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https://www.readbyqxmd.com/read/28514600/evaluating-five-different-loci-rbcl-rpob-rpoc1-matk-and-its-for-dna-barcoding-of-indian-orchids
#1
Iffat Parveen, Hemant Kumar Singh, Saloni Malik, Saurabh Raghuvanshi, Shashi Bhushan Babbar
Orchidaceae, one of the largest families of angiosperms, is represented in India by 1600 species distributed in diverse habitats. Orchids are in high demand due to their beautiful flowers and therapeutic properties. Overexploitation and habitat destruction have made many orchid species endangered. In the absence of effective identification methods, illicit trade of orchids continues unabated. Considering DNA barcoding as a potential identification tool, species discrimination capability of five loci, ITS matK, rbcL, rpoB and rpoC1, was tested in 393 accessions of 94 Indian orchid species belonging to 47 genera, including one listed in Appendix I of CITES and 26 medicinal species...
May 17, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28507815/a-new-molecular-diagnostic-tool-for-surveying-and-monitoring-triops-cancriformis-populations
#2
Graham S Sellers, Larry R Griffin, Bernd Hänfling, Africa Gómez
The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism's life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations...
2017: PeerJ
https://www.readbyqxmd.com/read/28499337/optically-encoded-semiconducting-polymer-dots-with-single-wavelength-excitation-for-barcoding-and-tracking-of-single-cells
#3
Chun-Ting Kuo, Hong-Shang Peng, Yu Rong, Jiangbo Yu, Wei Sun, Bryant S Fujimoto, Daniel T Chiu
Multiplexed optical encoding is emerging as a powerful technique for high-throughput cellular analysis and molecular assays. Most of the developed optical barcodes, however, either suffer from large particle size or are incompatible with most commercial optical instruments. Here, a new type of nanoscale fluorescent barcodes (Pdot barcodes) was prepared from semiconducting polymers. The Pdot barcodes possess the merits of small size (~20 nm in diameter), narrow emission bands (FWHM of 30-40 nm), three-color emissions (blue, green, and red) under single-wavelength excitation, a high brightness, good pH and thermal stability, and efficient cellular uptake...
May 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28493919/genomic-variation-in-plasmodium-vivax-malaria-reveals-regions-under-selective-pressure
#4
Ernest Diez Benavente, Zoe Ward, Wilson Chan, Fady R Mohareb, Colin J Sutherland, Cally Roper, Susana Campino, Taane G Clark
BACKGROUND: Although Plasmodium vivax contributes to almost half of all malaria cases outside Africa, it has been relatively neglected compared to the more deadly P. falciparum. It is known that P. vivax populations possess high genetic diversity, differing geographically potentially due to different vector species, host genetics and environmental factors. RESULTS: We analysed the high-quality genomic data for 46 P. vivax isolates spanning 10 countries across 4 continents...
2017: PloS One
https://www.readbyqxmd.com/read/28489817/selectivity-determinants-of-gpcr-g-protein-binding
#5
Tilman Flock, Alexander S Hauser, Nadia Lund, David E Gloriam, Santhanam Balaji, M Madan Babu
The selective coupling of G-protein-coupled receptors (GPCRs) to specific G proteins is critical to trigger the appropriate physiological response. However, the determinants of selective binding have remained elusive. Here we reveal the existence of a selectivity barcode (that is, patterns of amino acids) on each of the 16 human G proteins that is recognized by distinct regions on the approximately 800 human receptors. Although universally conserved positions in the barcode allow the receptors to bind and activate G proteins in a similar manner, different receptors recognize the unique positions of the G-protein barcode through distinct residues, like multiple keys (receptors) opening the same lock (G protein) using non-identical cuts...
May 10, 2017: Nature
https://www.readbyqxmd.com/read/28484128/characterizing-the-temporal-patterns-of-avian-influenza-virus-introduction-into-japan-by-migratory-birds
#6
Manabu Onuma, Masayoshi Kakogawa, Masae Yanagisawa, Atsushi Haga, Tomomi Okano, Yasuko Neagari, Tsukasa Okano, Koichi Goka, Mitsuhiko Asakawa
The objectives of the present study were to observe the temporal pattern of avian influenza virus (AIV) introduction into Japan and to determine which migratory birds play an important role in introducing AIV. In total, 19,407 fecal samples from migratory birds were collected at 52 sites between October 2008 and May 2015. Total nucleic acids extracted from the fecal samples were subjected to reverse transcription loop-mediated isothermal amplification to detect viral RNA. Species identification of host migratory birds was conducted by DNA barcoding for positive fecal samples...
