scholarly journals A SIMPLE METHOD OF DNA EXTRACTION OF MYCOBACTERIUM TUBERCULOSIS FROM SPUTUM CULTURES FOR SEQUENCING ANALYSIS

2021 ◽  
Vol 15 (2s) ◽  
pp. 19-22
Author(s):  
Maharani Pertiwi Koentjoro ◽  
Adyan Donastin ◽  
Endry Nugroho Prasetyo
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Dna Extraction ◽  
Pcr Amplification ◽  
Dna Integrity ◽  
Sequencing Analysis ◽  
Simple Method ◽  
Molecular Tests ◽  
Mycobacterial Genome ◽  
Complex Procedure ◽  
Species Specific

Background: Concern has been raised about DNA extraction from Mycobacterium tuberculosis due to its complex procedure. This study demonstrates a simple and fast DNA extraction method of mycobacterial genome to subsequent molecular investigation, such as Polymerization Chain Reaction (PCR) amplification, with species-specific primers and sequencing. Materials and Methods: Total DNA was isolated from M. tuberculosis cultured by using boil method. DNA was evaluated via measures of DNA quantity and quality (absorbance at 230, 260 and 280 nm), DNA integrity (electrophoresis). Molecular tests were tested namely PCR and sequencing. Conclusions: The quality of DNA obtained is acceptable for PCR and sequencing analysis. These findings demonstrate that the method used is inexpensive and suitable for minimum infrastructure facilities.

A simple method for discriminating Bursaphelenchus xylophilus and B. mucronatus by species-specific polymerase chain reaction primer pairs

Nematology ◽  
2004 ◽  
Vol 6 (2) ◽  
pp. 273-277 ◽  
Author(s):  
Koji Matsunaga ◽  
Katsumi Togashi
Keyword(s):  
Pcr Amplification ◽  
Nematode Species ◽  
Bursaphelenchus Xylophilus ◽  
Polymerase Chain Reaction Primer ◽  
Dna Fragments ◽  
Simple Method ◽  
Specific Pcr ◽  
Pcr Products ◽  
Specific Pcr Primer ◽  
Species Specific

Abstract Two species-specific PCR primer pairs were developed for identifying the two nematode species, Bursaphelenchus xylophilus and B. mucronatus. The primer pairs were developed from the sequence of ribosomal DNA (rDNA) repeats to produce DNA fragments of different lengths by PCR amplification. The DNA fragments for B. mucronatus and B. xylophilus were 210 bp and 557 bp, respectively. When mixed, neither primer pair inhibited the PCR amplification of the other. Five isolates of B. xylophilus and four isolates of B. mucronatus showed different band profiles of PCR products between the two species, but identical profiles among isolates of the same species.

A simple method of DNA extraction from Mycobacterium tuberculosis

1995 ◽  
Vol 76 (6) ◽  
pp. 578-581 ◽  
Author(s):  
M. Jaber ◽  
A. Rattan ◽  
A. Verma ◽  
J. Tyagi ◽  
R. Kumar
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Dna Extraction ◽  
Simple Method

Simple Method for DNA Extraction from Pancreatic Juice for PCR Amplification Assays

1999 ◽  
Vol 25 (1) ◽  
pp. 39-44 ◽  
Author(s):  
Petra Müller ◽  
Ralf Jesnowski ◽  
Stefan Liebe ◽  
Arndt Rolfs ◽  
Matthias Löhr
Keyword(s):  
Dna Extraction ◽  
Pancreatic Juice ◽  
Pcr Amplification ◽  
Simple Method

scholarly journals Authentication of the Herbal Medicine Angelicae Dahuricae Radix Using an ITS Sequence-Based Multiplex SCAR Assay

Molecules ◽  
2018 ◽  
Vol 23 (9) ◽  
pp. 2134 ◽  
Author(s):  
Pureum Noh ◽  
Wook Kim ◽  
Sungyu Yang ◽  
Inkyu Park ◽  
Byeong Moon
Keyword(s):  
Herbal Medicines ◽  
Morphological Characteristics ◽  
Pcr Amplification ◽  
Its Region ◽  
Sequencing Analysis ◽  
Accurate Identification ◽  
Republic Of China ◽  
Sequence Characterized Amplified Region ◽  
Angelicae Dahuricae Radix ◽  
Species Specific

