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https://www.readbyqxmd.com/read/28228677/review-of-neopalpa-povoln%C3%A3-1998-with-description-of-a-new-species-from-california-and-baja-california-mexico-lepidoptera-gelechiidae
#1
Vazrick Nazari
The monotypic genus Neopalpa was described in 1998 by Czech entomologist Dalibor Povolný based on two male specimens from Santa Catalina Island, California, which he named Neopalpa neonata. The female of this species was discovered recently based on a DNA barcode match and is described. In addition, a new species with marked differences in morphology and DNA barcodes from southern California and Baja California Mexico is described as Neopalpa donaldtrumpisp. n. Adults and genitalia of both species are illustrated, new diagnosis for the genus Neopalpa is provided, and its position within Gelechiidae is briefly discussed...
2017: ZooKeys
https://www.readbyqxmd.com/read/28228669/a-new-species-of-pristimantis-amphibia-anura-craugastoridae-from-a-montane-forest-of-the-pui-pui-protected-forest-in-central-peru-regi%C3%A3-n-jun%C3%A3-n
#2
Edgar Lehr, Jiří Moravec
A new species of frog of the genus Pristimantis is described from a montane forest between 1700 and 1800 m a.s.l. of the Pui Pui Protected Forest (Región Junín) in central Peru. Pristimantis ashaninkasp. n. is described based on five adult females (snout-vent length 23.1-26.7 mm) and ten juveniles (snout-vent length 10.6-13.4). It differs from its congeners by having the skin on dorsum shagreen with many conical tubercles giving it a spinose appearance, lacking a tympanum, having groin, anterior and posterior surfaces of thighs uniformly grayish brown, and a pale bronze iris with fine black reticulations, a median reddish hint horizontally across iris, and a black narrow vertical streak from pupil across lower and upper half of iris...
2017: ZooKeys
https://www.readbyqxmd.com/read/28228107/effectiveness-of-its-and-sub-regions-as-dna-barcode-markers-for-the-identification-of-basidiomycota-fungi
#3
Fernanda Badotti, Francislon Silva de Oliveira, Cleverson Fernando Garcia, Aline Bruna Martins Vaz, Paula Luize Camargos Fonseca, Laila Alves Nahum, Guilherme Oliveira, Aristóteles Góes-Neto
BACKGROUND: Fungi are among the most abundant and diverse organisms on Earth. However, a substantial amount of the species diversity, relationships, habitats, and life strategies of these microorganisms remain to be discovered and characterized. One important factor hindering progress is the difficulty in correctly identifying fungi. Morphological and molecular characteristics have been applied in such tasks. Later, DNA barcoding has emerged as a new method for the rapid and reliable identification of species...
February 23, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28224997/clonal-reversal-of-ageing-associated-stem-cell-lineage-bias-via-a-pluripotent-intermediate
#4
Martin Wahlestedt, Eva Erlandsson, Trine Kristiansen, Rong Lu, Cord Brakebusch, Irving L Weissman, Joan Yuan, Javier Martin-Gonzalez, David Bryder
Ageing associates with significant alterations in somatic/adult stem cells and therapies to counteract these might have profound benefits for health. In the blood, haematopoietic stem cell (HSC) ageing is linked to several functional shortcomings. However, besides the recent realization that individual HSCs might be preset differentially already from young age, HSCs might also age asynchronously. Evaluating the prospects for HSC rejuvenation therefore ultimately requires approaching those HSCs that are functionally affected by age...
February 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28223725/gut-microbial-diversity-analysis-using-illumina-sequencing-for-functional-dyspepsia-with-liver-depression-spleen-deficiency-syndrome-and-the-interventional-xiaoyaosan-in-a-rat-model
#5
Juan-Juan Qiu, Zhe Liu, Peng Zhao, Xue-Jun Wang, Yu-Chun Li, Hua Sui, Lawrence Owusu, Hui-Shu Guo, Zheng-Xu Cai
AIM: To investigate gut microbial diversity and the interventional effect of Xiaoyaosan (XYS) in a rat model of functional dyspepsia (FD) with liver depression-spleen deficiency syndrome. METHODS: The FD with liver depression-spleen deficiency syndrome rat model was established through classic chronic mild unpredictable stimulation every day. XYS group rats received XYS 1 h before the stimulation. The models were assessed by parameters including state of the rat, weight, sucrose test result and open-field test result...
