Genetics and Genomics Commons^™

Genetic Entropy: A Critical Examination, Sarah Hunter

Science, Faith, and Origins

Genetic entropy is a hypothesis proposing that genomes deteriorate over time due to the gradual accumulation of slightly harmful mutations that natural selection cannot effectively remove. This paper explores the scientific debate surrounding this claim by examining differing perspectives on the theory of genetic entropy. Proponents of genetic entropy, such as John Sanford, argue that most mutations are deleterious and fall within a “near-neutral” range, allowing them to accumulate since their effects are too small for natural selection to detect. Evidence to support this claim includes Robert Carter and John Sanford’s research on the deterioration of the H1N1 viral genome …

Dynamic Rewiring Of Microrna Networks In The Brainstem Autonomic Control Circuits During Hypertension Development In The Female Spontaneously Hypertensive Rat, Alison Moss, Ankita Srivastava, Lakshmi Kuttippurathu, James S. Schwaber, Rajanikanth Vadigepalli

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

We describe global microRNA (miRNA) changes in the central autonomic control circuits during the development of neurogenic hypertension. Using the female spontaneously hypertensive rat (SHR) and the normotensive Wistar Kyoto (WKY), we analyzed the dynamic miRNA expression changes in three brainstem regions-the nucleus of the solitary tract, caudal ventrolateral medulla, and rostral ventrolateral medulla-as a time series beginning at 8 wk of age before hypertension onset through to extended chronic hypertension. Our analysis yielded nine miRNAs that were significantly differentially regulated in all three regions between SHR and WKY over time. We collated computationally predicted gene targets of these nine …

Investigating The Presence Of R-Loops At The Centromeres Of Drosophila Melanogaster, Daniel D'Souza

Holster Scholar Projects

This study investigates the presence and localization of R-loops at the centromeres of Drosophila melanogaster. R-loops are non-canonical nucleic acid structures that have been implicated in various cellular processes, including genomic instability and accurate chromosome segregation. Although previous research has found R-loops at Drosophila satellite sequences and LTR retrotransposons, their presence and function at the centromeres of a whole organism remain largely unknown. Using IF-FISH (immunofluorescence-fluorescence in situ hybridization), we stained R-loops with the S9.6 antibody. A UAS-rnh1 overexpression line was used to induce the overexpression of RNase H1, an enzyme that resolves R-loops, to confirm the specificity of …

Integrating Multimodal Neuroimaging Of Error Monitoring To Estimate Future Anxiety In Adolescents, Emilio A. Valadez, Stefania Conte, John E. Richards, Yi Feng, Lucrezia Liuzzi, Marco Mcsweeney, Enda Tan, George A. Buzzell, Anderson M. Winkler, Daniel Samuel Pine

Human Genetics Publications

Importance Anxiety disorders are highly prevalent and associated with heightened error monitoring, the detection of one’s mistakes. However, error monitoring, anxiety, and their associations change throughout adolescence, limiting the ability to estimate future anxiety trajectories during this period.

Objective To ascertain whether measures of error monitoring obtained via the integration of electroencephalogram (EEG) and functional magnetic resonance imaging (fMRI) improve estimations of future anxiety compared with EEG or fMRI alone, in adolescents with or without a history of behaviorally inhibited temperament.

Design, Setting, and Participants This longitudinal cohort study was conducted at a university research laboratory and government research hospital. …

Penetrance Of Neurodevelopmental Copy Number Variants Is Associated With Variations In Cortical Morphology, Ana I. Silva, Ida E. Sønderby, George Kirov, Abdel Abdellaoui, Ingrid Agartz, David Ames, Nicola J. Armstrong, Eric Artiges, Tobias Banaschewski, John Blangero

Human Genetics Publications

Background: Copy number variants (CNVs) may increase the risk for neurodevelopmental conditions. The neurobiological mechanisms that link these high-risk genetic variants to clinical phenotypes are largely unknown. An important question is whether brain abnormalities in individuals who carry CNVs are associated with their degree of penetrance.

