Genetics and Genomics Commons^™

A Study Of The Snd1/Prmt5 Axis In Liver Cancer By Genetic Mouse Models, Tanner Wright, Tanner Wright

Dissertations and Theses (Open Access)

Arginine methylation is an essential post-translational modification (PTM) in cells. Protein arginine methyltransferase 5 (PRMT5) is the primary enzyme that catalyzes symmetric dimethyl arginine (SDMA) and requires methylosome protein 50 (MEP50) for stability and enzymatic activity which are necessary for life and development. Effector proteins bind different types of PTM’s to facilitate signaling. Staphylococcal nuclease Tudor domain containing 1 (SND1) is an effector that specifically binds SDMA via its single C-terminal Tudor domain. Both SND1 and PRMT5 have been implicated in hepatocellular carcinoma (HCC). SND1 has been confirmed as a driver of HCC using genetically engineered mouse models (GEMMs), though, …

The Discovery Of A Novel Bacteria From A Large Co-Assembly Of Metagenomes, Matthew Finkelberg

Masters Theses

In the summer of 2022, a co-assembly of metagenome was created using the microbes found at Barres Woods in Harvard Forest. 14 samples were taken, and sample was split into the organic and mineral layer, which totals 28 Bulk MAGs. Within this Co-assembly, 4 different genomes were found which were designated with the phylum of FCPU426. Three of which were considered medium quality and one being assigned high quality. The novel phyla first appeared in NCBI and GTDB databases in June 2018. The name FCPU426 dates to 2010 and was named based on the 16s amplicon sequencing.

The novel phylum …

Brown Anole (Anolis Sagrei) Hoxa5: Insights Into The Divergence Of Hoxa5 Gene Expression And Regulation Across Evolutionarily Divergent Gnathostome Vertebrates, Jennifer A. Lange, Amber L. Rittgers, Adam Davis

Georgia Journal of Science

Hox genes are evolutionarily conserved developmental regulatory genes that function, in part, to pattern the anterior-posterior (AP) axis of organs and organ systems during animal embryonic development. Hoxa5, specifically, is shown to be expressed in the spinal cord, somites, or transient compartments giving rise to the vertebrae and ribs, developing gut, lungs, and limbs of the mouse (Mus musculus). The cis-regulatory elements (CREs), or short DNA sequences, that direct Hoxa5 expression in these embryonic domains have been mapped and functionally tested in the mouse as well. Similar Hoxa5 expression patterns have been observed in chicken ( …

Development Of A Protocol For The Extraction Of Genomic Material From Fecal Matter For Metagenome And Virome Sequencing, Keith Coughlan

ORBioM (Open Research BioSciences Meeting)

With the advent of increasingly more accurate and reliable sequencing methods, the requirement for extraction methods yielding large volumes of high-quality genomic material has become progressively more significant. While the analysis of genomic material through bioinformatics can offer some methods of “cleaning” and standardizing data, it is essential that the “wet lab” aspects of data produce abundant amounts of high-quality genetic material. Therefore, the purpose of this project is to develop an optimized method of DNA extraction for fecal material sequencing in microbiome and virome investigations. The samples used for the optimized protocol are infant fecal samples collected and stored …

Impact Of Breeding For Dairy Traits On Beef Production, Shauna Mulhall

ORBioM (Open Research BioSciences Meeting)

Background

In recent years, there has been a large expansion in the dairy herd, accompanied by a reduction in the beef herd. Consequently, there has been a growing proportion of beef originating from the dairy herd. This study aims to investigate the impact of the current dairy cow breeding program on beef merit.

Methods

Following data edits, this study analysed 53,358 records of cow live weights and body condition scores, as well as slaughter records for 58,151 cows and 156,522 prime animals. Covariance components were estimated between various cow traits (BCS, live weight, carcass weight, conformation and fat score). Additionally, …

Characterisation Of Sex Chromosome Aneuploidy In Female Cattle Using Genotype Information, Cliona Ryan

ORBioM (Open Research BioSciences Meeting)

Background

Aneuploidy is a genetic condition characterized by the loss (monosomy) or gain (trisomy) of one or more chromosomes. Aneuploidy affecting the sex chromosomes often leads to infertility. The objective of this study was to estimate the prevalence of sex chromosome aneuploidy in a large juvenile population using routinely available genotype intensity information.

Methods

Genotype and genotype intensity data was available on 145,476 female dairy and beef cattle below 15 months of age at the time of genotyping, with no recorded progeny. Genotype intensity data included the LogR Ratio (LRR), R-value (the sum of X and Y SNP probe intensities), …

Phenotypic Correlations Between Enteric Methane Emissions And Feeding Behaviour Traits In Beef Cattle, Sean Crowley

ORBioM (Open Research BioSciences Meeting)

Background

Animal breeding for methane mitigation offers the unique potential to make cumulative and permanent improvements, setting it apart from nutritional or management strategies that require ongoing investment. Internationally multiple phenotypes for enteric methane emissions have been defined, however the complexity of the relationship between methane and feed intake and ultimately animal performance, has meant there has been little consensus on which methane definition should be used in breeding goals.