February 7, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28223460/mechanism-of-h2s-oxidation-by-the-dissimilatory-perchlorate-reducing-microorganism-azospira-suillum-ps
#6
Misha G Mehta-Kolte, Dana Loutey, Ouwei Wang, Matthew D Youngblut, Christopher G Hubbard, Kelly M Wetmore, Mark E Conrad, John D Coates
The genetic and biochemical basis of perchlorate-dependent H2S oxidation (PSOX) was investigated in the dissimilatory perchlorate-reducing microorganism (DPRM) Azospira suillum PS (PS). Previously, it was shown that all known DPRMs innately oxidize H2S, producing elemental sulfur (S(o)). Although the process involving PSOX is thermodynamically favorable (ΔG°' = -206 kJ ⋅ mol(-1) H2S), the underlying biochemical and genetic mechanisms are currently unknown. Interestingly, H2S is preferentially utilized over physiological electron donors such as lactate or acetate although no growth benefit is obtained from the metabolism...
February 21, 2017: MBio
https://www.readbyqxmd.com/read/28222945/nad9-nad7-mitochondrial-nicotinamide-adenine-dinucleotide-dehydrogenase-gene-a-new-holy-grail-phylogenetic-and-dna-barcoding-marker-for-arcellinida-amoebozoa
#7
Quentin Blandenier, Enrique Lara, Edward A D Mitchell, Daniel M C Alcantara, Ferry J Siemensma, Milcho Todorov, Daniel J G Lahr
Molecular phylogeny is an indispensable tool for assessing evolutionary relationships among protists. The most commonly used marker is the small subunit ribosomal RNA gene, a conserved gene present in many copies in the nuclear genomes. However, this marker is not variable enough at a fine-level taxonomic scale, and intra-genomic polymorphism has already been reported. Finding a marker that could be useful at both deep and fine taxonomic resolution levels seemed like a utopic dream. We designed Amoebozoa-specific primers to amplify a region including partial sequences of two subunits of the mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene (NAD9/NAD7)...
December 23, 2016: European Journal of Protistology
https://www.readbyqxmd.com/read/28222096/metacoder-an-r-package-for-visualization-and-manipulation-of-community-taxonomic-diversity-data
#8
Zachary S L Foster, Thomas J Sharpton, Niklaus J Grünwald
Community-level data, the type generated by an increasing number of metabarcoding studies, is often graphed as stacked bar charts or pie graphs that use color to represent taxa. These graph types do not convey the hierarchical structure of taxonomic classifications and are limited by the use of color for categories. As an alternative, we developed metacoder, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data. Metacoder includes a dynamic and flexible function that can parse most text-based formats that contain taxonomic classifications, taxon names, taxon identifiers, or sequence identifiers...
February 21, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28219759/reevaluating-species-number-distribution-and-endemism-of-the-coral-genus-pocillopora-lamarck-1816-using-species-delimitation-methods-and-microsatellites
#9
P Gélin, B Postaire, C Fauvelot, H Magalon
Species delimitation methods based on genetic information, notably using single locus data, have been proposed as means of increasing the rate of biodiversity description, but can also be used to clarify complex taxonomies. In this study, we explore the species diversity within the cnidarian genus Pocillopora, widely distributed in the tropical belt of the Indo-Pacific Ocean. From 943 Pocillopora colonies sampled in the Western Indian Ocean, the Tropical Southwestern Pacific and Southeast Polynesia, representing a huge variety of morphotypes, we delineated Primary Species Hypotheses (PSH) applying the Automatic Barcode Gap Discovery method, the Poisson tree processes algorithm and the Generalized mixed Yule-coalescent model on two mitochondrial markers (Open Reading Frame and Dloop) and reconstructing a haploweb using one nuclear marker (Internal Transcribed Spacer 2)...
