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https://www.readbyqxmd.com/read/28335433/evaluation-and-adaptation-of-a-laboratory-based-cdna-library-preparation-protocol-for-retrospective-sequencing-of-archived-micrornas-from-up-to-35-year-old-clinical-ffpe-specimens
#1
Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert Greenlee, Deborah Multerer, Stacey Honda, Yihe Daida, Heather Spencer Feigelson, Andrew Glass, Fergus J Couch, Thomas Rohan, Iddo Z Ben-Dov
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years...
March 14, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28334157/overview-of-freshwater-microbial-eukaryotes-diversity-a-first-analysis-of-publicly-available-metabarcoding-data
#2
Didier Debroas, Isabelle Domaizon, Jean-Francois Humbert, Ludwig Jardillier, Cécile Lepère, Anne Oudart, Najwa Taïb
Although they are widespread, diverse, and involved in biogeochemical cycles, microbial eukaryotes attract less attention than their prokaryotic counterparts in environmental microbiology. In this study, we used publicly available 18S barcoding data to define biases that may limit such analyses and to gain an overview of the planktonic microbial eukaryotic diversity in freshwater ecosystems. The richness of the microbial eukaryotes was estimated to 100,798 operational taxonomic units (OTUs) delineating 1267 clusters or phylogenetic units (PUs i...
March 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28331401/dna-barcoding-and-species-delimitation-of-chaitophorinae-hemiptera-aphididae
#3
Xi-Chao Zhu, Jing Chen, Rui Chen, Li-Yun Jiang, Ge-Xia Qiao
Chaitophorinae aphids are widespread across Eurasia and North America, and include some important agricultural and horticultural pests. So, accurate rapid species identification is very important. Here, we used three mitochondrial genes and one endosymbiont gene to calculate and analyze the genetic distances within different datasets. For species delimitation, two distance-based methods were employed, threshold with NJ (neighbor-joining) and ABGD (Automatic Barcode Gap Discovery), and two tree-based approaches, GMYC (General Mixed Yule Coalescent) and PTP (Poisson Tree Process)...
2017: ZooKeys
https://www.readbyqxmd.com/read/28329763/the-allosteric-inhibitor-abl001-enables-dual-targeting-of-bcr-abl1
#4
Andrew A Wylie, Joseph Schoepfer, Wolfgang Jahnke, Sandra W Cowan-Jacob, Alice Loo, Pascal Furet, Andreas L Marzinzik, Xavier Pelle, Jerry Donovan, Wenjing Zhu, Silvia Buonamici, A Quamrul Hassan, Franco Lombardo, Varsha Iyer, Michael Palmer, Giuliano Berellini, Stephanie Dodd, Sanjeev Thohan, Hans Bitter, Susan Branford, David M Ross, Timothy P Hughes, Lilli Petruzzelli, K Gary Vanasse, Markus Warmuth, Francesco Hofmann, Nicholas J Keen, William R Sellers
Chronic myeloid leukaemia (CML) is driven by the activity of the BCR-ABL1 fusion oncoprotein. ABL1 kinase inhibitors have improved the clinical outcomes for patients with CML, with over 80% of patients treated with imatinib surviving for more than 10 years. Second-generation ABL1 kinase inhibitors induce more potent molecular responses in both previously untreated and imatinib-resistant patients with CML. Studies in patients with chronic-phase CML have shown that around 50% of patients who achieve and maintain undetectable BCR-ABL1 transcript levels for at least 2 years remain disease-free after the withdrawal of treatment...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28303008/an-analysis-of-echinacea-chloroplast-genomes-implications-for-future-botanical-identification
#5
Ning Zhang, David L Erickson, Padmini Ramachandran, Andrea R Ottesen, Ruth E Timme, Vicki A Funk, Yan Luo, Sara M Handy
Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28296890/re-establishment-of-species-from-synonymies-based-on-dna-barcoding-and-phylogenetic-analysis-using-diplopterygium-simulans-gleicheniaceae-as-an-example
#6
Jiang-Ping Shu, Hui Shang, Dongmei Jin, Hong-Jin Wei, Xi-Le Zhou, Hong-Mei Liu, Yu-Feng Gu, Ying Wang, Fa-Guo Wang, Hui Shen, Rui Zhang, Bayu Adjie, Yue-Hong Yan
Because synonymy treatment traditionally relies on morphological judgments, it usually causes many problems in species delimitation and in the biodiversity catalogue. For example, Diplopterygium simulans, which belongs to the Gleicheniaceae family, has been considered to be synonymous with D. glaucum or D. giganteum based mainly on the morphology of its pinna rachis and blade. In the absence of molecular evidence, these revisions remain doubtful. DNA barcoding, which is considered to be a powerful method for species-level identification, was employed to assess the genetic distance among 9 members of the Diplopterygium genus...
