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Rare And Low Frequency Genomic Variants Impacting Neuronal Functions Modify The Dup7q11.23 Phenotype, Farah Qaiser, Yue Yin, Carolyn B. Mervis, Colleen A. Morris, Bonita P. Klein-Tasman, Elaine Tam, Lucy R. Osborne, Ryan K.C. Yuen 2021 University of Toronto

Rare And Low Frequency Genomic Variants Impacting Neuronal Functions Modify The Dup7q11.23 Phenotype, Farah Qaiser, Yue Yin, Carolyn B. Mervis, Colleen A. Morris, Bonita P. Klein-Tasman, Elaine Tam, Lucy R. Osborne, Ryan K.C. Yuen

School of Medicine Faculty Publications

© 2021, The Author(s). Background: 7q11.23 duplication (Dup7) is one of the most frequent recurrent copy number variants (CNVs) in individuals with autism spectrum disorder (ASD), but based on gold-standard assessments, only 19% of Dup7 carriers have ASD, suggesting that additional genetic factors are necessary to manifest the ASD phenotype. To assess the contribution of additional genetic variants to the Dup7 phenotype, we conducted whole-genome sequencing analysis of 20 Dup7 carriers: nine with ASD (Dup7-ASD) and 11 without ASD (Dup7-non-ASD). Results: We identified three rare variants of potential clinical relevance for ASD: a 1q21.1 microdeletion (Dup7-non-ASD) and two ...


Environmental Rnai Pathways In The Two-Spotted Spider Mite, Mosharrof Mondal, Jacob Peter, Obrie Scarbrough, Alex Flynt 2021 The University of Arizona

Environmental Rnai Pathways In The Two-Spotted Spider Mite, Mosharrof Mondal, Jacob Peter, Obrie Scarbrough, Alex Flynt

Faculty Publications

© 2020, The Author(s).

Background:RNA interference (RNAi) regulates gene expression in most multicellular organisms through binding of small RNA effectors to target transcripts. Exploiting this process is a popular strategy for genetic manipulation and has applications that includes arthropod pest control. RNAi technologies are dependent on delivery method with the most convenient likely being feeding, which is effective in some animals while others are insensitive. The two-spotted spider mite, Tetranychus urticae, is prime candidate for developing RNAi approaches due to frequent occurrence of conventional pesticide resistance. Using a sequencing-based approach, the fate of ingested RNAs was explored to identify ...


Comparison Of Multiple Imputation Algorithms And Verification Using Whole-Genome Sequencing In The Cmuh Genetic Biobank, Ting-Yuan Liu, Chih-Fan Lin, Hsing-Tsung Wu, Ya-Lun Wu, Yu-Chia Chen, Chi-Chou Liao, Yu-Pao Chou, Dysan Chao, Hsing-Fang Lu, Ya-Sian Chang, Jan-Gowth Chang, Kai-Cheng Hsu, Fuu‑Jen Tsai 2021 China Medical University Hospital, Taiwan

Comparison Of Multiple Imputation Algorithms And Verification Using Whole-Genome Sequencing In The Cmuh Genetic Biobank, Ting-Yuan Liu, Chih-Fan Lin, Hsing-Tsung Wu, Ya-Lun Wu, Yu-Chia Chen, Chi-Chou Liao, Yu-Pao Chou, Dysan Chao, Hsing-Fang Lu, Ya-Sian Chang, Jan-Gowth Chang, Kai-Cheng Hsu, Fuu‑Jen Tsai

BioMedicine

A genome-wide association study (GWAS) can be conducted to systematically analyze the contributions of genetic factors to a wide variety of complex diseases. Nevertheless, existing GWASs have provided highly ethnic specific data. Accordingly, to provide data specific to Taiwan, we established a large-scale genetic database in a single medical institution at the China Medical University Hospital. With current technological limitations, microarray analysis can detect only a limited number of single-nucleotide polymorphisms (SNPs) with a minor allele frequency of >1%. Nevertheless, imputation represents a useful alternative means of expanding data. In this study, we compared four imputation algorithms in terms of ...


