Genetics and Genomics Commons^™

Precision Metagenomics In Elder Care: Renovating Infection Diagnostics And Antimicrobial Stewardship, Rob E. Carpenter

Human Resource Development Faculty Publications and Presentations

Antimicrobial resistance (AMR) remains a critical challenge in elder care, where frequent infections, polypharmacy, and immunosenescence contribute to poor outcomes. Traditional diagnostic methods, including culture-based and polymerase chain reaction assays, often fail to provide timely, comprehensive microbial identification, leading to prolonged empirical antibiotic use and worsening resistance trends. Precision metagenomics, a clinically refined application of next-generation sequencing, represents a transformative advancement in infection diagnostics and antimicrobial stewardship. By enabling culture-independent, high-resolution pathogen detection directly from clinical samples, precision metagenomics provides real-time identification of bacterial, viral, fungal, and parasitic pathogens, along with their antimicrobial resistance profiles. This approach facilitates early intervention, …

Changing Fire Regimes In The Great Basin Usa, Eva K. Strand, Kori Blankenship, Corey Gucker, Mark Brunson, Eugénie Montblanc

Aspen Bibliography

Wildfire is a natural disturbance in landscapes of the Western United States, but the effects and extents of fire are changing. Differences between historical and contemporary fire regimes can help identify reasons for observed changes in landscape composition. People living and working in the Great Basin, USA, are observing altered fire conditions, but spatial information about the degree and direction of change and departure from historical fire regimes is lacking. This study estimates how fire regimes have changed in the major Great Basin vegetation types over the past 60 years with comparisons to historical (pre-1900) fire regimes. We explore potential …

Variation In Thermal Tolerance Plasticity And The Costs Of Heat Exposure In The Estuarine Sea Hare, Phyllaplysia Taylori, Richelle L. Tanner, Rauri C. K. Bowie, Cynthia Y. Wang-Claypool, Jonathan H. Stillman

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Climate change is increasing average temperatures and the frequency and intensity of thermal extremes in coastal marine environments. Organisms in coastal marine habitats are accustomed to environmental fluctuations and possess physiological plasticity that may be advantageous in response to increased occurrence of extremes. To examine whether such plasticity is locally adapted to environmental conditions, we investigated the relationship between genetic diversity and thermal tolerance plasticity in 11 populations of the direct-developing intertidal sea hare, Phyllaplysia taylori, on the western coast of the United States. Using whole-organism metrics of muscle function and metabolic rate and a ddRADseq genomic approach, we …

Microbial Source Tracking Protocols For Differentiation Of Fecal Bacteria From Cow, Deer, And Horse, Nika Shams, Michael Beach

Symposium of Student Scholars

Microbial source tracking (MST) attempts to identify specific animal sources of fecal contamination in the environment. While traditional fecal coliform enumeration can give a general measure of contamination, the specificity imparted by modern MST provides a more informative assessment of contaminants and their likelihood to affect human health outcomes.

We have been developing an MST system that detects DNA biomarkers from the gram-negative bacterial genus Bacteroides and the family Lachnospiraceae. They are strict anaerobes found in large quantities in the intestines of animals. Unlike E. coli or Enterococci, host-specific strains of Bacteroides and Lachnospiraceae exist. To this end, we …

Transcription Factor Binding And Discovery Of Novel Gene In The Opportunistic Human Pathogen, Pseudomonas Aeruginosa, Alaina Westee

Symposium of Student Scholars

Pseudomonas aeruginosa (PA) is a gram-negative, ubiquitously-found bacterium that primarily causes nosocomial, or hospital-borne, infections within immunocompromised patients. Therefore, it has been deemed a critical priority pathogen by the World Health Organization (WHO) and the Center for Disease Control (CDC), generating a need for research on its fundamental biology. The Van Dyke laboratory focuses on proteins called transcription factors, which promote or repress gene expression to regulate an organism’s functioning. We are specifically studying the cadmium-responsive transcription factor, CadR, due to the importance of metals in virulence and the lack of information on PA’s response to metal fluctuations. We intend …

