Life Sciences Commons^™

Identification Of Candidate Dna Methylation Biomarkers Related To Alzheimer’S Disease Risk By Integrating Genome And Blood Methylome Data, Yanfa Sun, Jingjing Zhu, Yaohua Yang, Zichen Zhang, Hua Zhong, Guanghua Zeng, Dan Zhou, Richard S Nowakowski, Jirong Long, Chong Wu, Lang Wu

Faculty, Staff and Student Publications

Alzheimer disease (AD) is a common neurodegenerative disease with a late onset. It is critical to identify novel blood-based DNA methylation biomarkers to better understand the extent of the molecular pathways affected in AD. Two sets of blood DNA methylation genetic prediction models developed using different reference panels and modelling strategies were leveraged to evaluate associations of genetically predicted DNA methylation levels with AD risk in 111,326 (46,828 proxy) cases and 677,663 controls. A total of 1,168 cytosine-phosphate-guanine (CpG) sites showed a significant association with AD risk at a false discovery rate (FDR) < 0.05. Methylation levels of 196 CpG sites were correlated with expression levels of 130 adjacent genes in blood. Overall, 52 CpG sites of 32 genes showed consistent association directions for the methylation-gene expression-AD risk, including nine genes (CNIH4, THUMPD3, SERPINB9, MTUS1, CISD1, FRAT2, CCDC88B, FES, and SSH2) firstly reported as AD risk genes. Nine of 32 genes were enriched in dementia and AD disease categories (P values ranged from 1.85 × 10-4 to 7.46 × 10-6), and 19 genes in a neurological disease network (score = 54) were also observed. Our findings improve the understanding of genetics and etiology for AD.

Epigenomic Mapping Reveals Distinct B Cell Acute Lymphoblastic Leukemia Chromatin Architectures And Regulators, Kelly R Barnett, Robert J Mobley, Jonathan D Diedrich, Brennan P Bergeron, Kashi Raj Bhattarai, Alexander C Monovich, Shilpa Narina, Wenjian Yang, Kristine R Crews, Christopher S Manring, Elias Jabbour, Elisabeth Paietta, Mark R Litzow, Steven M Kornblau, Wendy Stock, Hiroto Inaba, Sima Jeha, Ching-Hon Pui, Charles G Mullighan, Mary V Relling, Shondra M Pruett-Miller, Russell J H Ryan, Jun J Yang, William E Evans, Daniel Savic

Faculty, Staff and Student Publications

B cell lineage acute lymphoblastic leukemia (B-ALL) is composed of diverse molecular subtypes, and while transcriptional and DNA methylation profiling has been extensively examined, the chromatin landscape is not well characterized for many subtypes. We therefore mapped chromatin accessibility using ATAC-seq in primary B-ALL cells from 156 patients spanning ten molecular subtypes and present this dataset as a resource. Differential chromatin accessibility and transcription factor (TF) footprint profiling were employed and identified B-ALL cell of origin, TF-target gene interactions enriched in B-ALL, and key TFs associated with accessible chromatin sites preferentially active in B-ALL. We further identified over 20% of …

Monitoring Glucocorticoid Receptor In Plasma-Derived Extracellular Vesicles As A Marker Of Resistance To Androgen Receptor Signaling Inhibition In Prostate Cancer, Emanuela Gentile, Andrew W Hahn, Jian H Song, Anh Hoang, Peter D A Shepherd, Sumankalai Ramachandran, Nora M Navone, Eleni Efstathiou, Mark Titus, Paul G Corn, Sue-Hwa Lin, Christopher J Logothetis, Theocharis Panaretakis

Faculty, Staff and Student Publications

Disease progression following androgen ablation was shown to be associated with upregulation of the glucocorticoid receptor (GR). Longitudinal monitoring of GR expression in circulating extracellular vesicles (EV) may reflect changes in the tumor cell and facilitates detection of acquired resistance. We utilized LNCaP, LREX cells and a patient-derived xenograft, MDA PDX 322-2-6a, for in vitro and in vivo experiments. Plasma-derived EVs were isolated from patients with localized high-risk prostate cancer undergoing androgen ablation. The mRNA levels of GR in EVs and their responsive genes were detected by transcriptome analysis, qRT-PCR and the protein levels by Western blot analysis. We detected …

Where Did All The Bed Bugs Go?, Lauren Friedman

Capstones

In the early 2000s in New York City, everyone was talking about bed bugs. The disc-shaped, bloodsucking pests had been a common domestic nuisance up to the World War II era, but in the decades since, they’d mostly faded into obscurity. That was until bed bug infestations, which are often psychologically distressing and sometimes impossible to overcome, suddenly became routine across the five boroughs, driving people from their apartments and stoking fear about everything from upholstered theater seats to thrift stores.

