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https://www.readbyqxmd.com/read/28813413/polylox-barcoding-reveals-haematopoietic-stem-cell-fates-realized-in-vivo
#1
Weike Pei, Thorsten B Feyerabend, Jens Rössler, Xi Wang, Daniel Postrach, Katrin Busch, Immanuel Rode, Kay Klapproth, Nikolaus Dietlein, Claudia Quedenau, Wei Chen, Sascha Sauer, Stephan Wolf, Thomas Höfer, Hans-Reimer Rodewald
Developmental deconvolution of complex organs and tissues at the level of individual cells remains challenging. Non-invasive genetic fate mapping has been widely used, but the low number of distinct fluorescent marker proteins limits its resolution. Much higher numbers of cell markers have been generated using viral integration sites, viral barcodes, and strategies based on transposons and CRISPR-Cas9 genome editing; however, temporal and tissue-specific induction of barcodes in situ has not been achieved. Here we report the development of an artificial DNA recombination locus (termed Polylox) that enables broadly applicable endogenous barcoding based on the Cre-loxP recombination system...
August 16, 2017: Nature
https://www.readbyqxmd.com/read/28811535/delimiting-species-of-protaphorura-collembola-onychiuridae-integrative-evidence-based-on-morphology-dna-sequences-and-geography
#2
Xin Sun, Feng Zhang, Yinhuan Ding, Thomas W Davies, Yu Li, Donghui Wu
Species delimitation remains a significant challenge when the diagnostic morphological characters are limited. Integrative taxonomy was applied to the genus Protaphorura (Collembola: Onychiuridae), which is one of most difficult soil animals to distinguish taxonomically. Three delimitation approaches (morphology, molecular markers and geography) were applied providing rigorous species validation criteria with an acceptably low error rate. Multiple molecular approaches, including distance- and evolutionary model-based methods, were used to determine species boundaries based on 144 standard barcode sequences...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811315/quantitative-whole-genome-sequencing-of-circulating-tumor-cells-enables-personalized-combination-therapy-of-metastatic-cancer
#3
Natali Gulbahce, Mark Jesus M Magbanua, Robert Chin, Misha R Agarwal, Xuhao Luo, Jia Liu, Daniel M Hayden, Qing Mao, Serban Ciotlos, Zhenyu Li, Yanxiang Chen, Xingpeng Chen, Yuxiang Li, Rebecca Yu Zhang, Katharine Lee, Rick Tearle, Emily Park, Snezana Drmanac, Hope S Rugo, John W Park, Radoje Drmanac, Brock A Peters
Much effort has been dedicated to developing circulating tumor cells (CTC) as a noninvasive cancer biopsy, but with limited success as yet. In this study, we combine a method for isolation of highly pure CTCs using immunomagnetic enrichment/fluorescence-activated cell sorting with advanced whole genome sequencing (WGS), based on long fragment read technology, to illustrate the utility of an accurate, comprehensive, phased, and quantitative genomic analysis platform for CTCs. Whole genomes of 34 CTCs from a patient with metastatic breast cancer were analyzed as 3,072 barcoded subgenomic compartments of long DNA...
August 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28810700/a-single-mini-barcode-test-to-screen-for-australian-mammalian-predators-from-environmental-samples
#4
Elodie Modave, Anna J MacDonald, Stephen D Sarre
Identification of species from trace samples is now possible through the comparison of diagnostic DNA fragments against reference DNA sequence databases. DNA detection of animals from non-invasive samples, such as predator faeces (scats) that contain traces of DNA from their species of origin, has proved to be a valuable tool for the management of elusive wildlife. However, application of this approach can be limited by the availability of appropriate genetic markers. Scat DNA is often degraded, meaning that longer DNA sequences, including standard DNA barcoding markers, are difficult to recover...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28809924/species-delimitation-in-frogs-from-south-american-temperate-forests-the-case-of-eupsophus-a-taxonomically-complex-genus-with-high-phenotypic-variation
#5
Claudio Correa, Dayana Vásquez, Camila Castro-Carrasco, Álvaro Zúñiga-Reinoso, Juan Carlos Ortiz, R Eduardo Palma
One of the most characteristic and abundant amphibian taxa of South American temperate forests is Eupsophus. The ten currently recognized species of the genus have been divided in two species groups, roseus and vertebralis, but most of them, eight, belong to the roseus group. Recent phylogeographic and phylogenetic studies have suggested that species diversity of the roseus group could be underestimated. An examination of the literature shows that species of the roseus group exhibit high levels of variation in their external characteristics, particularly those used as diagnostic characters, which compromises their taxonomy and hinders their field recognition...
