm), high water solubility, low toxicity, and high metal affinity. Modification of CDs by Nitrogen functional groups (N-CDs) enhances their metal adsorption capacity. This study investigated the influences of pH (4, 6, and 9), ionic strength (1, 50, and 100 mM), and cation valency (Na⁺ and Ca²⁺) on the competitive adsorption of Pb to quartz and N-CD surfaces, the transport and retention of N-CDs in saturated porous media, and the capacity of N-CDs to mobilize pre-adsorbed Pb in quartz columns. Pb adsorption was higher on N-CDs than on quartz surfaces and decreased with increases in ionic strength (IS) and divalent cations (Ca²⁺) concentration. N-CD mobility in quartz columns was highest at pH of 9- and 1-mM monovalent cations …

Providing Transgender Patient Care: Athletic Trainers' Compassion And Lack Of Preparedness, Lindsey E. Eberman, Zachary K. Winkelmann Phd, Lat, Atc, Emma A. Nye, Kelcey C. Granger, Stacy E. Walker

Faculty Publications

Context

Previous researchers have indicated that athletic trainers (ATs) had a favorable view of treating transgender patients, yet the ATs did not perceive themselves as competent in their patient care knowledge or abilities.

Objective

To gain more in-depth information about ATs' knowledge and experiences regarding the health care needs of transgender student-athletes.

Design

Mixed-methods study.

Setting

Individual, semistructured follow-up interviews.

Patients or Other Participants

Fifteen ATs (4 men, 10 women, 1 transgender female; age = 34 ± 9 years, experience = 11 ± 8 years) who took part in a cross-sectional survey in April 2018.

Main Outcome Measure(s)

The interviews …

Weighing The Evidence For The Abundant-Center Hypothesis, Tad Dallas, Luca Santini, Alan Hastings

Faculty Publications

The abundant-center hypothesis posits that species density should be highest in the center of the geographic range or climatic niche of a species, based on the idea that the center of either will be the area with the highest demographic performance (e.g., greater fecundity, survival, or carrying capacity). While intuitive, current support for the hypothesis is quite mixed. Here, we discuss the current state of the abundant-center hypothesis, highlighting the relatively low level of support for the relationship. We then discuss the potential reasons for this lack of empirical support, emphasiz-ing the inherent ecological complexity which may prevent the observation …

Natalia Shustova Answers Questions About 15 Years Of Research On Covalent Organic Frameworks, Natalia B. Shustova Prof. Dr.

Faculty Publications

No abstract provided.

Interleukin-17a Facilitates Chikungunya Virus Infection By Inhibiting Ifn-Α2 Expression, Biswas Neupane, Dhiraj Acharya, Farzana Nazneen, Gabriel Gonzalez-Fernandez, Alex Sutton Flynt, Fengwei Bai

Faculty Publications

Interferons (IFNs) are the key components of innate immunity and are crucial for host defense against viral infections. Here, we report a novel role of interleukin-17A (IL-17A) in inhibiting IFN-α2 expression thus promoting chikungunya virus (CHIKV) infection. CHIKV infected IL-17A deficient (Il17a^−/−) mice expressed a higher level of IFN-α2 and developed diminished viremia and milder footpad swelling in comparison to wild-type (WT) control mice, which was also recapitulated in IL-17A receptor-deficient (Il17ra^−/−) mice. Interestingly, IL-17A selectively blocked IFN-α2 production during CHIKV, but not West Nile virus (WNV) or Zika virus (ZIKV), infections. Recombinant IL-17A …

Inferring Life History Characteristics Of The Oceanic Whitetip Shark Carcharhinus Longimanus From Vertebral Bomb Radiocarbon, Michelle S. Passerotti, Allen H. Andrews, Lisa J. Natanson

