Other Genetics and Genomics Commons^™

Gmr39h01, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 50066

• ID - GMR39H01
• Location - 2R: 18153797, 18156108
• Base pairs - 2311

Gmr42e10, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR42E10
• Location - 2R: 18133506, 18137474
• Base pairs - 3968

Gmr41c04, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR41C04
• Location -2R: 18143594, 18147064
• Base pairs - 3470

Gmr42h01, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 48150

• ID - GMR42H01
• Location - 2R: 18158419, 18162751
• Base pairs - 4332

Gmr35a04, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR35A04
• Location - 2R: 18125755, 18128365
• Base pairs - 2610

Gmr41h07, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 46241

• ID - GMR41H07
• Location - 2R: 18150920, 18154671
• Base pairs - 3751

Gmr41f05, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 50133

• ID - GMR41F05
• Location - 2R: 18139042, 18142672
• Base pairs - 3630

Gmr40c05, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 45682

• ID - GMR40C05
• Location - 2R: 18141630, 18144381
• Base pairs - 2751

Gmr40c09, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer

• ID - GMR40C09
• Location - 2R: 18132203, 18134987
• Base pairs - 2784

Gmr42a07, Anuradha Venkatakrishnan Chimata, Oorvashi Roy Puli, Amit Singh

DVE Enhancer Sequences Utilized in GMR Line

dve enhancer 45284

• ID - GMR42A07
• Location - 2R: 18146520, 18150306
• Base pairs - 3786

Divergent Transcriptional Regulation Of Suppressors Of Cytokine Signaling Genes In Adipocytes, Paula Mota De Sa

LSU Doctoral Dissertations

The Janus Kinase - Signal Transducer and Activator of Transcription (JAK-STAT) signaling pathway transduces several signals crucial for development and homeostasis. Suppressors of cytokine signaling (SOCS) proteins control JAK-STAT signaling via a negative feedback loop. The transcription factor STAT5 is known to play a significant role in fat cell development and function, and several studies suggest that acetylation may affect STAT5 transcriptional activity. To test this hypothesis, we treated 3T3-L1 adipocytes with growth hormone (GH) to activate STAT5 in the presence or absence of histone deacetylase (HDAC) inhibitors. STAT5 acetylation levels were low in adipocytes and mostly unchanged by the …

Deletion Of Uls1 Confers Damage Tolerance In Sgs1 Mutants Through A Top3-Dependent D-Loop Mediated Fork Restart Pathway, M. Rebecca Glineburg, Eleanor Johns, F. Brad Johnson

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Homologous recombination (HR)-based repair during DNA replication can apparently utilize several partially overlapping repair pathways in response to any given lesion. A key player in HR repair is the Sgs1-Top3-Rmi1 (STR) complex, which is critical for resolving X-shaped recombination intermediates formed following bypass of methyl methanesulfonate (MMS)-induced damage. STR mutants are also sensitive to the ribonucleotide reductase inhibitor, hydroxyurea (HU), but unlike MMS treatment, HU treatment is not accompanied by X-structure accumulation, and it is thus unclear how STR functions in this context. Here we provide evidence that HU-induced fork stalling enlists Top3 prior to recombination intermediate formation. The resistance …

Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards …

Supervised Dimension Reduction For Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

The past two decades have witnessed significant advances in high-throughput ``omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive ``omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential …

Exploring The Ipf Lung Through The Lens Of Single Cell Rna Sequencing, Taylor Adams, Jonas Schupp

Yale Day of Data

This poster illustrates the differences between the IPF disease-specific variety of lung macrophages and the two varieties of macrophages known to reside in the normal human lung.

Hnrnpa2 Mediated Acetylation Reduces Telomere Length In Response To Mitochondrial Dysfunction, Manti Guha, Satish Srinivasan, F. Bradley Johnson, Gordon Ruthel, Kip Guja, Miguel Garcia-Diaz, Brett A. Kaufman, M. Rebecca Glineburg, Jikang Fang, Hiroshi Nakagawa, Jeelan Basha, Tapas Kundu, Narayan G. Avadhani

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Telomeres protect against chromosomal damage. Accelerated telomere loss has been associated with premature aging syndromes such as Werner’s syndrome and Dyskeratosis Congenita, while, progressive telomere loss activates a DNA damage response leading to chromosomal instability, typically observed in cancer cells and senescent cells. Therefore, identifying mechanisms of telomere length maintenance is critical for understanding human pathologies. In this paper we demonstrate that mitochondrial dysfunction plays a causal role in telomere shortening. Furthermore, hnRNPA2, a mitochondrial stress responsive lysine acetyltransferase (KAT) acetylates telomere histone H4at lysine 8 of (H4K8) and this acetylation is associated with telomere attrition. Cells containing dysfunctional mitochondria …

Trim24 As An Oncogene In The Mammary Gland, Aundrietta Duncan

Dissertations and Theses (Open Access)

Despite the many advances made in breast cancer research and treatments, breast cancer remains one of the deadliest diseases plaguing women worldwide. While many findings on genetic mutations and their role in predisposing people to breast cancer have been uncovered, we are just beginning to understand the extent to which epigenetic regulators promote tumorigenic phenotypes, metastasis, and chemotherapeutic resistance. Moreover, new experimental tools offer the ability to address questions we were previously unable to assess. My project takes advantage of a new mouse model to understand the role of a proto-oncogenic, transcriptional co-regulator, TRIM24, in mammary gland development and disease. …

