Genetics and Genomics Commons^™

Microrna Profiling In The Weddell Seal Suggests Novel Regulatory Mechanisms Contributing To Diving Adaptation, Luca Penso-Dolfin, Wilfried Haerty, Allyson Hindle, Federica Di Palma

Life Sciences Faculty Publications

Background:The Weddell Seal (Leptonychotes weddelli) represents a remarkable example of adaptation to diving among marine mammals. This species is capable of diving... (See full abstract in article).

Cov Genome Tracker: Tracing Genomic Footprints Of Covid-19 Pandemic, Saymon Akther, Edgaras Bezrucenkovas, Brian Sulkow, Christopher Panlasigui, Li Li, Wei-Gang Qiu, Lia Di

Publications and Research

Genome sequences constitute the primary evidence on the origin and spread of the 2019-2020 Covid-19 pandemic. Rapid comparative analysis of coronavirus SARS-CoV-2 genomes is critical for disease control, outbreak forecasting, and developing clinical interventions. CoV Genome Tracker is a web portal dedicated to trace Covid-19 outbreaks in real time using a haplotype network, an accurate and scalable representation of genomic changes in a rapidly evolving population. We resolve the direction of mutations by using a bat-associated genome as outgroup. At a broader evolutionary time scale, a companion browser provides gene-by-gene and codon-by-codon evolutionary rates to facilitate the search for molecular ...

Evolutionary Ecology Of Host-Parasite Relationships: Role Of Host Ecology, Phylogeny, And Demographics In Shaping Parasite Evolution, Erika Taylor Gendron

Biology ETDs

Host-parasite systems exist across complex and ecologically heterogeneous landscapes, and may occur across taxonomically and ecologically disparate host species. Under these conditions, mechanisms underlying microevolutionary processes (i.e. gene flow, genetic drift) are not always clear, and may be mediated by numerous co-occurring factors specific to individual hosts. Host traits such as host immunology, demographics, phylogeny and ecology may act in concert to shape host-parasite relationships, and ultimately evolutionary processes. The research described herein used phylogeographic, phylogenomic, and population genetic methods to further understanding of how host traits impact the evolutionary ecology of trematode systems, using avian schistosomes (Digenea: Schistosomatidae ...

Examining Phenotypic Structural Traits As Indicators For Reproductive Longevity Success In Sows, Lindsay Kate Peters, Melanie Dawn Trenhaile-Grannemann, Benny Edd Mote

UCARE Research Products

The objective of this study was to examine structure and body conformation traits of 494 gilts/sows as a prediction of reproductive longevity in sows. This study focused on specific traits including body length, body depth, front and rear pastern angles, knee angle, and hock angle. The primary method of data collection was based on videos. Still images were pulled from the videos when the sow was standing in a natural stance. The images were analyzed and interpreted objectively with Image J which gives the availability to measure distance and angles given known references in the images. The structural data ...

Trim34 Restricts Hiv-1 And Siv Capsids In A Trim5alpha-Dependent Manner, Molly Ohainle, Kyusik Kim, Sevnur Komurlu Keceli, Abby Felton, Ed Campbell, Jeremy Luban, Michael Emerman

Open Access Articles

The HIV-1 capsid protein makes up the core of the virion and plays a critical role in early steps of HIV replication. Due to its exposure in the cytoplasm after entry, HIV capsid is a target for host cell factors that act directly to block infection such as TRIM5alpha and MxB. Several host proteins also play a role in facilitating infection, including in the protection of HIV-1 capsid from recognition by host cell restriction factors. Through an unbiased screening approach, called HIV-CRISPR, we show that the CPSF6-binding deficient, N74D HIV-1 capsid mutant is sensitive to restriction mediated by human TRIM34 ...

Identification Of Staphylococcus Aureus In State Fair Samples, Ana Castillo Jimenez

Research and Scholarship Symposium Posters

No abstract provided.