On Computing Relative Effective Population Size Estimates And Parameters From An Equilibrium Cycle Of Hermaphrodite Frequency Fluctuation Due To Mixed Reproductive Modes In Filamentous Fungi, Christopher Toomajian 2021 Kansas State University

On Computing Relative Effective Population Size Estimates And Parameters From An Equilibrium Cycle Of Hermaphrodite Frequency Fluctuation Due To Mixed Reproductive Modes In Filamentous Fungi, Christopher Toomajian

Fungal Genetics Reports

Many filamentous ascomycete fungi reproduce primarily asexually, with only occasional sexual generations. This can lead to a departure from the 1:1 mating type ratio that is expected in obligate sexual populations. The relaxed selection on sexual traits also can lead to a decrease in the frequency of female fertile strains in field populations, while male fertility does not similarly decrease since male gametes also can serve as asexual spores. Both changes ultimately impact the strength of genetic drift in populations. The frequency of female sterility likely increases with the time since the last generation of sexual reproduction, such that ...


Editorial For The Genetics Of Alzheimer’S Disease Special Issue: October 2021, Laura Ibanez, Justin B. Miller 2021 Washington University in St. Louis

Editorial For The Genetics Of Alzheimer’S Disease Special Issue: October 2021, Laura Ibanez, Justin B. Miller

Sanders-Brown Center on Aging Faculty Publications

No abstract provided.


Genomics Of Postprandial Lipidomics In The Genetics Of Lipid-Lowering Drugs And Diet Network Study, Marguerite R. Irvin, May E. Montasser, Tobias Kind, Sili Fan, Dinesh K. Barupal, Amit Patki, Rikki M. Tanner, Nicole D. Armstrong, Kathleen A. Ryan, Steven A. Claas, Jeffrey R. O’Connell, Hemant K. Tiwari, Donna K. Arnett 2021 University of Alabama at Birmingham

Genomics Of Postprandial Lipidomics In The Genetics Of Lipid-Lowering Drugs And Diet Network Study, Marguerite R. Irvin, May E. Montasser, Tobias Kind, Sili Fan, Dinesh K. Barupal, Amit Patki, Rikki M. Tanner, Nicole D. Armstrong, Kathleen A. Ryan, Steven A. Claas, Jeffrey R. O’Connell, Hemant K. Tiwari, Donna K. Arnett

Epidemiology Faculty Publications

Postprandial lipemia (PPL) is an important risk factor for cardiovascular disease. Inter-individual variation in the dietary response to a meal is known to be influenced by genetic factors, yet genes that dictate variation in postprandial lipids are not completely characterized. Genetic studies of the plasma lipidome can help to better understand postprandial metabolism by isolating lipid molecular species which are more closely related to the genome. We measured the plasma lipidome at fasting and 6 h after a standardized high-fat meal in 668 participants from the Genetics of Lipid-Lowering Drugs and Diet Network study (GOLDN) using ultra-performance liquid chromatography coupled ...


Estimation Of Genetic Diversity Among Canola Accessions Using Simple Sequence Repeat Markers, Jaleel Ahmad, Muhammad Baber, Wajid Nazeer, Sana Hamdullah, Aleena Ahmad Somroo, Shaiza Ali, Rameen Fatima, Seema Aslam 2021 Institute of Molecular Biology and Biotechnology Bahauddin Zakariya University Multan, Pakistan

Estimation Of Genetic Diversity Among Canola Accessions Using Simple Sequence Repeat Markers, Jaleel Ahmad, Muhammad Baber, Wajid Nazeer, Sana Hamdullah, Aleena Ahmad Somroo, Shaiza Ali, Rameen Fatima, Seema Aslam

Journal of Bioresource Management

Genetic studies through molecular markers proved important to find out the genetic diversity of canola. In this study, 50 lines of canola were used to find the polymorphism using 15 SSR primers and investigated the genetic diversity, PIC values, frequency-based genetic distance, and allelic frequencies. Mean gene diversity, frequency-based genetic distance, and PIC values were 0.8777, 0.233 and 0.8666, respectively for the canola lines. A good range of genetic diversity was found among studied canola lines with value 85.91% polymorphism. Maximum and minimum genetic distances among 50 lines were 1 and 0.26, respectively. Accessions ACC-26068 ...


Decoding The Equine Genome: Lessons From Encode, Sichong Peng, Jessica L. Petersen, Rebecca R. Bellone, Theodore S. Kalbfleisch, N. B. Kingsley, Alexa M. Barber, Eleonora Cappelletti, Elena Giulotto, Carrie J. Finno 2021 University of California, Davis

Decoding The Equine Genome: Lessons From Encode, Sichong Peng, Jessica L. Petersen, Rebecca R. Bellone, Theodore S. Kalbfleisch, N. B. Kingsley, Alexa M. Barber, Eleonora Cappelletti, Elena Giulotto, Carrie J. Finno

Veterinary Science Faculty Publications

The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has ...


