Life Sciences Commons^™

Nac1 Confines Virus‐Specific Memory Formation Of Cd4+ T Cells Through The Rock1‐Mediated Pathway, Liqing Wang, Hao-Yun Peng, Jugal Kishore Das, Anil Kumar, Yijie Ren, Darby J. Ballard, Xiaofang Xiong, Wen Yang, Xingcong Ren, Paul De Figueiredo, Jin-Ming Yang, Jianxun Song

Markey Cancer Center Faculty Publications

Nucleus accumbens‐associated protein 1 (NAC1), a transcriptional cofactor, has been found to play important roles in regulating regulatory T cells, CD8 + T cells, and antitumor immunity, but little is known about its effects on T‐cell memory. In this study, we found that NAC1 expression restricts memory formation of CD4 + T cells during viral infection. Analysis of CD4 + T cells from wild‐type (WT) and NAC1‐ deficient (−/−) mice showed that NAC1 is essential for T‐cell metabolism, including glycolysis and oxidative phosphorylation, and supports CD4 + T‐cell survival in vitro. We further demonstrated that a deficiency of NAC1 downregulates …

The Metabolomics Workbench File Status Website: A Metadata Repository Promoting Fair Principles Of Metabolomics Data, Christian D. Powell, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

Background: An updated version of the mwtab Python package for programmatic access to the Metabolomics Workbench (MetabolomicsWB) data repository was released at the beginning of 2021. Along with updating the package to match the changes to MetabolomicsWB’s ‘mwTab’ file format specification and enhancing the package’s functionality, the included validation facilities were used to detect and catalog file inconsistencies and errors across all publicly available datasets in MetabolomicsWB.

Results: The MetabolomicsWB File Status website was developed to provide continuous validation of MetabolomicsWB data files and a useful interface to all found inconsistencies and errors. This list of detectable issues/errors include format …

The Impact Of Progerin On Genome Maintenance In Mammalian Cells, Liza Alexandra Joudeh

Theses and Dissertations

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare genetic condition characterized by accelerated aging. The cause of HGPS is a point mutation in the LMNA gene, which encodes lamins A and the splice variant lamin C. Lamins are components of the nuclear lamina, a complex that plays structural and catalytic roles in the nucleus that are essential to chromatin organization, DNA replication, and DNA repair. The mutation associated with HGPS activates a cryptic splice donor site which alters the lamin A protein in a way that does not allow prelamin A to be fully processed, and ultimately results in the accumulation …

Advancing American Chestnut (Castanea Dentata) Restoration Through Science, Gis And Partnerships, Tyler Riendeau

All Theses And Dissertations

The American chestnut (Castanea dentata) was once a prominent hardwood species of the eastern United States forests. From Maine to Alabama, the chestnut provided many ecosystem and economic services to wildlife and humans alike. After an accidental importation of chestnut blight (Cryphonectria parasitica) from Asia, billions of American chestnuts succumbed to the disease. Since the 1980s, researchers have been working to develop a fungal blight-tolerant chestnut in hopes of restoring the species. By the early 1990s, Dr. William Powell and his fellow scientists at the State University of New York College of Environmental Science and Forestry (SUNY-ESF) successfully …

Federal Agency Perspectives And Funding Opportunities For Weed And Invasive Plant Research, Stephen L. Young, James J. Kells, Vijay K. Nandula

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Weeds and invasive plants know no borders and have collectively impacted many ecosystems worldwide, including croplands, forests, grasslands, rangelands, wetlands, and riparian areas. Losses continue to mount, affecting yield and productivity, species diversity, and ecosystem services, with both short- and long-term repercussions on the sustainability of plant and animal communities and the livelihoods of many. New and emerging invasive plants, along with many of the most intractable weeds, have undermined even the best control efforts, serving as a reminder of the constant need for improvements in science, application, and technology. One of the main reasons for the success of weeds …

