scholarly journals Detection of DNA mutations by PCR-TTGE method

2014 ◽  
pp. 21-25
Author(s):  
Ádám Csikós ◽  
Ádám Simon ◽  
Ákos Tisza ◽  
Gabriella Gulyás ◽  
András Jávor ◽  
...  
Keyword(s):  
High Temperature ◽  
Gene Polymorphism ◽  
Detection System ◽  
Target Sequence ◽  
Melting Profile ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Dna Mutations ◽  
Target Dna ◽  
Pituitary Adenylate Cyclase

In our study PCR-temporal temperature gelelectrophoresis (TTGE) and MeltINGENY bioinformatic program were used to analyse the mutations in the genes of melanocortin-1 receptor (MC1R) and pituitary adenylate-cyclase activating polypeptide (PACAP) in cattle. Amplification of target DNA by PCR was performed with GC-clamp primers and non-GC-clamp primers in simplex PCR reactions. The fragments were separated by denaturing polyacrylamide gelelectrophoresis (denaturing agents: high temperature, urea) after PCR reactions.MC1R homozygous individuals were used for the reaction. We concluded that MeltINGENY program makes the decision and detection system easier, and more simple as the melting profile of target sequence is determined by the software. In case of MC1R gene, PCR-TTGE method is appropriate for SNP detection, however PACAP gene polymorphism can not be identified by the method, because PACAP mutations are not included in melting domains, therefore PCR-TTGE cannot detect them.

Single-nucleotide polymorphism of MC1R, ASIP, and TYRP2 genes in wild and farmed foxes (Vulpes vulpes)

2016 ◽  
Vol 96 (2) ◽  
pp. 172-179 ◽  
Author(s):  
Andrzej Jakubczak ◽  
Magdalena Gryzinska ◽  
Beata Horecka ◽  
Marek Kowalczyk ◽  
Kornel Kasperek ◽  
...  
Keyword(s):  
Vulpes Vulpes ◽  
Related Protein ◽  
Nucleotide Polymorphism ◽  
Melanin Production ◽  
Single Nucleotide ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Dna Mutations ◽  
In The Wild ◽  
Tyrosinase Related Protein

DNA mutations within genes associated with melanogenesis can affect melanin production, leading to dyschromias. Genes that are involved in synthesis of melatonin and may affect the color of skin are melanocortin 1 receptor (MC1R), agouti locus (ASIP), and tyrosinase-related protein-2 (TYRP2). In this study, SNP identification within ASIP, MC1R, and TYRP2 gene fragments in wild and farmed foxes (Vulpes vulpes) was performed. Nine mutations in the ASIP gene which allowed us to distinguish seven SNP profiles, fourteen mutations and five SNP profiles in the MC1R gene, and seven SNP profiles based on four polymorphic nucleotides in the TYRP2 gene were detected. Analyses of obtained profiles indicate that ASIP did not undergo mutations in the wild, and significant variability of SNP profiles was found for TYRP2, with specific haplotypes noted for farm foxes and American and European wild foxes.

scholarly journals High Polymorphism at the Human Melanocortin 1 Receptor Locus

Genetics ◽  
1999 ◽  
Vol 151 (4) ◽  
pp. 1547-1557 ◽  
Author(s):  
Brinda K Rana ◽  
David Hewett-Emmett ◽  
Li Jin ◽  
Benny H-J Chang ◽  
Naymkhishing Sambuughin ◽  
...  
Keyword(s):  
Protein Sequence ◽  
Nucleotide Diversity ◽  
Coat Color ◽  
Low Frequency ◽  
Melanocortin Receptor ◽  
Human Populations ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Southeast Asians ◽  
Color Changes

