Genetics and Genomics Commons^™

Complete Genome Sequence Of Rothia Mucilaginosa D1, A Genetically Amenable Strain, Hemendra P. Dhaked, Isabella Andonie, Bo Yang, Vinayka M. Joshi, Zezhang T. Wen

School of Dentistry Faculty Publications

Here, we report the complete genome sequence of Rothia mucilaginosa D1. Unlike many other strains that have been sequenced, R. mucilaginosa D1, a clinical isolate, is genetically amenable. The complete sequencing of the genome provides potential for further studies on the genetics and pathophysiology of this emerging pathobiont.

The Interplay Of Cytokine Expression, Cardiac Phenotype, And Heritability In Cardiovascular Health In Mexican Americans., Veronica O'Brien, Ana Leandro, Marcio Almeida, John Blangero, Joanne Curran

Research Colloquium

Background: Cardiovascular disease (CVD) is the leading cause of death worldwide, and the Hispanic population has a significantly higher risk of developing CVD. In this study, we measured plasma cytokine levels, lipidomic data, and cardiac magnetic resonance imaging (CMRI) in individuals from the San Antonio Family Heart Study (SAFHS). Statistical analysis was implemented to determine the heritability, the correlation between cytokine expression and cardiac phenotype and lipid and cardiac phenotype.

Methods: We analyzed frozen plasma samples from 254 participants using the MILLIPLEX Human Cytokine/Chemokine/Growth Factor Panel A Magnetic Bead Panel. The panel included GM-CSF, IFNg, IL-1ß, IL-2, IL-4, IL-5, IL-6, …

From Venom To Medicine: Harnessing Animal Toxins For Drug Discovery, Christine Vega, Ying Jia

Research Colloquium

Background: Drug development research has long focused on synthesizing novel therapeutics while overlooking isolation from naturally available sources such as animal venoms. Recently, the discovery of the therapeutic effects of highly bioavailable animal venom caused the field of venom research to soar in popularity. Animal venom serves as a natural, sophisticated tool optimized over millions of years by evolution with the ability to bind to ion channels such as nAChRs, non-specific ligand-gated ion channels distributed throughout the human nervous system. However, purifying individual venom toxins from crude venom is challenging due to its availability. Therefore, synthesizing large quantities of venom …

The Chromosome Complement Of Male Chrysoperla Rufilabris (Burmeister, 1839), With Evidence Of Distance Segregation In Meiosis I, Valoria G. Maslin, Allison M. Eisenhauer, Leocadia V. Paliulis

Faculty Journal Articles

Neuropteran insects display a phenomenon called distance segregation during male meiosis I, where the X and Y chromosomes are unconnected from prometaphase I through anaphase I. Here we investigate chromosome number and patterns of chromosome segregation of a previously unstudied Neuropteran: the green lacewing, Chrysoperla rufilabris (Burmeister, 1839). Testes of male C. rufilabris were isolated and prepared following a chromosome squash method. Living meiosis I spermatocytes were also imaged. The data revealed a chromosome number of 2n=12 in males (2n=10+XY) and evidence of distance segregation of X and Y chromosomes in meiosis I spermatocytes.

Resolution Of Physics And Deep Learning-Based Protein Engineering Filters: A Case Study With A Lipase For Industrial Substrate Hydrolysis, Spencer Gardiner, Peter Dollinger, Filip Kovacic, Jörge Pietruszka, Daniel Ess, Karl-Erich Jaeger, Gunnar F. Schröder, Dennis Della Corte

Faculty Publications

Computational enzyme design remains a powerful yet imperfect tool for optimizing biocatalysts, especially when targeting non-natural substrates. Using design tools we investigated Pseudomonas aeruginosa LipA, a lipase with a flexible lid domain crucial for substrate binding and turnover, aiming to enhance its hydrolysis of the industrially relevant substrate Roche ester. We generated an initial set of single-point mutations based on structural proximity to the active site and evaluated their effects using a computational pipeline integrating molecular dynamics (MD) simulations, density functional theory (DFT) calculations, and ensemble-based energy scoring. While we identified several active variants, attempts to rank them by activity …

