Life Sciences Commons^™

Sustainability And Drivers Of Populus Tremuloides Regeneration And Recruitment Near The Southwestern Edge Of Its Range, Connor D. Crouch, Nicholas P. Wilhelmi, Paul C. Rogers, Margaret M. Moore, Kristen M. Waring

Aspen Bibliography

Quaking aspen (Populus tremuloides Michx.) ecosystems are highly valued in the southwestern United States because of the ecological, economic, and aesthetic benefits they provide. Aspen has experienced extensive mortality in recent decades, and there is evidence that many areas in Arizona, United States lack adequate recruitment to replace dying overstory trees. Maintaining sustainable levels of regeneration and recruitment (i.e. juveniles) is critical for promoting aspen ecosystem resilience and adaptive capacity, but questions remain about which factors currently limit juvenile aspen and which strategies are appropriate for managing aspen in an increasingly uncertain future. To fill these critical knowledge gaps, …

An Approach To Identify Gene-Environment Interactions And Reveal New Biological Insight In Complex Traits, Xiaofeng Zhu, Yihe Yang, Noah Lorincz-Comi, Gen Li, Amy R Bentley, Paul S De Vries, Michael Brown, Alanna C Morrison, Charles N Rotimi, W James Gauderman, Dabeeru C Rao, Hugues Aschard

Student and Faculty Publications

There is a long-standing debate about the magnitude of the contribution of gene-environment interactions to phenotypic variations of complex traits owing to the low statistical power and few reported interactions to date. to address this issue, the Gene-Lifestyle Interactions Working Group within the Cohorts for Heart and Aging Research in Genetic Epidemiology Consortium has been spearheading efforts to investigate G × E in large and diverse samples through meta-analysis. Here, we present a powerful new approach to screen for interactions across the genome, an approach that shares substantial similarity to the Mendelian randomization framework. We identify and confirm 5 loci …

Differential Behavioral Responses In Male And Female Mice Lacking Either Rgs2 Or Rgs4 Proteins After Acute Administration Of Antidepressants And Anxiolytics, Hiroyoshi Matsui, Sarah Seeley, Manoranjan S. D'Souza

ONU Student Research Colloquium

The overall objective of the study was to assess the acute behavioral effects of currently used antidepressants and anxiolytics in male and female mice lacking regulator of G protein-signaling (RGS) proteins 2 and 4 and their wild-type counterparts. RGS 2 and 4 proteins negatively modulate signaling pathways of G protein-coupled receptors (GPCRs), which play an important role in mediating the effects of monoamine neurotransmitters such as dopamine, norepinephrine, and serotonin. These neurotransmitters in turn play an important role in the action of antidepressant and anxiolytic medications. The study was undertaken because no studies till date have systematically assessed the behavioral …

Annotation Of Hypothetical Genes In Lactococcus Lactis Ssp. Il403, Jennifer A. Tangires

Student Scholar Showcase

The human gastrointestinal tract (GIT) harnesses various microbial organisms involved in almost all processes of physiological homeostasis, among these are lactic acid bacteria (LAB). These bacteria, almost all of which belong to the order Lactobacillales, are able to produce lactic acid, and play an important role in food preservation because they produce bacteriocins. Bacteriocins are antimicrobial proteins that are used to fight off related bacteria in their environment that are competing for the same resources. This study focuses on a specific LAB strain, Lactococcus lactis ssp. IL1403 where 21.9% of its predicted genes have not yet been assigned a function. …

Tissue-Specific Atlas Of Trans-Models For Gene Regulation Elucidates Complex Regulation Patterns, Robert Dagostino, Assaf Gottlieb

Student and Faculty Publications

BACKGROUND: Deciphering gene regulation is essential for understanding the underlying mechanisms of healthy and disease states. While the regulatory networks formed by transcription factors (TFs) and their target genes has been mostly studied with relation to cis effects such as in TF binding sites, we focused on trans effects of TFs on the expression of their transcribed genes and their potential mechanisms.