Faculty Publications

Oceanic whitetip sharks Carcharhinus longimanus are a cosmopolitan epipelagic species that was once prolific throughout the tropics and subtropics but was recently listed as Critically Endangered by the International Union for the Conservation of Nature and as Threatened under the United States Endangered Species Act. Although historically conspicuous in oceanic fisheries catches, relatively little is known about their habitat use, movement, and life history during migration. Given the paucity of data on migratory patterns and lack of age estimate validation available for this species, we evaluated vertebral growth bands for bomb radiocarbon (14C) patterns to derive additional information on these …

Collegiate Student-Athletes' Perceptions Of Patient-Centered Care Delivered By Athletic Trainers, Ansley Smallen Redinger, Zachary K. Winkelmann Phd, Lat, Atc, Lindsey E. Eberman

Faculty Publications

Context

The health care core competencies indicate that all medical professionals should provide patient-centered care (PCC), which is defined as care that is respectful and responsive to the patient's values and preferences, during each encounter. Objective

To identify collegiate student-athletes' definitions of PCC and measure their perceived level of PCC from an athletic trainer (AT). Design

Cross-sectional study. Setting

Mixed-methods survey. Patients or Other Participants

A total of 610 (age = 19 ± 1 year) National Collegiate Athletic Association student-athletes completed the survey. Main Outcome Measure(s)

The survey consisted of 1 open-ended question that prompted the participant to define PCC …

Classification Of Planetary Craters Using Outline-Based Morphometrics, Thomas J. Slezak, Jani Radebaugh, Eric H. Christiansen, Mark C. Belk

Faculty Publications

The morphologies of craters on planetary surfaces reveal clues about the geologic mechanisms by which they originate and subsequently evolve, as well as the materials and physical variables inherent to the environment in which they formed. We carried out a quantitative multivariate analysis of shape descriptors derived from the outlines of craters formed by volcanic processes on Mars, Io, and Earth and by impact cratering on the Moon using elliptic Fourier analysis (EFA) and the Zahn-Roskies (Z-R) shape function. Canonical variate analysis (CVA) was used to construct a statistical model of differences between the crater groups to classify …

Prevalence Of Eating Disorder Risk And Body Image Dissatisfaction Among Rotc Cadets, Allison Smith, Dawn Emerson, Zachary Winkelmann, Devin Potter, Toni Torres-Mcgehee

Faculty Publications

Injury risk is multifactorial including non-modifiable and modifiable factors such as nutrition and mental health. The purpose of this study was to estimate eating disorder risk and body image (BI) dissatisfaction among Reserve Officers Training Corps (ROTC) cadets. A total of 102 (male: = 75, female: = 27; age: 20 ± 2 years) ROTC cadets self-reported height, current and ideal weight, and completed the Eating Attitudes Test-26 (EAT-26) and self-perceived BI current and perceived sex-specific figural stimuli. The overall eating disorder risk for ROTC cadets was 32.4%. No significant differences were found when comparing sex, ethnicity, or military branch. Overall …

Microbiological, Physicochemical, And Immunological Analysis Of A Commercial Cashew Nut-Based Yogurt, Christopher P. Mattison, Kayanush Aryana, Kristen Clermont, Eric Prestenburg, Steven W. Lloyd, Casey .. Grimm, Richard L. Wasserman

Faculty Publications

Nut-based milks and yogurts are gaining popularity, but may not offer the same benefits as dairy yogurts to consumers. Cashew nuts often cause severe allergic reactions, and cashew nut allergens are stable to several types of processing. To compare its characteristics to dairy yogurt and characterize the effects of fermentation on the Ana o 1-3 cashew nut allergens, a commercial yogurt made from cashew nuts (Cashewgurt) was evaluated for microbiological, physiochemical, and immunological properties. Average counts for lactobacilli and Streptococcus thermophilus were greater than 10 million colony forming units per milliliter, indicating the capacity to provide a health benefit. Cashewgurt …

A Novel Mutation Of The Narrow Leaf 1 Gene Adversely Affects Plant Architecture In Rice (Oryza Sativa L.), Prasanta K. Subudhi, Richard S. Garcia, Sapphire Coronejo, Teresa B. De Leon

