scholarly journals Novel Single Nucleotide Polymorphisms of Lysozyme (C-Type) Gene in Donkey (Equus Asinus) Populations in Marmara Province of Turkey

2020 ◽  
Vol 8 (2) ◽  
pp. 495
Author(s):  
Raziye Işık
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Pathogenic Bacteria ◽  
Nucleotide Polymorphisms ◽  
Milk Traits ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Equus Asinus ◽  
Pcr Products ◽  
Exon 1 ◽  
Type Gene

The major antimicrobial proteins in donkey milk are lysozyme, lactoferrin, lactoperoxidase and immunoglobulins. Lysozyme has an important role in the host defense by way it inhibits the pathogenic bacteria. The aim of this study is to investigate the Lysozyme (LYZ) gene polymorphism in 82 donkeys reared in Thrace region of Turkey. 716 bp long partial 5’ UTR, exon 1, intron 1, exon 2 regions of LYZ gene were amplified and PCR products were analyzed via DNA sequencing. Three novel single nucleotide polymorphisms (SNPs) were identified as g.1782775A>G, g.1782924A>G and g.1782960T>C in the first intron of LYZ gene. The partial DNA sequence of LYZ gene in donkeys was reported in the present study and sequences of LYZ were entered to NCBI Genbank database with the accession number: MK984689-MK984692. This SNP may have an effect on immune system and milk traits in donkeys and additional studies are needed to confirm this assumption for donkey breeding.

scholarly journals Association of single nucleotide polymorphisms in the fatty acid synthase, LOC514211, and fat mass and obesity-associated genes with milk traits in Indonesian-Holstein dairy cattle

2019 ◽  
Vol 12 (7) ◽  
pp. 1160-1166
Author(s):  
Amalia Puji Rahayu ◽  
Tety Hartatik ◽  
Agung Purnomoadi ◽  
Edy Kurnianto
Keyword(s):  
Fatty Acid ◽  
Single Nucleotide Polymorphisms ◽  
Fat Mass ◽  
Milk Protein ◽  
Fatty Acid Synthase ◽  
Nucleotide Polymorphisms ◽  
Fat Percentage ◽  
Fto Gene ◽  
Milk Traits ◽  
Single Nucleotide

Aim: The study aimed to identify fatty acid synthase (FASN), LOC514211, and fat mass and obesity-associated (FTO) gene polymorphisms and to investigate their associations with milk traits in an Indonesian-Holstein dairy cow population. Materials and Methods: A total of 100 Indonesian-Holstein cows consisting of 50 heads (0th generation; G0) and 50 heads of their daughters (1st generation; G1) were used. Polymerase chain reaction-restriction fragment length polymorphism was performed to genotype three single nucleotide polymorphisms: rs41919985 in the FASN gene, rs42688595 in the LOC514211 gene, and g.1371T>A in the FTO gene. Results: FASN rs41919985 was associated with milk protein percentage (p<0.05), FTO g.1371T>A was associated with milk fat percentage (p<0.05), and LOC514211 rs42688595 was not associated with any trait (p>0.05). Heterozygote variants showed a higher protein percentage for FASN and the highest fat percentage for FTO. These associations were consistent in the G0 and G1 populations. Conclusion: Our results indicate that the milk protein and fat percentages can be improved by increasing the frequency of the AG genotype of FASN and the AT genotype of FTO, respectively.

Novel combined insulin-like 3 variations of a single nucleotide in cryptorchidism

2019 ◽  
Vol 32 (9) ◽  
pp. 987-994 ◽  
Author(s):  
Xenophon Sinopidis ◽  
Roza Mourelatou ◽  
Eirini Kostopoulou ◽  
Alexia Karvela ◽  
Andrea-Paola Rojas-Gil ◽  
...  
Keyword(s):  
Phenotypic Variability ◽  
Testicular Descent ◽  
Sequencing Analysis ◽  
Single Nucleotide ◽  
Allelic Variants ◽  
Exon 2 ◽  
Pcr Products ◽  
Exon 1 ◽  
Male Patients ◽  
Allelic Variations

Abstract Background Insulin-like 3 hormone (INSL3) is involved in the process of testicular descent, and has been thoroughly studied in cryptorchidism. However, INSL3 allelic variations found in the human genome were heterozygous and only a few of them were found exclusively in patients with cryptorchidism. Under this perspective, we aimed to study the presence of INSL3 allelic variations in a cohort of patients with cryptorchidism and to estimate their potential consequences. Methods Blood samples were collected from 46 male patients with non-syndromic cryptorchidism and from 43 age-matched controls. DNA extraction and polymerase chain reaction (PCR) were performed for exons 1 and 2 of the INSL3 gene in all subjects. Sequencing analysis was carried out on the PCR products. All data were grouped according to testicular location. Results Seven variations of a single nucleotide (SNVs) were identified both in patients with cryptorchidism and in controls: rs2286663 (c.27G > A), rs1047233 (c.126A > G) and rs6523 (c.178A > G) at exon 1, rs74531687 (c.191-30C > T) at the intron, rs121912556 (c.305G > A) at exon 2 and rs17750642 (c.*101C > A) and rs1003887 (c.*263G > A) at the untranslated region (UTR). The allelic variants rs74531687 and rs121912556 were found for the first time in the Greek population. The novel homozygotic combination of the three allelic variants rs1047233-rs6523-rs1003887 seemed to present a stronger correlation with more severe forms of cryptorchidism. Conclusions The combination of specific INSL3 SNVs rather than the existence of each one of them alone may offer a new insight into the involvement of allelic variants in phenotypic variability and severity.

