scholarly journals Computer-assisted selection of restriction enzymes for rrs genes PCR-RFLP discrimination of rhizobial species

1998 ◽  
Vol 30 (Suppl 1) ◽  
pp. S297 ◽  
Author(s):  
Marc Neyra ◽  
Bouchaib Khbaya ◽  
Philippe de Lajudie ◽  
Bernard Dreyfus ◽  
Philippe Normand
Keyword(s):  
Restriction Enzymes ◽  
Computer Assisted ◽  
Pcr Rflp ◽  
Rhizobial Species ◽  
Selection Of

​POU1F1 Gene Polymorphism and its Associations with Body Weight of Osmanabadi Goat

2021 ◽  
Author(s):  
Vikrant D. Pawar ◽  
Mahadeo P. Sawane ◽  
Aakash Y. Doiphode
Keyword(s):  
Body Weight ◽  
Gene Polymorphism ◽  
Age Groups ◽  
Restriction Enzymes ◽  
Nucleotide Position ◽  
Pou1f1 Gene ◽  
Body Weights ◽  
Pcr Rflp ◽  
Indigenous Goat ◽  
Selection Of

Background: Osmanabadi is the premium meat type goat breed of Maharashtra, known for its adaptability and reproductive efficiency. Identification of superior germplasm and incorporating them into breeding programme is the need of hour for augmenting productivity of Osmanabadi as well as other indigenous goat breeds. Hence, the present research was aimed to study Pituitary Specific Transcription Factor I (POU1F1) gene polymorphism and its associations with body weight of Osmanabadi goat. Methods: Genomic DNA was extracted from 217 blood samples of randomly selected Osmanabadi goats. The 450 bp fragment of POU1F1 gene encompassing exon-6 and its flanking region (3’UTR) was PCR amplified. The PCR amplicon was subjected to RFLP using AluI and PstI restriction enzymes to identify polymorphism at nucleotide position 174 (T greater than C) in exon 6 and at nucleotide position 110 (T greater than C) in the 3’UTR of POU1F1 gene, respectively. The association of the observed allelic variants / genotypes with body weight of the animals was performed using One-way ANOVA. Result: The AluI PCR-RFLP of 450 bp amplicon of POU1F1 gene in Osmanabadi goats revealed polymorphism with three different genotypes viz., ‘CC’, ‘TT’ and ‘TC’. The observed frequencies for TT, TC and CC genotypes were 0.604, 0.355 and 0.041 respectively. The frequencies of T and C alleles were found to be 0.781 and 0.219, respectively. However, PstI PCR-RFLP revealed monomorphic 3’UTR of POU1F1 gene with single TT genotype. We observed significant differences (P less than 0.01) between various genotypes at AluI exon-6 locus of POU1F1 gene and body weights at birth, 3 and 6 months of Osmanabadi goat. Highest body weight was recorded for TT genotype followed by TC and CC genotypes in all three age groups. Our findings indicate that the AluI PCR-RFLP locus of the exon-6 of POU1F1 gene can be used as a potent molecular marker for selection of superior stock of Osmanabadi goats.

scholarly journals Derived Polymorphic Amplified Cleaved Sequence (dPACS): A Novel PCR-RFLP Procedure for Detecting Known Single Nucleotide and Deletion–Insertion Polymorphisms

2019 ◽  
Vol 20 (13) ◽  
pp. 3193 ◽  
Author(s):  
Shiv Shankhar Kaundun ◽  
Elisabetta Marchegiani ◽  
Sarah-Jane Hutchings ◽  
Ken Baker
Keyword(s):  
Gel Electrophoresis ◽  
Restriction Site ◽  
Restriction Enzymes ◽  
Nucleotide Polymorphisms ◽  
Acetyl Coa Carboxylase ◽  
Wild Type ◽  
Single Nucleotide ◽  
Pcr Rflp ◽  
Broadleaf Species ◽  
Selection Of

