Genetics and Genomics Commons^™

Bridging The Gap In Science Research: Preparing Students For College- Level Research In The Sciences, Victoria Helwig, Yaoguang Li

UConn Library Presentations

Many first-year students enter college unprepared to fully engage with scientific literature and academic library resources. Drawing on experiences from academic librarians working with STEM students, this session explores common gaps in science research skills, including navigating databases, identifying scholarly sources, and understanding the structure of scientific literature. Participants will be introduced to practical strategies and classroom-ready activities to better prepare students for college-level research. Discussion questions: What science research skills do students struggle with most when entering college? How can high school instruction better support these skills? Where can librarians and educators collaborate to support student success?

From Chromosomes To Precision Therapy: Clinical Cytogenetics And Cytogenomics In The Era Of Genomic Medicine, Jinglan Liu

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

No abstract provided.

Epigenetic Regulators Mll3 And Mll4 Sustain Hematopoietic Stem Cell Multipotency, Helen Chenwei Wang

Arts & Sciences Graduate Student Theses and Dissertations

Hematopoietic stem cells (HSCs) maintain lifelong blood production by balancing self-renewal and multilineage differentiation. They are sustained by networks of transcription factors and epigenetic regulators that prime lineage-specific programs while simultaneously preventing activation of any one program up until the moment of lineage commitment. Despite extensive study, it remains unclear how these complex transcriptional programs are coordinated and how specific epigenetic regulators are deployed to reinforce specific cell fate decisions. Epigenetic regulators, MLL3 and MLL4, play a central role in pluripotent embryonic stem cell fate transitions, but their functions in multipotent somatic stem cells are less well characterized. MLL3 (also …

Summer Research Internships In Agricultural Biotechnology For Off-Campus Undergraduate Students, Aaron J. Thomas

Funded Research Records

No abstract provided.

Homocysteine Thiolactone From Translation Proofreading Is An Endogenous Ligand For Cell-Cell Signaling By The Receptor Sdia, Lorenzo Eugenio Leiva, Roberto A. Zúñiga, Gregory J. Phillips, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Several widespread mechanisms enable cellular communication and coordinate the behavior of bacterial populations. The modules responsible for cellular communication are often found in matching pairs: an enzyme that synthesizes a signal molecule and a specific receptor that decodes it. A notable exception is Escherichia coli SdiA, a homolog of known N-acyl-homoserine lactone (AHL) receptors, for which no corresponding AHL synthase exists. SdiA is an orphan receptor that enables cross-talk by sensing AHLs from other bacterial species. In this work, we investigated whether homocysteine thiolactone (HTL), an AHL-like molecule arising from a proofreading reaction of methionyl tRNA synthetase (MetRS) to correct …

Vertebrate Diversity In Cave Systems Of Colombia: An Approach Based On Environmental Dna Metabarcoding Analysis, Rita Daniela Martinelli Marín, Carlos Andres Lasso, Francesco Sauro, Susana Josefina Caballero

International Journal of Speleology

There is currently limited knowledge of the biological communities inhabiting cave ecosystems in South America. This study examines the vertebrate community composition of 21 caves across diverse subterranean ecosystems in Colombia using environmental DNA (eDNA) analysis. Water was collected from water bodies inside caves and subterranean systems in six of the eight speleological regions of Colombia in eight departments. Water was filtered manually through a 0.8 m pore size filter and preserved with Longmire solution. A 170-base pair (bp) fragment of the 12s mitochondrial gene specific for vertebrate identification was amplified by PCR and sequenced by Illumina (metabarcoding). Data corresponding …

Developmental Stability Of Task-Rest Neural Efficiency In Youth Using A Threat And Cognitive Control Task, Parmis Khosravi, Julia O. Linke, Anjali D. Poe, Chase Antonacci, Reut Naim, Elise M. Cardinale, Katharina Kircanski, Anderson M. Winkler, Nathan A. Fox, Daniel Samuel Pine, Simona P. Haller

School of Medicine Publications

Behaviors arise from coordinated neural activity across diverse spatial and temporal scales. Prior work has linked better task performance and cognitive functioning to patterns of global network connectivity requiring minimal reconfiguration when switching between task demands. This metric indexing similarity in functional connectivity across task and rest has been termed “neural efficiency.” Here we assess stability of neural efficiency over approximately 3 years in adolescence, specificity across two task-rest combinations and associations with anxiety. At approximately age 16 and/or 19, 95 participants completed a resting state scan alongside a cognitive control and/or threat task. Neural efficiency was quantified as partial …