Consumer Acceptance Of Gene-Edited Food: The Role Of Knowledge, Trust, And Information, Anubrata Deka, Syed Imran Ali Meerza, Amalia Yiannaka

Cornhusker Economics

The research aims to assess consumer preferences and attitudes toward CRISPR applications in the food sector and estimate consumer willingness to pay for a food product developed using CRISPR technology to enhance food safety and confer health benefits. Additionally, the research assesses the impact of information provision on perceptions, attitudes and willingness to pay. Specifically, we consider the potential effect of both the nature of information provided (i.e., whether it emphasizes the differences between GM and CRISPR technology or not) and the delivery format (i.e., text versus video) used to present content-equivalent information. In this context, we also assess consumer …

Identification Of Novel Argonaute Proteins Using A Metagenomic Mining Approach, Lobna Abdallah Ghonaim

Theses and Dissertations

Gene editing is one of the most promising tools in science. It enables precise modifications of an organism's genetic material. Metagenomics is considered a powerful tool that unlocks the broad genetic potential found in uncultured microbial communities. Exploring the genetic diversity of uncultured microbial communities helps identify novel functional proteins with unique properties and make the best use of these diverse microbial ecosystems.

We developed and employed a metagenomic-based approach to mine more than 1000 metagenomes for prokaryotic argonaute proteins (pAgos), a potential gene editing machinery encoded in bacterial and archaeal genomes. Our workflow involved strict quality control, sequence assembly, …

Drought Resilience And Legacy Effects In Two Forest Tree Species On Loess Plateau Of China: Growth And Water-Use Efficiency Under Different Drought Conditions, Lu Han, J. Julio Camarero, Guodong Jia, Zhiqiang Zhang, Lixin Chen

Aspen Bibliography

As droughts become more frequent and severer, understanding tree resilience and its role in mediating drought legacy effects (LEs) is critical for predicting forest ecosystem responses to future droughts and informing forest management. Both Pinus tabuliformis and Populus davidiana are widely distributed in the Loess Plateau region of western China and play important roles in provision of ecosystem services. In this study we quantified the LEs and resilience, including resistance (Rt) and recovery (Rc), of radial growth (BAI, basal area increment) and intrinsic water use efficiency (iWUE) of the two species, determined the external and internal factors influencing Rt and …

Exploring The Connection Between Rna Splicing And Intellectual Disability, Anthony Caputo, Ashleigh E. Schaffer

Faculty Scholarship

Intellectual disability (ID) is a broad diagnostic category that encompasses individuals with impaired cognitive ability. While these disorders have heterogeneous causes, recent developments in next-generation sequencing (NGS) are revealing the prevalence of genetic etiologies. In particular, germline mutations in genes that affect RNA splicing are increasingly common causes of ID disorders. Research to elucidate the functional relationship between splicing and neurodevelopment is critical since molecular therapeutics require a nuanced understanding of the pathological mechanism. In this review, we first summarize the trends that have led to the discovery of the RNA splicing–ID relationship, then discuss recent progress and future directions …

Genomic And Phenotypic Correlates Of Mosaic Loss Of Chromosome Y In Blood, Yasminka A Jakubek, Xiaolong Ma, Adrienne M Stilp, Fulong Yu, Jason Bacon, Justin W Wong, Francois Aguet, Kristin Ardlie, Donna K Arnett, Kathleen Barnes, Joshua C Bis, Tom Blackwell, Lewis C Becker, Eric Boerwinkle, Russell P Bowler, Matthew J Budoff, April P Carson, Jiawen Chen, Michael H Cho, Josef Coresh, Nancy J Cox, Paul S De Vries, Dawn L Demeo, David W Fardo, Myriam Fornage, Xiuqing Guo, Michael E Hall, Nancy Heard-Costa, Bertha Hidalgo, Marguerite Ryan Irvin, Andrew D Johnson, Eric Jorgenson, Eimear E Kenny, Michael D Kessler, Daniel Levy, Yun Li, Joao A C Lima, Yongmei Liu, Adam E Locke, Ruth J F Loos, Mitchell J Machiela, Rasika A Mathias, Braxton D Mitchell, Joanne M Murabito, Josyf C Mychaleckyj, Kari E North, Peter Orchard, Stephen C J Parker, Yash Pershad, Patricia A Peyser, Katherine A Pratte, Bruce M Psaty, Laura M Raffield, Susan Redline, Stephen S Rich, Jerome I Rotter, Sanjiv J Shah, Jennifer A Smith, Aaron P Smith, Albert Smith, Margaret A Taub, Hemant K Tiwari, Russell Tracy, Bjoernar Tuftin, Alexander G Bick, Vijay G Sankaran, Alexander P Reiner, Paul Scheet, Paul L Auer

