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https://www.readbyqxmd.com/read/28449274/a-dna-barcode-library-for-germany-s-mayflies-stoneflies-and-caddisflies-ephemeroptera-plecoptera-trichoptera
#1
Jérôme Morinière, Lars Hendrich, Michael Balke, Arne J Beermann, Tobias König, Monika Hess, Stefan Koch, Reinhard Müller, Florian Leese, Paul D N Hebert, Axel Hausmann, Christoph F Schubart, Gerhard Haszprunar
Mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are prominent representatives of aquatic macroinvertebrates, commonly used as indicator organisms for water quality and ecosystem assessments. However, unambiguous morphological identification of EPT species, especially their immature life stages, is a challenging, yet fundamental task. However, a comprehensive DNA barcode library based upon taxonomically well-curated specimens can overcome the problematic identification. Once available, this library will support the implementation of fast, cost-efficient, and reliable DNA-based identifications and assessments of ecological status...
April 27, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28449233/an-evaluation-of-the-international-society-for-animal-genetics-recommended-parentage-and-identification-panel-for-the-domestic-pigeon-columba-livia-domestica
#2
M de Groot, W A van Haeringen
In this study, the International Society for Animal Genetics (ISAG) recommended panel for the identification of the domestic pigeon (Columba livia domestica) is characterized based on commonly used statistical parameters. The marker panel is based on 16 short tandem repeat (STR) loci (PIGN15, PIGN10, PIGN57, PIGN26, CliμD16, CliμD19, PIGN12, CliμD17, CliμT17, PIGN04, CliμD01, CliμD11, CliμD35, CliμT02, CliμT13, CliμT43). The alleles of the 16 loci consist of a mixture of tri-, tetra-, penta- and hexameric repeat patterns...
April 27, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28448639/cryptic-diversity-of-the-subfamily-calaphidinae-hemiptera-aphididae-revealed-by-comprehensive-dna-barcoding
#3
Yerim Lee, Wonhoon Lee, Mariusz Kanturski, Robert G Foottit, Shin-Ichi Akimoto, Seunghwan Lee
Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank)...
2017: PloS One
https://www.readbyqxmd.com/read/28447972/wild-type-blocking-pcr-combined-with-direct-sequencing-as-a-highly-sensitive-method-for-detection-of-low-frequency-somatic-mutations
#4
Adam Z Albitar, Wanlong Ma, Maher Albitar
Accurate detection and identification of low frequency mutations can be problematic when assessing residual disease after therapy, screening for emerging resistance mutations during therapy, or when patients have few circulating tumor cells. Wild-type blocking PCR followed by sequencing analysis offers high sensitivity, flexibility, and simplicity as a methodology for detecting these low frequency mutations. By adding a custom designed locked nucleic acid oligonucleotide to a new or previously established conventional PCR based sequencing assay, sensitivities of approximately 1 mutant allele in a background of 1,000 WT alleles can be achieved (1:1,000)...
March 29, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28446964/strategies-for-the-acquisition-of-transcriptional-and-epigenetic-information-in-single-cells
#5
REVIEW
Guang Li, Elda Dzilic, Nick Flores, Alice Shieh, Sean M Wu
As the basic unit of living organisms, each single cell has unique molecular signatures and functions. Our ability to uncover the transcriptional and epigenetic signature of single cells has been hampered by the lack of tools to explore this area of research. The advent of microfluidic single cell technology along with single cell genome-wide DNA amplification methods had greatly improved our understanding of the expression variation in single cells. Transcriptional expression profile by multiplex qPCR or genome-wide RNA sequencing has enabled us to examine genes expression in single cells in different tissues...
March 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28446707/deterministic-versus-stochastic-model-of-reprogramming-new-evidence-from-cellular-barcoding-technique
#6
Anastasia M Yunusova, Veniamin S Fishman, Gennady V Vasiliev, Nariman R Battulin
Factor-mediated reprogramming of somatic cells towards pluripotency is a low-efficiency process during which only small subsets of cells are successfully reprogrammed. Previous analyses of the determinants of the reprogramming potential are based on average measurements across a large population of cells or on monitoring a relatively small number of single cells with live imaging. Here, we applied lentiviral genetic barcoding, a powerful tool enabling the identification of familiar relationships in thousands of cells...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28446605/crispr-cas9-mediated-gene-knockout-screens-and-target-identification-via-whole-genome-sequencing-uncover-host-genes-required-for-picornavirus-infection
#7
Heon Seok Kim, Kyungjin Lee, Sangsu Bae, Jeongbin Park, Chong-Kyo Lee, Meehyein Kim, Eunji Kim, Minju Kim, Seokjoong Kim, Chonsaeng Kim, Jin-Soo Kim
Several groups have used genome-wide libraries of lentiviruses encoding small-guide RNAs (sgRNAs) for genetic screens. In most cases, sgRNA expression cassettes are integrated into cells by using lentiviruses, and target genes are statistically estimated by the readout of sgRNA sequences after targeted sequencing. We present a new virus-free method for human gene-knockout screens using a genome-wide library of CRISPR/Cas9 sgRNAs based on plasmids, and target gene identification via whole-genome sequencing (WGS) confirming authentic mutations rather than statistical estimating through targeted amplicon sequencing...
