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Nature Biotechnology

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https://www.readbyqxmd.com/read/27893703/generation-of-genome-scale-metabolic-reconstructions-for-773-members-of-the-human-gut-microbiota
#1
Stefanía Magnúsdóttir, Almut Heinken, Laura Kutt, Dmitry A Ravcheev, Eugen Bauer, Alberto Noronha, Kacy Greenhalgh, Christian Jäger, Joanna Baginska, Paul Wilmes, Ronan M T Fleming, Ines Thiele
Genome-scale metabolic models derived from human gut metagenomic data can be used as a framework to elucidate how microbial communities modulate human metabolism and health. We present AGORA (assembly of gut organisms through reconstruction and analysis), a resource of genome-scale metabolic reconstructions semi-automatically generated for 773 human gut bacteria. Using this resource, we identified a defined growth medium for Bacteroides caccae ATCC 34185. We also showed that interactions among modeled species depend on both the metabolic potential of each species and the nutrients available...
November 28, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27893702/failure-to-detect-dna-guided-genome-editing-using-natronobacterium-gregoryi-argonaute
#2
Seung Hwan Lee, Giandomenico Turchiano, Hirotaka Ata, Somaira Nowsheen, Marianna Romito, Zhenkun Lou, Seuk-Min Ryu, Stephen C Ekker, Toni Cathomen, Jin-Soo Kim
No abstract text is available yet for this article.
November 28, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27842061/america-s-drug-problem
#3
Brady Huggett
No abstract text is available yet for this article.
November 14, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27819664/measurement-of-bacterial-replication-rates-in-microbial-communities
#4
Christopher T Brown, Matthew R Olm, Brian C Thomas, Jillian F Banfield
Culture-independent microbiome studies have increased our understanding of the complexity and metabolic potential of microbial communities. However, to understand the contribution of individual microbiome members to community functions, it is important to determine which bacteria are actively replicating. We developed an algorithm, iRep, that uses draft-quality genome sequences and single time-point metagenome sequencing to infer microbial population replication rates. The algorithm calculates an index of replication (iRep) based on the sequencing coverage trend that results from bi-directional genome replication from a single origin of replication...
November 7, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27798564/single-cell-sequencing-of-the-small-rna-transcriptome
#5
Omid R Faridani, Ilgar Abdullayev, Michael Hagemann-Jensen, John P Schell, Fredrik Lanner, Rickard Sandberg
Little is known about the heterogeneity of small-RNA expression as small-RNA profiling has so far required large numbers of cells. Here we present a single-cell method for small-RNA sequencing and apply it to naive and primed human embryonic stem cells and cancer cells. Analysis of microRNAs and fragments of tRNAs and small nucleolar RNAs (snoRNAs) reveals the potential of microRNAs as markers for different cell types and states.
October 31, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27798563/genome-scale-deletion-screening-of-human-long-non-coding-rnas-using-a-paired-guide-rna-crispr-cas9-library
#6
Shiyou Zhu, Wei Li, Jingze Liu, Chen-Hao Chen, Qi Liao, Ping Xu, Han Xu, Tengfei Xiao, Zhongzheng Cao, Jingyu Peng, Pengfei Yuan, Myles Brown, Xiaole Shirley Liu, Wensheng Wei
CRISPR-Cas9 screens have been widely adopted to analyze coding-gene functions, but high-throughput screening of non-coding elements using this method is more challenging because indels caused by a single cut in non-coding regions are unlikely to produce a functional knockout. A high-throughput method to produce deletions of non-coding DNA is needed. We report a high-throughput genomic deletion strategy to screen for functional long non-coding RNAs (lncRNAs) that is based on a lentiviral paired-guide RNA (pgRNA) library...
October 31, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27798562/adaptive-light-sheet-microscopy-for-long-term-high-resolution-imaging-in-living-organisms
#7
Loïc A Royer, William C Lemon, Raghav K Chhetri, Yinan Wan, Michael Coleman, Eugene W Myers, Philipp J Keller
Optimal image quality in light-sheet microscopy requires a perfect overlap between the illuminating light sheet and the focal plane of the detection objective. However, mismatches between the light-sheet and detection planes are common owing to the spatiotemporally varying optical properties of living specimens. Here we present the AutoPilot framework, an automated method for spatiotemporally adaptive imaging that integrates (i) a multi-view light-sheet microscope capable of digitally translating and rotating light-sheet and detection planes in three dimensions and (ii) a computational method that continuously optimizes spatial resolution across the specimen volume in real time...
October 31, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27748755/a-proteomic-atlas-of-the-legume-medicago-truncatula-and-its-nitrogen-fixing-endosymbiont-sinorhizobium-meliloti
#8
Harald Marx, Catherine E Minogue, Dhileepkumar Jayaraman, Alicia L Richards, Nicholas W Kwiecien, Alireza F Sihapirani, Shanmugam Rajasekar, Junko Maeda, Kevin Garcia, Angel R Del Valle-Echevarria, Jeremy D Volkening, Michael S Westphall, Sushmita Roy, Michael R Sussman, Jean-Michel Ané, Joshua J Coon
Legumes are essential components of agricultural systems because they enrich the soil in nitrogen and require little environmentally deleterious fertilizers. A complex symbiotic association between legumes and nitrogen-fixing soil bacteria called rhizobia culminates in the development of root nodules, where rhizobia fix atmospheric nitrogen and transfer it to their plant host. Here we describe a quantitative proteomic atlas of the model legume Medicago truncatula and its rhizobial symbiont Sinorhizobium meliloti, which includes more than 23,000 proteins, 20,000 phosphorylation sites, and 700 lysine acetylation sites...