Faculty, Staff and Student Publications

Mosaic loss of Y (mLOY) is the most common somatic chromosomal alteration detected in human blood. The presence of mLOY is associated with altered blood cell counts and increased risk of Alzheimer disease, solid tumors, and other age-related diseases. We sought to gain a better understanding of genetic drivers and associated phenotypes of mLOY through analyses of whole-genome sequencing (WGS) of a large set of genetically diverse males from the Trans-Omics for Precision Medicine (TOPMed) program. We show that haplotype-based calling methods can be used with WGS data to successfully identify mLOY events. This approach enabled us to identify differences …

Extracellular Vesicles Released By All Patients Contain Hne-Adducted Proteins: Implications Of Collateral Damage., Jenni Ho, Suriyan Sukati, Tamara Taylor, Sherry Carter, Brittany Fuller, Amy Marmo, Caryn Sorge, John D'Orazio, D Allan Butterfield, Subbarao Bondada, Heidi Weiss, Daret K St Clair, Luksana Chaiswing

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Off-target neuronal injury is a serious side-effect observed in cancer survivors. It has previously been shown that pediatric acute lymphoblastic leukemia (ALL) survivors have a decline in neurocognition compared to healthy age-matched counterparts. Elevated oxidative stress has been documented to be a mediator in off-target tissue damage in cancer survivors. Early detection of oxidative stress markers may provide an opportunity to prevent off-target tissue damage. Extracellular vesicles (EVs) have surfaced as a potential diagnostic tool due to molecular cargo they contain. We investigated the potential for EVs to be a sensitive indicator of oxidative stress and off-target tissue damage by …

The Role Of Secondary And Tertiary Structure In The Cap-Independent Translation Of Fgf-9 And Hif-1-Alpha, Amanda Michelle Whittaker

Dissertations, Theses, and Capstone Projects

Under normoxic conditions, eukaryotes initiate translation of RNA through eIF4E recognition of the 5’ cap. However, under cellular stress, eukaryotic translation must be initiated through a 4E-independent, or “cap-independent” mechanism, involving eukaryotic initiation factor 4G (eIF4G) binding directly to the 5’ untranslated regions (5’ UTR) of the RNA. eIF4G binding then recruits the ribosome to the transcript. While this mechanism is useful for translation of apoptotic transcripts and transcripts involved in cell survival, cap-independent translation is also utilized by oncogenic RNA for tumorigenesis. Previous work by our lab and others has categorized this recruitment and initiation mechanism as either internal-ribosome-entry-site …

Taming Biological Complexity Through The Use Of Symmetries, Luis A. Álvarez-García

Dissertations, Theses, and Capstone Projects

The study of biological systems is, inherently, the study of very complex systems. This is essentially due to the fact that they are made up of numerous, often very complicated, interactions between an extensive number of components. Often necessitating an abundance of quantitative parameters and details for a precise description. The human brain for ex- ample, consisting of ∼ 80 billion neurons with ∼ 800 to 100 trillion connections between them, each of them depending on a large set of parameters. Even simpler examples such as bacterial organisms, such as E. coli and B. subtilis, which we focus on …