RESULTS: We provide a comprehensive tissue-specific atlas, spanning 49 tissues of TF variations affecting gene expression through computational models considering two potential mechanisms, including combinatorial regulation by the expression of the TFs, and by genetic variants within the …

Unravelling The Genetic Basis Of Schizophrenia, Clara Casey, John F. Fullard, Roy D. Sleator

Department of Biological Sciences Publications

Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant genetic component, whereby an individual with an SCZ affected family member is eight times more likely to develop the disease than someone with no family history of SCZ. By examining a combination of genomic, transcriptomic and epigenomic datasets, large-scale ‘omics’ studies aim to delineate the relationship between genetic variation and abnormal cellular activity in the SCZ brain. Herein, we provide a brief overview of …

Comparative Genomics Of Selected Lactobacillus Helveticus Strains, Cain Petty

Undergraduate Research Conference

My research is to compare two strains (D76 and H10) of Lactobacillus helveticus and a shared gene between them. I would want to experiment with overexpression to test for any difference in the regulatory function of genes associated with CggR - the central glycolytic genes regulator. The poster I am presenting would outline this and provide a clearer understanding of genes and potential overexpression.

Determining The Effects Of Mistranslating Transfer Rna Variants On Drosophila Melanogaster, Joshua R. Isaacson

Electronic Thesis and Dissertation Repository

Transfer RNAs (tRNAs) play a central role in translation as adaptor molecules between mRNA and protein. Variant tRNAs can cause the misincorporation of an amino acid into a growing polypeptide. Mistranslating tRNA variants are surprisingly common in humans but the effects of mistranslating tRNA variants on eukaryotic biology are poorly understood. My thesis aimed to create a model of tRNA-induced mistranslation using the fruit fly Drosophila melanogaster and characterize the effects of mistranslating tRNA variants on eukaryotic biology.

I first integrated a gene encoding a serine tRNA variant that induced proline-to-serine (P>S) mistranslation into the fly genome. Proteins isolated …

"The Relevant History And Medical And Ethical Future Viability Of Xenotransplantation", Morgan Janes

Augustana Center for the Study of Ethics Essay Contest

Xenotransplantation, the transplantation of organs or tissues from one species to another, presents a complex nexus of medical, ethical, and cultural considerations. In this article, we delve into the multifaceted landscape of xenotransplantation, beginning with a thorough examination of its relevant historical trajectory. From early experiments to recent advancements, we chart the evolution of this field, setting the stage for a nuanced discussion. We then confront the central issue: the true medical viability of xenotransplantation and the looming specter of operative risk. By scrutinizing the ethical dilemmas inherent in xenotransplantation through a multicultural lens, we illuminate the diverse perspectives that …

Unsupervised Deep Representation Learning Enables Phenotype Discovery For Genetic Association Studies Of Brain Imaging, Khush Patel, Ziqian Xie, Hao Yuan, Sheikh Muhammad Saiful Islam, Yaochen Xie, Wei He, Wanheng Zhang, Assaf Gottlieb, Han Chen, Luca Giancardo, Alexander Knaack, Evan Fletcher, Myriam Fornage, Shuiwang Ji, Degui Zhi

Student and Faculty Publications

Understanding the genetic architecture of brain structure is challenging, partly due to difficulties in designing robust, non-biased descriptors of brain morphology. Until recently, brain measures for genome-wide association studies (GWAS) consisted of traditionally expert-defined or software-derived image-derived phenotypes (IDPs) that are often based on theoretical preconceptions or computed from limited amounts of data. Here, we present an approach to derive brain imaging phenotypes using unsupervised deep representation learning. We train a 3-D convolutional autoencoder model with reconstruction loss on 6130 UK Biobank (UKBB) participants' T1 or T2-FLAIR (T2) brain MRIs to create a 128-dimensional representation known as Unsupervised Deep learning …

Nodal Variants Are Associated With A Continuum Of Laterality Defects From Simple D-Transposition Of The Great Arteries To Heterotaxy, Zain Dardas, Jawid M Fatih, Angad Jolly, Moez Dawood, Haowei Du, Christopher M Grochowski, Edward G Jones, Shalini N Jhangiani, Xander H T Wehrens, Pengfei Liu, Weimin Bi, Eric Boerwinkle, Jennifer E Posey, Donna M Muzny, Richard A Gibbs, James R Lupski, Zeynep Coban-Akdemir, Shaine A Morris

Student and Faculty Publications

BACKGROUND: NODAL signaling plays a critical role in embryonic patterning and heart development in vertebrates. Genetic variants resulting in perturbations of the TGF-β/NODAL signaling pathway have reproducibly been shown to cause laterality defects in humans. To further explore this association and improve genetic diagnosis, the study aims to identify and characterize a broader range of NODAL variants in a large number of individuals with laterality defects.