Abstract Variation in human skin/hair pigmentation is due to varied amounts of eumelanin (brown/black melanins) and phaeomelanin (red/yellow melanins) produced by the melanocytes. The melanocortin 1 receptor (MC1R) is a regulator of eu- and phaeomelanin production in the melanocytes, and MC1R mutations causing coat color changes are known in many mammals. We have sequenced the MC1R gene in 121 individuals sampled from world populations with an emphasis on Asian populations. We found variation at five nonsynonymous sites (resulting in the variants Arg67Gln, Asp84Glu, Val92Met, Arg151Cys, and Arg163Gln), but at only one synonymous site (A942G). Interestingly, the human consensus protein sequence is observed in all 25 African individuals studied, but at lower frequencies in the other populations examined, especially in East and Southeast Asians. The Arg163Gln variant is absent in the Africans studied, almost absent in Europeans, and at a low frequency (7%) in Indians, but is at an exceptionally high frequency (70%) in East and Southeast Asians. The MC1R gene in common and pygmy chimpanzees, gorilla, orangutan, and baboon was sequenced to study the evolution of MC1R. The ancestral human MC1R sequence is identical to the human consensus protein sequence, while MC1R varies considerably among higher primates. A comparison of the rates of substitution in genes in the melanocortin receptor family indicates that MC1R has evolved the fastest. In addition, the nucleotide diversity at the MC1R locus is shown to be several times higher than the average nucleotide diversity in human populations, possibly due to diversifying selection.

A bioluminescent assay for detecting melanocortin-1 receptor (MC1R) gene polymorphisms R160W, R151C, and D294H

2015 ◽  
Vol 49 (6) ◽  
pp. 852-857 ◽  
Author(s):  
E. E. Bashmakova ◽  
V. V. Krasitskaya ◽  
A. A. Bondar ◽  
A. V. Kozlova ◽  
T. G. Ruksha ◽  
...  
Keyword(s):  
Gene Polymorphisms ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Bioluminescent Assay

scholarly journals Effects of melanocortin 1 receptor (MC1R) gene polymorphisms on plumage color in mule ducks

2019 ◽  
Vol 48 ◽  
Author(s):  
Yi-Chen Tu ◽  
Liang-Yuan Wei ◽  
Yi-Ying Chang ◽  
Hsiu-Chou Liu ◽  
Hsien-Hsiung Lee ◽  
...  
Keyword(s):  
Gene Polymorphisms ◽  
Plumage Color ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene

Characterisation of the melanocortin-1 receptor gene in alpaca and identification of possible markers associated with phenotypic variations in colour

2009 ◽  
Vol 49 (8) ◽  
pp. 675 ◽  
Author(s):  
N. L. Feeley ◽  
K. A. Munyard
Keyword(s):  
Mus Musculus ◽  
Bos Taurus ◽  
Receptor Gene ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene ◽  
Pcr Products ◽  
Phenotypic Variations

The aim of this study was to determine if any correlation exists between melanocortin-1 receptor (MC1R) polymorphisms and skin and fibre colour in alpacas. Primers capable of amplifying the entire alpaca MC1R gene were designed from a comparative alignment of Bos taurus and Mus musculus MC1R gene sequences. The complete MC1R gene of 41 alpacas exhibiting a range of fibre colours, and which were sourced from farms across Australia, was sequenced from PCR products. Twenty-one single nucleotide polymorphisms were identified within MC1R. Two of these polymorphisms (A82G and C901T) have the potential to reduce eumelanin production by disrupting the activity of MC1R. No agreement was observed between fibre colour alone and MC1R genotype in the 41 animals in this study. However, when the animals were assigned to groups based on the presence or absence of eumelanin in their fibre and skin, only animals that had at least one allele with the A82/C901 combination expressed eumelanin. We propose that A82/C901 is the wild-type dominant ‘E’ MC1R allele, while alpacas with either G82/T901 or G82/Y901 are homozygous for the recessive ‘e’ MC1R allele and are therefore unable to produce eumelanin.

scholarly journals Computational design of probes to detect bacterial genomes by multivalent binding

2020 ◽  
Vol 117 (16) ◽  
pp. 8719-8726 ◽  
Author(s):  
Tine Curk ◽  
Chris A. Brackley ◽  
James D. Farrell ◽  
Zhongyang Xing ◽  
Darshana Joshi ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Bacterial Infections ◽  
Bacterial Genome ◽  
Computational Design ◽  
Diagnostic Methods ◽  
Detection Sensitivity ◽  
Target Sequence ◽  
Inappropriate Use ◽  
Single Target ◽  
Target Dna