May 7, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28481646/barcode-index-number-taxonomic-rank-and-modes-of-speciation-examples-from-fish
#7
Yuri Phedorovich Kartavtsev
Species delimitation by DNA sequence data or DNA barcoding is successful, as confirmed by the vast BOLD data base. However, the theory that would explain this fact has not been developed yet. An approach based on Barcoding Index Number (BIN), suggested in the assignment, allows delimiting of taxa of three ranks (species, genera, and families) and statistical validation with a high precision of delimiting (over 80%), as well as shows for majority of Co-1-based single gene trees good correspondence between their topology and conventional taxa content for analyzed fish species (R(2) ≈ 0...
May 8, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28475621/mageri-computational-pipeline-for-molecular-barcoded-targeted-resequencing
#8
Mikhail Shugay, Andrew R Zaretsky, Dmitriy A Shagin, Irina A Shagina, Ivan A Volchenkov, Andrew A Shelenkov, Mikhail Y Lebedin, Dmitriy V Bagaev, Sergey Lukyanov, Dmitriy M Chudakov
Unique molecular identifiers (UMIs) show outstanding performance in targeted high-throughput resequencing, being the most promising approach for the accurate identification of rare variants in complex DNA samples. This approach has application in multiple areas, including cancer diagnostics, thus demanding dedicated software and algorithms. Here we introduce MAGERI, a computational pipeline that efficiently handles all caveats of UMI-based analysis to obtain high-fidelity mutation profiles and call ultra-rare variants...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28472365/deciphering-the-genic-basis-of-yeast-fitness-variation-by-simultaneous-forward-and-reverse-genetics
#9
Calum J Maclean, Brian P H Metzger, Jian-Rong Yang, Wei-Chin Ho, Bryan Moyers, Jianzhi Zhang
The budding yeast Saccharomyces cerevisiae is the best studied eukaryote in molecular and cell biology, but its utility for understanding the genetic basis of phenotypic variation in natural populations is limited by inefficient association mapping due to strong and complex population structure. To overcome this challenge, we generated genome sequences for 85 strains and performed a comprehensive population genomic survey of a total of 190 diverse strains. We identified considerable variation in population structure among chromosomes and identified 181 genes that are absent from the reference genome...
May 4, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28472156/genetically-barcoded-siv-facilitates-enumeration-of-rebound-variants-and-estimation-of-reactivation-rates-in-nonhuman-primates-following-interruption-of-suppressive-antiretroviral-therapy
#10
Christine M Fennessey, Mykola Pinkevych, Taina T Immonen, Arnold Reynaldi, Vanessa Venturi, Priyanka Nadella, Carolyn Reid, Laura Newman, Leslie Lipkey, Kelli Oswald, William J Bosche, Matthew T Trivett, Claes Ohlen, David E Ott, Jacob D Estes, Gregory Q Del Prete, Jeffrey D Lifson, Miles P Davenport, Brandon F Keele
HIV and SIV infection dynamics are commonly investigated by measuring plasma viral loads. However, this total viral load value represents the sum of many individual infection events, which are difficult to independently track using conventional sequencing approaches. To overcome this challenge, we generated a genetically tagged virus stock (SIVmac239M) with a 34-base genetic barcode inserted between the vpx and vpr accessory genes of the infectious molecular clone SIVmac239. Next-generation sequencing of the virus stock identified at least 9,336 individual barcodes, or clonotypes, with an average genetic distance of 7 bases between any two barcodes...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28468764/a-resource-for-functional-profiling-of-noncoding-rna-in-the-yeast-saccharomyces-cerevisiae
#11
Steven Parker, Marcin Fraczek, Jian Wu, Sara Shamsah, Alkisti Manousaki, Kobchai Dungrattanalert, Rogerio Alves de Almeida, Diego Estrada-Rivadeneyra, Walid Omara, Daniela Delneri, Raymond T O'Keefe
Eukaryotic genomes are extensively transcribed generating many different RNAs with no known function. We have constructed 1502 molecular barcoded ncRNA gene deletion strains encompassing 443 ncRNAs in the yeast Saccharomyces cerevisiae as tools for ncRNA functional analysis. This resource includes deletions of small nuclear RNAs (snRNAs), transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs) and other annotated ncRNAs as well as the more recently identified stable unannotated transcripts (SUTs) and cryptic unstable transcripts (CUTs) whose functions are largely unknown...
May 3, 2017: RNA
https://www.readbyqxmd.com/read/28467234/morphological-and-genetic-analyses-of-the-first-record-of-longrakered-trevally-ulua-mentalis-perciformes-carangidae-and-of-the-pinjalo-snapper-pinjalo-pinjalo-perciformes-lutjanidae-in-the-odisha-coast-bay-of-bengal
#12
Tapan K Barik, Surya N Swain, Bijayalaxmi Sahu, Bibarani Tripathy, Usha R Acharya
Identification of fish species have so far been carried out mostly by classical morpho-taxonomy. In the present study, however, an attempt has been taken to identify two species of fishes Ulua mentalis and Pinjalo pinjalo of order Perciformes which happens to be the first record in Odisha coast Bay of Bengal, India during the year 2015, using DNA barcoding technique for reconfirmation over conventional morpho-taxonomy. During recent past, study of molecular-taxonomical profile of mitochondrial DNA in general and Cytochrome Oxidase subunit I (COI) gene in particular has gained enormous importance for accurate identification of species...
