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https://www.readbyqxmd.com/read/28543666/high-resolution-melting-analysis-assay-for-identification-of-fonsecaea-species
#1
Minglan Shi, Xiqing Li, Jiao Feng, Shulin Jia, Xing Xiao, Chunmei Chen, Cindy Fransisca, Liyan Xi, Junmin Zhang
BACKGROUND: Chromoblastomycosis (CBM) is a chronic fungal disease. In China, the principle etiologic agent was a group of dematiaceous fungi, including Fonsecaea monophora, Fonsecaea nubica, and Cladophialophora carrionii. Although the Fonsecaea species have similar morphology, their pathogenicity is quite different. This study aims to establish a new solution for early identification of Fonsecaea species because of their distinctive potential infection risk. METHODS: Five reference strains and 35 clinical isolates from patients with CBM, preserved in our laboratory, were used in this study...
May 22, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28542313/environmental-dna-edna-metabarcoding-assays-to-detect-invasive-invertebrate-species-in-the-great-lakes
#2
Katy E Klymus, Nathaniel T Marshall, Carol A Stepien
Describing and monitoring biodiversity comprise integral parts of ecosystem management. Recent research coupling metabarcoding and environmental DNA (eDNA) demonstrate that these methods can serve as important tools for surveying biodiversity, while significantly decreasing the time, expense and resources spent on traditional survey methods. The literature emphasizes the importance of genetic marker development, as the markers dictate the applicability, sensitivity and resolution ability of an eDNA assay. The present study developed two metabarcoding eDNA assays using the mtDNA 16S RNA gene with Illumina MiSeq platform to detect invertebrate fauna in the Laurentian Great Lakes and surrounding waterways, with a focus for use on invasive bivalve and gastropod species monitoring...
2017: PloS One
https://www.readbyqxmd.com/read/28542301/electronic-cigarette-aerosols-suppress-cellular-antioxidant-defenses-and-induce-significant-oxidative-dna-damage
#3
Vengatesh Ganapathy, Jimmy Manyanga, Lacy Brame, Dehra McGuire, Balaji Sadhasivam, Evan Floyd, David A Rubenstein, Ilangovan Ramachandran, Theodore Wagener, Lurdes Queimado
BACKGROUND: Electronic cigarette (EC) aerosols contain unique compounds in addition to toxicants and carcinogens traditionally found in tobacco smoke. Studies are warranted to understand the public health risks of ECs. OBJECTIVE: The aim of this study was to determine the genotoxicity and the mechanisms induced by EC aerosol extracts on human oral and lung epithelial cells. METHODS: Cells were exposed to EC aerosol or mainstream smoke extracts and DNA damage was measured using the primer anchored DNA damage detection assay (q-PADDA) and 8-oxo-dG ELISA assay...
2017: PloS One
https://www.readbyqxmd.com/read/28540937/dental-caries
#4
REVIEW
Nigel B Pitts, Domenick T Zero, Phil D Marsh, Kim Ekstrand, Jane A Weintraub, Francisco Ramos-Gomez, Junji Tagami, Svante Twetman, Georgios Tsakos, Amid Ismail
Dental caries is a biofilm-mediated, sugar-driven, multifactorial, dynamic disease that results in the phasic demineralization and remineralization of dental hard tissues. Caries can occur throughout life, both in primary and permanent dentitions, and can damage the tooth crown and, in later life, exposed root surfaces. The balance between pathological and protective factors influences the initiation and progression of caries. This interplay between factors underpins the classification of individuals and groups into caries risk categories, allowing an increasingly tailored approach to care...
