scholarly journals Ovine Toll-like Receptor 9 (TLR9) Gene Variation and Its Association with Flystrike Susceptibility

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3549
Author(s):  
Xiu Liu ◽  
Huitong Zhou ◽  
Hua Gong ◽  
Wenting Liu ◽  
Qian Fang ◽  
...  
Keyword(s):  
Single Strand Conformation Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Innate Immune Responses ◽  
Single Nucleotide ◽  
Gene Variation ◽  
Tlr9 Gene ◽  
Polymerase Chain ◽  
Molecular Patterns ◽  
Unmethylated Cytosine ◽  
Conformation Polymorphism

Toll-like receptors (TLRs) are a family of proteins that play a role in innate immune responses by recognising pathogen-associated molecular patterns derived from various microbes. Of these receptors, TLR9 recognises bacterial and viral DNA containing unmethylated cytosine-phosphate-guanine (CpG) motifs, and variation in TLR9 has been associated with resistance to various infectious diseases. Flystrike is a problem affecting the sheep industry globally and the immune response of the sheep has been suggested as one factor that influences the response to the disease. In this study, variation in ovine TLR9 from 178 sheep with flystrike and 134 sheep without flystrike was investigated using a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) approach. These sheep were collected from both commercial and stud farms throughout New Zealand and they were of 13 different breeds, cross-breds and composites. Four alleles of TLR9 were detected, including three previously identified alleles (*01, *02 and *03) and a new allele (*04). In total six single nucleotide polymorphisms (SNPs) were found. Of the three common alleles in the sheep studied, the presence of *03 was found to be associated with a reduced likelihood of flystrike being present (OR = 0.499, p = 0.024). This suggests that variation in ovine TLR9 may affect a sheep’s response to flystrike, and thus the gene may have value as a genetic marker for improving resistance to the disease.

scholarly journals DETECTION SINGLE NUCLEOTIDE POLYMORPHISMS IN UROMODULIN PROMOTER REGION ASSOCIATED WITH RENAL DISEASES USING SINGLE-STRAND CONFORMATION POLYMORPHISM-POLYMERASE CHAIN POLYMORPHISMS TECHNIQUE

2018 ◽  
Vol 11 (1) ◽  
pp. 205
Author(s):  
Zahraa Isam ◽  
Rabab Omran Al-jelawi- ◽  
Ammad Hassan Mahmood
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Promoter Region ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Thick Ascending Limb ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Blood Samples ◽  
Polymerase Chain ◽  
Conformation Polymorphism

  Objective: The uromodulin, a glycoprotein, expressed and secreted by epithelial kidney cells lining the thick ascending limb of the Henle’s loop. It is encoded by the UMOD gene in humans. Our objective was to analyze single nucleotide polymorphisms (SNPs) in the UMOD promoter region in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD).Methods: The blood samples were collected from 100 patients with CKD (50) and ESRD (50), who admitted at Merjan Teaching Hospital in Babylon Province, Iraq (February-July 2016). In addition, 50 blood samples of healthy control. The SNPs of UMOD promoter region was investigated using single-strand conformation polymorphism-polymerase chain polymorphisms (SSCP-PCR) and DNA sequencing techniques.Results: UOMD promoter region polymorphisms using PCR-SSCP and sequencing DNA appeared three different conformational haplotypes, including A\G 49 haplotype (5 bands), A\G 49 and C\A 247 haplotype (5 bands), and C\G 45 and A\G 49 haplotype (6 bands) distributed among CKD and ESRD cases, due to the presence of three SNPs. There was no association between band numbers of PCR-SSCP with ESRD and CKD compared with a control group.Conclusion: SSCP-PCR is a good screening method to detect genetic variations in an uromodulin promoter region.

scholarly journals DETECTION SINGLE NUCLEOTIDE POLYMORPHISMS IN UROMODULIN PROMOTER REGION ASSOCIATED WITH RENAL DISEASES USING SINGLE-STRAND CONFORMATION POLYMORPHISM-POLYMERASE CHAIN POLYMORPHISMS TECHNIQUE

2018 ◽  
Vol 11 (1) ◽  
pp. 205 ◽  
Author(s):  
Zahraa Isam ◽  
Rabab Omran Al-jelawi- ◽  
Ammad Hassan Mahmood
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Promoter Region ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Thick Ascending Limb ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Blood Samples ◽  
Polymerase Chain ◽  
Conformation Polymorphism

