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https://www.readbyqxmd.com/read/28211676/electrochemical-genetic-profiling-of-single-cancer-cells
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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 whole-library 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 15, 2017: ACS Combinatorial Science
https://www.readbyqxmd.com/read/28199378/the-first-initiative-of-dna-barcoding-of-ornamental-plants-from-egypt-and-potential-applications-in-horticulture-industry
#7
Hosam O Elansary, Muhammad Ashfaq, Hayssam M Ali, Kowiyou Yessoufou
DNA barcoding relies on short and standardized gene regions to identify species. The agricultural and horticultural applications of barcoding such as for marketplace regulation and copyright protection remain poorly explored. This study examines the effectiveness of the standard plant barcode markers (matK and rbcL) for the identification of plant species in private and public nurseries in northern Egypt. These two markers were sequenced from 225 specimens of 161 species and 62 plant families of horticultural importance...
2017: PloS One
https://www.readbyqxmd.com/read/28199101/fungal-identification-using-molecular-tools-a-primer-for-the-natural-products-research-community
#8
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/28196276/pcr-fishing-for-red-endophytes-in-british-columbia-kallymeniaceae-gigartinales-florideophyceae-uncovers-the-species-rich-kallymenicola-gen-nov-palmariales-nemaliophycidae
#9
Joshua R Evans, Gary W Saunders
Unexpected contaminants uncovered during routine COI-5P DNA barcoding of British Columbia Kallymeniaceae indicated the presence of a novel lineage allied to the family Meiodiscaceae, Palmariales. Available rbcL data for species of this family were used to design specific primers to screen for the presence of the meiodiscacean species in 534 kallymeniacean specimens primarily from British Columbia, Canada. Ultimately, 43 positive PCR products representing six diverse genetic groups from nine host species were uncovered; three are described here in the new genus Kallymenicola gen...
February 14, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28193505/statistical-modelling-of-ion-pgm-hid-str-10-plex-mps-data
#10
Søren B Vilsen, Torben Tvedebrink, Helle Smidt Mogensen, Niels Morling
We investigated the results of short tandem repeat (STR) markers of dilution series experiments and reference profiles generated using the Ion PGM massively parallel sequencing platform utilising the HID STR 10-plex panel. The STR markers were identified by the marker specific flanking regions of the STR region. We investigated the following: (1) the usage of quality measures for identifying substitution errors, (2) the heterozygote balance and compared it to that of capillary electrophoresis (CE), (3) the stability of the coverage and the consequence of IonExpress Barcode adapter (IBA) sampling with decreasing amounts of template DNA, (4) the hypothesis that the parental longest uninterrupted stretch (LUS) is a better linear predictor of stutter ratio than the parent allele length, (5) the use of parental allele length as a predictor of shoulder ratio, and (6) the removal of non-systematic erroneous sequences using dynamic thresholds created by fitting the distribution of the non-systematic erroneous sequences...
February 3, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28192986/biosynthesis-based-quantitative-analysis-of-151-secondary-metabolites-of-licorice-to-differentiate-medicinal-glycyrrhiza-species-and-their-hybrids
#11
Wei Song, Xue Qiao, Kuan Chen, Ying Wang, Shuai Ji, Jin Feng, Kai Li, Yan Lin, Min Ye
Secondary metabolites are usually the bioactive components of medicinal plants. The difference in the secondary metabolisms of closely related plant species and their hybrids has rarely been addressed. In this study, we conducted a holistic secondary metabolomics analysis of three medicinal Glycyrrhiza species (G. uralensis, G. glabra, and G. inflata), which are used as the popular herbal medicine licorice. The Glycyrrhiza species (genotype) for 95 batches of samples were identified by DNA barcodes of the internal transcribed spacer and trnV-ndhC regions, and the chemotypes were revealed by LC/UV- or LC/MS/MS-based quantitative analysis of 151 bioactive secondary metabolites, including 17 flavonoid glycosides, 24 saponins, and 110 free phenolic compounds...
February 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28192446/range-extension-for-the-common-dolphin-delphinus-sp-to-the-colombian-caribbean-with-taxonomic-implications-from-genetic-barcoding-and-phylogenetic-analyses
#12
Nohelia Farías-Curtidor, Dalia C Barragán-Barrera, Paula Alejandra Chávez-Carreño, Cristina Jiménez-Pinedo, Daniel M Palacios, Dalila Caicedo, Fernando Trujillo, Susana Caballero
The nearest known population of common dolphins (Delphinus sp.) to the Colombian Caribbean occurs in a fairly restricted range in eastern Venezuela. These dolphins have not been previously reported in the Colombian Caribbean, likely because of a lack of study of the local cetacean fauna. We collected cetacean observations in waters of the Guajira Department, northern Colombia (~11°N, 73°W) during two separate efforts: (a) a seismic vessel survey (December 2009-March 2010), and (b) three coastal surveys from small boats (May-July 2012, May 2013, and May 2014)...