February 17, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28218638/metagaap-a-novel-pipeline-to-estimate-community-composition-and-abundance-from-non-model-sequence-data
#10
Christopher Noune, Caroline Hauxwell
Next generation sequencing and bioinformatic approaches are increasingly used to quantify microorganisms within populations by analysis of 'meta-barcode' data. This approach relies on comparison of amplicon sequences of 'barcode' regions from a population with public-domain databases of reference sequences. However, for many organisms relevant 'barcode' regions may not have been identified and large databases of reference sequences may not be available. A workflow and software pipeline, 'MetaGaAP,' was developed to identify and quantify genotypes through four steps: shotgun sequencing and identification of polymorphisms in a metapopulation to identify custom 'barcode' regions of less than 30 polymorphisms within the span of a single 'read', amplification and sequencing of the 'barcode', generation of a custom database of polymorphisms, and quantitation of the relative abundance of genotypes...
February 17, 2017: Biology
https://www.readbyqxmd.com/read/28218290/the-interaction-between-the-proliferating-macroalga-asparagopsis-taxiformis-and-the-coral-astroides-calycularis-induces-changes-in-microbiome-and-metabolomic-fingerprints
#11
Stéphane Greff, Tânia Aires, Ester A Serrão, Aschwin H Engelen, Olivier P Thomas, Thierry Pérez
Mediterranean Sea ecosystems are considered as hotspots of biological introductions, exposed to possible negative effects of non-indigenous species. In such temperate marine ecosystems, macroalgae may be dominant, with a great percentage of their diversity represented by introduced species. Their interaction with temperate indigenous benthic organisms have been poorly investigated. To provide new insights, we performed an experimental study on the interaction between the introduced proliferative red alga Asparagopsis taxiformis and the indigenous Mediterranean coral Astroides calycularis...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28216881/specific-pcr-identification-between-peucedanum-praeruptorum-and-angelica-decursiva-and-identification-between-them-and-adulterant-using-dna-barcode
#12
Bang-Xing Han, Yuan Yuan, Lu-Qi Huang, Qun Zhao, Ling-Ling Tan, Xiang-Wen Song, Xiao-Mei He, Tao Xu, Feng Liu, Jian Wang
BACKGROUND: The traditional Chinese medicine (TCM) Qianhu and Zihuaqianhu are the dried roots of Peucedanum praeruptorum and Angelica decursiva, respectively. Since the plant sources of Qianhu and Zihuaqianhu are more complex, the chemical compositions of P. praeruptorum and A. decursiva are significantly different, and many adulterants exist because of the differences in traditional understanding and medication habits. Therefore, the rapid and accurate identification methods are required...
January 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28215349/the-complete-mitochondrial-genome-of-the-conifer-needle-endophyte-phialocephala-scopiformis-daomc-229536-confirms-evolutionary-division-within-the-fungal-phialocephala-fortinii-s-l-%C3%A2-%C3%A2-acephala-appalanata-species-complex
#13
Brent M Robicheau, Alexander P Young, Kurt LaButti, Igor V Grigoriev, Allison K Walker
Despite the recent surge in mitochondrial (mt) genome sequencing, Kingdom Fungi remains underrepresented with respect to mtDNA. We describe the mt genome of the conifer needle endophyte, Phialocephala scopiformis DAOMC 229536 (Helotiales, Ascomycota). This strain is of interest to the Canadian forestry industry as it produces the anti-insectan compound rugulosin. Sequence was obtained from whole genome shotgun sequencing. Comparison to the only other published Phialocephala mt genome, Phialocephala subalpina, indicates that the suite of common mt genes - cox1-3, cob, nad1-6 and 4L, atp6, 8 and 9, as well as rrnL and rrnS - has retained an identical order...