2017: PloS One
https://www.readbyqxmd.com/read/28293890/characterizing-dynamic-protein-protein-interactions-using-the-genetically-encoded-split-biosensor-assay-technique-split-tev
#7
Jan P Wintgens, Moritz J Rossner, Michael C Wehr
Dynamic protein-protein interactions (PPIs) are fundamental building blocks of cellular signaling and monitoring their regulation promotes the understanding of signaling in health and disease. Genetically encoded split protein biosensor assays, such as the split TEV method, have proved to be highly valuable when studying regulated PPIs in living cells. Split TEV is based on the functional complementation of two previously inactive TEV protease fragments fused to interacting proteins and provides a robust, sensitive and flexible readout to monitor PPIs both at the membrane and in the cytosol...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28290550/abseq-ultrahigh-throughput-single-cell-protein-profiling-with-droplet-microfluidic-barcoding
#8
Payam Shahi, Samuel C Kim, John R Haliburton, Zev J Gartner, Adam R Abate
Proteins are the primary effectors of cellular function, including cellular metabolism, structural dynamics, and information processing. However, quantitative characterization of proteins at the single-cell level is challenging due to the tiny amount of protein available. Here, we present Abseq, a method to detect and quantitate proteins in single cells at ultrahigh throughput. Like flow and mass cytometry, Abseq uses specific antibodies to detect epitopes of interest; however, unlike these methods, antibodies are labeled with sequence tags that can be read out with microfluidic barcoding and DNA sequencing...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28290215/genetic-assessment-of-leech-species-from-yak-bos-grunniens-in-the-tract-of-northeast-india
#9
Nilkantha Chatterjee, Bishal Dhar, Debasis Bhattarcharya, Sourabh Deori, Juwar Doley, Joken Bam, Pranab J Das, Asit K Bera, Sitangshu M Deb, Ningthoujam Neelima Devi, Rajesh Paul, Sorokhaibam Malvika, Sankar Kumar Ghosh
Yak is an iconic symbol of Tibet and high altitudes of Northeast India. It is highly cherished for milk, meat, and skin. However, yaks suffer drastic change in milk production, weight loss, etc, when infested by parasites. Among them, infestation by leeches is a serious problem in the Himalayan belt of Northeast India. The parasite feeds on blood externally or from body orifices, like nasopharynx, oral, rectum, etc. But there has been limited data about the leech species infesting the yak in that region because of the difficulties in morphological identification due to plasticity of the body, changes in shape, and surface structure and thus, warrants for the molecular characterization of leech...
March 14, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28287390/species-of-philometra-nematoda-philometridae-from-fishes-off-the-mediterranean-coast-of-africa-with-a-description-of-philometra-rara-n-sp-from-hyporthodus-haifensis-and-a-molecular-analysis-of-philometra-saltatrix-from-pomatomus-saltatrix
#10
František Moravec, Amira Chaabane, Lassad Neifar, Delphine Gey, Jean-Lou Justine
Two gonad-infecting species of Philometra Costa, 1845 (Nematoda, Philometridae) were recorded for the first time from marine perciform fishes off Tunisia and Libya: Philometra rara n. sp. from the rare, deep-water Haifa grouper Hyporthodus haifensis (Serranidae) off Libya and Philometra saltatrix Ramachandran, 1973 from the bluefish Pomatomus saltatrix (Pomatomidae) off Tunisia. Identification of both fish species was confirmed by molecular barcoding. Light and scanning electron microscope studies of Ph. rara n...
2017: Parasite: Journal de la Société Française de Parasitologie
https://www.readbyqxmd.com/read/28278695/dna-barcoding-and-genetic-diversity-analyses-of-fishes-of-kaladan-river-of-indo-myanmar-biodiversity-hotspot
#11
Anindya Sundar Barman, Mamta Singh, Pramod Kumar Pandey
Species are considered as a fundamental unit of biodiversity. Therefore, the prerequisite for biodiversity management and conservation is to know the number of species one is dealing with. Consequently, the need of the present study was conceptualized, which dealt with the comprehensive molecular appraisal of Kaladan's Fish fauna. A total of 291 specimens representing 49 species, 28 genera, 11 families, and 4 orders, were collected from 11 sampling stations situated along the main Kaladan River and its four major tributaries, i...
