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Nature Biotechnology

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https://www.readbyqxmd.com/read/28922347/pearl-millet-genome-sequence-provides-a-resource-to-improve-agronomic-traits-in-arid-environments
#1
Rajeev K Varshney, Chengcheng Shi, Mahendar Thudi, Cedric Mariac, Jason Wallace, Peng Qi, He Zhang, Yusheng Zhao, Xiyin Wang, Abhishek Rathore, Rakesh K Srivastava, Annapurna Chitikineni, Guangyi Fan, Prasad Bajaj, Somashekhar Punnuri, S K Gupta, Hao Wang, Yong Jiang, Marie Couderc, Mohan A V S K Katta, Dev R Paudel, K D Mungra, Wenbin Chen, Karen R Harris-Shultz, Vanika Garg, Neetin Desai, Dadakhalandar Doddamani, Ndjido Ardo Kane, Joann A Conner, Arindam Ghatak, Palak Chaturvedi, Sabarinath Subramaniam, Om Parkash Yadav, Cécile Berthouly-Salazar, Falalou Hamidou, Jianping Wang, Xinming Liang, Jérémy Clotault, Hari D Upadhyaya, Philippe Cubry, Bénédicte Rhoné, Mame Codou Gueye, Ramanjulu Sunkar, Christian Dupuy, Francesca Sparvoli, Shifeng Cheng, R S Mahala, Bharat Singh, Rattan S Yadav, Eric Lyons, Swapan K Datta, C Tom Hash, Katrien M Devos, Edward Buckler, Jeffrey L Bennetzen, Andrew H Paterson, Peggy Ozias-Akins, Stefania Grando, Jun Wang, Trilochan Mohapatra, Wolfram Weckwerth, Jochen C Reif, Xin Liu, Yves Vigouroux, Xun Xu
Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication...
September 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28922346/grid-seq-reveals-the-global-rna-chromatin-interactome
#2
Xiao Li, Bing Zhou, Liang Chen, Lan-Tao Gou, Hairi Li, Xiang-Dong Fu
Higher eukaryotic genomes are bound by a large number of coding and non-coding RNAs, but approaches to comprehensively map the identity and binding sites of these RNAs are lacking. Here we report a method to capture in situ global RNA interactions with DNA by deep sequencing (GRID-seq), which enables the comprehensive identification of the entire repertoire of chromatin-interacting RNAs and their respective binding sites. In human, mouse, and Drosophila cells, we detected a large set of tissue-specific coding and non-coding RNAs that are bound to active promoters and enhancers, especially super-enhancers...
September 18, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28892078/detection-of-dysregulated-protein-association-networks-by-high-throughput-proteomics-predicts-cancer-vulnerabilities
#3
John D Lapek, Patricia Greninger, Robert Morris, Arnaud Amzallag, Iulian Pruteanu-Malinici, Cyril H Benes, Wilhelm Haas
The formation of protein complexes and the co-regulation of the cellular concentrations of proteins are essential mechanisms for cellular signaling and for maintaining homeostasis. Here we use isobaric-labeling multiplexed proteomics to analyze protein co-regulation and show that this allows the identification of protein-protein associations with high accuracy. We apply this 'interactome mapping by high-throughput quantitative proteome analysis' (IMAHP) method to a panel of 41 breast cancer cell lines and show that deviations of the observed protein co-regulations in specific cell lines from the consensus network affects cellular fitness...
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28892077/mapping-the-secrets-of-the-antibody-pool
#4
Jonathan R McDaniel, Gregory C Ippolito, George Georgiou
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28892076/single-cell-deep-phenotyping-of-igg-secreting-cells-for-high-resolution-immune-monitoring
#5
Klaus Eyer, Raphaël C L Doineau, Carlos E Castrillon, Luis Briseño-Roa, Vera Menrath, Guillaume Mottet, Patrick England, Alexei Godina, Elodie Brient-Litzler, Clément Nizak, Allan Jensen, Andrew D Griffiths, Jérôme Bibette, Pierre Bruhns, Jean Baudry
Studies of the dynamics of the antibody-mediated immune response have been hampered by the absence of quantitative, high-throughput systems to analyze individual antibody-secreting cells. Here we describe a simple microfluidic system, DropMap, in which single cells are compartmentalized in tens of thousands of 40-pL droplets and analyzed in two-dimensional droplet arrays using a fluorescence relocation-based immunoassay. Using DropMap, we characterized antibody-secreting cells in mice immunized with tetanus toxoid (TT) over a 7-week protocol, simultaneously analyzing the secretion rate and affinity of IgG from over 0...