March 2017: Fungal Biology
https://www.readbyqxmd.com/read/28215143/identifying-the-main-mosquito-species-in-the-taiwan-strait-using-dna-barcoding
#14
Bo Gao, Yiliang Fang, Jianqing Zhang, Rongquan Wu, Baohai Xu, Lianhui Xie
Mosquitoes can transmit many types of viruses such West Nile virus and Zika virus and are responsible for virus-causing diseases including malaria, Dengue fever, yellow fever, lymphatic filariasis, and Japanese B encephalitis. On January 19, 2016, the first case of Zika virus infection was identified in Taiwan, which presents the need for studying the mosquito species in the Taiwan Strait and evaluating the risk of the outbreak of this infection. In this study, we collected a total of 144 specimens from 42 mosquito specimens belonging to 9 genera from both sides of the Taiwan Strait during 2013 and 2014...
February 17, 2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28211676/electrochemical-genetic-profiling-of-single-cancer-cells
#15
Josep L Acero Sanchez, Hamdi Joda, Olivier Yves Henry, Beata W Solnestam, Linda Kvastad, Pelin S Akan, Joakim Lundeberg, Nadja Laddach, Dheeraj Ramakrishnan, Ian Riley, Carmen Schwind, Daniel Latta, Ciara K O' Sullivan
Recent understandings in the development and spread of cancer have lead to the realisation of novel single cell analysis platforms focused on circulating tumour cells (CTCs). A simple, rapid and inexpensive analytical platform capable of providing genetic information of these rare cells is highly desirable to support clinicians and researchers alike to either support the selection or adjustment of therapy or provide fundamental insights into cell function and cancer progression mechanisms. We report on the genetic profiling of single cancer cells, exploiting a combination of multiplex ligation-dependent probe amplification (MLPA) and electrochemical detection...
February 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28208623/fluorescence-lectin-bar-coding-of-glycoconjugates-in-the-extracellular-matrix-of-biofilm-and-bioaggregate-forming-microorganisms
#16
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/28208159/two-previously-unknown-phytophthora-species-associated-with-brown-rot-of-pomelo-citrus-grandis-fruits-in-vietnam
#17
Ivana Puglisi, Alessandro De Patrizio, Leonardo Schena, Thomas Jung, Maria Evoli, Antonella Pane, Nguyen Van Hoa, Mai Van Tri, Sandra Wright, Mauritz Ramstedt, Christer Olsson, Roberto Faedda, Gaetano Magnano di San Lio, Santa Olga Cacciola
Two distinct Phytophthora taxa were found to be associated with brown rot of pomelo (Citrus grandis), a new disease of this ancestral Citrus species, in the Vinh Long province, Mekong River Delta area, southern Vietnam. On the basis of morphological characters and using the ITS1-5.8S-ITS2 region of the rDNA and the cytochrome oxidase subunit 1 (COI) as barcode genes, one of the two taxa was provisionally named as Phytophthora sp. prodigiosa, being closely related to but distinct from P. insolita, a species in Phytophthora Clade 9, while the other one, was closely related to but distinct from the Clade 2 species P...
2017: PloS One
https://www.readbyqxmd.com/read/28202776/baring-cellular-souls
#18
Alex K Shalek
Coupling chemical approaches for disrupting DNA-protein complexes in intact nuclei with combinatorial barcoding enables high-throughput single-cell DNA sequencing.
February 15, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28202626/cancer-cells-exhibit-clonal-diversity-in-phenotypic-plasticity
#19
Robert Austin Mathis, Ethan S Sokol, Piyush B Gupta
Phenotypic heterogeneity in cancers is associated with invasive progression and drug resistance. This heterogeneity arises in part from the ability of cancer cells to switch between phenotypic states, but the dynamics of this cellular plasticity remain poorly understood. Here we apply DNA barcodes to quantify and track phenotypic plasticity across hundreds of clones in a population of cancer cells exhibiting epithelial or mesenchymal differentiation phenotypes. We find that the epithelial-to-mesenchymal cell ratio is highly variable across the different clones in cancer cell populations, but remains stable for many generations within the progeny of any single clone-with a heritability of 0...
February 2017: Open Biology
https://www.readbyqxmd.com/read/28199790/an-integrated-microfluidic-processor-for-dna-encoded-combinatorial-library-functional-screening
#20
Andrew B MacConnell, Alexander K Price, Brian M Paegel
DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits...
February 22, 2017: ACS Combinatorial Science
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