What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Friday, 2012 August 31
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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Item 1 of 1

1.	N Engl J Med. 2012 Aug 23;367(8):754-62. Case records of the Massachusetts General Hospital. Case 26-2012. A 70-year-old woman with fever and back pain. Drapkin MS, Kamath RS, Kim JY. Source Infectious Diseases Service, Newton–Wellesley Hospital, Newton, MA, USA.
	PMID: 22913686 [PubMed - indexed for MEDLINE]

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Wednesday, 2012 August 29
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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Item 1 of 1

1.	Science. 2012 Aug 17;337(6096):793-5. Climatology. Mountains of data. Service RF.
	PMID: 22903993 [PubMed - indexed for MEDLINE]

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Tuesday, 2012 August 28
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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Items 1 - 6 of 6

1.	N Engl J Med. 2012 Aug 9;367(6):e8. Images in clinical medicine. Green teeth in neonatal sepsis. Swann O, Powls A. Source Princess Royal Maternity Hospital, Glasgow, United Kingdom. livvyswann@doctors.org.uk Free Article
	PMID: 22873557 [PubMed - indexed for MEDLINE]
	Related citations

2.	Nature. 2012 Jul 25;487(7408):482-5. doi: 10.1038/nature11286. Administration of vorinostat disrupts HIV-1 latency in patients on antiretroviral therapy. Archin NM, Liberty AL, Kashuba AD, Choudhary SK, Kuruc JD, Crooks AM, Parker DC, Anderson EM, Kearney MF, Strain MC, Richman DD, Hudgens MG, Bosch RJ, Coffin JM, Eron JJ, Hazuda DJ, Margolis DM. Source The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA. Comment in HIV: Shock and kill. [Nature. 2012] HIV: Shock and kill.Deeks SG. Nature. 2012 Jul 25; 487(7408):439-40. Epub 2012 Jul 25. Abstract Despite antiretroviral therapy, proviral latency of human immunodeficiency virus type 1 (HIV-1) remains a principal obstacle to curing the infection. Inducing the expression of latent genomes within resting CD4(+) T cells is the primary strategy to clear this reservoir. Although histone deacetylase inhibitors such as suberoylanilide hydroxamic acid (also known as vorinostat, VOR) can disrupt HIV-1 latency in vitro, the utility of this approach has never been directly proven in a translational clinical study of HIV-infected patients. Here we isolated the circulating resting CD4(+) T cells of patients in whom viraemia was fully suppressed by antiretroviral therapy, and directly studied the effect of VOR on this latent reservoir. In each of eight patients, a single dose of VOR increased both biomarkers of cellular acetylation, and simultaneously induced an increase in HIV RNA expression in resting CD4(+) cells (mean increase, 4.8-fold). This demonstrates that a molecular mechanism known to enforce HIV latency can be therapeutically targeted in humans, provides proof-of-concept for histone deacetylase inhibitors as a therapeutic class, and defines a precise approach to test novel strategies to attack and eradicate latent HIV infection directly.
	PMID: 22837004 [PubMed - indexed for MEDLINE]
	Related citations

3.	Nature. 2012 Jul 25;487(7408):427-8. doi: 10.1038/487427a. Methods: Face up to false positives. Macarthur D. Source Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA. macarthur@atgu.mgh.harvard.edu
	PMID: 22836983 [PubMed - indexed for MEDLINE]
	Related citations

4.	Nature. 2012 Jul 23;487(7408):417. doi: 10.1038/487417a. Contest to sequence centenarians kicks off. Baker M.
	PMID: 22836978 [PubMed - indexed for MEDLINE]
	Related citations

5.	Nature. 2012 Jul 25;487(7408):406. doi: 10.1038/487406a. Error prone. [No authors listed]
	PMID: 22836962 [PubMed - indexed for MEDLINE]
	Related citations

