The Role Of Siamese In G2 Checkpoint Regulation In Arabidopsis Thaliana,
2024
Louisiana State University and Agricultural and Mechanical College
The Role Of Siamese In G2 Checkpoint Regulation In Arabidopsis Thaliana, Martha A. Schwall
LSU Doctoral Dissertations
Cyclin-cyclin dependent kinase (Cyclin-CDK) pairs regulate progression through the checkpoints of the cell cycle. They bind with some specificity and must be bound to for their regulative properties to be active. The presence of cyclin-CDKs is conserved throughout eukaryotes, while differences in specifics exist between yeast, animals, and plants. In Arabidopsis, SIAMESE (SIM) is a CDK inhibitor that restricts progression through mitosis. Overexpression of SIM is required for endoreplication in Arabidopsis trichomes, and overexpression of SIM results in increased endoreplication in leaf epidermal cells. SIM is expressed at high levels in the root elongation zone, where it plays a …
Dynamic Dysregulation Of Retrotransposons In Neurodegenerative Diseases At The Single-Cell Level\,
2024
The Texas Medical Center Library
Dynamic Dysregulation Of Retrotransposons In Neurodegenerative Diseases At The Single-Cell Level\, Wankun Deng, Citu Citu, Andi Liu, Zhongming Zhao
Faculty, Staff and Student Publications
Retrotransposable elements (RTEs) are common mobile genetic elements comprising ∼42% of the human genome. RTEs play critical roles in gene regulation and function, but how they are specifically involved in complex diseases is largely unknown. Here, we investigate the cellular heterogeneity of RTEs using 12 single-cell transcriptome profiles covering three neurodegenerative diseases, Alzheimer's disease (AD), Parkinson's disease, and multiple sclerosis. We identify cell type marker RTEs in neurons, astrocytes, oligodendrocytes, and oligodendrocyte precursor cells that are related to these diseases. The differential expression analysis reveals the landscape of dysregulated RTE expression, especially L1s, in excitatory neurons of multiple neurodegenerative diseases. …
Adding Gastrointestinal Parasite Resistance To The Breeding
Objective In Hair Sheep: Initial Step,
2024
University of Nebraska-Lincoln
Adding Gastrointestinal Parasite Resistance To The Breeding Objective In Hair Sheep: Initial Step, Robert M. Forbes, Thomas W. Murphy, Joan M. Burke, David R. Notter, Matthew L. Spangler, Michael D. Macneil, Ronald M. Lewis
Department of Animal Science: Faculty Publications
The U.S. Maternal Hair Index was designed by the National Sheep Improvement Program (NSIP) to increase total weight of lamb weaned per ewe lambing (TW). Producers are interested in adding gastrointestinal nematode (GIN) resistance to this breeding objective since parasitism causes substantial economic losses. The NSIP provides producers with estimated breeding values (EBV) for postweaning fecal egg count (PFEC), an indicator of GIN resistance. Our objective was to gauge the effects of including PFEC as another selection criterion and goal trait. Selection index theory was used to construct 11 indexes. …
Identification Of Allele-Specific Kiv-2 Repeats And Impact On Lp(A) Measurements For Cardiovascular Disease Risk,
2024
The Texas Medical Center Library
Identification Of Allele-Specific Kiv-2 Repeats And Impact On Lp(A) Measurements For Cardiovascular Disease Risk, Sairam Behera, Jonathan R Belyeu, Xiao Chen, Luis F Paulin, Ngoc Quynh H Nguyen, Emma Newman, Medhat Mahmoud, Vipin K Menon, Qibin Qi, Parag Joshi, Santica Marcovina, Massimiliano Rossi, Eric Roller, James Han, Vitor Onuchic, Christy L Avery, Christie M Ballantyne, Carlos J Rodriguez, Robert C Kaplan, Donna M Muzny, Ginger A Metcalf, Richard A Gibbs, Bing Yu, Eric Boerwinkle, Michael A Eberle, Fritz J Sedlazeck
Faculty, Staff and Students Publications
The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase approximately 50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 …
The Primacy Of Density-Mediated Indirect Effects In A Community Of Wolves, Elk, And Aspen,
2024
Utah State University
The Primacy Of Density-Mediated Indirect Effects In A Community Of Wolves, Elk, And Aspen, Elaine M. Brice, Eric J. Larsen, Daniel R. Stahler, Daniel R. Macnulty
Aspen Bibliography
The removal or addition of a predator in an ecosystem can trigger a trophic cascade, whereby the predator indirectly influences plants and/or abiotic processes via direct effects on its herbivore prey. A trophic cascade can operate through a density-mediated indirect effect (DMIE), where the predator reduces herbivore density via predation, and/or through a trait-mediated indirect effect (TMIE), where the predator induces an herbivore trait response that modifies the herbivore's effect on plants. Manipulative experiments suggest that TMIEs are an equivalent or more important driver of trophic cascades than are DMIEs. Whether this applies generally in nature is uncertain because few …