Gdp-Mannose 4,6-Dehydratase Is A Key Driver Of Mycn-Amplified Neuroblastoma Core Fucosylation And Tumorigenesis, Beibei Zhu, Michelle G. Pitts, Michael D. Buoncristiani, Lindsay T. Bryant, Oscar Lopez-Nunez, Juan P. Gurria, Cameron Shedlock, Roberto Ribas, Shannon Keohane, Jinpeng Liu, Chi Wang, Matthew S. Gentry, Nathan R. Shelman, Derek B. Allison, B. Mark Evers, Ramon C. Sun, Eric J. Rellinger

Markey Cancer Center Faculty Publications

MYCN-amplification is a genetic hallmark of ~40% of high-risk neuroblastomas (NBs). Altered glycosylation is a common feature of adult cancer progression, but little is known about how genetic signatures such as MYCN-amplification alter glycosylation profiles. Herein, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) revealed increased core fucosylated glycan abundance within neuroblast-rich regions of human MYCN-amplified NB tumors. GDP-mannose 4,6-dehydratase (GMDS) is responsible for the first-committed and rate-limiting step of de novo GDP-fucose synthesis. High GMDS expression was found to be associated with poor patient survival, advanced stage disease, and MYCN-amplification in human NB tumors. Chromatin immunoprecipitation and promoter reporter assays …

A Microrna-Regulated Transcriptional State Defines Intratumoral Cd8+ T Cells That Respond To Immunotherapy, William W. Tang, Ben Battistone, Kaylyn M. Bauer, Allison M. Weis, Cindy Barba, Muhammad Zaki Hidayatullah Fadlullah, Arevik Ghazaryan, Van B. Tran, Soh-Hyun Lee, Z. Busra Agir, Morgan C. Nelson, Emmanuel Stephen Victor, Amber Thibeaux, Colton Hernandez, Jacob Tantalla, Aik C. Tan, Dinesh Rao, Matthew Williams, Micah J. Drummond, Ellen J. Beswick, June L. Round, H. Atakan Ekiz, Warren P/ Voth, Ryan M. O’Connell

Markey Cancer Center Faculty Publications

The rising incidence of advanced-stage colorectal cancer (CRC) and poor survival outcomes necessitate new and effective therapies. Immune checkpoint inhibitors (ICIs), specifically anti-PD-1 therapy, show promise, yet clinical determinants of a positive response are suboptimal. Here, we identify microRNA-155 (miR-155) as necessary for CD8 + T cell-infiltrated tumors through an unbiased in vivo CRISPR-Cas9 screen identifying functional tumor antigen-specific CD8+ T cell-expressed microRNAs. T cell miR-155 is required for anti-PD-1 responses and for a vital intratumor CD8 + T cell differentiation cascade by repressing Ship-1, inhibiting Tcf-1 and stemness, and subsequently enhancing Cxcr6 expression, anti-tumor immunity, and effector functions. Based …

Gdp-Mannose 4,6-Dehydratase Is A Key Driver Of Mycn- Amplified Neuroblastoma Core Fucosylation And Tumorigenesis, Beibei Zhu, Michelle G. Pitts, Michael D. Buoncristiani, Lindsay T. Bryant, Oscar Lopez-Nunez, Juan P. Gurria, Cameron Shedlock, Roberto Ribas, Shannon Keohane, Jinpeng Liu, Chi Wang, Matthew S. Gentry, Nathan R. Shelman, Derek B. Allison, B. Mark Evers, Ramon C. Sun, Eric J. Rellinger

Markey Cancer Center Faculty Publications

MYCN-amplification is a genetic hallmark of ~40% of high-risk neuroblastomas (NBs). Altered glycosylation is a common feature of adult cancer progression, but little is known about how genetic signatures such as MYCN-amplification alter glycosylation profiles. Herein, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) revealed increased core fucosylated glycan abundance within neuroblast-rich regions of human MYCN-amplified NB tumors. GDP-mannose 4,6-dehydratase (GMDS) is responsible for the first-committed and rate-limiting step of de novo GDP-fucose synthesis. High GMDS expression was found to be associated with poor patient survival, advanced stage disease, and MYCN-amplification in human NB tumors. Chromatin immunoprecipitation and promoter reporter assays …