Amyloid-Beta Protein Concentration Dependence Of Reversible Aggregation Using Gold Colloid Particles, Renee Spencer, Lila Kocieniewski, Bryan Martinez, Kazushige Yokoyama

McNair Scholars Program

Although Alzheimer’s and COVID-19 are different diseases, the commonality between them is during the process of them developing in a person by fibrillogenesis. The product of fibrillogenesis results in the development of these diseases. We study the first stage of fibrillogenesis where the amyloid-beta peptide monomers are assembled into an oligomer. We want to isolate this oligomer using gold colloids because this step can be reversed. Utilizing gold colloids allows us to freeze fibrillogenesis in the first step by folding and unfolding the protein repeatedly through a series of pH changes from 4 or below to 10 or higher. At …

Decreased Moderate To Vigorous Physical Activity Levels In Children With Asthma Are Associated With Increased Traffic-Related Air Pollutants, Juan Aguilera, Soyoung Jeon, Amit U. Raysoni, Wen-Whai Li, Leah D. Whigham

School of Earth, Environmental, & Marine Sciences Faculty Publications

People with asthma, particularly young children, are more adversely aected by trac emissions-and regular exercise reduces asthma symptoms and improves lung function. We studied the relationship between air pollution and objectively measured physical activity in children with asthma who were attending a school near a freeway. We continuously monitored air pollutants-PM2.5, PM10, nitrogen dioxide (NO2), and ozone (O3)-at the school for 10 weeks and measured physical activity levels via accelerometry in children (n = 12, ages 6-12 years). Concentrations of PM2.5, PM10, and NO2 were negatively associated with moderate to vigorous physical activity (PM2.5 and PM10: p < .001; NO2: p = …

Oxygen And Hydrogen Isotopic Evidence That KamaʻEhuakanaloa (LōʻIhi) Seamount Hydrothermal Systems Are Recharged By Deep Pacific Seawater, Eric W. Chan, Brianna A. Alanis, Christopher R. German, Darlene S. S. Lim, John A. Breier

School of Earth, Environmental, & Marine Sciences Faculty Publications

We observed negative and positive δ18O and δ2H deviations from fluids collected at Kamaʻehuakanaloa (previously known as Lōʻihi) seamount relative to Pacific seawater from the same depth. Hydrothermal vents on the crater floor of Pele's Pit at Kamaʻehuakanaloa, at a depth of 1320 m, had δ18O and δ2H values as low as −0.19‰ and −0.3‰, respectively. Seawater collected within the caldera, within a zone 45 m above the crater floor, had δ18O and δ2H values as high as 1.15‰ and 6.5‰, respectively. In comparison, Pacific seawater at 1200 m and 1400 m at nearby station ALOHA exhibit intermediate δ18O and …

Exploring The Interactions Between Sars-Cov-2 And Host Proteins, Sojan Shrestha

School of Biological Sciences: Dissertations, Theses, and Student Research

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current pandemic, Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 is considered to be of zoonotic origin; it originated in non-human animals and was transmitted to humans. Since the early stage of the pandemic, however, the evidence of transmissions from humans to animals (reverse zoonoses) has been found in multiple animal species including mink, white-tailed deer, and pet and zoo animals. Furthermore, secondary zoonotic events of SARS-CoV-2, transmissions from animals to humans, have been also reported. It is suggested that non-human hosts can act as SARS-CoV-2 reservoirs where accumulated …

Comparative Analysis Of Soil Properties, Microbial Community Composition, And Yield Responses To Cover Crops In Different Ecoregions Of South Texas, Daphne Zapsas

Theses and Dissertations

Comprehensive understanding of soil properties, their interdependencies, and the effects of management practices is crucial for designing sustainable agricultural strategies. By adopting site-specific and need-based practices that enhance soil health, farmers can optimize crop growth, increase yield, and contribute to long-term environmental sustainability. Cover crops have been recognized for enhancing soil fertility, promoting microbial activity, and increasing organic matter content. However, while their effectiveness is well documented in temperate regions with readily available water, their impact in water limited systems in subtropical regions remains mixed. The aim of this study is to assess soil conditions in four different farms across …

Cover Crops Influence Arthropod Community Dynamics Through Seasonal Variation And Cascading Effects, Adegboyega Fajemisin

Theses and Dissertations

Chapter 1: This chapter gives an overview of how cover crops influence soil’s physical, chemical, and biological properties, and their role on mediating arthropod community dynamics with implications for pest management in the subsequent cash crop.

