scholarly journals Pengembangan Set Multipleks Penanda DNA Mikrosatelit untuk Analisis Variasi Genetik Padi dan Kedelai

2016 ◽  
Vol 5 (2) ◽  
pp. 57
Author(s):  
Chaerani Chaerani ◽  
Nurul Hidayatun ◽  
Dwinita W. Utami
Keyword(s):  
Fluorescent Dyes ◽  
Size Range ◽  
Detection System ◽  
Pcr Amplification ◽  
Specific Primers ◽  
Allele Size ◽  
Universal Primer ◽  
Allele Size Range ◽  
Capillary Array ◽  
Microsatellite Multiplex

<p>Detection of multiplex microsatellite markers in a<br />single capillary array on a laser detection system is traditionally<br />conducted with specific primers that are labelled with<br />fluorescent dyes. An alternative method using fluorescent<br />labels that are appended to 5’ end of universal primer M13<br />instead of to the specific primers offers flexibility in<br />designning multiplex panels and a less expensive method.<br />Allele size range of microsatellite loci that can be grouped in<br />multiplex panels can be accurately estimated by pooling and<br />analyzing DNA samples from several genotypes simultaneously.<br />This paper describes the procedure in development<br />of microsatellite multiplex panels using M13 fluorescentlylabelled<br />and estimation of allele size range based on pooled<br />DNA strategies. Two multiplex panels of PCR amplification<br />products for rice consisting of 15 loci and three panels for<br />soybean consisting of 10 loci have been designed. The<br />panels have been applied to 50 accessions of rice and soybean<br />with fairly good results. Further characterization of<br />allele size range, however, is required prior to the application<br />of these panels to diverse genotypes. The procedure<br />described here should be applicable in the development of<br />multiplex panels of other species.</p>

scholarly journals Molecular characterization and morphological clustering of exotic early maturing rice (Oryza sativa L.) lines

2014 ◽  
Vol 11 (2) ◽  
pp. 233-240 ◽  
Author(s):  
MM Sarker ◽  
L Hassan ◽  
MM Rashid ◽  
S Seraj
Keyword(s):  
Oryza Sativa ◽  
Size Range ◽  
Oryza Sativa L ◽  
Gene Diversity ◽  
Allele Size ◽  
Upgma Dendrogram ◽  
Allele Size Range ◽  
Early Maturing ◽  
Positive Correlations ◽  
Simple Sequence

Characterization and variability analysis is important for the improvement of crop plant. This study aimed to evaluate the morphological and molecular variation of exotic early maturing rice (Oryza sativa L.) lines. A total of 32 exotic rice lines collected from different locations were genotyped and clustered using selected SSR markers. Based on morphological dendrogram, the lines were grouped into three clusters viz.I, II and III. Cluster I, cluster II and cluster III had 12, 11, 9 lines respectively. The results showed that the varieties were closely related belonging to the same cluster. DNA Markers namely Simple Sequence Repeats (SSR) is a useful tool for assessing genetic variations and resolving cultivar identities. Positive correlations were found between gene diversity, number of allele, the allele size range and the maximum number of repeats. Among the primers used RM147 identified more number of alleles and average PIC was 0.88. The UPGMA dendrogram based on Nei’s (1972) genetic distance grouped the 32 rice lines into three major clusters. This result indicates that the line which formed grouped together, they are less diverse. A significant level of polymorphism based on morphological and molecular levels was observed. Being grouped into three clusters C1-4-11-7P-2P-1P and IR 79201-49-1-1-1 could be utilized as potential parents for the improvement of yield in early maturing rice lines. DOI: http://dx.doi.org/10.3329/jbau.v11i2.19900 J. Bangladesh Agril. Univ. 11(2): 233-240, 2013

scholarly journals Cross-Kingdom Amplification Using Bacteria-Specific Primers: Complications for Studies of Coral Microbial Ecology

2008 ◽  
Vol 74 (24) ◽  
pp. 7828-7831 ◽  
Author(s):  
Julia P. Galkiewicz ◽  
Christina A. Kellogg
Keyword(s):  
Microbial Ecology ◽  
Pcr Amplification ◽  
Rrna Genes ◽  
Specific Primers ◽  
Universal Primer ◽  
Bacterial Dna ◽  
Bacterial Interactions

ABSTRACT PCR amplification of pure bacterial DNA is vital to the study of bacterial interactions with corals. Commonly used Bacteria-specific primers 8F and 27F paired with the universal primer 1492R amplify both eukaryotic and prokaryotic rRNA genes. An alternative primer set, 63F/1542R, is suggested to resolve this problem.

