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https://www.readbyqxmd.com/read/28208623/fluorescence-lectin-bar-coding-of-glycoconjugates-in-the-extracellular-matrix-of-biofilm-and-bioaggregate-forming-microorganisms
#1
Thomas R Neu, Ute Kuhlicke
Microbial biofilm systems are defined as interface-associated microorganisms embedded into a self-produced matrix. The extracellular matrix represents a continuous challenge in terms of characterization and analysis. The tools applied in more detailed studies comprise extraction/chemical analysis, molecular characterization, and visualisation using various techniques. Imaging by laser microscopy became a standard tool for biofilm analysis, and, in combination with fluorescently labelled lectins, the glycoconjugates of the matrix can be assessed...
February 10, 2017: Microorganisms
https://www.readbyqxmd.com/read/28199101/fungal-identification-using-molecular-tools-a-primer-for-the-natural-products-research-community
#2
Huzefa A Raja, Andrew N Miller, Cedric J Pearce, Nicholas H Oberlies
Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi...
February 15, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28191885/molecular-definition-of-a-metastatic-lung-cancer-state-reveals-a-targetable-cd109-janus-kinase-stat-axis
#3
Chen-Hua Chuang, Peyton G Greenside, Zoë N Rogers, Jennifer J Brady, Dian Yang, Rosanna K Ma, Deborah R Caswell, Shin-Heng Chiou, Aidan F Winters, Barbara M Grüner, Gokul Ramaswami, Andrew L Spencley, Kimberly E Kopecky, Leanne C Sayles, E Alejandro Sweet-Cordero, Jin Billy Li, Anshul Kundaje, Monte M Winslow
Lung cancer is the leading cause of cancer deaths worldwide, with the majority of mortality resulting from metastatic spread. However, the molecular mechanism by which cancer cells acquire the ability to disseminate from primary tumors, seed distant organs, and grow into tissue-destructive metastases remains incompletely understood. We combined tumor barcoding in a mouse model of human lung adenocarcinoma with unbiased genomic approaches to identify a transcriptional program that confers metastatic ability and predicts patient survival...
February 13, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28187661/bird-droppings-on-chestnut-leaves-or-sawfly-larvae-dna-barcodes-verify-the-occurrence-of-the-archaic-i-megaxyela-i-i-togashii-i-hymenoptera-xyelidae-in-hokkaido-japan
#4
Akihiko Shinohara, Hideho Hara, Katja Kramp, Stephan M Blank, Yuichi Kameda
We made a molecular phylogenetic analysis using mitochondrial cytochrome oxidase subunit 1 (COI) gene sequences for ten unidentified Megaxyela larvae from Hokkaido, Honshu and Shikoku, Japan, and 15 identified adults of four Megaxyela, one Macroxyela and three Xyela species. It revealed that all larvae belonged to M. togashii Shinohara, 1992, which showed rather large intraspecific genetic variability even among the individuals from the same population. This is the first distribution record of M. togashii from Hokkaido...
January 17, 2017: Zootaxa
https://www.readbyqxmd.com/read/28169275/crispr-cas9-targeted-fragmentation-and-selective-sequencing-enable-massively-parallel-microsatellite-analysis
#5
GiWon Shin, Susan M Grimes, HoJoon Lee, Billy T Lau, Li C Xia, Hanlee P Ji
Microsatellites are multi-allelic and composed of short tandem repeats (STRs) with individual motifs composed of mononucleotides, dinucleotides or higher including hexamers. Next-generation sequencing approaches and other STR assays rely on a limited number of PCR amplicons, typically in the tens. Here, we demonstrate STR-Seq, a next-generation sequencing technology that analyses over 2,000 STRs in parallel, and provides the accurate genotyping of microsatellites. STR-Seq employs in vitro CRISPR-Cas9-targeted fragmentation to produce specific DNA molecules covering the complete microsatellite sequence...
