scholarly journals RANCANGAN PRIMER SPESIFIK GEN MACROPHAGE MANNOSE RECEPTOR (MMR) UNTUK POLYMERASE CHAIN REACTION (PCR) DAN SEKUENSING DEOXYRIBO NUCLEIC ACID (DNA)

2018 ◽  
Vol 22 (2) ◽  
pp. 158
Author(s):  
Yani Triyani ◽  
Nurizzatun Nafsi ◽  
Lelly Yuniarti ◽  
Nanan Sekarwana ◽  
Endang Sutedja ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequencing ◽  
Mannose Receptor ◽  
Primer Design ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Specific Pcr ◽  
Polymerase Chain ◽  
Dna Sequencing Analysis

The order (sequencing) determinationof DeoxyribonucleicAcid (DNA) bases is the gene’s most basic information, using the methodof Polymerase Chain Reaction (PCR) as its stage. A key factor of successful detection by PCR is specific PCR primer design choice. Thedetection of diversity of Mycobacterium Mannose Receptor (MMR) gene, responsible for recognizing mannosylated antigen structureof Mycobacterium tuberculosis (M.tb) by DNA sequencing of exon 7 chromosome 10p12, related to susceptiblity for PulmonaryTuberculosis(TB), was first performed in China in 2012. The purpose of this study was to find specific primerfromboth design originatedfrom the research in China/primer I and my own design/primer IIby using Primer3 software. This study was based on 10 healthy subjectsand was a preliminary study of a research titled. The Relationship of Single Nucleotide Polymorphisms (SNPs) of Macrophage MannoseReceptor Gene to Pulmonary Tuberculosis Cases. The examination materials consist of 3 mL of EDTA blood and DNA extraction from itsbuffy coat. The resulting DNA was processed by PCR to amplify MMR gene with primer I and II. The primer I successfully amplified DNAfragments up to 780bp while primer II only 329 bp. The MMR gene DNA sequencing analysis was performed on the amplification resultof both kinds primers by using DNA Baser and Ensembl−BLAST software. The results were different, DNA sequencing result by using theprimer I was found in several chromosomes and also in several loci. Whereas, by using the primer II, it was only found in chromosome10 and in the same locus. Based on this study, it can be concluded that the specific primer design is one of the most important factorsin the success of DNA sequencing.

scholarly journals Use of the polymerase chain reaction for detection of Fusarium graminearum in bulgur wheat

2012 ◽  
Vol 32 (1) ◽  
pp. 201-208 ◽  
Author(s):  
Carla Bertechini Faria ◽  
Giovana Caputo Almeida-Ferreira ◽  
Karina Bertechine Gagliardi ◽  
Tatiane Cristina Albuquerque Alves ◽  
Dauri José Tessmann ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Fusarium Graminearum ◽  
Genomic Dna ◽  
Solid Medium ◽  
Food Contamination ◽  
Chain Reaction ◽  
Specific Pcr ◽  
Culture Characteristics ◽  
Mycotoxigenic Fungi ◽  
Polymerase Chain

The detection of mycotoxigenic fungi in foodstuff is important because their presence may indicate the possible associated mycotoxin contamination. Fusarium graminearum is a wheat pathogen and a producer of micotoxins. The polymerase chain reaction (PCR) has been employed for the specific identification of F. graminearum. However, this methodology has not been commonly used for detection of F. graminearum in food. Thus, the objective of the present study was to develop a molecular methodology to detect F. graminearum in commercial samples of bulgur wheat. Two methods were tested. In the first method, a sample of this cereal was contaminated with F. graminearum mycelia. The genomic DNA was extracted from this mixture and used in a F. graminearum specific PCR reaction. The F. graminearum species was detected only in samples that were heavily contaminated. In the second method, samples of bulgur wheat were inoculated on a solid medium, and isolates having F. graminearum culture characteristics were obtained. The DNA extracted from these isolates was tested in F. graminearum specific PCR reactions. An isolate obtained had its trichothecene genotype identified by PCR. The established methodology could be used in surveys of food contamination with F. graminearum.

Human papillomavirus typing with GP5+/6+ polymerase chain reaction reverse line blotting and with commercial type-specific PCR kits

2006 ◽  
Vol 36 (2) ◽  
pp. 126-132 ◽  
Author(s):  
Anna Gillio-Tos ◽  
Laura De Marco ◽  
Valeria Ghisetti ◽  
Peter J.F. Snijders ◽  
Nereo Segnan ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Human Papillomavirus ◽  
Chain Reaction ◽  
Reverse Line Blotting ◽  
Specific Pcr ◽  
Polymerase Chain

scholarly journals Variation in the caprine keratin-associated protein 15-1 (KAP15-1) gene affects cashmere fibre diameter