The Giab Genomic Stratifications Resource For Human Reference Genomes,
2024
The Texas Medical Center Library
The Giab Genomic Stratifications Resource For Human Reference Genomes, Nathan Dwarshuis, Divya Kalra, Jennifer Mcdaniel, Philippe Sanio, Pilar Alvarez Jerez, Bharati Jadhav, Wenyu Eddy Huang, Rajarshi Mondal, Ben Busby, Nathan D Olson, Fritz J Sedlazeck, Justin Wagner, Sina Majidian, Justin M Zook
Faculty, Staff and Students Publications
Despite the growing variety of sequencing and variant-calling tools, no workflow performs equally well across the entire human genome. Understanding context-dependent performance is critical for enabling researchers, clinicians, and developers to make informed tradeoffs when selecting sequencing hardware and software. Here we describe a set of “stratifications,” which are BED files that define distinct contexts throughout the genome. We define these for GRCh37/38 as well as the new T2T-CHM13 reference, adding many new hard-to-sequence regions which are critical for understanding performance as the field progresses. Specifically, we highlight the increase in hard-to-map and GC-rich stratifications in CHM13 relative to the …
A Long-Recognized But Undescribed New Species Of Cyprinella (Cypriniformes: Leuciscidae) From North Carolina And South Carolina, United States,
2024
North Carolina Museum of Natural Sciences
A Long-Recognized But Undescribed New Species Of Cyprinella (Cypriniformes: Leuciscidae) From North Carolina And South Carolina, United States, Bryn H. Tracy, Fred C. Rohde, Michael A. Perkins, Laura M. Lee, Kara B. Carlson, Madelyn Mccutcheon, Brena K. Jones, Heather K. Evans
Southeastern Fishes Council Proceedings
Cyprinella leptocheilus sp. nov., Siouan Thinlip Chub, is described as a new species that is endemic to Sand Hills and upper Coastal Plain streams in North Carolina and South Carolina. Recognized as an undescribed species since the early 1970s, this fish was known in the literature and in museum electronic databases as Hybopsis n. sp., H. sp. cf. zanema, Cyprinella n. sp., and C. sp. cf. zanema. Unofficially, it had gone by the common name Thinlip Chub. It was thought to be closely related to the two other barbeled Cyprinella species: Thicklip Chub, …
Electric Potential Energy Optimized 3d Radial Sampling Trajectories For Mri,
2024
The Texas Medical Center Library
Electric Potential Energy Optimized 3d Radial Sampling Trajectories For Mri, Christopher Huynh, Datta Singh Goolaub, Christopher K Macgowan
Faculty, Staff and Students Publications
A novel method for creating “golden” 3D center-out radial MRI sampling trajectories was developed and analyzed. This method, called ELECTRO (ELECTRic potential energy Optimized), uses repulsive forces to minimize electric potential energy. An objective function , the electric potential energies of all subsets of consecutive readouts in a 3D radial trajectory, and its reduced form were minimized using a multi-stage optimization strategy. A metric called normalized mean nearest neighbor angular distance (NMNA) was proposed for describing distributions of points on a sphere. ELECTRO and other relevant golden trajectories were compared in silico using NMNA and point spread function analysis. Consecutive …
When Less Is More: Sketching With Minimizers In Genomics,
2024
The Texas Medical Center Library
When Less Is More: Sketching With Minimizers In Genomics, Malick Ndiaye, Silvia Prieto-Baños, Lucy M Fitzgerald, Ali Yazdizadeh Kharrazi, Sergey Oreshkov, Christophe Dessimoz, Fritz J Sedlazeck, Natasha Glover, Sina Majidian
Faculty, Staff and Students Publications
The exponential increase in sequencing data calls for conceptual and computational advances to extract useful biological insights. One such advance, minimizers, allows for reducing the quantity of data handled while maintaining some of its key properties. We provide a basic introduction to minimizers, cover recent methodological developments, and review the diverse applications of minimizers to analyze genomic data, including de novo genome assembly, metagenomics, read alignment, read correction, and pangenomes. We also touch on alternative data sketching techniques including universal hitting sets, syncmers, or strobemers. Minimizers and their alternatives have rapidly become indispensable tools for handling vast amounts of data.
