The development of diagnostic PCR primers for Cryptosporidium using RAPD-PCR

1996 ◽  
Vol 77 (1) ◽  
pp. 103-108 ◽  
Author(s):  
U Morgan
Keyword(s):  
Pcr Primers ◽  
Diagnostic Pcr ◽  
Rapd Pcr

scholarly journals CeMbio - The Caenorhabditis elegans Microbiome Resource

2020 ◽  
Vol 10 (9) ◽  
pp. 3025-3039 ◽  
Author(s):  
Philipp Dirksen ◽  
Adrien Assié ◽  
Johannes Zimmermann ◽  
Fan Zhang ◽  
Adina-Malin Tietje ◽  
...  
Keyword(s):  
Life History ◽  
Caenorhabditis Elegans ◽  
Meta Analysis ◽  
Microbial Community Composition ◽  
Network Models ◽  
Pcr Primers ◽  
Diagnostic Pcr ◽  
C Elegans ◽  
Natural Choice ◽  
Gnotobiotic Mice

Abstract The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.

scholarly journals Genomic Analysis of Blastocystis hominisStrains Isolated from Two Long-Term Health Care Facilities

2000 ◽  
Vol 38 (4) ◽  
pp. 1324-1330 ◽  
Author(s):  
Hisao Yoshikawa ◽  
Niichiro Abe ◽  
Mizue Iwasawa ◽  
Syoko Kitano ◽  
Isao Nagano ◽  
...  
Keyword(s):  
Health Care ◽  
Dna Analysis ◽  
Pcr Primers ◽  
Health Care Facilities ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Blastocystis Hominis ◽  
Diagnostic Pcr ◽  
Care Facilities

The genotype Blastocystis hominis is highly polymorphic. Therefore, a genetic marker would be a powerful tool for the identification or classification of B. hominis subtypes and could be used as a means to resolve the transmission route or origin of the parasite. To this end, 32 B. hominis isolates were collected from patients and/or staff members of two long-term health care facilities (facilities A and B), and these organisms were subjected to genotype analysis based on diagnostic PCR primers and restriction fragment length polymorphism (RFLP) of small subunit rRNA gene (rDNA). Based on PCR amplification using diagnostic primers which were developed from randomly amplified polymorphic DNA analysis of known strains of B. hominis, the 32 isolates of B. hominis were classified into three different subtypes. Thirty isolates, including twenty-four that were isolated from patients and a staff member, from facility A and all isolates isolated from six patients from facility B showed the same genotype. Two of six patients of facility B had been transferred from facility A, and these two patients also had the same-genotype B. hominis that corresponded to 24 isolates from facility A. This genotype strain may have been transmitted by these two patients from facility A to facility B, suggesting human-to-human transmission. In contrast, 2 of 26 isolates from facility A showed distinct genotypes, suggesting that the colonization by these two isolates is attributable to another infectious route. These different subtypes were subjected to RFLP analysis, and the RFLP profiles were correlated with the results obtained by diagnostic PCR primers. This study presents the first molecular evidence of possible human-to-human B. hominisinfection between and/or among two small communities.

scholarly journals The development of a novel diagnostic PCR for Madurella mycetomatis using a comparative genome approach

2020 ◽  
Vol 14 (12) ◽  
pp. e0008897
Author(s):  
Wilson Lim ◽  
Emmanuel Siddig ◽  
Kimberly Eadie ◽  
Bertrand Nyuykonge ◽  
Sarah Ahmed ◽  
...  
Keyword(s):  
Diagnostic Marker ◽  
Pcr Primers ◽  
Protein Coding ◽  
Diagnostic Pcr ◽  
Comparative Genome ◽  
Specific Pcr ◽  
Causative Agents ◽  
Madurella Mycetomatis ◽  
Species Specific ◽  
A New Species

Background Eumycetoma is a neglected tropical disease most commonly caused by the fungus Madurella mycetomatis. Identification of eumycetoma causative agents can only be reliably performed by molecular identification, most commonly by species-specific PCR. The current M. mycetomatis specific PCR primers were recently discovered to cross-react with Madurella pseudomycetomatis. Here, we used a comparative genome approach to develop a new M. mycetomatis specific PCR for species identification. Methodology Predicted-protein coding sequences unique to M. mycetomatis were first identified in BLASTCLUST based on E-value, size and presence of orthologues. Primers were then developed for 16 unique sequences and evaluated against 60 M. mycetomatis isolates and other eumycetoma causing agents including the Madurella sibling species. Out of the 16, only one was found to be specific to M. mycetomatis. Conclusion We have discovered a predicted-protein coding sequence unique to M. mycetomatis and have developed a new species-specific PCR to be used as a novel diagnostic marker for M. mycetomatis.

Differentiation of Potato virus Y strains using improved sets of diagnostic PCR-primers

2007 ◽  
Vol 140 (1-2) ◽  
pp. 66-74 ◽  
Author(s):  
Jörg Schubert ◽  
Victoria Fomitcheva ◽  
Joana Sztangret-Wiśniewska
Keyword(s):  
Potato Virus ◽  
Potato Virus Y ◽  
Pcr Primers ◽  
Diagnostic Pcr

The detection of Trichinella with polymerase chain reaction (PCR) primers constructed using sequences of random amplified polymorphic DNA (RAPD) or sequences of complementary DNA encoding excretory–secretory (E–S) glycoproteins

Parasitology ◽  
1998 ◽  
Vol 117 (2) ◽  
pp. 173-183 ◽  
Author(s):  
Z. WU ◽  
I. NAGANO ◽  
Y. TAKAHASHI
Keyword(s):  
Trichinella Spiralis ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Primers ◽  
Dna Encoding ◽  
Diagnostic Pcr ◽  
Complementary Dna ◽  
Trichinella Pseudospiralis ◽  
Secretory Glycoproteins ◽  
Polymerase Chain ◽  
Different Strains