Improved Radiation Expression Profiling In Blood By Sequential Application Of Sensitive And Specific Gene Signatures, Eliseos J. Mucaki, Ben C. Shirley, Peter K. Rogan 2021 Western University

Improved Radiation Expression Profiling In Blood By Sequential Application Of Sensitive And Specific Gene Signatures, Eliseos J. Mucaki, Ben C. Shirley, Peter K. Rogan

Biochemistry Publications

Purpose. Combinations of expressed genes can discriminate radiation-exposed from normal control blood samples by machine learning based signatures (with 8 to 20% misclassification rates). These signatures can quantify therapeutically-relevant as well as accidental radiation exposures. The prodromal symptoms of Acute Radiation Syndrome (ARS) overlap those present in Influenza and Dengue Fever infections. Surprisingly, these human radiation signatures misclassified gene expression profiles of virally infected samples as false positive exposures. The present study investigates these and other confounders, and then mitigates their impact on signature accuracy.

Methods. This study investigated recall by previous and novel radiation signatures independently derived from multiple ...


Metabolic Modeling Of Cystic Fibrosis Airway Microbiota From Patient Samples, Arsh Vyas 2021 University of Massachusetts Amherst

Metabolic Modeling Of Cystic Fibrosis Airway Microbiota From Patient Samples, Arsh Vyas

Masters Theses

Cystic Fibrosis (CF) is a genetic disorder, found with higher prevalence in the Caucasian population, affecting > 30,000 individuals in the United States and > 70,000 worldwide. Due to the astoundingly high rate of mortality among CF patients being attributed to respiratory failure brought on by chronic bacterial infections and subsequent airway inflammation, there has been a lot of focus on systematically analyzing CF lung airway communities. While it is observed traditionally that Pseudomonas aeruginosa is the most threatening and persistent CF colonizer due to high antibiotic resistance, recent studies have elicited the roles of other pathogens and it has ...


Structure-Function Studies Of The Trypanosome Mitochondrial Replication Protein Polib, Raveen Armstrong 2021 University of Massachusetts Amherst

Structure-Function Studies Of The Trypanosome Mitochondrial Replication Protein Polib, Raveen Armstrong

Masters Theses

Trypanosoma brucei and related protists are distinguished from all other eukaryotes by an unusual mitochondrial genome known as kinetoplast DNA (kDNA) that is a catenated network composed of minicircles and maxicircles. Replication of this single nucleoid involves a release, replicate, and reattach mechanism for the thousands of catenated minicircles and requires at least three DNA polymerase (POLIB, POLIC and POLID) with similarity to E. coli DNA polymerase I. Like other proofreading replicative DNA polymerases, POLIB has both an annotated polymerase domain and an exonuclease domain. Predictive modelling of POLIB indicates that it has the canonical right hand polymerase structure with ...


Discovering Mechanisms Driving Adaptive Evolution In The Cross-Kingdom Fungal Pathogen Fusarium Oxysporum, Dilay Hazal Ayhan 2021 University of Massachusetts Amherst

Discovering Mechanisms Driving Adaptive Evolution In The Cross-Kingdom Fungal Pathogen Fusarium Oxysporum, Dilay Hazal Ayhan

Doctoral Dissertations

Fusarium oxysporum is a cross-kingdom pathogenic fungus that can cause vascular wilt disease in many economically important plants and local or disseminated infections in humans. Although it lacks a sexual stage in its life cycle, F. oxysporum can adapt to a wide range of hosts because of accessory chromosomes (ACs) which are enriched in host-specific genes and repeat content. This dissertation investigates the mechanisms that drive the adaptive evolution in the cross-kingdom pathogen F. oxysporum using comparative genomics and an experimental evolution approach. The first chapter compares phenotypes and genomes of a plant pathogenic isolate F. oxysporum f. sp. lycopersici ...


