scholarly journals PHYLOGENETIC ANALYSIS OF COTTON SPECIES (DIPLOID GENOMES) USING SINGLE NUCLEOTIDE POLYMORPHISMS (SNPs) MARKERS

2016 ◽  
Vol 53 (02) ◽  
pp. 283-290 ◽  
Author(s):  
Tayyaba Shaheen ◽  
Yusuf Zafar ◽  
Mehboob-ur- Rehman
Keyword(s):  
Phylogenetic Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cotton Species

scholarly journals Single Nucleotide Polymorphisms in the Promoter of CYP19 Gene in Cattle Bred in Iraq

2020 ◽  
Vol 33 (1) ◽  
pp. 89-97
Author(s):  
Salah H. Faraj ◽  
Asaad Y. Ayied ◽  
Khalaf A. H. Al-Rishdy
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Diversity ◽  
Animal Species ◽  
Haplotype Diversity ◽  
Evolutionary Relationship ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cyp19 Gene

The present study was undertaken to characterize the genetic diversity of the aromatase cytochrome P450 (CYP19) gene in 34 cows (15 local, 14 Holstein, and 5 Crosses) in Iraq. The objectives of the present study are to detect SNPs (mutations) in promoter p1.1 of the CYP19 gene in cattle bred in Iraq using sequencing techniques. We identified five single-nucleotide polymorphisms (SNP) loci of the CYP19 gene that were detected, namely G933T, G994C, A1044G, A1062T, and C1468A. The results showed the presence of 3, 4, and 2 polymorphic sites leading to the construction of 4, 5, and 3 different haplotypes for Holstein, local, and crosses respectively. Haplotype diversity were 0.791, 0.752, and 0.700 respectively. While nucleotide diversity was 0.0017, 0.0022, and 0.0013 respectively. Besides, we carried out a phylogenetic analysis of these sequences to address the evolutionary relationship between the animal species. These fragments were assigned in the GenBank database under the accession numbers: LC490756, LC490757, LC491437, LC491438, LC491439, LC491588, and LC491589.

scholarly journals 189. Potential Tiger-to-Human Transmission of SARS-CoV-2 at a Tennessee Zoo: A One Health Approach to Outbreak Investigation

2021 ◽  
Vol 8 (Supplement_1) ◽  
pp. S114-S115
Author(s):  
Heather N Grome ◽  
Becky Meyer ◽  
Erin Read ◽  
Martha Buchanan ◽  
Andrew C Cushing ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Environmental Assessment ◽  
One Health ◽  
Observation Point ◽  
Outbreak Investigation ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Rt Pcr ◽  
Single Nucleotide

Abstract Background Human-to-feline and airborne transmission among cats of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been described, though documented feline-to-human transmission has not been reported. In October 2020, all 3 Malayan tigers at a Tennessee AZA accredited zoo were diagnosed with symptomatic SARS-CoV-2 infection. We investigated to determine source and prevent further transmission. Methods Tiger nasal swab specimens were tested at the National Veterinary Services Laboratories (NVSL). An environmental assessment at the zoo was completed. We interviewed 18 staff who interacted with the tigers during the 2 weeks before animal symptom onset. Confirmed human cases were defined as persons testing positive for SARS-CoV-2 by RT-PCR during September 28–October 29, with tiger interaction during their 14-day incubation period. Interviewed staff had repeat SARS-CoV-2 RT-PCR and serum IgG testing on October 29. Tigers and staff testing positive had specimens sent to CDC for genomic sequencing. Tiger sequences were compared phylogenetically with 30 geographically associated human cases collected within 2 weeks of the outbreak and > 200 background sequences from TN. Results NVSL confirmed SARS-CoV-2 infection in all 3 tigers. Environmental assessment identified fencing between humans and animals allowing airflow and an open outdoor exhibit observation point above the habitat. Confirmed cases were identified in a tiger keeper and veterinary assistant; both developed symptoms after exposure to symptomatic tigers and one sample was genotyped. Staff did not report known contact with ill visitors. All staff were negative for SARS-CoV-2 IgG. The tigers and most temporally and geographically associated cases had genetic sequences in clade 20G and B.1.2. Tiger sequences were 3-6 single nucleotide polymorphisms different from the positive tiger keeper (Figure). Figure. Whole-genome phylogenetic analysis. Whole-genome phylogenetic analysis from a portion of clade 20G showing divergence estimates from SARS-CoV-2 Wuhan-Hu-1 reference genome with sequences from humans living in Tennessee and Malayan tigers sampled during the outbreak investigation in October 2020. Sequence analysis showed 3-6 single nucleotide polymorphisms (SNPs) differences between one human tiger keeper and all three tiger sequences. Differences are indicated by one-step edges (lines) between colored dots (individual SARS-CoV-2 sequenced infections). Numbers indicate unique sequences. Note not all analyzed sequences are shown in this figure. Conclusion Using a One Health approach, we concluded the index tiger was likely infected via transmission from an ill visitor at an exhibit observation point or unidentified asymptomatic staff. Infection spread to the other 2 tigers and tiger-to-human transmission to 2 staff is possible thereafter. The zoo was advised on infection control practices for humans and animals, and no additional cases were identified. Disclosures William Schaffner, MD, VBI Vaccines (Consultant)