Polymorphisms of LHβ and GnRHR genes and their association with the number of embryos recovered in goats

2014 ◽  
Vol 54 (8) ◽  
pp. 987 ◽  
Author(s):  
M. Z. Fu ◽  
G. Li ◽  
Z. Q. Zhou
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Nucleotide Polymorphisms ◽  
Gene Polymorphism ◽  
Corpus Luteum ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Single Strand Conformational Polymorphism ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Polymerase Chain

The objective of the present study was to explore a predictor of superovulation response on the basis of associations between the number of embryos recovered and gene polymorphism. Variation in the goat LHβ and GnRHR genes was investigated using polymerase chain reaction–single-strand conformational polymorphism and DNA sequencing. Two single nucleotide polymorphisms (SNPs) were identified in the 5′-UTR of LHβ gene (A59C, P1 locus) and in the Exon 2 of GnRHR gene (T177A, P6 locus). At the P1 locus in both breeds, the frequencies of one allele were 0.46 and 0.51, respectively. At the P6 locus, the minor allele frequency was 0.23. Associations of both SNPs with the number of embryos recovered and the corpus luteum number were evaluated in Boer and Shaanbei goat breeds. Association analysis showed that both SNPs had significant (P < 0.05) effects on the number of embryos recovered and corpus luteum number. These results indicate that LHβ and GnRHR genes are potential markers for the number of embryos recovered.

scholarly journals Implications of single nucleotide polymorphisms in CD44 exon 2 for risk of breast cancer

2011 ◽  
Vol 20 (5) ◽  
pp. 396-402 ◽  
Author(s):  
Juhua Zhou ◽  
Prakash S. Nagarkatti ◽  
Yin Zhong ◽  
Jiajia Zhang ◽  
Mitzi Nagarkatti
Keyword(s):  
Breast Cancer ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Exon 2

MS for Identification of Single Nucleotide Polymorphisms and MS/MS for Discrimination of Isomeric PCR Products

2000 ◽  
Vol 72 (17) ◽  
pp. 4033-4040 ◽  
Author(s):  
Mark T. Krahmer ◽  
James J. Walters ◽  
Karen F. Fox ◽  
Alvin Fox ◽  
Kim E. Creek ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Pcr Products

scholarly journals Analysis of Clinically Relevant Single-Nucleotide Polymorphisms by Use of Microelectronic Array Technology

2002 ◽  
Vol 48 (12) ◽  
pp. 2124-2130 ◽  
Author(s):  
Rosa Santacroce ◽  
Antonia Ratti ◽  
Francesco Caroli ◽  
Barbara Foglieni ◽  
Alessandro Ferraris ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Factor Vii ◽  
Restriction Enzyme Digestion ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Ret Protooncogene ◽  
Mismatched Dna ◽  
Specific Pcr ◽  
Pcr Products ◽  
Allele Specific

Abstract Background: Microelectronic DNA chip devices represent an emerging technology for genotyping. We developed methods for detection of single-nucleotide polymorphisms (SNPs) in clinically relevant genes. Methods: Primer pairs, with one containing a 5′-biotin group, were used to PCR-amplify the region encompassing the SNP to be interrogated. After denaturation, the biotinylated strand was electronically targeted to discrete sites on streptavidin-coated gel pads surfaces by use of a Nanogen Molecular Workstation. Allele-specific dye-labeled oligonucleotide reporters were used for detection of wild-type and variant sequences. Methods were developed for SNPs in genes, including factor VII, β-globin, and the RET protooncogene. We genotyped 331 samples for five DNA variations in the factor VII gene, &gt;600 samples from patients with β-thalassemia, and 15 samples for mutations within the RET protooncogene. All samples were previously typed by various methods, including DNA sequence analysis, allele-specific PCR, and/or restriction enzyme digestion of PCR products. Results: Analysis of amplified DNA required 4–6 h. After mismatched DNA was removed, signal-to-noise ratios were &gt;5. More than 940 samples were typed with the microelectronic array platform, and results were totally concordant with results obtained previously by other genotyping methods. Conclusions: The described protocols detect SNPs of clinical interest with results comparable to those of other genotyping methods.

scholarly journals A Locked Nucleic Acid Probe Based on Selective Salt-Induced Effect Detects Single Nucleotide Polymorphisms

2015 ◽  
Vol 2015 ◽  
pp. 1-6
Author(s):  
Jing Zhang ◽  
Huizhe Wu ◽  
Qiuchen Chen ◽  
Pengfei Zhao ◽  
Haishan Zhao ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Single Nucleotide Polymorphisms ◽  
Room Temperature ◽  
Genetic Mutation ◽  
Locked Nucleic Acid ◽  
Nucleotide Polymorphisms ◽  
Buffer Solution ◽  
Single Nucleotide ◽  
Real Time Quantitative Pcr ◽  
Pcr Products

Detection of single based genetic mutation by using oligonucleotide probes is one of the common methods of detecting single nucleotide polymorphisms at known loci. In this paper, we demonstrated a hybridization system which included a buffer solution that produced selective salt-induced effect and a locked nucleic acid modified 12 nt oligonucleotide probe. The hybridization system is suitable for hybridization under room temperature. By using magnetic nanoparticles as carriers for PCR products, the SNPs (MDR1C3435T/A) from 45 volunteers were analyzed, and the results were consistent with the results from pyrophosphoric acid sequencing. The method presented in this paper differs from the traditional method of using molecular beacons to detect SNPs in that it is suitable for research institutions lacking real-time quantitative PCR detecting systems, to detect PCR products at room temperature.

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