2017: PloS One
https://www.readbyqxmd.com/read/28808384/molecular-authentication-of-the-traditional-medicinal-plant-lakshman-booti-smithia-conferta-sm-and-its-adulterants-through-dna-barcoding
#6
Suraj D Umdale, Parthraj R Kshirsagar, Manoj M Lekhak, Nikhil B Gaikwad
BACKGROUND: Smithia conferta Sm. is an annual herb widely used in Indian traditional medical practice and commonly known as "Lakshman booti" in Sanskrit. Morphological resemblance among the species of genus Smithia Aiton. leads to inaccurate identification and adulteration. This causes inconsistent therapeutic effects and also affects the quality of herbal medicine. AIM: This study aimed to generate potential barcode for authentication of S. conferta and its adulterants through DNA barcoding technique...
July 2017: Pharmacognosy Magazine
https://www.readbyqxmd.com/read/28807221/identification-of-processed-chinese-medicinal-materials-using-dna-mini-barcoding
#7
Ming Song, Gang-Qiang Dong, Ya-Qin Zhang, Xia Liu, Wei Sun
Most of Chinese medicinal herbs are subjected to traditional processing procedures, including stir-frying, charring, steaming, boiling, and calcining before they are released into dispensaries. The marketing and identification of processed medicinal materials is a growing issue in the marketplace. However, conventional methods of identification have limitations, while DNA mini-barcoding, based on the sequencing of a short-standardized region, has received considerable attention as a new potential means to identify processed medicinal materials...
July 2017: Chinese Journal of Natural Medicines
https://www.readbyqxmd.com/read/28803843/high-throughput-screening-of-hybridoma-supernatants-using-multiplexed-fluorescent-cell-barcoding-on-live-cells
#8
Mei Lu, Brian M Chan, Peter W Schow, Wesley S Chang, Chadwick T King
With current available assay formats using either immobilized protein (ELISA, enzyme-linked immunosorbent assay) or immunostaining of fixed cells for primary monoclonal antibody (mAb) screening, researchers often fail to identify and characterize antibodies that recognize the native conformation of cell-surface antigens. Therefore, screening using live cells has become an integral and important step contributing to the successful identification of therapeutic antibody candidates. Thus the need for developing high-throughput screening (HTS) technologies using live cells has become a major priority for therapeutic mAb discovery and development...
August 10, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28802879/quadrulella-texcalense-sp-nov-from-a-mexican-desert-an-unexpected-new-environment-for-hyalospheniid-testate-amoebae
#9
Horacio Pérez-Juárez, Angélica Serrano-Vázquez, Anush Kosakyan, Edward A D Mitchell, Víctor M Rivera Aguilar, Daniel J G Lahr, Mayra M Hernández Moreno, Humberto Macías Cuellar, Luis E Eguiarte, Enrique Lara
Quadrulella (Amoebozoa, Arcellinida, Hyalospheniidae) is a genus of testate amoebae with unmistakable morphology, which secretes characteristic square plates to reinforce the test. They are mainly known from fens and freshwater habitats and have never been documented in deserts. We describe a new species, Quadrulella texcalense, from biological soil crusts in the intertropical desert of Tehuacán (state of Puebla, Mexico). Quadrulella texcalense occurred only at altitudes between 2140 and 2221m.a.s.l., together with the bryophyte genera Pseudocrossidium, Weissia, Bryum, Didymodon, Neohyophyla and Aloina...
July 17, 2017: European Journal of Protistology
https://www.readbyqxmd.com/read/28799720/its-fungal-barcoding-primers-vs-18s-amf-specific-primers-reveal-similar-amf-based-diversity-patterns-in-roots-and-soils-of-three-mountain-vineyards
#10
A Berruti, A Desirò, S Visentin, O Zecca, P Bonfante
ITS primers commonly used to describe soil fungi are flawed for AMF although it is unknown the extent to which they distort the interpretation of community patterns. Here we focus on how the use of a specific ITS2 fungal barcoding primer pair biased for AMF changes the interpretation of AMF community patterns from three mountain vineyards compared to a novel AMF-specific approach on the 18S. We found that although discrepancies were present in the taxonomic composition of the two resulting datasets, the estimation of diversity patterns among AMF communities was similar and resulted in both primer systems being able to correctly assess the community-structuring effect of location, compartment (root vs...