But then, just as quickly as bed bugs had invaded, they seemed to fade away. In a 2022 study …

Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam

SMU Data Science Review

Abstract. This research used deep learning for image analysis by isolating and characterizing distinct DNA replication patterns in human cells. By leveraging high-resolution microscopy images of multiple cells stained with 5-Ethynyl-2′-deoxyuridine (EdU), a replication marker, this analysis utilized Convolutional Neural Networks (CNNs) to perform image segmentation and to provide robust and reliable classification results. First multiple cells in a field of focus were identified using a pretrained CNN called Cellpose. After identifying the location of each cell in the image a python script was created to crop out each cell into individual .tif files. After careful annotation, a CNN was …

Soybean Genetics, Genomics, And Breeding For Improving Nutritional Value And Reducing Antinutritional Traits In Food And Feed, William M. Singer, Yi-Chen Lee, Zachary Shea, Caio Canella Vieira, Dongho Lee, Xiaoying Li, Mia Cunicelli, Shaila S. Kadam, Mohammad Amir Waseem Khan, Grover Shannon, M. A. Rouf Mian, Henry T. Nguyen, Bo Zhang

Agriculture Faculty Publications

Soybean [Glycine max(L.) Merr.] is a globally important crop due to its valuable seed composition, versatile feed, food, and industrial end-uses, and consistent genetic gain. Successful genetic gain in soybean has led to widespread adaptation and increased value for producers, processors, and consumers. Specific focus on the nutritional quality of soybean seed composition for food and feed has further elucidated genetic knowledge and bolstered breeding progress. Seed components are historical and current targets for soybean breeders seeking to improve nutritional quality of soybean. This article reviews genetic and genomic foundations for improvement of nutritionally important traits, such as protein and …

The Mayfly Newsletter, Donna Giberson

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

Status Survey Of Eight Rare Aquatic Macroinvertebrates In East Texas, Alexandra Randall

Biology Theses

Freshwater is essential to human existence. The health of each freshwater source is connected to the survival of pollution intolerant species of aquatic macroinvertebrates in the orders Ephemeroptera, Plecoptera, and Trichoptera (EPT taxa). A higher presence of EPT taxa equates to better water quality because their water bound larvae assist in maintaining clean freshwater environments and will not survive in highly polluted water. Human disruption to natural environments is causing increases in polluted freshwater, leading to decreases in the presence of EPT taxa. Texas Parks and Wildlife Department documentation shows major concern for the populations of eight EPT species of …

The Dose-Response Effect Of Aerobic Exercise On Inflammation In Colon Cancer Survivors, Justin C. Brown, Stephanie L.E. Compton, Jeffrey A. Meyerhardt, Guillaume Spielmann, Shengping Yang

School of Medicine Faculty Publications

Background; Physical activity after surgical resection for colon cancer is associated with significantly longer disease-free survival. Inflammation is hypothesized to mediate the association between physical activity and disease-free survival in colon cancer. Methods; In this exploratory analysis of a randomized dose-response trial, 39 colon cancer survivors who completed standard therapy were stratified by cancer stage and randomized in a 1;1;1 ratio to one of three treatment groups for 24 weeks of usual-care control, 150 min/wk of moderate-intensity aerobic exercise (low-dose), or 300 min/wk of moderate-intensity aerobic exercise (high-dose). Inflammation outcomes included high-sensitivity C-reactive protein (hs-CRP), interleukin-6 (IL6), and soluble tumor …

Association Of Chlamydia Trachomatis Burden With The Vaginal Microbiota, Bacterial Vaginosis, And Metronidazole Treatment, Caleb M. Ardizzone, Christopher M. Taylor, Evelyn Toh, Rebecca A. Lillis, Jacob H. Elnaggar, John W. Lammons, Patricia Dehon Mott, Emily L. Duffy, Li Shen, Alison J. Quayle

