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1. Development of a PCR Kit for Detection of Coxiella burnetii in Ukraine

Author:
Lyudmyla V. Marushchak; Oleg N. Deriabin; Liudmyla Dedok; Elena Volosyanko; Tatyana Garcavenko
Source:
Vector borne and zoonotic diseases 2020 v.20 no.2 pp. 100-106
ISSN:
1557-7759
Subject:
Coxiella burnetii; DNA; DNA fragmentation; DNA primers; Q fever; World Organization for Animal Health; analytical kits; biotechnology; genes; humans; pathogens; quantitative polymerase chain reaction; Ukraine
Abstract:
... Coxiella burnetii is an obligate intracellular pathogen and the causative agent of Q fever. In Ukraine, 28 human cases of Q fever were reported between 1997 and 2006; however, there are no state-approved, standardized molecular diagnostic assays that can be used systematically to investigate C. burnetii transmission to humans and its distribution throughout Ukraine. To address this deficiency, we ...
DOI:
10.1089/vbz.2019.2518
PubMed:
31536465
PubMed Central:
PMC7041315

2. Survey for pestiviruses in backyard pigs in southern Brazil

Author:
Ana C. S. Mósena; Matheus N. Weber; Samuel P. Cibulski; Mariana S. Silva; Willian P. Paim; Gustavo S. Silva; Antônio A. Medeiros; Nathália A. Viana; Letícia F. Baumbach; Daniela E. Puhl; Simone Silveira; Luis G. Corbellini; Cláudio W. Canal
Source:
Journal of veterinary diagnostic investigation 2020 v.32 no.1 pp. 136-141
ISSN:
1943-4936
Subject:
Border disease virus; Bovine viral diarrhea virus 1; Classical swine fever virus; DNA primers; Suidae; World Organization for Animal Health; animal viruses; blood serum; herds; hosts; neutralization tests; reverse transcriptase polymerase chain reaction; ruminants; surveys; swine; swine diseases; viruses; Brazil
Abstract:
... The Pestivirus genus comprises species that affect animal health and productivity worldwide. Members of the Suidae family are hosts for classical swine fever virus (CSFV), an important pathogen tracked by the World Organization for Animal Health (OIE). However, swine are also susceptible to other pestivirus species that can result in disease or compromise CSFV detection. We searched for pestivirus ...
DOI:
10.1177/1040638719896303
PubMed:
31924139
PubMed Central:
PMC7003213

3. Truncated satratoxin gene clusters in selected isolates of the atranone chemotype of Stachybotrys chartarum (Ehrenb.) S. Hughes

Author:
Sebastian Ulrich; Ludwig Niessen; Julia Ekruth; Cornelius Schäfer; Florian Kaltner; Christoph Gottschalk
Source:
Mycotoxin research 2020 v.36 no.1 pp. 83-91
ISSN:
0178-7888
Subject:
DNA primers; Stachybotrys chartarum; animals; biosynthesis; chemotypes; construction materials; forage; fungi; herbs; hybrids; multigene family; polymerase chain reaction; trichothecenes
Abstract:
... The fungus Stachybotrys (S.) chartarum was isolated from culinary herbs, damp building materials, and improperly stored animal forage. Two distinct chemotypes of the fungus were described that produced either high-cytotoxic macrocyclic trichothecenes (S type) or low-cytotoxic atranones (A type). Recently, two distinct gene clusters were described that were found to be necessary for the biosynthesi ...
DOI:
10.1007/s12550-019-00371-x
PubMed:
31435889
PubMed Central:
PMC6971138

4. Validation of a quantitative PCR assay for the detection of 2 Flavobacterium columnare genomovars

Author:
Gordon D. Gibbs; Matthew J. Griffin; Michael J. Mauel; Mark L. Lawrence
Source:
Journal of veterinary diagnostic investigation 2020 v.32 no.3 pp. 356-362
ISSN:
1943-4936
Subject:
DNA; DNA primers; Flavobacterium columnare; Ictalurus punctatus; chondroitin; columnaris disease; etiological agents; fish; genes; kidneys; liver; quantitative polymerase chain reaction; spleen
Abstract:
... Flavobacterium columnare is the causative agent of columnaris disease in a variety of fish hosts. Using modifications to previously established protocols, a quantitative PCR (qPCR) assay was validated for the detection of 2 predominant F. columnare genomovars. The oligonucleotide primer and probe combination was designed to amplify a 203-bp region of the chondroitin AC lyase gene (GenBank AY912281 ...
DOI:
10.1177/1040638720915760
CHORUS:
10.1177/1040638720915760

5. A virome sequencing approach to feline oral squamous cell carcinoma to evaluate viral causative factors

Author:
Shirley Chu; Todd N. Wylie; Kristine M. Wylie; Gayle C. Johnson; Zachary L. Skidmore; Maren Fleer; Obi L. Griffith; Jeffrey N. Bryan
Source:
Veterinary microbiology 2020 v.240 pp. 108491
ISSN:
0378-1135
Subject:
Alphatorquevirus; DNA; DNA primers; Feline foamy virus; Human gammaherpesvirus 4; Lambdapapillomavirus 1; RNA viruses; cats; high-throughput nucleotide sequencing; humans; metagenomics; models; mucosa; polymerase chain reaction; squamous cell carcinoma
Abstract:
... Feline oral squamous cell carcinoma (FOSCC) may be the best naturally-occurring model of human head and neck squamous cell carcinoma (HNSCC). HNSCC can be broadly divided into human papillomavirus (HPV)-negative cancers and HPV-positive cancers where HPV is the causative agent. Previous studies in FOSCC have used both species-specific and species-nonspecific PCR primers that may be insensitive to ...
DOI:
10.1016/j.vetmic.2019.108491
PubMed:
31902496
PubMed Central:
PMC7117531

6. A Combination of Real-Time PCR and High-Resolution Melting Analysis to Detect and Identify CpGV Genotypes Involved in Type I Resistance

Author:
Aurélie Hinsberger; Stéphane Theulier Saint Germain; Patrice Guerrero; Christine Blachère-López; Miguel López-Ferber; Sandrine Bayle
Source:
Viruses 2019 v.11 no.8 pp. -
ISSN:
1999-4915
Subject:
Cydia pomonella; Cydia pomonella granulovirus; DNA primers; biological control; genes; genotype; insect control; larvae; melting; melting point; orchards; quantitative polymerase chain reaction; rapid methods
Abstract:
... Cydia pomonella granulovirus, in particular CpGV-M isolate, is used as a biological control against the codling moth (CM), Cydia pomonella. As a result of intensive control over the years, codling moth populations have developed resistance against this isolate. This resistance is now called type I resistance. Isolates, among them, CpGV-R5, have been found that are able to overcome type I resistanc ...
DOI:
10.3390/v11080723
PubMed:
31390849
PubMed Central:
PMC6723291

