Genetics Commons^™

Pyrus Calleryana Extracts Reduce Germination Of Native Grassland Species, Suggesting The Potential For Allelopathic Effects During Ecological Invasion, Michaela J. Woods, Jonathan T. Bauer, Dena Schaeffer, Ryan W. Mcewan

Biology Faculty Publications

Invasive plant species’ success may be a result of allelopathy, or the release of secondary metabolites that are harmful for surrounding plant species. Allelopathy can be mediated through the abiotic environment by chemical sorption or transformation, so the substrate on which interactions occur can lead to differential outcomes in allelopathic potential. One aggressive invader, Pyrus calleryana, has become dominant in many ecosystems throughout Eastern US, and has reduced the abundance of native species where it invades. Thus, our goal was to identify if P. calleryana had allelopathic potential by testing the impact of leaf and flower leachate on gemination …

Localization Of Ctg-Repeat-Containing Transgenes In Drosophila Melanogaster Myotonic Dystrophy Models, Andrea Waltrip

Departmental Honors & Graduate Capstone Projects

Myotonic Dystrophy Type 1, DM1, is a multi-systemic muscle wasting disorder that results from expression of expanded CTG repeats in the DMPK gene in humans. Three transgenic Drosophila melanogaster lines have been created containing 60, 250, or 480 CTG repeats to model DM1. The transgenic repeats are expressed using the GAL4/UAS system. Expression of long-repeat transgenes ((CTG)₂₅₀ and i(CTG)₄₈₀) produces phenotypes consistent with DM1, relative to control lines ((CTG)₆₀). The precise chromosomal location of insertion of the transgenes has not been reported. We used classical genetic approaches to localize CTG-repeat transgene insertion to a specific …

Soil Microbial Community Composition Of White Oak Mountain, Tennessee, Matthew Gano, Timothy D. Trott

Research in Biology

Abstract - Soil microbial communities are responsible for nutrient cycling in terrestrial ecosystems and have symbiotic and parasitic relationships with the plant community. However, little is known about the factors that determine the soil microbial community composition. In this study we examined how spring wildflower diversity and geographical factors influence the soil microbial community composition of the second growth oak hickory forests of White Oak Mountain in Southeast Tennessee. The characterization of the soil microbial community was completed with 16S/18S/ITS rDNA amplicon sequencing of total DNA extracted from soil samples that were normalized for each sample plot. Here we characterize …

Examining The Different Soil Horizons Of White Oak Mountain, Tn And Their Effect On The Soil Microbial Community, Ji Won Moon, Timothy D. Trott

Research in Biology

Soil microorganisms participate in the diverse interaction within virtually all ecosystems, consequently affecting the associated human and animal population. Identifying how edaphic variables alter the functional and taxonomic diversity of the soil microbial community requires an examination of total microbial soil diversity and abundance. This research study examined the effect of soil depth and horizon on the soil microbial community composition of White Oak Mountain. The soil microbial community was characterized by 16S/18S/ITS rDNA amplicon sequencing of the DNA extract of six samples from the three major soil types identified: HcE, MoE, and uMvC. OTU clustering analysis and both alpha …

A Meta-Narrative Review: Efficacy Of Non-Invasive Prenatal Testing (Nipt) In The Detection Of Sex Chromosomal Aneuploidy In Singleton Pregnancy, Tien T. Dao, Arianna Fields, Annie Huynh, Nikkita Mcghee, Christian Pellegrini

Research Methods Poster Session 2023

Abstract:

Objective: To assess the efficacy of Noninvasive Prenatal Testing (NIPT) as a screening method for Sex Chromosomal Aneuploidy (SCA) and its application in clinical practice.

Methods: Searches on Pubmed and M.D. Anderson Cancer Center Research Medical Library was performed to identify primary research articles published between January 2018 to April 2023.