February 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28166371/lineage-specific-and-highly-derived-gene-sequences-among-amoebozoa-revealed-by-the-comparative-analysis-of-transcriptomes-from-twelve-amoebozoan-species
#6
Natalya I Bondarenko, Anton S Bondarenko, Alexey V Smirnov
Amoebozoa represent a difficult group for traditional morphology-based taxonomy. Molecular approaches, such as gene sequencing and DNA barcoding have greatly enhanced our knowledge on the diversity of these organisms. However, metagenomic studies of Amoebozoa still did not provide as impressive results as they did among some other groups of protists. In environmental DNA surveys done on fragments of SSU rDNA gene and other traditional DNA barcodes, Amoebozoa genes normally constitute a minor part of the total gene diversity and represent only the most abundant lineages...
February 6, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28151699/cytogenetic-and-molecular-data-support-the-occurrence-of-three-gymnotus-species-gymnotiformes-gymnotidae-used-as-live-bait-in-corumb%C3%A3-brazil-implications-for-conservation-and-management-of-professional-fishing
#7
Tatiane Pires de Sousa, Débora Karla Silvestre Marques, Carla de Andrade Vitorino, Karina de Cassia Faria, Gisele da Silva Ferreira Braga, Daniela Cristina Ferreira, Paulo Cesar Venere
In the Pantanal of Mato Grosso do Sul, electric fish (Gymnotus spp.) are the primary source of live bait, accounting for more than three-quarters of total sales. Based on chromosomal and molecular markers, the present study attempted to identify the Gymnotus species used as bait in the region of Corumbá, Mato Grosso do Sul, Brazil. Three species were detected, based on their distinct karyotypes: G. paraguensis (2n = 54), G. sylvius (2n = 40), and G. pantanal (2n = 39-40, X1X2Y/X1X1X2X2), with no evidence being found of interspecific hybrids...
February 2, 2017: Zebrafish
https://www.readbyqxmd.com/read/28150727/development-of-a-multilocus-based-approach-for-sponge-phylum-porifera-identification-refinement-and-limitations
#8
Qi Yang, Christopher M M Franco, Shirley J Sorokin, Wei Zhang
For sponges (phylum Porifera), there is no reliable molecular protocol available for species identification. To address this gap, we developed a multilocus-based Sponge Identification Protocol (SIP) validated by a sample of 37 sponge species belonging to 10 orders from South Australia. The universal barcode COI mtDNA, 28S rRNA gene (D3-D5), and the nuclear ITS1-5.8S-ITS2 region were evaluated for their suitability and capacity for sponge identification. The highest Bit Score was applied to infer the identity...
February 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28138850/a-fosmid-pool-based-next-generation-sequencing-approach-to-haplotype-resolve-whole-genomes
#9
Eun-Kyung Suk, Sabrina Schulz, Birgit Mentrup, Thomas Huebsch, Jorge Duitama, Margret R Hoehe
Haplotype resolution of human genomes is essential to describe and interpret genetic variation and its impact on biology and disease. Our approach to haplotyping relies on converting genomic DNA into a fosmid library, which represents the entire diploid genome as a collection of haploid DNA clones of ~40 kb in size. These can be partitioned into pools such that the probability that the same pool contains both parental haplotypes is reduced to ~1 %. This is the key principle of this method, allowing entire pools of fosmids to be massively parallel sequenced, yielding haploid sequence output...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28126462/exploring-genetic-variation-in-haplotypes-of-the-filariasis-vector-culex-quinquefasciatus-diptera-culicidae-through-dna-barcoding
#10
Chithravel Vadivalagan, Pushparaj Karthika, Kadarkarai Murugan, Chellasamy Panneerselvam, Paola Del Serrone, Giovanni Benelli
Culex quinquefasciatus (Diptera: Culicidae) is a vector of many pathogens and parasites of humans, as well as domestic and wild animals. In urban and semi-urban Asian countries, Cx. quinquefasciatus is a main vector of nematodes causing lymphatic filariasis. In the African region, it vectors the Rift Valley fever virus, while in the USA it transmits West Nile, St. Louis encephalitis and Western equine encephalitis virus. In this study, DNA barcoding was used to explore the genetic variation of Cx. quinquefasciatus populations from 88 geographical regions...