7. Comparative analysis of apicoplast genomes of Babesia infective to small ruminants in China

Author:
Xiaoxing Wang; Jinming Wang; Junlong Liu; Aihong Liu; Xin He; Jianlin Xu; Zhi Li; Shuaiyang Zhao; Youquan Li; Hong Yin; Jianxun Luo; Guiquan Guan
Source:
Parasites & vectors 2019 v.12 no.1 pp. 312
ISSN:
1756-3305
Subject:
Babesia motasi; DNA primers; DNA-directed RNA polymerase; RNA; amino acid sequences; apicoplast genome; babesiosis; biochemical pathways; bioinformatics; biosynthesis; circular DNA; computer software; drugs; fatty acids; genes; genomics; isoprenoids; open reading frames; parasites; peptide elongation factors; phylogeny; proteinases; protists; sequence analysis; sheep; China
Abstract:
... BACKGROUND: Babesiosis is an economically important disease caused by tick-borne apicomplexan protists of the genus Babesia. Most apicomplexan parasites, including Babesia, have a plastid-derived organelle termed an apicoplast, which is involved in critical metabolic pathways such as fatty acid, iron-sulphur, haem and isoprenoid biosynthesis. Apicoplast genomic data can provide significant informa ...
DOI:
10.1186/s13071-019-3581-x
PubMed:
31234937
PubMed Central:
PMC6591869

8. Detection of fish allergen by droplet digital PCR

Author:
Cinzia Daga; Simona Cau; Maria Giovanna Tilocca; Barbara Soro; Aldo Marongiu; Bruna Vodret
Source:
Italian journal of food safety 2019 v.7 no.4 pp. -
ISSN:
2239-7132
Subject:
DNA; DNA primers; allergens; annealing; comparative study; droplets; fish; genes; ingredients; polymerase chain reaction; ribosomal RNA; temperature; zero tolerance
Abstract:
... Fish is one of fourteen allergens that must be highlighted on the label within the ingredients list. The European regulation is very restrictive to allergens with zero tolerance. Therefore, it is important to establish sensitive and specific methods for detecting fish allergen. Applicability to detect and quantify fish allergen by droplet digital polymerase chain reaction (ddPCR) has been evaluate ...
DOI:
10.4081/ijfs.2018.7264
PubMed:
30854336
PubMed Central:
PMC6379699

9. Development of conventional and real time PCR assays for rapid species authentication of mammalian cell lines commonly used in veterinary diagnostic laboratories

Author:
Amaresh Das; Lizhe Xu; Wei Jia
Source:
Research in veterinary science 2019 v.126 pp. 170-177
ISSN:
0034-5288
Subject:
DNA; DNA primers; Internet; National Center for Biotechnology Information; cattle; cell lines; computer simulation; cross reaction; detection limit; disease diagnosis; hamsters; high-throughput nucleotide sequencing; kidneys; mitochondrial genes; monkeys; quantitative polymerase chain reaction; rabbits; species identification; swine; tissues; vaccines
Abstract:
... Mammalian cell lines are valuable tools in biomedical fields, with applications ranging from disease diagnosis to the production of biological reagents and vaccines. Here we report the development of new conventional (cPCR) and real time PCR (qPCR) assays for species identification of several mammalian kidney cell lines originated from swine, green monkey, hamster and bovine tissues that are exten ...
DOI:
10.1016/j.rvsc.2019.08.029
CHORUS:
10.1016/j.rvsc.2019.08.029

10. Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers

Author:
Ahmad Ali; Yong-Bao Pan; Qin-Nan Wang; Jin-Da Wang; Jun-Lü Chen; San-Ji Gao
Source:
Scientific reports 2019 v.9 no.1 pp. -
ISSN:
2045-2322
Subject:
DNA primers; Saccharum arundinaceum; Saccharum barberi; Saccharum officinarum; Saccharum robustum; Saccharum sinense; Saccharum spontaneum; alleles; capillary electrophoresis; fluorescent labeling; genetic variation; genotype; genotyping; hybrids; microsatellite repeats; phylogeny; population structure; sugarcane
Abstract:
... In order to understand the genetic diversity and structure within and between the genera of Saccharum and Erianthus, 79 accessions from five species (S. officinarum, S. spontaneum, S. robustum, S. barberi, S. sinense), six accessions of E. arundinaceus, and 30 Saccharum spp. hybrids were analyzed using 21 pairs of fluorescence-labeled highly poloymorphic SSR primers and a capillary electrophoresis ...
Handle:
10113/6471198
DOI:
10.1038/s41598-018-36630-7
PubMed:
30674931
PubMed Central:
PMC6344583

11. High-resolution mapping of reciprocal translocation breakpoints using long-read sequencing

Author:
Judy F.C. Chow; Heidi H.Y. Cheng; Estella Y.L. Lau; William S.B. Yeung; Ernest H.Y. Ng
Source:
MethodsX 2019 v.6 pp. 2499-2503
ISSN:
2215-0161
Subject:
DNA primers; genomics; nanopores; polymerase chain reaction; reciprocal translocation
Abstract:
... Long-read nanopore sequencing enables direct high-resolution breakpoint mapping on balanced carriers of reciprocal translocation. The mean sequencing depth on the translocated chromosomes to achieve accurate mapping of breakpoints ranged from 2.5-fold to 6.2-fold. To speed up determination of the breakpoints from long-read sequencing data, alignment reads on the translocated chromosomes were extra ...
DOI:
10.1016/j.mex.2019.10.028
PubMed:
31908979
PubMed Central:
PMC6939040

12. International Commission on Trichinellosis: Recommendations for genotyping Trichinella muscle stage larvae

Author:
Edoardo Pozio; Dante Zarlenga
Source:
Food and Waterborne Parasitology 2019 v.15 pp. e00033
ISSN:
2405-6766
Subject:
DNA primers; Trichinella pseudospiralis; encapsulation; epidemiological studies; genotype; genotyping; larvae; meat products; muscles; polymerase chain reaction; restriction endonucleases; sequence analysis; trichinosis; wild animals
Abstract:
... Being able to identify the species or genotype of Trichinella is of paramount importance not only for epidemiological studies but to better ascertain the source of outbreaks that still occur worldwide. This has become more critical in recent years given the increase in imported meat products and the relationship that wild animals play in the domestic and sylvatic transmission cycles. In contrast t ...
DOI:
10.1016/j.fawpar.2018.e00033
PubMed:
32095609
PubMed Central:
PMC7034036

13. Isolation and Molecular Identification of Microsporidian Pathogen Causing Nosemosis in Muga Silkworm, Antheraea assamensis Helfer (Lepidoptera: Saturniidae)

Author:
G. Subrahmanyam; Vijaya Gowri Esvaran; Kangayam Muthusamy Ponnuvel; W. Hassan; M. Chutia; R. Das
Source:
Indian journal of microbiology 2019 v.59 no.4 pp. 525-529
ISSN:
0046-8991
Subject:
Antheraea assamensis; DNA primers; Nosema bombycis; Vairimorpha; bioassays; fungi; genes; molecular cloning; moths; nosema disease; parasites; pathogens; phylogeny; polymerase chain reaction; pupae; ribosomal RNA; sequence analysis; sericulture; silk; silkworms; India
Abstract:
... Microsporidia are intracellular fungal parasites and they are the most common pathogens for sericulture. Microsporidian sp. can cause pebrine, a dreadful disease and lead to destructive disorder in Muga silkworm, Antheraea assamensis Helfer by vertical and horizontal transmission. This disease is the key factor obstructing the developmental progress of Muga culture in India. Nevertheless, molecula ...
DOI:
10.1007/s12088-019-00822-0
PubMed:
31762517
PubMed Central:
PMC6842381