Deconstructing Systemic Sclerosis Heterogeneity: From Patient Subtypes To Pathogenic Fibroblasts, Rezvan Parvizi

Dartmouth College Ph.D Dissertations

This thesis advances heterogeneity as the central barrier both to interpreting therapeutic response and to identifying the molecular regulators that drive fibrosis in systemic sclerosis (SSc). In SSc, heterogeneity is manifest at every level at which the disease can be measured: clinically, in the variable extent of skin and organ involvement; molecularly, in the distinct gene-expression programs that distinguish otherwise comparable patients; and cellularly, in the diverse fibroblast populations from which the fibrotic signal ultimately arises.

Leveraging longitudinal skin transcriptomics from a large cohort treated with mycophenolate mofetil (MMF), the first study demonstrates that intrinsic molecular subtypes are dynamic rather …

Birds Of A Tether Flock Together: Examining Centromere Tethering And Chromosome Segregation In Caulobacter Crescentus, Jake Dwyer, Simon Kruczak, Rodrigo Arana-Garrido, Paola Mera

MICRO-CCS student projects

Introduction:

Chromosome segregation is essential for all domains of life. Caulobacter crescentus is a key model for studying this process. It divides asymmetrically into two morphologically distinct cells. Proteins can be seen directly with fluorescent tags.

Research done on Caulobacter can apply to many different bacteria. The ParABS system is integral to chromosome segregation in Caulobacter.

ParS – DNA sequence on the chromosome

ParB – CTP-binding protein that specifically recognizes parS

ParA – ATP-binding protein that non-specifically binds DNA and provides the force for segregation.

PopZ – Polar tethering protein via interactions with ParB.

TipN - Polar protein that …

Proteogenomics Of Hypertrophic Cardiomyopathy Reveals Subtype-Specific Therapy, Ke Ma, Jie Yang, Hongchang Guo, Ping Li, Xiaowei Li, Zhujun Dong, Jing Zhang, Congcong Zhang, Pengli Yang, Chongpei Hua, Shuolin Zhu, Guoqing Li, Jianchao Zhang, Ningyu Ding, Jizheng Wang, Xin-Liang Ma, Zhuofeng Lin, Jianzeng Dong, Yang Li, Yulin Li

Department of Emergency Medicine Faculty Papers

BACKGROUND: Hypertrophic cardiomyopathy (HCM) is a heterogeneous disease with diverse prognosis. The underlying mechanisms remain unknown, resulting in limited risk stratification and therapeutic strategies. This study aimed to elucidate molecular subtypes of HCM through integrated proteogenomic analysis and explore subtype-specific therapeutic strategies.

METHODS: We conducted an integrated proteogenomic analysis of 132 patients with HCM using myocardial samples, incorporating whole-exome sequencing, RNA sequencing, and proteomics. Unsupervised clustering was used to identify HCM subtypes, which were validated in heart tissues and human induced pluripotent stem cell-derived cardiomyocytes from 2 independent HCM subsets. Subtype-specific signatures and pathways were explored, and their causal link …

Pearson Syndrome: Expanding The Clinical Spectrum Of A Mitochondrial Cytopathy-A Case Report, Alizah Faisal, Hooria Waqas, Hania Masood, Armeen Butt, Saad Rahman, Muhammad Sheraz Hameed, Syed Rafay Hussain Zaidi, Ali Iqbal, Muhammad Usama Naveed

Department of Medicine Faculty Papers

BACKGROUND: Pearson syndrome (PS) is a rare multisystem mitochondrial disorder characterized by single large-scale mitochondrial DNA deletions (SLSMDs). It typically presents in infancy with refractory sideroblastic anemia, exocrine pancreatic insufficiency, and failure to thrive. Due to its heterogeneous manifestations and resemblance to other hematological conditions, early diagnosis remains a clinical challenge.