2017: PloS One
https://www.readbyqxmd.com/read/28192419/seq-well-portable-low-cost-rna-sequencing-of-single-cells-at-high-throughput
#13
Todd M Gierahn, Marc H Wadsworth, Travis K Hughes, Bryan D Bryson, Andrew Butler, Rahul Satija, Sarah Fortune, J Christopher Love, Alex K Shalek
Single-cell RNA-seq can precisely resolve cellular states, but applying this method to low-input samples is challenging. Here, we present Seq-Well, a portable, low-cost platform for massively parallel single-cell RNA-seq. Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells using a semipermeable membrane, enabling efficient cell lysis and transcript capture. We use Seq-Well to profile thousands of primary human macrophages exposed to Mycobacterium tuberculosis.
February 13, 2017: Nature Methods
https://www.readbyqxmd.com/read/28191885/molecular-definition-of-a-metastatic-lung-cancer-state-reveals-a-targetable-cd109-janus-kinase-stat-axis
#14
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/28190875/technique-barcoding-the-nucleus
#15
Dorothy Clyde
No abstract text is available yet for this article.
February 13, 2017: Nature Reviews. Genetics
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
#16
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/28187647/dna-barcoding-reveals-sexual-dimorphism-in-i-isotrias-i-i-penedana-i-trematerra-2013-lepidoptera-tortricidae-chlidanotinae
#17
Martin Francis Vanner Corley, Sónia Ferreira
Isotrias penedana Trematerra, 2013 was described from north Portugal based on males alone. Unidentified females were associated with the males using DNA barcoding, revealing sexual dimorphism in the species. Males and females differ in forewing shape, markings, and size, with females significantly smaller than males. The female is described and illustrated for the first time. We also document the species' occurrence in northern Spain.
January 20, 2017: Zootaxa
https://www.readbyqxmd.com/read/28187642/a-revision-of-the-genus-i-lepidobrya-i-womersley-collembola-entomobryidae-based-on-morphology-and-sequence-data-of-the-genotype
#18
Feng Zhang, Penelope Greenslade, Mark I Stevens
The genus Lepidobrya Womersley, previously placed in Willowsiini, is re-diagnosed based on a redescription of the type species L. mawsoni (Tillyard) and its DNA barcode. Specimens possess narrow, pointed scales on the dens, two inner teeth on unguis, a truncate unguiculus with an outer tooth, a bidentate mucro with a basal spine and ordinary tergal S-chaetae 2, 2|1, 2, 2, ?, 3, so belongs to the Entomobryinae. Its systematic position and relationships to other scaled Entomobryinae genera are discussed and comments are made on the distribution of the genus as well as on ecology...
January 20, 2017: Zootaxa
https://www.readbyqxmd.com/read/28187619/revision-of-the-nearctic-i-calliphora-i-robineau-desvoidy-diptera-calliphoridae
#19
Tarek I Tantawi, Terry L Whitworth, Bradley J Sinclair
The Nearctic species of Calliphora Robineau-Desvoidy are revised and all species are redescribed and/or diagnosed. Diagnostic characters to permit reliable identification of both sexes of Calliphora aldrichia (Shannon) and C. montana (Shannon) and detailed distributional records for both species are provided for the first time. A lectotype is designated for Calliphora loewi Enderlein, 1903. A revised key to the 13 species of Nearctic Calliphora is also included. The key is based on examination of over 1,000 specimens from across North America and the structure of the terminalia of both sexes of each species...
January 26, 2017: Zootaxa
https://www.readbyqxmd.com/read/28187592/-i-culicoides-i-latreille-biting-midges-diptera-ceratopogonidae-of-the-dongzhaigang-mangrove-forest-hainan-province-china
#20
Jia-Hui Li, David Gopurenko, DU-Cheng Cai, Ye-Meng Yang, Rong Hu, Arunrat Thepparat, April H Wardhana, Heung-Chul Kim, Terry A Klein, Myung-Soon Kim, Glenn A Bellis
The biting midge fauna of Dongzhaigang Mangrove Forest, Hainan Province, China was sampled on 14 October 2015 using three methods: a pan light trap operated from dusk until dawn the following morning and sweep net and human landing collections performed between 16:15-17:15 hr. Eight species, including two new records for China, Culicoides palawanensis and C. niphanae, and one new record for Hainan, C. circumbasalis, were collected. A key to assist with identification of specimens of these species is provided...
January 31, 2017: Zootaxa
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