Diagnostic PCR primers for Trichinella were constructed. Twelve pairs of primers were designed based on the sequences of random amplified polymorphic DNA, and 4 pairs of primers were designed based on the reported sequences of complementary DNA encoding excretory–secretory glycoproteins. With these primers, 31 samples of DNA from different strains of Trichinella including 5 species (Trichinella spiralis, Trichinella britovi, Trichinella nativa, Trichinella nelsoni and Trichinella pseudospiralis) and 3 phenotypes of uncertain taxonomic level (Trichinella T5, T6 and T8) were tested with PCR. Genus Trichinella can be identified by 4 different primer pairs (SB147D, SB372A, SB153, or Ts43). Trichinella spiralis can be identified by the presence of a 673 bp amplicon in PCR with the primer pair SB147B. Trichinella nelsoni can be identified using primer pair SB147F or by the presence of 673 bp and ca. 380 bp amplicon in PCR with the primer pair SB147B. Trichinella pseudospiralis can be identified by 2 primer pairs (SB147E or SB372B). Trichinella T5 can be identified by the primer pair SB147G. Trichinella T8 can be identified by its positivity by the primer pair SB147C and its negativity by the primer pair SB372C. A group of Trichinella species (T. britovi, T. nativa and Trichinella T6) can be identified by the primer pair SB372C.

scholarly journals CeMbio - The C. elegans microbiome resource

2020 ◽  
Author(s):  
Philipp Dirksen ◽  
Adrien Assié ◽  
Johannes Zimmermann ◽  
Fan Zhang ◽  
Adina-Malin Tietje ◽  
...  
Keyword(s):  
Life History ◽  
Meta Analysis ◽  
Microbial Community Composition ◽  
Network Models ◽  
Pcr Primers ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Diagnostic Pcr ◽  
C Elegans ◽  
Natural Choice

ABSTRACTThe study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g. human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.Dataset accession numbersWhole genome sequencing data (PRJNA624308); microbiome sequencing [PRJEB37101 and PRJEB37035]; data supplement on the GSA Figshare Portal.

scholarly journals Fur: Find unique genomic regions for diagnostic PCR

2021 ◽  
Author(s):  
Bernhard Haubold ◽  
Fabian Klötzl ◽  
Lars Hellberg ◽  
Daniel Thompson ◽  
Markus Cavalar
Keyword(s):  
Similarity Search ◽  
Pcr Primers ◽  
The Other ◽  
Supplementary Information ◽  
Lactobacillus Species ◽  
Diagnostic Pcr ◽  
Specific Pcr ◽  
The Many ◽  
Genomic Regions

Abstract Motivation Unique marker sequences are highly sought after in molecular diagnostics. Nevertheless, there are only few programs available to search for marker sequences, compared to the many programs for similarity search. We therefore wrote the program Fur for Finding Unique genomic Regions. Results Fur takes as input a sample of target sequences and a sample of closely related neighbors. It returns the regions present in all targets and absent from all neighbors. The recently published program genmap can also be used for this purpose and we compared it to fur. When analyzing a sample of 33 genomes representing the major phylogroups of E.coli, fur was 40 times faster than genmap but used three times more memory. On the other hand, genmap yielded three times more markers, but they were less accurate when tested in silico on a sample of 237 E.coli genomes. We also designed phylogroup-specific PCR primers based on the markers proposed by genmap and fur, and tested them by analyzing their virtual amplicons in GenBank. Finally, we used fur to design primers specific to a Lactobacillus species, and found excellent sensitivity and specificity in vitro. Availability and implementation Fur sources and documentation are available from https://github.com/evolbioinf/fur. The compiled software is posted as a docker container at https://hub.docker.com/r/haubold/fox. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals A PCR-Based Assay by Sequence-Characterized DNA Markers for the Identification and Detection of Aphanomyces euteiches

2000 ◽  
Vol 90 (10) ◽  
pp. 1137-1144 ◽  
Author(s):  
G. J. Vandemark ◽  
J. M. Kraft ◽  
R. C. Larsen ◽  
M. A. Gritsenko ◽  
W. L. Boge
Keyword(s):  
Dna Markers ◽  
Pcr Primers ◽  
Single Step ◽  
Aphanomyces Euteiches ◽  
Diagnostic Pcr ◽  
Trial Site ◽  
Pcr Product ◽  
Multiplex Reaction ◽  
Pcr Products ◽  
Time Required

Polymerase chain reaction (PCR) products were identified and amplified from isolates of Aphanomyces euteiches and A. cochlioides. The products were cloned and sequenced, and the data were used to design pairs of extended PCR primers to amplify sequence-characterized DNA markers. The primer pair OPC7-FS-30 and OPC7-RS-25 amplified a single 1,332-bp product from all isolates of A. euteiches that were not amplified from any other isolates tested. A single 718-bp product was selectively amplified only from isolates of A. cochlioides with the primer pair OPB10-FS-25 and OPB10-RS-25. A. euteiches was detected in roots of several varieties of field-grown peas collected from a root rot trial site. PCR also detected A. euteiches in the organic fraction of field soil samples. Both pairs of extended primers were used in a multiplex reaction to unambiguously discriminate between A. euteiches and A. cochlioides. Both pairs of primers were used in two-step PCR reactions in which annealing and extension was done in a single step at 72°C. This reduced the time required for amplification of the diagnostic PCR product and its resolution by electrophoresis to less than 3 h.

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