School of Graduate Studies Faculty Publications

Bacterial vaginosis (BV), a dysbiosis of the vaginal microbiota, is a common coinfection with Chlamydia trachomatis (Ct), and BV-associated bacteria (BVAB) and their products have been implicated in aiding Ct evade natural immunity. Here, we determined if a non-optimal vaginal microbiota was associated with a higher genital Ct burden and if metronidazole, a standard treatment for BV, would reduce Ct burden or aid in natural clearance of Ct infection. Cervicovaginal samples were collected from women at enrollment and, if testing positive for Ct infection, at a follow-up visit approximately one week later. Cervical Ct burden was assessed by inclusion forming …

Linking Individual Behavior With Physiology To Understand Complex Life Histories, Doreen Cabrera

Theses and Dissertations

Life history strategies encompass a suite of co-evolved traits crucial for ensuring an individual's fitness, often evolving from trade-offs between traits competing for the same resources. Adult male crayfish in the Cambaridae family undergo seasonal morphological changes linked to reproductive status, a process called cyclic dimorphism. In this dissertation, we attempt to understand how cyclic dimorphism evolved in non-native northern crayfish (Faxonius virilis). First, in Chapter 1, we review empirical studies that have assessed animal personality across developmental periods. The results show that personality traits tend to be stable within life stages but not across developmental events. In Chapter 2, …

12.04.2023 Orsp Connect, Liz Williamson

ORED Newsletter

Week of December 4, 2023

Oregon State Rank Assessment For Gold Beach Pocket Gopher (Thomomys Mazama Helleri), Misty Nelson

Institute for Natural Resources Publications

Oregon state conservation status assessment for Gold Beach pocket gopher (Thomomys mazama helleri) using NatureServe methodology, 2023.

Oregon State Rank Assessment For Pistol River Pocket Gopher (Thomomys Bottae Detumidus), Misty Nelson

Institute for Natural Resources Publications

Oregon state conservation status assessment for Pistol River pocket gopher (Thomomys bottae detumidus) using NatureServe methodology, 2023.

Formate Supplementation Enhances Antitumor Cd8+ T-Cell Fitness And Efficacy Of Pd-1 Blockade, Jared H Rowe, Ilaria Elia, Osmaan Shahid, Emily F Gaudiano, Natalia E Sifnugel, Sheila Johnson, Amy G Reynolds, Megan E Fung, Shakchhi Joshi, Martin W Lafleur, Joon Seok Park, Kristen E Pauken, Joshua D Rabinowitz, Gordon J Freeman, Marcia C Haigis, Arlene H Sharpe

Faculty, Staff and Student Publications

UNLABELLED: The tumor microenvironment (TME) restricts antitumor CD8+ T-cell function and immunotherapy responses. Cancer cells compromise the metabolic fitness of CD8+ T cells within the TME, but the mechanisms are largely unknown. Here we demonstrate that one-carbon (1C) metabolism is enhanced in T cells in an antigen-specific manner. Therapeutic supplementation of 1C metabolism using formate enhances CD8+ T-cell fitness and antitumor efficacy of PD-1 blockade in B16-OVA tumors. Formate supplementation drives transcriptional alterations in CD8+ T-cell metabolism and increases gene signatures for cellular proliferation and activation. Combined formate and anti-PD-1 therapy increases tumor-infiltrating CD8+ T cells, which are essential for …

Genetic Determinants Underlying The Progressive Phenotype Of Β-Lactam/Β-Lactamase Inhibitor Resistance In Escherichia Coli, William C Shropshire, Hatim Amiji, Jordan Bremer, Selvalakshmi Selvaraj Anand, Benjamin Strope, Pranoti Sahasrabhojane, Marc Gohel, Samuel Aitken, Sarah Spitznogle, Xiaowei Zhan, Jiwoong Kim, David E Greenberg, Samuel A Shelburne

Faculty, Staff and Student Publications

Currently, whole-genome sequencing (WGS) data have not shown strong concordance with Escherichia coli susceptibility profiles to the commonly used β-lactam/β-lactamase inhibitor (BL/BLI) combinations: ampicillin-sulbactam (SAM), amoxicillin-clavulanate (AMC), and piperacillin-tazobactam (TZP). Progressive resistance to these BL/BLIs in the absence of cephalosporin resistance, also known as extended-spectrum resistance to BL/BLI (ESRI), has been suggested to primarily result from increased copy numbers of bla TEM variants, which is not routinely assessed in WGS data. We sought to determine whether addition of gene amplification could improve genotype-phenotype associations through WGS analysis of 147 E. coli bacteremia isolates with increasing categories of BL/BLI non-susceptibility ranging …