May 25, 2017: Nature Reviews. Disease Primers
https://www.readbyqxmd.com/read/28540714/arbitrarily-primed-pcr-for-comparison-of-meta-genomes-and-extracting-useful-loci-from-them
#5
Leigh Burgoyne, Lin Y Koh, David Catcheside
A method is described that uses arbitrarily primed PCR followed by many cycles of amplification under stringent conditions and selection by computational means to obtain a set of sequence tags that can be used for the comparison of metagenomes. Relative to unselective shot-gun sequencing, the results are small data sets that can be csompared electronically or plotted as scattergrams that are simple to interpret. The method can be used to compare groups of samples of any size to build in-house databases from which, for example, the provenance of trace soil samples may be inferred...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540710/genetic-diversity-analysis-of-medicinally-important-horticultural-crop-aegle-marmelos-by-issr-markers
#6
Farina Mujeeb, Preeti Bajpai, Neelam Pathak, Smita Rastogi Verma
Inter simple sequence repeat (ISSR) markers help in identifying and determining the extent of genetic diversity in cultivars. Here, we describe their application in determining the genetic diversity of bael (Aegle marmelos Corr.). Universal ISSR primers are selected and their marker characteristics such as polymorphism information content, effective multiplex ratio and marker index have been evaluated. ISSR-PCR is then performed using universal ISSR primers to generate polymorphic bands. This information is used to determine the degree of genetic similarity among the bael varieties/accessions by cluster analysis using unweighted pair-group method with arithmetic averages (UPGMA)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540701/inverse-pcr-for-point-mutation-introduction
#7
Diogo Silva, Gustavo Santos, Mário Barroca, Tony Collins
Inverse PCR is a powerful tool for the rapid introduction of desired mutations at desired positions in a circular double-stranded DNA sequence. Here, custom-designed mutant primers oriented in the inverse direction are used to amplify the entire circular template with incorporation of the required mutation(s). By careful primer design it can be used to perform such diverse modifications as the introduction of point mutations and multiple mutations, the insertion of new sequences, and even sequence deletions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540700/strategies-to-improve-efficiency-and-specificity-of-degenerate-primers-in-pcr
#8
Maria Jorge Campos, Alberto Quesada
PCR with degenerate primers can be used to identify the coding sequence of an unknown protein or to detect a genetic variant within a gene family. These primers, which are complex mixtures of slightly different oligonucleotide sequences, can be optimized to increase the efficiency and/or specificity of PCR in the amplification of a sequence of interest by the introduction of mismatches with the target sequence and balancing their position toward the primers 5'- or 3'-ends. In this work, we explain in detail examples of rational design of primers in two different applications, including the use of specific determinants at the 3'-end, to: (1) improve PCR efficiency with coding sequences for members of a protein family by fully degeneration at a core box of conserved genetic information, with the reduction of degeneration at the 5'-end, and (2) optimize specificity of allelic discrimination of closely related orthologous by 5'-end degenerate primers...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540698/introduction-on-using-the-fastpcr-software-and-the-related-java-web-tools-for-pcr-and-oligonucleotide-assembly-and-analysis
#9
Ruslan Kalendar, Timofey V Tselykh, Bekbolat Khassenov, Erlan M Ramanculov
This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540697/in-silico-pcr-tools-for-a-fast-primer-probe-and-advanced-searching
#10
Ruslan Kalendar, Alexandr Muterko, Malika Shamekova, Kabyl Zhambakin
The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory "wet bench" experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540488/an-18s-rrna-workflow-for-characterizing-protists-in-sewage-with-a-focus-on-zoonotic-trichomonads
#11
Julia M Maritz, Krysta H Rogers, Tara M Rock, Nicole Liu, Susan Joseph, Kirkwood M Land, Jane M Carlton
Microbial eukaryotes (protists) are important components of terrestrial and aquatic environments, as well as animal and human microbiomes. Their relationships with metazoa range from mutualistic to parasitic and zoonotic (i.e., transmissible between humans and animals). Despite their ecological importance, our knowledge of protists in urban environments lags behind that of bacteria, largely due to a lack of experimentally validated high-throughput protocols that produce accurate estimates of protist diversity while minimizing non-protist DNA representation...
May 24, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28539917/diversity-of-extremely-halophilic-archaeal-and-bacterial-communities-from-commercial-salts
#12
Ashagrie Gibtan, Kyounghee Park, Mingyeong Woo, Jung-Kue Shin, Dong-Woo Lee, Jae Hak Sohn, Minjung Song, Seong Woon Roh, Sang-Jae Lee, Han-Seung Lee
Salting is one of the oldest food preservation techniques. However, salt is also the source of living halophilic microorganisms that may affect human health. In order to determine the microbial communities of commercial salts, an investigation were done using amplicon sequencing approach in four commercial salts: Ethiopian Afdera salt (EAS), Ethiopian rock salt (ERS), Korean Jangpan salt (KJS), and Korean Topan salt (KTS). Using domain-specific primers, a region of the 16S rRNA gene was amplified and sequenced using a Roche 454 instrument...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28539346/rapid-and-accurate-molecular-identification-of-the-emerging-multidrug-resistant-pathogen-candida-auris
#13
Milena Kordalewska, Yanan Zhao, Shawn R Lockhart, Anuradha Chowdhary, Indira Berrio, David S Perlin
Candida auris is an emerging multidrug resistant fungal pathogen causing nosocomial and invasive infections associated with high mortality. C. auris is commonly misidentified as several different yeast species by commercially available phenotypic identification platforms. Thus, there is an urgent need for a reliable diagnostic method. In this paper we present fast, robust, easy to perform and interpret PCR and real-time PCR assays to identify C. auris and related species: Candida duobushaemulonii, Candida haemulonii, and Candida lusitaniae Targeting rDNA region nucleotide sequences, primers specific for C...
May 24, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28538739/multiplex-pcr-method-for-minion-and-illumina-sequencing-of-zika-and-other-virus-genomes-directly-from-clinical-samples
#14
Joshua Quick, Nathan D Grubaugh, Steven T Pullan, Ingra M Claro, Andrew D Smith, Karthik Gangavarapu, Glenn Oliveira, Refugio Robles-Sikisaka, Thomas F Rogers, Nathan A Beutler, Dennis R Burton, Lia Laura Lewis-Ximenez, Jaqueline Goes de Jesus, Marta Giovanetti, Sarah C Hill, Allison Black, Trevor Bedford, Miles W Carroll, Marcio Nunes, Luiz Carlos Alcantara, Ester C Sabino, Sally A Baylis, Nuno R Faria, Matthew Loose, Jared T Simpson, Oliver G Pybus, Kristian G Andersen, Nicholas J Loman
Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples (i.e., without isolation and culture) remains challenging for viruses such as Zika, for which metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence-complete genomes, comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimized library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences...
