keyword
MENU ▼
Read by QxMD icon Read
search

barcoding

keyword
https://www.readbyqxmd.com/read/28439859/genome-wide-profiling-of-histone-modifications-and-histone-variants-in-arabidopsis-thaliana-and-marchantia-polymorpha
#1
Ramesh Yelagandula, Akihisa Osakabe, Elin Axelsson, Frederic Berger, Tomokazu Kawashima
Histone modifications and histone variants barcode the genome and play major roles in epigenetic regulations. Chromatin immunoprecipitation (ChIP) coupled with next-generation sequencing (NGS) is a well-established method to investigate the landscape of epigenetic marks at a genomic level. Here, we describe procedures for conducting ChIP, subsequent NGS library construction, and data analysis on histone modifications and histone variants in Arabidopsis thaliana. We also describe an optimized nuclear isolation procedure to prepare chromatin for ChIP in the liverwort, Marchantia polymorpha, which is the emerging model plant ideal for evolutionary studies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439828/interrogation-of-functional-mirna-target-interactions-by-crispr-cas9-genome-engineering
#2
Yale S Michaels, Qianxin Wu, Tudor A Fulga
Post-transcriptional silencing by microRNAs (miRNAs) is a critical constituent of eukaryotic gene regulation. miRNAs are short (~22nt) noncoding RNAs capable of specifically targeting the miRNA-induced-silencing-complex (miRISC) to transcripts bearing a complementary miRNA response element (MRE). Although recent methodological advances have greatly improved our understanding of miRNA biogenesis and the mechanisms by which miRNAs repress their cognate targets, exploring the physiological relevance of direct miRNA-target interactions in vivo has remained an outstanding challenge...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28437475/the-school-malaise-trap-program-coupling-educational-outreach-with-scientific-discovery
#3
Dirk Steinke, Vanessa Breton, Emily Berzitis, Paul D N Hebert
The School Malaise Trap Program (SMTP) provides a technologically sophisticated and scientifically relevant educational experience that exposes students to the diversity of life, enhancing their understanding of biodiversity while promoting environmental stewardship. Since 2013, the SMTP has allowed 15,000 students at 350 primary and secondary schools to explore insect diversity in Canadian schoolyards. Students at each school collected hundreds of insects for an analysis of DNA sequence variation that enabled their rapid identification to a species...
April 2017: PLoS Biology
https://www.readbyqxmd.com/read/28431212/dna-barcoding-and-traditional-taxonomy-an-integrated-approach-for-biodiversity-conservation
#4
Bhavisha P Sheth, Vrinda S Thaker
Biological diversity is depleting at an alarming rate. Additionally, a vast amount of biodiversity still remains undiscovered. Taxonomy has been serving the purpose of describing, naming, and classifying species for more than 250 years. DNA taxonomy and barcoding have accelerated the rate of this process, thereby providing a tool for conservation practice. DNA barcoding and traditional taxonomy have their own inherent merits and demerits. The synergistic use of both methods, in the form of integrative taxonomy, has the potential to contribute to biodiversity conservation in a pragmatic timeframe and overcome their individual drawbacks...
April 21, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28431084/sonographic-barcode-sign-of-pneumothorax
#5
Tai-Jen Chuang, Chih-Cheng Lai
No abstract text is available yet for this article.
April 18, 2017: QJM: Monthly Journal of the Association of Physicians
https://www.readbyqxmd.com/read/28430956/achieving-high-reliability-in-histology-%C3%A2-an-improvement-series-to-reduce-errors
#6
Yael K Heher, Yigu Chen, Sergey Pyatibrat, Edward Yoon, Jeffrey D Goldsmith, Kenneth E Sands
Objectives: Despite sweeping medical advances in other fields, histology processes have by and large remained constant over the past 175 years. Patient label identification errors are a known liability in the laboratory and can be devastating, resulting in incorrect diagnoses and inappropriate treatment. The objective of this study was to identify vulnerable steps in the histology workflow and reduce the frequency of labeling errors (LEs). Methods: In this 36-month study period, a numerical step key (SK) was developed to capture LEs...
November 1, 2016: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28430780/the-importance-of-standardization-for-biodiversity-comparisons-a-case-study-using-autonomous-reef-monitoring-structures-arms-and-metabarcoding-to-measure-cryptic-diversity-on-mo-orea-coral-reefs-french-polynesia
#7
Emma Ransome, Jonathan B Geller, Molly Timmers, Matthieu Leray, Angka Mahardini, Andrianus Sembiring, Allen G Collins, Christopher P Meyer
The advancement of metabarcoding techniques, declining costs of high-throughput sequencing and development of systematic sampling devices, such as autonomous reef monitoring structures (ARMS), have provided the means to gather a vast amount of diversity data from cryptic marine communities. However, such increased capability could also lead to analytical challenges if the methods used to examine these communities across local and global scales are not standardized. Here we compare and assess the underlying biases of four ARMS field processing methods, preservation media, and current bioinformatic pipelines in evaluating diversity from cytochrome c oxidase I metabarcoding data...