6.	Nature. 2012 Jul 26;487(7408):500-4. Tumour micro-environment elicits innate resistance to RAF inhibitors through HGF secretion. Straussman R, Morikawa T, Shee K, Barzily-Rokni M, Qian ZR, Du J, Davis A, Mongare MM, Gould J, Frederick DT, Cooper ZA, Chapman PB, Solit DB, Ribas A, Lo RS, Flaherty KT, Ogino S, Wargo JA, Golub TR. Source The Eli and Edythe L. Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA. Abstract Drug resistance presents a challenge to the treatment of cancer patients. Many studies have focused on cell-autonomous mechanisms of drug resistance. By contrast, we proposed that the tumour micro-environment confers innate resistance to therapy. Here we developed a co-culture system to systematically assay the ability of 23 stromal cell types to influence the innate resistance of 45 cancer cell lines to 35 anticancer drugs. We found that stroma-mediated resistance is common, particularly to targeted agents. We characterized further the stroma-mediated resistance of BRAF-mutant melanoma to RAF inhibitors because most patients with this type of cancer show some degree of innate resistance. Proteomic analysis showed that stromal cell secretion of hepatocyte growth factor (HGF) resulted in activation of the HGF receptor MET, reactivation of the mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-OH kinase (PI(3)K)-AKT signalling pathways, and immediate resistance to RAF inhibition. Immunohistochemistry experiments confirmed stromal cell expression of HGF in patients with BRAF-mutant melanoma and showed a significant correlation between HGF expression by stromal cells and innate resistance to RAF inhibitor treatment. Dual inhibition of RAF and either HGF or MET resulted in reversal of drug resistance, suggesting RAF plus HGF or MET inhibitory combination therapy as a potential therapeutic strategy for BRAF-mutant melanoma. A similar resistance mechanism was uncovered in a subset of BRAF-mutant colorectal and glioblastoma cell lines. More generally, this study indicates that the systematic dissection of interactions between tumours and their micro-environment can uncover important mechanisms underlying drug resistance.
	PMID: 22763439 [PubMed - indexed for MEDLINE]
	Related citations

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Saturday, 2012 August 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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Item 1 of 1

1.	N Engl J Med. 2012 Aug 16;367(7):636-46. Franklin H. Epstein Lecture. Both ends of the leash--the human links to good dogs with bad genes. Ostrander EA. Source National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. eostrand@mail.nih.gov Free Article
	PMID: 22894576 [PubMed - indexed for MEDLINE]

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Friday, 2012 August 24
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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Items 1 - 3 of 3

1.	Nature. 2012 Jul 4;487(7405):43-5. doi: 10.1038/487043a. Stem cells: a sporadic super state. Surani A, Tischler J. Source Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK. a.surani@gurdon.cam.ac.uk Comment on Embryonic stem cell potency fluctuates with endogenous retrovirus activity. [Nature. 2012] Embryonic stem cell potency fluctuates with endogenous retrovirus activity.Macfarlan TS, Gifford WD, Driscoll S, Lettieri K, Rowe HM, Bonanomi D, Firth A, Singer O, Trono D, Pfaff SL. Nature. 2012 Jul 5; 487(7405):57-63.
	PMID: 22763548 [PubMed - indexed for MEDLINE]
	Related citations

2.	Nature. 2012 Jul 5;487(7405):57-63. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Macfarlan TS, Gifford WD, Driscoll S, Lettieri K, Rowe HM, Bonanomi D, Firth A, Singer O, Trono D, Pfaff SL. Source Howard Hughes Medical Institute, Gene Expression Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines, La Jolla, California 92037, USA. Comment in Stem cells: a sporadic super state. [Nature. 2012] Stem cells: a sporadic super state.Surani A, Tischler J. Nature. 2012 Jul 4; 487(7405):43-5. Epub 2012 Jul 4. Abstract Embryonic stem (ES) cells are derived from blastocyst-stage embryos and are thought to be functionally equivalent to the inner cell mass, which lacks the ability to produce all extraembryonic tissues. Here we identify a rare transient cell population within mouse ES and induced pluripotent stem (iPS) cell cultures that expresses high levels of transcripts found in two-cell (2C) embryos in which the blastomeres are totipotent. We genetically tagged these 2C-like ES cells and show that they lack the inner cell mass pluripotency proteins Oct4 (also known as Pou5f1), Sox2 and Nanog, and have acquired the ability to contribute to both embryonic and extraembryonic tissues. We show that nearly all ES cells cycle in and out of this privileged state, which is partially controlled by histone-modifying enzymes. Transcriptome sequencing and bioinformatic analyses showed that many 2C transcripts are initiated from long terminal repeats derived from endogenous retroviruses, suggesting this foreign sequence has helped to drive cell-fate regulation in placental mammals. PMCID: PMC3395470 [Available on 2013/1/5]
	PMID: 22722858 [PubMed - indexed for MEDLINE]
	Related citations