Chapter 2: This chapter examines the effects of cover-cash crop rotation on arthropod community dynamics on four growers fields in the Lower Rio Grande Valley, Texas. We assessed the impact of cover crops planted in the summer months on the subsequent cash crops planted in the winter. Our results showed that cover crops had a differential effect on the population of beneficials and herbivores …

Linking The Metabolic And Ecological Fate Of Caribbean Ciguatoxins And Related Neurotoxins In Reef Herbivores, Jessica K. Gwinn

Graduate Theses and Dissertations (2019 - present)

Ciguatera poisoning (CP) is one of the most prominent seafood-borne illnesses worldwide, affecting between 25,000–500,000 people annually. Ciguatera is caused by the ingestion of seafood contaminated with algal-derived ciguatoxins (CTX), the precursors of which are produced by benthic and toxigenic dinoflagellates in the genera Gambierdiscus and Fukuyoa. These compounds enter marine food webs through herbivory and are subsequently transferred to higher trophic levels, undergoing complex metabolic biotransformations, which produce structurally related CTX derivatives. Consumption of CTX induces a variety of severe neurological, gastrointestinal, and/or cardiovascular symptoms beginning within hours and lasting for weeks to months following exposure. Despite the impact …

Cadmium And Salinity Stressor Antagonism On Vallisneria Neotropicalis, Christopher P. Mikolaitis

Graduate Theses and Dissertations (2019 - present)

Submerged macrophytes form the foundation of freshwater ecosystems. These organisms are sessile and are very susceptible to shifts in their environment. Heavy metals are of particular concern as they can be sequestered indefinitely in sediments and are readily taken up by rooted vegetation. In the presence of saltwater intrusions, these metals can interact with salt ions potentially changing their availability to submerged vegetation. In this study a freshwater macrophyte, Vallisneria neotropicalis, was used as a test species for interactive effects between Cd, a non-essential heavy metal, and salt stress. The metrics used to establish the individual as well as …

Effects Of Heterozygous Deletion Of Autism-Related Gene Cullin-3 In Mice, Qiang-Qiang Xia, Angela K. Walker, Chenghu Song, Jing Wang, James A. Mobley, Jeffrey Singer, Anju Singh, Craig M. Powell

Biology Faculty Publications and Presentations

Autism Spectrum Disorder (ASD) is a developmental disorder in which children display repetitive behavior, restricted range of interests, and atypical social interaction and communication. CUL3, coding for a Cullin family scaffold protein mediating assembly of ubiquitin ligase complexes through BTB domain substrate-recruiting adaptors, has been identified as a high-risk gene for autism. Although complete knockout of Cul3 results in embryonic lethality, Cul3 heterozygous mice have reduced CUL3 protein, demonstrate comparable body weight, and display minimal behavioral differences including decreased spatial object recognition memory. In measures of reciprocal social interaction, Cul3 heterozygous mice behaved similarly to their wild-type littermates. In …

Growing South Dakota (Summer 2023), College Of Agriculture, Food And Environmental Sciences

Growing South Dakota (Publication of the College of Agriculture, Food and Environmental Sciences)

3 SDSU Little International Celebrates 100 years of Tradition
7 2023 CAFES Celebration of Faculty Excellence
11 South Dakota Agricultural Experiment Station Locations and Research Initiatives
15 Every Acre Counts
16 Undergraduate Research
19 Tanner Sloan: South Dakota State Wrestler & Animal Science Student Takes Home NCAA Division I & U23 World Silver Medals
21 2023 CAFES Outstanding Seniors
23 Robert Streeter: International Advocate for Wildlife Conservation
25 Collegiate Cattlemen's Club
27 Jim and Melody Mielke: Lifelong Donors Contribute to Agriculture in More Ways than One
29 Jackrabbits Now and Then

