Life Sciences Commons^™

Large-Scale Integrative Analysis Of Soybean Transcriptome Using An Unsupervised Autoencoder Model, Lingtao Su, Chunhui Xu, Shuai Zeng, Li Su, Trupti Joshi, Gary Stacey, Dong Xu

Biomedical Sciences

Plant tissues are distinguished by their gene expression patterns, which can help identify tissue-specific highly expressed genes and their differential functional modules. For this purpose, large-scale soybean transcriptome samples were collected and processed starting from raw sequencing reads in a uniform analysis pipeline. To address the gene expression heterogeneity in different tissues, we utilized an adversarial deconfounding autoencoder (AD-AE) model to map gene expressions into a latent space and adapted a standard unsupervised autoencoder (AE) model to help effectively extract meaningful biological signals from the noisy data. As a result, four groups of 1,743, 914, 2,107, and 1,451 genes were …

Teen Reactions To A Self-Representational Avatar: A Qualitative Exploration, Emily Baysden, Ninna Mendoza, Chishinga Callender, Zhigang Deng, Debbe Thompson

Children’s Nutrition Research Center Staff Publications

Purpose: This research presents findings from a qualitative exploration of the reactions of adolescents (12-14 years old) to navigating an exergame with an avatar created from multiple scans of the player (referred to as a self-representational avatar).

Methods: Post-gameplay interviews were conducted with adolescents following participation in a 20-min laboratory session (21.2 ± 0.8 min, mean ± SD) where the self-representational avatar was navigated through an exergame. Verbatim transcripts (n = 40) were coded and analyzed by 2 independent coders using hybrid thematic analysis for this secondary data analysis. Codes were reviewed to identify themes representing adolescents' reactions.

Results: Four …

C.T. Trowell Collection Of Roland M. Harper, Zach S. Henderson Library Special Collections

Finding Aids

This collection consists of photocopies of articles and book excerpts written by Roland M. Harper for publication in scholarly journals and various other botanical bulletins. Harper's works focus on botany, conservation, and social conditions, primarily in the southeastern United States. Spanning from 1900 - 2008, additional documents, photographs and audio visual materials pertaining to Roland M. Harper's family history is included.

Find this collection in the University Libraries' catalog.

Global Education In Stem And Healthcare: Implications Of Covid-19, Jessica Hallet, Santanu De

Biology Faculty Articles

The Coronavirus Infectious Disease 2019 (COVID-19) was declared a pandemic in March of 2020. Since then, most schools, colleges, and universities across the globe stopped delivering classes face-to-face and transitioned into virtual modalities of instruction. This reformation of academics has had an impact on every field of study, especially those students in the areas of Science, Technology, Engineering, and Mathematics (STEM), and in the realm of healthcare education. Ranging from middle/high school to undergraduate and graduate programs, STEM degrees require intensive curricula integrating extensive lectures on theoretical topics and laboratory exercises to apply those concepts in a practical setting. Likewise, …

Mitonuclear Mismatch Is Associated With Increased Male Frequency, Outcrossing, And Male Sperm Size In Experimentally-Evolved C. Elegans, Brent W. Bever, Zachary P. Dietz, Jennifer Anne Sullins, Ariana M. Montoya, Ulfar Bergthorsson, Vaishali Katju, Suzanne Estes

Biology Faculty Publications and Presentations

We provide a partial test of themitonuclear sex hypothesiswith the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. Among facultatively outcrossing lines, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested—nuclear isp-1, mitochondrial cox-1 and ctb-1, and an isp-1 IV; ctb-1M mitonuclear double mutant—and confirmed for …

A Literary Examination Of The Efficacy Of Zoological Conservation In The United States Versus Foreign Efforts, Madeleine M. Lecorre

University Honors Theses

Falling into the top four threats to biodiversity, human activity is impacting species around the globe like never before. Zoological conservation of threatened species aids in the support and reestablishment of these dwindling populations. The examination of conservation work done in the U.S compared to foreign efforts provides insight into strengths, reveals weaknesses, and will help us better serve threatened species around the world. The status of conservation in the U.S. as well as foreign efforts were assessed through literary review of published reports from accredited organizations. As zoologic conservation aims to conserve threatened species, it is also important to …

Impacts Of Temperature And Carbon Dioxide On Boro Rice Production, Sabiha Ferdous

