1,720,982 research outputs found
A Nonsense Variant in Hephaestin Like 1 (HEPHL1) Is Responsible for Congenital Hypotrichosis in Belted Galloway Cattle
Get PDFGenodermatosis such as hair disorders mostly follow a monogenic mode of inheritance. Congenital hypotrichosis (HY) belong to this group of disorders and is characterized by abnormally reduced hair since birth. The purpose of this study was to characterize the clinical phenotype of a breed-specific non-syndromic form of HY in Belted Galloway cattle and to identify the causative genetic variant for this recessive disorder. An affected calf born in Switzerland presented with multiple small to large areas of alopecia on the limbs and on the dorsal part of the head, neck, and back. A genome-wide association study using Swiss and US Belted Galloway cattle encompassing 12 cases and 61 controls revealed an association signal on chromosome 29. Homozygosity mapping in a subset of cases refined the HY locus to a 1.5 Mb critical interval and subsequent Sanger sequencing of protein-coding exons of positional candidate genes revealed a stop gain variant in the HEPHL1 gene that encodes a multi-copper ferroxidase protein so-called hephaestin like 1 (c.1684A>T; p.Lys562*). A perfect concordance between the homozygous presence of this most likely pathogenic loss-of-function variant and the HY phenotype was found. Genotyping of more than 700 purebred Swiss and US Belted Galloway cattle showed the global spread of the mutation. This study provides a molecular test that will permit the avoidance of risk matings by systematic genotyping of relevant breeding animals. This rare recessive HEPHL1-related form of hypotrichosis provides a novel large animal model for similar human conditions. The results have been incorporated in the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 002230-9913)
Sequence characterization of the HSA12/22/12 evolutionary breakpoint region on SSC5q21
Get PDFThe HSA12/22/12 evolutionary breakpoint region on SSC5q21 has been sequenced, further localized, and preliminarily characterized. The existence and location of the breakpoint regions were originally determined in the human-porcine comparative map constructed by Meyers and colleagues. Bacterial artificial chromosome (BAC) fingerprint analysis and radiation hybrid mapping of BAC-end sequences was used to construct a minimum tiling path (MTP) encompassing each breakpoint region. The MTP clones were sequenced. The MTP sequences were then evaluated for similarity to human sequences using the NCBI cross-species megaBLAST program on Build 37.3 of the human genome. The more centromeric HSA12/22 breakpoint region displays sequence similarity to megabase (Mb) positions 2.593-2.807 on HSA12 and 17.583-17.672 on HSA22, and the more telomeric HSA22/12 breakpoint region displays sequence similarity to Mb positions 18.566-18.660 on HSA22 and 34.252-49.523 on HSA12. The human genome coordinates corresponding to the HSA12/22 breakpoint region also suggest an alternative marker order to the marker order proposed by Meyers and colleagues, although additional research is necessary to finalize the true marker order. The sequence evidence indicates the presence of transposable elements and AT-rich sequence composition in the areas surrounding each of the breakpoint regions. The sequence characterization results are in agreement with several previous studies of evolutionary breakpoint regions and therefore suggest potential involvement of such factors in evolutionary breakpoint generation, although underlying molecular mechanisms remain poorly understood at this point in time.Item withdrawn by Mark Zulauf ([email protected]) on 2012-04-27T12:44:41Z
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University of Illinois Theses & Dissertations (ID: 1)
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Molecular characterization of ovine GM1 gangliosidosis
Get PDFOvine GM1-gangliosidosis is an autosomal recessive lysosomal storage disorder. Affected lambs are born relatively normal, however at approximately four months of age they begin exhibiting severe neurological symptoms. Pathology progresses rapidly in affected lambs ultimately resulting in death by five to six months of age. In humans and other species, mutations in the β-galactosidase (GLB1) gene are responsible for similar disease phenotypes. The production of non-functional β-galactosidase results in a buildup of GM1 gangliosides and other terminally linked galactose-containing molecules in the brain and visceral tissues. Using the Illumina® OvineSNP50 BeadChip platform, seven affected and ten unaffected animals were genotyped and a genome wide association analysis was performed using PLINK. A significant association was detected for multiple SNPs on OAR19; further investigation showed this area was orthologous to HSA3 containing GLB1. Sequence analysis revealed a G to T nucleotide transversion in exon six of ovine GLB1 resulting in a nonsynonymous cysteine to phenylalanine (Cys229Phe) amino acid substitution. A PCR-RFLP assay using AciI restriction enzyme was designed for genotyping lambs. To date, 1664 animals have been genotyped using the DNA-based diagnostic and all affected lambs were homozygous for this mutation. Conversely, individuals with normal phenotypes were either heterozygous or homozygous for the alternative allele. Affected lambs will be used as an animal model to further explore the disease and potentially identify therapies for humans.Item withdrawn by Mark Zulauf ([email protected]) on 2012-12-07T21:18:40Z
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QTL Mapping and Molecular Dissection of Meat Quality Traits in Swine
