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https://www.readbyqxmd.com/read/28921904/developing-a-dna-barcode-library-for-perciform-fishes-in-the-south-china-sea-species-identification-accuracy-and-cryptic-diversity
#1
Gang Hou, Wei-Tao Chen, Huo-Sheng Lu, Fei Cheng, Song-Guang Xie
DNA barcodes were studied for 1,353 specimens representing 272 morphological species belonging to 149 genera and 55 families of Perciformes from the South China Sea (SCS). The average Kimura 2-parameter (K2P) distances within species, genera, and families were 0.31%, 8.71%, and 14.52%, respectively. A Neighbor-joining (NJ) tree, Bayesian inference (BI) and maximum-likelihood (ML) trees and Automatic Barcode Gap Discovery (ABGD) revealed 260, 253 and 259 single-species-representing clusters, respectively. Barcoding Gap Analysis (BGA) demonstrated that barcode gaps were present for 178 of 187 species analysed with multiple specimens (95...
September 15, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28919968/a-new-species-of-melitaea-from-israel-with-notes-on-taxonomy-cytogenetics-phylogeography-and-interspecific-hybridization-in-the-melitaea-persea-complex-lepidoptera-nymphalidae
#2
Vladimir A Lukhtanov
Specimens with intermediate morphology are often considered to be the result of ongoing interspecific hybridization; however, this conclusion is difficult to prove without analysis of chromosomal and/or molecular markers. In the butterfly genus Melitaea, such an intermediacy can be detected in male genitalia, and is more or less regularly observed in localities where two closely related, presumably parental species are found in sympatry. Here I analyze a high altitude Melitaea population from Mt. Hermon in north Israel and show that its male genitalia are clearly differentiated from those found in phenotypically similar M...
2017: Comparative Cytogenetics
https://www.readbyqxmd.com/read/28915829/how-often-do-mosquitoes-bite-humans-in-southern-england-a-standardised-summer-trial-at-four-sites-reveals-spatial-temporal-and-site-related-variation-in-biting-rates
#3
Victor A Brugman, Marion E England, Joanne Stoner, Laura Tugwell, Lara E Harrup, Anthony J Wilson, Jolyon M Medlock, James G Logan, Anthony R Fooks, Peter P C Mertens, Nicholas Johnson, Simon Carpenter
BACKGROUND: This field-based study examined the abundance and species complement of mosquitoes (Diptera: Culicidae) attracted to humans at four sites in the United Kingdom (UK). The study used a systematic approach to directly measure feeding by mosquitoes on humans at multiple sites and using multiple volunteers. Quantifying how frequently humans are bitten in the field by mosquitoes is a fundamental parameter in assessing arthropod-borne virus transmission. METHODS: Human landing catches were conducted using a standardised protocol by multiple volunteers at four rural sites between July and August 2013...
September 15, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28914776/worldwide-occurrence-and-investigations-of-contamination-of-herbal-medicines-by-tropane-alkaloids
#4
REVIEW
Thomas Y K Chan
Tropane alkaloids occur mainly in Solanaceae plants. In the present review, the main objective is to describe the worldwide occurrence and investigations of anticholinergic poisoning due to the contamination of herbal teas and herbs by tropane alkaloids. Tropane alkaloid poisoning can occur after consumption of any medicinal plant if Solanaceae plants or plant parts are present as contaminants. Globally, almost all reports in 1978-2014 involve herbal teas and one of the prescribed herbs in composite formulae...
September 15, 2017: Toxins
https://www.readbyqxmd.com/read/28914591/mucosa-associated-microbiota-dysbiosis-in-colitis-associated-cancer
#5
Mathias L Richard, Giuseppina Liguori, Bruno Lamas, Giovanni Brandi, Gregory da Costa, Thomas W Hoffmann, Massimo Pierluigi Di Simone, Carlo Calabrese, Gilberto Poggioli, Philippe Langella, Massimo Campieri, Harry Sokol
Gut microbiota dysbiosis has been associated with inflammatory bowel diseases (IBD). In colorectal cancer, the gut microbiota has also been recognized as potentially involved in aggravating or favoring the tumor development. However, very little is known on the structure and role of the microbiota in colitis associated cancer (CAC), an important complication of IBD in human. Here we analyzed the bacterial and fungal composition of the mucosa associated microbiota of patients suffering CAC, sporadic cancer (SC) and of healthy subjects (HS) by barcode sequences analysis on the following cohort: 7 CAC patients, 10 SC patients and 10 HS using 16S (MiSeq) and ITS2 (pyrosequencing) sequencing, for bacteria and fungi respectively...