June 2017: Nature Protocols
https://www.readbyqxmd.com/read/28538144/probing-the-potential-role-of-non-b-dna-structures-at-yeast-meiosis-specific-dna-double-strand-breaks
#15
Rucha Kshirsagar, Krishnendu Khan, Mamata V Joshi, Ramakrishna V Hosur, K Muniyappa
A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28536711/a-target-triggered-proximity-combination-based-fluorescence-sensing-strategy-for-adenosine-detection
#16
Xiaowen Xu, Haiping Wei, Wei Jiang
Adenosine is a potent physiological and pharmacological regulator, and its abnormal level is closely related to disease development. The sensitive and specific detection of adenosine is crucial for health evaluation and disease diagnosis. In this work, a target triggered proximity combination-based fluorescence sensing strategy is developed for the sensitive and specific detection of adenosine. A difunctional probe showing target recognition and signal amplification is designed, by integration of DNA linker-connected split aptamer fragments with a fragment-elongated polymerase/nicking template...
May 24, 2017: Analyst
https://www.readbyqxmd.com/read/28536590/miniature-inverted-repeat-transposable-element-insertions-provide-a-source-of-intron-length-polymorphism-markers-in-the-carrot-daucus-carota-l
#17
Katarzyna Stelmach, Alicja Macko-Podgórni, Gabriela Machaj, Dariusz Grzebelus
The prevalence of non-autonomous class II transposable elements (TEs) in plant genomes may serve as a tool for relatively rapid and low-cost development of gene-associated molecular markers. Miniature inverted-repeat transposable element (MITE) copies inserted within introns can be exploited as potential intron length polymorphism (ILP) markers. ILPs can be detected by PCR with primers anchored in exon sequences flanking the target introns. Here, we designed primers for 209 DcSto (Daucus carota Stowaway-like) MITE insertion sites within introns along the carrot genome and validated them as candidate ILP markers in order to develop a set of markers for genotyping the carrot...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28536584/genotyping-by-sequencing-and-its-exploitation-for-forage-and-cool-season-grain-legume-breeding
#18
Paolo Annicchiarico, Nelson Nazzicari, Yanling Wei, Luciano Pecetti, Edward C Brummer
Genotyping-by-Sequencing (GBS) may drastically reduce genotyping costs compared with single nucleotide polymorphism (SNP) array platforms. However, it may require optimization for specific crops to maximize the number of available markers. Exploiting GBS-generated markers may require optimization, too (e.g., to cope with missing data). This study aimed (i) to compare elements of GBS protocols on legume species that differ for genome size, ploidy, and breeding system, and (ii) to show successful applications and challenges of GBS data on legume species...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28536431/novel-highly-divergent-sapoviruses-detected-by-metagenomics-analysis-in-straw-colored-fruit-bats-in-cameroon
#19
Claude Kwe Yinda, Nádia Conceição-Neto, Mark Zeller, Elisabeth Heylen, Piet Maes, Stephen Mbigha Ghogomu, Marc Van Ranst, Jelle Matthijnssens
Sapoviruses (SaVs) belong to the Sapovirus genus, in the family Caliciviridae. They have been associated with gastroenteritis in humans and in pigs but not in other animals. In addition, some strains from pigs, chimpanzees and rodents show close sequence identity with human SaVs thereby suggesting the possibility of interspecies transmissions. Bats are known to be a major reservoir of zoonotic viruses, however, very little is known about the genetic diversity of SaVs in bats. To explore the genetic diversity of bat SaVs, fecal samples of Eidolon helvum and Epomophorus gambianus were treated according to the NetoVIR protocol and sequenced by Illumina technology...
May 24, 2017: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/28536161/correction-for-evans-et-al-informing-antibiotic-treatment-decisions-evaluating-rapid-molecular-diagnostics-to-identify-susceptibility-and-resistance-to-carbapenems-against-acinetobacter-spp-in-primers-iii
#20
Scott R Evans, Andrea M Hujer, Hongyu Jiang, Carol B Hill, Kristine M Hujer, Jose R Mediavilla, Claudia Manca, Thuy Tien T Tran, T Nicholas Domitrovic, Paul G Higgins, Harald Seifert, Barry N Kreiswirth, Robin Patel, Michael R Jacobs, Liang Chen, Rangarajan Sampath, Thomas Hall, Christine Marzan, Vance G Fowler, Henry F Chambers, Robert A Bonomo
No abstract text is available yet for this article.
June 2017: Journal of Clinical Microbiology
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