Aims

Previous enteric methane research focused on traditional methane metrics like yield, intensity and residual emissions, leaving a gap in understanding how alternative traits, such as feeding behaviour, impact methane …

The Detection Of Putative Recessive Lethal Haplotypes In Irish Sheep Populations, Rory Mcauley

ORBioM (Open Research BioSciences Meeting)

In livestock populations, recessive lethal alleles are a known contributor to poor reproductive performance due to embryonic death in homozygous individuals. Despite their lethal effect in the recessive form, these alleles may be maintained at high frequencies among carrier animals because of their positive pleiotropic effects on economically important traits. Although several such recessive alleles have been identified in cattle and pig populations, limited studies have been completed in sheep, and none within Irish sheep populations. Genotype data for 69,034 animals from five major Irish sheep breeds genotyped on a variety of panels was available for this study. Only animals …

Genetic Evaluation Of Enteric Methane For Sustainable Irish Beef Cattle, Clodagh Ryan

ORBioM (Open Research BioSciences Meeting)

Background:

Globally, livestock agriculture significantly contributes to human-induced greenhouse gas emissions, particularly through methane production. A potential approach to effectively, durably, and progressively reduce enteric methane emissions at a reasonable cost is through animal breeding.

Methods:

Individual animal methane records were available from 1,508 multi-breed growing beef cattle using GreenFeed Emission Monitoring systems. The objective of this study was to derive genetic parameters for a series of definitions of enteric methane, carbon dioxide, and dry matter intake (DMI). Estimated breeding values (EBVs) were generated for nine alternative definitions of enteric methane and EBVs were validated against phenotypic performance (adjusted for …

Tracing Evolution Of Gene Transfer Agents Using Comparative Genomics, Roman Kogay

Dartmouth College Ph.D Dissertations

The accumulating evidence suggest that viruses and their components can be domesticated by their hosts, equipping them with convenient molecular toolkits for various functions. One of such domesticated system is Gene Transfer Agents (GTAs) that are produced by some bacteria and archaea. GTAs morphologically resemble small phage-like particles and contain random fragments of their host genome. They are produced only by a small fraction of the microbial population and are released through a lysis of the host cell. Bioinformatic analyses suggest that GTAs are especially abundant in the taxonomic class of Alphaproteobacteria, where they are vertically inherited and evolve …

Multiple Light Signaling Pathways Control Solar Tracking In Sunflowers, Christopher J. Brooks, Hagop S. Atamian, Stacey L. Harmer

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Sunflowers are famous for their ability to track the sun throughout the day and then reorient at night to face east the following morning. This occurs by differential growth patterns, with the east sides of stems growing more during the day and the west sides of stems growing more at night. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism, we compared gene expression patterns in plants undergoing phototropism in a controlled environment and in plants initiating and maintaining heliotropic growth in the field. We …

Book Review: Habitantes De La Obscuridad (Fauna Ibero-Balear De Las Cuevas) – Inhabitants Of The Darkness (Ibero-Baleric Fauna Of Caves), Oana Teodora Moldovan

International Journal of Speleology

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Genomic Insights Into The Mystery Of Mouse Mummies On The Summits Of Atacama Volcanoes, Jay F. Storz, Schuyler Liphardt, Marcial Quiroga-Carmona, Naim M. Bautista, Juan C. Opazo, Guillermo D’Elía, Jeffrey M. Good

Jay F. Storz Publications

Our understanding of the limits of animal life is continually revised by scientific exploration of extreme environments. Here we report the discovery of mummified cadavers of leaf-eared mice, Phyllotis vaccarum, from the summits of three different Andean volcanoes at elevations 6,029–6,233 m above sea level in the Puna de Atacama in Chile and Argentina. Such extreme elevations were previously assumed to be completely uninhabitable by mammals. In combination with a live-captured specimen of the same species from the nearby summit of Volcán Llullaillaco (6,739 m),¹ the summit mummies represent the highest altitude physical records of mammals in the …

Tox3 Rs3803662 Polymorphism Is Associated With Breast Cancer Protection In Northeastern Mexican Woman, Orlando D. Solis-Coronado, Hazyadee F. Rodríguez-Gutiérrez, Monica P. Villarreal-Vela, Ricardo M. Cerda-Flores, Juan F. González-Guerrero, Oscar Vidal-Gutiérrez, Diana C. Pérez-Ibave, Maria Lourdes Garza-Rodríguez

Research Symposium

Introduction: Low penetrance genes are involved in breast cancer (BC) and confer risk for the development of this neoplasia. Different single nucleotide polymorphisms (SNPs) associated with BC have been identified, such as rs3803662 (TOX3), which is related to estrogen receptors in European and African-American women. The contribution of this variant in the Mexican population is unknown. The objective of this study was to evaluate, through a case-control design, the association of the SNP rs3803662 (TOX3), with the risk of BC in women from northeastern Mexico.