14. Merkel cell polyomavirus is implicated in a subset of Merkel cell carcinomas, in the Indian subcontinent

Author:
Reety Arora; Bharat Rekhi; Pratik Chandrani; Sudhir Krishna; Amit Dutt
Source:
Microbial pathogenesis 2019 v.137 pp. 103778
ISSN:
0882-4010
Subject:
DNA primers; Human polyomavirus 5; antibodies; antigens; carcinogenesis; carcinoma; histopathology; immunohistochemistry; mechanoreceptors; mutation; polymerase chain reaction; viruses; India
Abstract:
... Merkel cell carcinoma is a rare, lethal cancer histopathologically composed of cells showing similarity with mechanoreceptor Merkel cells. Merkel cell tumors manifest in two distinct forms. While a virus called Merkel cell polyomavirus is involved in the pathogenesis of one form of Merkel tumors, the other is driven by ultraviolet (UV)-linked mutations. In this study we investigated 18 cases, from ...
DOI:
10.1016/j.micpath.2019.103778
PubMed:
31600537
PubMed Central:
PMC7166130

15. New genus-specific primers for PCR identification of Rubrobacter strains

Author:
Jean Franco Castro; Imen Nouioui; Juan A. Asenjo; Barbara Andrews; Alan T. Bull; Michael Goodfellow
Source:
Antonie van Leeuwenhoek 2019 v.112 no.12 pp. 1863-1874
ISSN:
0003-6072
Subject:
DNA; DNA libraries; DNA primers; Rubrobacter; Thermoleophilum; clones; ecosystems; evolutionary radiation; genes; nucleotide sequences; polymerase chain reaction; ribosomal RNA; soil sampling
Abstract:
... A set of oligonucleotide primers, Rubro223f and Rubro454r, were found to amplify a 267 nucleotide sequence of 16S rRNA genes of Rubrobacter type strains. The primers distinguished members of this genus from other deeply-rooted actinobacterial lineages corresponding to the genera Conexibacter, Gaiella, Parviterribacter, Patulibacter, Solirubrobacter and Thermoleophilum of the class Thermoleophilia. ...
DOI:
10.1007/s10482-019-01314-3
PubMed:
31407134
PubMed Central:
PMC6834744

16. Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification

Author:
Jordan Cannon; Robert A. Sanford; Lynn Connor; Wendy H. Yang; Joanne Chee-Sanford
Source:
Journal of microbiological methods 2019 v.160 pp. 49-59
ISSN:
0167-7012
Subject:
DNA; DNA primers; ammonification; ammonium; bacteria; cytochrome c; gene amplification; genes; genetic traits; groundwater; heme; high-throughput nucleotide sequencing; nitrate reduction; nitrite reductase; nitrites; phylogeny; quantitative polymerase chain reaction; terrestrial ecosystems; translation (genetics)
Abstract:
... Dissimilatory nitrate reduction to ammonium (DNRA) is now known to be a more prevalent process in terrestrial ecosystems than previously thought. The key enzyme, a pentaheme cytochrome c nitrite reductase NrfA associated with respiratory nitrite ammonification, is encoded by the nrfA gene in a broad phylogeny of bacteria. The lack of reliable and comprehensive molecular tools to detect diverse nrf ...
DOI:
10.1016/j.mimet.2019.03.020
CHORUS:
10.1016/j.mimet.2019.03.020
Chorus Open Access:
10.1016/j.mimet.2019.03.020

17. Papillomavirus DNA is not Amplifiable from Bladder, Lung, or Mammary Gland Cancers in Dogs or Cats

Author:
John S. Munday; Chloe B. MacLachlan; Matthew R. Perrott; Danielle Aberdein
Source:
Animals 2019 v.9 no.9 pp. -
ISSN:
2076-2615
Subject:
DNA; DNA primers; Papillomaviridae; bladder; breasts; cats; cattle; dogs; epithelium; histology; human cell lines; human diseases; lungs; mammary glands; polymerase chain reaction; skin neoplasms; urinary bladder neoplasms; uterine cervical neoplasms; viruses
Abstract:
... Papillomaviruses (PVs) cause around 5% of all human cancers, including most cervical cancers and around a quarter of all oral cancers. Additionally, some studies have suggested that PVs could cause a proportion of human lung, breast, and bladder cancers. As PVs have been associated with skin cancer in cats and, more rarely, dogs, it was hypothesized that these viruses could also contribute to epit ...
DOI:
10.3390/ani9090668
PubMed:
31500370
PubMed Central:
PMC6770269

18. Rapid high throughput template preparation (rHTTP) method: a novel cost effective method of direct PCR for a wide range of plants

Author:
Prassan Choudhary; Sudipta Das; Hillol Chakdar; Arjun Singh; Sanjay Kumar Goswami; Anil Kumar Saxena
Source:
BMC biotechnology 2019 v.19 no.1 pp. 69
ISSN:
1472-6750
Subject:
Amaryllis; Bougainvillea; Brassicaceae; Cajanus cajan; Chrysanthemum; DNA; DNA primers; Duranta; Dypsis lutescens; Gaillardia pulchella; Glycine max; Nerium; Oryza sativa; Petunia; Pisum sativum; Solanum lycopersicum; Tradescantia spathacea; Triticum; Vinca; Zea mays; ambient temperature; analytical kits; corn; cost effectiveness; diagnostic techniques; grinding; internal transcribed spacers; isolation techniques; liquid nitrogen; microsatellite repeats; peas; pigeon peas; plant tissues; random amplified polymorphic DNA technique; rice; shelf life; soybeans; storage temperature; tomatoes; toxic substances; wheat; xerophytes
Abstract:
... BACKGROUND: Conventional plant DNA isolation methods are complex, time consuming and require technical expertise. These limitations were overcome using the DNA isolation kits which, however significantly add to the research costs. Hence the present study was aimed to develop a high throughput, rapid and inexpensive method of PCR ready DNA template preparation from plant materials. METHODS: Concent ...
DOI:
10.1186/s12896-019-0560-4
PubMed:
31655574
PubMed Central:
PMC6815007

19. A deletion in the STA1 promoter determines maltotriose and starch utilization in STA1+ Saccharomyces cerevisiae strains

Author:
Kristoffer Krogerus; Frederico Magalhães; Joosu Kuivanen; Brian Gibson
Source:
Applied microbiology and biotechnology 2019 v.103 no.18 pp. 7597-7615
ISSN:
0175-7598
Subject:
DNA primers; Saccharomyces cerevisiae; beers; dextrins; fermentation; gene editing; genes; glucan 1,4-alpha-glucosidase; hydrolysis; maltotriose; nucleotide sequences; polymerase chain reaction; starch; wort (brewing)
Abstract:
... Diastatic strains of Saccharomyces cerevisiae are common contaminants in beer fermentations and are capable of producing an extracellular STA1-encoded glucoamylase. Recent studies have revealed variable diastatic ability in strains tested positive for STA1, and here, we elucidate genetic determinants behind this variation. We show that poorly diastatic strains have a 1162-bp deletion in the promot ...
DOI:
10.1007/s00253-019-10021-y
PubMed:
31346683
PubMed Central:
PMC6719335

