scholarly journals Prevalence and molecular identification of Mycobacteria isolated from animals slaughtered at Sokoto modern abattoir, Sokoto State, Nigeria

2021 ◽  
Vol 19 (3) ◽  
pp. 217-224
Author(s):  
A.I. Musawa ◽  
A.A. Magaji ◽  
M.D. Salihu ◽  
A.C. Kudi ◽  
A.U. Junaidu ◽  
...  
Keyword(s):  
Similarity Search ◽  
Pcr Amplification ◽  
Genomic Region ◽  
Specific Primers ◽  
Suspected Tuberculosis ◽  
Lowenstein Jensen ◽  
Hsp65 Gene ◽  
Polymerase Chain ◽  
Ncbi Blast ◽  
Control And Eradication

This study investigated the molecular epidemiology of Mycobacteria isolated from animals slaughtered at Sokoto modern abattoir. During meat inspection, 104 suspected tuberculosis lesions were sampled from a total of 102,681 animals slaughtered between November 2016 and January 2018. These samples were subjected to Ziehl Neelsen staining, followed by culture on Lowenstein-Jensen media. Subsequently, polymerase chain reaction (PCR) and sequencing of the 65KDa heat shock protein (hsp65) gene were performed to identify and phylogenetically characterize the cultured organisms. Because sequencing of the hsp65 gene was unable to distinguish between Mycobacterium bovis (M. bovis) and M. tuberculosis, PCR was performed to amplify a genomic region-specific to M. bovis in order to differentiate them from M. tuberculosis. Results showed that, 14 samples yielded growth after culture. Furthermore, hsp65 was detected in 9 out of the 14 isolates screened, 5 of the amplicons were successfully sequenced. Similarity search using NCBI BLAST tool showed the five sequences to share highest identities with Mycobacterium novocastrense (95.99%), M. canettii (94.54%), and M. tuberculosis/M. bovis (100%). Two out of the 5 isolates were confirmed to be M. bovis after PCR amplification using M. bovis specific primers. Phylogenetic tree further confirmed the identity of these isolates by placing them close to species of their kind. Further studies should be conducted to establish the transmission dynamics of the zoonotic Mycobacteria between animals and their owners, to facilitate control and eradication of tuberculosis.

scholarly journals Differential effects of distamycin analogues on amplification of human gene sequences by polymerase-chain reaction

1995 ◽  
Vol 308 (2) ◽  
pp. 513-519 ◽  
Author(s):  
M Passadore ◽  
N Bianchi ◽  
G Feriotto ◽  
C Mischiati ◽  
P Giacomini ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Pyrrole Ring ◽  
Human Gene ◽  
Pcr Amplification ◽  
Genomic Region ◽  
Ras Oncogene ◽  
Gene Sequences ◽  
Chain Reaction ◽  
Sequence Preference ◽  
Polymerase Chain

In this report we analyse the effects of distamycin and five distamycin analogues on amplification by polymerase-chain reaction (PCR) of two gene sequences displaying a different A+T/G+C content. The first was a 5′ region of the human oestrogen receptor (ER) gene, containing a (TA)26 stretch; the second was a CG-rich sequence of the human Ha-ras oncogene. The results obtained unequivocally demonstrate that the addition of one pyrrole ring significantly improves the ability of distamycin derivatives to interfere with PCR-mediated amplification of the human ER genomic region carrying a (TA)26 stretch. The distamycin analogues analysed differ in the number of pyrrole rings and in the presence of an N-formyl, an N-formimidoyl or a retroamide group at position X1. Among compounds carrying the same number of pyrrole rings, those carrying an N-formyl or an N-formimidoyl group retain a similar inhibitory activity. The retroamide analogues, on the contrary, are much less efficient in inhibiting PCR-mediated amplification of the 5′ER region. With respect to sequence selectivity both distamycin and distamycin analogues exhibit a sequence preference, since they do not inhibit PCR amplification of Ha-ras CG-rich gene regions, with the exception of a distamycin analogue carrying four pyrrole rings.

scholarly journals Detection of Pythium ultimum Using Polymerase Chain Reaction with Species-Specific Primers

