Towards a high reliability of the PCR amplification process in DNA computing

2002 ◽  
Author(s):  
M. Nakatsugawa ◽  
S. Kashiwamura ◽  
M. Yamamoto ◽  
T. Shiba ◽  
A. Ohuchi
Keyword(s):  
Dna Computing ◽  
High Reliability ◽  
Pcr Amplification ◽  
Amplification Process

TOWARDS A HIGH RELIABILITY OF THE PCR AMPLIFICATION PROCESS IN DNA COMPUTING

2002 ◽  
Vol 02 (04) ◽  
pp. 423-432
Author(s):  
MASASHI NAKATSUGAWA ◽  
SATOSHI KASHIWAMURA ◽  
AZUMA OHUCHI ◽  
MASAHITO YAMAMOTO ◽  
TOSHIKAZU SHIBA
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequence ◽  
Calculation Result ◽  
Dna Computing ◽  
High Reliability ◽  
Pcr Amplification ◽  
Small Concentration ◽  
Chain Reaction ◽  
Amplification Process ◽  
Polymerase Chain

Polymerase Chain Reaction (PCR) is the most important experimental technique in DNA computing. When a concentration of DNA sequence is too small to investigate, PCR amplifies the DNA sequence by the addition of a polymerase. PCR is frequently used in DNA computing, because the calculation result is usually represented by a small concentration of DNA sequence. Therefore, PCR has a crucial influence on the calculation result. The reliability of PCR needs to be improved for DNA computing. In this paper, the reliability of PCR is defined by the reproducibility of the amplified concentration of DNA sequence. The PCR protocol is adjusted to improve the reliability. Quality Engineering efficiently supports this adjustment.

Modelling the PCR amplification process by a size-dependent branching process and estimation of the efficiency

2004 ◽  
Vol 36 (2) ◽  
pp. 602-615 ◽  
Author(s):  
N. Lalam ◽  
C. Jacob ◽  
P. Jagers
Keyword(s):  
Branching Process ◽  
Good Accuracy ◽  
Critical Size ◽  
Pcr Amplification ◽  
Stochastic Modelling ◽  
Transient Phase ◽  
Size Dependent ◽  
Dna Molecule ◽  
Amplification Process

We propose a stochastic modelling of the PCR amplification process by a size-dependent branching process starting as a supercritical Bienaymé-Galton-Watson transient phase and then having a saturation near-critical size-dependent phase. This model allows us to estimate the probability of replication of a DNA molecule at each cycle of a single PCR trajectory with a very good accuracy.

scholarly journals Use of an Amplified-Fragment Length Polymorphism Technique To Fingerprint and Differentiate Isolates of Helicobacter pylori

1998 ◽  
Vol 36 (9) ◽  
pp. 2580-2585 ◽  
Author(s):  
J. R. Gibson ◽  
E. Slater ◽  
J. Xerry ◽  
D. S. Tompkins ◽  
R. J. Owen
Keyword(s):  
Helicobacter Pylori ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Pcr Amplification ◽  
Amplified Fragment Length Polymorphism ◽  
Aflp Analysis ◽  
Modified Technique ◽  
Amplification Process ◽  
H Pylori

Amplified-fragment length polymorphism (AFLP) analysis is the name given to a genotypic technique in which adapter oligonucleotides are ligated to restriction enzyme fragments and then used as target sites for primers in a PCR amplification process. The amplified fragments are electrophoretically separated to give strain-specific band profiles. We have developed a single-enzyme approach that did not require costly equipment or reagents for the fingerprinting of strains ofHelicobacter pylori. The method was assessed with 46 isolates of H. pylori from 28 patients, and the results were compared with those from other genotypic tests. The AFLP profiles derived from HindIII fragments differentiated strains ofH. pylori from unrelated individuals and confirmed the common origin of strains in some family members. AFLP analysis was also applied to investigate persistent infection following antibiotic therapy. Overall, the modified technique was relatively rapid and technically simple yet gave reproducible and discriminatory results. AFLP analysis samples variation throughout the genome and is a valuable addition to the existing genotypic fingerprinting methods for H. pylori.