20. An evaluation of primers for detecting denitrifiers via their functional genes

Author:
Yanjun Ma; Julie L. Zilles; Angela D. Kent
Source:
Environmental microbiology 2019 v.21 no.4 pp. 1196-1210
ISSN:
1462-2912
Subject:
DNA; DNA primers; climate change; data collection; denitrification; denitrifying microorganisms; ecosystem services; environmental quality; genes; greenhouse gases; metagenomics; microbial ecology; models; moieties; nitrogen; nitrogen cycle; nucleotide sequences; pollution
Abstract:
... Microbial populations provide nitrogen cycling ecosystem services at the nexus of agriculture, environmental quality and climate change. Denitrification, in particular, impacts socio‐environmental systems in both positive and negative ways, through reduction of aquatic and atmospheric nitrogen pollution, but also reduction of soil fertility and production of greenhouse gases. However, denitrificat ...
DOI:
10.1111/1462-2920.14555
CHORUS:
10.1111/1462-2920.14555

21. A pathway-focused RT-qPCR array study on immune relevant genes in rainbow trout (Oncorhynchus mykiss) harboring cecropin P1 transgene

Author:
Yueh-Chiang Han; Thomas T. Chen
Source:
Fish & shellfish immunology 2019 v.89 pp. 1-11
ISSN:
1050-4648
Subject:
DNA microarrays; DNA primers; Oncorhynchus mykiss; Toll-like receptors; antigens; arachidonic acid; cecropins; chemokines; complement; complementary DNA; extracellular matrix; fish; gene expression; gene expression regulation; high-throughput nucleotide sequencing; immunomodulators; kidneys; leukocytes; lipid metabolism; liver; messenger RNA; pathogens; peroxisome proliferator-activated receptors; phagocytosis; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; spleen; tissues; transgenes; transgenic animals
Abstract:
... Recently, our laboratory had produced five families of transgenic rainbow trout harboring cecropin P1 transgene, and via repeated challenge studies these fish exhibited a significant elevation of resistance to infection by microbial pathogens. By cDNA microarray and mRNA deep sequencing (mRNA-seq) analyses on two of the five families of cecropin P1 transgenic fish, differentially expressed genes ( ...
DOI:
10.1016/j.fsi.2019.03.027
CHORUS:
10.1016/j.fsi.2019.03.027

22. Application of Bacillus velezensis NJAU-Z9 Enhanced Plant Growth Associated with Efficient Rhizospheric Colonization Monitored by qPCR with Primers Designed from the Whole Genome Sequence

Author:
Yang Zhang; Xu Gao; Shuai Wang; Chengzhi Zhu; Rong Li; Qirong Shen
Source:
Current microbiology 2018 v.75 no.12 pp. 1574-1583
ISSN:
0343-8651
Subject:
DNA primers; biomass; colonizing ability; genome; monitoring; nutrient uptake; pepper; plant growth; plant growth-promoting rhizobacteria; quantitative polymerase chain reaction; rhizosphere; seedlings; soil
Abstract:
... Plant growth-promoting rhizobacteria (PGPR) have been reported to influence plant growth, yield, and nutrient uptake by an array of mechanisms. Uncovering the behavioral dynamics of PGPR is one of the most important issues necessary for understanding their functional performances. In this study, strain NJAU-Z9 which was found to possess complex functions and efficient rhizospheric colonization abi ...
DOI:
10.1007/s00284-018-1563-4
PubMed:
30194479
PubMed Central:
PMC6208667

23. Assessment of genetic diversity in lettuce (Lactuca sativa L.) germplasm using RAPD markers

Author:
Shubhangi Sharma; Pankaj Kumar; Geetika Gambhir; Ramesh Kumar; D. K. Srivastava
Source:
3 Biotech 2018 v.8 no.1 pp. 9
ISSN:
2190-572X
Subject:
DNA primers; Lactuca sativa; arithmetics; breeding programs; genetic background; genetic markers; genetic similarity; genetic variation; germplasm; germplasm evaluation; lettuce; plant genetic resources; random amplified polymorphic DNA technique
Abstract:
... The importance of germplasm characterization is an important link between the conservation and utilization of plant genetic resources in various breeding programmes. In the present study, genetic variability and relationships among 25 Lactuca sativa L. genotypes were tested using random amplified polymorphic DNA (RAPD) molecular markers. A total of 45 random decamer oligonucleotide primers were ex ...
DOI:
10.1007/s13205-017-1039-4
PubMed:
29259884
PubMed Central:
PMC5723581

24. Chromogenic detection of yam mosaic virus by closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP)

Author:
Chukwuemeka K. Nkere; Joshua O. Oyekanmi; Gonçalo Silva; Moritz Bömer; Gabriel I. Atiri; Joseph Onyeka; Norbert G. Maroya; Susan E. Seal; P. Lava Kumar
Source:
Archives of virology 2018 v.163 no.4 pp. 1057-1061
ISSN:
0304-8608
Subject:
DNA primers; Dioscorea; Yam mosaic virus; coat proteins; leaves; reverse transcriptase polymerase chain reaction; reverse transcription loop-mediated isothermal amplification; tubers; yams
Abstract:
... A closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP) assay was developed for the detection of yam mosaic virus (YMV, genus Potyvirus) infecting yam (Dioscorea spp.). The assay uses a set of six oligonucleotide primers targeting the YMV coat protein region, and the amplification products in YMV-positive samples are visualized by chromogenic detection with SYBR Gre ...
DOI:
10.1007/s00705-018-3706-0
PubMed:
29308543
PubMed Central:
PMC5854734

25. Clinical and epidemiological use of nested PCR targeting the repetitive element IS1111 associated with the transposase gene from Coxiella burnetii

Author:
Maria Angélica M.M. Mares-Guia; Alexandro Guterres; Tatiana Rozental; Michelle dos Santos Ferreira; Elba R.S. Lemos
Source:
Brazilian journal of microbiology 2018 v.49 no.1 pp. 138-143
ISSN:
1517-8382
Subject:
Coxiella burnetii; DNA; DNA primers; Gram-negative bacteria; Q fever; aerosols; airborne transmission; amniotic fluid; breathing; detection limit; feces; genes; humans; milk; placenta; polymerase chain reaction; raw milk; rodents; spleen; ticks; urine; wool; zoonoses
Abstract:
... Q fever is a worldwide zoonosis caused by Coxiella burnetii—a small obligate intracellular Gram-negative bacterium found in a variety of animals. It is transmitted to humans by inhalation of contaminated aerosols from urine, feces, milk, amniotic fluid, placenta, abortion products, wool, and rarely by ingestion of raw milk from infected animals. Nested PCR can improve the sensitivity and specifici ...
DOI:
10.1016/j.bjm.2017.04.009
PubMed:
28899604
PubMed Central:
PMC5790644