2017: PloS One
https://www.readbyqxmd.com/read/28428844/stable-isotope-analyses-a-method-to-distinguish-intensively-farmed-from-wild-frogs
#8
Carolin Dittrich, Ulrich Struck, Mark-Oliver Rödel
Consumption of frog legs is increasing worldwide, with potentially dramatic effects for ecosystems. More and more functioning frog farms are reported to exist. However, due to the lack of reliable methods to distinguish farmed from wild-caught individuals, the origin of frogs in the international trade is often uncertain. Here, we present a new methodological approach to this problem. We investigated the isotopic composition of legally traded frog legs from suppliers in Vietnam and Indonesia. Muscle and bone tissue samples were examined for δ(15)N, δ(13)C, and δ(18)O stable isotope compositions, to elucidate the conditions under which the frogs grew up...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28427715/multiplexed-dynamic-imaging-of-genomic-loci-by-combined-crispr-imaging-and-dna-sequential-fish
#9
Yodai Takei, Sheel Shah, Sho Harvey, Lei S Qi, Long Cai
Visualization of chromosome dynamics allows the investigation of spatiotemporal chromatin organization and its role in gene regulation and other cellular processes. However, current approaches to label multiple genomic loci in live cells have a fundamental limitation in the number of loci that can be labeled and uniquely identified. Here we describe an approach we call "track first and identify later" for multiplexed visualization of chromosome dynamics by combining two techniques: CRISPR imaging and DNA sequential fluorescence in situ hybridization...
April 17, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28420399/distinct-parasite-populations-infect-individuals-identified-through-passive-and-active-case-detection-in-a-region-of-declining-malaria-transmission-in-southern-zambia
#10
Kelly M Searle, Ben Katowa, Tamaki Kobayashi, Mwiche N S Siame, Sungano Mharakurwa, Giovanna Carpi, Douglas E Norris, Jennifer C Stevenson, Philip E Thuma, William J Moss
BACKGROUND: Substantial reductions in the burden of malaria have been documented in parts of sub-Saharan Africa, with elimination strategies and goals being formulated in some regions. Within this context, understanding the epidemiology of low-level malaria transmission is crucial to achieving and sustaining elimination. A 24 single-nucleotide-polymorphism Plasmodium falciparum molecular barcode was used to characterize parasite populations from infected individuals identified through passive and active case detection in an area approaching malaria elimination in southern Zambia...
April 19, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28419161/unidentifiable-by-morphology-dna-barcoding-of-plant-material-in-local-markets-in-iran
#11
Abdolbaset Ghorbani, Yousef Saeedi, Hugo J de Boer
Local markets provide a rapid insight into the medicinal plants growing in a region as well as local traditional health concerns. Identification of market plant material can be challenging as plants are often sold in dried or processed forms. In this study, three approaches of DNA barcoding-based molecular identification of market samples are evaluated, two objective sequence matching approaches and an integrative approach that coalesces sequence matching with a priori and a posteriori data from other markers, morphology, ethnoclassification and species distribution...
2017: PloS One
https://www.readbyqxmd.com/read/28418812/phellinopsis-lonicericola-and-p-tibetica-spp-nov-hymenochaetales-basidiomycota-from-tibet-with-a-key-to-worldwide-species
#12
Li-Wei Zhou, Jie Song
Phellinopsis (Hymenochaetaceae) was recently segregated from Phellinus. Phellinopsis differs from other genera segregated from Phellinus in a combination of hymenial setae, if present, mostly originating from tramal hyphae and hyaline basidiospores becoming pale yellowish with age. In this study, two new species of Phellinopsis, P. lonicericola and P. tibetica, from Tibet in southwestern China were described and illustrated. Morphological data and sequences of the nuc rDNA ITS1-5.8S-ITS2 region (internal transcribed spacer [ITS] barcode) support the recognition of these taxa as distinct...
March 3, 2017: Mycologia
https://www.readbyqxmd.com/read/28417591/effective-mosquito-and-arbovirus-surveillance-using-metabarcoding
#13
J Batovska, S E Lynch, N O I Cogan, K Brown, J M Darbro, E A Kho, M J Blacket
Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next-generation sequencing (NGS) is a high-throughput technology that has the potential to modernise vector surveillance. When combined with DNA barcoding, it is termed 'metabarcoding'. The aim of our study was to establish a metabarcoding protocol to characterise pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%...
April 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28417460/effect-of-high-fat-diet-and-growth-stage-on-the-diversity-and-composition-of-intestinal-microbiota-in-healthy-bovine-livestock
#14
Shengyin Jiao, Hui Cao, Yue Dai, Junhui Wu, Jia Lv, Renjia Du, Bei Han
BACKGROUND: This study aimed to investigate the composition of bacteria in the bovine rectum and their functions during growth, in relation to different diets. Fecal samples were collected from 6-, 12-, 18- and 24-month cattle fed high-fat diet, and healthy female parents fed regular-diet. Total DNA was amplified (V3-V4 of 16S rRNA) and submitted to barcode-DNA-pyrosequencing. Then, intestinal microbiota profiles and functions were analysed. RESULTS: A total of 114,512 OTUs were detected from the 1,802,243 sequences obtained...
