Isolation and species delineation of genus Bifidobacterium using PCR-RFLP of partial hsp60 gene fragment

LWT ◽  
2017 ◽  
Vol 80 ◽  
pp. 286-293 ◽  
Author(s):  
Rajashree Jena ◽  
Prasanta Kumar Choudhury ◽  
Anil Kumar Puniya ◽  
Sudhir Kumar Tomar
Keyword(s):  
Gene Fragment ◽  
Species Delineation ◽  
Hsp60 Gene ◽  
Pcr Rflp

scholarly journals Identification of species belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60 gene fragment

2013 ◽  
Vol 13 (1) ◽  
pp. 149 ◽  
Author(s):  
Loredana Baffoni ◽  
Verena Stenico ◽  
Erwin Strahsburger ◽  
Francesca Gaggìa ◽  
Diana Di Gioia ◽  
...  
Keyword(s):  
Rflp Analysis ◽  
Gene Fragment ◽  
Hsp60 Gene ◽  
Pcr Rflp ◽  
Identification Of Species

scholarly journals Genetic identification of bovine leukaemia virus

2018 ◽  
Vol 6 (2) ◽  
pp. 314-324 ◽  
Author(s):  
Irina Donnik ◽  
Irina Donnik ◽  
Ramil Vafin ◽  
Ramil Vafin ◽  
Aram Galstyan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Research Methods ◽  
Bovine Leukemia Virus ◽  
Leukemia Virus ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Genetic Identification ◽  
Gene Fragment ◽  
Phylogenetic Classification ◽  
Pcr Rflp

Molecular genetic research methods make it possible to evaluate the genetic diversity of bovine leukemia virus (BLV) and are the most informative approaches to its genetic identification. Molecular genetic research methods work well for the phylogenetic analysis of sequenced nucleotide DNA sequences of the provirus, as well as for the polymerase chain reaction-restriction fragment length polymorphism analysis (PCR-RFLP) according to the phylogenetic classification of the pathogen. The purpose of the research was to study the scientific and methodological approaches to the genetic identification of bovine leukemia virus, integrated into the molecular monitoring of infection of cattle with BLV genotypes. The authors used PCR-RFLP-genotyping and comparative phylogenetic analysis of aligned nucleotide sequences of the env gene fragment of the BLV provirus isolates to detect the genotypic affiliation of the cattle from twenty-one livestock farms of the Republic of Tatarstan. As a result, isolates of four out of ten BLV genotypes were found in the Tatarstani cattle, namely genotypes 1, 4, 7, and 8. The research involved a comparative analysis of 505 nucleotide sequences of a fragment of the BLV env gene, including those deposited in GenBank NCBI. The analysis confirms the inconsistency of several earlier PCR-RFLP typing strategies with the current approach in assessing the genotypic diversity by phylogenetic analysis. The improved strategy of PCR-RFLP genotyping of BLV corresponds with its modern phylogenetic classification. The strategy makes it possible to identify all the known genotypes of the viral pathogen. Its validity has been proved by in silico modelling of restrictogrammes and a phylogenetic analysis of the env gene fragment of 57 reference isolates of ten BLV genotypes that generate 57 genotype-associated combinations of diagnostically significant PCR-RFLP profiles.

Molecular identification of cephalopod species by FINS and PCR-RFLP of a cytochrome b gene fragment

2003 ◽  
Vol 217 (6) ◽  
pp. 524-529 ◽  
Author(s):  
Mar�a Jos� Chapela ◽  
Carmen G. Sotelo ◽  
Ricardo I. P�rez-Mart�n
Keyword(s):  
Cytochrome B ◽  
Molecular Identification ◽  
Cytochrome B Gene ◽  
Gene Fragment ◽  
Cephalopod Species ◽  
Pcr Rflp