September 15, 2017: Gut Microbes
https://www.readbyqxmd.com/read/28911667/dna-barcode-and-identification-of-the-varieties-and-provenances-of-taiwan-s-domestic-and-imported-made-teas-using-ribosomal-internal-transcribed-spacer-2-sequences
#6
Shih-Chieh Lee, Chia-Hsiang Wang, Cheng-En Yen, Chieh Chang
The major aim of made tea identification is to identify the variety and provenance of the tea plant. The present experiment used 113 tea plants [Camellia sinensis (L.) O. Kuntze] housed at the Tea Research and Extension Substation, from which 113 internal transcribed spacer 2 (ITS2) fragments, 104 trnL intron, and 98 trnL-trnF intergenic sequence region DNA sequences were successfully sequenced. The similarity of the ITS2 nucleotide sequences between tea plants housed at the Tea Research and Extension Substation was 0...
April 2017: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/28911333/profiling-bacterial-communities-by-minion-sequencing-of-ribosomal-operons
#7
Lee J Kerkhof, Kevin P Dillon, Max M Häggblom, Lora R McGuinness
BACKGROUND: An approach utilizing the long-read capability of the Oxford Nanopore MinION to rapidly sequence bacterial ribosomal operons of complex natural communities was developed. Microbial fingerprinting employs domain-specific forward primers (16S rRNA subunit), reverse primers (23S rRNA subunit), and a high-fidelity Taq polymerase with proofreading capabilities. Amplicons contained both ribosomal subunits for broad-based phylogenetic assignment (~ 3900 bp of sequence), plus the intergenic spacer (ITS) region (~ 300 bp) for potential strain-specific identification...
September 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28910286/potential-dna-barcodes-for-melilotus-species-based-on-five-single-loci-and-their-combinations
#8
Fan Wu, Jinxing Ma, Yuqin Meng, Daiyu Zhang, Blaise Pascal Muvunyi, Kai Luo, Hongyan Di, Wenli Guo, Yanrong Wang, Baochang Feng, Jiyu Zhang
Melilotus, an annual or biennial herb, belongs to the tribe Trifolieae (Leguminosae) and consists of 19 species. As an important green manure crop, diverse Melilotus species have different values as feed and medicine. To identify different Melilotus species, we examined the efficiency of five candidate regions as barcodes, including the internal transcribed spacer (ITS) and two chloroplast loci, rbcL and matK, and two non-coding loci, trnH-psbA and trnL-F. In total, 198 individuals from 98 accessions representing 18 Melilotus species were sequenced for these five potential barcodes...
2017: PloS One
https://www.readbyqxmd.com/read/28906059/benefits-and-limitations-of-dna-barcoding-and-metabarcoding-in-herbal-product-authentication
#9
REVIEW
Ancuta Cristina Raclariu, Michael Heinrich, Mihael Cristin Ichim, Hugo de Boer
INTRODUCTION: Herbal medicines play an important role globally in the health care sector and in industrialised countries they are often considered as an alternative to mono-substance medicines. Current quality and authentication assessment methods rely mainly on morphology and analytical phytochemistry-based methods detailed in pharmacopoeias. Herbal products however are often highly processed with numerous ingredients, and even if these analytical methods are accurate for quality control of specific lead or marker compounds, they are of limited suitability for the authentication of biological ingredients...
September 14, 2017: Phytochemical Analysis: PCA
https://www.readbyqxmd.com/read/28906012/pacbio-metabarcoding-of-fungi-and-other-eukaryotes-errors-biases-and-perspectives
#10
Leho Tedersoo, Ave Tooming-Klunderud, Sten Anslan
Second-generation, high-throughput sequencing methods have greatly improved our understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) provide limited taxonomic and phylogenetic information for species discrimination and taxonomic assignment. Here, we utilized the third-generation Pacific Biosciences (PacBio) RSII and Sequel instruments to evaluate the suitability of full-length internal transcribed spacer (ITS) barcodes and longer rRNA gene amplicons for metabarcoding Fungi, Oomycetes and other eukaryotes in soil samples...