Faculty Publications

Plant architecture is critical for enhancing the adaptability and productivity of crop plants. Mutants with an altered plant architecture allow researchers to elucidate the genetic network and the underlying mechanisms. In this study, we characterized a novel nal1 rice mutant with short height, small panicle, and narrow and thick deep green leaves that was identified from a cross between a rice cultivar and a weedy rice accession. Bulked segregant analysis coupled with genome re-sequencing and cosegregation analysis revealed that the overall mutant phenotype was caused by a 1395-bp deletion spanning over the last two exons including the transcriptional end site …

Speciation-By-Depth On Coral Reefs: Sympatric Divergence With Gene Flow Or Cryptic Transient Isolation?, Carlos Prada, Michael E. Hellberg

Faculty Publications

The distributions of many sister species in the sea overlap geographically but are partitioned along depth gradients. The genetic changes leading to depth segregation may evolve in geographic isolation as a prerequisite to coexistence or may emerge during primary divergence leading to new species. These alternatives can now be distinguished via the power endowed by the thousands of scorable loci provided by second-generation sequence data. Here, we revisit the case of two depth-segregated, genetically isolated ecotypes of the nominal Caribbean candelabrum coral Eunicea flexuosa. Previous analyses based on a handful of markers could not distinguish between models of genetic exchange …

Significance Of Viral Activity For Regulating Heterotrophic Prokaryote Community Dynamics Along A Meridional Gradient Of Stratification In The Northeast Atlantic Ocean, Kristina D.A. Mojica, Corina P.D. Brussaard

Faculty Publications

How microbial populations interact influences the availability and flux of organic carbon in the ocean. Understanding how these interactions vary over broad spatial scales is therefore a fundamental aim of microbial oceanography. In this study, we assessed variations in the abundances, production, virus and grazing induced mortality of heterotrophic prokaryotes during summer along a meridional gradient in stratification in the North Atlantic Ocean. Heterotrophic prokaryote abundance and activity varied with phytoplankton biomass, while the relative distribution of prokaryotic subpopulations (ratio of high nucleic acid fluorescent (HNA) and low nucleic acid fluorescent (LNA) cells) was significantly correlated to phytoplankton mortality mode …

Predators As Agents Of Selection And Diversification, Jerald B. Johnson, Mark C. Belk

Faculty Publications

Predation is ubiquitous in nature and can be an important component of both ecological and evolutionary interactions. One of the most striking features of predators is how often they cause evolutionary diversification in natural systems. Here, we review several ways that this can occur, exploring empirical evidence and suggesting promising areas for future work. We also introduce several papers recently accepted in Diversity that demonstrate just how important and varied predation can be as an agent of natural selection. We conclude that there is still much to be done in this field, especially in areas where multiple predator species prey …

Patterning A Leaf By Establishing Polarities, Darren Manuela, Mingli Xu

Faculty Publications

Leaves are the major organ for photosynthesis in most land plants, and leaf structure is optimized for the maximum capture of sunlight and gas exchange. Three polarity axes, the adaxial–abaxial axis, the proximal-distal axis, and the medial-lateral axis are established during leaf development to give rise to a flattened lamina with a large area for photosynthesis and blades that are extended on petioles for maximum sunlight. Adaxial cells are elongated, tightly packed cells with many chloroplasts, and their fate is specified by HD-ZIP III and related factors. Abaxial cells are rounder and loosely packed cells and their fate is established …

Hydroxychloroquine Prophylaxis For Covid-19, David D. Busath

Faculty Publications

It is common in medicine that simple, inexpensive remedies are held hostage to medical prejudice, financial or political interest, and legal precedent. The purpose of this review is to take the point of view of the victims of COVID-19 and address whether scientific information, including randomized-control trials, can answer whether the hydroxychloroquine should be dispensed for those testing positive and their immediate recent contacts at the point of testing. Although the FDA in the United States is yet to be convinced, the demonstration of positive effects in clinical trials cannot be ignored and there is a large amount of information …