CASE PRESENTATION: A south asian male infant presented with persistent pancytopenia, severe anemia unresponsive to intravenous and oral iron and multivitamin supplements, exocrine pancreatic insufficiency, failure to thrive, and metabolic acidosis. Born to consanguineous parents, the child had a significant family history of early infant deaths and hematological abnormalities. …

Multi-Ancestry Polygenic Risk Scores For The Prediction Of Type 2 Diabetes And Complications In Diverse Ancestries, Alicia Huerta-Chagoya, Joohyun Kim, Ravi Mandla, Yingchang Lu, Ken Suzuki, Lauren E. Petty, Hong Kiat Ng, Jaewon Choi, Simon Lee, John Blangero

Human Genetics Publications

Background: Polygenic risk scores (PRSs) improve prediction of the development of type 2 diabetes over the use of clinical risk factors alone; however, they perform poorly in populations of non-European ancestry, limiting their global clinical utility. We aimed to deliver comprehensive and rigorously tested multi-ancestry PRSs for prediction in type 2 diabetes.

Methods: We conducted meta-analyses using data from type 2 diabetes genome-wide association studies (GWAS) across cohorts from five major global ancestries: European, African or African American, Admixed American, South Asian, and East Asian. We used summary statistics from the GWAS to construct single-ancestry PRSs (using the continuous-shrinkage PRS-CS …

Association Of Ultra-Processed Food Intake With Insulin Secretion And Sensitivity In Mexican American Children: Results From The Safari Study, Hemant Kulkarni, Rector Arya, Srinivas Mummidi, Sharon P. Fowler, Roy G. Resendez, Juan C. Lopez-Alvarenga, Vidya Farook, John Blangero

Human Genetics Publications

Background/Objectives: There is increasing interest in and evidence for the role of ultra-processed foods (UPFs) in cardiometabolic risk. We tested the hypothesis that UPF intake score derived from dietary history is associated with measures of insulin secretion and sensitivity in a family setting even when the process of type 2 diabetes is still to ensue. Methods: We used data from our well-characterized San Antonio Family Assessment of Metabolic Risk Indicators in Youth (SAFARI) study cohort of nondiabetic children (aged 6–17 years). Dietary history was assessed using the Block Food Frequency Questionnaire. Outcomes of interest were 19 clinically useful indexes of …

Mosaic Loss Of Y Chromosome Associates With Lung Function, Emphysema, And Epigenetic Aging, Woei Yuh Saw, Kangjin Kim, Yichen Huang, Jeong H. Yun, Xiaolong Ma, Jason Bacon, Yash Pershad, Daniel Levy, George T. O’Connor, John Blangero

Human Genetics Publications

Rationale: As the global population ages, identifying risk factors for age-related diseases, such as COPD, is crucial for public health. Mosaic loss of Y chromosome (mLOY) in blood cells is an age-related somatic mosaicism event, but its relationship with pulmonary health remains undercharacterized. Objectives: To examine the association between mLOY and pulmonary outcomes in men. Methods: Leveraging mLOY assessment (cell fraction ≥ 5%) in over 12 000 men, including 5097 from the COPDGene Study and 7235 from six additional cohorts in the Trans-Omics for Precision Medicine program, we investigated mLOY associations with respiratory outcomes and epigenetic aging using multivariable cross-sectional, …

Crispr/Cas9-Based Genome Editing: Understanding Differences In Dna Repair Pathways, Profiles, And Outcomes, Samuel Effah, Shirley Barrera, Nahia Urturi Ortiz, Will Dampier, Michael Nonnemacher, Brian Wigdahl

Kimmel Cancer Center Faculty Papers

Over a decade of advances in Clustered Regularly Interspersed Short Palindromic Repeats (CRISPR) and CRISPR-associated protein 9 (Cas9)-based technologies have culminated in the first-ever FDA-approved CRISPR/Cas-based therapy. Aside from this approved therapy for sickle cell anemia, several CRISPR/Cas-based therapies are currently under development or testing for a range of chronic diseases, including viral diseases like human immunodeficiency virus type 1 (HIV-1) infection, genetic diseases like familial hypercholesterolemia, and cancer. The success of these therapies hinges on the effective delivery of CRISPR/Cas9 components to target regions, efficient Cas endonuclease editing, repair profiles generated, and their resulting outcomes. Here, we discuss the …

