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Clinical Utility Of Exon Deletion/Duplication Microarray Testing - A Children’S Mercy Kansas City Two-Year Experience, Binu Porath 2019 Children's Mercy Kansas City

Clinical Utility Of Exon Deletion/Duplication Microarray Testing - A Children’S Mercy Kansas City Two-Year Experience, Binu Porath

Research Days

No abstract provided.


A Discrepancy Between The Human Reference Genome (Grch37) And Transcriptome (Refseq) Results In The Incorrect Annotation Of A Clinically-Relevant Sequence Variant In Recql4, Lisa A. Lansdon 2019 Children's Mercy Kansas City

A Discrepancy Between The Human Reference Genome (Grch37) And Transcriptome (Refseq) Results In The Incorrect Annotation Of A Clinically-Relevant Sequence Variant In Recql4, Lisa A. Lansdon

Research Days

No abstract provided.


Circadian Rhythmicity And Neurodevelopment Of Disco And Grim Mutations In Drosophila Melanogaster, John Patrick Story 2019 University of Tennessee, Knoxville

Circadian Rhythmicity And Neurodevelopment Of Disco And Grim Mutations In Drosophila Melanogaster, John Patrick Story

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

The death gene grim and its pathway for apoptosis has been studied extensively in Drosophila Melanogaster. The effects of grim mutations on circadian neurodevelopment and locomotor assays have yet to be investigated. Mutations in the gene disconnected (disco) has been shown to disrupt the normal development of the circadian circuitry, specifically the small ventro-lateral neurons (s-LNv’s). Which has shown to severely decrease rhythmicity during free-running periods. Alternatively, we have observed an increase in rhythmicity during free-running periods in grim mutations. Our goal is to investigate the neurodevelopment of the circadian circuitry and their associated locomotor activities in these Drosophila ...


A Polymorphism In The Fatty Acid Desaturase-2 Gene Is Associated With The Arachidonic Acid Metabolism In Pigs, Sofia Gol, Ramona N. Pena, Max F. Rothschild, Marc Tor, Joan Estany 2019 Universitat de Lleida

A Polymorphism In The Fatty Acid Desaturase-2 Gene Is Associated With The Arachidonic Acid Metabolism In Pigs, Sofia Gol, Ramona N. Pena, Max F. Rothschild, Marc Tor, Joan Estany

Max Rothschild

Arachidonic acid (C20:4) is related to a wide range of biological effects including lipid homeostasis. The fatty acid desaturase-2 (FADS2) gene encodes for the delta-6-desaturase, which is involved in the biosynthesis of C20:4 from linoleic acid (C18:2). The purpose of this study was to characterise mutations in the promoter of the porcine FADS2, evaluating in particular the effect of one haplotype tagging polymorphism (rs321384923A > G) on the biosynthesis pathway of C20:4. A total of 1,192 Duroc barrows with records on fatty acid composition in muscle and subcutaneous fat were genotyped. Pigs carrying the A allele ...


Genome-Wide Snp Profiling Of Worldwide Goat Populations Reveals Strong Partitioning Of Diversity And Highlights Post-Domestication Migration Routes, Licia Colli, Marco Milanesi, Andrea Talenti, Francesca Bertolini, Minhui Chen, Alessandra Crisà, Kevin Gerard Daly, Marcello Del Corvo, Bernt Guldbrandtsen, Johannes A. Lenstra, Benjamin D. Rosen, Elia Vajana, Gennaro Catillo, Stéphane Joost, Ezequiel Luis Nicolazzi, Estelle Rochat, Max F. Rothschild, Bertrand Servin, Tad S. Sonstegard, Roberto Steri, Curtis P. Van Tassell, Paolo Ajmone‑Marsan, Paola Crepaldi, Alessandra Stella 2019 Università Cattolica del S. Cuore

Genome-Wide Snp Profiling Of Worldwide Goat Populations Reveals Strong Partitioning Of Diversity And Highlights Post-Domestication Migration Routes, Licia Colli, Marco Milanesi, Andrea Talenti, Francesca Bertolini, Minhui Chen, Alessandra Crisà, Kevin Gerard Daly, Marcello Del Corvo, Bernt Guldbrandtsen, Johannes A. Lenstra, Benjamin D. Rosen, Elia Vajana, Gennaro Catillo, Stéphane Joost, Ezequiel Luis Nicolazzi, Estelle Rochat, Max F. Rothschild, Bertrand Servin, Tad S. Sonstegard, Roberto Steri, Curtis P. Van Tassell, Paolo Ajmone‑Marsan, Paola Crepaldi, Alessandra Stella

Max Rothschild

Background: Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats.