METHODS: We re-analyzed a cohort of 321 proband-only exomes of individuals with clinically diagnosed laterality congenital heart disease (CHD) using family-based, rare variant genomic analyses. To this cohort we added 12 affected subjects with …

Swine Influenza A Virus: Challenges And Novel Vaccine Strategies, Erika Petro-Turnquist, Matthew J. Pekarek, Eric A. Weaver

Nebraska Center for Virology: Faculty Publications

Swine Influenza A Virus (IAV-S) imposes a significant impact on the pork industry and has been deemed a significant threat to global public health due to its zoonotic potential. The most effective method of preventing IAV-S is vaccination. While there are tremendous efforts to control and prevent IAV-S in vulnerable swine populations, there are considerable challenges in developing a broadly protective vaccine against IAV-S. These challenges include the consistent diversification of IAV-S, increasing the strength and breadth of adaptive immune responses elicited by vaccination, interfering maternal antibody responses, and the induction of vaccine-associated enhanced respiratory disease after vaccination. Current vaccination …

Hira Gene Mutation In Arabidopsis Via Crispr, Kelly Chen, Claire Shippy, Tara Phelps-Durr

SACAD: John Heinrichs Scholarly and Creative Activity Days

The purpose of this study is to mutate the Histone Repressor A (HIRA) gene in a mustard plant (Arabidopsis) using CRISPR technology. HIRA is a chromatin-remodeling protein that is required for proper development in both plants and animals. Creating new changes (mutations) in HIRA will help us better understand the mechanism of how HIRA regulates transcription, which is important for understanding developmental disorders in animals, as well as how improper development leads to a reduction in crop yields in plants

Where Have All The Flowers Gone? A Call For Federal Leadership In Deer Management In The United States, Bernd Blossey, Darragh Hare, Donald M. Waller

Aspen Bibliography

Forests in the United States continue to lose biodiversity and many fail to regenerate due to high deer (family Cervidae) abundance. Declines in biodiversity and overall ecosystem health due to high deer populations increases prevalence of wildlife and human diseases associated with increasing tick abundances and decreases forest resilience and the ability to deliver benefits provided by healthy ecosystems. In the eastern and midwestern United States, white-tailed deer (Odocoileus virginianus) are the main stressor, while in the western U.S. elk (Cervus elaphus) and black-tailed and mule deer (Odocoileus hemionus) can become equally problematic. Federal …

Genome-Wide Crispr Screen Reveals The Synthetic Lethality Between Bcl2l1 Inhibition And Radiotherapy, Ling Yin, Xiaoding Hu, Guangsheng Pei, Mengfan Tang, You Zhou, Huimin Zhang, Min Huang, Siting Li, Jie Zhang, Citu Citu, Zhongming Zhao, Bisrat G Debeb, Xu Feng, Junjie Chen

Student and Faculty Publications

Radiation therapy (RT) is one of the most commonly used anticancer therapies. However, the landscape of cellular response to irradiation, especially to a single high-dose irradiation, remains largely unknown. In this study, we performed a whole-genome CRISPR loss-of-function screen and revealed temporal inherent and acquired responses to RT. Specifically, we found that loss of the IL1R1 pathway led to cellular resistance to RT. This is in part because of the involvement of radiation-induced IL1R1-dependent transcriptional regulation, which relies on the NF-κB pathway. Moreover, the mitochondrial anti-apoptotic pathway, particularly the BCL2L1 gene, is crucially important for cell survival after radiation. BCL2L1 …

Exploring The Potential Pathogenicity Of A Type 2 Diabetes Mellitus Associated Insr Missense Variant Of Uncertain Significance Through Daf-2 In The Caenorhabditis Elegans Model, Brittany White

Theses

Type 2 diabetes mellitus (T2DM) is hallmarked by insulin resistance, with the INSR gene identified as a key player in this condition in humans. This gene is known to harbor genetic variants with a wide range of clinical significance from pathogenic to variants of uncertain significance (VUS) to benign. This project investigates a VUS associated with T2DM identified through ClinVar. A gene mutational analysis, predictive amino acid substitution analysis, and protein modeling predict INSR c.1628C>T (p. Thr543Met) to be likely pathogenic or damaging. PolyPhen-2 predicts this variant to be probably damaging (HumDiv score of 1.000).