Using Machine Learning And Distributed Hydrologic Modeling To Predict Soil Texture, Surface Soil Moisture And Evapotranspiration In Jornada Experimental Range, Southwestern U.S., Jorge Andres Mayo

Open Access Theses & Dissertations

In water-limited ecosystems, detailed knowledge of the soil, vegetation, and atmosphere interactions is critical to understand the processes that control the partitioning of energy, water fluxes, and biogeochemical cycles within the critical zone. This Master's thesis is divided into two main contributing sections. The first, is on the use of machine learning to reconstruct missing soil type information, and the second, on the calibration and validation of a physically-based distributed hydrological model to estimate soil moisture and evapotranspiration within the Jornada Experimental Range of the U.S. in southern New Mexico. For the first contribution, three explainable, shallow machine-learning techniques are …

Biofilms And Their Role On Diseases, Vijay Singh Gondil, Bindu Subhadra

Faculty Publications - Biological Sciences

Biofilms are complex, three-dimensional structures that provide a long-established survival mechanism for microorganisms. Biofilms play a substantial role in pathogenesis as they can evade the immune response and be highly resistant to conventional antimicrobials, thus impacting the human health and healthcare system. To address this issue, BMC Microbiology invites submissions to the collection ‘Biofilms and its impact on disease’.

Diversity, Function, And Phenotypic Plasticity Of Cryptophyte Phycobiliproteins, Kristiaän Merritt

Theses and Dissertations

Cryptophytes are a group of unicellular eukaryotic algae that can be found in a wide range of underwater habitats. Part of their ecological success can be attributed to their diverse array of cryptophyte phycobiliproteins (Cr-PBPs), a pigment class that captures wavelengths of light that are poorly absorbed by chlorophylls. Cryptophytes gained photosynthesis via secondary endosymbiosis in which their ancestor engulfed a red algal endosymbiont. Following endosymbiosis, they deconstructed the red algal photosynthetic machinery to form the Cr-PBP. Since then, the Cr-PBPs have diversified into at least 9 spectrally distinct forms. I investigated the diversity of Cr-PBP light absorption across 76 …

Effect Of Supplementation Prior To Artificial Insemination And During Gestation In Beef Females, Landon Folsom Tadich

Department of Animal Science: Dissertations, Theses, and Student Research

Objectives of Experiment 1 was to evaluate the impact of increased energy prior to AI on BW, ADG, and reproductive efficiency in heifers developed on range or in a dry lot. During the winter development period (131 ± 3.5 d/yr) heifers (n = 100/yr) were assigned to either upland range (RANGE) or fed a dry lot diet in two pens that either remained constant (DLLO) or increased in energy prior to AI (DLHI). Heifers developed on RANGE grazed upland winter range until 38 d prior to AI where they then received the DLLO diet. Pre-breeding BW was greater ( …

Mid-Gestation Maternofetal Inflammation Impacts Growth, Skeletal Muscle Glucose Metabolism, And Inflammatory Tone In The Ovine Fetus During Late Gestation, Zena Mariah Hicks

Department of Animal Science: Dissertations, Theses, and Student Research

Our 1^st and 2^nd studies assessed the impact of mid-gestation maternofetal inflammation on growth, skeletal muscle glucose metabolism, and inflammatory tone in the late gestation ovine fetus. The objective was to determine if inducing maternofetal inflammation during peak placental growth would lead to more profound IUGR characteristics in the fetus. MI-IUGR fetuses exhibited reduced body and skeletal muscle weights and hallmark asymmetric growth at late gestations. Fetuses had higher baseline glucose:insulin ratios and reduced glucose-stimulated insulin secretion. Moreover, hindlimb glucose oxidation was impaired independent of glucose uptake. Skeletal muscle specific glucose uptake and oxidation was reduced in MI-IUGR …