Interpretation Of The Epigenetic Signature Of Facioscapulohumeral Muscular Dystrophy In Light Of Genotype-Phenotype Studies, Ana Nikolic, Louise Maranda, Rossella Ginevra Tupler

Open Access Articles

Facioscapulohumeral muscular dystrophy (FSHD) is characterized by incomplete penetrance and intra-familial clinical variability. The disease has been associated with the genetic and epigenetic features of the D4Z4 repetitive elements at 4q35. Recently, D4Z4 hypomethylation has been proposed as a reliable marker in the FSHD diagnosis. We exploited the Italian Registry for FSHD, in which FSHD families are classified using the Clinical Comprehensive Evaluation Form (CCEF). A total of 122 index cases showing a classical FSHD phenotype (CCEF, category A) and 110 relatives were selected to test with the receiver operating characteristic (ROC) curve, the diagnostic and predictive value of D4Z4 ...

Histone Deacetylases 1 And 2 Silence Cryptic Transcription To Promote Mitochondrial Function During Cardiogenesis, Zachary J. Milstone, Sherin Saheera, Lauren Bourke, Tomer Shpilka, Cole M. Haynes, Chinmay M. Trivedi

Open Access Articles

Cryptic transcription occurs widely across the eukaryotic genome; however, its regulation during vertebrate development is not understood. Here, we show that two class I histone deacetylases, Hdac1 and Hdac2, silence cryptic transcription to promote mitochondrial function in developing murine hearts. Mice lacking Hdac1 and Hdac2 in heart exhibit defective developmental switch from anaerobic to mitochondrial oxidative phosphorylation (OXPHOS), severe defects in mitochondrial mass, mitochondrial function, and complete embryonic lethality. Hdac1/Hdac2 promotes the transition to OXPHOS by enforcing transcriptional fidelity of metabolic gene programs. Mechanistically, Hdac1/Hdac2 deacetylates histone residues including H3K23, H3K14, and H4K16 to suppress cryptic transcriptional initiation ...

Comparative Lipidomics Of 5-Fluorouracil-Sensitive And -Resistant Colorectal Cancer Cells Reveals Altered Sphingomyelin And Ceramide Controlled By Acid Sphingomyelinase (Smpd1)., Jae Hun Jung, Kohei Taniguchi, Hyeong Min Lee, Min Young Lee, Raju Bandu, Kazumasa Komura, Kil Yeon Lee, Yukihiro Akao, Kwang Pyo Kim

Articles, Abstracts, and Reports

5-Fluorouracil (5-FU) is a chemotherapeutic drug widely used to treat colorectal cancer. 5-FU is known to gradually lose its efficacy in treating colorectal cancer following the acquisition of resistance. We investigated the mechanism of 5-FU resistance using comprehensive lipidomic approaches. We performed lipidomic analysis on 5-FU-resistant (DLD-1/5-FU) and -sensitive (DLD-1) colorectal cancer cells using MALDI-MS and LC-MRM-MS. In particular, sphingomyelin (SM) species were significantly up-regulated in 5-FU-resistant cells in MALDI-TOF analysis. Further, we quantified sphingolipids including SM and Ceramide (Cer) using Multiple Reaction Monitoring (MRM), as they play a vital role in drug resistance. We found that 5-FU resistance ...

Dugesia Japonica Is The Best Suited Of Three Planarian Species For High-Throughput Toxicology Screening, D. Ireland, Veronica Bochenek , '22, Daniel Chaiken , '20, C. Rabeler, Sumi Onoe , '21, Ameet Soni, Eva-Maria S. Collins

Biology Faculty Works

High-throughput screening (HTS) using new approach methods is revolutionizing toxicology. Asexual freshwater planarians are a promising invertebrate model for neurotoxicity HTS because their diverse behaviors can be used as quantitative readouts of neuronal function. Currently, three planarian species are commonly used in toxicology research: Dugesia japonica, Schmidtea mediterranea, and Girardia tigrina. However, only D. japonica has been demonstrated to be suitable for HTS. Here, we assess the two other species for HTS suitability by direct comparison with D. japonica. Through quantitative assessments of morphology and multiple behaviors, we assayed the effects of 4 common solvents (DMSO, ethanol, methanol, ethyl acetate ...