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28892075/analysis-of-somatic-microsatellite-indels-identifies-driver-events-in-human-tumors
#6
Yosef E Maruvka, Kent W Mouw, Rosa Karlic, Prasanna Parasuraman, Atanas Kamburov, Paz Polak, Nicholas J Haradhvala, Julian M Hess, Esther Rheinbay, Yehuda Brody, Amnon Koren, Lior Z Braunstein, Alan D'Andrea, Michael S Lawrence, Adam Bass, Andre Bernards, Franziska Michor, Gad Getz
Microsatellites (MSs) are tracts of variable-length repeats of short DNA motifs that exhibit high rates of mutation in the form of insertions or deletions (indels) of the repeated motif. Despite their prevalence, the contribution of somatic MS indels to cancer has been largely unexplored, owing to difficulties in detecting them in short-read sequencing data. Here we present two tools: MSMuTect, for accurate detection of somatic MS indels, and MSMutSig, for identification of genes containing MS indels at a higher frequency than expected by chance...
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28892074/replacing-reprogramming-factors-with-antibodies-selected-from-combinatorial-antibody-libraries
#7
Joel W Blanchard, Jia Xie, Nadja El-Mecharrafie, Simon Gross, Sohyon Lee, Richard A Lerner, Kristin K Baldwin
The reprogramming of differentiated cells into induced pluripotent stem cells (iPSCs) is usually achieved by exogenous induction of transcription by factors acting in the nucleus. In contrast, during development, signaling pathways initiated at the membrane induce differentiation. The central idea of this study is to identify antibodies that can catalyze cellular de-differentiation and nuclear reprogramming by acting at the cell surface. We screen a lentiviral library encoding ∼100 million secreted and membrane-bound single-chain antibodies and identify antibodies that can replace either Sox2 and Myc (c-Myc) or Oct4 during reprogramming of mouse embryonic fibroblasts into iPSCs...
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28854175/multiplexed-quantification-of-proteins-and-transcripts-in-single-cells
#8
Vanessa M Peterson, Kelvin Xi Zhang, Namit Kumar, Jerelyn Wong, Lixia Li, Douglas C Wilson, Renee Moore, Terrill K McClanahan, Svetlana Sadekova, Joel A Klappenbach
We present a tool to measure gene and protein expression levels in single cells with DNA-labeled antibodies and droplet microfluidics. Using the RNA expression and protein sequencing assay (REAP-seq), we quantified proteins with 82 barcoded antibodies and >20,000 genes in a single workflow. We used REAP-seq to assess the costimulatory effects of a CD27 agonist on human CD8(+) lymphocytes and to identify and characterize an unknown cell type.
August 30, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898207/shotgun-metagenomics-from-sampling-to-analysis
#9
Christopher Quince, Alan W Walker, Jared T Simpson, Nicholas J Loman, Nicola Segata
Diverse microbial communities of bacteria, archaea, viruses and single-celled eukaryotes have crucial roles in the environment and in human health. However, microbes are frequently difficult to culture in the laboratory, which can confound cataloging of members and understanding of how communities function. High-throughput sequencing technologies and a suite of computational pipelines have been combined into shotgun metagenomics methods that have transformed microbiology. Still, computational approaches to overcome the challenges that affect both assembly-based and mapping-based metagenomic profiling, particularly of high-complexity samples or environments containing organisms with limited similarity to sequenced genomes, are needed...
September 12, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898230/massachusetts-injects-more-cash-into-jobs
#10
(no author information available yet)
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898229/what-faculty-hiring-committees-want
#11
Charles B Wright, Nathan L Vanderford
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898228/vertex-cf-data-wow-wall-street
#12
(no author information available yet)
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898227/challenges-in-the-gene-therapy-commercial-ecosystem
#13
Rahul Kapoor, Thomas Klueter, James M Wilson
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898226/after-myriad-what-makes-a-gene-patent-claim-markedly-different-from-nature
#14
Mateo Aboy, Johnathon Liddicoat, Kathleen Liddell, Matthew Jordan, Cristina Crespo
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898225/adenosine-checkpoint-agent-blazes-a-trail-joins-immunotherapy-roster
#15
Ken Garber
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898224/buying-time-for-transplants
#16
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898223/recent-patents-related-to-clinical-applications-of-sequencing
#17
(no author information available yet)
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898222/around-the-world-in-a-month
#18
(no author information available yet)
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898221/go-ahead-for-first-anti-il-23-mab-to-treat-psoriasis
#19
(no author information available yet)
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28898220/podcast-first-rounders-greg-winter
#20
(no author information available yet)
No abstract text is available yet for this article.
September 11, 2017: Nature Biotechnology
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