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https://www.readbyqxmd.com/read/27934409/kinetically-inert-lanthanide-complexes-as-reporter-groups-for-binding-of-potassium-by-18-crown-6
#1
Anne Kathrine R Junker, Manuel Tropiano, Stephen Faulkner, Thomas Just Sørensen
The barcode-like spectrum of lanthanide-centered emission has been used in imaging and to make responsive luminescent reporters. The intensities and the shapes of each line in the luminescence spectrum can also report on the coordination environment of the lanthanide ion. Here, we used lanthanide-centered emission to report on the binding of potassium in an 18-crown-6 binding pocket. The responsive systems were made by linking a crown ether to a kinetically inert lanthanide binding pocket using a molecular building block approach...
December 5, 2016: Inorganic Chemistry
https://www.readbyqxmd.com/read/27932930/testing-the-global-malaise-trap-program-how-well-does-the-current-barcode-reference-library-identify-flying-insects-in-germany
#2
Matthias F Geiger, Jerome Moriniere, Axel Hausmann, Gerhard Haszprunar, Wolfgang Wägele, Paul D N Hebert, Björn Rulik
BACKGROUND: Biodiversity patterns are inherently complex and difficult to comprehensively assess. Yet, deciphering shifts in species composition through time and space are crucial for efficient and successful management of ecosystem services, as well as for predicting change. To better understand species diversity patterns, Germany participated in the Global Malaise Trap Program, a world-wide collection program for arthropods using this sampling method followed by their DNA barcode analysis...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27932928/metabarcoding-of-marine-nematodes-evaluation-of-similarity-scores-used-in-alignment-based-taxonomy-assignment-approach
#3
Oleksandr Holovachov
BACKGROUND: The diversity of organisms is being commonly accessed using metabarcoding of environmental samples. Reliable identification of barcodes is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task, including alignment-based approach that uses Basic Local Alignment Search Tool (BLAST) algorithm. This publication evaluates the variability of 5' end of 18S rRNA barcoding region as expressed by similarity scores (alignment score and identity score) produced by BLAST, and its impact on barcode identification to family-level taxonomic categories...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27932926/a-dataset-of-fishes-in-and-around-inle-lake-an-ancient-lake-of-myanmar-with-dna-barcoding-photo-images-and-ct-3d-models
#4
Yuichi Kano, Prachya Musikasinthorn, Akihisa Iwata, Sein Tun, Lkc Yun, Seint Seint Win, Shoko Matsui, Ryoichi Tabata, Takeshi Yamasaki, Katsutoshi Watanabe
BACKGROUND: Inle (Inlay) Lake, an ancient lake of Southeast Asia, is located at the eastern part of Myanmar, surrounded by the Shan Mountains. Detailed information on fish fauna in and around the lake has long been unknown, although its outstanding endemism was reported a century ago. NEW INFORMATION: Based on the fish specimens collected from markets, rivers, swamps, ponds and ditches around Inle Lake as well as from the lake itself from 2014 to 2016, we recorded a total of 948 occurrence data (2120 individuals), belonging to 10 orders, 19 families, 39 genera and 49 species...
2016: Biodiversity Data Journal
https://www.readbyqxmd.com/read/27929523/single-cell-barcoding-and-sequencing-using-droplet-microfluidics
#5
Rapolas Zilionis, Juozas Nainys, Adrian Veres, Virginia Savova, David Zemmour, Allon M Klein, Linas Mazutis
Single-cell RNA sequencing has recently emerged as a powerful tool for mapping cellular heterogeneity in diseased and healthy tissues, yet high-throughput methods are needed for capturing the unbiased diversity of cells. Droplet microfluidics is among the most promising candidates for capturing and processing thousands of individual cells for whole-transcriptome or genomic analysis in a massively parallel manner with minimal reagent use. We recently established a method called inDrops, which has the capability to index >15,000 cells in an hour...