Rapid methods for diagnosis of bacterial infections are urgently needed to reduce inappropriate use of antibiotics, which contributes to antimicrobial resistance. In many rapid diagnostic methods, DNA oligonucleotide probes, attached to a surface, bind to specific nucleotide sequences in the DNA of a target pathogen. Typically, each probe binds to a single target sequence; i.e., target–probe binding is monovalent. Here we show using computer simulations that the detection sensitivity and specificity can be improved by designing probes that bind multivalently to the entire length of the pathogen genomic DNA, such that a given probe binds to multiple sites along the target DNA. Our results suggest that multivalent targeting of long pieces of genomic DNA can allow highly sensitive and selective binding of the target DNA, even if competing DNA in the sample also contains binding sites for the same probe sequences. Our results are robust to mild fragmentation of the bacterial genome. Our conclusions may also be relevant for DNA detection in other fields, such as disease diagnostics more broadly, environmental management, and food safety.

scholarly journals Enhancement of target specificity of CRISPR–Cas12a by using a chimeric DNA–RNA guide

2020 ◽  
Vol 48 (15) ◽  
pp. 8601-8616 ◽  
Author(s):  
Hanseop Kim ◽  
Wi-jae Lee ◽  
Yeounsun Oh ◽  
Seung-Hun Kang ◽  
Junho K Hur ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genome Engineering ◽  
Target Genes ◽  
Target Sequence ◽  
Energy Potential ◽  
Guide Rna ◽  
Sequence Recognition ◽  
Protospacer Adjacent Motif ◽  
Effective Manner ◽  
Target Dna

Abstract The CRISPR–Cas9 system is widely used for target-specific genome engineering. CRISPR–Cas12a (Cpf1) is one of the CRISPR effectors that controls target genes by recognizing thymine-rich protospacer adjacent motif (PAM) sequences. Cas12a has a higher sensitivity to mismatches in the guide RNA than does Cas9; therefore, off-target sequence recognition and cleavage are lower. However, it tolerates mismatches in regions distant from the PAM sequence (TTTN or TTN) in the protospacer, and off-target cleavage issues may become more problematic when Cas12a activity is improved for therapeutic purposes. Therefore, we investigated off-target cleavage by Cas12a and modified the Cas12a (cr)RNA to address the off-target cleavage issue. We developed a CRISPR–Cas12a that can induce mutations in target DNA sequences in a highly specific and effective manner by partially substituting the (cr)RNA with DNA to change the energy potential of base pairing to the target DNA. A model to explain how chimeric (cr)RNA guided CRISPR–Cas12a and SpCas9 nickase effectively work in the intracellular genome is suggested. Chimeric guide-based CRISPR- Cas12a genome editing with reduced off-target cleavage, and the resultant, increased safety has potential for therapeutic applications in incurable diseases caused by genetic mutations.

scholarly journals A composite six bp in-frame deletion in the melanocortin 1 receptor (MC1R) gene is associated with the Japanese brindling coat colour in rabbits (Oryctolagus cuniculus)

BMC Genetics ◽  
2010 ◽  
Vol 11 (1) ◽  
pp. 59 ◽  
Author(s):  
Luca Fontanesi ◽  
Emilio Scotti ◽  
Michela Colombo ◽  
Francesca Beretti ◽  
Lionel Forestier ◽  
...  
Keyword(s):  
Oryctolagus Cuniculus ◽  
Coat Colour ◽  
Melanocortin 1 Receptor ◽  
Mc1r Gene

scholarly journals Fire Detection Technology for Turbine-Powered Transportation

1970 ◽  
Author(s):  
T. M. Trumble
Keyword(s):  
High Temperature ◽  
Detection System ◽  
Fire Detection ◽  
Vehicle Design ◽  
Design Phase ◽  
Detection Systems ◽  
Detection Technology ◽  
Operational Envelope

The problems of providing a fire and overheat detection system for turbine-powered vehicles must be solved during the design phase of the vehicle. In order to accomplish this goal the vehicle design engineer must be aware of the basic constraints involved in the application of fire detection technology. This paper presents a condensed method for understanding, designing and evaluating fire and overheat detection systems. Advanced concepts and technologies such as optical redundancy and high temperature ultraviolet sensors are discussed. Performance of fire and overheat detection systems designed using this approach will provide maximum safety for those using the vehicles, as well as those in its operational envelope.

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