Most methods developed for detecting known single nucleotide polymorphisms (SNP) and deletion–insertion polymorphisms (DIP) are dependent on sequence conservation around the SNP/DIP and are therefore not suitable for application to heterogeneous organisms. Here we describe a novel, versatile and simple PCR-RFLP procedure baptised ‘derived Polymorphic Amplified Cleaved Sequence’ (dPACS) for genotyping individual samples. The notable advantage of the method is that it employs a pair of primers that cover the entire fragment to be amplified except for one or few diagnostic bases around the SNP/DIP being investigated. As such, it provides greater opportunities to introduce mismatches in one or both of the 35–55 bp primers for creating a restriction site that unambiguously differentiates wild from mutant sequences following PCR-RFLP and horizontal MetaPhorTM gel electrophoresis. Selection of effective restriction enzymes and primers is aided by the newly developed dPACS 1.0 software. The highly transferable dPACS procedure is exemplified here with the positive detection (in up to 24 grass and broadleaf species tested) of wild type proline106 of 5-enolpyruvylshikimate-3-phosphate synthase and its serine, threonine and alanine variants that confer resistance to glyphosate, and serine264 and isoleucine2041 which are key target-site determinants for weed sensitivities to some photosystem II and acetyl-CoA carboxylase inhibiting herbicides, respectively.

scholarly journals Genetic variation among pathogens causing "Helminthosporium" diseases of rice, maize and wheat

2002 ◽  
Vol 27 (6) ◽  
pp. 639-643 ◽  
Author(s):  
RITA C. B. WEIKERT-OLIVEIRA ◽  
M. APARECIDA DE RESENDE ◽  
HENRIQUE M. VALÉRIO ◽  
RACHEL B. CALIGIORNE ◽  
EDILSON PAIVA
Keyword(s):  
Triticum Aestivum ◽  
Genetic Variation ◽  
Climatic Factors ◽  
Rapd Analysis ◽  
Its Region ◽  
Restriction Enzymes ◽  
Fungal Species ◽  
High Similarity ◽  
Pcr Rflp ◽  
Upgma Phenogram

Twenty isolates of four fungal species, agents of "Helminthosporium" diseases in cereals, were collected from different regions: nine Bipolarisoryzae isolated from rice (Oryza sativa), seven B.sorokiniana from wheat (Triticum aestivum), two B. maydis, and two Exserohilumturcicum from maize (Zea mays). The strains were compared by PCR-RFLP and RAPD analysis. Size polymorphism among the isolates in the ITS region comprising the 5.8 S rDNA indicated genetic differences among the isolates, while a UPGMA phenogram constructed after the digestion of this region with restriction enzymes showed inter- and intra-specific polymorphism. The RAPD profiles indicated an expressive level of polymorphism among different species, compared with a low level of polymorphism among isolates of the same species. A UPGMA phenogram grouped the isolates according to the species and their host plant. RAPD profiles did not reveal polymorphism that directly correlated climatic factors with geographic source of the isolates of B. sorokiniana, and B. oryzae. Teleomorphic species revealed high similarity with their correspondent anamorphs.

scholarly journals Genetic Polymorphism of SCD1 Gene of Holstein-Friesian Cows in Indonesia

2019 ◽  
Vol 24 (2) ◽  
pp. 56
Author(s):  
Ari Sulistyo Wulandari ◽  
HD Rahayu ◽  
SD Volkandari ◽  
N Herlina ◽  
S Anwar ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Genetic Polymorphism ◽  
Breeding Strategy ◽  
Holstein Friesian ◽  
Pcr Rflp ◽  
Hardy Weinberg Equilibrium ◽  
Molecular Selection ◽  
Friesian Cattle ◽  
Selection Of ◽  
Friesian Cows

<p class="abstrak2">Stearoyl-Coenzyme A desaturase 1 (SCD1) belongs to the fatty acid family of desaturases. In lactating ruminants, the SCD1 protein is highly expressed in the mammary gland and is relevant for the fatty acid composition of milk and dairy products. Polymorphism of SCD1 gene in Holstein-Friesian (HF) cows could be used as a basis of molecular selection of cattle in order to increase their productivity. The aim of this study was to investigate the polymorphism of SCD1 gene of Holstein-Friesian cows in Indonesia. A total of 162 blood samples of HF cows were collected from four different locations i.e. Bogor, Sukabumi, Tasikmalaya and Enrekang districts. Genotyping of SCD1 gene used PCR-RFLP method with NcoI restriction enzyme. The result showed that three genotypes (AA, AV and VV) and two alleles (A and V) have successfully found and polymorphic. A allele was dominant in all populations (0.63) and in Hardy Weinberg Equilibrium. The highest A allele was found in Sukabumi (0.78) and the lowest was in Bogor (0.55). Heterozigosity observed and expected reached 0.471 and 0.470, respectively. In conclusion, genetic polymorphism was found in all population with dominant of A allele. This finding can be used as a early genetic information of Holstein-Friesian cattle in Indonesia and to build breeding strategy for improving of productivity especially improving of healthy fat milk. </p><p class="abstrak2"><span><br /></span></p>

scholarly journals Identification of restriction enzyme in the FSHR gene of indonesian local cattle