Impact Of Distillers' Removal And Impact Of Lowering Inclusions Of Distillers’ Grains Plus Solubles And Different Roughage Quality On Finishing Cattle Performance, Sofia Suarez Lorences

Department of Animal Science: Dissertations, Theses, and Student Research

A feedlot trial (Exp. 1) was conducted to evaluate the impact of removing modified distillers grains plus solubles (MDGS) on performance and carcass characteristics. Cattle with MDGS removed on either d 79 or d 43 had reduced final BW, DMI, and ADG. Cattle with MDGS removed on d 43 were 5% less efficient than cattle fed 20% MDGS throughout the entire 124-d feeding period. Cattle fed 20% MDGS throughout the whole feeding had the greatest HCW and LM area. There were no differences in backfat and marbling scores among treatments, and no differences in percent of abscessed livers. In conclusion, …

Arkansas Corn And Grain Sorghum Research Studies 2022, Victor Ford, Jason Kelley, Nathan Mckinney Ii

Arkansas Agricultural Experiment Station Research Series

The 2022 edition of the Arkansas Corn and Grain Sorghum Research Studies Series includes research results on topics pertaining to corn and grain sorghum production, including weed, disease, and insect management; economics; sustainability; irrigation; post-harvest drying; soil fertility; mycotoxins; cover crop management; and research verification program results. Our objective is to capture and broadly distribute the results of research projects funded by the Arkansas Corn and Grain Sorghum Board. The intended audience includes producers and their advisors, current investigators, and future researchers. The Series serves as a citable archive of research results.

Reports in this publication are 2–3 year summaries. …

State Of The Fisheries: Status Reports And Aquatic Resources Of Western Australia 2021/22, Department Of Primary Industries And Regional Development, Western Australia, S J. Newman, B S. Wise, K G. Santaro, D J. Gaughan

Status Reports of the Fisheries and Aquatic Resources

Aquatic resources within Western Australia (WA) are in good condition, and this has positioned WA as a global leader in sustainable fisheries management. The sustainable fisheries of WA continue to support our strong economy and regional communities. Nonetheless, the lack of a consistent approach to build in the knowledge of Traditional Owners remains a gap in our longer-term fisheries science in Western Australia.

Climate change and climate variability continues to impact fish stocks, challenging our ability to effectively monitor, assess, and manage fish stocks. We are continually working with our stakeholders, and the broader community to be adaptive, responsive, and …

Enhancement Of Tki Sensitivity In Lung Adenocarcinoma Through M6a-Dependent Translational Repression Of Wnt Signaling By Circ-Fbxw7, Kai Li, Zi-Yang Peng, Rui Wang, Xiang Li, Ning Du, Da-Peng Liu, Jia Zhang, Yun-Feng Zhang, Lei Ma, Ye Sun, Shou-Ching Tang, Hong Ren, Yi-Ping Yang, Xin Sun

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

BACKGROUND: Tyrosine kinase inhibitors (TKIs) that specifically target mutational points in the EGFR gene have significantly reduced suffering and provided greater relief to patients with lung adenocarcinoma (LUAD). The third-generation EGFR-TKI, Osimertinib, has been successfully employed in clinical treatments to overcome resistance to both original and acquired T790M and L858R mutational points. Nevertheless, the issue of treatment failure response has emerged as an insurmountable problem.

METHODS: By employing a combination of multiple and integrated approaches, we successfully identified a distinct population within the tumor group that plays a significant role in carcinogenesis, resistance, and recurrence. Our research suggests that addressing …

School Of Biological Sciences News, 2023, School Of Biological Sciences

School of Biological Sciences News

Alumni newsletter of Illinois State University's School of Biological Sciences.