Global Gene Expression Analysis Of Systemic Sclerosis Myofibroblasts Demonstrates A Marked Increase In The Expression Of Multiple Nbpf Genes, Giuseppina Abignano, Heidi Hermes, Sonsoles Piera-Velazquez, Sankar Addya, Francesco Del Galdo, Sergio A. Jimenez 2021 University of Leeds

Global Gene Expression Analysis Of Systemic Sclerosis Myofibroblasts Demonstrates A Marked Increase In The Expression Of Multiple Nbpf Genes, Giuseppina Abignano, Heidi Hermes, Sonsoles Piera-Velazquez, Sankar Addya, Francesco Del Galdo, Sergio A. Jimenez

Kimmel Cancer Center Faculty Papers

Myofibroblasts are the key effector cells responsible for the exaggerated tissue fibrosis in Systemic Sclerosis (SSc). Despite their importance to SSc pathogenesis, the specific transcriptome of SSc myofibroblasts has not been described. The purpose of this study was to identify transcriptome differences between SSc myofibroblasts and non-myofibroblastic cells. Alpha smooth muscle actin (α-SMA) expressing myofibroblasts and α-SMA negative cells were isolated employing laser capture microdissection from dermal cell cultures from four patients with diffuse SSc of recent onset. Total mRNA was extracted from both cell populations, amplified and analyzed employing microarrays. Results for specific genes were validated by Western blots ...


Determining The Primary Dna Substrates Of Shld2'S Ob-Fold Domains, Hari Patchigolla 2021 University of Connecticut - Storrs

Determining The Primary Dna Substrates Of Shld2'S Ob-Fold Domains, Hari Patchigolla

Holster Scholar Projects

Failure to repair DNA double-stranded breaks leads to cell death. Radiation therapy is commonly used to kill cancer cells by inducing these breaks. However resistance to radiation therapy, due to a hyperactive DNA double-stranded break repair pathway, is a common occurrence that makes cancer patients more prone to relapse. The Shieldin complex is shown to promote DNA-double stranded break repair by binding to DNA at sites of damage. Thus, the objective of this project is to understand the affinity and type of DNA that Shieldin binds to, through gel-shift assays, for the eventual creation of an inhibitor for this protein ...


Establishment Of A Pesticide Resistance Monitoring Tool For The Two-Spotted Spider Mite, Tetranychus Urticae, Hanna Varonina 2021 The University of Western Ontario

Establishment Of A Pesticide Resistance Monitoring Tool For The Two-Spotted Spider Mite, Tetranychus Urticae, Hanna Varonina

Electronic Thesis and Dissertation Repository

Two-spotted spider mite (TSSM), or Tetranychus urticae (Koch), is a major agriculture pest known for its rapid development of resistance to pesticides. The analysis of spider mites’ pesticide resistance demonstrated that resistance patterns and frequencies vary between T. urticae strains collected from different geographic locations and host plants. This research aims at characterization of pesticide resistance patterns in mite populations present in greenhouses in the Southwestern Ontario by identifying genetic and metabolic markers of their pesticide resistance. The establishment of these markers lays the basis for development of a pesticide resistance diagnostic tool that will enable prediction of population resistance ...


Against The Odds: Hybrid Zones Between Mangrove Killifish Species With Different Mating Systems, Waldir M. Berbel-Filho, Andrey Tatarenkov, George Pacheco, Helder M. V. Espírito-Santo, Mateus G. Lira, Carlos Garcia de Leaniz, John C. Avise, Sergio M. Q. Lima, Carlos M. Rodriguez Lopez, Sofia Consuegra 2021 University of Oklahoma

Against The Odds: Hybrid Zones Between Mangrove Killifish Species With Different Mating Systems, Waldir M. Berbel-Filho, Andrey Tatarenkov, George Pacheco, Helder M. V. Espírito-Santo, Mateus G. Lira, Carlos Garcia De Leaniz, John C. Avise, Sergio M. Q. Lima, Carlos M. Rodriguez Lopez, Sofia Consuegra

Horticulture Faculty Publications

Different mating systems are expected to affect the extent and direction of hybridization. Due to the different levels of sexual conflict, the weak inbreeder/strong outbreeder (WISO) hypothesis predicts that gametes from self-incompatible (SI) species should outcompete gametes from self-compatible (SC) ones. However, other factors such as timing of selfing and unilateral incompatibilities may also play a role on the direction of hybridization. In addition, differential mating opportunities provided by different mating systems are also expected to affect the direction of introgression in hybrid zones involving outcrossers and selfers. Here, we explored these hypotheses with a unique case of recent ...


The Effects Of Ppal-1 In Arabidopsis Gamete Development, Amanda J White, Susana Perez-Martinez, Mark P. Running 2021 University of Louisville

The Effects Of Ppal-1 In Arabidopsis Gamete Development, Amanda J White, Susana Perez-Martinez, Mark P. Running

The Cardinal Edge

Prenylation is a type of post-translational modification in which a 15- or 20-carbon lipid is added to the carboxyl (C) terminus of the protein. Arabidopsis thaliana contains the PROTEIN PRENYLTRANSFERASE ALPHA SUBUNIT-LIKE (PPAL) gene, which encodes a protein with homology to the α-subunits of the three known prenylation enzymes, PFT, PGGT, and Rab-GGT. We previously identified two mutations in PPAL, one of which is ppal-1, which contains a T-DNA insertion in the fourth intron. We have previously observed that self-fertilizing heterozygous ppal-1 plants produce progeny in which homozygous ppal-1 is underrepresented. This project attempts to ascertain possible affects of ppal-1 ...