Oncogenic Kras Drives Lipofibrogenesis To Promote Angiogenesis And Colon Cancer Progression, Wen-Hao Hsu, Kyle A Labella, Yiyun Lin, Ping Xu, Rumi Lee, Cheng-En Hsieh, Lei Yang, Ashley Zhou, Jonathan M Blecher, Chang-Jiun Wu, Kangyu Lin, Xiaoying Shang, Shan Jiang, Denise J Spring, Yan Xia, Peiwen Chen, John Paul Shen, Scott Kopetz, Ronald A Depinho

Faculty, Staff and Student Publications

Oncogenic KRAS (KRAS*) contributes to many cancer hallmarks. In colorectal cancer, KRAS* suppresses antitumor immunity to promote tumor invasion and metastasis. Here, we uncovered that KRAS* transforms the phenotype of carcinoma-associated fibroblasts (CAF) into lipid-laden CAFs, promoting angiogenesis and tumor progression. Mechanistically, KRAS* activates the transcription factor CP2 (TFCP2) that upregulates the expression of the proadipogenic factors BMP4 and WNT5B, triggering the transformation of CAFs into lipid-rich CAFs. These lipid-rich CAFs, in turn, produce VEGFA to spur angiogenesis. In KRAS*-driven colorectal cancer mouse models, genetic or pharmacologic neutralization of TFCP2 reduced lipid-rich CAFs, lessened tumor angiogenesis, and improved overall survival. …

Analyzing The Shark Paleoecology Of Coastal Georgia From The Miocene And Pliocene Epochs, Joshua Lee Clark, Benjamin Angalet

Georgia Journal of Science

The field of shark paleoecology often yields indecisive conclusions based on the limited fossilization of their anatomical structures, with the exception of their teeth. The majority of the Atlantic coast has been studied regarding the presence of certain prehistoric shark species from the Miocene, Pliocene, and Pleistocene epochs. However, information pertaining to the Georgia coast and understanding its potential community structure is relatively understudied. This study was conducted in which thousands of fossil shark specimens and subsequent marine fauna were collected from dredge spoils created by the US Army Corps of Engineers (USACE): Savannah District. A total of 5,127 fossil …

Volatiles And Interspecific Competition, Stephen T. Trumbo

EEB Articles

No abstract provided.

On Some Teratological Scorpions In The Natural History Museum, London And Checklist Of The Scorpiological Literature On Morphological Anomalies (Arachnida: Scorpiones), Danniella Sherwood, Luis F. De Armas

Euscorpius

Whilst undertaking curation in the collections of the Natural History Museum, London, the senior author came across a jar of scorpions marked ‘scorpions with curled feet’. Further investigation showed this jar was full of scorpions with teratological anatomy. We hereby document and illustrate all of the specimens and discuss their respective anomalies. Furthermore, a comprehensive checklist of the literature on anomalies in scorpions, including giving the life stage and sex where known, is compiled for the benefit of future workers.

Smokejumper Obituary: Graves, Thomas Harry "Tom" (North Cascades 1949), National Smokejumper Association

Smokejumper Obituaries

No abstract provided.

Silla De Ruedas Para La Práctica Del Rugby, Diana Yaquelin Barrero Malagón, Jonathan Steven Vargas Cañón

Documentos de Trabajo CTeI

El rugby en silla de ruedas, como una opción de promoción de la actividad física para personas con discapacidades físicas, se convierte en un área de investigación de gran interés. Esta disciplina se aborda desde una perspectiva de salud, alentando la prevención de comorbilidades en esta población. Simultáneamente, se considera un enfoque deportivo que requiere estrategias para mejorar el desempeño atlético de los participantes.