Comparative Efficacies Of Calmare Therapy And Transcutaneous Electrical Nerve Stimulation In Randomized Peripheral Neuropathy Subjects With Resting State Fmri Monitoring, Ty A. Bodily, Logan Edvalson, Jordan B. Peacock, Zack M. Bradshaw, Carson Hart, Cameron Ernst, Samuel Biggs, David D. Busath

Faculty Publications

Clinical reports of Calmare protocol efficacy suggest enhanced durability compared to TENS and the possibility changes in resting fMRI connectivity. The objective was to compare peripheral neuropathy pain relief and resting fMRI changes with Calmare and TENS treatments. Randomized double-blind trials performed in August 2015 and between August 2016 and November 2017, with 18 and 20 human peripheral neuropathy subjects, respectively. The initial trial examined effects of a single session while the latter trial examined the effects of a course of ten treatment sessions on consecutive weekdays. fMRI scans were examined for changes in blood flow correlations and connectivity. Subjective …

Use Of Altmetrics To Analyze Scholarworks In Natural Resource Management, David L. Kulhavy, R Philip Reynolds, Daniel R. Unger, Matthew W. Mcbroom, I-Kuai Hung, Yanli Zhang

Faculty Publications

Digital preservation of library materials has increased the need for methods to access the documents and contents maintained in digital archives. The use of altmetrics to quantify the impact of scholarly works, including PlumX, is increasing readership by listing articles in reference services. The outreach from the digital repository ScholarWorks at Stephen F. Austin State University (SFASU) highlights the impact within the natural resources community from Digital Commons, Forest Sciences Commons; and from the Natural Products Chemistry and Pharmacognosy Commons. The use of PlumX altmetrics was examined to evaluate usage, impact, and digital audience downloads for the Arthur Temple College …

A Review Of Integrative Imputation For Multi-Omics Datasets, Meng Song, Jonathan Greenbaum, Joseph Luttrell, Weihua Zhou, Chong Wu, Hui Shen, Ping Gong, Chaoyang Zhang, Hong Wen Deng

Faculty Publications

Multi-omics studies, which explore the interactions between multiple types of biological factors, have significant advantages over single-omics analysis for their ability to provide a more holistic view of biological processes, uncover the causal and functional mechanisms for complex diseases, and facilitate new discoveries in precision medicine. However, omics datasets often contain missing values, and in multi-omics study designs it is common for individuals to be represented for some omics layers but not all. Since most statistical analyses cannot be applied directly to the incomplete datasets, imputation is typically performed to infer the missing values. Integrative imputation techniques which make use …

Reconstruction Of Piñon–Juniper Woodlands In The Sky Islands Of The Davis Mountains, Texas, Usa, Mohammad Bataineh, Brian P. Oswald, Hans M. Williams, Dan Unger, I-Kuai Hung

Faculty Publications

Piñon (Pinus spp. L.)–juniper (Juniperus spp. L.) woodlands’ historical stand structures were recreated to provide reference conditions and document long‐term changes in the Sky Islands of the Davis Mountains, Texas. Restoration of these isolated woodlands requires insights into the range of variability in current and historical stand structures, as well as an understanding of the spatiotemporal establishment and recruitment patterns of tree species. With drastic changes in forests and woodlands of the Southwestern United States widely reported, the main objective of this study was to reconstruct woodland tree temporal and spatial establishment patterns. A stratified random sampling approach was used …

The Dynamic Trophic Niche Of An Island Bird Of Prey, Ulises Balza, Nicolas A. Lois, Michael J. Polito, Klemens Puetz, Amira Saalom, Andrea Raya Rey