No full text134 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2007.Improvement of meat quality is important for consumer satisfaction. As many pork quality traits cannot be assessed in the live animal, selection for these traits must rely upon genetic determinants known as quantitative trait loci (QTL). To facilitate fine-mapping of swine QTL, a ∼1 Mb-resolution human-pig comparative map, composed of 2,274 markers in 34 linkage groups, was constructed using the radiation hybrid method. Comparative analyses revealed 51 conserved synteny groups, including 173 conserved segments, and overall comparative coverage greater than 90%. This map was used, together with porcine linkage and bacterial artificial chromosome (BAC) physical maps, to fine-map a QTL affecting pork tenderness that was detected, on the q arm of porcine chromosome 2 (SSC2q), within the Illinois Meat Quality Pedigree (IMQP). Nine novel microsatellite markers within the ∼30-Mb region surrounding the most likely QTL position, including one within the candidate gene calpastatin (CAST), were developed. These markers, along with nine publicly-available markers, were used to perform linkage and haplotype analyses within the IMQP. Within-family linkage analyses revealed at least two families segregating for a highly-significant QTL in strong positional agreement with CAST. A combined analysis of these two families yielded QTL intervals of 36 cM and 7 cM for Instron shear force and taste panel tenderness, respectively, while haplotype analyses suggested further refinement to a 1.8 cM interval containing CAST. To identify allelic variation that may influence pork tenderness, the complete genomic sequence of porcine CAST was determined. Nearly 77.6% of this gene was then re-sequenced from each of six IMQP F1 boars. Based on heterozygosity, 393 of 896 discovered polymorphisms appeared concordant with previous QTL data. The location of this variation within the CAST gene suggests that a causative mutation is likely to be regulatory. Functional characterization of CAST variation should enhance understanding of the molecular basis of pork tenderness, and thus allow for genetic improvement of pork products. The effectiveness of CAST polymorphisms for marker-assisted selection (MAS) of pork tenderness can now be assessed. Furthermore, genomic resources developed in this study may be used to investigate many other porcine QTL, including additional tenderness QTL suggested on SSC2q.U of I OnlyRestricted to the U of I community idenfinitely during batch ingest of legacy ETD
QTL Mapping and Molecular Dissection of Meat Quality Traits in Swine
No full textImprovement of meat quality is important for consumer satisfaction. As many pork quality traits cannot be assessed in the live animal, selection for these traits must rely upon genetic determinants known as quantitative trait loci (QTL). To facilitate fine-mapping of swine QTL, a ∼1 Mb-resolution human-pig comparative map, composed of 2,274 markers in 34 linkage groups, was constructed using the radiation hybrid method. Comparative analyses revealed 51 conserved synteny groups, including 173 conserved segments, and overall comparative coverage greater than 90%. This map was used, together with porcine linkage and bacterial artificial chromosome (BAC) physical maps, to fine-map a QTL affecting pork tenderness that was detected, on the q arm of porcine chromosome 2 (SSC2q), within the Illinois Meat Quality Pedigree (IMQP). Nine novel microsatellite markers within the ∼30-Mb region surrounding the most likely QTL position, including one within the candidate gene calpastatin (CAST), were developed. These markers, along with nine publicly-available markers, were used to perform linkage and haplotype analyses within the IMQP. Within-family linkage analyses revealed at least two families segregating for a highly-significant QTL in strong positional agreement with CAST. A combined analysis of these two families yielded QTL intervals of 36 cM and 7 cM for Instron shear force and taste panel tenderness, respectively, while haplotype analyses suggested further refinement to a 1.8 cM interval containing CAST. To identify allelic variation that may influence pork tenderness, the complete genomic sequence of porcine CAST was determined. Nearly 77.6% of this gene was then re-sequenced from each of six IMQP F1 boars. Based on heterozygosity, 393 of 896 discovered polymorphisms appeared concordant with previous QTL data. The location of this variation within the CAST gene suggests that a causative mutation is likely to be regulatory. Functional characterization of CAST variation should enhance understanding of the molecular basis of pork tenderness, and thus allow for genetic improvement of pork products. The effectiveness of CAST polymorphisms for marker-assisted selection (MAS) of pork tenderness can now be assessed. Furthermore, genomic resources developed in this study may be used to investigate many other porcine QTL, including additional tenderness QTL suggested on SSC2q.Made available in DSpace on 2015-09-25T21:08:26Z (GMT). No. of bitstreams: 3
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Reason: Restricted to the U of I community idenfinitely during batch ingest of legacy ETDsRestricted to the U of I community idenfinitely during batch ingest of legacy ETDsU of I Only134 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2007
Characterization of NHLRC2 gene-edited mice: a model for bovine developmental duplications
