scholarly journals Gonadotropine Releasing Hormone (GnRH) Receptor Profile from Cow’s Hypothalamus

2020 ◽  
Vol 38 (2) ◽  
pp. 188
Author(s):  
Irma Dian Nurani
Keyword(s):  
Bos Taurus ◽  
Gnrh Receptor ◽  
Genomic Variation ◽  
Coding Region ◽  
Government Programs ◽  
Single Nucleotide ◽  
Releasing Hormone ◽  
Pcr Product ◽  
Receptor Profile ◽  
Exon 1

Gonadotropine Releasing Hormone (GnRH) is one of the recommended hormones to overcome ovulation problems and it can increase pregnancy rate so that it is used in government programs to increase cattle population in Indonesia, although the results are not yet optimal. The purpose of this study is to compare the composition of bovine GnRH receptor nucleotides with the GenBank reference so that the level of genetic diversity of bovine receptors in Indonesia is known. PCR product sequencing using Promoter F and Exon 1 R primers were further aligned with the reference sequences of Bos Taurus GnRHR mRNA GenBank using the MEGA X program. The results of the analysis found the presence of Single Nucleotide Polymorphism (SNP) in the coding region  of 1st cow  position 38(A> T), 261(C > T), 342(C >T), 411(C >T) and 495(C > T) and 2nd cow positions 261(C >T). Changes in amino acids were also detected in 1st cow position 13 (H> L). The presence of SNP was found to indicate genomic variation between individuals at cattle receptors in Indonesia.

Classification of wheat PPO genes and effect of non-synonymous cSNP on kernel PPO activity

2008 ◽  
Vol 5 (1) ◽  
pp. 81-86 ◽  
Author(s):  
Wang Xiao-Bo ◽  
Ma Chuan-Xi ◽  
Si Hong-Qi ◽  
He Xian-Fang
Keyword(s):  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Chain Reaction ◽  
Wheat Varieties ◽  
Single Nucleotide ◽  
Pcr Product ◽  
Dnaman Software ◽  
Dna Fragment ◽  
Polymerase Chain

AbstractPolyphenol oxidase (PPO) activity is highly related to the undesirable browning of wheat-based end products. In this study, wheat PPO sequences (mRNA) were searched/BLASTed in the NCBI database and aligned using DNAMAN software. The results showed that wheat PPO genes could be divided into two clusters (I and II) and that three genes (‘i’) of cluster II seemed not to be located on chromosomes 2A and 2D. Ninety-four single nucleotide polymorphisms (SNPs) were detected between two haplotypes of the PPO gene on chromosome 2D. Eighty of these were found in the coding region (coding (c) SNPs) and 36 were non-synonymous cSNPs, which could affect the PPO amino acid sequence. Primers (STS-H) were designed at some non-synonymous cSNPs sites and were used to investigate the correlations between allelic variants and PPO activity of seeds – a total of 130 common wheat varieties were evaluated in 2 years. The results showed that STS-H could amplify a 460 bp DNA fragment in most cultivars with high PPO activity, while no PCR product was detected in most cultivars with low PPO activity. To improve the selection efficiency of a single dominance molecular marker, the multiplex polymerase chain reaction (PCR) system of STS-H and STS01 markers was also studied, based on the complementary between them.

Molecular characterization and SNP identification in HSPB1 gene in Murrah buffalo

2015 ◽  
Author(s):  
Ashwani Arya ◽  
Archana Verma ◽  
I. D. Gupta ◽  
Shahid A. Shergojry ◽  
Ankit Magotra ◽  
...  
Keyword(s):  
Heat Shock ◽  
Marker Assisted Selection ◽  
Bos Taurus ◽  
Nucleotide Position ◽  
Coding Region ◽  
Murrah Buffalo ◽  
Future Improvement ◽  
Pcr Products ◽  
Exon 1 ◽  
Heat Shock Protein Genes

Present study was conducted on 100 lactating Murrah buffaloes maintained at LRC, NDRI Karnal (Haryana) to characterize and to identify genetic polymorphisms in HSPB1 gene. Two sets of primers specific to coding sequence of HSPB1 gene were designed using Primer3 software and PCR products of 631 bp and 670 bp were obtained. Amplicons were custom sequenced and subjected to ClustalW analysis which revealed 8 nucleotide changes, 7 in non coding region and one in coding region in Murrah buffalo sequence as compared to Bos taurus. Only one SNP at nucleotide position G225A in exon 1 of HSPB1 gene was observed in Murrah buffalo, which resulted in two genotypes GG and AG with respective frequency of 0.84 and 0.16 indicating the existence of variability in the sampled population. The study has opened the possibility of identifying and using genetic variations in major heat shock protein genes, for the future improvement of livestock through marker assisted selection.