Faculty Publications

Optimal foraging theory predicts an inverse relationship between the availability of preferred prey and niche width in animals. Moreover, when individuals within a population have identical prey preferences and preferred prey is scarce, a nested pattern of trophic niche is expected if opportunistic and selective individuals can be identified. Here, we examined intraspecific variation in the trophic niche of a resident population of striated caracara (Phalcoboenus australis) on Isla de los Estados (Staten Island), Argentina, using pellet and stable isotope analyses. While this raptor specializes on seabird prey, we assessed this population's potential to forage on terrestrial prey, especially invasive …

Fish Assemblages Associated With Artificial Reefs Assessed Using Multiple Gear Types In The Northwest Gulf Of Mexico, Jeffrey D. Plumlee, Kaylan M. Dance, Michael A. Dance, Hay R. Rooker, Thomas C. Tinhan, J. Brooke Shipley, R. J. David Wells

Faculty Publications

Quantitative surveys of fishes associated with artificial reefs in the northwest Gulf of Mexico were conducted over a 4-yr period (2014-2017). Artificial reefs surveyed were comprised of three types: concrete structures, rig jackets, and decommissioned ships. All reefs were surveyed using vertical long line ( VLL), fish traps, and Adaptive Resolution Imaging Sonar (ARIS 1800). Mean fish abundance did not significantly differ using VLL [1.7 ind set(-1) (SD 2.2)] among the three reef types. However, relative abundance among all fishes collected was significantly highest on rig reefs using traps [6.2 ind soak(-1) (SD 3.8)], while results from sonar surveys indicated …

All-Atomic Molecular Dynamic Studies Of Human And Drosophila Cdk8: Insights Into Their Kinase Domains, The Lxxll Motifs, And Drug Binding Site, Wu Xu, Xiao-Jun Xie, Ali K. Faust, Mengmeng Liu, Xiao Li, Feng Chen, Ashlin A. Naquin, Avery C. Walton, Peter W. Kishbaugh, Jun-Yuan Ji

Faculty Publications

Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using molecular dynamics simulations, combined with functional analyses in Drosophila. Specifically, we evaluated the structural differences between hCDK8 and dCDK8 to predict the effects of the LXXLL motif mutation (AQKAA), the P154L mutations, and drug binding on local structures of the CDK8 proteins. First, we have observed that both the LXXLL motif and the kinase activity of CDK8 …

Reducing Host Dna Contamination In 16s Rrna Gene Surveys Of Anthozoan Microbiomes Using Pna Clamps, Alicia M. Reigel, Sarah M. Owens, Michael E. Hellberg

Faculty Publications

Efforts to study the microbial communities associated with corals can be limited by inefficiencies in the sequencing process due to high levels of host amplification by universal bacterial 16S rRNA gene primers. Here, we develop an inexpensive peptide nucleic acid (PNA) clamp that binds to a target sequence of host DNA during PCR and blocks amplification. We then test the ability of this PNA clamp to mitigate host contamination and increase overall microbial sequence coverage on samples from three coral species: the gorgoniansEunicea flexuosaandGorgonia ventalina,and the scleractinianPorites panamensis. The 20-bp PNA clamp was designed using DNA fromE. flexuosa. Adding the …

Oil-Producing Metabolons Containing Dgat1 Use Separate Substrate Pools From Those Containing Dgat2 Or Pdat, Anushobha Regmi, Jay Shockey, Hari Kiran Kotapati, Philip D. Bates

Faculty Publications

© 2020 American Society of Plant Biologists. All rights reserved. Seed triacylglycerol (TAG) biosynthesis involves a metabolic network containing multiple different diacylglycerol (DAG) and acyl donor substrate pools. This network of pathways overlaps with those for essential membrane lipid synthesis and utilizes multiple different classes of TAG biosynthetic enzymes. Acyl flux through this network ultimately dictates the final oil fatty acid composition. Most strategies to alter seed oil composition involve the overexpression of lipid biosynthetic enzymes, but how these enzymes are assembled into metabolons and which substrate pools are used by each is still not well understood. To understand the …