Results: The average combined SCA's PPV was 46.08%. The average PPV for 45, X, 47, XXX, 47, XXY, and 47, XYY was 26.05%, 44.82%, 50.21%, and 62.99%, respectively. The average PPV for 46, XY was 1.18%; however, there is a lack of statistical data for 46, XY. NIPT …

The Presence Of Tetracycline-Resistant Bacteria In A Kean University Campus Soil Sample, Esther Blankson, Jessica Kobilas, Gianna Medeiros

Kean Quest

The spread of antimicrobial resistance (AMR) in the environment is a worldwide problem that threatens human health. Bacteria are becoming increasingly resistant to antibiotics as the consumption of antibiotics grows. In particular, soil can be contaminated with bacteria that are resistant to antibiotics. As of today, there is no surveillance system that tracks the spread of antibiotic-resistant bacteria, however, Tufts University aims to change this by implementing the Prevalence of Antibiotic Resistance in the Environment (PARE) project. The course-based PARE project consists of research students sampling soil in diverse locations and reporting the prevalence of antibiotic-resistant bacteria. The purpose of …

The Role Of Community In Immunity Against Sars-Cov-2, Jessica Kobilas

Kean Quest

This literature review investigated the roles genes activated by social interactions had in helping to build immunity against COVID-19. Past studies have shown that individuals who are more socially connected are less likely to become ill due to social interactions strengthening the immune system through optimal exposure to bacteria and viruses in the environment. The IL-6 and TLR4 genes that are activated through social interactions and associated with cytokines have been analyzed in cases of various viral infections. Cytokines play a role in inflammation and have both pro-inflammatory and anti-inflammatory responses to infections and viruses. The results suggest that the …

The Genomics Of Autism-Related Genes Il1rapl1 And Il1rapl2: Insights Into Their Cortical Distribution, Cell-Type Specificity, And Developmental Trajectories, Jacob Weaver

MUSC Theses and Dissertations

Neuropsychiatric disorders have a significant impact on modern society. These disorders affect a large percentage of the population: schizophrenia has a world-wide prevalence of 1% and autism spectrum disorders (ASD) affects 1 in 59 school-aged children in the US. There is substantial evidence that most neuropsychiatric disorders have a genetic component. Thus, with the advent of high throughput sequencing much effort has gone into identifying genetic variants associated with these disorders. The emerging picture from these studies is a complex one where hundreds of genes with small effects interact with a varied landscape of common variants to result in disease. …

Physiological And Transcriptomic Responses Of Two Artemisia Californica Populations To Drought: Implications For Restoring Drought-Resilient Native Communities, Hagop S. Atamian Dr., Jennifer L. Funk

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

As climate change brings drier and more variable rainfall patterns to many arid and semi-arid regions, land managers must re-assemble appropriate plant communities for these conditions. Transcriptome sequencing can elucidate the molecular mechanisms underlying plant responses to changing environmental conditions, potentially enhancing our ability to screen suitable genotypes and species for restoration. We examined physiological and morphological traits and transcriptome sequences of coastal and inland populations of California sagebrush (Artemisia californica), a critical shrub used to restore coastal sage scrub vegetation communities, grown under low and high rainfall environments. The populations are located approximately 36 km apart but …

How Accurately Structure Can Identify Hybrids When Comparing Different Numbers Of Species And Marker Types And Numbers, Chloe Hendrikse

2023 Midwest Ecology & Evolution Conference

Hybridization is a common problem in conservation. It can be difficult to identify hybrid individuals but doing so is often necessary in order to make conservation recommendations. For example, botanical gardens and seed banks want to identify if individuals are hybrids of two or more species to determine if offspring could be used for conservation or restoration, and to analyze the risk of possible extinction via introgression. Our project looks at how well the program STRUCTURE can detect and cluster hybrids, their parent species, and other pure species, which we created using simulations. We build on past studies, which typically …

Qtl Analysis Of Body Size And Development Time In Dendroctonus Ponderosae, Camille M. Pushman

2023 Midwest Ecology & Evolution Conference

The mountain pine beetle (MPB, Dendroctonus ponderosae) is a pest species found in western Norh America that attacks and kills Pinus host trees. Previous studies have identified genetic divergence between populations and variation in life-history traits (body size and development time) that are likely important in local adaptation. To understand the underlying genetic architecture of MPB adaptation and divergence, we performed an F₁ intercross between two distinct populations (Utah & Arizona) and performed a QTL analysis. We analyzed double digest RAD sequencing data from 181 F2 individuals. Our final dataset consists of 986 SNPs and we were able to …

