scholarly journals Parallel implementation of the primer search algorithm for loop-mediated isothermal amplification

2021 ◽  
Vol 2131 (2) ◽  
pp. 022004
Author(s):  
L U Akhmetzianova ◽  
T M Davletkulov ◽  
I M Gubaidullin ◽  
A R Islamgulov
Keyword(s):  
Dna Sequence ◽  
Parallel Implementation ◽  
Search Algorithm ◽  
Isothermal Amplification ◽  
Parallel Search ◽  
Specific Primers ◽  
Loop Mediated Isothermal Amplification ◽  
Search Result

Abstract In the paper, the implementation of an algorithm of search for primers in a DNA sequence with a size varying between one nucleotide and multiple million nucleotides was discussed. This analysis was done within the objective of finding a set of six specific primers that are used for a conduction of the loop-mediated isothermal amplification (LAMP). For the fastest search result possible, a parallel search for the primer with the use of the Rabin-Karp Algorithm which enables the search for a primer’s entry in DNA sequence in each thread was proposed. A new software for search for primers was developed using Python with BioPython library which implements the algorithm.

scholarly journals Loop-Mediated Isothermal Amplification for Detection ofStaphylococcus aureusin Dairy Cow Suffering from Mastitis

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Zhang Tie ◽  
Wang Chunguang ◽  
Wei Xiaoyuan ◽  
Zhao Xinghua ◽  
Zhong Xiuhui
Keyword(s):  
Staphylococcus Aureus ◽  
High Sensitivity ◽  
High Specificity ◽  
Isothermal Amplification ◽  
Lamp Method ◽  
Specific Primers ◽  
Loop Mediated Isothermal Amplification ◽  
Reaction Tube ◽  
Specificity And Sensitivity ◽  
Detectable Concentration

To develop a rapid detection method ofStaphylococcus aureususing loop-mediated isothermal amplification (LAMP), four specific primers were designed according to six distinct sequences of thenucgene. In addition, the specificity and sensitivity of LAMP were verified and compared with those of PCR. Results showed that the LAMP reaction was completed within 45 min at 62.5°C, and ladder bands were appeared in LAMP products analyzed by gel electrophoresis. After adding 1x SYBR Green l, the positive reaction tube showed green color and the negative reaction tube remained orange, indicating that the LAMP has high specificity. The minimal detectable concentration of LAMP was1×102 CFU/mL and that of PCR was1×104 CFU/mL, indicating that the LAMP was 100 times more sensitive than the PCR. The LAMP method for detection ofStaphylococcus aureushas many advantages, such as simple operation, high sensitivity, high specificity, and rapid analysis. Therefore, this method is more suitable for the rapid on-site detection ofStaphylococcus aureus.

scholarly journals Earlyin plantadetection ofXanthomonas axonopodispv.punicaein pomegranate using enhanced loop-mediated isothermal amplification assay

2018 ◽  
Author(s):  
M.K. PrasannaKumar ◽  
P. Buela Parivallal ◽  
C. Manjunath ◽  
H.B. Mahesh ◽  
Karthik S Narayan ◽  
...  
Keyword(s):  
Post Infection ◽  
Bacterial Blight ◽  
Lamp Assay ◽  
Isothermal Amplification ◽  
Economic Losses ◽  
Specific Primers ◽  
Loop Mediated Isothermal Amplification ◽  
Negative Results ◽  
Hydroxynaphthol Blue ◽  
Amplification Assay

AbstractBacterial blight in pomegranate caused byXanthomonas axonopodispv.punicae(Xap) is an increasing threat for pomegranate cultivation in India. To prevent the economic losses, it is pivotal to detect the infection in latent stages rather than in later stages. We have developed an enhanced method termed as loop-mediated isothermal amplification (LAMP) technique to evaluate for the latent detection of Xap in pomegranate using six set of specific primers. Three DNA intercalating dyes were used, such as Ethidium bromide, hydroxynaphthol blue (HNB) and SYBR Green resulted in visualising the positivity for LAMP assay. The reaction time and temperature were to be 65°C from 30 min onwards, for the dyes and its sensitivity was observed up to 10−7ng in the LAMP assay. For field applicability, LAMP assay detected Xap on 7thday post infection while the PCR amplified Xap after 11thday post infection. Finally, the specificity of LAMP assay was validated to be positive with ten Xap isolates for its accuracy and 29 non-Xap bacterial isolates showed negative results. Moreover, this method could be used as a better alternative to PCR based methods, for early detection of the pathogens.

scholarly journals Loop-Mediated Isothermal Amplification as a Simple Molecular Method for the Detection of Derzsy’s Disease Virus

2013 ◽  
Vol 57 (1) ◽  
pp. 19-23 ◽  
Author(s):  
Karolina Tarasiuk ◽  
Grzegorz Woźniakowski ◽  
Elżbieta Samorek-Salamonowicz
Keyword(s):  
Disease Virus ◽  
Isothermal Amplification ◽  
Optimum Temperature ◽  
Molecular Method ◽  
Specific Primers ◽  
Loop Mediated Isothermal Amplification ◽  
Specific Assay ◽  
Goose Parvovirus

Abstract The objective of the study was to develop a simple and rapid molecular method for the detection of GPV. Twenty seven goose parvovirus (GPV) isolates collected from geese flocks in Poland were examined. Three pairs of specific primers: two outer primers (F3 and B3), two inner primers (FIP and BIP), and two loop primers (FL and BL) were used to accelerate the reaction. The optimum temperature and time of the reaction were 60°C and 30 min. The sensitivity of the method was 10-times higher than PCR. The method proved to be a sensitive, rapid, and specific assay for detecting GPV.

Detection of Pythium aphanidermatum in tomato using loop-mediated isothermal amplification (LAMP) with species-specific primers

2013 ◽  
Vol 136 (4) ◽  
pp. 689-701 ◽  
Author(s):  
Shiro Fukuta ◽  
Reiko Takahashi ◽  
Satoru Kuroyanagi ◽  
Noriyuki Miyake ◽  
Hirofumi Nagai ◽  
...  
Keyword(s):  
Pythium Aphanidermatum ◽  
Isothermal Amplification ◽  
Specific Primers ◽  
Loop Mediated Isothermal Amplification ◽  
Species Specific

scholarly journals Metode Loop-Mediated Isothermal Amplification (LAMP) dan Aplikasinya untuk Deteksi Penyakit Ikan

2006 ◽  
Vol 8 (1) ◽  
pp. 1
Author(s):  
Murwantoko Murwantoko
Keyword(s):  
Isothermal Condition ◽  
Isothermal Amplification ◽  
Lamp Method ◽  
Fish Pathogens ◽  
Specific Primers ◽  
Molecular Biology Technique ◽  
Loop Mediated Isothermal Amplification ◽  
Target Dna ◽  
Polymerase Chain ◽  
Short Time

Polymerase chain reaction (PCR) is a method that amplifies DNA which have been widely used in molecular biology technique. Based on the PCR, many methods have been developed on isothermal condition and the useful one is loop-mediated isothermal amplification of DNA (LAMP). LAMP reaction employs a Bst DNA polymerase and a set of four specific primers that recognizes a total of six distinct sequences of the target DNA and produces amount of different size of DNA. Many advantages have been achieved in LAMP such as the simple equipment for reaction and observation, short time, highly specific and sensitive procedure. LAMP has been used as a tools for detection many pathogens for human, animals and plants. Some fish pathogens as parasites, bacteria and viruses have been detected by LAMP. The principles and application of LAMP method are discussed in this paper.

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