August 11, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28798064/accurate-rna-consensus-sequencing-for-high-fidelity-detection-of-transcriptional-mutagenesis-induced-epimutations
#11
Kate S Reid-Bayliss, Lawrence A Loeb
Transcriptional mutagenesis (TM) due to misincorporation during RNA transcription can result in mutant RNAs, or epimutations, that generate proteins with altered properties. TM has long been hypothesized to play a role in aging, cancer, and viral and bacterial evolution. However, inadequate methodologies have limited progress in elucidating a causal association. We present a high-throughput, highly accurate RNA sequencing method to measure epimutations with single-molecule sensitivity. Accurate RNA consensus sequencing (ARC-seq) uniquely combines RNA barcoding and generation of multiple cDNA copies per RNA molecule to eliminate errors introduced during cDNA synthesis, PCR, and sequencing...
August 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28797253/first-record-of-anopheles-stephensi-in-sri-lanka-a-potential-challenge-for-prevention-of-malaria-reintroduction
#12
A G Gayan Dharmasiri, A Yashan Perera, Jeevanie Harishchandra, Hemantha Herath, Kandasamy Aravindan, H T R Jayasooriya, Gaya R Ranawaka, Mihirini Hewavitharane
BACKGROUND: The major malaria vector in Sri Lanka is reported to be Anopheles culicifacies with Anopheles subpictus, Anopheles annularis, and Anopheles varuna considered as potential vectors. The occurrence of Anopheles stephensi, which is the key vector of urban malaria in India and the Middle East, had never been reported from Sri Lanka. METHODS: A series of entomological investigations were carried out by the Anti Malaria Campaign, Ministry of Health, Sri Lanka during December 2016 to April 2017 in two localities of the Mannar District in the Northern Province of the country...
August 10, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28795701/a-dna-assisted-immunoassay-for-enzyme-activity-via-a-dna-linked-activity-based-probe
#13
Dongwook Kim, Rachael R Jetson, Casey J Krusemark
Here, we describe an immunoassay approach for the detection of enzyme activity by quantitative PCR (qPCR) or parallel DNA sequencing which relies on activity-based probes linked to barcoding DNAs. We demonstrate this technique in the detection of serine hydrolase activities using a fluorophosphonate-oligonucleotide conjugate.
August 10, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28794574/pseudodidymellaceae-fam-nov-phylogenetic-affiliations-of-mycopappus-like-genera-in-dothideomycetes
#14
A Hashimoto, M Matsumura, K Hirayama, R Fujimoto, K Tanaka
The familial placement of four genera, Mycodidymella, Petrakia, Pseudodidymella, and Xenostigmina, was taxonomically revised based on morphological observations and phylogenetic analyses of nuclear rDNA SSU, LSU, tef1, and rpb2 sequences. ITS sequences were also provided as barcode markers. A total of 130 sequences were newly obtained from 28 isolates which are phylogenetically related to Melanommataceae (Pleosporales, Dothideomycetes) and its relatives. Phylogenetic analyses and morphological observation of sexual and asexual morphs led to the conclusion that Melanommataceae should be restricted to its type genus Melanomma, which is characterised by ascomata composed of a well-developed, carbonaceous peridium, and an aposphaeria-like coelomycetous asexual morph...
June 2017: Studies in Mycology
https://www.readbyqxmd.com/read/28793855/contrasting-morphology-with-molecular-data-an-approach-to-revision-of-species-complexes-based-on-the-example-of-european-phoxinus-cyprinidae
#15
Anja Palandačić, Alexander Naseka, David Ramler, Harald Ahnelt
BACKGROUND: Molecular taxonomy studies and barcoding projects can provide rapid means of detecting cryptic diversity. Nevertheless, the use of molecular data for species delimitation should be undertaken with caution. Especially the single-gene approaches are linked with certain pitfalls for taxonomical inference. In the present study, recent and historical species descriptions based upon morphology were used as primary species hypotheses, which were then evaluated with molecular data (including in type and historical museum material) to form secondary species hypotheses...