Methods: We investigated whether increased CNV penetrance for schizophrenia and other developmental disorders was associated with variations in cortical and subcortical morphology. We pooled T1-weighted brain magnetic resonance imaging and genetic data from 22 cohorts from the ENIGMA (Enhancing Neuro Imaging Genetics through Meta Analysis)-CNV consortium. In the main analyses, we included 9268 individuals …

Clinical And Genetic Studies Of Hypotrichosis In District Pakpattan, Punjab, Pakistan, Amir Anees, Muhammad Abdullah, Khawar Hayyat, Muhammad Irshad, Muhammad Iqbal Usama, Muhammad Saleem Khan, Muhammad Rizwan, Muhammad Wajid

Journal of Bioresource Management

Hypotrichosis is a hereditary hair development condition that results in thin or little hair on the head and other regions of the body due to diminished or non-existent hair growth. To investigate the prevalence rate, the mechanism of inheritance, and the genetic counselling of people affected by these conditions. To determine the number of cases of familial hypotrichosis, a survey was done at various schools, colleges, hospitals, and communities to identify those affected by this ailment. A study of eleven families with consanguineous marriages found that 10.52 % of the population had hypotrichosis. The affected individuals had limited hair growth …

Uncovering The Pml::Rara Fusion In Cytogenetically Cryptic And Fish-Negative Acute Promyelocytic Leukemia-A Case Report And Comprehensive Literature Review, Busra Delikkaya, Jaime Eberle-Singh, Arianna Morton, Jerald Gong, Jinglan Liu

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

The PML::RARA fusion resulting from t(15;17) is the genetic hallmark of acute promyelocytic leukemia (APL), typically detected by cytogenetics and/or fluorescence in situ hybridization (FISH) studies. Rarely, APL patients present with normal cytogenetics and FISH findings, complicating diagnosis and delaying life-saving therapy. We report a 23-year-old male with clinical, morphologic and immunophenotypic features consistent with APL but negative for FISH studies. Despite prompt initiation of all-trans retinoic acid (ATRA) based on clinical suspicion, the patient succumbed to intracranial hemorrhage. Quantitative reverse transcriptase PCR (qRT-PCR) confirmed a long isoform PML::RARA fusion. A review of 34 published cytogenetics- and FISH-negative cases since …

The Evaluation Of Variants Within Eight Collagen Genes Col1a1, Col1a2, Col3a1, Col5a1, Col11a1, Col15a1, Col22a1, And Col27a1 And A Risk Of Non-Contact Knee Ligament Rupture In Elite Handball Players: A Case-Control Study, Katarzyna Krawczak-Wójcik, Andrzej Mastalerz, Aleksandra Bojarczuk, Monika Johne, Alison V. September, Aleksandra Garbacz, Katarzyna Komar, Ewelina Maculewicz

Baltic Journal of Health and Physical Activity

Introduction: Knee ligament ruptures are common injuries among athletes. While most previous studies examined single collagen gene polymorphisms, few have investigated haplotype-level associations across multiple genes, particularly in elite handball players. Materials and methods: This case-control study analyzed variants in eight collagen genes (COL1A1, COL1A2, COL3A1, COL5A1, COL11A1, COL15A1, COL22A1, and COL27A1) in 103 elite Polish handball players with non-contact knee ligament rupture and 226 matched controls. Results: The COL22A1 rs11784270 CC genotype was associated with an increased risk (OR = 2.88, p = 0.01), with the strongest effect in the …

Early-Life Exposure To Organic Chemical Pollutants As Assessed In Primary Teeth And Cardiometabolic Risk In Mexican American Children: A Pilot Study, Vidya S. Farook, Feroz Akhtar, Rector Arya, Alice Yau, Srinivas Mummidi, Juan Lopez Alvarenga, Alvaro Diaz-Badillo, Roy G. Resendez, John Blangero

Human Genetics Publications

Early-life exposure to organic chemicals (OCs) may influence childhood obesity and associated cardiometabolic risk. These conditions have been shown to disproportionately affect minority populations such as Mexican Americans (MAs). However, information on the impact of organic chemicals on cardiometabolic risk in MA children is limited. Therefore, we conducted a pilot study to assess the extent to which exposure to organic chemicals influences cardiometabolic traits (CMTs) in MA children. We recalled 25 children from a previous study and collected 25 primary teeth from them. Chemical analyses of the teeth were performed using established protocols. Target analytes included acetaminophen (APAP); 3,5,6-trichloro-2-pyridinol (TCPy), …

Teaching Molecular Genetics Using Paramecium And Rna Interference: Research-Based Learning And Project Ownership, M. S. Valentine, K. Johnson, M. B. Veramendi, C. James, J. Kozak, A. Patwardhan, R. Quartey

Montclair State University Scholarship & Creative Works

Research-based course design is beneficial to both the instructor and the students by providing project ownership, independence, increased engagement, and publishable results. Paramecium, a single-celled eukaryote, is a common organism observed in many high school and college classrooms that can be easily cultured and manipulated to navigate through guided student-driven research projects. Presented here are research-centered student projects that include designing and creating an RNA interference (RNAi) plasmid to deplete a gene product in Paramecium. Because RNAi can be used in a large number of model organisms, the techniques presented can be applied in a variety of ways. …