scholarly journals Applicability of human-specific STR systems, GlobalFiler™ PCR Amplification Kit, Investigator 24plex QS Kit, and PowerPlex® Fusion 6C in chimpanzee (Pan troglodytes)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Abhishek Singh ◽  
Vivek Sahajpal ◽  
Mukesh Thakur ◽  
Lalit Kumar Sharma ◽  
Kailash Chandra ◽  
...  
Keyword(s):  
Population Genetics ◽  
Pan Troglodytes ◽  
Human Population ◽  
Pcr Amplification ◽  
Forensic Analysis ◽  
Cross Reactivity ◽  
Allele Size ◽  
Male And Female ◽  
Successful Amplification ◽  
Human Specific

Abstract Objectives Human identification systems based on STRs are widely used in human population genetics and forensic analysis. This study aimed to validate the cross-reactivity of three widely known human-specific STR identification systems i.e. GlobalFiler™ PCR Amplification Kit, Investigator 24plex QS Kit, and PowerPlex® Fusion 6C in chimpanzee. Results The present study revealed the successful amplification of 18 loci using GlobalFiler™ PCR Amplification Kit, 18 loci using Investigator 24plex QS Kit, and 20 loci using PowerPlex® Fusion 6C system. The marker Amelogenin (AMEL) showed differential allele size between male and female revealing the gender identity of chimpanzees and thus validates their application concerning forensic examination, population estimation, and genetic analysis.

Organization, Expression and Evolution of a Disease Resistance Gene Cluster in Soybean

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1961-1977
Author(s):  
Michelle A Graham ◽  
Laura Fredrick Marek ◽  
Randy C Shoemaker
Keyword(s):  
Disease Resistance ◽  
Resistance Gene ◽  
Resistance Genes ◽  
Developmental Stages ◽  
Gene Evolution ◽  
Pcr Amplification ◽  
Disease Resistance Genes ◽  
Disease Resistance Gene ◽  
R Genes ◽  
Specific Primers

Abstract PCR amplification was previously used to identify a cluster of resistance gene analogues (RGAs) on soybean linkage group J. Resistance to powdery mildew (Rmd-c), Phytophthora stem and root rot (Rps2), and an ineffective nodulation gene (Rj2) map within this cluster. BAC fingerprinting and RGA-specific primers were used to develop a contig of BAC clones spanning this region in cultivar “Williams 82” [rps2, Rmd (adult onset), rj2]. Two cDNAs with homology to the TIR/NBD/LRR family of R-genes have also been mapped to opposite ends of a BAC in the contig Gm_Isb001_091F11 (BAC 91F11). Sequence analyses of BAC 91F11 identified 16 different resistance-like gene (RLG) sequences with homology to the TIR/NBD/LRR family of disease resistance genes. Four of these RLGs represent two potentially novel classes of disease resistance genes: TIR/NBD domains fused inframe to a putative defense-related protein (NtPRp27-like) and TIR domains fused inframe to soybean calmodulin Ca2+-binding domains. RT-PCR analyses using gene-specific primers allowed us to monitor the expression of individual genes in different tissues and developmental stages. Three genes appeared to be constitutively expressed, while three were differentially expressed. Analyses of the R-genes within this BAC suggest that R-gene evolution in soybean is a complex and dynamic process.

scholarly journals Specific DNA identification of Pheretima in the Naoxintong capsule

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
Xiaoxiao Zhu ◽  
Hoi-Yan Wu ◽  
Pang-Chui Shaw ◽  
Wei Peng ◽  
Weiwei Su
Keyword(s):  
Pcr Amplification ◽  
Cerebrovascular Diseases ◽  
Coi Gene ◽  
Chemical Marker ◽  
Dna Identification ◽  
Specific Primers ◽  
Blast Search ◽  
Pcr Products ◽  
Crude Drugs ◽  
Nucleotide Database