Identification of Single Nucleotide Polymorphism in GnRHR gene in Murrah bulls

2018 ◽  
Author(s):  
J. K. Reen ◽  
K. P. Ramesha ◽  
Preeti . ◽  
D. Revanasiddu ◽  
M. Ahirwar
Keyword(s):  
Bos Taurus ◽  
Reference Sequence ◽  
Coding Region ◽  
Single Nucleotide ◽  
Training Centre ◽  
Blood Samples ◽  
Livestock Breeding ◽  
Single Stranded Conformational Polymorphism ◽  
Similar Band ◽  
And Training

The present study was undertaken with the objectives of molecular characterization and detection of genetic polymorphism in the GnRHR gene in Murrah bulls. Blood samples were collected from 109 Murrah bulls maintained at three different organized semen stations viz., Centralized Semen Collection Centre of Livestock Breeding and Training Centre, Dharwad; Nandini Sperm Station and State Livestock Breeding and Training Centre, Hessarghatta, Bengaluru, Karnataka, India. Genomic DNA was isolated from the blood samples within 24 hours of collection . Mutations were screened using Polymerase Chain Reaction – Single Stranded Conformational Polymorphism (PCR-SSCP) technique followed by Sanger Sequencing. PCR-SSCP method revealed similar band pattern within Murrah bulls. To confirm monomorphism in the studied population with respect to GnRHR gene, duplicate samples from each primer fragment were custom sequenced. PCR-SSCP and sequence analysis revealed monomorphism within the studied population that is coding region as well as exon-intron boundaries of GnRHR gene is highly conserved among Murrah bulls. However, a total of 28 Single Nucleotide variations (SNV’s) have been found when compared with Bos Taurus reference sequence for GnRHR gene.

EVALUATION OF PTYCHOBOTHRIDEAN CESTODES USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS FROM FRESH WATER FISHES IN GODAVARI BASIN (M.S.) INDIA

2017 ◽  
Vol 23 (2) ◽  
Author(s):  
SUNITA BORDE ◽  
ASAWARI FARTADE ◽  
AMOL THOSAR ◽  
RAHUL KHAWAL
Keyword(s):  
Fresh Water ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Band Pattern ◽  
Genomic Variation ◽  
Polymorphic Band ◽  
Rapd Profile ◽  
Band Size ◽  
Pcr Product ◽  
The Common

Ptychobothridean genera like Senga and Circumoncobothrium are the common parasites of fresh water fishes. The genotypic study of these parasites was taken by RAPD. The RAPD profile of these two parasites were not similar to each other as depicted by the band pattern in picture. These results suggest the presence of inter-specific polymorphism among cestode parasites of two different genera for RAPD analysis. The present study demonstrated that genetic differentiation of cestode parasites could be accomplished on the basis of genomic variation with polymorphic band pattern using RAPD. All the detected bands (PCR product) were polymorphic and band size ranged from 500-5000 bp in length. The RAPD of profiles using GBO-31, GBO-32, GBO-33, GBO-34, GBO-35 and GBO-36. Primers were able to characterize inter-specific polymorphism among the two genus ( Senga and Circumoncobothrium ). Genetic analysis suggests that Senga and Circumoncobothrium show genetic diversity with respect to RAPD patterns using all the six primers used for the present study. The genetic distance between the analyzed genuses ranged from 0.14 to 0.80. The differentiation of the two parasites on the basis of genetic markers could greatly facilitate study on the biology of these parasites.

scholarly journals Identification of a novel homozygous loss-of-function mutation in FUCA1 gene causing severe fucosidosis: A case report

2021 ◽  
Vol 49 (4) ◽  
pp. 030006052110059
Author(s):  
Xinwen Zhang ◽  
Shaozhi Zhao ◽  
Hongwei Liu ◽  
Xiaoyan Wang ◽  
Xiaolei Wang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Lysosomal Storage Disorder ◽  
Autosomal Recessive ◽  
Signs And Symptoms ◽  
Lysosomal Storage ◽  
Loss Of Function ◽  
Wild Type ◽  
Single Nucleotide ◽  
Whole Exome ◽  
Exon 1

Fucosidosis is a rare lysosomal storage disorder characterized by deficiency of α-L-fucosidase with an autosomal recessive mode of inheritance. Here, we describe a 4-year-old Chinese boy with signs and symptoms of fucosidosis but his parents were phenotypically normal. Whole exome sequencing (WES) identified a novel homozygous single nucleotide deletion (c.82delG) in the exon 1 of the FUCA1 gene. This mutation will lead to a frameshift which will result in the formation of a truncated FUCA1 protein (p.Val28Cysfs*105) of 132 amino acids approximately one-third the size of the wild type FUCA1 protein (466 amino acids). Both parents were carrying the mutation in a heterozygous state. This study expands the mutational spectrum of the FUCA1 gene associated with fucosidosis and emphasises the benefits of WES for accurate and timely clinical diagnosis of this rare disease.