Evolutionary conservation of the …

An Exploration Of The Genetics Of The Mutant Huntingtin (Mhtt) Gene In A Cohort Of Patients With Chorea From Different Ethnic Groups In Sub-Saharan Africa, Mendi J. Muthinja, Carlos Othon Guelngar, Maouly Fall, Fatumah Jama, Huda Aldeen Shuja, Jamila Nambafu, Daniel Gams Massi, Oluwadamilola Ojo, Juzar Hooker, Dilraj Sokhi

Internal Medicine, East Africa

Background: Africans are underrepresented in Huntington's disease (HD) research. A European ancestor was postulated to have introduced the mutant Huntingtin (mHtt) gene to the continent; however, recent work has shown the existence of a unique Htt haplotype in South-Africa specific to indigenous Africans.

Objective: We aimed to investigate the CAG trinucleotide repeats expansion in the Htt gene in a geographically diverse cohort of patients with chorea and unaffected controls from sub-Saharan Africa.

Methods: We evaluated 99 participants: 43 patients with chorea, 21 asymptomatic first-degree relatives of subjects with chorea, and 35 healthy controls for the presence of the mHtt. Participants …

Rainwater Harvesting Systems Metagenomics, Jade Riddle, Julia Parsons

Spring Showcase for Research and Creative Inquiry

Climate change induced water scarcity has led to an increasing interest in non-traditional water sources such as rainwater. However, there are lingering health and safety concerns due to the lack of research into the microbial communities contained within collection systems. To address this gap, water samples were collected from rain barrels around northern Virginia for microbial analysis. Each microbe within the sample has a unique genome subject to DNA testing. Environmental DNA was prepared from the collected water samples. To characterize the microbial community, both targeted sequencing and whole genome sequencing approaches were used. Using targeted sequencing of the 16s …

Search, The Jackson Laboratory

Search Magazine

No abstract provided.

Documenting The Southern Range Terminus Of The Wood Frog (Lithobates Sylvaticus) In North America, Christian Braswell

Theses

The Wood Frog (Lithobates sylvaticus) holds a remarkable position in North American amphibian biology, with its range extending from the Arctic Circle down to the near sub-tropical southeastern United States. This thesis presents a novel quantitative polymerase chain reaction analysis (qPCR) primer specific to L. sylvaticus and a survey effort regarding the southernmost distribution and detection of this species in Alabama through the application of environmental DNA (eDNA) sampling techniques. By investigating historical data and employing advanced genetic methodologies, this research provides insights into the contemporary status and distribution of the Wood Frog. This research is important to …

Deciphering The Functional Connections Between The Nuclear Paraspeckle And Rad51 Homologous Recombination Proteins Using A Yeast Protein Interaction System, Eric J. Nutz

Senior Theses

Homologous recombination (HR) is a repair pathway for DNA double-stranded breaks. Mutations in HR genes contribute to genomic instability and increase the prevalence of cancer. Exploiting HR deficiency in tumor cells has led to improved synthetic lethality outcomes. RAD51 paralogue protein complexes are known to be involved with HR. Proteomic analysis of RAD51 paralogues reveals a connection to the nuclear paraspeckle. A paraspeckle is a little-known, specialized organelle found in the interchromatin space of the nucleus in mammalian cells. Its three central protein components include SFPQ, NONO, and PSPC1. RAD51D is an HR protein shown previously to interact with SFPQ …

Case Of Human Orthohantavirus Infection, Michigan, Usa, 2021, Samuel M Goodfellow, Robert A Nofchissey, Dustin Arsnoe, Chunyan Ye, Seonghyeon Lee, Jieun Park, Won-Keun Kim, Kartik Chandran, Shannon L M Whitmer, John D Klena, Jonathan W Dyal, Trevor Shoemaker, Diana Riner, Mary Grace Stobierski, Kimberly Signs, Steven B Bradfute

Student and Faculty Publications

Orthohantaviruses cause hantavirus cardiopulmonary syndrome; most cases occur in the southwest region of the United States. We discuss a clinical case of orthohantavirus infection in a 65-year-old woman in Michigan and the phylogeographic link of partial viral fragments from the patient and rodents captured near the presumed site of infection.