Results: A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within ...


Genome-Wide Association Studies Of Inflammatory Bowel Disease In German Shepherd Dogs, Atiyeh Peiravan, Francesca Bertolini, Max Rothschild, Kenneth W. Simpson, Albert E. Jergens, Karin Allenspach, Dirk Werling 2019 University of London, North Mymms

Genome-Wide Association Studies Of Inflammatory Bowel Disease In German Shepherd Dogs, Atiyeh Peiravan, Francesca Bertolini, Max Rothschild, Kenneth W. Simpson, Albert E. Jergens, Karin Allenspach, Dirk Werling

Max Rothschild

Canine Inflammatory Bowel Disease (IBD) is considered a multifactorial disease caused by complex interactions between the intestinal immune system, intestinal microbiota and environmental factors in genetically susceptible individuals. Although IBD can affect any breed, German shepherd dogs (GSD) in the UK are at increased risk of developing the disease. Based on previous evidence, the aim of the present study was to identify single nucleotide polymorphisms (SNPs), which may confer genetic susceptibility or resistance to IBD using a genome-wide association study (GWAS). Genomic DNA was extracted from EDTA blood or saliva samples of 96 cases and 98 controls. Genotyping of cases ...


A Screen For Genetic Modifiers Of Protein Phosphatase 1 Function In Drosophila Collective Cell Cohesion And Migration, Carmen F. Del Real, Yujun Chen, Marissa Komp, Jocelyn A. McDonald 2019 Kansas State University

A Screen For Genetic Modifiers Of Protein Phosphatase 1 Function In Drosophila Collective Cell Cohesion And Migration, Carmen F. Del Real, Yujun Chen, Marissa Komp, Jocelyn A. Mcdonald

Kansas State University Undergraduate Research Conference

Cells can migrate collectively in tightly or loosely-associated groups during tissue and organ formation, during embryonic development, in tumor metastases, and in wound healing. Drosophilaborder cellsserve as an excellent genetic model of collective cell migration inside a developing tissue. During ovarian development, 6-8 cells form the border cell cluster and migrate together as a cohesive group to reach the large oocyte. Previous experiments have shown that Nuclear inhibitor of Protein Serine Threonine Phosphatase 1 (NiPP1) causes border cells to separate into single cells, rather than stay in a group, and limits their ability to migrate. NiPP1 inhibits the ...


An Integrative Transcriptome Analysis Indicates Regulatory Mrna-Mirna Networks For Residual Feed Intake In Nelore Cattle, Priscila S.N. De Oliveira, Luiz L. Coutinho, Polyana C. Tizioto, Aline S. M. Cesar, Gabriella B. de Oliveira, Wellison J. da S. Diniz, Andressa O. De Lima, James M. Reecy, Gerson B. Mourão, Adhemar Zerlotini, Luciana C. A. Regitano 2019 Embrapa Pecuária Sudeste

An Integrative Transcriptome Analysis Indicates Regulatory Mrna-Mirna Networks For Residual Feed Intake In Nelore Cattle, Priscila S.N. De Oliveira, Luiz L. Coutinho, Polyana C. Tizioto, Aline S. M. Cesar, Gabriella B. De Oliveira, Wellison J. Da S. Diniz, Andressa O. De Lima, James M. Reecy, Gerson B. Mourão, Adhemar Zerlotini, Luciana C. A. Regitano

James M Reecy

Residual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such ...


Differences In The Skeletal Muscle Transcriptome Profile Associated With Extreme Values Of Fatty Acids Content, Aline S. M. Cesar, Luciana C. A. Regitano, Mirele D. Poleti, Sónia C. S. Andrade, Polyana C. Tizioto, Priscila S. N. Oliveira, Andrezza M. Felício, Michele L. do Nascimento, Amália S. Chaves, Dante P. D. Lanna, Rymer R. Tullio, Renata T. Nassu, James E. Koltes, Eric Frtiz-Waters, Gerson B. Mourão, Adhemar Zerlotini-Neto, James M. Reecy, Luiz L. Coutinho 2019 Iowa State University

Differences In The Skeletal Muscle Transcriptome Profile Associated With Extreme Values Of Fatty Acids Content, Aline S. M. Cesar, Luciana C. A. Regitano, Mirele D. Poleti, Sónia C. S. Andrade, Polyana C. Tizioto, Priscila S. N. Oliveira, Andrezza M. Felício, Michele L. Do Nascimento, Amália S. Chaves, Dante P. D. Lanna, Rymer R. Tullio, Renata T. Nassu, James E. Koltes, Eric Frtiz-Waters, Gerson B. Mourão, Adhemar Zerlotini-Neto, James M. Reecy, Luiz L. Coutinho

James M Reecy

Background: Lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. In the last few decades, it has been reported that long-chain fatty acids (FAs) are involved in several biological functions from transcriptional regulation to physiological processes. Several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. To gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes (DEGs) and functional pathways related to gene ...