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

There are different anticipated impacts of climate change (CC) on agriculture all over the world. Bangladesh as a developing country has potential vulnerability and negative impacts on CC. This change in meteorological parameters creates negative impacts on agricultural production which is a threat to food security and economic development. The country has recently achieved food security in rice which is mainly due to increased yields and area coverage of irrigated dry season (Boro) rice over the last decades. It is necessary to predict the future Boro rice production in accordance with CC as well as take supplementary actions to ensure …

Effects Of Methyl Salicylate (Mesa) On The Physiology And Biochemical Characteristics Of Rice Under Salinity Stress At Seedling Stage, Thu Ha Thi Pham, Truong Minh Tuan, Pham Thi Thu Hien, Tran Thi My Hiep, Chau Thi Da

The Philippine Agricultural Scientist

Salt stress negatively affects crop survival, growth, development, and yield. Methyl salicylate (MeSA) is synthesized from salicylic acid (SA) which is a volatile organic compound that is responsible for inducing defense mechanisms in plants and also has a protective role in stress sensitivity. The objective of this study was to examine the effect of different concentrations of methyl salicylate (MeSA) on the physiological and biochemical characteristics of two rice varieties GRIS4 (G1) and GRIS5 (G2) under salt stress at the seedling stage. Five hundred seeds of each variety were treated with different doses of MeSA (0, 0.1, 0.5, and 1.0 …

Effect Of Workers Density On Insect Pest Incidence And Colony Development Of Bumblebees, Bombus Terrestris (L.) (Hymenoptera: Apidae), Marium Fatima, Asim Gulzar, Munir Ahmed, Farid Asif Shaheen, Muhammad Tariq, Tariq Mukhtar

The Philippine Agricultural Scientist

Insect pollination improves essential nutrients and qualities of pollinating plants. Approximately 90% of flowering plants and 35% of crops require insect pollination. Bees play a vital role in pollination in natural and agricultural systems. Managed bees have extensively been used for pollination. Unfortunately, the native bee population has been waning globally. Commercial bee-rearing experiences different rearing problems i.e. food, environment, and spatial conditions within colonies. In this research, the impact of different densities of workers within colonies of Bombus terrestris L. was observed on colony development and pest incidence. Different worker densities i.e. 60-70, 80-90,110-120 and 140-150, respectively, were maintained …

Relating Metabolic Phenotypes To Movement Behavior In Brook Trout, Jacob E. Bowman

All NMU Master's Theses

Brook trout movement-related life history strategies vary considerably and range from individuals that stay within the same 100 meters their entire life to individuals that are potamodromous or anadromous. Potential drivers of movement life histories have been the subject of much research in fish, with genetic subpopulation explanations often failing to explain the phenomenon. Metabolic phenotypes have been suggested as a possible driver for expression of different movement life histories. I investigated if metabolic phenotypes are related to movement strategies within a population of brook trout (Salvelinus fontinalis) in Unnamed Creek, a tributary to the Rock River, Alger …

Comparative Evaluation Of Physicochemical And Fermentative Responses Of Three Sorghum Varieties From Dryland And Irrigated Land And The Properties Of Proteins From Distillers’ Grains, Jikai Zhao, Thomas Weiss, Zhenjiao Du, Shan Hong, Scott R. Bean, Yonghui Li, Donghai Wang

School of Earth, Environmental, & Marine Sciences Faculty Publications

Three sorghum varieties [waxy sorghum (WS), high protein sorghum (HPS), and normal sorghum (NS)] grown under dryland and irrigated conditions were evaluated with respect to the physicochemical and fermentative properties. The proteins were extracted from wet distillers' grains with solubles (WDGS) and characterized in terms of purity and in vitro digestibility. Starch, crude protein, crude fat, and fiber contents of the sorghums ranged from 64.16 to 68.05 g/100 g, 11.49–13.54 g/100 g, 2.45–2.98 g/100 g, and 1.62–1.80 g/100 g, respectively. For the same variety, the sorghums grown under dryland conditions had higher protein (0.33–0.91 g/100 g) and lower …

Geospatial Assessment Of Groundwater Quality With The Distinctive Portrayal Of Heavy Metals In The United Arab Emirates, Imen Ben Salem, Yousef Nazzal, Fares M. Howari, Manish Sharma, Jagadish Kumar Mogaraju, Cijo M. Xavier

All Works

Groundwater is a valuable resource, and its quality is critical to human survival. Optimal farming and urbanization degraded groundwater reserves. This research investigates and reports the spatial variability of selected heavy metals developed in the Liwa area of the United Arab Emirates. Forty water samples were collected from existing wells and analyzed for different elements. Principal components analysis was applied to a subgroup of the data set in terms of their usefulness for determining the variability of groundwater quality variables. Geographic information systems were used to produce contour maps to analyze the distribution of heavy metals. Ordinary kriging was used …