Gaming To Learn Genetics, Sarah Wolfe

Undergraduate Honors Thesis Projects

Digital game-based learning is an alternative to traditional lecture learning. It involves active engagement with concepts in a digital game setting and can apply to a variety of subjects, including STEM fields. We examined this type of learning in the context of an undergraduate introductory genetics course: specifically, use of a genetics video game for teaching. There were two groups: an experimental group that played the genetics game Geniventure, and a control group that read and studied Powerpoint lecture slides. Both groups took a pretest and posttest, as well as completed an I/D (interest/deprivation) scale and workload scale. There …

A Kinome-Wide Crispr Screen Identifies Ck1Α As A Target To Overcome Enzalutamide Resistance Of Prostate Cancer, Jinghui Liu, Yue Zhao, Daheng He, Katelyn M. Jones, Shan Tang, Derek B. Allison, Yanquan Zhang, Jing Chen, Qiongsi Zhang, Xinyi Wang, Chaohao Li, Chi Wang, Lang Li, Xiaoqi Liu

Markey Cancer Center Faculty Publications

Enzalutamide (ENZA), a second-generation androgen receptor antagonist, has significantly increased progression-free and overall survival of patients with metastatic prostate cancer (PCa). However, resistance remains a prominent obstacle in treatment. Utilizing a kinome-wide CRISPR-Cas9 knockout screen, we identified casein kinase 1a (CK1a) as a therapeutic target to overcome ENZA resistance. Depletion or pharmacologic inhibition of CK1a enhanced ENZA efficacy in ENZA-resistant cells and patient-derived xenografts. Mechanistically, CK1a phosphorylates the serine residue S1270 and modulates the protein abundance of ataxia telangiectasia mutated (ATM), a primary initiator of DNA double-strand break (DSB)-response signaling, which is compromised in ENZA-resistant cells and patients. Inhibition of …

Identification Of A Nacc1-Regulated Gene Signature Implicated In The Features Of Triple-Negative Breast Cancer, Chrispus Ngule, Hami Hemati, Xingcong Ren, Oluwafunminiyi Obaleye, Amos O. Akinyemi, Felix Oyelami, Xiaofang Xiong, Jianxun Song, Xia Liu, Jin-Ming Yang

Markey Cancer Center Faculty Publications

Triple-negative breast cancer (TNBC), characterized by a deficiency in estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor2 (HER2), is among the most lethal subtypes of breast cancer (BC). Nevertheless, the molecular determinants that contribute to its malignant phenotypes such as tumor heterogeneity and therapy resistance, remain elusive. In this study, we sought to identify the stemness-associated genes involved in TNBC progression. Using bioinformatics approaches, we found 55 up- and 9 downregulated genes in TNBC. Out of the 55 upregulated genes, a 5 gene-signature (CDK1, EZH2, CCNB1, CCNA2, and AURKA) involved in cell regeneration was positively correlated …

Leukocyte Tyrosine Kinase (Ltk) Is The Mendelian Determinant Of The Axolotl Melanoid Color Variant, Mirindi Kabangu, Raissa Cecil, Lloyd Strohl Ii, Nataliya Y. Timoshevskaya, Jeramiah James Smith, Stephen Randal Voss

Markey Cancer Center Faculty Publications

The great diversity of color patterns observed among amphibians is largely explained by the differentiation of relatively few pigment cell types during development. Mexican axolotls present a variety of color phenotypes that span the continuum from leucistic to highly melanistic. The melanoid axolotl is a Mendelian variant characterized by large numbers of melanophores, proportionally fewer xanthophores, and no iridophores. Early studies of melanoid were influential in developing the single-origin hypothesis of pigment cell development, wherein it has been proposed that all three pigment cell types derive from a common progenitor cell, with pigment metabolites playing potential roles in directing the …

In Situ Microwave Fixation Provides An Instantaneous Snapshot Of The Brain Metabolome, Jelena A. Juras, Madison B. Webb, Lyndsay E. A. Young, Kia H. Markussen, Tara R. Hawkinson, Michael D. Buoncristiani, Kayli E. Bolton, Peyton T. Coburn, Meredith I. Williams, Lisa P. Y. Sun, William C. Sanders, Ronald C. Bruntz, Lindsey R. Conroy, Chi Wang, Matthew S. Gentry, Bret N. Smith, Ramon C. Sun