Plant Disease ◽  
1997 ◽  
Vol 81 (10) ◽  
pp. 1155-1160 ◽  
Author(s):  
K. Kageyama ◽  
A. Ohyama ◽  
M. Hyakumachi
Keyword(s):  
Polymerase Chain Reaction ◽  
Internal Transcribed Spacer ◽  
Pcr Amplification ◽  
Its Region ◽  
Pythium Ultimum ◽  
Pythium Species ◽  
Chain Reaction ◽  
Specific Primers ◽  
Polymerase Chain ◽  
Species Specific

This study was conducted to sequence the rDNA internal transcribed spacer (ITS) region of Pythium ultimum and Pythium group HS, design species-specific primers for polymerase chain reaction (PCR), and detect P. ultimum from diseased seedlings using PCR. The sequence of the ITS region of P. ultimum was identical with that of Pythium group HS. The results support the reports that the HS group is an asexual strain of P. ultimum. Using PCR, the primer pair K1+K3, designed on portions of the sequence of the ITS region, amplified isolates of P. ultimum and the HS group but not isolates of 20 other Pythium species. DNA extracts from damped-off seedlings were not amplified, but a 10-fold dilution of the extracts with Tris-EDTA (TE) buffer diluted the inhibitors and allowed PCR amplification. The primer pair used detected P. ultimum from a single diseased seedling.

scholarly journals ABO glycosyltransferase genotyping by polymerase chain reaction using sequence-specific primers

Blood ◽  
1996 ◽  
Vol 88 (5) ◽  
pp. 1852-1856 ◽  
Author(s):  
C Gassner ◽  
A Schmarda ◽  
W Nussbaumer ◽  
D Schonitzer
Keyword(s):  
Pcr Amplification ◽  
Abo Blood Groups ◽  
Chain Reaction ◽  
Specific Primers ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Serological Typing ◽  
Modern Molecular Biology ◽  
Specific Nucleotide Sequence ◽  
Polymerase Chain

Serological typing for the classical ABO blood groups is routinely performed using anti-A and anti-B antisera of polyclonal or monoclonal origin, which are able to distinguish four phenotypes (A, B, AB, and O). Modern molecular biology methods offer the possibility of direct ABO genotyping without the need for family investigations. Typing can be done with small amounts of DNA and without detection of blood group molecules on the surface of red blood cells. We developed a system of eight polymerase chain reactions (PCR) to detect specific nucleotide sequence differences between the ABO alleles O1, O2, A1, A2, and B. PCR amplification using sequence-specific primers and detection of amplification products by agarose gel electrophoresis is one of the fastest genotyping methods and is easy to handle. With our method we tested the A1,2BO1,2 genotypes of 300 randomly chosen persons out of a pool of platelet donors and found the results to be consistent with ABO glycosyltransferase phenotypes. We also identified a presumably new ABO allele, which may be the result of a crossing-over event between alleles O1 and A2.

The Polymerase Chain Reaction with Sequence Specific Primers for the Detection of the Factor V Mutation Associated with Activated Protein C Resistance

1995 ◽  
Vol 74 (03) ◽  
pp. 874-878 ◽  
Author(s):  
Nancy E Kirschbaum ◽  
Paul A Foster
Keyword(s):  
Protein C ◽  
Activated Protein C ◽  
Pcr Amplification ◽  
Factor V ◽  
Activated Protein C Resistance ◽  
Chain Reaction ◽  
Specific Primers ◽  
Allele Specific ◽  
Fv Leiden ◽  
Polymerase Chain

SummaryThe prevalence of the Factor V (FV) mutation associated with activated protein C resistance (FV Leiden) and its significance as a genetic risk factor for venous thrombosis have necessitated the development of a simple, rapid, and accurate assay for its detection. The polymerase chain reaction with sequence specific primers (PCR-SSP) provides a powerful technique for the discrimination of alleles resulting from single base substitutions. PCR amplification was performed using a sense primer complementary to both FV alleles coupled with either of two antisense allele specific primers, one complementary to the normal FV allele and one complementary to the FV Leiden allele. PCR conditions were developed that favored amplification only in the case of perfect complementation between template DNA and allele specific primer. The FV genotype was assigned based on whether or not each allele specific primer set produced an amplified product. Assignment of genotypes correlated 100% with those determined by the method of PCR amplification followed by MnII digestion. PCR-SSP allows the rapid and accurate identification of carriers of the Factor V Leiden mutation by a simple PCR reaction without the need for the usual post-amplification specificity step.

