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https://www.readbyqxmd.com/read/28533898/reconstructing-a-herbivore-s-diet-using-a-novel-rbcl-dna-mini-barcode-for-plants
#1
David L Erickson, Elizabeth Reed, Padmini Ramachandran, Norman A Bourg, William J McShea, Andrea Ottesen
Next Generation Sequencing and the application of metagenomic analyses can be used to answer questions about animal diet choice and study the consequences of selective foraging by herbivores. The quantification of herbivore diet choice with respect to native versus exotic plant species is particularly relevant given concerns of invasive species establishment and their effects on ecosystems. While increased abundance of white-tailed deer (Odocoileus virginianus) appears to correlate with increased incidence of invasive plant species, data supporting a causal link is scarce...
May 2017: AoB Plants
https://www.readbyqxmd.com/read/28530655/a-quantitative-and-multiplexed-approach-to-uncover-the-fitness-landscape-of-tumor-suppression-in-vivo
#2
Zoë N Rogers, Christopher D McFarland, Ian P Winters, Santiago Naranjo, Chen-Hua Chuang, Dmitri Petrov, Monte M Winslow
Cancer growth is a multistage, stochastic evolutionary process. While cancer genome sequencing has been instrumental in identifying the genomic alterations that occur in human tumors, the consequences of these alterations on tumor growth remain largely unexplored. Conventional genetically engineered mouse models enable the study of tumor growth in vivo, but they are neither readily scalable nor sufficiently quantitative to unravel the magnitude and mode of action of many tumor-suppressor genes. Here, we present a method that integrates tumor barcoding with ultradeep barcode sequencing (Tuba-seq) to interrogate tumor-suppressor function in mouse models of human cancer...
May 22, 2017: Nature Methods
https://www.readbyqxmd.com/read/28530222/ultrasensitive-and-high-efficiency-screen-of-de-novo-low-frequency-mutations-by-o2n-seq
#3
Kaile Wang, Shujuan Lai, Xiaoxu Yang, Tianqi Zhu, Xuemei Lu, Chung-I Wu, Jue Ruan
Detection of de novo, low-frequency mutations is essential for characterizing cancer genomes and heterogeneous cell populations. However, the screening capacity of current ultrasensitive NGS methods is inadequate owing to either low-efficiency read utilization or severe amplification bias. Here, we present o2n-seq, an ultrasensitive and high-efficiency NGS library preparation method for discovering de novo, low-frequency mutations. O2n-seq reduces the error rate of NGS to 10(-5)-10(-8). The efficiency of its data usage is about 10-30 times higher than that of barcode-based strategies...
May 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28529702/assessing-the-species-composition-of-tropical-eels-anguillidae-in-aceh-waters-indonesia-with-dna-barcoding-gene-cox1
#4
Zainal A Muchlisin, Agung Setia Batubara, Nur Fadli, Abdullah A Muhammadar, Afrita Ida Utami, Nurul Farhana, Mohd Nor Siti-Azizah
The objective of the present study was to evaluate the species diversity of eels native to Aceh waters based on genetic data. Sampling was conducted in western coast waters of Aceh Province, Indonesia, from July to August 2016. Genomic DNA was extracted from the samples, a genomic region from the 5' region of the cox1 gene was amplified and sequenced, and this was then used to analyse genetic variation. The genetic sequences were blasted into the NCBI database. Based on this analysis there were three valid species of eels that occurred in Aceh waters, namely Anguilla marmorata, A...