  Objective: The uromodulin, a glycoprotein, expressed and secreted by epithelial kidney cells lining the thick ascending limb of the Henle’s loop. It is encoded by the UMOD gene in humans. Our objective was to analyze single nucleotide polymorphisms (SNPs) in the UMOD promoter region in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD).Methods: The blood samples were collected from 100 patients with CKD (50) and ESRD (50), who admitted at Merjan Teaching Hospital in Babylon Province, Iraq (February-July 2016). In addition, 50 blood samples of healthy control. The SNPs of UMOD promoter region was investigated using single-strand conformation polymorphism-polymerase chain polymorphisms (SSCP-PCR) and DNA sequencing techniques.Results: UOMD promoter region polymorphisms using PCR-SSCP and sequencing DNA appeared three different conformational haplotypes, including A\G 49 haplotype (5 bands), A\G 49 and C\A 247 haplotype (5 bands), and C\G 45 and A\G 49 haplotype (6 bands) distributed among CKD and ESRD cases, due to the presence of three SNPs. There was no association between band numbers of PCR-SSCP with ESRD and CKD compared with a control group.Conclusion: SSCP-PCR is a good screening method to detect genetic variations in an uromodulin promoter region.

Promoter region single nucleotide polymorphism of siglec-8 gene associates with susceptibility to allergic asthma

2020 ◽  
Vol 17 (3) ◽  
pp. 195-201 ◽  
Author(s):  
Mohammad Sajay-asbaghi ◽  
Mahnaz Sadeghi-shabestrai ◽  
Amir Monfaredan ◽  
Narges Seyfizadeh ◽  
Alireza Razavi ◽  
...  
Keyword(s):  
Allergic Asthma ◽  
Normal Subjects ◽  
Single Strand Conformation Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Nucleotide Polymorphism ◽  
Potential Therapeutic Target ◽  
Single Nucleotide ◽  
Study Materials ◽  
Protective Allele ◽  
Conformation Polymorphism

Aim: Siglec-8 is exclusively expressed on mast cells, eosinophils and basophils. Possible association of six siglec-8 single nucleotide polymorphisms (SNPs) with susceptibility to allergic asthma in the Azeri population of Iran was investigated in this study. Materials & methods: A total of 194 patients and 190 normal subjects were enrolled. PCR single strand conformation polymorphism (PCR-SSCP) was used to determine the genotypes of the studied SNPs. Results: The rs36498 showed significant association with allergic asthma (odds ratio [OR]: 0.65; p = 0.022) and the T allele was found as a protective allele (OR: 0.61; p = 0.008). Also, eosinophil count in the CC genotype was significantly higher than that in the other genotypes (p = 0.026). Conclusion: The rs36498 is thought to influence the expression level of siglec-8. Siglec-8 could be a potential therapeutic target for allergic asthma.

A963G single nucleotide variant of BMP15 is not common bio-marker for fecundity in goat

2016 ◽  
Author(s):  
Guang-Xin E ◽  
Yong-Fu Huang ◽  
Jian-Ning He ◽  
Wei-Wei Ni ◽  
Yong-Ju Zhao
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Strand Conformation Polymorphism ◽  
Single Nucleotide Variant ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Morphogenetic Protein ◽  
Polymerase Chain ◽  
Bone Morphogenetic Protein 15 ◽  
Conformation Polymorphism

Bone morphogenetic protein 15 (BMP15) is crucial factor for ovulation as well as for increasing litter size. In the present investigation efforts had been carried out to assess the genetic variations in Exon 2 region of BMP15 in goat, using polymerase chain reaction single strand conformation polymorphism (PCR-SSCP) sequencing methods and cooperated frequency distribution to discuss its possibility of related fecundity. Across the 144samples from six breeds were identified in the A963G location of BMP15 using PCR-SSCP and sequences technology. A963A genotype was the most frequent (85.4%) and G963G was the least frequent with a frequency of 4.2% and A963G is 10.4%. It revealed non significant different between high and low fecundity breed. Therefore, this single nucleotide variant is not common Bio-Marker for fecundity in Goat.