A Multitrait Genetic Study Of Hemostatic Factors And Hemorrhagic Transformation After Stroke Treatment, Cristina Gallego-Fabrega, Gerard Temprano-Sagrera, Jara Cárcel-Márquez, Elena Muiño, Natalia Cullell, Miquel Lledós, Laia Llucià-Carol, Jesús M Martin-Campos, Tomás Sobrino, José Castillo, Mònica Millán, Lucía Muñoz-Narbona, Elena López-Cancio, Marc Ribó, Jose Alvarez-Sabin, Jordi Jiménez-Conde, Jaume Roquer, Silvia Tur, Victor Obach, Juan F Arenillas, Tomas Segura, Gemma Serrano-Heras, Joan Marti-Fabregas, Marimar Freijo-Guerrero, Francisco Moniche, Maria Del Mar Castellanos, Alanna C Morrison, Nicholas L Smith, Paul S De Vries, Israel Fernández-Cadenas, Maria Sabater-Lleal

Student and Faculty Publications

BACKGROUND: Thrombolytic recombinant tissue plasminogen activator (r-tPA) treatment is the only pharmacologic intervention available in the ischemic stroke acute phase. This treatment is associated with an increased risk of intracerebral hemorrhages, known as hemorrhagic transformations (HTs), which worsen the patient's prognosis.

OBJECTIVES: to investigate the association between genetically determined natural hemostatic factors' levels and increased risk of HT after r-tPA treatment.

METHODS: Using data from genome-wide association studies on the risk of HT after r-tPA treatment and data on 7 hemostatic factors (factor [F]VII, FVIII, von Willebrand factor [VWF], FXI, fibrinogen, plasminogen activator inhibitor-1, and tissue plasminogen activator), we performed …

Pedigree Analysis Of Congenital Stationary Night Blindness And Surveillance Of Related Problems In The Area Of Depalpur, Okara-Pakistan, Muhammad Abdullah, Muhammad Sajjad Sarwar, Muhammad Rizwan, Muhammad Iqbal Usama, Hamza Zulfiqar, Muhammad Wajid, Saira Ashfaq

Journal of Bioresource Management

Congenital stationary night blindness (CSNB) is described as a set of inherited, non-progressive retinal conditions in which the rod pathway is primarily affected, resulting in difficulty adapting to low-light situations due to impaired photoreceptor transmission. Objectives of study was to identify patients with CSNB and explore their lifestyle and the impact of CSNB on their daily routines in selected areas. Total seven families having CSNB, belonging to five villages (Abadi Haji Ismaeel, Sunari wala, Tibba, Shamdin, and Chorasta Mian Khan) of Depalpur, district Okara, were investigated in March 2023. The CSNB prevalence was calculated as 2.528 % in all selected …

Eurasian Aspen (Populus Tremula L.): Central Europe's Keystone Species 'Hiding In Plain Sight', Antonín Kusbach, Jan Šebesta, Robert Hruban, Pavel Peška, Paul C. Rogers

Aspen Bibliography

Knowledge of Eurasian aspen’s (Populus tremula L.) ecological and growth characteristics is of high importance to plant and wildlife community ecology, and noncommercial forest ecosystem services. This research assessed these characteristics, identified aspen’s habitat optimum, and examined causality of its current scarce distribution in central Europe. We analyzed a robust database of field measurements (4,656,130 stands) for forest management planning over 78,000 km² of the Czech territory. Our analysis we used GIS techniques, with basic and multivariate statistics such as general linear models, ordination, and classification. Results describe a species of broad ecological amplitude that has heretofore attracted …

Genetic Impact Of External Targhee Sires At The U.S. Sheep Experiment Station: A Case Study Of Introgression, Carrie S. Wilson, J. Bret Taylor, Ronald M. Lewis, David R. Notter

