What's new for 'JKB_daily1' in PubMed

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Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Thursday, 2014 September 25
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

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PubMed Results

Items 1 - 3 of 3

1.	Nature. 2014 Sep 4;513(7516):40-1. doi: 10.1038/nature13659. Epub 2014 Aug 20. Biological techniques: Edit the genome to understand it. Urnov FD. Comment on Saturation editing of genomic regions by multiplex homology-directed repair. [Nature. 2014] Saturation editing of genomic regions by multiplex homology-directed repair.Findlay GM, Boyle EA, Hause RJ, Klein JC, Shendure J. Nature. 2014 Sep 4; 513(7516):120-3.
	PMID: 25141180 [PubMed - indexed for MEDLINE]
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2.	Nature. 2014 Sep 4;513(7516):120-3. doi: 10.1038/nature13695. Saturation editing of genomic regions by multiplex homology-directed repair. Findlay GM1, Boyle EA1, Hause RJ2, Klein JC2, Shendure J2. Author information: 11] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2]. 2Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA. Comment in Biological techniques: Edit the genome to understand it. [Nature. 2014] Biological techniques: Edit the genome to understand it.Urnov FD. Nature. 2014 Sep 4; 513(7516):40-1. Epub 2014 Aug 20. Abstract Saturation mutagenesis--coupled to an appropriate biological assay--represents a fundamental means of achieving a high-resolution understanding of regulatory and protein-coding nucleic acid sequences of interest. However, mutagenized sequences introduced in trans on episomes or via random or "safe-harbour" integration fail to capture the native context of the endogenous chromosomal locus. This shortcoming markedly limits the interpretability of the resulting measurements of mutational impact. Here, we couple CRISPR/Cas9 RNA-guided cleavage with multiplex homology-directed repair using a complex library of donor templates to demonstrate saturation editing of genomic regions. In exon 18 of BRCA1, we replace a six-base-pair (bp) genomic region with all possible hexamers, or the full exon with all possible single nucleotide variants (SNVs), and measure strong effects on transcript abundance attributable to nonsense-mediated decay and exonic splicing elements. We similarly perform saturation genome editing of a well-conserved coding region of an essential gene, DBR1, and measure relative effects on growth that correlate with functional impact. Measurement of the functional consequences of large numbers of mutations with saturation genome editing will potentially facilitate high-resolution functional dissection of both cis-regulatory elements and trans-acting factors, as well as the interpretation of variants of uncertain significance observed in clinical sequencing. PMCID: PMC4156553 [Available on 2015/3/4]
	PMID: 25141179 [PubMed - indexed for MEDLINE]
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3.	Nature. 2014 Sep 4;513(7516):59-64. doi: 10.1038/nature13568. Epub 2014 Jul 23. Alterations of the human gut microbiome in liver cirrhosis. Qin N1, Yang F2, Li A2, Prifti E3, Chen Y2, Shao L1, Guo J4, Le Chatelier E5, Yao J6, Wu L4, Zhou J4, Ni S4, Liu L4, Pons N5, Batto JM5, Kennedy SP5, Leonard P5, Yuan C4, Ding W4, Chen Y4, Hu X4, Zheng B6, Qian G4, Xu W4, Ehrlich SD7, Zheng S8, Li L6. Author information: 11] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [3]. 21] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2]. 31] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2]. 4State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China. 5Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France. 61] State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, College of Medicine, Zhejiang University, 310003 Hangzhou, China [2] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China. 71] Metagenopolis, Institut National de la Recherche Agronomique, 78350 Jouy en Josas, France [2] King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London Bridge, London SE1 9RT, UK. 81] Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, 310003 Hangzhou, China [2] Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University, 310003 Hangzhou, China. Abstract Liver cirrhosis occurs as a consequence of many chronic liver diseases that are prevalent worldwide. Here we characterize the gut microbiome in liver cirrhosis by comparing 98 patients and 83 healthy control individuals. We build a reference gene set for the cohort containing 2.69 million genes, 36.1% of which are novel. Quantitative metagenomics reveals 75,245 genes that differ in abundance between the patients and healthy individuals (false discovery rate < 0.0001) and can be grouped into 66 clusters representing cognate bacterial species; 28 are enriched in patients and 38 in control individuals. Most (54%) of the patient-enriched, taxonomically assigned species are of buccal origin, suggesting an invasion of the gut from the mouth in liver cirrhosis. Biomarkers specific to liver cirrhosis at gene and function levels are revealed by a comparison with those for type 2 diabetes and inflammatory bowel disease. On the basis of only 15 biomarkers, a highly accurate patient discrimination index is created and validated on an independent cohort. Thus microbiota-targeted biomarkers may be a powerful tool for diagnosis of different diseases.
	PMID: 25079328 [PubMed - indexed for MEDLINE]
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