Design And Validation Of A 90k Snp Genotyping Assay For The Water Buffalo (Bubalus Bubalis), Daniela Iamartino, Ezequiel L. Nicolazzi, Curtis P. Van Tassell, James M. Reecy, Eric R. Fritz-Waters, James E. Koltes, Stefano Biffani, Tad S. Sonstegard, Steven G. Schroeder, Paolo Ajmone-Marsan, Riccardo Negrini, Rolando Pasquariello, Paola Ramell, Angelo Coletta, Jose F. Garcia, Ahmad Ali, Luigi Ramunno, Gianfranco Cosenza, Denise A. A. de Oliveira, Marcela G. Drummond, Eduardo Bastianetto, Alessandro Davassi, Ali Pirani, Fiona Brew, John L. Williams 2019 AIA-LGS Associazione Italiana Allevatori±Laboratorio Genetica e Servizi

Design And Validation Of A 90k Snp Genotyping Assay For The Water Buffalo (Bubalus Bubalis), Daniela Iamartino, Ezequiel L. Nicolazzi, Curtis P. Van Tassell, James M. Reecy, Eric R. Fritz-Waters, James E. Koltes, Stefano Biffani, Tad S. Sonstegard, Steven G. Schroeder, Paolo Ajmone-Marsan, Riccardo Negrini, Rolando Pasquariello, Paola Ramell, Angelo Coletta, Jose F. Garcia, Ahmad Ali, Luigi Ramunno, Gianfranco Cosenza, Denise A. A. De Oliveira, Marcela G. Drummond, Eduardo Bastianetto, Alessandro Davassi, Ali Pirani, Fiona Brew, John L. Williams

James M Reecy

Background The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here.

Methods The genomes of 73 buffaloes of 4 different breeds were sequenced and ...


Investigating Comt Influence On The Proactive-Reactive Stress Coping Axis In Zebrafish, Sean T. Bresnahan, Ryan Y. Wong 2019 University of Nebraska at Omaha

Investigating Comt Influence On The Proactive-Reactive Stress Coping Axis In Zebrafish, Sean T. Bresnahan, Ryan Y. Wong

Student Research and Creative Activity Fair

Individuals of the same species often display differences in correlated suites of behaviors which are made conspicuous when challenges – stressful, fear-inducing, etc. – are presented. In many species, a specific suite of behaviors (risk-aversion, aggression, exploration, learning, and memory) characterize an alternative set of stress coping styles (proactive and reactive). Such behaviors are regulated in the brain by specific neurotransmitters along with proteins that regulate them. One neurotransmitter regulator protein, catechol-O-methyltransferase (COMT) shows higher baseline whole-brain expression in proactive relative to reactive animals. However, it is not known whether its expression is a cause or a consequence of the stress coping ...


Synder: Inferring Genomic Orthologs From Synteny Maps, Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, Eve Syrkin Wurtele 2019 Iowa State University

Synder: Inferring Genomic Orthologs From Synteny Maps, Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, Eve Syrkin Wurtele

Genetics, Development and Cell Biology Publications

Ortholog inference is a key step in understanding the evolution and function of a gene or other genomic feature. Yet often no similar sequence can be identified, or the true ortholog is hidden among false positives. A solution is to consider the sequence's genomic context. We present the generic program, synder, for tracing features of interest between genomes based on a synteny map. This approach narrows genomic search-space independently of the sequence of the feature of interest. We illustrate the utility of synder by finding orthologs for the Arabidopsis thaliana 13-member gene family of Nuclear Factor YC transcription factor ...


Mrub_3018 Is Orthologous To E. Coli B2759 (Casb), Kyle Parker, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

Mrub_3018 Is Orthologous To E. Coli B2759 (Casb), Kyle Parker, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We studied the biological activity of the Mrub_3018 gene, which we hypothesize is orthologous to E. coli gene B2759. We predicted that Mrub_3018(DNA coordinates 3057916… 3058524) encodes the protein CasB. CasB is a protein in the CRISPR CASCADE that will function as a structural protein. When the rest of the proteins form an “S” formation CasB will connect the front and back of the “S” creating a back bone for the structure. It will help bind ...


Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This research is part of the Meiothermus ruber genome annotation project which aims to predict gene function with various bioinformatics tools. We investigated the function of Mrub_3019, which encodes the CasA protein involved in the multi-subunit effector complex for the CRISPR-Cas immunity system and predicted it to be an ortholog of E. coli K12 MG1655 b2760 (casA). We predicted that Mrub_3019 encodes the protein CasA, which is involved in PAM recognition of CRISPR interference pathway. Foreign DNA will bind to CasA, which signals Cas3 for helicase-mediated DNA degradation. Our hypothesis is supported by low E-values for pairwise alignment in NCBI ...


Mrub_3015 Is Orthologous To The B2757 Gene Found In Escherichia Coli Coding For Casd, Ramona Collins, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

Mrub_3015 Is Orthologous To The B2757 Gene Found In Escherichia Coli Coding For Casd, Ramona Collins, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3015, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3015 (DNA coordinates 3055550...3056245) encodes the the CRISPR-associated protein cas5, which is integral in maintaining the crRNA-DNA structure, keeping the complex from base pairing with the target phage DNA. Our hypothesis is supported by identical hits for Mrub_3015 and b2527 to the KEGG, Pfam, TIGRfam, CDD and PDB databases as well as ...


Phylogenetic History Of The Amy Gene Cluster In Catarrhines, Christian M. Gagnon 2019 CUNY Hunter College

Phylogenetic History Of The Amy Gene Cluster In Catarrhines, Christian M. Gagnon

School of Arts & Sciences Theses

This study phylogenetically analyzed 30 AMY-related genes from 11 primates. The results show the gradual expansion of the AMY gene family which could have allowed primates to adapt to various ecological landscapes and maximize energy intake from starch-rich foods in periods of food scarcity.


Effects Of Temperature On Crispr/Cas System, Eddie Beckom, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

Effects Of Temperature On Crispr/Cas System, Eddie Beckom, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the effect of temperature on the complexity of CRISPR/Cas systems in bacterial organisms across temperature classifications. We predict that temperature extremes would result in CRISPR/Cas systems with multiple operons, repeating cas genes, and complex systems. CRISPR/Cas systems can be classified into three types with a number of subtypes based on the CRISPR-associated genes, cas genes, present in a given organism. Our hypothesis is supported by the presence of multiple operons in thermophilic ...


Mrub_3014 Is Orthologous To B2756, Samir Abdelkarim, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

Mrub_3014 Is Orthologous To B2756, Samir Abdelkarim, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3014, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3014 (DNA coordinates 3054943..3055575) encodes CRISPR-associated protein Cse3/case which function as an endonuclease. Our hypothesis is supported by identical hits for Mrub_3014 and b2756 to the KEGG, Pfam, TIGRfam, CDD and PDB databases, as well as a low E-value for a pairwise NCBI BLAST comparison. Both protein products are predicted to ...


M. Ruber Mrub_3013 Is Orthologous To E. Coli B2755, Laura Butcher, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

M. Ruber Mrub_3013 Is Orthologous To E. Coli B2755, Laura Butcher, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of gene Mrub_3013, which we hypothesize is orthologous to b2755 in E. coli K12 MG1655 (a.k.a. Cas1). We investigated the biological function of a gene with the M. ruber locus tag of Mrub_3013, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system in M. ruber. We predict that Mrub_3013 (DNA coordinates 3,053,978-3,054,940) encodes the protein Cas1 which as part of the CRISPR-Cas system ...


An Investigation Into The Relationship Between Mrub_3013, Mrub_1477, And Mrub_0224: Are They Paralogs?, Melette DeVore, Dr. Lori Scott 2019 Augustana College, Rock Island Illinois

An Investigation Into The Relationship Between Mrub_3013, Mrub_1477, And Mrub_0224: Are They Paralogs?, Melette Devore, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of mrub_3013 and the nature of its relationship with mrub_1477 and mrub_0224. We hypothesized that mrub_3013 is orthologous to b2755 in E. coli K12 MG1655 (a.k.a. cas1). We predict that mrub_3013 encodes the enzyme Cas1, which is involved in spacer acquisition in the CRISPR-Cas prokaryotic defense system. Our hypothesis is supported by identical hits for b2755, mrub_3013, mrub_1477, and mrub_0224 from the CDD and Pfam databases and highly similar hits ...


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