scholarly journals ABO glycosyltransferase genotyping by polymerase chain reaction using sequence-specific primers

Blood ◽  
1996 ◽  
Vol 88 (5) ◽  
pp. 1852-1856 ◽  
Author(s):  
C Gassner ◽  
A Schmarda ◽  
W Nussbaumer ◽  
D Schonitzer
Keyword(s):  
Pcr Amplification ◽  
Abo Blood Groups ◽  
Chain Reaction ◽  
Specific Primers ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Serological Typing ◽  
Modern Molecular Biology ◽  
Specific Nucleotide Sequence ◽  
Polymerase Chain

Abstract Serological typing for the classical ABO blood groups is routinely performed using anti-A and anti-B antisera of polyclonal or monoclonal origin, which are able to distinguish four phenotypes (A, B, AB, and O). Modern molecular biology methods offer the possibility of direct ABO genotyping without the need for family investigations. Typing can be done with small amounts of DNA and without detection of blood group molecules on the surface of red blood cells. We developed a system of eight polymerase chain reactions (PCR) to detect specific nucleotide sequence differences between the ABO alleles O1, O2, A1, A2, and B. PCR amplification using sequence-specific primers and detection of amplification products by agarose gel electrophoresis is one of the fastest genotyping methods and is easy to handle. With our method we tested the A1,2BO1,2 genotypes of 300 randomly chosen persons out of a pool of platelet donors and found the results to be consistent with ABO glycosyltransferase phenotypes. We also identified a presumably new ABO allele, which may be the result of a crossing-over event between alleles O1 and A2.

Molecular Differentiation of Two Strains of the Parasitoid Anisopteromalus calandrae (Hymenoptera: Pteromalidae) Using Specific PCR Primers

2004 ◽  
Vol 39 (1) ◽  
pp. 1-10 ◽  
Author(s):  
Yu Cheng Zhu ◽  
Alan K. Dowdy ◽  
James E. Baker
Keyword(s):  
Dna Markers ◽  
Natural Populations ◽  
Pcr Amplification ◽  
Pcr Primers ◽  
Dna Fragments ◽  
Chain Reaction ◽  
Specific Primers ◽  
Specific Pcr ◽  
Anisopteromalus Calandrae ◽  
Polymerase Chain

Two strains (Sav and Bam) of the parasitoid Anisopteromalus calandrae (Howard) (Hymenoptera: Pteromalidae) showed different sensitivity to organophosphate insecticides. By using polymerase chain reaction (PCR) and DNA sequencing, we demonstrated clear molecular difference between these two strains. DNA markers that are specific for the Bam strain were developed, and PCR-generated DNA fragments were cloned and sequenced. Two DNA fragments unique to the Bam strain contained 365 and 584 nucleotides. A pair of specific primers was designed from each fragment. PCR-amplification of the DNA from individual wasps generated fragments of the expected sizes only in the Bam strain. Studies conducted on F1 and F2 hybrids produced from crossing and backcrossing between resistant and susceptible strains indicated that these DNA markers are located on mitochondria and inherited exclusively maternally. Probes developed from these fragments may be used in assessing genetic information of natural populations and in studies on physiological or biochemical differences between the strains of this beneficial insect.

scholarly journals Intraspecific Variations of Epimedium koreanum by Randomly and Specifically Amplified Polymorphic DNA Markers

HortScience ◽  
1997 ◽  
Vol 32 (3) ◽  
pp. 454D-454
Author(s):  
Hak-Tae Lim
Keyword(s):  
Genetic Relationships ◽  
Pcr Amplification ◽  
Morphological Characters ◽  
Pcr Analysis ◽  
Specific Primers ◽  
Banding Patterns ◽  
Intraspecific Variations ◽  
Similarity Indices ◽  
Leaflet Number ◽  
Polymerase Chain