New polymorphisms of PAPPA and PAPPA2 genes and their associations with egg production traits in Chinese Dagu chickens

2017 ◽  
Author(s):  
D. Liu ◽  
X. L. Niu ◽  
T. L. Tyasi ◽  
N. Qin ◽  
H. Zhu ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Egg Production ◽  
Protein A ◽  
Follicular Development ◽  
Single Strand Conformation Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Single Nucleotide ◽  
Egg Weight ◽  
Conformation Polymorphism

Pregnancy-associated plasma protein A, pappalysin1 (PAPPA) and pappalysin2 (PAPPA2) genes were implicated in regulation of hen ovarian follicular development and growth. Four novel single nucleotide polymorphisms (SNPs) were identified using PCR-single strand conformation polymorphism (PCR-SSCP) and DNA sequencing. Among them, A/G transition at position 172864 and T/C mutation at position 172952 in 3‘-untranslated region (UTR) of PAPPA named SNP A172864G and T172952C, respectively. A/G transition at position 77421 and T/C at position 77455 in 3‘-UTR of PAPPA2 gene named as SNP A77421G and T77455C, respectively. For SNP A172864G and T172952C (PAPPA), 360 Dagu hens were classified as AA, AB and BB genotypes based on PCR-SSCP patterns, and BB genotype correlated significantly (P less than 0.05) with higher hen-housed egg production (HHEP) at 30 and 57 weeks (wks) of age and higher egg weight (EW) at 43 wks of age. Consequently, these SNPs identified will be potential genetic markers to improve egg productivity in chicken breeding.

scholarly journals Haplotype Analysis of Norwegian and Swedish Patients with Acute Intermittent Porphyria (AIP): Extreme Haplotype Heterogeneity for the Mutation R116W

2003 ◽  
Vol 19 (1) ◽  
pp. 41-46 ◽  
Author(s):  
Kjersti Tjensvoll ◽  
Ove Bruland ◽  
Ylva Floderus ◽  
Øyvind Skadberg ◽  
Sverre Sandberg ◽  
...  
Keyword(s):  
Acute Intermittent Porphyria ◽  
Single Strand Conformation Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Gene Encoding ◽  
Single Nucleotide ◽  
Cpg Dinucleotides ◽  
High Prevalence ◽  
Different Populations ◽  
Acute Porphyrias ◽  
Conformation Polymorphism

Acute intermittent porphyria (AIP), the most common of the acute porphyrias, is caused by mutations in the gene encoding hydroxymethylbilane synthase (HMBS) also called porphobilinogen deaminase (PBGD). The mutation spectrum in the HMBS gene is characterized by a majority of family specific mutations. Among the exceptions are R116W and W198X, with high prevalence in both the Dutch and Swedish populations. These two mutations were also detected in unrelated Norwegian patients. Thus, Norwegian and Swedish patients were haplotyped using closely linked flanking microsatellites and intragenic single nucleotide polymorphisms (SNPs) to see if the high frequency of these two mutations is due to a founder effect. Twelve intragenic SNPs were determined by a method based on fluorescent restriction enzyme fingerprinting single-strand conformation polymorphism (F-REF-SSCP).W198X occurred exclusively on one haplotype in both Norwegian and Swedish patients, showing that it has originated from a common gene source. In contrast, R116W was found on three different haplotypes in three Norwegian families, and in five Swedish families on four or five haplotypes. This extreme haplotype heterogeneity indicates that R116W is a recurrent mutation, maybe explained by the high mutability of CpG dinucleotides. This can also explain why it is the only AIP mutation reported to occur in seven different populations (Norway, Sweden, Finland, Netherlands, France, Spain and South Africa).

SSCP Analysis of cDNA Markers Provides a Dense Linkage Map of theAedes aegyptiGenome

Genetics ◽  
2001 ◽  
Vol 158 (2) ◽  
pp. 715-726 ◽  
Author(s):  
Ruth E Fulton ◽  
Michael L Salasek ◽  
Nancy M DuTeau ◽  
William C Black
Keyword(s):  
Population Genetics ◽  
Drosophila Melanogaster ◽  
Linkage Map ◽  
Single Strand Conformation Polymorphism ◽  
Genome Project ◽  
Sscp Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
F2 Progeny ◽  
Conformation Polymorphism