January 23, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28117350/overlap-extension-barcoding-for-the-next-generation-sequencing-and-genotyping-of-plasmodium-falciparum-in-individual-patients-in-western-kenya
#11
Brandt Levitt, Andrew Obala, Scott Langdon, David Corcoran, Wendy Prudhomme O'Meara, Steve M Taylor
Large-scale molecular epidemiologic studies of Plasmodium falciparum parasites have provided insights into parasite biology and transmission, can identify the spread of drug resistance, and are useful in assessing vaccine targets. The polyclonal nature infections in high transmission settings is problematic for traditional genotyping approaches. Next-generation sequencing (NGS) approaches to parasite genotyping allow sensitive detection of minority variants, disaggregation of complex parasite mixtures, and scalable processing of large samples sets...
January 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28114306/new-evidences-of-mitochondrial-dna-heteroplasmy-by-putative-paternal-leakage-between-the-rock-partridge-alectoris-graeca-and-the-chukar-partridge-alectoris-chukar
#12
Andrea Gandolfi, Barbara Crestanello, Anna Fagotti, Francesca Simoncelli, Stefania Chiesa, Matteo Girardi, Eleonora Giovagnoli, Carla Marangoni, Ines Di Rosa, Livia Lucentini
The rock partridge, Alectoris graeca, is a polytypic species declining in Italy mostly due to anthropogenic causes, including the massive releases of the closely related allochthonous chukar partridge Alectoris chukar which produced the formation of hybrids. Molecular approaches are fundamental for the identification of evolutionary units in the perspective of conservation and management, and to correctly select individuals to be used in restocking campaigns. We analyzed a Cytochrome oxidase I (COI) fragment of contemporary and historical A...
2017: PloS One
https://www.readbyqxmd.com/read/28110431/a-report-on-identification-of-sequence-polymorphism-in-barcode-region-of-six-commercially-important-cymbopogon-species
#13
Ashok Kumar Bishoyi, Aarti Kavane, Anjali Sharma, K A Geetha
CYMBOPOGON: is an important member of grass family Poaceae, cultivated for essential oils which have greater medicinal and industrial value. Taxonomic identification of Cymbopogon species is determined mainly by morphological markers, odour of essential oils and concentration of bioactive compounds present in the oil matrices which are highly influenced by environment. Authenticated molecular marker based taxonomical identification is also lacking in the genus; hence effort was made to evaluate potential DNA barcode loci in six commercially important Cymbopogon species for their individual discrimination and authentication at the species level...
January 21, 2017: Molecular Biology Reports
https://www.readbyqxmd.com/read/28108445/multi-rate-poisson-tree-processes-for-single-locus-species-delimitation-under-maximum-likelihood-and-markov-chain-monte-carlo
#14
P Kapli, S Lutteropp, J Zhang, K Kobert, P Pavlidis, A Stamatakis, T Flouri
MOTIVATION: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28107413/improving-the-conservation-of-mediterranean-chondrichthyans-the-elasmomed-dna-barcode-reference-library
#15
Alessia Cariani, Silvia Messinetti, Alice Ferrari, Marco Arculeo, Juan J Bonello, Leanne Bonnici, Rita Cannas, Pierluigi Carbonara, Alessandro Cau, Charis Charilaou, Najib El Ouamari, Fabio Fiorentino, Maria Cristina Follesa, Germana Garofalo, Daniel Golani, Ilaria Guarniero, Robert Hanner, Farid Hemida, Omar Kada, Sabrina Lo Brutto, Cecilia Mancusi, Gabriel Morey, Patrick J Schembri, Fabrizio Serena, Letizia Sion, Marco Stagioni, Angelo Tursi, Nedo Vrgoc, Dirk Steinke, Fausto Tinti
Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles...