Relaxation Of The Leaf Economics Spectrum Within And Across Quaking Aspen Populus Tremuloides Genotypes, Jolanta Rieksta, Bente J. Graae, Kenny Helsen, Rozália E. Kapás, Richard Strimbeck, Benjamin W. Blonder

Aspen Bibliography

Plant functional traits typically show strong covariation, e.g. as in the worldwide leaf economics spectrum (LES). Covariation is thought to arise from selective forces and physical constraints. However, processes shaping covariation at interspecific scales may differ from those at intraspecific scales. Potential sources of intraspecific trait variation include variation in genetics, abiotic environment, and biotic environment; any of these factors may cause divergence from interspecific patterns. Quaking aspen, Populus tremuloides (Salicaceae), is a widespread tree species ideal for assessing these processes' role in the intraspecific LES, due to its clonal growth along environmental gradients, intraspecific variation in cytotype (ploidy level), …

Increased Circulating Th17 Cells And Altered Cd4 T Cell Maturation And Differentiation In Active Tuberculosis With Type 2 Diabetes: A Pilot Study, Paul Ogongo, Yoscelina Estrella Martinez-Lopez, Anthony Tran, Cecilia S. Lindestam Arlehamn, Alessandro Sette, Ilse A. Dominguez-Trejo, Genesis P. Aguillón-Durán, Esperanza M. Garcia-Oropeza, Blanca I. Restrepo

School of Medicine Publications

Introduction: Type 2 diabetes (T2D) is a major risk factor for developing tuberculosis (TB). However, understanding the role of defective T cell responses in T2D and TB has been difficult, largely due to inconsistencies across studies. These discrepancies often stem from T cell subset classification primarily relying on cytokine expression profiles, which may not fully capture the complexity of T cell maturation, differentiation, and function in TB patients with T2D.

Objective and methods: In this pilot study, we sought to identify alterations in phenotypic and ex vivo responses of CD4 T cells to Mycobacterium tuberculosis (Mtb) antigens in people with …

Improving Efficiency Of Prime Editing For Superior Genetic Traits In Livestock, Iuri Viótti Périssé

Funded Research Records

No abstract provided.

Subtype-Specific Her3 Enrichment In Basal-Like Breast Cancer Is Regulated Via The Gata2/Gata3–Foxa1 Axis, Congcong Tan, Hui Lyu, Sanbao Ruan, Yakun Wu, Margaret E. Larsen, Shou Ching Tang, Bolin Liu

School of Medicine Faculty Publications

Basal-like breast cancer (BLBC) is a major subtype of triple-negative breast cancer (TNBC), characterized by aggressive behavior, limited treatment options, and poor prognosis. While HER3 overexpression is frequently observed in TNBC and associated with poor outcomes, its subtype-specific expression and therapeutic potential remain unclear. Here, we demonstrated that HER3 signaling is selectively hyperactivated in BLBC compared to claudin-low breast cancer (CLBC) using transcriptomic profiling. Histone deacetylase inhibitors (HDACi), Romidepsin and Panobinostat, exerted potent antitumor effects on BLBC by selectively downregulating HER3 expression. HER3 levels were positively correlated with FOXA1, a key transcriptional activator. Mechanistically, we identified GATA2 and GATA3 as …

A Complicated History Of Mitogenome Introgression Among Luxilus Species (Teleostei, Family Leuciscidae) In The Ozark Highlands, David D. Duvernell, Carson Arnold, Shila Koju, Abby J. Wicks, Thomas E. Dowling

Biological Sciences Faculty Research & Creative Works

Hybridization is common among minnows and shiners in the family Leuciscidae, and mitonuclear discordance can reveal evidence of historical hybridization and introgression events that have shaped extant species and populations. We have identified a notable case of serial mitogenome replacement in populations of two shiner species, Luxilus zonatus and L. chrysocephalus, which are syntopic in drainages throughout the northern and eastern Ozark Interior Highlands of North America. These mitogenome replacement events involved L. zonatus acquiring the mitogenome of L. chrysocephalus, and populations of L. chrysocephalus acquiring the mitogenome of an allopatric congeneric species, L. cornutus. The latter species has a …