En este contexto, esta propuesta se basa en un objetivo a corto plazo, que implica caracterizar el estado inicial de salud y realizar un análisis biomecánico del rendimiento deportivo en esta población. Luego, a largo plazo, …

Combined Purebred And Crossbred Genetic Evaluation Of Columbia, Suffolk, And Crossbred Lamb Birth And Weaning Weights: Systematic Effects And Heterogeneous Variances, Napoleón Vargas Jurado, David R. Notter, Joshua B. Taylor, Daniel J. Brown, Michelle R. Mousel, Ronald M. Lewis

Department of Animal Science: Faculty Publications

Despite the benefits of crossbreeding on animal performance, genetic evaluation of sheep in the U.S. does not directly incorporate records from crossbred lambs. Crossbred animals may be raised in different environments as compared to purebreds. Systemic factors such as age of dam and birth and rearing type may, therefore, affect purebred and crossbred performance differently. Furthermore, crossbred performance may benefit from heterozygosity, and genetic and environmental variances may be heterogeneous in different breeds and their crosses. Such issues must be accounted for in a combined (purebred and crossbred) genetic evaluation. The objectives of this study were to i) determine the …

Techniques In Multi-Omics Data Integration To Develop A Novel Proteogenomics Framework For Identification Of Proteoforms, Kanishka Manna

Theses and Dissertations

Multi-omics experimental approaches are becoming a mainstream practice in systems biology underlining the need to design new integrative techniques and applications to enable the multi-scale characterization of different types of diseases for targeted therapy. Proteogenomics, a sub-field within the broad field of multi-omics incorporates techniques to integrate genomics, transcriptomics and proteomics data for efficient identification of novel proteoforms or protein isoforms. There are multitude of challenges when applying proteogenomics analyses, such as improper integration of each omics data type, missing structural annotations, inefficient identification of splice-junctions, novel genes, etc. This dissertation will outline a novel and integrative proteogenomics pipeline that …

Isolation And Characterization Of Nut Shell Proteins From Arachis Hypogea Linn. And Cocos Nucifera Linn. And Its Effect On Macrophage Activation To Treat Visceral Leishmaniasis, Suhatha S

Theses and Dissertations

Glycoproteins are among several immunomodulatory agents known to activate the innate immune system. Plant derived glycoproteins are a generous source of glycoproteins that could be utilized as cost effective preparations for therapeutics. Isolating glycoproteins from agricultural by- products with the intention to use them against Visceral Leishmaniasis (VL) was the focus in this doctoral study. The two nut shells, Arachis hypogea L. (Groundnut) and Cocos nucifera L. (Coconut), were used for the isolation of glycoprotein used in the study. Crude glycoproteins from the A. hypogea L. (AHP-C) were isolated and fractioned. AHP-F2 was identified as 28.37 kDa Mannose/Glucose binding lectin …

Managing Soil Ph For Crop Production In Calcareous-Alkaline Soil, Cody Zesiger, Jody Gale, Matt Yost, Grant Cardon

All Current Publications

In semiarid soils of the Western U.S., altering soil pH is not easily accomplished nor straightforward. Utah’s soil pH range can be 1,000 times more acidic or alkaline than neutral (7.0) pH soils. In semiarid regions, typical high-pH soils are also calcareous, meaning there is a large amount of solid calcium carbonate (lime) in the soil. When soil-acidifying amendments are added to these soils, the lime dissolves and counteracts any of the applied soil-acidifying amendments. This fact sheet explains how to identify whether crop symptoms are related to soil pH, how to perform an in-field test for soil pH buffering …

Investigating Telomere Lengths In Chestnut-Crowned Babblers, Gabriella Rose Beberg

Honors Thesis

Telomeres are chromosomal elements that protect and maintain genes as DNA replicates in many organisms. As individuals age and DNA replicates, telomeres often shorten; thus, telomere length often corresponds with an individual’s lifespan, and early-life decreases in telomere length can be predictive of longevity. Here, I investigated the relationship between telomere length and developmental environment in a cooperatively breeding species, the chestnut-crowned babbler (Pomatostomus ruficeps; CCB). Cooperative species are unique, as some individuals give up their own breeding opportunities to help rear the offspring of others; further, cooperative breeding systems generate considerably more variation in adult carers, which …

12.11.2023 Orsp Connect, Liz Williamson

ORED Newsletter

December 11, 2023 Newsletter

Oregon State Ranking Assessment For Morrison Bumblebee (Bombus Morrisoni), Misty Nelson

Institute for Natural Resources Publications

Oregon state conservation status assessment for Morrison bumblebee (Bombus morrisoni) using NatureServe methodology, 2023.

Oregon State Rank Assessment For Yellow Bumblebee (Bombus Fervidus), Misty Nelson

Institute for Natural Resources Publications

Oregon state conservation status assessment for Yellow bumblebee (Bombus fervidus) using NatureServe methodology, 2023.