February 16, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28264285/description-of-the-female-of-i-ceromya-i-i-glaucescens-i-tachi-amp-shima-diptera-tachinidae-and-discovery-of-unusual-sexual-dimorphism-in-this-species
#12
Takuji Tachi
Sexual dimorphism is a phenomenon in which the male and female of a species differ in features of the external morphology such as size, shape, colour, or the development of appendages. In the Diptera, stalked compound eyes, leg modifications and wing patterns are well-known examples of sexual dimorphism (McAlpine 1979; Zeil 1983; Adler & Adler 1991; Meyerrochow & Reid 1994; Wilkinson & Dodson 1996; Sivinski 1997; Baker & Wilkinson 2001; Eberhard 2002; Puniamoorthy et al. 2008). Males and females of sexually dimorphic species are often described as separate species due to the dissimilarity in external characters, thus leading to problems in identification and proper association of the sexes...
March 1, 2017: Zootaxa
https://www.readbyqxmd.com/read/28262023/ground-state-depletion-nanoscopy-resolves-semiconductor-nanowire-barcode-segments-at-room-temperature
#13
Joanna Oracz, Karl Adolfsson, Volker Westphal, Czeslaw Radzewicz, Magnus T Borgstrom, Steffen Sahl, Christelle Prinz, Stefan W Hell
Nanowires hold great promise as tools for probing and interacting with various molecular and biological systems. Their unique geometrical properties (typically <100 nm in diameter and a few µm in length) enable minimally invasive interactions with living cells, so that electrical signals or forces can be monitored. All such experiments require in situ high-resolution imaging to provide context. While there is a clear need to extend visualization capabilities to the nanoscale, no suitable super-resolution far-field photoluminescence microscopy of extended semiconductor emitters has been described...
March 6, 2017: Nano Letters
https://www.readbyqxmd.com/read/28257512/quantitative-molecular-diagnostic-assays-of-grain-washes-for-claviceps-purpurea-are-correlated-with-visual-determinations-of-ergot-contamination
#14
Alexia Comte, Tom Gräfenhan, Matthew G Links, Sean M Hemmingsen, Tim J Dumonceaux
We examined the epiphytic microbiome of cereal grain using the universal barcode chaperonin-60 (cpn60). Microbial community profiling of seed washes containing DNA extracts prepared from field-grown cereal grain detected sequences from a fungus identified only to Class Sordariomycetes. To identify the fungal sequence and to improve the reference database, we determined cpn60 sequences from field-collected and reference strains of the ergot fungus, Claviceps purpurea. These data allowed us to identify this fungal sequence as deriving from C...
2017: PloS One
https://www.readbyqxmd.com/read/28253235/simple-multiplexed-pcr-based-barcoding-of-dna-for-ultrasensitive-mutation-detection-by-next-generation-sequencing
#15
Anders Ståhlberg, Paul M Krzyzanowski, Matthew Egyud, Stefan Filges, Lincoln Stein, Tony E Godfrey
Detection of extremely rare variant alleles within a complex mixture of DNA molecules is becoming increasingly relevant in many areas of clinical and basic research, such as the detection of circulating tumor DNA in the plasma of cancer patients. Barcoding of DNA template molecules early in next-generation sequencing (NGS) library construction provides a way to identify and bioinformatically remove polymerase errors that otherwise make detection of these rare variants very difficult. Several barcoding strategies have been reported, but all require long and complex library preparation protocols...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28228107/effectiveness-of-its-and-sub-regions-as-dna-barcode-markers-for-the-identification-of-basidiomycota-fungi
#16
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
#17
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/28222945/nad9-nad7-mitochondrial-nicotinamide-adenine-dinucleotide-dehydrogenase-gene-a-new-holy-grail-phylogenetic-and-dna-barcoding-marker-for-arcellinida-amoebozoa
#18
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/28208623/fluorescence-lectin-bar-coding-of-glycoconjugates-in-the-extracellular-matrix-of-biofilm-and-bioaggregate-forming-microorganisms
#19
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
#20
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
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