Randomly and specifically amplified polymorphic DNA banding patterns based on polymerase chain reaction (PCR) analysis were used to assess the intraspecific genetic variations and relationships within Epimedium koreanum populations. A collection of 21 individuals were classified as different accessions by morphological characters such as leaflet number, shape of leaf base, cauline length, plant height, and leaf area. PCR amplification using 12 primers out of 62 [60 random (10-mer) primers, one 15-mer primer (M13 core sequence), and (GGAT)4] resulted in 89 amplified DNA fragments with polymorphisms (80.9%) in all of the tested plants. Similarity indices between accessions were computed from PCR data, and genetic relationships among intraspecific variations were closely related at the levels ranging from 0.66 to 0.93. These DNA data were not matched well with those of morphological characters because they were divided into two major groups at the similarity coefficient value of 0.74. Primers (VII, VIII) gave rise to monomorphic bands in all of examined plants, but specific primers (M13 core and (GGAT)4 sequences) were found to be very valuable molecular markers to evaluate the interspecific variations in Epimedium koreanum.

scholarly journals A simple and reliable method for the screening of transgenic tobacco plants

2003 ◽  
Vol 38 (7) ◽  
pp. 893-896
Author(s):  
Juliana Freitas-Astua ◽  
Gustavo Astua-Monge ◽  
Jane Elisabeth Polston ◽  
Ernest Hiebert
Keyword(s):  
Transgenic Plants ◽  
Pcr Amplification ◽  
Plant Leaves ◽  
Specific Primers ◽  
Transformed Plants ◽  
Polymerase Chain ◽  
Transformation Methods ◽  
Non Destructive ◽  
Laborious Work ◽  
Made In

Even though much improvement has been made in plant transformation methods, the screening of transgenic plants is often a laborious work. Most approaches for detecting the transgene in transformed plants are still timeconsuming, and can be quite expensive. The objective of this study was to search for a simpler method to screen for transgenic plants. The infiltration of kanamycin (100 mg/mL) into tobacco leaves resulted in conspicuous chlorotic spots on the non-transgenic plant leaves, while no spots were seen on the leaves of transformed plants. This reaction occurred regardless of age of the tested plants, and the method has proven to be simple, fast, non-destructive, relatively cheap, and reliable. These results were comparable to those obtained by the polymerase chain reaction (PCR) amplification of the transgene using specific primers.

scholarly journals Gaeumannomyces graminis vars. avenae, graminis, and tritici Identified Using PCR Amplification of Avenacinase-like Genes

Plant Disease ◽  
2002 ◽  
Vol 86 (6) ◽  
pp. 652-660 ◽  
Author(s):  
Sansanalak Rachdawong ◽  
Carole L. Cramer ◽  
Elizabeth A. Grabau ◽  
Verlyn K. Stromberg ◽  
George H. Lacy ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Rapid Identification ◽  
Gaeumannomyces Graminis ◽  
Specific Primers ◽  
Single Tube ◽  
Pcr Products ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Cereal Fields ◽  
Take All

Identifying take-all pathogens, Gaeumannomyces graminis varieties avenae (Gga), graminis (Ggg), and tritici (Ggt), is difficult. Rapid identification is important for development of disease thresholds. We developed a single-tube, polymerase chain reaction (PCR) method differentiating among Gga, Ggg, and Ggt. Nucleotide base sequence analyses of avenacinase-like genes from Gga, Ggg, and Ggt isolates provided the basis for designing variety-specific primers. Sequences from Ggg and Ggt were highly related (99% identity), but Gga sequences were <95% identical to Ggg and Ggt sequences. Three 5′ primers specific for Gga, Ggt, and Ggg and a single 3′ common primer allowed amplification of variety-specific fragments of 617, 870, and 1,086 bp, respectively. Each 5′ primer was specific in mixed populations of primers and templates. No PCR products were amplified from related fungi including Gaeumannomyces cylindrosporus and Phialophora spp. We surveyed 16 putative Ggt isolates using our assay; nine produced Ggt-specific fragments and seven produced Ggg-specific fragments. Five Gga isolates produced Gga-specific fragments. However, Gga- and Ggt-specific fragments were observed from a sixth Gga isolate, RB-W, which indicates a mixed culture or a heterokaryon. Our single-tube, PCR method rapidly differentiates among the important take-all pathogens commonly encountered together in cereal fields.

Sign in / Sign up

Export Citation Format

Share Document