scholarly journals Electric LAMP: Virtual Loop-Mediated Isothermal AMPlification

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Nelson R. Salinas ◽  
Damon P. Little
Keyword(s):  
New York ◽  
York Botanical ◽  
Regular Expressions ◽  
Whole Genome ◽  
Graphical Interface ◽  
Genome Sequences ◽  
Perl Script ◽  
Approximate Matching ◽  
Primer Sets ◽  
Virtual Loop

We present eLAMP, a PERL script, with Tk graphical interface, that electronically simulates Loop-mediated AMPlification (LAMP) allowing users to efficiently test putative LAMP primers on a set of target sequences. eLAMP can match primers to templates using either exact (via builtin PERL regular expressions) or approximate matching (via the tre-agrep library). Performance was tested on 40 whole genome sequences of Staphylococcus. eLAMP correctly predicted that the two tested primer sets would amplify from S. aureus genomes and not amplify from other Staphylococcus species. Open source (GNU Public License) PERL scripts are available for download from the New York Botanical Garden's website.

scholarly journals Whole-Genome Sequences of 13 Endophytic Bacteria Isolated from Shrub Willow (Salix) Grown in Geneva, New York

2014 ◽  
Vol 2 (3) ◽  
Author(s):  
H. Y. Gan ◽  
H. M. Gan ◽  
M. A. Savka ◽  
A. J. Triassi ◽  
M. S. Wheatley ◽  
...  
Keyword(s):  
New York ◽  
Endophytic Bacteria ◽  
Whole Genome ◽  
Genome Sequences ◽  
Shrub Willow

scholarly journals Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Noam B. Teyssier ◽  
Anna Chen ◽  
Elias M. Duarte ◽  
Rene Sit ◽  
Bryan Greenhouse ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Dropout Rate ◽  
Dried Blood Spots ◽  
High Ratio ◽  
Low Density ◽  
Whole Genome ◽  
Cross Sectional ◽  
Modest Improvement ◽  
Primer Sets

Abstract Background Whole-genome sequencing (WGS) is becoming increasingly useful to study the biology, epidemiology, and ecology of malaria parasites. Despite ease of sampling, DNA extracted from dried blood spots (DBS) has a high ratio of human DNA compared to parasite DNA, which poses a challenge for downstream genetic analyses. The effects of multiple methods for DNA extraction, digestion of methylated DNA, and amplification were evaluated on the quality and fidelity of WGS data recovered from DBS. Methods Low parasite density mock DBS samples were created, extracted either with Tween-Chelex or QIAamp, treated with or without McrBC, and amplified with one of three different amplification techniques (two sWGA primer sets and one rWGA). Extraction conditions were evaluated on performance of sequencing depth, percentiles of coverage, and expected SNP concordance. Results At 100 parasites/μL, Chelex-Tween-McrBC samples had higher coverage (5 × depth = 93% genome) than QIAamp extracted samples (5 × depth = 76% genome). The two evaluated sWGA primer sets showed minor differences in overall genome coverage and SNP concordance, with a newly proposed combination of 20 primers showing a modest improvement in coverage over those previously published. Conclusions Overall, Tween-Chelex extracted samples that were treated with McrBC digestion and are amplified using 6A10AD sWGA conditions had minimal dropout rate, higher percentages of coverage at higher depth, and more accurate SNP concordance than QiaAMP extracted samples. These findings extend the results of previously reported methods, making whole genome sequencing accessible to a larger number of low density samples that are commonly encountered in cross-sectional surveys.

scholarly journals Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1017
Author(s):  
Hirohisa Mekata ◽  
Tomohiro Okagawa ◽  
Satoru Konnai ◽  
Takayuki Miyazawa
Keyword(s):  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Virus Family ◽  
Bovine Foamy Virus ◽  
Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

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