3.	Nature. 2012 Jul 5;487(7405):94-8. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Heliconius Genome Consortium. Collaborators: Dasmahapatra KK, Walters JR, Briscoe AD, Davey JW, Whibley A, Nadeau NJ, Zimin AV, Hughes DS, Ferguson LC, Martin SH, Salazar C, Lewis JJ, Adler S, Ahn SJ, Baker DA, Baxter SW, Chamberlain NL, Chauhan R, Counterman BA, Dalmay T, Gilbert LE, Gordon K, Heckel DG, Hines HM, Hoff KJ, Holland PW, Jacquin-Joly E, Jiggins FM, Jones RT, Kapan DD, Kersey P, Lamas G, Lawson D, Mapleson D, Maroja LS, Martin A, Moxon S, Palmer WJ, Papa R, Papanicolaou A, Pauchet Y, Ray DA, Rosser N, Salzberg SL, Supple MA, Surridge A, Tenger-Trolander A, Vogel H, Wilkinson PA, Wilson D, Yorke JA, Yuan F, Balmuth AL, Eland C, Gharbi K, Thomson M, Gibbs RA, Han Y, Jayaseelan JC, Kovar C, Mathew T, Muzny DM, Ongeri F, Pu LL, Qu J, Thornton RL, Worley KC, Wu YQ, Linares M, Blaxter ML, ffrench-Constant RH, Joron M, Kronforst MR, Mullen SP, Reed RD, Scherer SE, Richards S, Mallet J, McMillan W, Jiggins CD. Abstract The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation. PMCID: PMC3398145 [Available on 2013/1/5]
	PMID: 22722851 [PubMed - indexed for MEDLINE]
	Related citations

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Saturday, 2012 August 18
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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Item 1 of 1

1.	Nature. 2012 Jul 18;487(7407):282-3. doi: 10.1038/487282a. Gene data to hit milestone. Baker M.
	PMID: 22810669 [PubMed - indexed for MEDLINE]

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Friday, 2012 August 17
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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Item 1 of 1

1.	Nature. 2012 Jun 26;486(7404):449-50. doi: 10.1038/486449a. Freeze on mutant-flu research set to thaw. Butler D.
	PMID: 22739287 [PubMed - indexed for MEDLINE]

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Wednesday, 2012 August 15
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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Items 1 - 2 of 2

1.	Nature. 2012 May 2;486(7403):420-8. doi: 10.1038/nature10831. Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. Imai M, Watanabe T, Hatta M, Das SC, Ozawa M, Shinya K, Zhong G, Hanson A, Katsura H, Watanabe S, Li C, Kawakami E, Yamada S, Kiso M, Suzuki Y, Maher EA, Neumann G, Kawaoka Y. Source Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53711, USA. Comment in Virology: bird flu in mammals. [Nature. 2012] Virology: bird flu in mammals.Yen HL, Peiris JS. Nature. 2012 May 2; 486(7403):332-3. Epub 2012 May 2. Abstract Highly pathogenic avian H5N1 influenza A viruses occasionally infect humans, but currently do not transmit efficiently among humans. The viral haemagglutinin (HA) protein is a known host-range determinant as it mediates virus binding to host-specific cellular receptors. Here we assess the molecular changes in HA that would allow a virus possessing subtype H5 HA to be transmissible among mammals. We identified a reassortant H5 HA/H1N1 virus-comprising H5 HA (from an H5N1 virus) with four mutations and the remaining seven gene segments from a 2009 pandemic H1N1 virus-that was capable of droplet transmission in a ferret model. The transmissible H5 reassortant virus preferentially recognized human-type receptors, replicated efficiently in ferrets, caused lung lesions and weight loss, but was not highly pathogenic and did not cause mortality. These results indicate that H5 HA can convert to an HA that supports efficient viral transmission in mammals; however, we do not know whether the four mutations in the H5 HA identified here would render a wholly avian H5N1 virus transmissible. The genetic origin of the remaining seven viral gene segments may also critically contribute to transmissibility in mammals. Nevertheless, as H5N1 viruses continue to evolve and infect humans, receptor-binding variants of H5N1 viruses with pandemic potential, including avian-human reassortant viruses as tested here, may emerge. Our findings emphasize the need to prepare for potential pandemics caused by influenza viruses possessing H5 HA, and will help individuals conducting surveillance in regions with circulating H5N1 viruses to recognize key residues that predict the pandemic potential of isolates, which will inform the development, production and distribution of effective countermeasures. PMCID: PMC3388103 [Available on 2012/12/21]
	PMID: 22722205 [PubMed - indexed for MEDLINE]
	Related citations