26. A Comparative Study of Three Detection Techniques for Leifsonia xyli Subsp. xyli, the Causal Pathogen of Sugarcane Ratoon Stunting Disease Subsp. the Causal Pathogen of Sugarcane Ratoon

Author:
Qibin Wu; Yong-Bao Pan; Dinggang Zhou; Michael Grisham P.; Shiwu Gao; Yachun Su; Jinlong Guo; Liping Xu; Youxiong Que
Source:
BioMed research international 2018 v.2018 no. pp. -
ISSN:
2314-6141
Subject:
DNA primers; Leifsonia xyli subsp. xyli; Saccharum; comparative study; detection limit; disease detection; loop-mediated isothermal amplification; microbial detection; plant pathogenic bacteria; quantitative polymerase chain reaction; ratoon stunting disease; stems; sugarcane juice
Abstract:
... The ratoon stunting disease (RSD), caused by the bacterium Leifsonia xyli subsp. xyli (Lxx), is one of the most economically devastating diseases impacting sugarcane. RSD causes significant yield losses and variety degradation. Diagnosis of RSD is challenging because it does not exhibit any discernible internal and external symptoms. Moreover, the Lxx bacteria are very small and difficult to isola ...
Handle:
10113/6740177
DOI:
10.1155/2018/2786458
PubMed:
29951532
PubMed Central:
PMC5989284

27. Development and validation of a real-time PCR specific for the leukotoxin gene of Bibersteinia trehalosi

Author:
Halcyon J. Killion; William Edwards; Jessica Jennings-Gaines; Mary Wood; Karen Fox; Kerry Sondgeroth
Source:
Journal of veterinary diagnostic investigation v.30 no.4 pp. 589-592
ISSN:
1943-4936
Subject:
DNA; DNA primers; Ovis canadensis; Pasteurellaceae; genes; leukotoxins; pathogens; quantitative polymerase chain reaction; respiratory tract diseases; sheep diseases
Abstract:
... A real-time PCR assay for the leukotoxin gene of Bibersteinia trehalosi was developed and validated to better identify this pathogen, which is a cause of respiratory disease in bighorn sheep. The specificity of the PCR primers was evaluated with DNA from 59 known isolates of the Pasteurellaceae family. For validation, 162 field samples were compared using both the new assay and an indirect method ...
DOI:
10.1177/1040638717753497
PubMed:
29601780
PubMed Central:
PMC6505900

28. Development of PCR-based molecular marker for screening of disease-suppressive composts against Fusarium wilt of tomato (Solanum lycopersicum L.)

Author:
C. M. Mehta; Ramesh N. Pudake; Rashmi Srivastava; Uma Palni; Anil K. Sharma
Source:
3 Biotech 2018 v.8 no.7 pp. 306
ISSN:
2190-572X
Subject:
DNA primers; Fusarium; Fusarium wilt; Solanum lycopersicum; bacterial communities; bioassays; biological control; composts; disease control; genetic markers; melting; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; screening; tomatoes
Abstract:
... The present study was carried out to develop a PCR-based molecular marker suitable for screening of disease-suppressive composts against Fusarium wilt of tomato. An effective uncultured bacterial community was screened from our previous study on investigation of microbial communities in composts for their potential for biocontrol of Fusarium wilt. Based on available sequence information (Accession ...
DOI:
10.1007/s13205-018-1331-y
PubMed:
30002996
PubMed Central:
PMC6035786

29. Development of a one-step RT-PCR assay for detection of pancoronaviruses (α-, β-, γ-, and δ-coronaviruses) using newly designed degenerate primers for porcine and avian `fecal samples

Author:
Hui Hu; Kwonil Jung; Qiuhong Wang; Linda J. Saif; Anastasia N. Vlasova
Source:
Journal of virological methods 2018 v.256 pp. 116-122
ISSN:
0166-0934
Subject:
Chiroptera; DNA primers; Deltacoronavirus; Porcine epidemic diarrhea virus; RNA; RNA-directed RNA polymerase; animal pathogens; birds; blood serum; control methods; disease outbreaks; feces; genes; humans; phylogeny; protein domains; reverse transcriptase polymerase chain reaction; swine; transmissible gastroenteritis; Asia; United States
Abstract:
... Coronaviruses (CoVs) are critical human and animal pathogens because of their potential to cause severe epidemics of respiratory or enteric diseases. In pigs, the newly emerged porcine deltacoronavirus (PDCoV) and re-emerged porcine epidemic diarrhea virus (PEDV) reported in the US and Asia, as well as the discovery of novel CoVs in wild bats or birds, has necessitated development of improved dete ...
DOI:
10.1016/j.jviromet.2018.02.021
PubMed:
29499225
PubMed Central:
PMC7113874

30. Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free‐living Giant Amoebae

Author:
Georgia M. Ward; Sigrid Neuhauser; René Groben; Stefan Ciaghi; Cédric Berney; Sarah Romac; David Bass
Source:
journal of eukaryotic microbiology 2018 v.65 no.5 pp. 574-586
ISSN:
1066-5234
Subject:
Bivalvia; Copepoda; DNA; DNA primers; Haplosporida; Paramyxida; invertebrates; new order; parasites; phylogeny; plankton; polymerase chain reaction; sequence diversity
Abstract:
... Class Ascetosporea (Rhizaria; Endomyxa) comprises many parasites of invertebrates. Within this group, recent group‐specific environmental DNA (eDNA) studies have contributed to the establishment of the new order Mikrocytida, a new phylogeny and characterization of Paramyxida, and illuminated the diversity and distribution of haplosporidians. Here, we use general and lineage‐specific PCR primers to ...
DOI:
10.1111/jeu.12501
PubMed:
29336517
PubMed Central:
PMC6173291

31. First Report of a New Isolate of Metarhizium rileyi from Maize Fields of Quivicán, Cuba

Author:
Sandra Pérez Álvarez; Amaury Méndez Guerrero; Bernardo Nayar Débora Duarte; Marco Antonio Magallanes Tapia; Jesús Alicia Chávez Medina; Yoannis Domínguez Rodríguez
Source:
Indian journal of microbiology 2018 v.58 no.2 pp. 222-226
ISSN:
0046-8991
Subject:
DNA; DNA primers; Lepidoptera; Metarhizium; Zea mays; ampicillin; biodiversity; cetyltrimethylammonium bromide; color; conidia; consensus sequence; corn; entomopathogenic fungi; integrated pest management; internal transcribed spacers; larvae; mycelium; new geographic records; transcription (genetics); Cuba
Abstract:
... Metarhizium rileyi (Farlow) Samson is an important entomopathogenic fungus of more than 30 species of Lepidoptera larvae. The aim of this research was to characterize isolate of M. rileyi from Quivicán, Cuba on the basis of morphological and molecular approaches. The fungus was isolated from samples of S. frugiperda larvae collected from maize fields of Quivicán municipality, Mayabeque province, C ...
DOI:
10.1007/s12088-018-0721-5
PubMed:
29651182
PubMed Central:
PMC5891484