January 2017: Nature Protocols
https://www.readbyqxmd.com/read/27929459/perturbations-of-circulating-mirnas-in-irritable-bowel-syndrome-detected-using-a-multiplexed-high-throughput-gene-expression-platform
#6
Nicolaas H Fourie, Ralph M Peace, Sarah K Abey, LeeAnne B Sherwin, John W Wiley, Wendy A Henderson
The gene expression platform assay allows for robust and highly reproducible quantification of the expression of up to 800 transcripts (mRNA or miRNAs) in a single reaction. The miRNA assay counts transcripts by directly imaging and digitally counting miRNA molecules that are labeled with color-coded fluorescent barcoded probe sets (a reporter probe and a capture probe). Barcodes are hybridized directly to mature miRNAs that have been elongated by ligating a unique oligonucleotide tag (miRtag) to the 3' end...
November 30, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27928939/developing-an-ecologically-relevant-heterogeneous-biofilm-model-for-dental-unit-waterlines
#7
Sham Lal, Mark Pearce, Undine E M Achilles-Day, John G Day, L H Glyn Morton, St John Crean, Sim K Singhrao
This study monitored the biodiversity of microbes cultured from a heterogeneous biofilm which had formed on the lumen of a section of dental waterline tubing over a period of 910 days. By day 2 bacterial counts on the outlet-water showed that contamination of the system had occurred. After 14 days, a biofilm comparable to that of clinical waterlines, consisting of bacteria, fungi and amoebae had formed. This showed that the proprietary silver coating applied to the luminal surface of the commercial waterline tubing failed to prevent biofilm formation...
December 8, 2016: Biofouling
https://www.readbyqxmd.com/read/27926379/a-comparative-analysis-of-chaotic-particle-swarm-optimizations-for-detecting-single-nucleotide-polymorphism-barcodes
#8
Li-Yeh Chuang, Sin-Hua Moi, Yu-Da Lin, Cheng-Hong Yang
OBJECTIVE: Evolutionary algorithms could overcome the computational limitations for the statistical evaluation of large datasets for high-order single nucleotide polymorphism (SNP) barcodes. Previous studies have proposed several chaotic particle swarm optimization (CPSO) methods to detect SNP barcodes for disease analysis (e.g., for breast cancer and chronic diseases). This work evaluated additional chaotic maps combined with the particle swarm optimization (PSO) method to detect SNP barcodes using a high-dimensional dataset...
October 2016: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/27924952/a-competitive-bio-barcode-amplification-immunoassay-for-small-molecules-based-on-nanoparticles
#9
Pengfei Du, Maojun Jin, Ge Chen, Chan Zhang, Zejun Jiang, Yanxin Zhang, Pan Zou, Yongxin She, Fen Jin, Hua Shao, Shanshan Wang, Lufei Zheng, Jing Wang
A novel detection method of small molecules, competitive bio-barcode amplification immunoassay, was developed and described in this report. Through the gold nanoparticles (AuNPs) probe and magnetic nanoparticles (MNPs) probe we prepared, only one monoclonal antibody can be used to detect small molecules. The competitive bio-barcode amplification immunoassay overcomes the obstacle that the bio-barcode assay cannot be used in small molecular detection, as two antibodies are unable to combine to one small molecule due to its small molecular structure...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27923552/preleukaemic-clonal-haemopoiesis-and-risk-of-therapy-related-myeloid-neoplasms-a-case-control-study
#10
Koichi Takahashi, Feng Wang, Hagop Kantarjian, Denaha Doss, Kanhav Khanna, Erika Thompson, Li Zhao, Keyur Patel, Sattva Neelapu, Curtis Gumbs, Carlos Bueso-Ramos, Courtney D DiNardo, Simona Colla, Farhad Ravandi, Jianhua Zhang, Xuelin Huang, Xifeng Wu, Felipe Samaniego, Guillermo Garcia-Manero, P Andrew Futreal
BACKGROUND: Therapy-related myeloid neoplasms are secondary malignancies that are often fatal, but their risk factors are not well understood. Evidence suggests that individuals with clonal haemopoiesis have increased risk of developing haematological malignancies. We aimed to identify whether patients with cancer who have clonal haemopoiesis are at an increased risk of developing therapy-related myeloid neoplasms. METHODS: We did this retrospective case-control study to compare the prevalence of clonal haemopoiesis between patients treated for cancer who later developed therapy-related myeloid neoplasms (cases) and patients who did not develop these neoplasms (controls)...