April 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28446571/a-core-genome-multi-locus-sequence-typing-scheme-for-stable-comparative-analyses-of-campylobacter-jejuni-and-c-coli-human-disease-isolates
#8
Alison J Cody, James E Bray, Keith A Jolley, Noel D McCarthy, C J Maiden Martin
Human campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterisation methods. Whole genome sequencing (WGS) data enables the improvement of sequence-based typing approaches, such as multi locus sequence typing (MLST), by substantially increasing the number of loci examined...
April 26, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28445483/community-barcoding-reveals-little-effect-of-ocean-acidification-on-the-composition-of-coastal-plankton-communities-evidence-from-a-long-term-mesocosm-study-in-the-gullmar-fjord-skagerrak
#9
Julia A F Langer, Rahul Sharma, Susanne I Schmidt, Sebastian Bahrdt, Henriette G Horn, María Algueró-Muñiz, Bora Nam, Eric P Achterberg, Ulf Riebesell, Maarten Boersma, Marco Thines, Klaus Schwenk
The acidification of the oceans could potentially alter marine plankton communities with consequences for ecosystem functioning. While several studies have investigated effects of ocean acidification on communities using traditional methods, few have used genetic analyses. Here, we use community barcoding to assess the impact of ocean acidification on the composition of a coastal plankton community in a large scale, in situ, long-term mesocosm experiment. High-throughput sequencing resulted in the identification of a wide range of planktonic taxa (Alveolata, Cryptophyta, Haptophyceae, Fungi, Metazoa, Hydrozoa, Rhizaria, Straminipila, Chlorophyta)...
2017: PloS One
https://www.readbyqxmd.com/read/28444200/the-mediterranean-the-cradle-of-anthoxanthum-poaceae-diploid-diversity
#10
Zuzana Chumová, Eliška Záveská, Terezie Mandáková, Karol Krak, Pavel Trávnícek
Background and Aims: Knowledge of diploid phylogeny and ecogeography provide a foundation for understanding plant evolutionary history, diversification patterns and taxonomy. The genus Anthoxanthum (vernal grasses, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and poorly resolved evolutionary relationships. The aims of the study were to reveal: (1) evolutionary lineages of the diploid taxa and their genetic differentiation; (2) the past distribution of the rediscovered 'Mediterranean diploid'; and (3) possible migration routes of diploids in the Mediterranean...
April 21, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28443105/identification-of-microrna-targets-of-capsicum-spp-using-mirtrans-a-trans-omics-approach
#11
Lu Zhang, Cheng Qin, Junpu Mei, Xiaocui Chen, Zhiming Wu, Xirong Luo, Jiaowen Cheng, Xiangqun Tang, Kailin Hu, Shuai C Li
The microRNA (miRNA) can regulate the transcripts that are involved in eukaryotic cell proliferation, differentiation, and metabolism. Especially for plants, our understanding of miRNA targets, is still limited. Early attempts of prediction on sequence alignments have been plagued by enormous false positives. It is helpful to improve target prediction specificity by incorporating the other data sources such as the dependency between miRNA and transcript expression or even cleaved transcripts by miRNA regulations, which are referred to as trans-omics data...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28443103/genotyping-by-sequencing-for-snp-based-linkage-analysis-and-identification-of-qtls-linked-to-fruit-quality-traits-in-japanese-plum-prunus-salicina-lindl
#12
Juan A Salazar, Igor Pacheco, Paulina Shinya, Patricio Zapata, Claudia Silva, Mallikarjuna Aradhya, Dianne Velasco, David Ruiz, Pedro Martínez-Gómez, Rodrigo Infante
Marker-assisted selection (MAS) in stone fruit (Prunus species) breeding is currently difficult to achieve due to the polygenic nature of the most relevant agronomic traits linked to fruit quality. Genotyping by sequencing (GBS), however, provides a large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from a reference genome. In this study, GBS was used to genotype 272 seedlings of three F1 Japanese plum (Prunus salicina Lindl) progenies derived from crossing "98-99" (as a common female parent) with "Angeleno," "September King," and "September Queen" as male parents...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28441969/molecular-identification-of-plasmodium-spp-and-blood-meal-sources-of-anophelines-in-environmental-reserves-on-s%C3%A3-o-lu%C3%A3-s-island-state-of-maranh%C3%A3-o-brazil
#13
Mayra Araguaia Pereira Figueiredo, Silvia Maria Di Santi, Wilson Gómez Manrique, Luiz Ricardo Gonçalves, Marcos Rogério André, Rosangela Zacarias Machado
BACKGROUND: Considering the diversity of feeding habits that females of some species of anophelines present, it is important to understand which vertebrates are part of blood food sources and how important is the role of each in the ecoepidemiology of malaria. There are many vector species for Plasmodium spp. in the State of Maranhão, Brazil. In São Luís Island, Anopheles aquasalis is the main vector for human malaria; this species is abundant in areas with primates that are positive for Plasmodium...