Kaempferol Regresses Carcinogenesis Through A Molecular Cross Talk Involved In Proliferation, Apoptosis And Inflammation On Human Cervical Cancer Cells, Hela, Nazia Afroze, Sreepoorna Pramodh, Abdulmajeed G. Almutary, Tahir A. Rizvi, Naushad Rais, Ritu Raina, Md Faiyazuddin, Abdullah M. Alnuqaydan, Arif Hussain

All Works

Kaempferol, a flavonoid, contains a plethora of therapeutic properties and has demonstrated its efficacy against cancer. This study aims to unravel the molecular targets that are being modulated by kaempferol on HeLa cells. Various assays were performed, namely: MTT assay, flow cytometry to analyze DNA content and quantitate apoptosis. Quantitative PCR and protein profiling were performed to evaluate the modulated manifestation of different genes involved in apoptosis, cell growth and inflammation. Kaempferol exhibited reduction in cell viability of HeLa cells (IC50 = 50 µM 48 h), whereas it did not show any significant effect on viability of the AC-16 cell …

Predation In Many Dimensions: Spatial Context Is Important For Meaningful Functional Response Experiments, Steven A. Juliano, Jonah A. Goughnour, Geoffrey D. Ower

Faculty Publications – Biological Sciences

For simplicity and to minimize variation, functional response experiments frequently use environments of simple physical structure and small size. Less attention is paid to similarity of the experimental environment to the natural environment where predation occurs. Assumptions about predator and prey use of space are often implied in the choice of experimental environment. We illustrate how these assumptions may affect conclusions with an experiment testing how arena size affects a functional response. Toxorhynchites rutilus preyed upon larval Culex restuans in containers differing in volume by 15x, but spanning a similar range of prey/liter. The most plausible Type II model included …

Collective Cognitive Capital, Emily R. D. Murphy

William & Mary Law Review

This Article calls for a new project for law and neuroscience. It outlines a structural, not individual, application of brain and behavioral science that is aligned with the general goal of basic science research: improving the lives of citizens with a better understanding of the human experience. It asks brain and behavioral science to move explicitly into public policy territory, and specifically onto ground more traditionally occupied by economists—but in ways the project of “behavioral economics” has not yet ventured. Put simply, policy analysts should focus on brains—“collective cognitive capital”—with the same intensity with which they focus on money, rights, …

Using Burdens Of Proof To Allocate The Risk Of Error When Assessing Developmental Maturity Of Youthful Offenders, David L. Faigman, Kelsey Geiser

William & Mary Law Review

Behavioral and neuroscientific research provides a relatively clear window into the timing of developmental maturity from adolescence to early adulthood. We know with considerable confidence that, on average, sixteen-year-olds are less developmentally mature than nineteen-year-olds, who are less developmentally mature than twenty-three-year-olds, who are less developmentally mature than twenty-six-year-olds. However, in the context of a given case, the question presented might be whether a particular seventeen-year-old defendant convicted of murder is “developmentally mature enough” that a sentence of life without parole can be constitutionally imposed on him or her. While developmental maturity can be accurately measured in group data, it …

The Diversity Of Norm Psychologies: A Challenge For The Law, Paul Sheldon Davies

William & Mary Law Review

Can we craft a coherent set of laws applicable to populations with deep cultural diversity? The full force of this question—call it the generalization challenge—has emerged recently thanks to advances in the sciences of the human, especially theories of neuroscience and psychology framed by theories of biological and especially cultural evolution. The goal of this Article is to describe enough of those advances to make clear the force of the challenge. The motivation is simple: as we endeavor to imagine the future of law in light of discoveries in neuroscience and related disciplines, being apprised of the generalization challenge may …

Neuroscience And Criminal Justice: Time For A "Copernican Revolution"?, John S. Callender

William & Mary Law Review

The main purpose of this Article is to argue for a fundamental change in the conceptual orientation of criminal justice: from one based on concepts such as free will, desert, and moral responsibility, to one based on empirical science. The Article describes research in behavioral genetics, acquired brain injuries, and psychological traumatization in relation to criminality. This research has reached a level of development at which the traditional approach to criminality is no longer tenable and should be discarded. I argue that mental health legislation provides a model that could be adapted and applied to offenders.