32. Genetic diversity and structure of tea plant in Qinba area in China by three types of molecular markers

Author:
Yu Zhang; Xiaojuan Zhang; Xi Chen; Wang Sun; Jiao Li
Source:
Hereditas 2018 v.155 no.1 pp. 22
ISSN:
1601-5223
Subject:
Camellia sinensis; DNA primers; alleles; expressed sequence tags; gene pool; genetic distance; genetic markers; genetic similarity; genetic variation; germplasm; introduced plants; microsatellite repeats; planting; population structure; principal component analysis; spatial data; tea; China
Abstract:
... BACKGROUND: Qinba area has a long history of tea planting and is a northernmost region in China where Camellia sinensis L. is grown. In order to provide basic data for selection and optimization of molecular markers of tea plants. 118 markers, including 40 EST-SSR, 40 SRAP and 38 SCoT markers were used to evaluate the genetic diversity of 50 tea plant (Camellia sinensis.) samples collected from Qi ...
DOI:
10.1186/s41065-018-0058-4
PubMed:
29773972
PubMed Central:
PMC5944026

33. Identification of Mx gene nucleotide dimorphism (G/A) as genetic marker for antiviral activity in Egyptian chickens

Author:
Mohamed S. Hassanane; Amal A.M. Hassan; Fatma M. Ahmed; Esteftah M. El-Komy; Khaled M. Roushdy; Nagwa A. Hassan
Source:
Journal of Genetic Engineering and Biotechnology (Print) 2018 v.16 no.1 pp. 83-88
ISSN:
1687-157X
Subject:
DNA; DNA fragmentation; DNA primers; alleles; antiviral properties; biotechnology; breeding programs; chicken breeds; chickens; dimorphism; disease resistance; exons; gene frequency; genetic engineering; genetic markers; genotype; genotyping; livestock breeding; polymerase chain reaction; restriction endonucleases; restriction fragment length polymorphism; Egypt
Abstract:
... Egyptian chickens, representing 2 breeds and 7 strains, were genotyped using the PCR-RFLP and sequencing techniques for detection of a non-synonymous dimorphism (G/A) in exon 14 of chicken Myxovirus resistance (Mx) gene. This dimorphic position is responsible for altering Mx protein’s antiviral activity. Polymerase Chain reactions were performed using Egyptian chickens DNA and specific primer set ...
DOI:
10.1016/j.jgeb.2017.11.002
PubMed:
30647709
PubMed Central:
PMC6296577

34. Improved multiplex PCR primers for rapid identification of coagulase-negative staphylococci

Author:
Jonguk Kim; Jisoo Hong; Jeong-A Lim; Sunggi Heu; Eunjung Roh
Source:
Archives of microbiology 2018 v.200 no.1 pp. 73-83
ISSN:
0302-8933
Subject:
DNA primers; Staphylococcus epidermidis; antibiotics; biofilm; carboxylic ester hydrolases; coagulase negative staphylococci; deoxyribonucleases; hemolysins; human diseases; human health; nucleotide sequences; phenotype; polymerase chain reaction; proteinases; ribosomal RNA; secondary infection; sequence analysis
Abstract:
... Coagulase-negative staphylococci (CNS) are opportunistic pathogens that are currently emerging as causative agents of human disease. Though CNS are widespread in the clinic and food, their precise identification at species level is important. Here, using 16S rRNA sequencing, 55 staphylococcal isolates were identified as S. capitis, S. caprae, S. epidermidis, S. haemolyticus, S. pasteuri, S. saprop ...
DOI:
10.1007/s00203-017-1415-9
PubMed:
28795230
PubMed Central:
PMC5758691

35. Loop‐mediated isothermal amplification (LAMP): a versatile technique for detection of micro‐organisms

Author:
Y.‐P. Wong; S. Othman; Y.‐L. Lau; S. Radu; H.‐Y. Chee
Source:
Journal of applied microbiology 2018 v.124 no.3 pp. 626-643
ISSN:
1364-5072
Subject:
DNA; DNA primers; DNA-directed DNA polymerase; colorimetry; commercialization; diagnostic techniques; freeze drying; humans; infectious diseases; livestock; loop-mediated isothermal amplification; microorganisms; monitoring; reverse transcription; turbidity
Abstract:
... Loop‐mediated isothermal amplification (LAMP) amplifies DNA with high specificity, efficiency and rapidity under isothermal conditions by using a DNA polymerase with high displacement strand activity and a set of specifically designed primers to amplify targeted DNA strands. Following its first discovery by Notomi et al. (Nucleic Acids Res 28: E63), LAMP was further developed over the years which ...
DOI:
10.1111/jam.13647
PubMed:
29165905
PubMed Central:
PMC7167136

36. Numerical Relationships Between Archaeal and Bacterial amoA Genes Vary by Icelandic Andosol Classes

Author:
Hendrikus J. Laanbroek; Peter T. M. Veenhuizen; Rosalinde M. Keijzer; Mariet M. Hefting
Source:
Microbial ecology 2018 v.75 no.1 pp. 204-215
ISSN:
0095-3628
Subject:
Andosols; Archaea; DNA primers; ammonia; genes; nitrification inhibitors; nitrifying bacteria; oxidation; quantitative polymerase chain reaction; soil sampling
Abstract:
... Bacterial amoA genes had not been detectable by qPCR in freshly sampled Icelandic Andosols thus far. Hence, a new primer set yielding shorter gene fragments has been designed to verify the absence of ammonia-oxidizing bacteria in different Icelandic Andosol classes. At the same time, a new primer set was also constructed for archaeal amoA genes that should improve the quality of PCR products. Alth ...
DOI:
10.1007/s00248-017-1032-9
PubMed:
28707145
PubMed Central:
PMC5742608

37. Optimization of a magnetic capture RT-LAMP assay for fast and real-time detection of potato virus Y and differentiation of N and O serotypes

Author:
Krzysztof Treder; Joanna Chołuj; Bogumiła Zacharzewska; Lavanya Babujee; Mateusz Mielczarek; Adam Burzyński; Aurélie M. Rakotondrafara
Source:
Archives of virology 2018 v.163 no.2 pp. 447-458
ISSN:
0304-8608
Subject:
DNA primers; DNA replication; Potato virus Y; RNA; annealing; certification; coat proteins; disease control; genes; magnetism; potatoes; reverse transcriptase polymerase chain reaction; reverse transcription; reverse transcription loop-mediated isothermal amplification; serotypes; temperature; viruses
Abstract:
... Potato virus Y (PVY) infection has been a global challenge for potato production and the leading cause of downgrading and rejection of seed crops for certification. Accurate and timely diagnosis is a key for effective disease control. Here, we have optimized a reverse transcription loop-mediated amplification (RT-LAMP) assay to differentiate the PVY O and N serotypes. The RT-LAMP assay is based on ...
DOI:
10.1007/s00705-017-3635-3
PubMed:
29119360
PubMed Central:
PMC5799334

38. Rhizarian ‘Novel Clade 10’ Revealed as Abundant and Diverse Planktonic and Terrestrial Flagellates, including Aquavolon n. gen.