Effects Of Cadherin Mediated Contact Normalization On Oncogenic Src Kinase Mediated Gene Expression And Protein Phosphorylation,
2024
Rowan University
Effects Of Cadherin Mediated Contact Normalization On Oncogenic Src Kinase Mediated Gene Expression And Protein Phosphorylation, Rachel E Nicoletto, Cayla J Holdcraft, Ariel C Yin, Edward P Retzbach, Stephanie A Sheehan, Amanda A Greenspan, Christopher M Laugier, Jason Trama, Caifeng Zhao, Haiyan Zheng, Gary S Goldberg
Rowan-Virtua School of Osteopathic Medicine Departmental Research
Nontransformed cells form heterotypic cadherin junctions with adjacent transformed cells to inhibit tumor cell growth and motility. Transformed cells must override this form of growth control, called "contact normalization", to invade and metastasize during cancer progression. Heterocellular cadherin junctions between transformed and nontransformed cells are needed for this process. However, specific mechanisms downstream of cadherin signaling have not been clearly elucidated. Here, we utilized a β-catenin reporter construct to determine if contact normalization affects Wnt signaling in transformed cells. β-catenin driven GFP expression in Src transformed mouse embryonic cells was decreased when cultured with cadherin competent nontransformed cells compared to …
Stratomod: Predicting Sequencing And Variant Calling Errors With Interpretable Machine Learning,
2024
The Texas Medical Center Library
Stratomod: Predicting Sequencing And Variant Calling Errors With Interpretable Machine Learning, Nathan Dwarshuis, Peter Tonner, Nathan D Olson, Fritz J Sedlazeck, Justin Wagner, Justin M Zook
Faculty, Staff and Students Publications
Despite the variety in sequencing platforms, mappers, and variant callers, no single pipeline is optimal across the entire human genome. Therefore, developers, clinicians, and researchers need to make tradeoffs when designing pipelines for their application. Currently, assessing such tradeoffs relies on intuition about how a certain pipeline will perform in a given genomic context. We present StratoMod, which addresses this problem using an interpretable machine-learning classifier to predict germline variant calling errors in a data-driven manner. We show StratoMod can precisely predict recall using Hifi or Illumina and leverage StratoMod's interpretability to measure contributions from difficult-to-map and homopolymer regions for …
Mates: A Deep Learning-Based Model For Locus-Specific Quantification Of Transposable Elements In Single Cell,
2024
The Texas Medical Center Library
Mates: A Deep Learning-Based Model For Locus-Specific Quantification Of Transposable Elements In Single Cell, Ruohan Wang, Yumin Zheng, Zijian Zhang, Kailu Song, Erxi Wu, Xiaopeng Zhu, Tao P Wu, Jun Ding
Faculty, Staff and Students Publications
Transposable elements (TEs) are crucial for genetic diversity and gene regulation. Current single-cell quantification methods often align multi-mapping reads to either 'best-mapped' or 'random-mapped' locations and categorize them at the subfamily levels, overlooking the biological necessity for accurate, locus-specific TE quantification. Moreover, these existing methods are primarily designed for and focused on transcriptomics data, which restricts their adaptability to single-cell data of other modalities. To address these challenges, here we introduce MATES, a deep-learning approach that accurately allocates multi-mapping reads to specific loci of TEs, utilizing context from adjacent read alignments flanking the TE locus. When applied to diverse single-cell …
Larp1 Haploinsufficiency Is Associated With An Autosomal Dominant Neurodevelopmental Disorder,
2024
The Texas Medical Center Library