Genetic And Geographic Profiling Of Fragrance-Associated Badh2 Mutations In Rice From China, Laos, And Vietnam, Lenie A. Quiatchon-Baeza, Venea Dara Daygon, Mariafe N. Calingacion, Melissa A. Fitzgerald

The Philippine Agricultural Scientist

Fragrance in rice is a culturally and economically significant trait in Asia and around the world. This study aimed to develop a genetic and geographic profile of the fragrance-associated BADH2 mutations (badh2.1 and badh2.11) in 1,067 rice varieties from China, Laos, and Vietnam, which are part of the International Rice Genebank Collection. Seventy-three varieties were found to carry the common eight-base pair (bp) deletion in exon 7 of the genes (badh2.1, also known as badh2.7), primarily from indica varieties, with some belonging to japonica, javanica, and intermediate varieties. Conversely, 59 varieties possess the recently identified badh2 allele, badh2.11 (also known …

Gene Expression Of Anthocyanin Pigments In The California Native Plant Leptosiphon Parviflorus: Interactions Between Flower Color Morphology And Abiotic Stressors, Weston Gonor

Master's Theses

For plants to survive in harsh conditions imposed by abiotic stressors, they must develop mechanisms of adaptation. One of the common types of adaptation seen in plants is the production of anthocyanin pigments, which have been shown to protect plants from UV radiation, metabolic stress, and drought. In this study, we used the flower color polymorphic species Leptosiphon parviflorus to investigate the role of anthocyanin pigments in protecting plants from abiotic stress. To accomplish this, RNA samples were taken from flower, leaf and root tissue of different flower color morphs of Leptosiphon parviflorus (Polemoniaceae) grown in high magnesium and water …

Impact Of Sowing Time And Plant Density On Selected Traits And Yield Of Cotton Genotypes In Pakistan, Muhammad Rizwan Jamil, Kalim Ullah, Muhammad Mohibullah, Saeed Muhammad, Hafiz Abdul Haq, Sundas Batool, Rashida Aslam, Wasif Rasool

The Philippine Agricultural Scientist

Extremely diversified cropping environments prevail in most cotton-growing areas of Pakistan due to prevailing rainfed conditions, prolonging the crop’s cultivation period. To contribute to the development of desired breeding traits for effective breeding programs, this study examined the production and growth pattern of 8 cotton genotypes. Four experiments were conducted in 2018 and 2019 at 2 locations in Dera Ismail Khan, Pakistan, to evaluate the performance of the studied genotypes at 3 plant densities and 2 sowing dates. Traits such as days to first flower opening, flowering duration, monopodial branches per plant, plant height at harvest, height-to-node ratio, fruiting branch …

Ai-Powered Multi-Omics Integration For Predictive Modeling Of Genotype-Environment-Phenotype Relationships, You Wu

Dissertations, Theses, and Capstone Projects

This dissertation presents a series of machine learning frameworks for modeling genotype–environment–phenotype relationships through integrative predictive modeling of multi-omics data. The work addresses three major axes of biological complexity: modeling biological information transmission cross-levels from genes to proteins to phenotypes, predicting molecular features cross-scale from cells to tissues to organisms, and translating phenotypes cross-species from model systems to humans. Each proposed method also tackles key machine learning (ML) challenges in the biomedical domain, including data scarcity, domain shift, out-of-distribution (OOD) generalization, and hierarchical modeling. Specifically, this dissertation introduces five novel deep learning algorithms: MultiDCP predicts drug-induced transcriptomic and viability responses …

Origin And Maintenance Of The Andean Bird Fauna, Elkin A. Tenorio

Dissertations, Theses, and Capstone Projects

The origin and maintenance of the tropical montane diversity have been evaluated over multiple decades using various techniques and perspectives. Despite major progress in understanding phylogenetic relationships, diversification patterns, distributional data, and general ecology in the Andean biota, large gaps in our understanding remain, particularly in the synthesis across scales. To fill these gaps, I aimed to explore patterns and processes that underlie species diversification in birds of the tropical Andes of South America by combining different approaches using phenotypic, phylogenetic, and genomic data in multiple temporal and spatial scales.