Author:
David Bass; Denis Victorovich Tikhonenkov; Rachel Foster; Patricia Dyal; Jan Janouškovec; Patrick J. Keeling; Michelle Gardner; Sigrid Neuhauser; Hanna Hartikainen; Alexandre P. Mylnikov; Cédric Berney
Source:
journal of eukaryotic microbiology 2018 v.65 no.6 pp. 828-842
ISSN:
1066-5234
Subject:
Cercozoa; DNA; DNA primers; Retaria; flagellum; freshwater; genes; habitats; marine environment; new genus; new order; phylogeny; plankton; polymerase chain reaction; protists; ribosomal RNA; screening; sediments; sequence analysis; soil; swimming
Abstract:
... Rhizarian ‘Novel Clade 10’ (NC10) is frequently detected by 18S rRNA gene sequencing studies in freshwater planktonic samples. We describe a new genus and two species of eukaryovorous biflagellate protists, Aquavolon hoantrani n. gen. n. sp. and A. dientrani n. gen. n. sp., which represent the first morphologically characterized members of NC10, here named Aquavolonida ord. nov. The slightly metab ...
DOI:
10.1111/jeu.12524
PubMed:
29658156
PubMed Central:
PMC6282753

39. Widespread occurrence of Sinorhizobium meliloti strains with a type IV secretion system

Author:
Yuanyuan Cao; Susan S. Miller; Melinda R. Dornbusch; Sarah S. Castle; Peter Lenz; John Ferguson; Michael J. Sadowsky; Matthew S. Nelson; Christian Klatt; Deborah A. Samac
Source:
Symbiosis 2018 v.75 no.2 pp. 81-91
ISSN:
0334-5114
Subject:
DNA fingerprinting; DNA primers; Ensifer meliloti; Medicago sativa; Sinorhizobium; alfalfa; bacteria; mineral fertilizers; multigene family; nitrogen fixation; nodulation; packaging; polymerase chain reaction; root nodules; seeds; soil; symbiosis; type IV secretion system
Abstract:
... Improving symbiotic nitrogen fixation would reduce reliance on synthetic fertilizers, but establishment of effective bacterial strains is hampered due to competition by indigenous, less effective rhizobia. This study investigated the origins, diversity, and competitiveness of Sinorhizobium meliloti (syn. Ensifer meliloti) strains isolated from root nodules of alfalfa (lucerne; Medicago sativa L.) ...
DOI:
10.1007/s13199-018-0547-2
CHORUS:
10.1007/s13199-018-0547-2

40. A qPCR method to quantify bioavailable phosphorus using indigenous aquatic species

Author:
Yanan Yang; Jianghua Yang; Xiaowei Zhang
Source:
Environmental sciences Europe 2018 v.30 no.1 pp. 32
ISSN:
2190-4707
Subject:
Anabaena; DNA primers; algae; alkaline phosphatase; aquatic environment; bioassays; bioavailability; environmental monitoring; eutrophication; gel electrophoresis; genes; lakes; phosphates; phosphorus; quantitative polymerase chain reaction; China
Abstract:
... BACKGROUND: Bioavailable phosphorus (BAP) represents the sum of phosphorus that is readily available for algae growth and is useful to indicate the severity of eutrophication in aquatic environments. RESULTS: Here, a quantitative real-time PCR (qPCR)-based bioassay was developed to quantify BAP using the indigenous cyanobacterium species Anabaena sp. of Lake Tai, a large and shallow eutrophic lake ...
DOI:
10.1186/s12302-018-0163-z
PubMed:
30221104
PubMed Central:
PMC6132795

41. The use of extracellular DNA as a proxy for specific microbial activity

Author:
Magdalena Nagler; Sabine Marie Podmirseg; Gareth Wyn Griffith; Heribert Insam; Judith Ascher-Jenull
Source:
Applied microbiology and biotechnology 2018 v.102 no.6 pp. 2885-2898
ISSN:
0175-7598
Subject:
Archaea; DNA; DNA primers; Neocallimastigales; anaerobes; bacteria; fungi; medicine; methanogens; microbial activity; quantitative polymerase chain reaction; ribosomal RNA
Abstract:
... The ubiquity and relevance of extracellular DNA (exDNA) are well-known and increasingly gaining importance in many fields of application such as medicine and environmental microbiology. Although sources and types of exDNA are manifold, ratios of specific DNA-molecules inside and outside of living cells can give reliable information about the activity of entire systems and of specific microbial gro ...
DOI:
10.1007/s00253-018-8786-y
PubMed:
29423636
PubMed Central:
PMC5847193

42. Analysis of genetic structure and interrelationships in lentil species using morphological and SSR markers

Author:
Priyanka Mohan Koul; Vikas Sharma; Maneet Rana; Rakesh K. Chahota; Shiv Kumar; Tilak R. Sharma
Source:
3 Biotech 2017 v.7 no.1 pp. 83
ISSN:
2190-572X
Subject:
DNA primers; Lens; alleles; breeding; cluster analysis; genetic background; genetic markers; genetic variance; genetic variation; lentils; microsatellite repeats; variance
Abstract:
... Genetic structure and relationships of 130 lentil accessions belonging to six taxa were analysed. For this purpose, seven morphological traits and 31 polymorphic simple sequence repeat (SSR) primers were used for this purpose. Morphological traits grouped lentil accessions into five main clusters. SSR primers collectively amplified 139 polymorphic alleles in a range of 2–10 with an average of 4.48 ...
DOI:
10.1007/s13205-017-0683-z
PubMed:
28500404
PubMed Central:
PMC5429312

43. CO2 assimilation strategies in stratified lakes: Diversity and distribution patterns of chemolithoautotrophs

Author:
Albin Alfreider; Andreas Baumer; Teresa Bogensperger; Thomas Posch; Michaela M. Salcher; Monika Summerer
Source:
Environmental microbiology 2017 v.19 no.7 pp. 2754-2768
ISSN:
1462-2912
Subject:
DNA primers; Nitrosospira; carbon dioxide; carbon dioxide fixation; epsilon-Proteobacteria; freshwater lakes; prokaryotic cells; ribulose-bisphosphate carboxylase; surface water
Abstract:
... While mechanisms of different carbon dioxide (CO₂) assimilation pathways in chemolithoautotrohic prokaryotes are well understood for many isolates under laboratory conditions, the ecological significance of diverse CO₂ fixation strategies in the environment is mostly unexplored. Six stratified freshwater lakes were chosen to study the distribution and diversity of the Calvin‐Benson‐Bassham (CBB) c ...
DOI:
10.1111/1462-2920.13786
PubMed:
28474482
PubMed Central:
PMC5619642

44. Demonstration that a Klebsiella pneumoniae subsp. pneumoniae isolated from an insect (Nezara viridula) harbors a plasmid-borne type IV secretion system