Larp1 Haploinsufficiency Is Associated With An Autosomal Dominant Neurodevelopmental Disorder, James Chettle, Raymond J Louie, Olivia Larner, Robert Best, Kevin Chen, Josephine Morris, Zinaida Dedeic, Anna Childers, R Curtis Rogers, Barbara R Dupont, Cindy Skinner, Sébastien Küry, Kevin Uguen, Marc Planes, Danielle Monteil, Megan Li, Aviva Eliyahu, Lior Greenbaum, Nofar Mor, Thomas Besnard, Bertrand Isidor, Benjamin Cogné, Alyssa Blesson, Anne Comi, Ingrid M Wentzensen, Blake Vuocolo, Seema R Lalani, Roberta Sierra, Lori Berry, Kent Carter, Stephan J Sanders, Sarah P Blagden
Faculty, Staff and Students Publications
Autism spectrum disorder (ASD) is a neurodevelopmental disorder (NDD) that affects approximately 4% of males and 1% of females in the United States. While causes of ASD are multi-factorial, single rare genetic variants contribute to around 20% of cases. Here, we report a case series of seven unrelated probands (6 males, 1 female) with ASD or another variable NDD phenotype attributed to de novo heterozygous loss of function or missense variants in the gene LARP1 (La ribonucleoprotein 1). LARP1 encodes an RNA-binding protein that post-transcriptionally regulates the stability and translation of thousands of mRNAs, including those regulating cellular metabolism and …
Single-Cell Somatic Copy Number Variants In Brain Using Different Amplification Methods And Reference Genomes,
2024
The Texas Medical Center Library
Single-Cell Somatic Copy Number Variants In Brain Using Different Amplification Methods And Reference Genomes, Ester Kalef-Ezra, Zeliha Gozde Turan, Diego Perez-Rodriguez, Ida Bomann, Sairam Behera, Caoimhe Morley, Sonja W Scholz, Zane Jaunmuktane, Jonas Demeulemeester, Fritz J Sedlazeck, Christos Proukakis
Faculty, Staff and Students Publications
The presence of somatic mutations, including copy number variants (CNVs), in the brain is well recognized. Comprehensive study requires single-cell whole genome amplification, with several methods available, prior to sequencing. Here we compare PicoPLEX with two recent adaptations of multiple displacement amplification (MDA): primary template-directed amplification (PTA) and droplet MDA, across 93 human brain cortical nuclei. We demonstrate different properties for each, with PTA providing the broadest amplification, PicoPLEX the most even, and distinct chimeric profiles. Furthermore, we perform CNV calling on two brains with multiple system atrophy and one control brain using different reference genomes. We find that 20.6% …
Unravelling The Impact Of Blood Metabolites, And Lifestyle Factors On Periodontal Disease Using Mendelian Randomization,
2024
University of South Florida
Unravelling The Impact Of Blood Metabolites, And Lifestyle Factors On Periodontal Disease Using Mendelian Randomization, Rhea Charles
USF Tampa Graduate Theses and Dissertations
Periodontal disease remains a global public health concern. Despite the availability of preventive and therapeutic strategies, the multifactorial nature of periodontitis complicates its understanding and management. Periodontal disease is associated with an increased risk of chronic conditions, including ischemic heart disease (IHD), gestational hypertension, respiratory diseases such as COPD and bronchitis, and various cancers, including kidney and pancreatic cancers. Moreover, individuals with diabetes, autoimmune diseases like lupus and Crohn’s disease, and osteoporosis are more likely to develop periodontitis. The ambiguity in the direction of causality between periodontal disease and its associated conditions poses challenges for effective treatment. Mendelian randomization offers …
Whole Genomes Of Amazonian Uakari Monkeys Reveal Complex Connectivity And Fast Differentiation Driven By High Environmental Dynamism,
2024
The Texas Medical Center Library
Whole Genomes Of Amazonian Uakari Monkeys Reveal Complex Connectivity And Fast Differentiation Driven By High Environmental Dynamism, Núria Hermosilla-Albala, Felipe Ennes Silva, Sebastián Cuadros-Espinoza, Claudia Fontsere, Alejandro Valenzuela-Seba, Harvinder Pawar, Marta Gut, Joanna L Kelley, Sandra Ruibal-Puertas, Pol Alentorn-Moron, Armida Faella, Esther Lizano, Izeni Farias, Tomas Hrbek, Joao Valsecchi, Ivo G Gut, Jeffrey Rogers, Kyle Kai-How Farh, Lukas F K Kuderna, Tomas Marques-Bonet, Jean P Boubli