2.	Nature. 2012 Apr 18;486(7403):346-52. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G , Haffari G, Bashashati A, Russell R, McKinney S; METABRIC Group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale AL, Brenton JD, Tavaré S, Caldas C, Aparicio S. Collaborators: Caldas C, Aparicio S, Curtis C, Shah SP, Caldas C, Aparicio S, Brenton JD, Ellis I, Huntsman D, Pinder S, Purushotham A, Murphy L, Caldas C, Aparicio S, Caldas C, Bardwell H, Chin SF, Curtis C, Ding Z, Gräf S, Jones L, Liu B, Lynch AG, Papatheodorou I, Sammut SJ, Wishart G, Aparicio S, Chia S, Gelmon K, Huntsman D, McKinney S, Speers C, Turashvili G, Watson P, Ellis I, Blamey R, Green A, Macmillan D, Rakha E, Purushotham A, Gillett C, Grigoriadis A, Pinder S, de Rinaldis E, Tutt A, Murphy L, Parisien M, Troup S, Caldas C, Chin SF, Chan D, Fielding C, Maia AT, McGuire S, Osborne M, Sayalero SM, Spiteri I, Hadfield J, Aparicio S, Turashvili G, Bell L, Chow K, Gale N, Huntsman D, Kovalik M, Ng Y, Prentice L, Caldas C, Tavaré S, Curtis C, Dunning MJ, Gräf S, Lynch AG, Rueda OM, Russell R, Samarajiwa S, Speed D, Markowetz F, Yuan Y, Brenton JD, Aparicio S, Shah SP, Bashashati A, Ha G, Haffari G, McKinney S. Source Department of Oncology, University of Cambridge, Hills Road, Cambridge CB2 2XZ, UK. Comment in Copy number aberrations define breast cancer subgroups. [Cancer Discov. 2012] Copy number aberrations define breast cancer subgroups.[No authors listed]Cancer Discov. 2012 Jun; 2(6):OF6. Epub 2012 Apr 26. Genomics: the breast cancer landscape. [Nature. 2012] Genomics: the breast cancer landscape.Gray J, Druker B. Nature. 2012 Jun 20; 486(7403):328-9. Epub 2012 Jun 20. Abstract The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in ~40% of genes, with the landscape dominated by cis- and trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the 'CNA-devoid' subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome.
	PMID: 22522925 [PubMed - indexed for MEDLINE]
	Related citations

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Friday, 2012 August 10
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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Item 1 of 1

1.	Nature. 2012 Jul 11;487(7406):190-5. doi: 10.1038/nature11236. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Zaranek AW, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R. Source Complete Genomics, Inc., 2071 Stierlin Court, Mountain View, California 94043, USA. bpeters@completegenomics.com Abstract Recent advances in whole-genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, long fragment read (LFR) technology, which is similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ∼100 picograms of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants were assembled into long haplotype contigs. Removal of false positive single nucleotide variants not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 megabases. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications. PMCID: PMC3397394 [Available on 2013/1/12]
	PMID: 22785314 [PubMed - indexed for MEDLINE]

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Thursday, 2012 August 09
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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Items 1 - 4 of 4

1.	Science. 2012 Jul 27;337(6093):426-7. IBI series winner. Engaging students in molecular biology via case-based learning. Bergland M, Klyczek K, Lin CC, Lundeberg M, Tosado-Acevedo R, Toro A, White D, Wolter B. Source Biology Department, University of Wisconsin-River Falls, River Falls, WI 54022, USA. mark.s.bergland@uwrf.edu Free Article
	PMID: 22837518 [PubMed - indexed for MEDLINE]
	Related citations