Author:
Enrique Gino Medrano; Alois A. Bell
Source:
Current microbiology 2017 v.74 no.9 pp. 1033-1042
ISSN:
0343-8651
Subject:
DNA primers; Klebsiella pneumoniae; Nezara viridula; antibiotic resistance; genes; genome mining; insects; molecular cloning; nucleic acid hybridization; pests; plasmids; polymerase chain reaction; sequence analysis; type IV secretion system; virulence
Abstract:
... Previously, we reported the isolation of Klebsiella pneumoniae subspecies pneumoniae strain Kp 5-1 from a southern green stink bug (Nezara viridula) that is a significant pest of numerous economically important crops. We subsequently sequenced the strains whole genome. Here, we report the presence of a functional plasmid-borne type IV secretion (TFSS) system that was identified using genomic minin ...
DOI:
10.1007/s00284-017-1277-z
CHORUS:
10.1007/s00284-017-1277-z

45. Development of a realtime RT-PCR assay for the rapid detection of influenza A(H2) viruses

Author:
Andrey Komissarov; Artem Fadeev; Anna Kosheleva; Kseniya Sintsova; Mikhail Grudinin
Source:
Molecular and cellular probes 2017 v.35 pp. 57-63
ISSN:
0890-8508
Subject:
DNA primers; Influenza A virus; analytical specificity; binding sites; clinical trials; databases; detection limit; diagnostic techniques; genes; hemagglutinins; human population; humans; immunity; influenza; morbidity; mortality; pandemic; plasmids; poultry; public health; rapid methods; reverse transcriptase polymerase chain reaction; screening; vaccines; viruses; wild birds
Abstract:
... Influenza and other acute respiratory infections are of great concern for public health, causing excessive morbidity and mortality throughout the world. Influenza virus A(H2N2), which caused a pandemic of so called “Asian flu” in 1957 was expelled from the human population by the new pandemic virus subtype H3N2 in 1968, however, influenza A(H2) viruses continue to circulate in wild birds and poult ...
DOI:
10.1016/j.mcp.2017.06.005
PubMed:
28652020
PubMed Central:
PMC7126497

46. Development of microsatellite markers in Garcinia paucinervis (Clusiaceae), an endangered species of karst habitats

Author:
Gang Hu; Zhong‐Hua Zhang; Ping Yang; Qi‐Wei Zhang; Chang‐An Yuan
Source:
Applications in plant sciences 2017 v.5 no.1 pp. e1600131
ISSN:
2168-0450
Subject:
DNA primers; Garcinia; alleles; endangered species; genetic markers; genetic variation; habitats; heterozygosity; indigenous species; karsts; linkage disequilibrium; loci; microsatellite repeats; population structure; sequence analysis
Abstract:
... PREMISE OF THE STUDY: Microsatellite markers were developed for Garcinia paucinervis (Clusiaceae), an endangered and endemic tree species of karst habitats, to analyze its genetic diversity and genetic structure. METHODS AND RESULTS: Using shotgun sequencing on an Illumina MiSeq platform, a total of 22 microsatellite primer sets were characterized, of which 17 were identified as polymorphic. For t ...
DOI:
10.3732/apps.1600131
PubMed:
28090413
PubMed Central:
PMC5231918

47. Direct detection of falciparum and non-falciparum malaria DNA from a drop of blood with high sensitivity by the dried-LAMP system

Author:
Kyoko Hayashida; Kiichi Kajino; Humphrey Simukoko; Martin Simuunza; Joseph Ndebe; Amos Chota; Boniface Namangala; Chihiro Sugimoto
Source:
Parasites & vectors 2017 v.10 no.1 pp. 26
ISSN:
1756-3305
Subject:
DNA primers; Plasmodium falciparum; blood; blood sampling; carrier state; diagnostic techniques; epidemiology; humans; malaria; mitochondrial DNA; point-of-care testing; polymerase chain reaction; Zambia
Abstract:
... BACKGROUND: Because of the low sensitivity of conventional rapid diagnostic tests (RDTs) for malaria infections, the actual prevalence of the diseases, especially those caused by non-Plasmodium falciparum (non-Pf) species, in asymptomatic populations remain less defined in countries lacking in well-equipped facilities for accurate diagnoses. Our direct blood dry LAMP system (CZC-LAMP) was applied ...
DOI:
10.1186/s13071-016-1949-8
PubMed:
28086864
PubMed Central:
PMC5237333

48. Evaluation and optimization of PCR primers for selective and quantitative detection of marine ANME subclusters involved in sulfate-dependent anaerobic methane oxidation

Author:
Peer H. A. Timmers; H. C. Aura Widjaja-Greefkes; Caroline M. Plugge; Alfons J. M. Stams
Source:
Applied microbiology and biotechnology 2017 v.101 no.14 pp. 5847-5859
ISSN:
0175-7598
Subject:
Archaea; DNA primers; genes; marine sediments; methane; methanogens; oxidation; quantitative polymerase chain reaction; ribosomal RNA; sulfates
Abstract:
... Since the discovery that anaerobic methanotrophic archaea (ANME) are involved in the anaerobic oxidation of methane coupled to sulfate reduction in marine sediments, different primers and probes specifically targeting the 16S rRNA gene of these archaea have been developed. Microbial investigation of the different ANME subtypes (ANME-1; ANME-2a, b, and c; and ANME-3) was mainly done in sediments wh ...
DOI:
10.1007/s00253-017-8338-x
PubMed:
28620686
PubMed Central:
PMC5501906

49. Genetic and phytochemical diversity analysis in Bunium persicum populations of north-western Himalaya

Author:
Rakesh Kumar Chahota; Vikas Sharma; Minerva Ghani; Tilak Raj Sharma; Jai Chand Rana; Shyam Kumar Sharma
Source:
Physiology and molecular biology of plants 2017 v.23 no.2 pp. 429-441
ISSN:
0971-5894
Subject:
Bayesian theory; Bunium persicum; DNA primers; breeding programs; essential oils; phenylacetic acid; population structure; random amplified polymorphic DNA technique; sabinene; Himalayan region
Abstract:
... The present study explores morphological, genetic and phytochemical composition of Bunium persicum populations belonging to high altitudinal areas of Indian Himalayan region. In total, 23 morphological traits (13 quantitative and 10 qualitative traits) and 32 Random Amplified Polymorphic DNA primers were employed to infer the population structure of the species. Of the fourteen populations, five g ...
DOI:
10.1007/s12298-017-0428-9
PubMed:
28461730
PubMed Central:
PMC5391360

50. Identification and monitoring of Korean medicines derived from Cinnamomum spp. by using ITS and DNA marker

Author:
Eui Jeong Doh; Jung-Hoon Kim; Seung eun Oh; Guemsan Lee
Source:
Genes & genomics 2017 v.39 no.1 pp. 101-109
ISSN:
1976-9571
Subject:
Cinnamomum aromaticum; DNA; DNA barcoding; DNA primers; cortex; genetic markers; genetic relationships; internal transcribed spacers; markets; medicinal plants; monitoring; polymerase chain reaction; traditional medicine; China; Japan
Abstract:
... In this study, we identified and evaluated the genetic relationships among Cinnamomum plants, which are used in traditional medicine. We also attempted to monitor the distribution of traditional medicines derived from Cinnamomum cassia by using DNA barcoding and a species-specific DNA marker. Plants of the genus Cinnamomum, and in particular C. cassia, are commonly used as medicinal herbs in the f ...
DOI:
10.1007/s13258-016-0476-5
PubMed:
28090265
PubMed Central:
PMC5196016