scholarly journals Interference in PCR: Transcription amplifications of mixed PVY isolates

2010 ◽  
Vol 41 (No. 4) ◽  
pp. 125-131 ◽  
Author(s):  
A. Rosner ◽  
L. Maslenin
Keyword(s):  
Virus Infection ◽  
Virus Strain ◽  
Rna Synthesis ◽  
Virus Isolate ◽  
Pcr Amplification ◽  
Target Sequence ◽  
Specific Primers ◽  
Pcr Products ◽  
Amplification Process ◽  
Mixed Virus Infection

Interference in PCR and transcription amplifications by mixed virus templates is described. The yields of PCR amplification of closely related PVY isolates in a mixture were lower than those of the separate amplification of each individual virus strain, i.e. the two virus templates mutually interfered in their amplification process. When PCR products of mixed PVY isolates served as templates for transcription, RNA synthesis was also inhibited. This interference could be avoided by applying strain-specific primers in the separate amplification of each target sequence in the mixture. The use of strain-specific primers in PCR amplification of a mixed virus infection thus enabled detection of each virus isolate without interference.

scholarly journals Analisis Cemaran DNA Tikus pada Bakso Daging Sapi yang Beredar di Makassar dengan Metode Polymerase Chain Reaction (PCR)

2019 ◽  
Vol 5 (1) ◽  
pp. 93-100
Author(s):  
Aminah Aminah ◽  
Ristieyen Ramadini ◽  
Tadjuddin Naid
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Analysis ◽  
Uv Light ◽  
Pcr Amplification ◽  
Polymerase Chain Reaction Method ◽  
Chain Reaction ◽  
Reaction Method ◽  
Amplification Process ◽  
Three Stages ◽  
Polymerase Chain

Analysis of rat DNA contamination in meatball meat circulating in Makassar by PCR (Polymerase Chain Reaction) method has been carried out. In this study, a polymerase chain reaction method will be developed to analyze the presence of rat meat contamination in beef meatballs. There are three stages in the PCR amplification process carried out with 30 cycles, which are 95oC temperature denaturation, 51oC attachment, and 72oC extension. DNA analysis included agarose gel electrophoresis, measurement of concentration and purification, and analysis of rat DNA using PCR. The results of PCR amplification using mouse-specific primers namely primary ND1 (NADH dehydrogenase 1) showed no bands seen in UV light. So that it can be proven that beef meatball samples in the Makassar region did not contain rat DNA. t.  

scholarly journals Effect of POU1F1 Gene Haplotypes on Eights and Milk Production of Awassi Sheep

2019 ◽  
Vol 32 (2) ◽  
pp. 85-94
Author(s):  
Azhar A. Jaffar ◽  
Amad F. Hassan ◽  
Waleed Y. Kassim
Keyword(s):  
Statistical Analysis ◽  
Gel Electrophoresis ◽  
Pcr Amplification ◽  
Gene Bank ◽  
College Of Agriculture ◽  
Pou1f1 Gene ◽  
Nitrogen Bases ◽  
Awassi Sheep ◽  
Amplification Process ◽  
Productive Traits

The aim of the study was to detect polymorphism in the POU1F1 gene in Iraqi Awassi sheep breed, as well as to establish if haplotype of POU1F1 gene could be associated with productive traits. This study was carried out at Al-Kafeel station, Karbala city during the period of 01/10/2017 until 01/08/2018. The study included 46 Awassi ewes with their 52 lambs. The laboratory analyses were conducted at the Laboratory of Molecular Genetics, College of Agriculture, University of Basrah. Results showed the successfulness of the PCR amplification process for all six examined fragments of the POU1F1 gene. Gel electrophoresis was conducted using agarose 2%, the product sizes were 637bp, 789bp, 999bp, 868bp, 1190 bp, and 469bp for the fragments P1, P2, P3, P4, P5, and P6 respectively. The analysis of the nitrogen bases sequences of the POU1F1 gene for the studied fragments showed a change in 12 different sites of the gene. These changes resulted in 7 haplotypes of H1-H7. The results showed significant influence (P<0.05) in haplotypes of the POU1F1 gene on birth weight . However, haplotypes showed no significant effect on lambs’ weights at weaning, six months and daily weight gains during all periods. Statistical analysis showed that different haplotypes of the POU1F1 gene did not influence on milk productive traits. The examined fragments of the POU1F1 Awassi gene have been submitted to Gene Bank under the accession numbers (LC469323 to LC469349).