April 18, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28416672/bisulfite-converted-duplexes-for-the-strand-specific-detection-and-quantification-of-rare-mutations
#15
Austin K Mattox, Yuxuan Wang, Simeon Springer, Joshua D Cohen, Srinivasan Yegnasubramanian, William G Nelson, Kenneth W Kinzler, Bert Vogelstein, Nickolas Papadopoulos
The identification of mutations that are present at low frequencies in clinical samples is an essential component of precision medicine. The development of molecular barcoding for next-generation sequencing has greatly enhanced the sensitivity of detecting such mutations by massively parallel sequencing. However, further improvements in specificity would be useful for a variety of applications. We herein describe a technology (BiSeqS) that can increase the specificity of sequencing by at least two orders of magnitude over and above that achieved with molecular barcoding and can be applied to any massively parallel sequencing instrument...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28416409/-recommendations-for-the-unequivocal-identification-of-the-newborn
#16
Ester Sanz López, Manuel Sánchez Luna, Segundo Rite Gracia, Isabel Benavente Fernández, José Luis Leante Castellanos, Alejandro Pérez Muñuzuri, César W Ruiz Campillo, María Dolores Sánchez Redondo
Newborn identification is a legal right recognised by international and national laws. Moreover, improving the accuracy of correct patient identification is an important goal of patient safety solutions programs. In this article, the Standards Committee of the Spanish Society of Neonatology establishes recommendations to ensure correct identification of the newborn whilst in hospital. Currently, the most reliable method of identification of the newborn is the combination of identification cord clamp and bracelets (mother bracelet, newborn bracelet and cord clamp with the same number and identical and exclusive barcode system for each newborn) and the collection of maternal and umbilical cord blood samples (for DNA testing only for identification purposes)...
April 14, 2017: Anales de Pediatría: Publicación Oficial de la Asociación Española de Pediatría (A.E.P.)
https://www.readbyqxmd.com/read/28416141/multiplexed-engineering-and-analysis-of-combinatorial-enhancer-activity-in-single-cells
#17
Shiqi Xie, Jialei Duan, Boxun Li, Pei Zhou, Gary C Hon
The study of enhancers has been hampered by the scarcity of methods to systematically quantify their endogenous activity. We develop Mosaic-seq to systematically perturb enhancers and measure their endogenous activities at single-cell resolution. Mosaic-seq uses a CRISPR barcoding system to jointly measure a cell's transcriptome and its sgRNA modulators, thus quantifying the effects of dCas9-KRAB-mediated enhancer repression in single cells. Applying Mosaic-seq to 71 constituent enhancers from 15 super-enhancers, our analysis of 51,448 sgRNA-induced transcriptomes finds that only a small number of constituents are major effectors of target gene expression...
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28414813/dna-barcoding-evaluation-and-implications-for-phylogenetic-relationships-in-lauraceae-from-china
#18
Zhi-Fang Liu, Xiu-Qin Ci, Lang Li, Hsi-Wen Li, John G Conran, Jie Li
Lauraceae are an important component of tropical and subtropical forests and have major ecological and economic significance. Owing to lack of clear-cut morphological differences between genera and species, this family is an ideal case for testing the efficacy of DNA barcoding in the identification and discrimination of species and genera. In this study, we evaluated five widely recommended plant DNA barcode loci matK, rbcL, trnH-psbA, ITS2 and the entire ITS region for 409 individuals representing 133 species, 12 genera from China...
2017: PloS One
https://www.readbyqxmd.com/read/28407939/dna-barcoding-coupled-to-hrm-analysis-as-a-new-and-simple-tool-for-the-authentication-of-gadidae-fish-species
#19
Telmo J R Fernandes, Joana Costa, M Beatriz P P Oliveira, Isabel Mafra
This work aimed to exploit the use of DNA mini-barcodes combined with high resolution melting (HRM) for the authentication of gadoid species: Atlantic cod (Gadus morhua), Pacific cod (Gadus macrocephalus), Alaska pollock (Theragra chalcogramma) and saithe (Pollachius virens). Two DNA barcode regions, namely cytochrome c oxidase subunit I (COI) and cytochrome b (cytb), were analysed in silico to identify genetic variability among the four species and used, subsequently, to develop a real-time PCR method coupled with HRM analysis...
September 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28407723/dna-barcodes-and-insights-into-the-phylogenetic-relationships-of-corvidae-aves-passeriformes
#20
Zuhao Huang, Rujue Ruan
DNA barcoding has become a promising tool for species identification and phylogeny in a wide range of animal taxa using mitochondrial cytochrome c oxidase subunit I (COI). The Corvidae (Aves: Passeriformes) is a species rich and morphologically diverse family. In the present study, we analyzed the COI barcodes of 39 species from 12 genera of Corvidae. COI gene was also used to examine phylogenetic relationships of Corvidae. Every species possessed a barcode distinct from that of other species. Kimura two-parameter distances were calculated between species barcodes...
April 13, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
keyword
keyword
75802
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"