Abstract Background Pheretima is a minister drug in Naoxintong capsule (NXTC), a well-known traditional Chinese medicine (TCM) formula for the treatment of cardiovascular and cerebrovascular diseases. Owing to the loss of morphological and microscopic characteristics and the lack of recognized chemical marker, it is difficult to identify Pheretima in NXTC. This study aims to evaluate the feasibility of using DNA techniques to authenticate Pheretima, especially when it is processed into NXTC. Methods DNA was extracted from crude drugs of the genuine and adulterant species, as well as nine batches of NXTCs. Based on mitochondrial cytochrome c oxidase subunit I (COI) gene, specific primers were designed for two genera of genuine species, Metaphire and Amynthas, respectively. PCR amplification was performed with the designed primers on crude drugs of Pheretima and NXTCs. The purified PCR products were sequenced and the obtained sequences were identified to species level with top hit of similarity with BLAST against GenBank nucleotide database. Results Primers MF2R2 and AF3R1 could amplify specific DNA fragments with sizes around 230–250 bp, both in crude drugs and NXTC. With sequencing and the BLAST search, identities of the tested samples were found. Conclusion This study indicated that the molecular approach is effective for identifying Pheretima in NXTC. Therefore, DNA identification may contribute to the quality control and assurance of NXTC.

Automation of HLA class II genotyping by PCR amplification with sequence-specific primers

1994 ◽  
Vol 39 (2) ◽  
pp. 141
Author(s):  
P. Merel ◽  
F. Comeau ◽  
B. Dupin ◽  
R. Destrebecq ◽  
G. Vezon
Keyword(s):  
Pcr Amplification ◽  
Class Ii ◽  
Hla Class Ii ◽  
Specific Primers

Hardware Design for Multiple Gas Detection System Using Zeolite Coated with Nile Red

2011 ◽  
Vol 2011 (1) ◽  
pp. 000861-000867
Author(s):  
Son Nguyen ◽  
Z. Joan Delalic ◽  
David M. Kargbo ◽  
Joel B. Sheffield ◽  
Zameer Hasan
Keyword(s):  
Fluorescent Dyes ◽  
Detection System ◽  
Nile Red ◽  
Sensor Arrays ◽  
Gas Absorption ◽  
Fully Integrated ◽  
Vlsi Chip ◽  
Dye Sensing ◽  
Different Gases ◽  
Nanoporous Structures

The goal of this research is to develop a nanosensor that integrates a zeolite/dye sensing unit with an optoelectronic detector, fully integrated into a portable gas sensor. The device will detect and measure more than one target gas at the same time. Since nanoporous structures of zeolites are manipulated, the device is expected to be more accurate, more sensitive, is able to better differentiate and detect any one target in a mixture of different gases. This is achieved by incorporating fluorescent dyes into the zeolites’ cavities, measuring gas absorption, desorption and photo-chromic interaction of dye and gases, interfacing the zeolite/dye sensor arrays with light source and electronic detectors. The electronic part of the device is fully customized VLSI chip. The final device will be packaged into a portable unit. The designed and packaged prototype will be presented.

scholarly journals Field and Laboratory Methods for DNA Studies on Deep-sea Isopod Crustaceans

2014 ◽  
Vol 35 (2) ◽  
pp. 203-224 ◽  
Author(s):  
Torben Riehl ◽  
Nils Brenke ◽  
Saskia Brix ◽  
Amy Driskell ◽  
Stefanie Kaiser ◽  
...  
Keyword(s):  
Deep Sea ◽  
Pcr Amplification ◽  
The Other ◽  
Universal Primers ◽  
Success Rates ◽  
Specific Primers ◽  
Scientific Publications ◽  
Cycle Sequencing ◽  
Laboratory Methods ◽  
Set Up

AbstractField and laboratory protocols that originally led to the success of published studies have previously been only briefly laid out in the methods sections of scientific publications. For the sake of repeatability, we regard the details of the methodology that allowed broad-range DNA studies on deep-sea isopods too valuable to be neglected. Here, a comprehensive summary of protocols for the retrieval of the samples, fixation on board research vessels, PCR amplification and cycle sequencing of altogether six loci (three mitochondrial and three nuclear) is provided. These were adapted from previous protocols and developed especially for asellote Isopoda from deep-sea samples but have been successfully used in some other peracarids as well. In total, about 2300 specimens of isopods, 100 amphipods and 300 tanaids were sequenced mainly for COI and 16S and partly for the other markers. Although we did not set up an experimental design, we were able to analyze amplification and sequencing success of different methods on 16S and compare success rates for COI and 16S. The primer pair 16S SF/SR was generally reliable and led to better results than universal primers in all studied Janiroidea, except Munnopsidae and Dendrotionidae. The widely applied universal primers for the barcoding region of COI are problematic to use in deep-sea isopods with a success rate of 45–79% varying with family. To improve this, we recommend the development of taxon-specific primers.

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