2017: F1000Research
https://www.readbyqxmd.com/read/28525570/droplet-barcode-sequencing-for-targeted-linked-read-haplotyping-of-single-dna-molecules
#5
David Redin, Erik Borgström, Mengxiao He, Hooman Aghelpasand, Max Käller, Afshin Ahmadian
Data produced with short-read sequencing technologies result in ambiguous haplotyping and a limited capacity to investigate the full repertoire of biologically relevant forms of genetic variation. The notion of haplotype-resolved sequencing data has recently gained traction to reduce this unwanted ambiguity and enable exploration of other forms of genetic variation; beyond studies of just nucleotide polymorphisms, such as compound heterozygosity and structural variations. Here we describe Droplet Barcode Sequencing, a novel approach for creating linked-read sequencing libraries by uniquely barcoding the information within single DNA molecules in emulsion droplets, without the aid of specialty reagents or microfluidic devices...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28521438/identification-of-differentially-expressed-genes-between-early-stage-adenocarcinoma-and-squamous-cell-carcinoma-lung-cancer-using-meta-analysis-methods
#6
Tianjiao Wang, Lei Zhang, Pu Tian, Suyan Tian
Lung adenocarcinoma (AC) and squamous cell lung carcinoma (SCC) are two major subtypes of non-small cell lung cancer (NSCLC). Previous studies have demonstrated that fundamental differences exist in the underlying mechanisms of tumor development, growth and invasion between these subtypes. The investigation of differentially-expressed genes (DEGs) between these two NSCLC subtypes is useful for determining and understanding such differences. The present study aimed to identify those DEGs using meta-analysis and the data from four microarray experiments, consisting of 164 AC and 161 SCC samples...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28521130/seqfish-accurately-detects-transcripts-in-single-cells-and-reveals-robust-spatial-organization-in-the-hippocampus
#7
Sheel Shah, Eric Lubeck, Wen Zhou, Long Cai
We recently applied multiplexed seqFISH to profile expressions of hundreds of genes at the single-cell level in situ (Shah et al., 2016) and provided a map of spatial heterogeneity within each subregion, reconciling previously contradictory descriptions of CA1 at lower spatial resolutions. The accompanying Matters Arising paper from Cembrowski and Spruston questions the spatial organization described for CA1 and raise concerns that the results were determined only by high expression, non-barcoded genes...
May 17, 2017: Neuron
https://www.readbyqxmd.com/read/28521129/integrating-results-across-methodologies-is-essential-for-producing-robust-neuronal-taxonomies
#8
Mark S Cembrowski, Nelson Spruston
Elucidating the diversity and spatial organization of cell types in the brain is an essential goal of neuroscience, with many emerging technologies helping to advance this endeavor. Using a new in situ hybridization method that can measure the expression of hundreds of genes in a given mouse brain section (amplified seqFISH), Shah et al. (2016) describe a spatial organization of hippocampal cell types that differs from previous reports. In seeking to understand this discrepancy, we find that many of the barcoded genes used by seqFISH to characterize this spatial organization, when cross-validated by other sensitive methodologies, exhibit negligible expression in the hippocampus...
May 17, 2017: Neuron
https://www.readbyqxmd.com/read/28515454/a-quantitative-shrna-screen-identifies-atp1a1-as-a-gene-that-regulates-cytotoxicity-by-aurilide-b
#9
Shohei Takase, Rumi Kurokawa, Daisuke Arai, Kind Kanemoto Kanto, Tatsufumi Okino, Yoichi Nakao, Tetsuo Kushiro, Minoru Yoshida, Ken Matsumoto
Genome-wide RNA interference (RNAi) with pooled and barcoded short-hairpin RNA (shRNA) libraries provides a powerful tool for identifying cellular components that are relevant to the modes/mechanisms of action (MoA) of bioactive compounds. shRNAs that affect cellular sensitivity to a given compound can be identified by deep sequencing of shRNA-specific barcodes. We used multiplex barcode sequencing technology by adding sample-specific index tags to PCR primers during sequence library preparation, enabling parallel analysis of multiple samples...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28515435/genetic-diversity-of-armored-scales-hemiptera-diaspididae-and-soft-scales-hemiptera-coccidae-in-chile
#10
P Amouroux, D Crochard, J-F Germain, M Correa, J Ampuero, G Groussier, P Kreiter, T Malausa, T Zaviezo
Scale insects (Sternorrhyncha: Coccoidea) are one of the most invasive and agriculturally damaging insect groups. Their management and the development of new control methods are currently jeopardized by the scarcity of identification data, in particular in regions where no large survey coupling morphological and DNA analyses have been performed. In this study, we sampled 116 populations of armored scales (Hemiptera: Diaspididae) and 112 populations of soft scales (Hemiptera: Coccidae) in Chile, over a latitudinal gradient ranging from 18°S to 41°S, on fruit crops, ornamental plants and trees...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28514600/evaluating-five-different-loci-rbcl-rpob-rpoc1-matk-and-its-for-dna-barcoding-of-indian-orchids
#11
Iffat Parveen, Hemant Kumar Singh, Saloni Malik, Saurabh Raghuvanshi, Shashi Bhushan Babbar
Orchidaceae, one of the largest families of angiosperms, is represented in India by 1600 species distributed in diverse habitats. Orchids are in high demand due to their beautiful flowers and therapeutic properties. Overexploitation and habitat destruction have made many orchid species endangered. In the absence of effective identification methods, illicit trade of orchids continues unabated. Considering DNA barcoding as a potential identification tool, species discrimination capability of five loci, ITS matK, rbcL, rpoB and rpoC1, was tested in 393 accessions of 94 Indian orchid species belonging to 47 genera, including one listed in Appendix I of CITES and 26 medicinal species...