Markey Cancer Center Faculty Publications

Brain glucose metabolism is highly heterogeneous among brain regions and continues postmortem. In particular, we demonstrate exhaustion of glycogen and glucose and an increase in lactate production during conventional rapid brain resection and preservation by liquid nitrogen. In contrast, we show that these post- mortem changes are not observed with simultaneous animal sacrifice and in situ fixation with focused, high- power microwave. We further employ microwave fixation to define brain glucose metabolism in the mouse model of streptozotocin-induced type 1 diabetes. Using both total pool and isotope tracing analyses, we identified global glucose hypometabolism in multiple brain regions, evidenced by …

Targeting Lncrna Ddit4-As1 Sensitizes Triple Negative Breast Cancer To Chemotherapy Via Suppressing Of Autophagy, Ting Jiang, Jiaojiao Zhu, Shilong Jiang, Zonglin Chen, Ping Xu, Rong Gong, Changxin Zhong, Yueying Cheng, Xinyuan Sun, Wenjun Yi, Jinming Yang, Wenhu Zhou, Yan Cheng

Markey Cancer Center Faculty Publications

In this study, it is found that the lncRNA, DNA damage inducible transcript 4 antisense RNA1 (DDIT4-AS1), is highly expressed in triple-negative breast cancer (TNBC) cell lines and tissues due to H3K27 acetylation in the promoter region, and promotes the proliferation, migration, and invasion of TNBC cells via activating autophagy. Mechanistically, it is shown that DDIT4-AS1 induces autophagy by stabilizing DDIT4 mRNA via recruiting the RNA binding protein AUF1 and promoting the interaction between DDIT4 mRNA and AUF1, thereby inhibiting mTOR signaling pathway. Furthermore, silencing of DDIT4-AS1 enhances the sensitivity of TNBC cells to chemotherapeutic agents such as paclitaxel both …

Surveillance And Stewardship: Where Infection Prevention And Antimicrobial Stewardship Intersect, Fred C. Tenover, Debra A. Goff

Biology Faculty Publications

Colonization with multidrug-resistant organisms (MDROs) is a risk factor for subsequent infection. Surveillance for MDROs, including methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum beta-lactamase-producing Enterobacterales, and carbapenemase-producing organisms, is commonly conducted in hospitals to prevent spread of MDROs, in part to reduce the potential for additional infections. Although colonization is a risk factor for infection, data on colonization with various MDROs are often not considered when selecting anti-infective therapy. There are conflicting data on the strength of the positive and negative predictive values of the colonization test results to guide therapeutic strategies. Defining therapeutic strategies for patients with complicated or …

Protocol To Identify The Core Gene Supported By An Essential Gene In E. Coli Bacteria Using A Genome-Wide Suppressor Screen, Isao Masuda, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).

Rare Variant Enrichment Analysis Supports Greb1l As A Contributory Driver Gene In The Etiology Of Mayer-Rokitansky-Küster-Hauser Syndrome, Angad Jolly, Haowei Du, Christelle Borel, Na Chen, Sen Zhao, Christopher M Grochowski, Ruizhi Duan, Jawid M Fatih, Moez Dawood, Sejal Salvi, Shalini N Jhangiani, Donna M Muzny, André Koch, Konstantinos Rouskas, Stavros Glentis, Efthymios Deligeoroglou, Flora Bacopoulou, Carol A Wise, Jennifer E Dietrich, Ignatia B Van Den Veyver, Antigone S Dimas, Sara Brucker, V Reid Sutton, Richard A Gibbs, Stylianos E Antonarakis, Nan Wu, Zeynep H Coban-Akdemir, Lan Zhu, Jennifer E Posey, James R Lupski

Faculty, Staff and Student Publications

Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by aplasia of the female reproductive tract; the syndrome can include renal anomalies, absence or dysgenesis, and skeletal anomalies. While functional models have elucidated several candidate genes, only WNT4 (MIM: 603490) variants have been definitively associated with a subtype of MRKH with hyperandrogenism (MIM: 158330). DNA from 148 clinically diagnosed MRKH probands across 144 unrelated families and available family members from North America, Europe, and South America were exome sequenced (ES) and by family-based genomics analyzed for rare likely deleterious variants. A replication cohort consisting of 442 Han Chinese individuals with MRKH was …