Department of Animal Science: Faculty Publications

Sheep breeders requested that the U.S. Sheep Experiment Station (USSES) to participate in national genetic evaluation through the National Sheep Improvement Program (NSIP). The reasons included the need for (1) a comparison of the productivity of industry and United States Department of Agriculture (USDA) lines, (2) transparency of USDA flocks, (3) genetic ties for NSIP by sampling of industry flocks, and (4) development of premium genetic lines for public release. In response, USSES began to incorporate external sires from NSIP participating flocks into the USSES Targhee flock. Our objective, based on a pedigree analysis, was to test if introgression of …

In Silico Analysis Of C-Type Lectins As Co-Infection Receptors Of Dengue And Chikungunya Viruses In Aedes Aegypti, Munawir Sazali, R. C. Hidayat Soesilohadi, Nastiti Wijayanti, Tri Wibawa, Arif Nur Muhammad Ansori

Makara Journal of Science

Aedes aegypti is a primer vector of dengue virus (DENV) and chikungunya virus (CHIKV). The susceptibility of mosquitoes to DENV and CHIKV depends on their recognition receptor of pathogens. C-type lectins (CTLs) are an important mediator of virus infection in A. aegypti. This study aims to identify potential receptors and determine the binding affinity between ligand–receptor interaction, CTLs and virus envelopes (DENV-1, 2, 3, and 4 and CHIKV) interaction based on in silico analysis. Sample sequences were obtained from GenBank (NCBI), and 10 CTLs were acquired from VectorBase. Homology modeling based on a minimum standard of 20% was processed …

Advancing Primary Ciliary Dyskinesia Diagnosis Through High-Speed Video Microscopy Analysis, Wilfredo De Jesús-Rojas, Zachary J Demetriou, José Muñiz-Hernández, Gabriel Rosario-Ortiz, Frances M Quiñones, Marcos J Ramos-Benitez, Ricardo A Mosquera

Student and Faculty Publications

Primary ciliary dyskinesia (PCD) is an inherited disorder that impairs motile cilia, essential for respiratory health, with a reported prevalence of 1 in 16,309 within Hispanic populations. Despite 70% of Puerto Rican patients having the RSPH4A [c.921+3_921+6del (intronic)] founder mutation, the characterization of the ciliary dysfunction remains unidentified due to the unavailability of advanced diagnostic modalities like High-Speed Video Microscopy Analysis (HSVA). Our study implemented HSVA for the first time on the island as a tool to better diagnose and characterize the RSPH4A [c.921+3_921+6del (intronic)] founder mutation in Puerto Rican patients. By applying HSVA, we analyzed the ciliary beat frequency …

Leucine Lock: A Diagnostic Tool To Revolutionize Rapid Antigen Testing, Kaitlyn Robinson, Jonathon Hill, Benjamin Johnson, Matt Goff

Library/Life Sciences Undergraduate Poster Competition 2024

• The current field of rapid testing uses antigen tests that are ELISA-based.

• ELISA tests are expensive and can only provide results for high-antigen loads. (asymptomatic patients and/or low-antigen samples generate inaccurate results).1

• We aim to provide a cheaper rapid test that produces both quantitative and qualitative results.

The Genome Of Huauzontle (Chenopodium Berlandieri), A North American Relative Of Quinoa, Ashley K. Marcheschi, Jeff Maughan, Peter J. Maughan, David E. Jarvis, Kate E. Jaggi, Eric N. Jellen

Library/Life Sciences Undergraduate Poster Competition 2024

Quinoa (Chenopodium quinoa) is a popular Andean seed crop that has a reduced ability to thrive outside of its native range. A related member of the Allotetraploid Goosefoot Complex (ATGC), pitseed goosefoot (Chenopodium berlandieri), is a minimally invasive North American weed that is able to survive in climates and environments that are restrictive to quinoa growth. C. berlandieri has been independently domesticated at least three times, including in Mesoamerica as the immature panicle vegetable ‘huauzontle.’ To assess the capacity of C. berlandieri as a genetic resource for improvement of C. quinoa, we sequenced the whole genome of a huauzontle accession …