2021 ◽  
Vol 888 (1) ◽  
pp. 012024
Author(s):  
P W Prihandini ◽  
A Primasari ◽  
M Luthfi ◽  
D Pamungkas ◽  
A P Z N L Sari ◽  
...  
Keyword(s):  
Restriction Enzyme ◽  
Restriction Site ◽  
Follicle Stimulating Hormone ◽  
Restriction Enzymes ◽  
Future Studies ◽  
Fshr Gene ◽  
Pcr Rflp ◽  
Mapping Analysis ◽  
Pcr Products ◽  
Enzyme Mapping

Abstract The restriction enzyme is important for genotyping using the PCR-RFLP technique. Therefore, this study aims to identify the restriction enzyme mapping in the partial sequence of the follicle-stimulating hormone receptor (FSHR) gene in Indonesian local cattle. A total of 29 samples sized 306 bp, were aligned with Genbank sequence acc no. NC_032660, resulting three polymorphic sites, namely g.193G>C, g.227T>C, and g.275A>C. Furthermore, the restriction mapping analysis using the NEBcutter program V2.0 showed that no enzyme recognized the SNP g.275A>C, while the SNP g.193G>C and g.227T>C were identified by the AluI and MscI enzymes, respectively. The AluI enzyme cuts at two positions (193 bp and 243 bp) in the G allele sample producing three fragments namely 50 bp, 63 bp, and 193 bp, meanwhile, in the C allele, the AluI cuts only in position 243 bp, hence, the fragment products are 63 bp and 243 bp. In contrast, the MscI enzyme was only recognized in the T allele, producing fragments sized 77 bp and 229 bp but failed to identify the restriction site along with the PCR products in the C allele. Based on the results, the SNPs (g.193G>C and g.227T>C) and restriction enzymes (AluI and MscI) are applicable for genotyping local Indonesian cattle using the PCR-RFLP technique in future studies.

scholarly journals Molecular Characterization ofCryptosporidiumspp. in Wild Rodents of Southwestern Iran Using 18s rRNA Gene Nested-PCR-RFLP and Sequencing Techniques

2016 ◽  
Vol 2016 ◽  
pp. 1-6 ◽  
Author(s):  
Jasem Saki ◽  
Masoud Foroutan-Rad ◽  
Reza Asadpouri
Keyword(s):  
Molecular Characterization ◽  
Nested Pcr ◽  
18S Rrna ◽  
Restriction Enzymes ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Wild Rodents ◽  
Nested Polymerase Chain Reaction ◽  
Pcr Rflp ◽  
Southwest Of Iran

Background. Rodents could act as reservoir forCryptosporidiumspp. speciallyC. parvum, a zoonotic agent responsible for human infections. Since there is no information aboutCryptosporidiuminfection in rodents of Ahvaz city, southwest of Iran, hence, this survey was performed to determine the prevalence and molecular characterization ofCryptosporidiumspp. in this region.Materials and Methods. One hundred rodents were trapped from different regions of Ahvaz city. Intestine contents and fecal specimens of rodents were studied using both microscopy examination to identify oocyst and nested-polymerase chain reaction (PCR) technique for 18s rRNA gene detection. Eventually restriction fragment length polymorphism (RFLP) method usingSspIandVspIrestriction enzymes was carried out to genotype the species and then obtained results were sequenced.Results. Three out of 100 samples were diagnosed as positive and overall prevalence ofCryptosporidiumspp. was 3% using both modified Ziehl-Neelsen staining under light microscope and nested-PCR (830 bp) methods. Afterwards, PCR-RFLP was performed on positive samples andC. parvumpattern was identified. Finally PCR-RFLP findings were sequenced and presence ofC. parvumwas confirmed again.Conclusions. Our study showed rodents could be potential reservoir forC. parvum. So an integrated program for control and combat with them should be adopted and continued.