Sequence And Phylogenetic Analysis Of Citrus Maxima (Burm.) Merr. From Tomini Bay, Sulawesi Island, Based On The Maturase K Gene, Brenda Febrina Zusriadi, Novri Youla Kandowangko, Febriyanti Febriyanti

Makara Journal of Science

This study was conducted in the coastal area of Tomini Bay, Sulawesi Island, and it focused on Citrus maxima, a plant known for its unique fruit flesh colors, which range from yellow to pink, and its varying leaf stalk wings. The study aimed to analyze the variations in maturase K (matK) sequences, molecular characteristics, and phylogenetic relationships of two C. maxima samples from Tomini Bay compared to other C. maxima and Citrus species using data available in GenBank. The study utilized DNA barcoding with matK molecular markers, followed by phylogenetic tree construction using the maximum likelihood method …

Detection Method For Escherichia Coli Using Real-Time Polymerase Chain Reaction Targeting The Yhav Gene, Muktiningsih Nurjayadi, Anisa Fitriyanti, Royna Rahma Musie, Gusti Angieta Putri, Puan Aqila Azizah, Helzi Angelina, Grace Grace, Ananda Indah Putri Sihombing, Agus Setiawan, Jefferson Lynford Declan, Gladys Indira Putri, Dandy Akbar Juliansyah, Siti Fatimah, Ayu Berkahingrum, Irma Ratna Kartika, Fera Kurniadewi, Vira Saamia, Shyi-Tien Chen, Bassam Aboemolak, Hesham Ali El Enshasy

Makara Journal of Science

Escherichia coli is a foodborne pathogenic bacterium that can cause diarrhea, while yhaV is a virulence-associated gene linked to the toxin–antitoxin system in E. coli. This study was aimed at evaluating the confirmation, specificity, and sensitivity of a yhaV gene primer using real-time polymerase chain reaction. The yhaV-targeting PCR successfully amplified a DNA fragment with an amplicon length of 207 bp (base pairs) under an annealing temperature optimized to a range of 54 °C to 62 °C via gradient PCR. The PCR using the primer pair produced a consistent Ct (cycle threshold) of 14.14 ± 0.05 and showed …

Where The Buffalo Roam: Ungulate Influences On Quaking Aspen And Willow Communities In The Greater Yellowstone Ecosystem, J. Boone Kauffman, Dian L. Cummings, Robert L. Beschta, William J. Ripple

Aspen Bibliography

Quaking aspen (Populus tremuloides) and willows (Salix spp.) are keystone species of montane and shrub-steppe landscapes of the Western United States. Intact communities dominated by these species provide a wide range of ecosystem services, harboring an exceptional proportion of landscape biodiversity. Land use, especially overgrazing by large ungulates, is among the greatest threats to these ecosystems. To examine the effects of wild ungulates and levels of grazing at Yellowstone National Park (YNP) and the adjacent Gallatin National Forest, we sampled plant community composition and vegetation structure of aspen and willow communities both inside and outside of exclosures. …

Association Of Genetic Scores Related To Insulin Resistance With Neurological Outcomes In Ancestrally Diverse Cohorts From The Trans-Omics For Precision Medicine (Topmed) Program, Chloé Sarnowski, Yixin Zhang, Farah Ammous, Lincoln M. P. Shade, Daniel Dicorpo, Xueqiu Jian, Donna K. Arnett, Thomas R. Austin, John Blangero, Joanne E. Curran

School of Medicine Publications

To better characterize the potential biological mechanisms underlying insulin resistance (IR) and dementia, we derive cross-population and population specific polygenic scores [PSs] for fasting insulin and IR-related partitioned PSs [pPSs]. We conduct a cross-sectional study of the associations of these genetic scores with neurological outcomes in >17k participants (36% men, mean age 55 yrs) from the Trans-Omics for Precision Medicine (TOPMed) program (50% Non-Hispanic White, 23% Black/African American, 21% Hispanic/Latino American, and 4% Asian American). We report significant negative associations (P <  0.002) of the cross-population (P = 1.3 × 10-5) and European (PEA = 3.0 × 10-8) fasting insulin PSs with total cranial volume, and of a metabolic syndrome European PS with general cognitive function (BEA = -0.13, PEA = 0.0002) and lateral ventricular volume (BEA = 0.09, PEA = 0.002). We identify suggestive negative associations (P <  0.007) of metabolic syndrome and obesity pPSs with general cognitive function, and of lipodystrophy pPSs with total cranial volume. A higher genetic predisposition to IR is associated with lower brain size, and a genetic predisposition to specific IR-related type 2 diabetes subtypes, such as metabolic syndrome and mechanisms of IR mediated through obesity and lipodystrophy, is potentially involved in cognitive decline.

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), …