scholarly journals TECHNOLOGY OF BOVINE LEUKEMIA VIRUS GENODIAGNOSTICS IN CATTLE, IN PRODUCED RAW MATERIALS AND PRODUCTS

2021 ◽  
pp. 119-125
Author(s):  
R. R. Vafin ◽  
Kh. Kh. Gilmanov ◽  
A. G. Galstyan ◽  
N. S. Pryanichnikova ◽  
A. V. Bigaeva ◽  
...  
Keyword(s):  
Bovine Leukemia Virus ◽  
Raw Materials ◽  
Leukemia Virus ◽  
Raw Milk ◽  
Gene Identification ◽  
Gene Fragment ◽  
Viral Pathogen ◽  
Cattle Industry ◽  
Pcr Rflp ◽  
Gene Diagnostics

The most important task of the dairy cattle industry is to obtain high quality raw milk. To achieve it, a set of measures is required, including aimed at increasing the biological safety of produced raw materials. The aim of the study was to create a scientific and methodological basis for the Bovine leukemia virus (BLV) gene diagnostics in a combined format of pathogen indication and identification. This required updating the strategy of BLV PCR-RFLP genotyping, consistent with its phylogenetic classification, taking into account the growing knowledge about the genetic diversity of 11 genotypes of the studied viral pathogen. When staging nested PCR, oligonucleotide primers were used, which initiate at the final stage of the reaction the production of a 444 bp env-gene fragment of the pathogen. Five restriction endonucleases were used in PCR-RFLP BLV genotyping of: PvuII, SspI, AsuHPI, HaeIII, and BstX2I. As a result of verification of the developed Bovine leukemia virus method for gene identification with an updated genotyping strategy, a technical result was obtained, expressed in the ability to identify all 11 BLV genotypes discovered to date by interpreting the generated 58 genotype-associated combinations of PCR-RFLP profiles.

scholarly journals VALIDATION OF PCR-RFLP TESTING METHOD TO DETECT PORCINE CONTAMINATION IN CHICKEN NUGGET

2012 ◽  
Vol 12 (3) ◽  
pp. 302-307 ◽  
Author(s):  
Tri Joko Raharjo ◽  
Winda Cahyaningtyas ◽  
Surajiman Surajiman ◽  
Istini Istini ◽  
Deni Pranowo
Keyword(s):  
Mitochondrial Dna ◽  
Rflp Analysis ◽  
Cytb Gene ◽  
Dna Fragments ◽  
Gene Fragment ◽  
Chicken Nugget ◽  
Testing Method ◽  
Pcr Product ◽  
Pcr Rflp ◽  
Dna Fragment

PCR-RFLP technique to detect porcine contamination in chicken nugget has been developed and validated in this research. Various concentrations of pork were fortified during preparation of the nugget. DNA was then isolated from the nugget followed by PCR employed primers which targeted a 359 bp cytB gene fragment of mitochondrial DNA. For RFLP, the PCR product was digested by means of BamHI and BseDI enzymes. Cutting DNA fragments from nugget containing pork using BseDI enzyme produced DNA fragment with size 228 and 131 bp, while cutting with BamHI enzyme produce DNA fragments with sizes 244 and 115 bp. All of these fragments were not present in RFLP analysis of pork-free nugget. The method shows good specificity and precision and could detect porcine contamination in the nugget up to 5%. The method has been applied to test commercial nugget. Four brand of Halal-labeled commercial nugget as well as four brand of non labeled one gave negative porcine contamination.

scholarly journals Analysis of calpastatin and сallipyge genes polymorphism in Prydniprovska meat sheep

2019 ◽  
Vol 6 (2) ◽  
pp. 58-65
Author(s):  
I. Pomitun ◽  
V. Rossokha ◽  
Ye. Boyko ◽  
O. Guzevatyi ◽  
M. Shpilka ◽  
...  
Keyword(s):  
Gene Polymorphism ◽  
Muscle Hypertrophy ◽  
Restriction Endonucleases ◽  
Gene Fragment ◽  
Cross Breeding ◽  
Pcr Rflp ◽  
Meat Sheep ◽  
Cast Gene