Beyond A Vision For The Future: Tangible Steps To Engage Diverse Participants In Inclusive Field Experiences, Robin M. Verble, Corinne L. Richards-Zawacki, Vanessa K.H. Young

Biological Sciences Faculty Research & Creative Works

Synopsis Recent strides toward improving diversity, equity, and inclusion (DEI) in field biology present a unique opportunity for transdisciplinary exploration of the impacts and state of a topic that has remained hereto largely underexplored and under-discussed in the academic setting. Within current literature, themes of racial and gender inequity, power imbalances, unsafe environments, and underdeveloped infrastructure and resources are widespread. Thus, we organized a symposium that addressed these compelling issues in field biology DEI through a multitude of experiential and academic lenses. This article will orient the reader to the special issue and offer summative goals and outcomes of the …

Clonal Hematopoiesis Is Associated With Protection From Alzheimer's Disease, Chloé Sarnowski, Matthew R Chrostek, Herra Ahmad, Daniel Nachun, Winnie Yao, Alexa Beiser, Alexander G Bick, Joshua C Bis, Myriam Fornage, William T Longstreth, Oscar L Lopez, Pradeep Natarajan, Bruce M Psaty, Claudia L Satizabal, Joshua Weinstock, Eric B Larson, Paul K Crane, C Dirk Keene, Ansuman T Satpathy, Thomas J Montine, Siddhartha Jaiswal

Faculty, Staff and Student Publications

Clonal hematopoiesis of indeterminate potential (CHIP) is a premalignant expansion of mutated hematopoietic stem cells. As CHIP-associated mutations are known to alter the development and function of myeloid cells, we hypothesized that CHIP may also be associated with the risk of Alzheimer's disease (AD), a disease in which brain-resident myeloid cells are thought to have a major role. To perform association tests between CHIP and AD dementia, we analyzed blood DNA sequencing data from 1,362 individuals with AD and 4,368 individuals without AD. Individuals with CHIP had a lower risk of AD dementia (meta-analysis odds ratio (OR) = 0.64, P …

Fast Inference Of Genetic Recombination Rates In Biobank Scale Data

Faculty, Staff and Student Publications

Although rates of recombination events across the genome (genetic maps) are fundamental to genetic research, the majority of current studies only use one standard map. There is evidence suggesting population differences in genetic maps, and thus estimating population-specific maps, are of interest. Although the recent availability of biobank-scale data offers such opportunities, current methods are not efficient at leveraging very large sample sizes. The most accurate methods are still linkage disequilibrium (LD)-based methods that are only tractable for a few hundred samples. In this work, we propose a fast and memory-efficient method for estimating genetic maps from population genotyping data. …

Weakly Supervised Spatial Relation Extraction From Radiology Reports

Faculty, Staff and Student Publications

OBJECTIVE: Weak supervision holds significant promise to improve clinical natural language processing by leveraging domain resources and expertise instead of large manually annotated datasets alone. Here, our objective is to evaluate a weak supervision approach to extract spatial information from radiology reports.

MATERIALS AND METHODS: Our weak supervision approach is based on data programming that uses rules (or labeling functions) relying on domain-specific dictionaries and radiology language characteristics to generate weak labels. The labels correspond to different spatial relations that are critical to understanding radiology reports. These weak labels are then used to fine-tune a pretrained Bidirectional Encoder Representations from …

Multi-Task Learning With Dynamic Re-Weighting To Achieve Fairness In Healthcare Predictive Modeling, Xiaoqian Jiang, Kai Zhang

Faculty, Staff and Student Publications

The emphasis on fairness in predictive healthcare modeling has increased in popularity as an approach for overcoming biases in automated decision-making systems. The aim is to guarantee that sensitive characteristics like gender, race, and ethnicity do not influence prediction outputs. Numerous algorithmic strategies have been proposed to reduce bias in prediction results, mitigate prejudice toward minority groups and promote prediction fairness. The goal of these strategies is to ensure that model prediction performance does not exhibit significant disparity among sensitive groups. In this study, we propose a novel fairness-achieving scheme based on multitask learning, which fundamentally differs from conventional fairness-achieving …