May 3, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28453569/molecular-exploration-of-hidden-diversity-in-the-indo-west-pacific-sciaenid-clade
#13
Pei-Chun Lo, Shu-Hui Liu, Siti Azizah Mohd Nor, Wei-Jen Chen
The family Sciaenidae, known as croakers or drums, is one of the largest perciform fish families. A recent multi-gene based study investigating the phylogeny and biogeography of global sciaenids revealed that the origin and early diversification of this family occurred in tropical America during the Late Oligocene-Early Miocene before undergoing range expansions to other seas including the Indo-West Pacific, where high species richness is observed. Despite this clarification of the overall evolutionary history of the family, knowledge of the taxonomy and phylogeny of sciaenid genera endemic to the Indo-West Pacific is still limited due to lack of a thorough survey of all taxa...
2017: PloS One
https://www.readbyqxmd.com/read/28453559/evaluation-of-the-reproducibility-of-amplicon-sequencing-with-illumina-miseq-platform
#14
Chongqing Wen, Liyou Wu, Yujia Qin, Joy D Van Nostrand, Daliang Ning, Bo Sun, Kai Xue, Feifei Liu, Ye Deng, Yuting Liang, Jizhong Zhou
Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as reproducibility, still exist. To assess reproducibility, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33...
2017: PloS One
https://www.readbyqxmd.com/read/28449274/a-dna-barcode-library-for-germany-s-mayflies-stoneflies-and-caddisflies-ephemeroptera-plecoptera-trichoptera
#15
Jérôme Morinière, Lars Hendrich, Michael Balke, Arne J Beermann, Tobias König, Monika Hess, Stefan Koch, Reinhard Müller, Florian Leese, Paul D N Hebert, Axel Hausmann, Christoph F Schubart, Gerhard Haszprunar
Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. However, a comprehensive DNA barcode library based upon taxonomically well-curated specimens can overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient, and reliable DNA-based identifications and assessments of ecological status...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28448639/cryptic-diversity-of-the-subfamily-calaphidinae-hemiptera-aphididae-revealed-by-comprehensive-dna-barcoding
#16
Yerim Lee, Wonhoon Lee, Mariusz Kanturski, Robert G Foottit, Shin-Ichi Akimoto, Seunghwan Lee
Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank)...
2017: PloS One
https://www.readbyqxmd.com/read/28443113/barcode-system-for-genetic-identification-of-soybean-glycine-max-l-merrill-cultivars-using-indel-markers-specific-to-dense-variation-blocks
#17
Hwang-Bae Sohn, Su-Jeong Kim, Tae-Young Hwang, Hyang-Mi Park, Yu-Young Lee, Kesavan Markkandan, Dongwoo Lee, Sunghoon Lee, Su-Young Hong, Yun-Ho Song, Bon-Cheol Koo, Yul-Ho Kim
For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28439828/interrogation-of-functional-mirna-target-interactions-by-crispr-cas9-genome-engineering
#18
Yale S Michaels, Qianxin Wu, Tudor A Fulga
Post-transcriptional silencing by microRNAs (miRNAs) is a critical constituent of eukaryotic gene regulation. miRNAs are short (~22nt) noncoding RNAs capable of specifically targeting the miRNA-induced-silencing-complex (miRISC) to transcripts bearing a complementary miRNA response element (MRE). Although recent methodological advances have greatly improved our understanding of miRNA biogenesis and the mechanisms by which miRNAs repress their cognate targets, exploring the physiological relevance of direct miRNA-target interactions in vivo has remained an outstanding challenge...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28431212/dna-barcoding-and-traditional-taxonomy-an-integrated-approach-for-biodiversity-conservation
#19
Bhavisha P Sheth, Vrinda S Thaker
Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks...
April 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28420399/distinct-parasite-populations-infect-individuals-identified-through-passive-and-active-case-detection-in-a-region-of-declining-malaria-transmission-in-southern-zambia
#20
Kelly M Searle, Ben Katowa, Tamaki Kobayashi, Mwiche N S Siame, Sungano Mharakurwa, Giovanna Carpi, Douglas E Norris, Jennifer C Stevenson, Philip E Thuma, William J Moss
BACKGROUND: Substantial reductions in the burden of malaria have been documented in parts of sub-Saharan Africa, with elimination strategies and goals being formulated in some regions. Within this context, understanding the epidemiology of low-level malaria transmission is crucial to achieving and sustaining elimination. A 24 single-nucleotide-polymorphism Plasmodium falciparum molecular barcode was used to characterize parasite populations from infected individuals identified through passive and active case detection in an area approaching malaria elimination in southern Zambia...
April 19, 2017: Malaria Journal
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