August 9, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28792677/deciphering-the-origin-of-mito-nuclear-discordance-in-two-sibling-caddisfly-species
#16
Hannah Weigand, Martina Weiss, Huimin Cai, Yongping Li, Lili Yu, Christine Zhang, Florian Leese
An increasing number of phylogenetic studies have reported discordances among nuclear and mitochondrial markers. These discrepancies are highly relevant to widely used biodiversity assessment approaches, such as DNA barcoding, that rely almost exclusively on mitochondrial markers. Although the theoretical causes of mito-nuclear discordances are well understood, it is often extremely challenging to determine the principal underlying factor in a given study system. In this study, we uncovered significant mito-nuclear discordances in a pair of sibling caddisfly species...
August 9, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28791769/fluorescent-polymer-nanoparticles-for-cell-barcoding-in-vitro-and-in-vivo
#17
Bohdan Andreiuk, Andreas Reisch, Marion Lindecker, Gautier Follain, Nadine Peyriéras, Jacky G Goetz, Andrey S Klymchenko
Fluorescent polymer nanoparticles for long-term labeling and tracking of living cells with any desired color code are developed. They are built from biodegradable poly(lactic-co-glycolic acid) polymer loaded with cyanine dyes (DiO, DiI, and DiD) with the help of bulky fluorinated counterions, which minimize aggregation-caused quenching. At the single particle level, these particles are ≈20-fold brighter than quantum dots of similar color. Due to their identical 40 nm size and surface properties, these nanoparticles are endocytosed equally well by living cells...
August 9, 2017: Small
https://www.readbyqxmd.com/read/28791201/comparative-mitogenomic-analysis-of-mirid-bugs-hemiptera-miridae-and-evaluation-of-potential-dna-barcoding-markers
#18
Juan Wang, Li Zhang, Qi-Lin Zhang, Min-Qiang Zhou, Xiao-Tong Wang, Xing-Zhuo Yang, Ming-Long Yuan
The family Miridae is one of the most species-rich families of insects. To better understand the diversity and evolution of mirids, we determined the mitogenome of Lygus pratenszs and re-sequenced the mitogenomes of four mirids (i.e., Apolygus lucorum, Adelphocoris suturalis, Ade. fasciaticollis and Ade. lineolatus). We performed a comparative analysis for 15 mitogenomic sequences representing 11 species of five genera within Miridae and evaluated the potential of these mitochondrial genes as molecular markers...
2017: PeerJ
https://www.readbyqxmd.com/read/28780857/barcode-dna-mediated-signal-amplifying-strategy-for-ultrasensitive-biomolecular-detection-on-matrix-assisted-laser-desorption-ionization-time-of-flight-maldi-tof-mass-spectrometry
#19
Raheel Ahmad, Hyowon Jang, Bhagwan S Batule, Hyun Gyu Park
We have devised a barcode DNA-mediated signal amplifying strategy for ultrasensitive biomolecular detection by utilizing matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). As a model target, thrombin was first captured by specific aptamer15 functionalized on magnetic beads (MBs-apt15) and sandwiched through the simultaneous interaction with gold nanoparticles modified with another specific aptamer29 and barcode DNA molecules (apt29-AuNPs-bcDNAs). The sandwiched complex was collected by convenient magnetic separation and then treated with potassium cyanide (KCN) to dissolve the gold nanoparticles (AuNPs) and consequently release the barcode DNA molecules (bcDNAs), which were then again magnetically separated and analyzed by using MALDI-TOF MS...
August 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28776479/parenteral-product-error-detection-before-and-after-implementation-of-intravenous-workflow-management-technology
#20
Kelly R Wright, Brian Dekarske, John S Clark, Bruce W Chaffee
Objective To assess the difference in pharmacy error detection rates when using a manual process compared to an intravenous workflow management system for the preparation of parenteral medications. Methods Baseline error data were collected by staff using a standard form over a four-day time period before intravenous workflow management system implementation and compared to 48 weeks of electronically collected data following implementation. The chi-square test was used for statistical comparisons. Results The ability to detect an error during the intravenous preparation process increased immediately following implementation, but this difference was not sustained and was not statistically different when the entire post-implementation time period was compared to the baseline sample...
January 1, 2017: Journal of Oncology Pharmacy Practice
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