Neuroscience, Criminal Sentencing, And Human Rights, Elizabeth Shaw

William & Mary Law Review

This Article discusses ways in which neuroscience should inform criminal sentencing in the future. Specifically, it compares the ethical permissibility of traditional forms of punishment, such as incarceration, on the one hand, and rehabilitative “neurointerventions” on the other. Rehabilitative neurointerventions are interventions that aim directly to modify brain activity in order to reduce reoffending. Various jurisdictions are already using techniques that could be classed as neurointerventions, and research suggests that, potentially, an even wider range of rehabilitative neurointerventions may be developed. This Article examines the role of human rights (in particular, the moral right to mental integrity and the legal …

An Abductive Argument From Depression And Anxiety To Christian Personal Holiness, Kelly Douglas Burchett

Masters Theses

The science on pathological depression and anxiety (D&A) describes religion and spirituality's (R/S) insulating and immunizing effects in roughly 72 to 85 percent of all relevant articles. But the descriptivism of science cannot assign any normative value to a theological worldview. Deductive logic favors theism via Leibnizian contingency, Kalām cosmology, objective morality, fine-tuning of the universe, and abstract conceptualism. The information in DNA, the irreducible complexity of intracellular machinery, the improbability of folded proteins, and the support for common modular design over common ancestry establish a design inference for all of life. Unguided naturalistic simulations fail to surmount the complexity …

Habitat Restoration Restores Underwater Soundscapes And Larval Recruitment, Jack Butler, Emily R. Anderson, Mark J. Butler

Biological Sciences Faculty Publications

Habitat degradation alters many ecosystem processes, and the potential for the reestablishment of ecosystem function through restoration is an area of active research. Among marine systems, coastal habitats are particularly vulnerable to anthropogenic degradation and, in response, are the focus of marine ecological restoration. One of the crucial functions of structurally complex coastal habitats (e.g., saltmarshes, seagrass meadows, kelp forests, coral reefs) are as nurseries to coastal and offshore species, many of whose larvae utilize sound to locate suitable nursery habitat. However, the effect of habitat degradation and subsequent restoration on underwater soundscapes and their function as navigational cues for …

Lytic Bacteriophages And Lactic Acid As Processing Aids Against Salmonella Spp. And Escherichia Coli O157:H7 On Marinated And Tenderized Pork Loins, Sherita Li

Master's Theses

Within the last decade, pork consumption has steadily increased and continues to be the most consumed meat globally. However, pathogenic bacterial strains resistant to antibiotics have also been increasingly found in pig farms, animals, and the environment. Bacterial food poisoning cases due to Salmonella spp. and Escherichia coli (E. coli) O157:H7 appear to be linked with a variety of pork products. The meat industry has recognized that research is needed to combat the multi-drug resistance in foodborne pathogens with alternative methods of control. This study evaluated the effects of both E. coli- and Salmonella-specific lytic bacteriophages and …

Nohwere, Peter A. Alces, Robert M. Sapolsky

William & Mary Law Review

Imagine the frustration of Samuel Butler’s protagonist, Higgs, with the strange society he encounters in Erewhon:

"Was there nothing which I could say to make them feel that the constitution of a person’s body was a thing over which he or she had had at any rate no initial control whatever, while the mind was a perfectly different thing, and capable of being created anew and directed according to the pleasure of its possessor? Could I never bring them to see that while habits of mind and character were entirely independent of initial mental force and early education, the body …

How Experts Have Dominated The Neuroscience Narrative In Criminal Cases For Twelve Decades: A Warning For The Future, Deborah W. Denno

William & Mary Law Review

Phineas Gage, the man who survived impalement by a rod through his head in 1848, is considered “one of the great medical curiosities of all time.” While expert accounts of Gage's post-accident personality changes are often wildly damning and distorted, recent research shows that Gage mostly thrived, despite his trauma. Studying past cases such as Gage’s helps us imagine—and prepare for—a future of law and neuroscience in which scientific debates over the brain’s functions remain fiery, and experts divisively control how we characterize brain-injured defendants.