scholarly journals Polymorphic status and phylogenetic analysis of myostatin gene in pak-thoroughbred

Genetika ◽  
2020 ◽  
Vol 52 (3) ◽  
pp. 1281-1290
Author(s):  
Zeshan Raza ◽  
Asif Nadeem ◽  
Maryam Javed ◽  
Faiz-Ul Hassan ◽  
Wasim Shehzad ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Myostatin Gene ◽  
Thoroughbred Horse ◽  
Mstn Gene ◽  
Thoroughbred Horses

Myostatin is a protein translated by the the MSTN gene (also known as GDF8), is responsible for limiting muscle growth and strength. In thoroughbred horse (Equus Caballus), limited studies have been designed to examine the variants in the coding region of MSTN gene. However, no data is available regarding the single nucleotide polymorphisms (SNPs) of the MSTN about racing performance in thoroughbred horses of Pakistan. In this study blood samples of fifteen Pakistani thoroughbred horses were collected from Race Club Lahore and immediately transferred into the ice box. The DNA was extracted by using phenol-chloroform method. Primers were designed for the amplification of all exons of the MSTN gene. The amplified PCR products were precipitated and sequenced for the identification of SNPs. SNPs were identified by visualizing the peaks of sequenced data by using Chromas Software. Phylogenetic analysis of MSTN gene in Pak-thoroughbred with racing species and some breeds of horses like Marwari Indian breed, Sindhi breed, Kathlawari breed, Italian breed and Chines breed was done separately by using MEGA 6 software. The analysis of identified SNPs were carried out by software SNPator. The sequenced data with altered protein was published in GenBank with accession number MN604194. Results have shown a total of 3 single nucleotide polymorphisms through Blast with reference sequences. Two SNPs were found in exon 2 at position of 2406 (C/T) and 2408 (C/T) respectively. One SNP (T/C) was detected in exon 3 at the position of 4661. In conclusion, Pak-thoroughbred horse population has 3 polymorphisms in their coding region which can be used as a biological marker for athletic abilities in Pak- thoroughbred.

Development of a simple method for the determination of single nucleotide polymorphisms

2010 ◽  
Vol 34 (8) ◽  
pp. S75-S75
Author(s):  
Weifeng Zhu ◽  
Zhuoqi Liu ◽  
Daya Luo ◽  
Xinyao Wu ◽  
Fusheng Wan
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Simple Method ◽  
Single Nucleotide

Sex Differences in Childhood Associations between DNA Markers and General Cognitive Ability

2007 ◽  
Vol 28 (3) ◽  
pp. 161-164 ◽  
Author(s):  
Rosalind Arden ◽  
Nicole Harlaar ◽  
Robert Plomin
Keyword(s):  
Sex Differences ◽  
Single Nucleotide Polymorphisms ◽  
Cognitive Ability ◽  
Dna Markers ◽  
Community Sample ◽  
Nucleotide Polymorphisms ◽  
General Cognitive Ability ◽  
Single Nucleotide ◽  
The Difference

Abstract. An association between intelligence at age 7 and a set of five single-nucleotide polymorphisms (SNPs) has been identified and replicated. We used this composite SNP set to investigate whether the associations differ between boys and girls for general cognitive ability at ages 2, 3, 4, 7, 9, and 10 years. In a longitudinal community sample of British twins aged 2-10 (n > 4,000 individuals), we found that the SNP set is more strongly associated with intelligence in males than in females at ages 7, 9, and 10 and the difference is significant at 10. If this finding replicates in other studies, these results will constitute the first evidence of the same autosomal genes acting differently on intelligence in the two sexes.

Sign in / Sign up

Export Citation Format

Share Document