April 26, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28441930/ribosomal-subunit-protein-typing-using-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry-maldi-tof-ms-for-the-identification-and-discrimination-of-aspergillus-species
#14
Sayaka Nakamura, Hiroaki Sato, Reiko Tanaka, Yoko Kusuya, Hiroki Takahashi, Takashi Yaguchi
BACKGROUND: Accurate identification of Aspergillus species is a very important subject. Mass spectral fingerprinting using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is generally employed for the rapid identification of fungal isolates. However, the results are based on simple mass spectral pattern-matching, with no peak assignment and no taxonomic input. We propose here a ribosomal subunit protein (RSP) typing technique using MALDI-TOF MS for the identification and discrimination of Aspergillus species...
April 26, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28441426/identification-of-genes-associated-with-dissociation-of-cognitive-performance-and-neuropathological-burden-multistep-analysis-of-genetic-epigenetic-and-transcriptional-data
#15
Charles C White, Hyun-Sik Yang, Lei Yu, Lori B Chibnik, Robert J Dawe, Jingyun Yang, Hans-Ulrich Klein, Daniel Felsky, Alfredo Ramos-Miguel, Konstantinos Arfanakis, William G Honer, Reisa A Sperling, Julie A Schneider, David A Bennett, Philip L De Jager
INTRODUCTION: The molecular underpinnings of the dissociation of cognitive performance and neuropathological burden are poorly understood, and there are currently no known genetic or epigenetic determinants of the dissociation. METHODS AND FINDINGS: "Residual cognition" was quantified by regressing out the effects of cerebral pathologies and demographic characteristics on global cognitive performance proximate to death. To identify genes influencing residual cognition, we leveraged neuropathological, genetic, epigenetic, and transcriptional data available for deceased participants of the Religious Orders Study (n = 492) and the Rush Memory and Aging Project (n = 487)...
April 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28440326/complex-multifractal-nature-in-mycobacterium-tuberculosis-genome
#16
Saurav Mandal, Tanmoy Roychowdhury, Keilash Chirom, Alok Bhattacharya, R K Brojen Singh
The mutifractal and long range correlation (C(r)) properties of strings, such as nucleotide sequence can be a useful parameter for identification of underlying patterns and variations. In this study C(r) and multifractal singularity function f(α) have been used to study variations in the genomes of a pathogenic bacteria Mycobacterium tuberculosis. Genomic sequences of M. tuberculosis isolates displayed significant variations in C(r) and f(α) reflecting inherent differences in sequences among isolates. M. tuberculosis isolates can be categorised into different subgroups based on sensitivity to drugs, these are DS (drug sensitive isolates), MDR (multi-drug resistant isolates) and XDR (extremely drug resistant isolates)...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28440291/identifying-n-6-methyladenosine-sites-using-multi-interval-nucleotide-pair-position-specificity-and-support-vector-machine
#17
Pengwei Xing, Ran Su, Fei Guo, Leyi Wei
N6-methyladenosine (m(6)A) refers to methylation of the adenosine nucleotide acid at the nitrogen-6 position. It plays an important role in a series of biological processes, such as splicing events, mRNA exporting, nascent mRNA synthesis, nuclear translocation and translation process. Numerous experiments have been done to successfully characterize m(6)A sites within sequences since high-resolution mapping of m(6)A sites was established. However, as the explosive growth of genomic sequences, using experimental methods to identify m(6)A sites are time-consuming and expensive...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28439835/the-uea-small-rna-workbench-a-suite-of-computational-tools-for-small-rna-analysis
#18
Irina Mohorianu, Matthew Benedict Stocks, Christopher Steven Applegate, Leighton Folkes, Vincent Moulton
RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439832/computational-and-experimental-identification-of-tissue-specific-microrna-targets
#19
Raheleh Amirkhah, Hojjat Naderi Meshkin, Ali Farazmand, John E J Rasko, Ulf Schmitz
In this chapter we discuss computational methods for the prediction of microRNA (miRNA) targets. More specifically, we consider machine learning-based approaches and explain why these methods have been relatively unsuccessful in reducing the number of false positive predictions. Further we suggest approaches designed to improve their performance by considering tissue-specific target regulation. We argue that the miRNA targetome differs depending on the tissue type and introduce a novel algorithm that predicts miRNA targets specifically for colorectal cancer...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439758/molecular-phylogeny-of-21-tropical-bamboo-species-reconstructed-by-integrating-non-coding-internal-transcribed-spacer-its1-and-2-sequences-and-their-consensus-secondary-structure
#20
Jayadri Sekhar Ghosh, Samik Bhattacharya, Amita Pal
The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses...
April 24, 2017: Genetica
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