AbstractAn intensive linkage map of the yellow fever mosquito, Aedes aegypti, was constructed using single-strand conformation polymorphism (SSCP) analysis of cDNA markers to identify single nucleotide polymorphisms (SNPs). A total of 94 A. aegypti cDNAs were downloaded from GenBank and primers were designed to amplify fragments <500 bp in size. These primer pairs amplified 94 loci, 57 (61%) of which segregated in a single F1 intercross family among 83 F2 progeny. This allowed us to produce a dense linkage map of one marker every 2 cM distributed over a total length of 134 cM. Many A. aegypti cDNAs were highly similar to genes in the Drosophila melanogaster genome project. Comparative linkage analysis revealed areas of synteny between the two species. SNP polymorphisms are abundant in A. aegypti genes and should prove useful in both population genetics and mapping studies.

Intra-species variability in ITS-1 sequences of Haemonchus contortus isolated from goats in West Bengal, India

2010 ◽  
Vol 85 (2) ◽  
pp. 204-209
Author(s):  
S. Bandyopadhyay ◽  
A.K. Bera ◽  
S. Sikdar ◽  
S. De ◽  
S. Das ◽  
...  
Keyword(s):  
Haemonchus Contortus ◽  
West Bengal ◽  
Single Strand Conformation Polymorphism ◽  
Nucleotide Position ◽  
Loop Structure ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Evolutionary Changes ◽  
Interior Loop ◽  
Conformation Polymorphism

AbstractThis study evaluated the existence of different genotypes of Haemonchus contortus prevailing among goats in West Bengal, India. These parasites were isolated from the abomasum of goat intestine and the molecular characterization was performed by comparing variation of nucleotide sequences of the internal transcribed spacer 1 (ITS-1) gene region. Single-strand conformation polymorphism (SSCP) analysis of ITS-1 amplified product showed the presence of three distinct conformations both in male and female parasites. The sequence analysis of conformations showed two single nucleotide polymorphisms (SNP) in male parasites at nucleotide positions 106 and 107 and one SNP was detected in female parasites at nucleotide position 157. These nucleotide variations in different isolates did not alter the interior loop structure of the predicted secondary RNA, therefore we believe these variations may not be responsible for any evolutionary changes among conformations.

scholarly journals Variation in the Caprine Keratin-Associated Protein 27-1 Gene is Associated with Cashmere Fiber Diameter

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 934
Author(s):  
Mengli Zhao ◽  
Huitong Zhou ◽  
Yuzhu Luo ◽  
Jiqing Wang ◽  
Jiang Hu ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Fiber Diameter ◽  
Single Strand Conformation Polymorphism ◽  
Chromosome 1 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Longissimus Dorsi Muscle ◽  
Cashmere Goats ◽  
Kidney Liver ◽  
Conformation Polymorphism

Variation in some caprine keratin-associated protein (KAP) genes has been associated with cashmere fiber traits, but many KAP genes remain unidentified in goats. In this study, we confirm the identification of a KAP27-1 gene (KRTAP27-1) and describe its effect on cashmere traits in 248 Longdong cashmere goats. A polymerase chain reaction–single strand conformation polymorphism (PCR-SSCP) analysis was used to screen for sequence variation in this gene, and three sequence variants (named A to C) were found. These sequences have the highest similarity (77% identity) to a human KRTAP27-1 sequence, while sharing some homology with a predicted caprine KRTAP27-1 sequence ENSCHIG00000023347 in the goat genome construct (ARS1:CM004562.1) at chromosome 1 position 3,966,193–3,973,677 in the forward strand. There were two single nucleotide polymorphisms (SNPs) detected in the coding sequence, including one nonsynonymous SNP (c.413C/T; p.Ala138Val) and one synonymous SNP (c.495C/T). The C variant differed from A and B at c.413C/T, having cytosine in its nucleotide sequence, while the B variant differed from A and C at c.495C/T, having thymine in its nucleotide sequence. Goats of the genotypes AB and BB produced cashmere fibers of higher mean fiber diameter (MFD) than goats of genotype AA, but no difference in MFD was detected between the AB and BB goats. These results suggest that B is associated with increased MFD. Expression of the caprine KRTAP27-1 sequence was predominantly detected in the skin tissue of goats but not or only weakly detected in other tissues, including longissimus dorsi muscle, heart, kidney, liver, lung and spleen.

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