Mobile Genetic Elements Shape Microbial Diversity And Functions In Thawing Permafrost Soils, Jiarong Guo, Samuel T. N. Aroney, Guillermo Domínguez-Huerta, Derek Smith, Dean Vik, Carlos Owusu-Ansah, Akbar Adjie Pratama, Sergei Solonenko, Funing Tian, Cristina Howard-Varona, Zhi-Ping Zhong, Aminata Fofana, Garrett J. Smith, Suzanne B. Hodgkins, Dylan Cronin, Isogenie Field Teams 2010–2017, 2019, Emerge Coordinators, Ben J. Woodcroft, Gene W. Tyson, Virginia I. Rich, Matthew B. Sullivan, Simon Roux, Sarah C. Bagby, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current …

Morphometric And Genetic Analyses Of The Sheat Catfish Genus Ompok And Kryptopterus (Siluriidae) From The Mahakam River, East Kalimantan, Indone-Sia, Jusmaldi Jusmaldi, Rudhy Gustiano, Haryono Haryono, Rusdianto Rusdianto, Gema Wahyudewantoro, Syahroma Husni Nasution, Yulianto Yulianto, Muhammad Hunaina Fariduddin Aththar, Safar Dody, Amran Ronny Syam, Irin Iriana Kusmini, Yosmaniar Yosmaniar

Makara Journal of Science

Anthropogenic impacts within the watershed threaten the survival of sheat catfish. Therefore, species of the genera Ompok and Kryptopterus should be conserved and domesticated to ensure their long-term persistence. Moreover, the accurate documentation of the existence and taxonomic validity of Ompok and Kryptopterus species is crucial. Accordingly, this study aims to assess the species diversity of the genera Ompok and Kryptopterus in the Mahakam River, East Kalimantan, Indonesia. The study was conducted between June and December 2014, with an update in August 2024. Fish samples were collected from the upstream and middle reaches of the Mahakam River. A total of …

Regional, Functional And Transcriptomic Decoding Of Multidimensional Brain Structure Alterations In Obsessive-Compulsive Disorder, Leonardo Cardoso Saraiva, João Ricardo Sato, Isaac Sebenius, Nadza Dzinalija, Carla Del Río-Torné, Fábio Godinho, Antonio C. Lopes, Thomas V. Fernandez, Monicke O. Lima, Anderson M. Winkler

Human Genetics Publications

Studies of brain morphology in mental illness often focus on a few neuroimaging phenotypes. Here we present a comprehensive morphological characterization in obsessive-compulsive disorder (OCD) in a large sample (2255 OCD, 2264 controls) using nine cortical and four subcortical phenotypes, including several not previously examined in OCD, among them a subcortical structural similarity network phenotype developed here. Spatially distinct regional alterations emerged across structural phenotypes: cortical curvature alterations in default mode and frontoparietal networks, increased structural similarity network node degree in sensorimotor regions, widespread volume reductions associated with medication use, and localized subcortical shape alterations. In brain-behavior predictive models, curvature …

Advocating For A Care-Based Ethic: Stories Of Pregnancy And Birth From Caregivers Of Children With Down Syndrome, Lydia Ocasio-Stoutenburg, Nayma Sultana Mim

Developmental Disabilities Network Journal

Down syndrome (DS) impacts about 1 in every 640 childbirths in the United States. While quality of life has improved for people with DS, systemic inequities and deficit-based perceptions have persisted throughout history, with material impacts on people with DS and their caregivers. Researchers have documented how caregivers of children with DS have had negative experiences with healthcare providers and genetic counselors, whose biased views about DS translate into subtle and overt pressures. Few studies explicitly focus on the experiences of Caregivers of Color, multilingual families, as well as families with varying economic experiences who have children with DS. This …

Quantitative Genetic Analysis Of Baboon Facial Variation Challenges A Classic Papionin Trait, A. Thiebaut, C. C. Roseman, Michael Mahaney, Leslea J. Hlusko

Human Genetics Publications

The Linnaean family of monkeys that includes baboons, macaques, and mandrills (among others) is notably characterized by large, extended muzzles that vary in lateral nasal dorsum profile. In paleontological studies, this variation is referred to as the anteorbital drop (AOD). Here, we first devise a method to quantify this phylogenetic character. We then employ quantitative genetic analyses using a MCMCglmm model of facial variation in a captive, pedigreed baboon colony (n = 934), including admixed individuals derived from at least two Papio species, from the Southwest National Primate Research Center to assess the quantitative variation of the AOD, its …