October 17, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27748754/differentiation-of-human-embryonic-stem-cells-to-hoxa-hemogenic-vasculature-that-resembles-the-aorta-gonad-mesonephros
#9
Elizabeth S Ng, Lisa Azzola, Freya F Bruveris, Vincenzo Calvanese, Belinda Phipson, Katerina Vlahos, Claire Hirst, Vanta J Jokubaitis, Qing C Yu, Jovana Maksimovic, Simone Liebscher, Vania Januar, Zhen Zhang, Brenda Williams, Aude Conscience, Jennifer Durnall, Steven Jackson, Magdaline Costa, David Elliott, David N Haylock, Susan K Nilsson, Richard Saffery, Katja Schenke-Layland, Alicia Oshlack, Hanna K A Mikkola, Edouard G Stanley, Andrew G Elefanty
The ability to generate hematopoietic stem cells from human pluripotent cells would enable many biomedical applications. We find that hematopoietic CD34(+) cells in spin embryoid bodies derived from human embryonic stem cells (hESCs) lack HOXA expression compared with repopulation-competent human cord blood CD34(+) cells, indicating incorrect mesoderm patterning. Using reporter hESC lines to track the endothelial (SOX17) to hematopoietic (RUNX1C) transition that occurs in development, we show that simultaneous modulation of WNT and ACTIVIN signaling yields CD34(+) hematopoietic cells with HOXA expression that more closely resembles that of cord blood...
October 17, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27669167/modeling-of-rna-seq-fragment-sequence-bias-reduces-systematic-errors-in-transcript-abundance-estimation
#10
Michael I Love, John B Hogenesch, Rafael A Irizarry
We find that current computational methods for estimating transcript abundance from RNA-seq data can lead to hundreds of false-positive results. We show that these systematic errors stem largely from a failure to model fragment GC content bias. Sample-specific biases associated with fragment sequence features lead to misidentification of transcript isoforms. We introduce alpine, a method for estimating sample-specific bias-corrected transcript abundance. By incorporating fragment sequence features, alpine greatly increases the accuracy of transcript abundance estimates, enabling a fourfold reduction in the number of false positives for reported changes in expression compared with Cufflinks...
September 26, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27669166/enhancing-the-pharmaceutical-properties-of-protein-drugs-by-ancestral-sequence-reconstruction
#11
Philip M Zakas, Harrison C Brown, Kristopher Knight, Shannon L Meeks, H Trent Spencer, Eric A Gaucher, Christopher B Doering
Optimization of a protein's pharmaceutical properties is usually carried out by rational design and/or directed evolution. Here we test an alternative approach based on ancestral sequence reconstruction. Using available genomic sequence data on coagulation factor VIII and predictive models of molecular evolution, we engineer protein variants with improved activity, stability, and biosynthesis potential and reduced inhibition by anti-drug antibodies. In principle, this approach can be applied to any protein drug based on a conserved gene sequence...
September 26, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27606440/applications-of-crispr-technologies-in-research-and-beyond
#12
Rodolphe Barrangou, Jennifer A Doudna
Programmable DNA cleavage using CRISPR-Cas9 enables efficient, site-specific genome engineering in single cells and whole organisms. In the research arena, versatile CRISPR-enabled genome editing has been used in various ways, such as controlling transcription, modifying epigenomes, conducting genome-wide screens and imaging chromosomes. CRISPR systems are already being used to alleviate genetic disorders in animals and are likely to be employed soon in the clinic to treat human diseases of the eye and blood...
September 8, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27824856/amgen-s-migraine-antibody-advances
#13
(no author information available yet)
No abstract text is available yet for this article.
November 8, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27824855/confounding-factors-in-identification-of-disease-resilient-individuals
#14
David S Rosenblatt, David Watkins, Farrah Rajabi, Harvey L Levy
No abstract text is available yet for this article.
November 8, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27824854/revealing-the-vectors-of-cellular-identity-with-single-cell-genomics
#15
Allon Wagner, Aviv Regev, Nir Yosef
Single-cell genomics has now made it possible to create a comprehensive atlas of human cells. At the same time, it has reopened definitions of a cell's identity and of the ways in which identity is regulated by the cell's molecular circuitry. Emerging computational analysis methods, especially in single-cell RNA sequencing (scRNA-seq), have already begun to reveal, in a data-driven way, the diverse simultaneous facets of a cell's identity, from discrete cell types to continuous dynamic transitions and spatial locations...
November 8, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27824853/microcantilevers-track-single-cell-mass
#16
Rashid Bashir
No abstract text is available yet for this article.
November 8, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27824852/people
#17
(no author information available yet)
No abstract text is available yet for this article.
November 8, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27824851/regulation-of-synthetic-biology-under-the-nagoya-protocol
#18
Bruce S Manheim
No abstract text is available yet for this article.
November 8, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27824850/the-discombobulation-of-de-identification
#19
Mark Phillips, Bartha M Knoppers
No abstract text is available yet for this article.
November 8, 2016: Nature Biotechnology
https://www.readbyqxmd.com/read/27824849/recent-patents-in-rna-based-therapies
#20
(no author information available yet)
No abstract text is available yet for this article.
November 8, 2016: Nature Biotechnology
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