Methods: We included 434 cases and 228 controls. Genotyping was carried out using RFLPs. The …

South Coast Offshore Crustacean Resource Of Western Australia Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries management papers

Harvest strategies for aquatic resources in Western Australia (WA) that are managed by the Department of Primary Industries and Regional Development (DPIRD, the Department) are formal documents that ensures decision-making processes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA) and the Aquatic Resources Management Act 2016 (ARMA), which is anticipated replace the FRMA once enacted. At this point, the Fish Resources Management Regulations 1995 (FRMR) is also anticipated to …

The Role Of Non-Coding Rnas In Myelodysplastic Neoplasms, Vasileios Georgoulis, Epameinondas Koumpis, Eleftheria Hatzimichael

Computational Medicine Center Faculty Papers

Myelodysplastic syndromes or neoplasms (MDS) are a heterogeneous group of myeloid clonal disorders characterized by peripheral blood cytopenias, blood and marrow cell dysplasia, and increased risk of evolution to acute myeloid leukemia (AML). Non-coding RNAs, especially microRNAs and long non-coding RNAs, serve as regulators of normal and malignant hematopoiesis and have been implicated in carcinogenesis. This review presents a comprehensive summary of the biology and role of non-coding RNAs, including the less studied circRNA, siRNA, piRNA, and snoRNA as potential prognostic and/or predictive biomarkers or therapeutic targets in MDS.

Trimeric Complex Interactions Of Antp-Tbp With Tfiieb And Exd Are Involved In The Genetic Control Of Drosophila Melanogaster, Gustavo Jiménez Mejía, Ruben De Jesus Montalvo Mendez, Claudia Dalila Altamirano Torres, Diana Reséndez Pérez

Research Symposium

Background: Homeoproteins are transcriptional factors (TFs) that shape animal body axes during development. These TFs are highly conserved and represent one of the most fascinating groups of regulatory molecules. Reports shown the multiplicity of interactions in hox proteins, as complexes trimeric involved to transcriptional activity. The study of trimeric complexes in Hox interactome will allow the better understanding of Hox genetic regulation during embryonic development.

Methodology: Using a new combination BiFCFRET approach performed in HEK293, the quantification was performed by FRETTY of ImageJ. Fly crosses were incubated at 25ºC on standard yeast-agar-cornmeal medium. Embryo cuticle preparations were carried out according …

Multiple Rsv Strains Infecting Hep-2 And A549 Cells Reveal Cell Line-Dependent Differences In Resistance To Rsv Infection, Anubama Rajan, Felipe-Andres Piedra, Letisha Aideyan, Trevor Mcbride, Matthew Robertson, Hannah L. Johnson, Gina Marie Aloisio, David Henke, Cristian Coarfa, Fabio Stossi, Vipin Kumar Menon, Harshavardhan Doddapaneni, Donna Marie Muzny, Sara Joan Javornik Cregeen, Kristi Louise Hoffman, Joseph Petrosino, Richard A. Gibbs, Vasanthi Avadhanula, Pedro A. Piedra

Research Symposium

Background: Respiratory syncytial virus (RSV) is the major viral driver of a global pediatric respiratory disease burden disproportionately borne by the poor¹. Thus, RSV, like SARS-CoV-2, combines with congenital and environmental and host-history-dependent factors to create a spectrum of disease with greatest severity most frequently occurring in those least able to procure treatment.

Methods: Here we apply whole genome sequencing and a suite of other molecular biological techniques to survey host-virus dynamics in infections of two distinct cell lines (HEp2 and A549) with four strains representative of known RSV genetic diversity.

Results: We observed non-gradient patterns of RSV …

Human Ipsc Derived Cardiomyocyte Model Reveals The Transcriptomic Bases Of Covid-19 Associated Myocardial Injury, Kashish Kumar, Satish Kumar, Erica De Leon, Joanne E. Curran, Sarah Williams-Blangero, John Blangero

Research Symposium

Background: Multi-organ complications have been the hallmark of severe COVID-19; cardiac injuries were reported in 20% to 30% of hospitalized COVID-19 patients, although the disease etiology remains poorly understood. This study leveraged genome-wide RNA-sequence data generated using induced pluripotent stem cell (iPSC) differentiated cardiomyocytes (CMs) and in vitro modeling of SARS-CoV-2 infection in CMs, to understand the molecular mechanisms of COVID-19 myocardial injuries for novel diagnostic and therapeutic development.

Methods: Raw RNA-sequence data sets, GSE165242 and GSE150392 were aligned to human genome assembly GRCh38 and gene expressions were quantified. Differentially expressed (DE) genes between experimental groups were identified using moderated …

Gene-By-Environment Expression And Calculation Of The Frailty Index, Eron G. Manuosv, Vincent P. Diego, John Blangero, Michael C. Mahaney, Sarah Williams-Blangero

Research Symposium

Background: Frailty can be described as a phenotype (e.g., sarcopenia, reduced grip strength, decreased VO2 max) or as a ratio of deficits, i.e., a Frailty Index (FI). FI predicts survival, death, cognitive impairment, falls, and hospitalizations. Frailty is influenced by both genes and environment. We calculated the FI as the sum of measured deficits divided by the total number of items assessed in a pedigree-based sample of 1,029 Mexican Americans participants in the San Antonio Family Heart Study. We performed a novel search for genotype-by-environment interactions (GXE) influencing FI. Such interactions lead to heritable differences between individuals in their responses …