Environmental Dna Metabarcoding Detects Mammal Use Of Stock Tanks And Natural Springs On The Prescott National Forest, K. A. Smith, Berenice Carreras Mendiolea, C. E. Benson, F. B. Anaya

Discovery Day - Prescott

Recent research has shown the viability of environmental DNA (eDNA) analysis as a tool for identifying species presence in aquatic ecosystems. However, there is limited research indicating the feasibility of eDNA as a survey tool in water sources such as springs and stock tanks. Because of the scarcity of water in the high desert landscape of Arizona, natural springs and stock tanks are an important water resource. In this study, we examined whether 16S rRNA metabarcoding could detect mammal eDNA in springs and stock tanks in the Prescott National Forest. During summer 2019, we collected and analyzed water samples at ...

Relative Model Fit Does Not Predict Topological Accuracy In Single-Gene Protein Phylogenetics, Stephanie J. Spielman

Faculty Scholarship for the College of Science & Mathematics

It is regarded as best practice in phylogenetic reconstruction to perform relative model selection to determine an appropriate evolutionary model for the data. This procedure ranks a set of candidate models according to their goodness of fit to the data, commonly using an information theoretic criterion. Users then specify the best-ranking model for inference. Although it is often assumed that better-fitting models translate to increase accuracy, recent studies have shown that the specific model employed may not substantially affect inferences. We examine whether there is a systematic relationship between relative model fit and topological inference accuracy in protein phylogenetics, using ...

Npgreat: Hybrid Assembly Of Human Subtelomeres With The Use Of Nanopore And Linked-Read Datasets, Eleni Adam, Desh Ranjan, Harold Riethman

College of Sciences Posters

The telomeres are vitally important regions that are located at the tips of the chromosomes. Their dysfunction, caused by length shortening can lead to senescent cells, which in turn cause age-related diseases, including cancer. The subtelomeres, located next to the telomeres, possess the critical role of regulating the adjacent telomere lengths. Even after many years of research, human subtelomeres have proven to be very hard to assemble due to their morphology. In order to overcome these problems, the hybrid assembly method we develop utilizes two of the latest available types of data, which complement each other: Linked-Reads and ultralong Nanopore ...

Tip60 Regulation Of Δnp63Α Is Associated With Cisplatin Resistance, Akshay Hira, Andrew Stacy, Jin Zhang, Michael P. Craig, Madhavi Kadakia

Symposium of Student Research, Scholarship, and Creative Activities Materials

About 5.4 million basal and squamous cell skin cancers are diagnosed every year in the US. ΔNp63a, a member of the p53 transcription factor family, is overexpressed in non-melanoma skin cancer and regulates cell survival, migration and invasion. TIP60 is histone acetyltransferase (HAT) which mediates cellular processes such as transcription and the DNA damage response (DDR). Previous studies in our lab have shown that overexpression of TIP60 induces ΔNp63a protein stabilization in a catalytic-dependent manner. Since ΔNp63a is known to transcriptionally regulate several DDR genes and promote cisplatin resistance, its stabilization by TIP60 may contribute to the failure of ...

Conservation Of Bta-Mir-29b And Its Effect On Human Gene Expression, Anna Barent, Katie Meinders, Daniel Gutzmann, Audrey L. Atkin

UCARE Research Products

The purposeof this work was to examine conservation of miR-29b and its binding sites in target mRNAs as well as co-expression of bta-miR-29b in bovine milk exosomes and its target mRNAs in HEK293 cells

•miRNAs are often highly conserved across species and bind to target mRNAs resulting in decreased gene expression. •Bovine milk exosomes contain miRNAs and most of these miRNAs are identical to human miRNAs. •Because these miRNAs are so conserved, it is hypothesized that bovine miRNAs can regulate gene expression and be linked to disease risk.