In the first chapter, I examined the macroevolutionary patterns of …

Bmp Signaling Co-Regulation Of Immune Response And Lipid Metabolism, Katerina K. Yamamoto

Dissertations, Theses, and Capstone Projects

The Bone Morphogenetic Proteins (BMPs) are secreted peptide ligands of the Transforming Growth Factor beta (TGF-β) family, initially identified for their roles in development and differentiation across animal species. They are now increasingly recognized for their roles in physiology and infectious disease. In the nematode Caenorhabditis elegans, the BMP ligand DBL-1 controls fat metabolism and immune response, in addition to its roles in body size regulation and development. DBL-1 regulates classical aspects of innate immunity, including the induction of anti-microbial peptides. We theorized that BMP-dependent regulation of fat metabolism could also promote resilience against microbial pathogens. We found that …

Retinal Precursor Cell Enriched Multiomic And Pseudo-Time Analysis Of Developing And Reprogrammed Photoreceptors, Brendon M. Patierno

Dissertations, Theses, and Capstone Projects

The vertebrate retina is a complex tissue made up of seven major cell subtypes which during development must differentiate and localize into a highly organized structure. These neuronal cells do not regenerate if damaged or diseased, and the progressive deterioration of cone photoreceptor cells is the leading cause of age related blindness. Currently there are no cures for this disease, but one promising therapeutic avenue is cell transplantation research. If we can further elucidate the gene regulatory networks that define cone cell development, this knowledge could be applied to the generation of healthy cone cells in clinically relevant models.

The …

Exploring The Role Of Ecological Traits In Shaping Spatial Patterns Of Genetic Diversity, Rilquer Mascarenhas Da Silva

Dissertations, Theses, and Capstone Projects

The field of comparative phylogeography aims at uncovering common underlying causes for shared patterns of diversity and diversification at the population level. However, it is now widely accepted that intraspecific genetic diversity patterns can differ considerably across co-occurring taxa due to ecological processes acting at the population level (and influencing individual movement and abundance). To model the processes underlying lineage diversification and demographic shifts in response to environmental changes, phylogeographers and population geneticists are now faced with the challenge of incorporating measurements of species ecological traits into their molecular studies. This dissertation aimed at investigating how different types of ecological …

Ibi-Dt: A Novel Approach Combining Individualized Bayesian Inference And Decision Tree For Identifying Cancer Drivers And Their Interactions, Md Asad Rahman, Gregory F. Cooper, Jinying Zhao, Xinghua Lu, Jinling Liu

Engineering Management and Systems Engineering Faculty Research & Creative Works

Cancer is mainly caused by a relatively small portion of somatic genome alterations (SGAs), called cancer drivers. Despite success in identifying a good number of cancer drivers, many more remain to be discovered to explain various cancers. Moreover, limited tools are available to identify potential interactions among cancer drivers for a better understanding of oncogenesis. To tackle these challenges, we have developed a novel approach called individualized Bayesian inference using a decision tree (IBI-DT). IBI-DT recognizes the genetic heterogeneity among cancer patients, where different individuals or patient subgroups of distinct genomic makeup may have different drivers. IBI-DT works by constructing …

Single Nuclei Transcriptomics Reveals Cellular Diversity In Tsc Subependymal Giant Cell Astrocytomas, Jennie C. Holmberg, Vijay Shankar, Rachel A. Lyman, Trudy F.C. Mackay, David M. Feliciano

Publications

Tuberous sclerosis complex (TSC) is a genetic disorder characterized by benign growths called hamartomas that are a significant cause of morbidity and mortality. Hamartomas are found along the neurocutaneous axis including along the brain’s ventricles near the boundaries of the striatum. They can be categorized by size and include small subependymal nodules (SENs) or larger subependymal giant cell astrocytomas (SEGAs). Here, we describe a quantitative analysis of SEGA cell identities based on single nuclei RNA sequencing. SEGAs contain several cell types. In contrast to unaffected samples, SEGAs have pronounced vasculature, more endothelial cells, increased perivascular macrophages, less myelination, and altered …