Get PDFDevelopmental duplications (DD) is a genetic condition recently characterized in Angus cattle. It is a congenital abnormality where duplication of neural crest derived tissues occurs during embryonic development. A common phenotypic presentation of the condition includes calves born with polymelia most frequently involving duplication of the front limbs that protrude from the neck or shoulder region. Aside from polymelia, DD affected individuals present malformations associated with neural tube defects (NTDs). Genome-wide association studies have identified a single locus associated with this disease phenotype. Further investigation has identified the putative mutation as a nonsynonymous substitution (p.Val311Ala) in the NHL repeat-containing 2 (NHLRC2) gene. Transcription activator-like effector nucleases (TALENs) targeting exon 5 of NHLRC2 were used for gene-editing of the orthologous locus in mice to further investigate the role of NHLRC2 in development. Three mouse lines were generated with mutations having varying impacts on the NHLRC2 protein. Two mutations, -2 bp and -19 bp, are predicted to cause a prematurely truncated protein and one mutation, -12 bp, the deletion of four amino acids, residues 307 through 310, adjacent to the corresponding bovine substitution. Heterozygous mice of each line were intermated to phenotypically characterize homozygous progeny. Genotyping of the offspring revealed absence of homozygous individuals suggesting embryonic lethality. Because initiation of neural tube closure in mice occurs at day E8.5, embryonic death was assessed at this developmental day by harvesting embryos from heterozygous matings at day E8.5 with subsequent genotyping. Again, no homozygous embryos could be detected, however yolk sacs containing no embryos were observed. Furthermore, the number of yolk sacs exceeded the average number of live births by 68% (11.3 vs. 6.7), indicating embryonic lethality of homozygous individuals most likely occurs between fertilization and E8.5. Thus, we suggest that NHLRC2 is essential during mammalian development and hypothesize NHLRC2 plays a significant role in neurulation.Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2016-11-09 without embargo termsThe student, Jocelyn Delhotal, accepted the attached license on 2016-07-12 at 18:01.The student, Jocelyn Delhotal, submitted this Thesis for approval on 2016-07-12 at 18:07.This Thesis was approved for publication on 2016-07-14 at 10:34.DSpace SAF Submission Ingestion Package generated from Vireo submission #9908 on 2016-11-09 at 10:24:31Made available in DSpace on 2016-11-10T17:55:02Z (GMT). No. of bitstreams: 2
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Previous issue date: 2016-07-1
Comparison of the molecular phenotypes of pigs carrying different IGF2 alleles at four developmental time points
Get PDFA single nucleotide polymorphism in insulin-like growth factor 2 (IGF2 intron3-G3072A) is associated with greater muscle mass and decreased subcutaneous fat deposition in pigs carrying a paternal copy of the A allele (Apat). While many studies have focused on the differences in between the gross phenotypes of these animals, relatively little has been done to understand how these animals differ at the molecular level. It was the objective of this study to compare the molecular phenotypes of animals carrying the Apat allele and those carrying the Gpat allele in order to gain insight into how those differences may result in the differences seen at the whole-animal level. RNA was extracted from longissimus (LM) samples taken from six animals of each genotype (Apat and Gpat) at four different time points, fetal day 90 (d90), birth (0d), weaning (21d), and market weight (176d). In total 46 samples were sequenced on the Illumina HiSeq 2000 with a target depth of 20 million reads per sample. Analysis of the RNA-seq data using tweeDEseq determined differentially expressed genes between Apat and Gpat pigs at each time point. Additionally, IPA analysis was used to determine if there were any differentially activated pathways between the two phenotypes. IGF2 was not found to be upregulated in Apat pigs compared to Gpat at d90 or 0d; however, IGF2 expression was found to be increased in Apat pigs compared to Gpat pigs at 21d and 176d. Though there was not differential expression of IGF2 at d90 and 0d, there was still differential expression of several other genes at these time points. At d90, Apat pigs tended to have an increase in the expression anti-apoptotic genes and a decrease in pro-apoptotic genes, possibly indicating enhanced myoblast survival, while Gpat pigs had greater expression of genes associated with protein synthesis. At 0d, there was an increased expression of genes associated with proliferation and protein synthesis in Apat pigs, and Gpat pigs appeared to have upregulation of genes involved in inflammation. At both 0d and 21d Apat and Gpat pigs had displayed upregulation of markers of myogenesis, suggesting different stages of muscle development. At 176d, Apat animals had decreased expression of genes involved in adipose signaling, including inflammation, stress, and autophagy and greater expression of genes associated with tissue development and the cell cycle. Thus, throughout the developmental timepoints, there appear to be markedly different processes taking place in the muscle tissue of Apat pigs and Gpat pigs.Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2017-08-10 without embargo termsThe student, Marissa Keever, accepted the attached license on 2017-04-04 at 20:48.The student, Marissa Keever, submitted this Thesis for approval on 2017-04-04 at 20:55.This Thesis was approved for publication on 2017-04-05 at 16:32.DSpace SAF Submission Ingestion Package generated from Vireo submission #10647 on 2017-08-10 at 13:38:45Made available in DSpace on 2017-08-10T19:14:43Z (GMT). No. of bitstreams: 2
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Previous issue date: 2017-04-0
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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