May 17, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28512377/species-delimitation-and-description-of-mesocriconema-nebraskense-n-sp-nematoda-criconematidae-a-morphologically-cryptic-parthenogenetic-species-from-north-american-grasslands
#12
Magdalena Olson, Timothy Harris, Rebecca Higgins, Peter Mullin, Kirsten Powers, Sean Olson, Thomas O Powers
Nematode surveys of North American grasslands conducted from 2010 to 2015 frequently recovered a species of criconematid nematode morphologically resembling Mesocriconema curvatum. These specimens were recovered from remnant native prairies in the central tallgrass ecoregion of North America, and not from surrounding agroecosystems. Historical records indicate that M. curvatum is a cosmopolitan species feeding on a wide range of agronomic and native plants. DNA barcoding indicates North American grasslands contain at least 10 phylogenetically distinct lineages of Mesocriconema that resemble, but are not, M...
March 2017: Journal of Nematology
https://www.readbyqxmd.com/read/28507815/a-new-molecular-diagnostic-tool-for-surveying-and-monitoring-triops-cancriformis-populations
#13
Graham S Sellers, Larry R Griffin, Bernd Hänfling, Africa Gómez
The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism's life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations...
2017: PeerJ
https://www.readbyqxmd.com/read/28503829/unravelling-seed-dispersal-through-fragmented-landscapes-frugivore-species-operate-unevenly-as-mobile-links
#14
Juan P González-Varo, Carolina S Carvalho, Juan M Arroyo, Pedro Jordano
Seed dispersal constitutes a pivotal process in an increasingly fragmented world, promoting population connectivity, colonization and range shifts in plants. Unveiling how multiple frugivore species disperse seeds through fragmented landscapes, operating as mobile links, has remained elusive owing to methodological constraints for monitoring seed dispersal events. We combine for the first time DNA barcoding and DNA microsatellites to identify, respectively, the frugivore species and the source trees of animal-dispersed seeds in forest and matrix of a fragmented landscape...
May 14, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28502206/dna-barcoding-and-phylogenetic-analysis-of-five-ascidians-phlebobranchia-distributed-in-gulf-of-mannar-india
#15
Soban Akram, Kaleem M L Arshan, Jaffarali H Abdul
DNA barcoding has played a significant role in biodiversity assessment as well as its conservation. This technique involves sequencing of mitochondrial marker gene including a short COI gene, known as barcode gene. It has proved its efficiency in identifying several species and resolving the limitations incurred during identification through conventional taxonomy. This study involves the use of DNA barcoding of ascidian species belonging to order Phlebobranchia. A total of 14 individuals, covering two families, three genera and five species, were barcoded...