Using Beet Pulp To Adapt Cattle To Finishing Diets Compared To Traditional Grain Adaptation With Alfalfa Hay, C. J. Schneider, Matt K. Luebbe, K. H. Jenkins, Stephanie A. Furman Furman, Galen E. Erickson, Terry J. Klopfenstein 2021 University of Nebraska-Lincoln

Using Beet Pulp To Adapt Cattle To Finishing Diets Compared To Traditional Grain Adaptation With Alfalfa Hay, C. J. Schneider, Matt K. Luebbe, K. H. Jenkins, Stephanie A. Furman Furman, Galen E. Erickson, Terry J. Klopfenstein

Faculty Papers and Publications in Animal Science

A study was conducted to compare grain adaptation programs using beet pulp (BP) to traditional grain adaptation with alfalfa hay (AH). Yearling crossbred steers (n = 232; BW = 326 ± 14.5 kg) were separated into 3 weight blocks, stratified by BW, and assigned randomly, within strata, to 18 feedlot pens, with 12 or 13 steers per pen. Treatments were imposed during grain adaptation (21 d) using 3 grain adaptation programs. Within each grain adaptation program, 4 step rations were fed for 3, 4, 7, and 7 d. Each program increased dry-rolled corn inclusion while roughage inclusion decreased. In the control treatment ...


Systematic Evaluation Of Chromosome Conformation Capture Assays, Betul Akgol-Oksuz, Liyan Yang, Sameer Abraham, Sergey V. Venev, Nils Krietenstein, Krishna M. Parsi, Hakan Ozadam, Marlies E. Oomen, Ankita Nand, Hui Mao, Ryan Genga, Rene Maehr, Oliver J. Rando, Leonid A. Mirny, Johan H. Gibcus, Job Dekker 2021 University of Massachusetts Medical School

Systematic Evaluation Of Chromosome Conformation Capture Assays, Betul Akgol-Oksuz, Liyan Yang, Sameer Abraham, Sergey V. Venev, Nils Krietenstein, Krishna M. Parsi, Hakan Ozadam, Marlies E. Oomen, Ankita Nand, Hui Mao, Ryan Genga, Rene Maehr, Oliver J. Rando, Leonid A. Mirny, Johan H. Gibcus, Job Dekker

Program in Molecular Medicine Publications

Chromosome conformation capture (3C) assays are used to map chromatin interactions genome-wide. Chromatin interaction maps provide insights into the spatial organization of chromosomes and the mechanisms by which they fold. Hi-C and Micro-C are widely used 3C protocols that differ in key experimental parameters including cross-linking chemistry and chromatin fragmentation strategy. To understand how the choice of experimental protocol determines the ability to detect and quantify aspects of chromosome folding we have performed a systematic evaluation of 3C experimental parameters. We identified optimal protocol variants for either loop or compartment detection, optimizing fragment size and cross-linking chemistry. We used this ...


Mutations In Several Auxin Biosynthesis Genes And Their Effects On Plant Phenotypes In Arabidopsis, Gabriela Hernandez, Lauren Huebner, Bethany Karlin Zolman 2021 University of Missouri-St. Louis

Mutations In Several Auxin Biosynthesis Genes And Their Effects On Plant Phenotypes In Arabidopsis, Gabriela Hernandez, Lauren Huebner, Bethany Karlin Zolman

Undergraduate Research Symposium

Auxins are important hormones in plants that regulate growth and development. Disruptions in the auxin biosynthesis pathway result in morphological changes in phenotypes in the model plant Arabidopsis thaliana, including differences in root and leaf formation. Mutations in the Tryptophan Aminotransferase of Arabidopsis (TAA1) and YUCCA (YUC4) genes interfere with the plant's ability to synthesize Indole-3-acetic acid (IAA), the primary auxin involved in plant development. IBR1 and IBR3 act in the multistep conversion of indole-3-butyric acid (IBA) to IAA. ILL2, IAR3, and ILR1 hydrolyze IAA-amino acid conjugates into free IAA. The goal of our study was to determine the ...


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