September 14, 2017: New Phytologist
https://www.readbyqxmd.com/read/28905379/a-new-species-of-pomatoschistus-teleostei-gobiidae-the%C3%A2-mediterranean-s-smallest-marine-fish
#11
S Engin, D Seyhan
The new sand goby species Pomatoschistus nanus (Teleostei: Gobiidae) is described from the northern coast of the Levantine Sea (eastern Mediterranean Sea) based on both morphological and DNA barcoding data. The new species is the smallest fish in the Mediterranean Sea and may be distinguished from congeners by the following features: predorsal area, first dorsal-fin base and breast naked; δ-pore missing; anterior point of the suborbital row b not reaching level of posterior point of suborbital row d; slightly emarginated caudal fin and nape coloration pattern...
September 14, 2017: Journal of Fish Biology
https://www.readbyqxmd.com/read/28905200/development-of-a-stable-lung-microbiome-in-healthy-neonatal-mice
#12
Matea Kostric, Katrin Milger, Susanne Krauss-Etschmann, Marion Engel, Gisle Vestergaard, Michael Schloter, Anne Schöler
The lower respiratory tract has been previously considered sterile in a healthy state, but advances in culture-independent techniques for microbial identification and characterization have revealed that the lung harbors a diverse microbiome. Although research on the lung microbiome is increasing and important questions were already addressed, longitudinal studies aiming to describe developmental stages of the microbial communities from the early neonatal period to adulthood are lacking. Thus, little is known about the early-life development of the lung microbiome and the impact of external factors during these stages...
September 13, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28905136/highly-sensitive-detection-of-esr1-mutations-in-cell-free-dna-from-patients-with-metastatic-breast-cancer-using-molecular-barcode-sequencing
#13
Nanae Masunaga, Naofumi Kagara, Daisuke Motooka, Shota Nakamura, Tomohiro Miyake, Tomonori Tanei, Yasuto Naoi, Masafumi Shimoda, Kenzo Shimazu, Seung Jin Kim, Shinzaburo Noguchi
PURPOSE: We aimed to develop a highly sensitive method to detect ESR1 mutations in cell-free DNA (cfDNA) using next-generation sequencing with molecular barcode (MB-NGS) targeting the hotspot segment (c.1600-1713). METHODS: The sensitivity of MB-NGS was tested using serially diluted ESR1 mutant DNA and then cfDNA samples from 34 patients with metastatic breast cancer were analyzed with MB-NGS. The results of MB-NGS were validated in comparison with conventional NGS and droplet digital PCR (ddPCR)...
September 13, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28904776/escaping-introns-in-coi-through-cdna-barcoding-of-mushrooms-pleurotus-as-a-test-case
#14
Farhat A Avin, Bhassu Subha, Yee-Shin Tan, Thomas W A Braukmann, Sabaratnam Vikineswary, Paul D N Hebert
DNA barcoding involves the use of one or more short, standardized DNA fragments for the rapid identification of species. A 648-bp segment near the 5' terminus of the mitochondrial cytochrome c oxidase subunit I (COI) gene has been adopted as the universal DNA barcode for members of the animal kingdom, but its utility in mushrooms is complicated by the frequent occurrence of large introns. As a consequence, ITS has been adopted as the standard DNA barcode marker for mushrooms despite several shortcomings. This study employed newly designed primers coupled with cDNA analysis to examine COI sequence diversity in six species of Pleurotus and compared these results with those for ITS...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28902202/responsive-photonic-barcodes-for-sensitive-multiplex-bioassay
#15
Chengxin Luan, Yueshuang Xu, Fanfan Fu, Huan Wang, Qionghua Xu, Baoan Chen, Yuanjin Zhao
Barcodes have a demonstrated value for multiplex high-throughput bioassays. The tendency of this technology is to pursue high sensitivity target screening. Herein, we presented a new type of inverse opal-structured poly(N-isopropylacrylamide) (pNIPAM) hydrogel photonic crystal (PhC) barcodes with the function of fluorescent signal self-amplification for the detection. During the bio-reaction process at body temperature, the pNIPAM hydrogel barcodes kept swelling, and their inverse opal structure with interconnected pores provided unblocked channels for the targets to diffuse into the voids of the barcodes and react...