2.	Science. 2012 Jul 27;337(6093):424-5. IBI series winner. Aipotu: simulation from nucleotides to populations and back again. White BT. Source Biology Department, University of Massachusetts, Boston, 100 Morrissey Boulevard, Boston, MA 02125, USA. brian.white@umb.edu Free Article
	PMID: 22837517 [PubMed - indexed for MEDLINE]
	Related citations

3.	Science. 2012 Jul 27;337(6093):463-6. Epub 2012 Jun 14. Adenylate cyclases of Trypanosoma brucei inhibit the innate immune response of the host. Salmon D, Vanwalleghem G, Morias Y, Denoeud J, Krumbholz C, Lhommé F, Bachmaier S, Kador M, Gossmann J, Dias FB, De Muylder G, Uzureau P, Magez S, Moser M, De Baetselier P, Van Den Abbeele J, Beschin A, Boshart M, Pays E. Source Laboratory of Molecular Parasitology, Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, 12, rue des Professeurs Jeener et Brachet, B6041 Gosselies, Belgium. salmon@bioqmed.ufrj.br Abstract The parasite Trypanosoma brucei possesses a large family of transmembrane receptor-like adenylate cyclases. Activation of these enzymes requires the dimerization of the catalytic domain and typically occurs under stress. Using a dominant-negative strategy, we found that reducing adenylate cyclase activity by about 50% allowed trypanosome growth but reduced the parasite's ability to control the early innate immune defense of the host. Specifically, activation of trypanosome adenylate cyclase resulting from parasite phagocytosis by liver myeloid cells inhibited the synthesis of the trypanosome-controlling cytokine tumor necrosis factor-α through activation of protein kinase A in these cells. Thus, adenylate cyclase activity of lyzed trypanosomes favors early host colonization by live parasites. The role of adenylate cyclases at the host-parasite interface could explain the expansion and polymorphism of this gene family.
	PMID: 22700656 [PubMed - indexed for MEDLINE]
	Related citations

4.	Nature. 2012 Jun 6;486(7401):17. doi: 10.1038/486017a. Ancestry testing goes for pinpoint accuracy. Callaway E.
	PMID: 22678260 [PubMed - indexed for MEDLINE]
	Related citations

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

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

Sent on Saturday, 2012 August 04
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]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.

PubMed Results

Items 1 - 3 of 3

1.	Nat Genet. 2012 May 29;44(6):623-30. doi: 10.1038/ng.2303. Exome sequencing and the genetic basis of complex traits. Kiezun A, Garimella K, Do R, Stitziel NO, Neale BM, McLaren PJ, Gupta N, Sklar P, Sullivan PF, Moran JL, Hultman CM, Lichtenstein P, Magnusson P, Lehner T, Shugart YY, Price AL, de Bakker PI, Purcell SM, Sunyaev SR. Source Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
	PMID: 22641211 [PubMed - indexed for MEDLINE]
	Related citations

2.	Nat Genet. 2012 May 29;44(6):619-22. doi: 10.1038/ng.2287. The Pediatric Cancer Genome Project. Downing JR, Wilson RK, Zhang J, Mardis ER, Pui CH, Ding L, Ley TJ, Evans WE. Source St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project, Memphis, Tennessee, USA. james.downing@stjude.org
	PMID: 22641210 [PubMed - indexed for MEDLINE]
	Related citations

3.	Nat Genet. 2012 May 20;44(6):725-31. doi: 10.1038/ng.2285. A model-based approach for analysis of spatial structure in genetic data. Yang WY, Novembre J, Eskin E, Halperin E. Source Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California, USA. Abstract Characterizing genetic diversity within and between populations has broad applications in studies of human disease and evolution. We propose a new approach, spatial ancestry analysis, for the modeling of genotypes in two- or three-dimensional space. In spatial ancestry analysis (SPA), we explicitly model the spatial distribution of each SNP by assigning an allele frequency as a continuous function in geographic space. We show that the explicit modeling of the allele frequency allows individuals to be localized on the map on the basis of their genetic information alone. We apply our SPA method to a European and a worldwide population genetic variation data set and identify SNPs showing large gradients in allele frequency, and we suggest these as candidate regions under selection. These regions include SNPs in the well-characterized LCT region, as well as at loci including FOXP2, OCA2 and LRP1B.
	PMID: 22610118 [PubMed - indexed for MEDLINE]
	Related citations