scholarly journals The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Rajiv Sharma ◽  
Daniel P. Dever ◽  
Ciaran M. Lee ◽  
Armon Azizi ◽  
Yidan Pan ◽  
...  
Keyword(s):  
Genetic Diseases ◽  
Basic Research ◽  
Gene Correction ◽  
Coding Region ◽  
Hematopoietic Stem ◽  
Hematopoietic Reconstitution ◽  
Exon 1 ◽  
Template Library ◽  
Donor Template

AbstractTargeted DNA correction of disease-causing mutations in hematopoietic stem and progenitor cells (HSPCs) may enable the treatment of genetic diseases of the blood and immune system. It is now possible to correct mutations at high frequencies in HSPCs by combining CRISPR/Cas9 with homologous DNA donors. Because of the precision of gene correction, these approaches preclude clonal tracking of gene-targeted HSPCs. Here, we describe Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a methodology that utilizes barcoded AAV6 donor template libraries, carrying in-frame silent mutations or semi-randomized nucleotides outside the coding region, to track the in vivo lineage contribution of gene-targeted HSPC clones. By targeting the HBB gene with an AAV6 donor template library consisting of ~20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-skewed, lymphoid-skewed, and balanced multi-lineage repopulating human HSPC clones in mice. We anticipate this methodology could potentially be used for HSPC clonal tracking of Cas9 RNP and AAV6-mediated gene targeting outcomes in translational and basic research settings.

scholarly journals Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections

2021 ◽  
Vol 9 (7) ◽  
pp. 1416
Author(s):  
Karen Leth Nielsen ◽  
Marc Stegger ◽  
Kristoffer Kiil ◽  
Berit Lilje ◽  
Karen Ejrnæs ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Genomic Variation ◽  
Whole Genome Sequencing Data ◽  
Phenotypic Traits ◽  
Recurrent Infections ◽  
Single Nucleotide ◽  
Recurrent Urinary Tract Infections ◽  
Tract Infections

Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0–13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny.

scholarly journals A single nucleotide substitution in the coding region of Ogura male sterile gene, orf138, determines effectiveness of a fertility restorer gene, Rfo, in radish

2021 ◽  
Author(s):  
Hiroshi Yamagishi ◽  
Megumi Jikuya ◽  
Kanako Okushiro ◽  
Ayako Hashimoto ◽  
Asumi Fukunaga ◽  
...  
Keyword(s):  
Male Sterility ◽  
Nucleotide Substitution ◽  
Fertility Restoration ◽  
Type A ◽  
Restorer Gene ◽  
Single Nucleotide Substitution ◽  
Coding Region ◽  
Fertility Restorer ◽  
Single Nucleotide ◽  
Fertility Restorer Gene

AbstractCytoplasmic male sterility (CMS) observed in many plants leads defect in the production of functional pollen, while the expression of CMS is suppressed by a fertility restorer gene in the nuclear genome. Ogura CMS of radish is induced by a mitochondrial orf138, and a fertility restorer gene, Rfo, encodes a P-type PPR protein, ORF687, acting at the translational level. But, the exact function of ORF687 is still unclear. We found a Japanese variety showing male sterility even in the presence of Rfo. We examined the pollen fertility, Rfo expression, and orf138 mRNA in progenies of this variety. The progeny with Type H orf138 and Rfo showed male sterility when their orf138 mRNA was unprocessed within the coding region. By contrast, all progeny with Type A orf138 were fertile though orf138 mRNA remained unprocessed in the coding region, demonstrating that ORF687 functions on Type A but not on Type H. In silico analysis suggested a specific binding site of ORF687 in the coding region, not the 5′ untranslated region estimated previously, of Type A. A single nucleotide substitution in the putative binding site diminishes affinity of ORF687 in Type H and is most likely the cause of the ineffectiveness of ORF687. Furthermore, fertility restoration by RNA processing at a novel site in some progeny plants indicated a new and the third fertility restorer gene, Rfs, for orf138. This study clarified that direct ORF687 binding to the coding region of orf138 is essential for fertility restoration by Rfo.

scholarly journals Temporal fluctuations of Y-chromosomal variation in Bos taurus

2008 ◽  
Vol 4 (6) ◽  
pp. 752-754 ◽  
Author(s):  
Emma Svensson ◽  
Anders Götherström
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bos Taurus ◽  
Demographic History ◽  
Northern Europe ◽  
Chromosomal Gene ◽  
Chromosomal Variation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Domestic Species ◽  
History Of

Phylogeography has recently become more abundant in studies of demographic history of both wild and domestic species. A single nucleotide polymorphism (SNP) in the intron of the Y-chromosomal gene UTY19 displays a north–south gradient in modern cattle. Support for this geographical distribution of haplogroups has previously also been seen in ancient cattle from Germany. However, when analysing 38 historic remains of domestic bulls and three aurochs from northern Europe for this SNP we found no such association. Instead, we noted extensive amounts of temporal variation that can be attributed to transportation of cattle and late breed formation.

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