2017: PloS One
https://www.readbyqxmd.com/read/28104454/ecology-of-trypanosoma-cruzi-i-genotypes-across-rhodnius-prolixus-captured-in-attalea-butyracea-palms
#16
Cristina Poveda, Adriana Higuera, Plutarco Urbano, Juan David Ramírez
Trypanosoma cruzi, the agent of Chagas disease exhibits significant genetic diversity. This parasite is divided into six discrete typing units (DTUs) where T. cruzi I (TcI) is the most widespread in the Americas. TcI genotypes have been associated to domestic and sylvatic cycles of transmission (TcIDom and sylvatic TcI). Due to the importance of the enzootic transmission, we determined the frequency of TcI genotypes present in Rhodnius prolixus captured in different regions of the palm A. butyracea to understand the ecology of the disease and the importance of A...
January 16, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28104086/identification-of-triplophysa-species-from-the-qinghai-tibetan-plateau-qtp-and-its-adjacent-regions-through-dna-barcodes
#17
Jiuxuan Li, Ying Wang, Huifang Jin, Wujiao Li, Chaochao Yan, Pengfei Yan, Xiuyue Zhang, Shunping He, Zhaobin Song
The genus Triplophysa is the largest and most difficult to identity morphologically fish group of superfamily Cobitoidea with 140 currently valid species, and is mainly distributed in the Qinghai-Tibetan Plateau (QTP) and adjacent regions. Most species within this genus possess highly similar morphological characteristics for adaption to the highland environment and are very difficult to be identified only based on morphology. The traditional species identification, mainly based on external morphological diagnostic characters, leads to inconsistent results in many cases...
March 20, 2017: Gene
https://www.readbyqxmd.com/read/28100584/umi-tools-modelling-sequencing-errors-in-unique-molecular-identifiers-to-improve-quantification-accuracy
#18
Tom Sean Smith, Andreas Heger, Ian Sudbery
Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR-amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalised. In particular, sequencing errors in the UMI sequence are often ignored, or else resolved in an ad-hoc manner. We show that errors in the UMI sequence are common and introduce network based methods to account for these errors when identifying PCR duplicates...
January 18, 2017: Genome Research
https://www.readbyqxmd.com/read/28099773/comparison-of-green-and-albino-individuals-of-the-partially-mycoheterotrophic-orchid-epipactis-helleborine-on-molecular-identities-of-mycorrhizal-fungi-nutritional-modes-and-gene-expression-in-mycorrhizal-roots
#19
Kenji Suetsugu, Masahide Yamato, Chihiro Miura, Katsushi Yamaguchi, Kazuya Takahashi, Yoshiko Ida, Shuji Shigenobu, Hironori Kaminaka
Some green orchids obtain carbon from their mycorrhizal fungi, as well as from photosynthesis. These partially mycoheterotrophic orchids sometimes produce fully achlorophyllous, leaf-bearing (albino) variants. Comparing green and albino individuals of these orchids will help to uncover the molecular mechanisms associated with mycoheterotrophy. We compared green and albino Epipactis helleborine by molecular barcoding of mycorrhizal fungi, nutrient sources based on (15) N and (13) C abundances, and gene expression in their mycorrhizae by RNA-seq and cDNA de novo assembly...
January 18, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28094568/barcode-based-species-delimitation-in-the-marine-realm-a-test-using-hexanauplia-multicrustacea-thecostraca-and-copepoda
#20
Robert G Young, Cathryn L Abbott, Thomas W Therriault, Sarah J Adamowicz
DNA barcoding has been used successfully for identifying specimens belonging to marine planktonic groups. However, the ability to delineate species within taxonomically diverse and widely distributed marine groups, such as the Copepoda and Thecostraca, remains largely untested. We investigate whether a cytochrome c oxidase subunit I (COI-5P) global pairwise sequence divergence threshold exists between intraspecific and interspecific divergences in the copepods plus the thecostracans (barnacles and allies). Using publicly accessible sequence data, we applied a graphical method to determine an optimal threshold value...
October 21, 2016: Genome Génome / Conseil National de Recherches Canada
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