Aim. To study calpastatin (CAST) and сallipyge (CLPG) genes polymorphism in Prydniprovska meat sheep. Methods. The studies were conducted using PCR-RFLP method. DNA was isolated from 47 animals. The amplicons were treated with restriction endonucleases MspI and FaqI for genes CAST and CLPG, respectively. Results. The study determined the polymorphism of CAST gene fragment. Two alleles – M (336, 286 b.p.) and N (622 b.p.) with the frequency of 0.83 and 0.17, respectively, were detected. The frequency of genotypes was as follows: ММ – 0.77, MN – 0.13 and NN – 0.10. There was a noted tendency towards the increase in live bodyweight of 4-month-old lambs, carriers of N allele (genotypes NN and MN), compared to the index for the lambs of the same age with genotype MM. Locus CLPG was monomorphic, only allele A was determined (278, 117 and 31 b.p.). Allele G with the mutation, manifested in muscle hypertrophy phenotype, was not detected, all the animals under investigation had genotype AA. Conclusions. CAST gene polymorphism was deter- mined in Prydniprovska meat sheep during our work. The tendency towards the increase in live bodyweight of 90-day-old lambs, carriers of allele N, was established which demonstrated promising perspectives of further studies on associations of this gene and meat qualities of Prydniprovska meat sheep. The obtained results on the monomorphic nature of locus CLPG and the absence of mutation, related to muscle hypertrophy phenotype, demonstrated that the mutation of this gene may be built into the genome of domestic breeds of sheep only via cross-breeding with foreign breeds, in which this trait is manifested.

scholarly journals Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment

Microbiology ◽  
2002 ◽  
Vol 148 (2) ◽  
pp. 583-595 ◽  
Author(s):  
Małgorzata Waleron ◽  
Krzysztof Waleron ◽  
Anna J Podhajska ◽  
Ewa Łojkowska
Keyword(s):  
Geographic Origin ◽  
Rflp Analysis ◽  
Erwinia Carotovora ◽  
Pcr Primers ◽  
Reca Gene ◽  
Gene Fragment ◽  
Erwinia Tracheiphila ◽  
Pcr Product ◽  
Pcr Rflp ◽  
Erwinia Stewartii

Genotypic characterization, based on the analysis of restriction fragment length polymorphism of the recA gene fragment PCR product (recA PCR-RFLP), was performed on members of the former Erwinia genus. PCR primers deduced from published recA gene sequences of Erwinia carotovora allowed the amplification of an approximately 730 bp DNA fragment from each of the 19 Erwinia species tested. Amplified recA fragments were compared using RFLP analysis with four endonucleases (AluI, HinfI, TasI and Tru1I), allowing the detection of characteristic patterns of RFLP products for most of the Erwinia species. Between one and three specific RFLP groups were identified among most of the species tested (Erwinia amylovora, Erwinia ananas, Erwinia cacticida, Erwinia cypripedii, Erwinia herbicola, Erwinia mallotivora, Erwinia milletiae, Erwinia nigrifluens, Erwinia persicina, Erwinia psidii, Erwinia quercina, Erwinia rhapontici, Erwinia rubrifaciens, Erwinia salicis, Erwinia stewartii, Erwinia tracheiphila, Erwinia uredovora, Erwinia carotovora subsp. atroseptica, Erwinia carotovora subsp. betavasculorum, Erwinia carotovora subsp. odorifera and Erwinia carotovora subsp. wasabiae). However, in two cases, Erwinia chrysanthemi and Erwinia carotovora subsp. carotovora, 15 and 18 specific RFLP groups were detected, respectively. The variability of genetic patterns within these bacteria could be explained in terms of their geographic origin and/or wide host-range. The results indicated that PCR-RFLP analysis of the recA gene fragment is a useful tool for identification of species and subspecies belonging to the former Erwinia genus, as well as for differentiation of strains within E. carotovora subsp. carotovora and E. chrysanthemi.

Sign in / Sign up

Export Citation Format

Share Document