May 13, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28499337/optically-encoded-semiconducting-polymer-dots-with-single-wavelength-excitation-for-barcoding-and-tracking-of-single-cells
#16
Chun-Ting Kuo, Hong-Shang Peng, Yu Rong, Jiangbo Yu, Wei Sun, Bryant S Fujimoto, Daniel T Chiu
Multiplexed optical encoding is emerging as a powerful technique for high-throughput cellular analysis and molecular assays. Most of the developed optical barcodes, however, either suffer from large particle size or are incompatible with most commercial optical instruments. Here, a new type of nanoscale fluorescent barcodes (Pdot barcodes) was prepared from semiconducting polymers. The Pdot barcodes possess the merits of small size (~20 nm in diameter), narrow emission bands (FWHM of 30-40 nm), three-color emissions (blue, green, and red) under single-wavelength excitation, a high brightness, good pH and thermal stability, and efficient cellular uptake...
May 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28499063/high-efficient-multi-sites-genome-editing-in-allotetraploid-cotton-gossypium-hirsutum-using-crispr-cas9-system
#17
Pengcheng Wang, Jun Zhang, Lin Sun, Yizan Ma, Jiao Xu, Sijia Liang, Jinwu Deng, Jiafu Tan, Qinghua Zhang, Lili Tu, Henry Daniell, Shuangxia Jin, Xianlong Zhang
Gossypium hirsutum is an allotetraploid with a complex genome. Most genes have multiple copies that belong to At and Dt subgenomes. Sequence similarity is also very high between gene homologs. To efficiently achieve site/gene-specific mutation is quite needed. Due to its high efficiency and robustness, the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 system has exerted broad site-specific genome editing from prokaryotes to eukaryotes. In this study, we utilized a CRISPR/Cas9 system to generate two sgRNAs in a single vector to conduct multiple sites genome editing in allotetraploid cotton...
May 12, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28493919/genomic-variation-in-plasmodium-vivax-malaria-reveals-regions-under-selective-pressure
#18
Ernest Diez Benavente, Zoe Ward, Wilson Chan, Fady R Mohareb, Colin J Sutherland, Cally Roper, Susana Campino, Taane G Clark
BACKGROUND: Although Plasmodium vivax contributes to almost half of all malaria cases outside Africa, it has been relatively neglected compared to the more deadly P. falciparum. It is known that P. vivax populations possess high genetic diversity, differing geographically potentially due to different vector species, host genetics and environmental factors. RESULTS: We analysed the high-quality genomic data for 46 P. vivax isolates spanning 10 countries across 4 continents...
2017: PloS One
https://www.readbyqxmd.com/read/28493414/investigating-niche-partitioning-of-ectomycorrhizal-fungi-in-specialized-rooting-zones-of-the-monodominant-leguminous-tree-dicymbe-corymbosa
#19
Matthew E Smith, Terry W Henkel, Gwendolyn C Williams, M Catherine Aime, Alexander K Fremier, Rytas Vilgalys
Temperate ectomycorrhizal (ECM) fungi show segregation whereby some species dominate in organic layers and others favor mineral soils. Weak layering in tropical soils is hypothesized to decrease niche space and therefore reduce the diversity of ectomycorrhizal fungi. The Neotropical ECM tree Dicymbe corymbosa forms monodominant stands and has a distinct physiognomy with vertical crown development, adventitious roots and massive root mounds, leading to multi-stemmed trees with spatially segregated rooting environments: aerial litter caches, aerial decayed wood, organic root mounds and mineral soil...
May 11, 2017: New Phytologist
https://www.readbyqxmd.com/read/28493387/current-advances-in-highly-multiplexed-antibody-based-single-cell-proteomic-measurements
#20
Lu Huang, Sean Alan Michael, Yangfan Chen, Hongkai Wu
Single cell measurements have played a critical role in revealing the complex signaling dynamics and heterogeneity present in cells but there is still much to learn. Measuring samples from bulk populations of cells often masks information and dynamics present in subsets of cells. Common single cell protein studies rely on fluorescent microscopy and flow cytometry but are limited in multiplexing ability due to spectral overlap. Recently, technology advancements in single cell proteomics have allowed highly multiplexed measurement of multiple parameters simultaneously using barcoded microfluidic enzyme-linked immunosorbent assays (ELISA) and mass cytometry techniques...
May 11, 2017: Chemistry, An Asian Journal
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