The accurate identification of plant species is of great concern for the quality control of herbal medicines. The Korean Pharmacopoeia and the Pharmacopoeia of the People’s Republic of China define Angelicae Dahuricae Radix (Baek-Ji in Korean and Bai-zhi in Chinese) as the dried roots of Angelica dahurica or A. dahurica var. formosana belonging to the family Apiaceae. Discrimination among Angelica species on the basis of morphological characteristics is difficult due to their extremely polymorphic traits and controversial taxonomic history. Furthermore, dried roots processed for medicinal applications are indistinguishable using conventional methods. DNA barcoding is a useful and reliable method for the identification of species. In this study, we sequenced the internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes in A. dahurica, A. dahurica var. formosana, and the related species A. anomala and A. japonica. Using these sequences, we designed species-specific primers, and developed and optimized a multiplex sequence-characterized amplified region (SCAR) assay that can simply and rapidly identify respective species, and verify the contamination of adulterant depending on the polymerase chain reaction (PCR) amplification without sequencing analysis in a single PCR reaction. This assay successfully identified commercial samples of Angelicae Dahuricae Radix collected from Korean and Chinese herbal markets, and distinguished them from adulterants. This multiplex SCAR assay shows a great potential in reducing the time and cost involved in the identification of genuine Angelicae Dahuricae Radix and adulterant contamination.

Rapid and simple method for DNA extraction from plant and algal species suitable for PCR amplification using a chelating resin Chelex 100

2009 ◽  
Vol 4 (1) ◽  
pp. 49-52 ◽  
Author(s):  
Kwon HwangBo ◽  
Su Hyun Son ◽  
Jong Suk Lee ◽  
Sung Ran Min ◽  
Suk Min Ko ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Algal Species ◽  
Pcr Amplification ◽  
Chelating Resin ◽  
Simple Method ◽  
Chelex 100

scholarly journals Inactivation of Mycobacterium tuberculosis for DNA Typing Analysis

1999 ◽  
Vol 37 (7) ◽  
pp. 2350-2351 ◽  
Author(s):  
P. Bemer-Melchior ◽  
H. B. Drugeon
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Dna Fingerprinting ◽  
Dna Extraction ◽  
Culture Media ◽  
Dna Typing ◽  
Epidemiological Studies ◽  
Dna Integrity ◽  
Cross Contamination ◽  
Laboratory Staff ◽  
A New Technique

DNA fingerprinting analysis of Mycobacterium tuberculosis is used for epidemiological studies and the control of laboratory cross-contamination. Because standardized procedures are not entirely safe for mycobacteriology laboratory staff, the paper proposes a new technique for the processing of specimens. The technique ensures the inactivation of M. tuberculosis before DNA extraction without the loss of DNA integrity. The control of inactivated cultures should be rigorous and should involve the use of two different culture media incubated for at least 4 months.

scholarly journals DNA extraction and pattern of crab and macrobentos from North Sumatran mangrove forest, Indonesia

2021 ◽  
Vol 912 (1) ◽  
pp. 012046
Author(s):  
A M Harahap ◽  
M Basyuni ◽  
I E Susetya
Keyword(s):  
Dna Extraction ◽  
Mangrove Forest ◽  
Morphological Analysis ◽  
Animal Species ◽  
Pcr Amplification ◽  
Sequencing Analysis ◽  
Chain Reaction ◽  
Mangrove Ecosystems ◽  
Polymerase Chain ◽  
North Sumatra