Evaluation Of Variable Selection Techniques On The Genetic Architecture Of Flowering Time In Maize, Felix Yeboah

Data Science and Data Mining

In this project, we investigate several variable selection procedures to give an overview of how well they perform on a genomic dataset using three different penalized regression approaches. Comparisons between different methods were performed. These methods include Ridge, lasso, and Elastic Net. We utilized 4494 observations with 7389 SNPs gene scores to predict time to male flowering (dtoa). We assessed the performance of these three models in terms of mean square error. Not surprisingly, Lasso and Elastic Net perform better than Ridge Regression. Overall, Elastic Net performed better in predicting the time of male flowering (dtoa).

Role Of An Smc-Like Protein, Recn, In Reca-Mediated Homology Search During Double-Strand Break Repair Via Homologous Recombination, Afroze Abdehaque Chimthanawala

Theses and Dissertations

The most deleterious form of DNA damage is the formation of a double-strand break (DSB). If left unrepaired or repaired incorrectly, DSBs can result in genome rearrangements, mutations, or even cell death. Hence, cells across domains of life have resorted to homologous recombination (HR) for the faithful repair of DSBs. A critical step in homologous recombination is the search for the intact homologous sequence by the break ends, termed ‘homology search’. This process is not well understood in vivo, especially when the break site and intact homologous template are not positioned adjacently.

Spatial reorganization of chromosomes is maintained by structural …

Mitochondrial Mrna And The Small Subunit Rrna In Budding Yeasts Undergo 3'-End Processing At Conserved Species-Specific Elements, Michael Anikin, Michael F Henry, Viktoria Hodorova, Hristo B Houbaviy, Jozef Nosek, Dimitri G Pestov, Dmitriy A Markov

Rowan-Virtua School of Osteopathic Medicine Departmental Research

Respiration in eukaryotes depends on mitochondrial protein synthesis, which is performed by organelle-specific ribosomes translating organelle-encoded mRNAs. Although RNA maturation and stability are central events controlling mitochondrial gene expression, many of the molecular details in this pathway remain elusive. These include

Timber Harvesting Was The Most Important Factor Driving Changes In Vegetation Composition, As Compared To Climate And Fire Regime Shifts, In The Mixedwood Temperate Forests Of Temiscamingue Since Ad 1830, Daniela Robles, Yan Boulanger, Jesus Pascual, Victor Danneyrolles, Yves Bergeron, Igor Drobyshev

Aspen Bibliography

Context The vegetation composition of northeastern North American forests has significantly changed since pre-settlement times, with a marked reduction in conifer-dominated stands, taxonomic and functional diversity. These changes have been attributed to fire regime shifts, logging, and climate change.

Methods In this study, we disentangled the individual effects of these drivers on the forest composition in southwestern Quebec from 1830 to 2000 by conducting retrospective modelling using the LANDIS-II forest landscape model. The model was run based on pre-settlement forest composition and fire history reconstructions, historical timber harvest records, and climate reanalysis data. We compared counterfactual scenarios excluding individual factors …

Protein Translation Rates Are Negatively Correlated With Lifespan In Inbred Drosophila Strains, Harper S Kim, Madison M Hardiman, Andrew M Pickering

Faculty, Staff and Student Publications

No abstract provided.