scholarly journals Identification of Pneumococcal Serotypes by PCR–Restriction Fragment Length Polymorphism

Diagnostics ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 196 ◽  
Author(s):  
García-Suárez ◽  
González-Rodríguez ◽  
Cima-Cabal ◽  
Yuste ◽  
Vazquez ◽  
...  
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Dna Sequences ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Pcr Rflp ◽  
Restriction Fragment Length

Streptococcus pneumoniae shows more than 90 capsular serotypes that can be distinguished by their reactivity against antisera. The main objective of this work was the development of a molecular method for serotyping without the use of antisera. A computer program containing an algorithm was used to search in a database for potentially useful enzymes for Restriction Fragment Length Polymorphism-RFLP typing, in order to maximize the discrimination between different serotypes. DNA sequences of 90 serotypes for the region between dexB and aliA genes were compiled, and a computer screening of restriction enzymes was performed. The wzg–wzh–wzd–wze region and Sse9I restriction predicted unique PCR-RFLP patterns for 39 serotypes and eight serogroups. A second restriction enzyme resolved fragment specific patterns for 25 serotypes. The method was tested with 98 serotype-unknown clinical isolates. PCR-RFLP analysis deduced correct serotypes that were confirmed by Quellung reaction for 78.5% of the isolates.

PCR-based genetic identification of marlin and other billfish

1998 ◽  
Vol 49 (5) ◽  
pp. 383 ◽  
Author(s):  
B. H. Innes ◽  
P. M. Grewe ◽  
R. D. Ward
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Test ◽  
Rflp Analysis ◽  
Restriction Enzymes ◽  
Genetic Identification ◽  
Dna Molecule ◽  
Pcr Rflp ◽  
D Loop ◽  
Specific Variation ◽  
Species Specific

A genetic test was developed for the identification of the six species of billfish found in Australian waters (black marlin, Indo–Pacific blue marlin, striped marlin, Indo–Pacific sailfish, shortbill spearfish and broadbill swordfish). The test was based on the PCR–RFLP analysis of a 1400 bp region of the mitochondrial DNA molecule, the d-loop, using four restriction enzymes (Hinf I, Rsa I and Sau3A I andTaq I). A total of 33 composite haplotypes were observed among 160 fish; all were species-specific. Three of the species—black marlin, striped marlin and broadbill swordfish—showed sufficient intra-specific variation to be useful in population structure analyses.

Computers and Aboriginal Literacy

1986 ◽  
Vol 14 (4) ◽  
pp. 3-10 ◽  
Author(s):  
K. Darvall
Keyword(s):  
Everyday Life ◽  
Computer Technology ◽  
Computer Assisted ◽  
Computer Assisted Learning ◽  
Job Opportunities ◽  
Hands On ◽  
The Right ◽  
Selection Of

Kids love computers. Computers are not seen as work but rather, games.I believe this to be true for most children. The exception would be the young computer buffs who become hooked on computer technology, and even for these computer buffs, it is probably still a game.Computer technology has become a fact of everyday life. We‘re all affected by computer technology. With this in mind, I believe it is essential that all children become familiar with computers, with regular ‘hands on’ experience. With the right selection of software, schools can incorporate computer-assisted learning across the curriculum. The experiences children have now with computers can lead to a variety of job opportunities in future years.

scholarly journals ICT in varied language learning environments: Selected papers from EUROCALL 1999

ReCALL ◽  
2000 ◽  
Vol 12 (1) ◽  
pp. 1-4
Author(s):  
THIERRY CHANIER
Keyword(s):  
Language Learning ◽  
Learning Environments ◽  
European Association ◽  
Large Scale ◽  
Computer Assisted ◽  
Computer Assisted Language Learning ◽  
Special Issue ◽  
French Speaking ◽  
Selection Of

This special issue offers a selection of papers presented at the 1999 annual EUROCALL conference, held last September in Besançon, France. Although CALL has a deep rooted tradition in France, EUROCALL’99 was the first large scale international CALL conference to take place in this country. Initiated by the European Association for Computer Assisted Language Learning and the French speaking CALL journal ALSIC (2000), the conference attracted more than 370 full participants coming from 30 countries.

Sign in / Sign up

Export Citation Format

Share Document