December 2, 2016: Lancet Oncology
https://www.readbyqxmd.com/read/27923068/gene-expression-correlates-with-the-number-of-herpes-viral-genomes-initiating-infection-in-single-cells
#11
Efrat M Cohen, Oren Kobiler
Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants...
December 6, 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27922451/direct-screening-for-chromatin-status-on-dna-barcodes-in-yeast-delineates-the-regulome-of-h3k79-methylation-by-dot1
#12
Hanneke Vlaming, Thom M Molenaar, Tibor van Welsem, Deepani W Poramba-Liyanage, Desiree E Smith, Arno Velds, Liesbeth Hoekman, Tessy Korthout, Sjoerd Hendriks, Af Maarten Altelaar, Fred van Leeuwen
Given the frequent misregulation of chromatin in cancer, it is important to understand the cellular mechanisms that regulate chromatin structure. However, systematic screening for epigenetic regulators is challenging and often relies on laborious assays or indirect reporter read-outs. Here we describe a strategy, Epi-ID, to directly assess chromatin status in thousands of mutants. In Epi-ID, chromatin status on DNA barcodes is interrogated by chromatin immunoprecipitation followed by deep sequencing, allowing for quantitative comparison of many mutants in parallel...
December 6, 2016: ELife
https://www.readbyqxmd.com/read/27918555/gene-expression-profiling-of-anti-ctla4-treated-metastatic-melanoma-in-patients-with-treatment-induced-autoimmunity
#13
Scott C Bresler, Le Min, Scott J Rodig, Andrew C Walls, Shuyun Xu, Songmei Geng, F Stephen Hodi, George F Murphy, Christine G Lian
Ipilimumab (IPI) is a monoclonal antibody that targets the inhibitory CTLA4 receptor of T cells, enhancing T-cell-driven antitumor responses. IPI therapy in metastatic melanoma results in significant improvement in disease-free and overall survival, although after initial responses disease progression generally ensues. Identification of specific responses in tissue where melanoma tumor cells are subjected to IPI-driven immune attack may reveal mechanisms of treatment efficacy or resistance, permitting refinement of targeted therapeutic approaches...
December 5, 2016: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/27918539/rapidly-evolving-homing-crispr-barcodes
#14
Reza Kalhor, Prashant Mali, George M Church
We present an approach for engineering evolving DNA barcodes in living cells. A homing guide RNA (hgRNA) scaffold directs the Cas9-hgRNA complex to the DNA locus of the hgRNA itself. We show that this homing CRISPR-Cas9 system acts as an expressed genetic barcode that diversifies its sequence and that the rate of diversification can be controlled in cultured cells. We further evaluate these barcodes in cell populations and show that they can be used to record lineage history and that the barcode RNA can be amplified in situ, a prerequisite for in situ sequencing...
December 5, 2016: Nature Methods
https://www.readbyqxmd.com/read/27918193/dna-barcodes-identify-medically-important-tick-species-in-canada
#15
Danielle A Ondrejicka, Kevin C Morey, Robert H Hanner
Medically important ticks (Acari: Ixodidae) are often difficult to identify morphologically. A standardized, molecular approach using a 658 base pair DNA barcode sequence (from the 5' region of the mitochondrial cytochrome c oxidase subunit I gene) was evaluated for its effectiveness in discriminating ticks in North America, with an emphasis on Canadian ticks. DNA barcodes were generated for 96 of 154 specimens representing 26 ixodid species. A genetic cluster analysis was performed on the barcode sequences, which separated specimens into haplogroups closely corresponding with morphologically identified species...