Mga-Related Syndrome: A Proposed Novel Disorder, Bobbi Mcgivern, Michelle M Morrow, Erin Torti, Kirsty Mcwalter, Ingrid M Wentzensen, Kristin G Monaghan, Amanda Gerard, Laurie Robak, David Chitayat, Claire Botsford, Sarah Jurgensmeyer, Peter Leahy, Paul Kruszka

Faculty, Staff and Students Publications

MGA (OMIM: 616061) encodes a dual-specificity transcription factor that regulates the expression of Max-network and T-box family target genes, important in embryogenesis. Previous studies have linked MGA to various phenotypes, including neurodevelopmental disorders, congenital heart disease, and early-onset Parkinson's disease. Here, we describe the clinical phenotype of individuals with de novo, heterozygous predicted loss-of-function variants in MGA, suggesting a unique disorder involving both neurodevelopmental and congenital anomalies. In addition to developmental delays, certain congenital anomalies were present in all individuals in this cohort including cardiac anomalies, male genital malformations, and craniofacial dysmorphisms. Additional findings seen in multiple individuals in this …

Bone Marrow Transplantation Reverses Metabolic Alterations In Multiple Sulfatase Deficiency: A Case Series, Nishitha R Pillai, Ning Liu, Xiyuan Li, Xiqi Li, Rebecca Ahrens-Nicklas, Laura Adang, Julie B Eisengart, Grace Bronken, Ashish Gupta, Troy C Lund, Chester B Whitley, Sarah H Elsea, Paul J Orchard

Faculty, Staff and Students Publications

BACKGROUND: Multiple sulfatase deficiency (MSD) is an exceptionally rare neurodegenerative disorder due to the absence or deficiency of 17 known cellular sulfatases. The activation of all these cellular sulfatases is dependent on the presence of the formylglycine-generating enzyme, which is encoded by the SUMF1 gene. Disease-causing homozygous or compound heterozygous variants in SUMF1 result in MSD. Other than symptomatic treatment, no curative therapy exists as of yet for MSD. Eight out of these 17 sulfatases are primarily localized in the lysosome.

METHODS: Two siblings with attenuated MSD underwent hematopoietic cell transplantation (HCT), evaluating the possibility of lysosomal enzymatic cross-correction from …

Evaluating Elk Distribution And Conflict Under Proposed Management Alternatives At The National Elk Refuge In Jackson, Wyoming, Gavin G. Cotterill, Paul C. Cross, Eric K. Cole, Jonathan D. Cook, Margaret C. Mceachran, Tabitha A. Graves

Aspen Bibliography

We evaluated measurable attributes describing the current and future distribution of Cervus elaphus canadensis (elk) across a region surrounding Jackson, Wyoming, for five feedground management alternatives proposed by the U.S. Fish and Wildlife Service as a revision to 2007 "Bison and Elk Management Plan" of the National Elk Refuge. A resource selection function evaluated measurable attributes of interest to managers, including elk use of private property and sensitive habitat types at monthly timesteps and varying winter conditions. The study area boundaries were created through an expert elicitation process and consist of the Jackson Elk Herd Unit, Grand Teton National Park, …

Exploring The Role Of Brain Angiogenesis Inhibitor 3 (Bai3) In Regulating Body Weight, Haifa Alsahrif

All ETDs from UAB

Obesity is a significant public health issue, strongly associated with various metabolic disorders, including type 2 diabetes and cardiovascular disease. Understanding the mechanisms that contribute to obesity is essential for developing effective interventions. One critical area of interest involves G-protein-coupled receptors (GPCRs), which are important in regulating metabolic health. These receptors are known to be involved in critical metabolic functions such as insulin secretion, lipid metabolism, and glucose uptake. The role of the GPCR, brain angiogenesis inhibitor-3 (BAI3), in metabolic regulation has not been fully explored. This dissertation focuses on the known functions of the BAI isoforms (BAI1-3) and presents …

Small Variant Benchmark From A Complete Assembly Of X And Y Chromosomes, Justin Wagner, Nathan D Olson, Jennifer Mcdaniel, Lindsay Harris, Brendan J Pinto, David Jáspez, Adrián Muñoz-Barrera, Luis A Rubio-Rodríguez, José M Lorenzo-Salazar, Carlos Flores, Sayed Mohammad Ebrahim Sahraeian, Giuseppe Narzisi, Marta Byrska-Bishop, Uday S Evani, Chunlin Xiao, Juniper A Lake, Peter Fontana, Craig Greenberg, Donald Freed, Mohammed Faizal Eeman Mootor, Paul C Boutros, Lisa Murray, Kishwar Shafin, Andrew Carroll, Fritz J Sedlazeck, Melissa Wilson, Justin M Zook