September 13, 2017: Nanoscale
https://www.readbyqxmd.com/read/28902130/the-chloroplast-genome-sequence-of-scutellaria-baicalensis-provides-insight-into-intraspecific-and-interspecific-chloroplast-genome-diversity-in-scutellaria
#16
Dan Jiang, Zhenyu Zhao, Teng Zhang, Wenhao Zhong, Chunsheng Liu, Qingjun Yuan, Luqi Huang
Scutellaria baicalensis Georgi (Lamiaceae) is the source of the well-known traditional Chinese medicine "HuangQin" (Radix Scutellariae). Natural sources of S. baicalensis are rapidly declining due to high market demand and overexploitation. Moreover, the commercial products of Radix Scutellariae have often been found to contain adulterants in recent years, which may give rise to issues regarding drug efficacy and safety. In this study, we developed valuable chloroplast molecular resources by comparing intraspecific and interspecific chloroplast genome...
September 13, 2017: Genes
https://www.readbyqxmd.com/read/28901371/synthesis-of-a-multi-functional-dna-nanosphere-barcode-system-for-direct-cell-detection
#17
Sangwoo Han, Jae Sung Lee, Jong Bum Lee
Nucleic acid-based technologies have been applied to numerous biomedical applications. As a novel material for target detection, DNA has been used to construct a barcode system with a range of structures. This paper reports multi-functionalized DNA nanospheres (DNANSs) by rolling circle amplification (RCA) with several functionalized nucleotides. DNANSs with a barcode system were designed to exhibit fluorescence for coding enhanced signals and contain biotin for more functionalities, including targeting through the biotin-streptavidin (biotin-STA) interaction...
September 13, 2017: Nanoscale
https://www.readbyqxmd.com/read/28895964/dynamic-sers-nanosensor-for-neurotransmitter-sensing-near-neurons
#18
Félix Lussier, Thibault Brulé, Marie-Josée Bourque, Charles Ducrot, Louis-Éric Trudeau, Jean-François Masson
Current electrophysiology and electrochemistry techniques have provided unprecedented understanding of neuronal activity. However, these techniques are suited to a small, albeit important, panel of neurotransmitters such as glutamate, GABA and dopamine, and these constitute only a subset of the broader range of neurotransmitters involved in brain chemistry. Surface-enhanced Raman scattering (SERS) provides a unique opportunity to detect a broader range of neurotransmitters in close proximity to neurons. Dynamic SERS (D-SERS) nanosensors based on patch-clamp-like nanopipettes decorated with gold nanoraspberries can be located accurately under a microscope using techniques analogous to those used in current electrophysiology or electrochemistry experiments...
September 12, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28894108/description-of-two-three-gendered-nematode-species-in-the-new-genus-auanema-rhabditina-that-are-models-for-reproductive-mode-evolution
#19
Natsumi Kanzaki, Karin Kiontke, Ryusei Tanaka, Yuuri Hirooka, Anna Schwarz, Thomas Müller-Reichert, Jyotiska Chaudhuri, Andre Pires-daSilva
The co-existence of males, females and hermaphrodites, a rare mating system known as trioecy, has been considered as an evolutionarily transient state. In nematodes, androdioecy (males/hermaphrodites) as found in Caenorhabditis elegans, is thought to have evolved from dioecy (males/females) through a trioecious intermediate. Thus, trioecious species are good models to understand the steps and requirements for the evolution of new mating systems. Here we describe two new species of nematodes with trioecy, Auanema rhodensis and A...
September 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28892487/transcriptome-sequencing-and-delimitation-of-sympatric-oscarella-species-o-carmela-and-o-pearsei-sp-nov-from-california-usa
#20
Alexander V Ereskovsky, Daniel J Richter, Dennis V Lavrov, Klaske J Schippers, Scott A Nichols
The homoscleromorph sponge Oscarella carmela, first described from central California, USA is shown to represent two superficially similar but both morphologically and phylogenetically distinct species that are co-distributed. We here describe a new species as Oscarella pearsei, sp. nov. and re-describe Oscarella carmela; the original description was based upon material from both species. Further, we correct the identification of published genomic/transcriptomic resources that were originally attributed to O...
2017: PloS One
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