July 19, 2016: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/27917695/nanostring-a-novel-digital-color-coded-barcode-technology-current-and-future-applications-in-molecular-diagnostics
#16
Hin-Fung Tsang, Vivian Weiwen Xue, Su-Pin Koh, Ya-Ming Chiu, Lawrence Po-Wah Ng, Sze-Chuen Cesar Wong
Formalin-fixed, paraffin-embedded (FFPE) tissue sample is a gold mine of resources for molecular diagnosis and retrospective clinical studies. Although molecular technologies have expanded the range of mutations identified in FFPE samples, the applications of existing technologies are limited by the low nucleic acids yield and poor extraction quality. As a result, the routine clinical applications of molecular diagnosis using FFPE samples has been associated with many practical challenges. NanoString technologies utilize a novel digital color-coded barcode technology based on direct multiplexed measurement of gene expression and offer high levels of precision and sensitivity...
December 3, 2016: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/27917059/a-survey-of-pireneitega-from-tajikistan-agelenidae-coelotinae
#17
Xiaoqing Zhang, Yuri M Marusik
Five new species of Pireneitega species from Tajikistan are described: Pireneitega zonsteinisp. n. (♂♀), Pireneitega muratovisp. n. (♀), Pireneitega tyuraisp. n. (♀), Pireneitega ramitensissp. n. (♀) and Pireneitega kovblyukisp. n. (♂). Pireneitega major (Kroneberg, 1875) is redescribed for the first time based on the lectotype designated here. DNA barcodes for the five new species are documented for future use and as proof of molecular differences between these species.
2016: ZooKeys
https://www.readbyqxmd.com/read/27917041/the-jumping-spiders-from-xishuangbanna-yunnan-china-araneae-salticidae
#18
Qi Cao, Shuqiang Li, Marek Żabka
Twenty one jumping spider species from South Yunnan are reported, diagnosed, described and illustrated; 19 of them are described as new: Afraflacilla ballarini Cao & Li, sp. n. (♂), Agorius tortilis Cao & Li, sp. n. (♂♀), Bavia exilis Cao & Li, sp. n. (♂), Carrhotus kevinlii Cao & Li, sp. n. (♂♀), Carrhotus sarahcrewsae Cao & Li, sp. n. (♂), Chinattus wengnanensis Cao & Li, sp. n. (♂♀), Chinophrys mengyangensis Cao & Li, sp. n. (♂♀), Cocalus menglaensis Cao & Li, sp. n. (♂♀), Cosmophasis xiaolonghaensis Cao & Li, sp...
2016: ZooKeys
https://www.readbyqxmd.com/read/27917038/revised-classification-and-catalogue-of-global-nepticulidae-and-opostegidae-lepidoptera-nepticuloidea
#19
Erik J van Nieukerken, Camiel Doorenweerd, Robert J B Hoare, Donald R Davis
A catalogue of all named Nepticulidae and Opostegidae is presented, including fossil species. The catalogue is simultaneously published online in the scratchpad http://nepticuloidea.info/ and in Catalogue of Life (http://www.catalogueoflife.org/col/details/database/id/172). We provide a historical overview of taxonomic research on Nepticuloidea and a brief 'state of the art'. A DNA barcode dataset with 3205 barcodes is made public at the same time, providing DNA barcodes of ca. 779 species, of which 2563 are identified as belonging to 444 validly published species...
2016: ZooKeys
https://www.readbyqxmd.com/read/27916561/finding-srna-associated-phenotypes-by-competition-assays-an-example-with-staphylococcus-aureus
#20
Thao Nguyen Le Lam, Claire Morvan, Wenfeng Liu, Chantal Bohn, Yan Jaszczyszyn, Philippe Bouloc
Bacteria optimize their fitness in response to a changing environment by tight regulation of gene expression. Regulation can be controlled at both transcriptional and post-transcriptional levels via key players such as sigma factors, regulatory proteins and regulatory RNAs. The identification of phenotypes associated with gene deletions is the established method for finding gene functions but may require testing many conditions for each studied mutant. As regulatory RNAs often contribute to fine-tuning gene expression, phenotypes associated with their inactivation are often weak and difficult to detect...
December 1, 2016: Methods: a Companion to Methods in Enzymology
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