Faculty, Staff and Students Publications

The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To enable technology developers along with research and clinical laboratories to evaluate variant detection on male sex chromosomes X and Y, we create a small variant benchmark set with 111,725 variants for the Genome in a Bottle HG002 reference material. We develop an active evaluation approach to demonstrate the benchmark set reliably identifies errors in challenging genomic regions and across short and long read callsets. We show how complete assemblies can expand benchmarks to difficult regions, but highlight …

Increased Positive Tree Species Mixture Effects On The Abundance And Richness Of Collembola With Stand Development In Canadian Boreal Forests, Yakun Zhang, Sai Peng, Zilong Ma, Chen Chen, Bilei Gao, Xinli Chen, Han Y.H. Chen

Aspen Bibliography

It is well established that species mixtures could enhance ecosystem functioning in diverse ecosystem types, with these benefits increasing over time. However, the impact of tree mixtures on Collembola communities following stand development in natural forests remains unclear, despite the critical roles Collembola plays in litter decomposition and nutrient cycling. We investigated the effects of tree species mixtures on Collembola abundance, diversity, and community structure by sampling pure and mixed jack pine (Pinus banksiana Lamb.) and trembling aspen (Populus tremuloides Michx.) of 15-year-old and 41-year-old stands in natural boreal forest. In total, 6,620 individuals of Collembola were identified …

Gene Model For The Ortholog Of Glys In Drosophila Simulans, Madeline L. Gruys, Madison A. Sharp, Zachary Lill, Caroline Xiong, Amy T. Hark, James J. Youngblom, Chinmay P. Rele, Laura K. Reed

Faculty Journal Articles

Gene model for the ortholog of glycogen synthase ( Glys ) in the Drosophila simulans May 2017 (Princeton ASM75419v2/DsimGB2) Genome Assembly (GenBank Accession: GCA_000754195.3 ). This ortholog was characterized as part of a developing dataset to study the evolution of the Insulin/insulin-like growth factor signaling pathway (IIS) across the genus Drosophila using the Genomics Education Partnership gene annotation protocol for Course-based Undergraduate Research Experiences.

Rpa And Rad27 Limit Templated And Inverted Insertions At Dna Breaks, Yang Yu, Xin Wang, Jordan Fox, Qian Li, Yang Yu, P J Hastings, Kaifu Chen, Grzegorz Ira

Faculty, Staff and Students Publications

Formation of templated insertions at DNA double-strand breaks (DSBs) is very common in cancer cells. The mechanisms and enzymes regulating these events are largely unknown. Here, we investigated templated insertions in yeast at DSBs using amplicon sequencing across a repaired locus. We document very short (most ∼5-34 bp), templated inverted duplications at DSBs. They are generated through a foldback mechanism that utilizes microhomologies adjacent to the DSB. Enzymatic requirements suggest a hybrid mechanism wherein one end requires Polδ-mediated synthesis while the other end is captured by nonhomologous end joining (NHEJ) or by alternative end joining (Alt-EJ). This process is exacerbated …

Investigating The Thermodynamic Properties Of Fat10 And Fat10ylated Proteins, Aravind R

Theses and Dissertations

Degradation of proteins by the proteasome is crucial in regulating protein levels in the cell. Post-translational modifications, such as ubiquitylation and Fat10ylation, trigger proteasomal degradation of the substrate proteins. While ubiquitylation orchestrates multiple cellular processes, Fat10ylation is primarily involved in the inflammatory response. Unlike ubiquitin, recycled upon substrate degradation, Fat10 is degraded along with its substrate. Although the thermodynamic properties of the substrate are critical for effective proteasomal degradation, they remain poorly understood for the Fat10-proteasome pathway.

Here, we demonstrate that Fat10 exhibits markedly lower thermodynamic stability and faster unfolding kinetics compared to ubiquitin. This is due to the absence …