Abstract Mangrove forest ecosystem is one of the most productive and unique ecosystems that serves to protect coastal areas from various disturbances, as well as provide habitat for various animal species. The large number of crab species and macrobentos in mangrove ecosystems results in frequent errors in the naming of species that have similarities in morphological features. This problem can be solved through a comprehensive approach by combining morphological analysis with genetic analysi.This study aims to report a DNA extraction and PCR amplification prior was used for the identification of crab and macrozoobentos from mangrove forest, North Sumatra. Primer 16S has a conserved area so it is appropriately used in Polymerase Chain Reaction (PCR) and sequencing analysis to determine taxonomy, phylogeny and diversity between specie. Visualization of PCR amplification results with primer16S from crab samples and macrobentos resulting a low DNA band with a size of 206 bp and a high of 678bp

Development of rapid and simple method for DNA extraction from cannabis resin based on the evaluation of relative PCR amplification ability

2018 ◽  
Vol 287 ◽  
pp. 176-182 ◽  
Author(s):  
Tadashi Yamamuro ◽  
Yuko T. Iwata ◽  
Hiroki Segawa ◽  
Kenji Kuwayama ◽  
Kenji Tsujikawa ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Pcr Amplification ◽  
Simple Method

scholarly journals Listeriosis in a peri-urban area: Cultural and molecular characterization of Listeria monocytogenes isolated from encephalitic goats

2020 ◽  
Vol 13 (9) ◽  
pp. 1743-1749
Author(s):  
Nagendra Nath Barman ◽  
Anjan Jyoti Nath ◽  
Sharmita Doley ◽  
Shameem Ara Begum ◽  
Parikshit Kakati ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
16S Rrna ◽  
Molecular Characterization ◽  
Early Stage ◽  
Meat Products ◽  
Pcr Amplification ◽  
High Dose ◽  
Molecular Tests ◽  
Species Specific

Background and Aim: Listeriosis in food animals bears a significant threat to human health. Detailed investigations into the cause facilitate proper management of the disease. This study reports the cultural, pathological, and molecular characterization of Listeria monocytogenes isolated from encephalitic goats from peri-urban Guwahati, Assam. Materials and Methods: Out of nine suspected samples, five positive isolates of L. monocytogenes were subjected to bacteriological, biochemical, and molecular tests. The genus and species-specific L. monocytogenes 16S rRNA and prs genes were amplified by polymerase chain reaction (PCR) to yield 1200 and 370 bp sized products, respectively. The encephalitic form of the disease was characterized by circling movement, high fever, and terminal recumbence. Results: All the five isolates were confirmed to be L. monocytogenes based on PCR amplification of genus and species-specific 16S rRNA and prs gene products. The isolates were sensitive to ciprofloxacin, oxytetracycline (OTC), and norfloxacin, but resistant to doxycycline and erythromycin. A high dose of OTC was used in a goat at the early stage of clinical symptom and the animal recovered clinically. Conclusion: Listeriosis in goats could pose a significant public health threat as the meat (occasionally milk) or meat products from goats are widely consumed by the people of Assam. Understanding the molecular epidemiological aspects of L. monocytogenes infections of food animal species should, therefore, be the priority in this part of the country.

scholarly journals Relationship between rifampin MICs for and rpoB mutations of Mycobacterium tuberculosis strains isolated in Japan.

1996 ◽  
Vol 40 (4) ◽  
pp. 1053-1056 ◽  
Author(s):  
H Ohno ◽  
H Koga ◽  
S Kohno ◽  
T Tashiro ◽  
K Hara
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Point Mutation ◽  
Rpob Gene ◽  
The Other ◽  
Clinical Isolates ◽  
Sequencing Analysis ◽  
The Relationship

We analyzed the relationship between rifampin MICs and rpoB mutations of 40 clinical isolates of Mycobacterium tuberculosis. A point mutation in either codon 516, 526, or 531 was found in 13 strains requiring MICs of > or = 64 micrograms/ml, while 21 strains requiring MICs of < or = 1 microgram/ml showed no alteration in these codons. However, 3 of these 21 strains contained a point mutation in either codon 515 or 533. Of the other six strains requiring MICs between 2 and 32 micrograms/ml, three contained a point mutation in codon 516 or 526, while no alteration was detected in the other three. Our results indicate that the sequencing analysis of a 69-bp fragment in the rpoB gene is useful in predicting rifampin-resistant phenotypes.

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