This Article examines how experts have long dominated the neuroscience narrative in U.S. criminal cases, …

Genome-Wide Identification Of Novel Srnas In Streptococcus Mutans, Madeline Claire Krieger, Justin Merritt, Rahul Raghavan

Biology Faculty Publications and Presentations

Streptococcus mutans is a major pathobiont involved in the development of dental caries. Its ability to utilize numerous sugars and to effectively respond to environmental stress promotes S. mutans proliferation in oral biofilms. Because of their quick action and low energetic cost, non-coding small RNAs (sRNAs) represent an ideal mode of gene regulation in stress response networks, yet their roles in oral pathogens have remained largely unexplored. We identified 15 novel sRNAs in S. mutans and show that they respond to four stress-inducing conditions commonly encountered by the pathogen in human mouth: sugar-phosphate stress, hydrogen peroxide exposure, high temperature, and …

Studying Acetylation Of Aconitase Isozymes By Genetic Code Expansion, Jessica Araujo, Sara Ottinger, Sumana Venkat, Qinglei Gan, Chenguang Fan

Chemistry & Biochemistry Faculty Publications and Presentations

Aconitase catalyzes the second reaction of the tricarboxylic acid cycle, the reversible conversion of citrate and isocitrate. Escherichia coli has two isoforms of aconitase, AcnA and AcnB. Acetylomic studies have identified acetylation at multiple lysine sites of both E. coli aconitase isozymes, but the impacts of acetylation on aconitases are unknown. In this study, we applied the genetic code expansion approach to produce 14 site-specifically acetylated aconitase variants. Enzyme assays and kinetic analyses showed that acetylation of AcnA K684 decreased the enzyme activity, while acetylation of AcnB K567 increased the enzyme activity. Further in vitro acetylation and deacetylation assays were …

0876: Lloyd Kiff Ornithology Collection, 1872-1997, Marshall University Special Collections

Guides to Manuscript Collections

Lloyd Kiff graduated from Marshall University in 1964 and later taught as instructor in Zoology in the late 1960s. Kiff has worked as an ornithologist for more than 50 years. His father earned a master’s degree in organic chemistry and his mother earned a master’s degree in both biology and Library Science at Marshall. Kiff’s mother was also the editor for Bird Calls, a periodical issued by the Huntington Bird Club.

Lloyd Kiff has also published various works included in this collection, such as Birds of the Lower Ohio River Valley in West Virginia (1960 and 1986) that can be …

Glutathione S-Transferase: A Candidate Gene For Berry Color In Muscadine Grapes (Vitis RotundifoliA), Aruna Varanasi, Margaret Worthington, Lacy Nelson, Autumn Brown, Thomas Mason Chizk, Renee Threlfall, Luke Howard, Patrick Conner, Rosa Figueroa-Balderas, Melanie Massonnet, Dario Cantu, John R. Clark

Horticulture Faculty Publications and Presentations

Muscadine grapes (Vitis rotundifolia Michx.) are a specialty crop cultivated in the southern United States. Muscadines (2n = 40) belong to the Muscadinia subgenus of Vitis, while other cultivated grape species belong to the subgenus Euvitis (2n = 38). The muscadine berry color locus was mapped to a 0.8 Mbp region syntenic with chromosome 4 of Vitis vinifera. In this study, we identified glutathione S-transferase4 as a likely candidate gene for anthocyanin transport within the berry color locus. PCR and Kompetitive allele-specific PCR genotyping identified a single intragenic SNP (C/T) marker corresponding to a proline …

Genetic Diversity Of Wild And Cultivated Muscadine Grapes (Vitis Rotundifolia Michx.), Kenneth Buck, Margaret Worthington

Horticulture Faculty Publications and Presentations

The muscadine (Vitis rotundifolia syn. Muscadinia rotundifolia) is an American grape species native to the southeastern United States that has been cultivated for centuries. Muscadines are one of three grape species in subgenus Muscadinia with a chromosome number of 2n = 40 (V. rotundifolia, Vitis munsoniana, and Vitis popenoei), making them genetically distinct from the European wine and table grape (Vitis vinifera) and other species in subgenus Euvitis. Crop improvement efforts have been continuous since the late 19th century, yet the germplasm that served as the foundation for early muscadine …

Ecopsychologists' Vital Importance In The Time Of Climate Crises, Nicole B. Auckerman Psyd

Antioch University Dissertations & Theses

Ecopsychology is a systems-based philosophy that expands the therapeutic lens to include client interactions with and perceptions of the natural environment as an integral element of well-being or pathology. Ecopsychology, known forward as EP, also looks at the pathology of our culture and what kind of diagnoses lead to practices that put our planet at risk. In recent decades, the field has amassed a substantial amount of empirical evidence supporting its effectiveness but remains largely underutilized. First generation EP suggested a cultural reordering shifting away from consumer culture and reordering our way of life. Second generation posits working within the …