2019 ◽  
Vol 62 (1) ◽  
pp. 125-133 ◽  
Author(s):  
Mengli Zhao ◽  
Huitong Zhou ◽  
Jon G. H. Hickford ◽  
Hua Gong ◽  
Jiqing Wang ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Fibre Diameter ◽  
Kidney Tissue ◽  
Single Strand Conformation Polymorphism ◽  
Hair Follicles ◽  
Pcr Analysis ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Association Analyses ◽  
Polymerase Chain

Abstract. Keratin-associated proteins (KAPs) are a structural component of cashmere fibre, and variation in some KAP genes (KRTAPs) has been associated with a number of caprine fibre traits. In this study, we report the identification of KRTAP15-1 in goats. Sequence variation in the gene was detected using the polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) technique in 250 Longdong goats, and six variants (named A to F) containing eight single nucleotide polymorphisms (SNPs) were identified. Five of the SNPs were non-synonymous and would lead to putative amino acid changes. Reverse-transcription polymerase chain reaction (RT-PCR) analysis revealed that KRTAP15-1 was expressed in secondary hair follicles but not in heart tissue, liver tissue, lung tissue, kidney tissue or the longissimus dorsi muscle. Despite being rich in cysteine, the caprine KAP15-1 protein possesses a high content of serine and moderate content of glycine and phenylalanine. Association analyses revealed that KRTAP15-1 variant A was associated with decreased mean fibre diameter (MFD), and this effect appeared to be dominant; while variant C was found to be associated with increased MFD, the effect being recessive. The findings suggest that caprine KRTAP15-1 is highly polymorphic and that variation in this gene affects cashmere MFD.

Direct sequencing analysis of transmembrane region of human neu gene by polymerase chain reaction

2006 ◽  
Vol 3 (4) ◽  
pp. 198-201 ◽  
Author(s):  
Hideyuki Saya ◽  
Seiji Ara ◽  
Polly S. Y. Lee ◽  
Jungsil Ro ◽  
Mien-Chie Hung
Keyword(s):  
Polymerase Chain Reaction ◽  
Direct Sequencing ◽  
Sequencing Analysis ◽  
Transmembrane Region ◽  
Chain Reaction ◽  
Polymerase Chain

scholarly journals Multiplex-Polymerase Chain Reaction Assay for the Authentication of the Mackerel Scomber colias in Commercial Canned Products

2006 ◽  
Vol 89 (3) ◽  
pp. 708-711 ◽  
Author(s):  
Carlos Infante ◽  
Manuel Manchado
Keyword(s):  
Polymerase Chain Reaction ◽  
Multiplex Polymerase Chain Reaction ◽  
Rrna Gene ◽  
Chain Reaction ◽  
Nontranscribed Spacer ◽  
Specific Pcr ◽  
Scomber Colias ◽  
Pcr Product ◽  
Polymerase Chain ◽  
Specific Fragment

Abstract A multiplex-polymerase chain reaction (PCR) system was developed for the authentication of the mackerel Scomber colias in commercial canned products. This novel method consists of an S. colias-specific fragment [159 base pairs (bp)] located in the nontranscribed spacer (NTS) sequence, and a Scomber genus-specific PCR product in the 5S rRNA gene (196201 bp) as a positive amplification control. The system was assayed using 18 different canned products labeled as S. colias. A positive identification was made in all but one sample, revealing this methodology as a potential molecular tool for direct application in the authentication of S. colias canned products.

Polymorphisms of LHβ and GnRHR genes and their association with the number of embryos recovered in goats

2014 ◽  
Vol 54 (8) ◽  
pp. 987 ◽  
Author(s):  
M. Z. Fu ◽  
G. Li ◽  
Z. Q. Zhou
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Nucleotide Polymorphisms ◽  
Gene Polymorphism ◽  
Corpus Luteum ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Single Strand Conformational Polymorphism ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Polymerase Chain

The objective of the present study was to explore a predictor of superovulation response on the basis of associations between the number of embryos recovered and gene polymorphism. Variation in the goat LHβ and GnRHR genes was investigated using polymerase chain reaction–single-strand conformational polymorphism and DNA sequencing. Two single nucleotide polymorphisms (SNPs) were identified in the 5′-UTR of LHβ gene (A59C, P1 locus) and in the Exon 2 of GnRHR gene (T177A, P6 locus). At the P1 locus in both breeds, the frequencies of one allele were 0.46 and 0.51, respectively. At the P6 locus, the minor allele frequency was 0.23. Associations of both SNPs with the number of embryos recovered and the corpus luteum number were evaluated in Boer and Shaanbei goat breeds. Association analysis showed that both SNPs had significant (P < 0.05) effects on the number of embryos recovered and corpus luteum number. These results indicate that LHβ and GnRHR genes are potential markers for the number of embryos recovered.

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