Modelling the PCR amplification process by a size-dependent branching process and estimation of the efficiency

2004 ◽  
Vol 36 (02) ◽  
pp. 602-615 ◽  
Author(s):  
N. Lalam ◽  
C. Jacob ◽  
P. Jagers
Keyword(s):  
Branching Process ◽  
Good Accuracy ◽  
Critical Size ◽  
Pcr Amplification ◽  
Stochastic Modelling ◽  
Transient Phase ◽  
Size Dependent ◽  
Dna Molecule ◽  
Amplification Process

We propose a stochastic modelling of the PCR amplification process by a size-dependent branching process starting as a supercritical Bienaymé-Galton-Watson transient phase and then having a saturation near-critical size-dependent phase. This model allows us to estimate the probability of replication of a DNA molecule at each cycle of a single PCR trajectory with a very good accuracy.

scholarly journals DESAIN PRIMER UNTUK AMPLIFIKASI REGIO PROMOTER GEN inhA ISOLAT P016 MULTIDRUG RESISTANCE Mycobacterium tuberculosis DENGAN METODE POLYMERASE CHAIN REACTION

2018 ◽  
pp. 34
Author(s):  
Eka Nata Sari
Keyword(s):  
Polymerase Chain Reaction ◽  
Promoter Region ◽  
Pcr Amplification ◽  
Promoter Sequence ◽  
Cross Resistance ◽  
Chain Reaction ◽  
Pcr Products ◽  
Amplification Process ◽  
Polymerase Chain

Mutations in the inhA promoter region are responsible for isoniazid resistance and cross-resistance to ethionamide. To identify mutations with polymerase chain reaction (PCR), a pair of primers that can amplify the target region. This aim of this study was to obtain the best primer pair to amplify the inhA promoter region using the Clone Manager Suite 6 program. The inhA promoter sequence (Genbank: U66801) obtained from the www.ncbi.nlm.nih.gov was used as a template. The design results obtained the best primer pair tested in vitro using Polymerase Chain Reaction (PCR) method. The PCR amplification process was performed for 40 cycles with the following conditions: predenaturase (95oC for 15 minutes), denaturation (94 oC for 1 minute), annealing (56 oC for 1 minute 30 seconds), elongation (72 oC for 2 minutes), and final elongation (72 oC for 10 minutes). Detection of PCR products was performed in agarose gel electrophoresis 1.3% w / v and visualized by UV transluminator tool. The results obtained were forward primers of 5'-GGTCGAAGTGTGCTGAGTC-3 'and reverse primer 5'-TGCTCTTCTACCGCCGTGA-3' which met the good primary criterion based on Clone Manager Suite 6. The pair of primers has been able to amplify the inhA promoter region by the length of product produced at 373 bp.

Failure Analysis With the Scanning Electron Microscope

1972 ◽  
Vol 30 ◽  
pp. 482-483
Author(s):  
John R. Devaney
Keyword(s):  
Electron Microscope ◽  
Scanning Electron Microscope ◽  
Integrated Circuits ◽  
Failure Analysis ◽  
High Reliability ◽  
Military Applications ◽  
Small Structure ◽  
Useful Life ◽  
Insight Into ◽  
Scanning Electron

Occasionally in history, an event may occur which has a profound influence on a technology. Such an event occurred when the scanning electron microscope became commercially available to industry in the mid 60's. Semiconductors were being increasingly used in high-reliability space and military applications both because of their small volume but, also, because of their inherent reliability. However, they did fail, both early in life and sometimes in middle or old age. Why they failed and how to prevent failure or prolong “useful life” was a worry which resulted in a blossoming of sophisticated failure analysis laboratories across the country. By 1966, the ability to build small structure integrated circuits was forging well ahead of techniques available to dissect and analyze these same failures. The arrival of the scanning electron microscope gave these analysts a new insight into failure mechanisms.

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