48839 (Gmr19b04), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48839

• Id - GMR19B04,
• Location - 2L:2432214,2435785
• Base pairs – 3571 bp

47472 (Gmr16g02), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 47472

• Id - GMR16G02
• Location 2L:2425041, 2428154
• Base pairs – 3113 bp

48770 (Gmr17e04), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48770

• Id - GMR17E04
• Location 2L: 2428913..2432834
• Base pairs – 3921 bp

45833 (Gmr19d09), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45833

• Id - GMR19D09
• Location - 2L:2435128,2438996
• Base pairs – 3868 bp

48784 (Gmr17g08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 48784

• Id - GMR 17G08
• Location 2L:2450278,2451074
• Base pairs – 796 bp

45437 (Gmr18b08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45437

• Id - GMR18B08
• Location - 2L:2455899,2457734
• Base pairs – 1835 bp

45442 (Gmr18d08), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 45442

• Id - GMR 18D08
• Location - 2L:2446783,2449086
• Base pairs – 2303 bp

49283 (Gmr19c03), Neha Gogia, Ankita Sarkar, Amit Singh

Dpp Enhancer Sequences Utilized in GMR Line

dpp enhancer - 49283

• Id - GMR19C03
• Location - 2L:2440970,2444735
• Base pairs – 3765 bp

Epigenetic Modifications Of Human Placenta Associated With Preterm Birth, Drissa Toure

Theses & Dissertations

Preterm birth is a complex multifactorial process. Despite the well-known role of the placenta in supporting the fetal development and maternal-fetal tolerance, the placental epigenetic modifications and preterm birth (PTB) remains poorly understood and under investigated. Various maternal and environment factors can influence epigenetic programming during fetal development to affect the functioning and structures of organs, including the placenta, which can lead to adverse pregnancy outcomes, including PTB. The understanding of the placental epigenetic alterations and maternal determinants associated with PTB are apparently indispensable for the development of actual diagnosis and methods of prevention and treatment of premature labor. The …

Lymphoid Hematopoiesis And The Role Of B-Cells In Transgenic Mouse Model Of Sickle Cell Disease, Christina Cotte

University Scholar Projects

Sickle cell disease (SCD) has been shown to be associated with decreased baseline immunity and thus increased susceptibility to infection. I sought to discern possible causes of this by looking into the correlations between SCD and hematopoiesis, the immune system and the neuroendocrine system, and ultimately by conducting experiments surrounding the impaired immune system of SCD. These experiments focused on the potential causes and effects of the diminution of B-1a cells in the SCD spleen. Adoptive transfers, infections with Streptococcus pneumoniae, and histologic imaging were conducted to establish if the diminution of the B-1a cells in the SCD spleen …

Punctuated Evolution Within A Eurythermic Genus (Mesenchytraeus) Of Segmented Worms: Genetic Modification Of The Glacier Ice Worm F1f0 Atp Synthase, Shirley A. Lang

Graduate School of Biomedical Sciences Theses and Dissertations

Segmented worms (Annelida) are among the most successful animal inhabitants of extreme environments worldwide. An unusual group of Mesenchytraeus worms endemic to the Pacific Northwest of North America occupy geographically proximal ecozones ranging from low elevation temperate rainforests to high altitude glaciers. Along this altitudinal transect, Mesenchytraeus representatives from disparate habitat types were collected and subjected to deep mitochondrial and nuclear phylogenetic analyses. Evidence presented here employing modern bioinformatic analyses (i.e., maximum likelihood, Bayesian inference, multi-species coalescent) supports a Mesenchytraeus “explosion” in the upper Miocene (5-10 million years ago) that gave rise to ice, snow and terrestrial worms, derived from …

Optimization Of A Genomic Editing System Using Crispr/Cas9-Induced Site-Specific Gene Integration, Jillian L. Mccool Ms., Nick Hum, Gabriela G. Loots

STAR Program Research Presentations

The CRISPR-Cas system is an adaptive immune system found in bacteria which helps protect against the invasion of other microorganisms. This system induces double stranded breaks at precise genomic loci (1) in which repairs are initiated and insertions of a target are completed in the process. This mechanism can be used in eukaryotic cells in combination with sgRNAs (1) as a tool for genome editing. By using this CRISPR-Cas system, in addition to the “safe harbor locus,” ROSAβ26, the incorporation of a target gene into a site that is not susceptible to gene silencing effects can be achieved through few …

Genetic Analysis Reveals A Hierarchy Of Interactions Between Polycystin-Encoding Genes And Genes Controlling Cilia Function During Left-Right Determination, Daniel T. Grimes, Jennifer L. Keynton, Maria T. Buenavista, Xingjian Jin, Saloni H. Patel, Shinohara Kyosuke, Jennifer Vibert, Debbie J. Williams, Hiroshi Hamada, Rohana Hussain, Surya M. Nauli, Dominic P. Norris

Pharmacy Faculty Articles and Research

During mammalian development, left-right (L-R) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node. This ‘nodal flow’ is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca²⁺ channel PKD2. The interaction of flow and crown cell cilia promotes left side-specific expression of Nodal in the lateral plate mesoderm (LPM). Whilst the PKD2-interacting protein PKD1L1 has also been implicated in L-R patterning, the underlying mechanism by which flow is detected and the genetic relationship between Polycystin function and asymmetric gene expression remains unknown. Here, we …