•miR-29b is highly conserved. •Identified 17 experimentally validated miR-29b target mRNAs. •The ...

Antibiotic Resistant Bacteria, Antibiotic Resistance Genes And Potential Drivers In The Aquatic Environments, Shuo Shen

Dissertations

As antibiotic resistance genes in aquatic environment have been increasing across the world, affecting water quality and public health, many studies documented concentrations of antibiotic resistance genes and some studies discussed their potential drivers. However, systematic and quantitative reviews that link antibiotic resistance genes (ARGs) to anthropogenic and environmental factors are limited. Nevertheless, this information will be important for developing regulation policy on controlling antibiotic use and therefore reducing potential risks to antibiotic resistance. I conducted meta-analysis of ARGs concentration at a global scale using Bayesian inference to explore climatic and socio-economic factors as drivers. I found local-scale climatic variables ...

The Ecology And Evolutionary History Of Two Musk Turtles In The Southeastern United States, Grover Brown

Dissertations

Turtles are among one of the most imperiled vertebrate groups on the planet with more than half of all species worldwide listed as threatened, endangered or extinct by the International Union of the Conservation of Nature. The Southeastern United States is a global biodiversity hotspot for turtles, and it likely represents the last area on the planet of both high diversity and high abundance of turtle species. In the past century, there has been an exponential increase in the number of publications on turtles in the United States and Canada, however a recent review of the literature suggests that this ...

Publisher Correction: Memote For Standardized Genome-Scale Metabolic Model Testing., Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Parizad Babaei, Jennifer A Bartell, Lars M Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta E Ebert, Janaka N Edirisinghe, José P Faria, Adam M Feist, Georgios Fengos, Ronan M T Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout Van Helvoirt, Christopher S Henry, Henning Hermjakob, Markus J Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary King, Steffen Klamt, Edda Klipp, Jasper J Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L Medlock, Jonathan M Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O Palsson, Jason A Papin, Kiran R Patil, Mark Poolman, Nathan D Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J Sánchez, Peter J Schaap, Rahuman S Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A H Wodke, Joana C Xavier, Qianqian Yuan, Maksim Zakhartsev, Cheng Zhang

Articles, Abstracts, and Reports

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Assessing Social Media For Themes Of Trisomy 18 And 13, Falecia Metcalf

Theses and Dissertations

Themes within virtual communities have been explored examining topics such as prenatal diagnosis and termination for fetal anomalies, and it is known that when receiving a diagnosis of trisomy 18 or 13 parents may turn to online resources for information and emotional support. Knowledge of what content patients may encounter on various social media platforms about prenatal testing for trisomy 18 and 13 at large has not yet been established. However, this information would aid healthcare professionals in providing anticipatory guidance for patients using social media.

This study is a preliminary scan of social media to identify content areas and ...

A Novel Landscape Of Nuclear Human Cdk2 Substrates Revealed By In Situ Phosphorylation., Yong Chi, John H Carter, Jherek Swanger, Alexander V Mazin, Robert L Moritz, Bruce E Clurman

Articles, Abstracts, and Reports

Cyclin-dependent kinase 2 (CDK2) controls cell division and is central to oncogenic signaling. We used an "in situ" approach to identify CDK2 substrates within nuclei isolated from cells expressing CDK2 engineered to use adenosine 5'-triphosphate analogs. We identified 117 candidate substrates, ~40% of which are known CDK substrates. Previously unknown candidates were validated to be CDK2 substrates, including LSD1, DOT1L, and Rad54. The identification of many chromatin-associated proteins may have been facilitated by labeling conditions that preserved nuclear architecture and physiologic CDK2 regulation by endogenous cyclins. Candidate substrates include proteins that regulate histone modifications, chromatin, transcription, and RNA/DNA ...