Faculty, Staff and Students Publications
Despite showing the greatest primate diversity on the planet, genomic studies on Amazonian primates show very little representation in the literature. With 48 geolocalized high coverage whole genomes from wild uakari monkeys, we present the first population-level study on platyrrhines using whole genome data. In a very restricted range of the Amazon rainforest, eight uakari species (Cacajao genus) have been described and categorized into the bald and black uakari groups, based on phenotypic and ecological differences. Despite a slight habitat overlap, we show that posterior to their split 0.92 Mya, bald and black uakaris have remained independent, without gene flow. …
The Short Allele Of The Serotonin Transporter Gene (Slc6a4) Increases Predisposition To Anxiety And Negative Emotional States,
2024
University of North Florida
The Short Allele Of The Serotonin Transporter Gene (Slc6a4) Increases Predisposition To Anxiety And Negative Emotional States, Gabriella Hitti
PANDION: The Osprey Journal of Research and Ideas
Mental disorders, such as anxiety and mood disorders, have long been a focus of psychological research, and increasing evidence points to a genetic basis for their occurrence. Polymorphisms of the serotonin transporter (5-HTT) gene (SLC6A4) may predispose an individual to anxiety-related symptoms. SLC6A4 has two common alleles: the short (s) allele, which results in less 5-HTT protein production, and the long (l) allele, which results in more 5-HTT. Integrated findings from psychometric evaluations, behavioral animal models, and biological assessments establish a link between the s allele of SLC6A4 and heightened anxiety phenotypes. The allele’s influence on serotonin levels and brain …
Sars-Cov-2 Vaccine Improved Hemostasis Of A Patient With Protein S Deficiency: A Case Report,
2024
LSU Health Sciences Center - New Orleans
Sars-Cov-2 Vaccine Improved Hemostasis Of A Patient With Protein S Deficiency: A Case Report, Mohammad A. Mohammad, Alaa Malik, Lekha Thangada, Diana Polanía-Villanueva, Jovanny Zabaleta, Rinku Majumder
School of Medicine Faculty Publications
A 16-year-old patient, while an infant, incurred right-sided hemiparesis and had difficulty breast feeding. She was later diagnosed with a neonatal stroke and her genetic testing showed a missense mutation in her PROS1 (Protein S) gene. Both her grandfather and father, but not her mother, had hereditary Protein S (PS) deficiency. The patient was not prescribed any mediation due to her young age but was frequently checked by her physician. The patient’s plasma was first collected at the age of 13, and the isolated plasma from the patient and her father were analyzed by aPTT, thrombin generation, and enzyme-linked immunosorbent …
Analyses Of Whole-Genome
Sequences From 185 North
American Thoroughbred Horses,
Spanning 5 Generations,
2024
University of Kentucky
Analyses Of Whole-Genome Sequences From 185 North American Thoroughbred Horses, Spanning 5 Generations, Ernie Bailey, Carrie J. Finno, Jonah N. Cullen, Ted Kalbfleisch, Jessica Lynn Petersen
Department of Animal Science: Faculty Publications
Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5–5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Individual coefficients of inbreeding, estimated from ROH, averaged 0.266 (Group 1) and …
Cross-Species Analysis Of Rpl24 Knockout For Cftr Function Restoration,
2024
University of Alabama at Birmingham
Cross-Species Analysis Of Rpl24 Knockout For Cftr Function Restoration, Brittany Jackson, Ryan Mancinone, John L. Hartman Iv
Expo Student Presentations
2024 Fall Expo Poster Presentation
