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  • Humans  (9)
  • *Electric Conductivity  (1)
  • Nature Publishing Group (NPG)  (10)
  • Blackwell Publishing Ltd
  • Nature Publishing Group
  • Oxford University Press
  • 2010-2014  (10)
  • 1945-1949
  • 2012  (5)
  • 2011  (5)
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  • 2010-2014  (10)
  • 1945-1949
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  • 1
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    A SUMOylation-defective MITF germline mutation predisposes to melanoma and renal carcinoma (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-10-21
    Description: So far, no common environmental and/or phenotypic factor has been associated with melanoma and renal cell carcinoma (RCC). The known risk factors for melanoma include sun exposure, pigmentation and nevus phenotypes; risk factors associated with RCC include smoking, obesity and hypertension. A recent study of coexisting melanoma and RCC in the same patients supports a genetic predisposition underlying the association between these two cancers. The microphthalmia-associated transcription factor (MITF) has been proposed to act as a melanoma oncogene; it also stimulates the transcription of hypoxia inducible factor (HIF1A), the pathway of which is targeted by kidney cancer susceptibility genes. We therefore proposed that MITF might have a role in conferring a genetic predisposition to co-occurring melanoma and RCC. Here we identify a germline missense substitution in MITF (Mi-E318K) that occurred at a significantly higher frequency in genetically enriched patients affected with melanoma, RCC or both cancers, when compared with controls. Overall, Mi-E318K carriers had a higher than fivefold increased risk of developing melanoma, RCC or both cancers. Codon 318 is located in a small-ubiquitin-like modifier (SUMO) consensus site (PsiKXE) and Mi-E318K severely impaired SUMOylation of MITF. Mi-E318K enhanced MITF protein binding to the HIF1A promoter and increased its transcriptional activity compared to wild-type MITF. Further, we observed a global increase in Mi-E318K-occupied loci. In an RCC cell line, gene expression profiling identified a Mi-E318K signature related to cell growth, proliferation and inflammation. Lastly, the mutant protein enhanced melanocytic and renal cell clonogenicity, migration and invasion, consistent with a gain-of-function role in tumorigenesis. Our data provide insights into the link between SUMOylation, transcription and cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bertolotto, Corine -- Lesueur, Fabienne -- Giuliano, Sandy -- Strub, Thomas -- de Lichy, Mahaut -- Bille, Karine -- Dessen, Philippe -- d'Hayer, Benoit -- Mohamdi, Hamida -- Remenieras, Audrey -- Maubec, Eve -- de la Fouchardiere, Arnaud -- Molinie, Vincent -- Vabres, Pierre -- Dalle, Stephane -- Poulalhon, Nicolas -- Martin-Denavit, Tanguy -- Thomas, Luc -- Andry-Benzaquen, Pascale -- Dupin, Nicolas -- Boitier, Francoise -- Rossi, Annick -- Perrot, Jean-Luc -- Labeille, Bruno -- Robert, Caroline -- Escudier, Bernard -- Caron, Olivier -- Brugieres, Laurence -- Saule, Simon -- Gardie, Betty -- Gad, Sophie -- Richard, Stephane -- Couturier, Jerome -- Teh, Bin Tean -- Ghiorzo, Paola -- Pastorino, Lorenza -- Puig, Susana -- Badenas, Celia -- Olsson, Hakan -- Ingvar, Christian -- Rouleau, Etienne -- Lidereau, Rosette -- Bahadoran, Philippe -- Vielh, Philippe -- Corda, Eve -- Blanche, Helene -- Zelenika, Diana -- Galan, Pilar -- French Familial Melanoma Study Group -- Aubin, Francois -- Bachollet, Bertrand -- Becuwe, Celine -- Berthet, Pascaline -- Bignon, Yves Jean -- Bonadona, Valerie -- Bonafe, Jean-Louis -- Bonnet-Dupeyron, Marie-Noelle -- Cambazard, Frederic -- Chevrant-Breton, Jacqueline -- Coupier, Isabelle -- Dalac, Sophie -- Demange, Liliane -- d'Incan, Michel -- Dugast, Catherine -- Faivre, Laurence -- Vincent-Fetita, Lynda -- Gauthier-Villars, Marion -- Gilbert, Brigitte -- Grange, Florent -- Grob, Jean-Jacques -- Humbert, Philippe -- Janin, Nicolas -- Joly, Pascal -- Kerob, Delphine -- Lasset, Christine -- Leroux, Dominique -- Levang, Julien -- Limacher, Jean-Marc -- Livideanu, Cristina -- Longy, Michel -- Lortholary, Alain -- Stoppa-Lyonnet, Dominique -- Mansard, Sandrine -- Mansuy, Ludovic -- Marrou, Karine -- Mateus, Christine -- Maugard, Christine -- Meyer, Nicolas -- Nogues, Catherine -- Souteyrand, Pierre -- Venat-Bouvet, Laurence -- Zattara, Helene -- Chaudru, Valerie -- Lenoir, Gilbert M -- Lathrop, Mark -- Davidson, Irwin -- Avril, Marie-Francoise -- Demenais, Florence -- Ballotti, Robert -- Bressac-de Paillerets, Brigitte -- England -- Nature. 2011 Oct 19;480(7375):94-8. doi: 10.1038/nature10539.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] INSERM, U895 (equipe 1), Equipe labelisee Ligue Contre le Cancer, C3M, 06204 Nice, France [2] Universite of Nice Sophia-Antipolis, UFR Medecine, 06204 Nice, France [3] Centre Hospitalier Universitaire de Nice, Service de Dermatologie, 06204 Nice, France [4].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22012259" target="_blank"〉PubMed〈/a〉
    Keywords: Carcinoma, Renal Cell/*genetics ; Cell Movement/genetics ; Gene Frequency ; *Genetic Predisposition to Disease ; *Germ-Line Mutation ; Humans ; Melanoma/*genetics ; Microphthalmia-Associated Transcription Factor/*genetics ; Neoplasm Invasiveness/genetics ; Sumoylation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
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    Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-07-29
    Description: Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) are the two most common non-Hodgkin lymphomas (NHLs). Here we sequenced tumour and matched normal DNA from 13 DLBCL cases and one FL case to identify genes with mutations in B-cell NHL. We analysed RNA-seq data from these and another 113 NHLs to identify genes with candidate mutations, and then re-sequenced tumour and matched normal DNA from these cases to confirm 109 genes with multiple somatic mutations. Genes with roles in histone modification were frequent targets of somatic mutation. For example, 32% of DLBCL and 89% of FL cases had somatic mutations in MLL2, which encodes a histone methyltransferase, and 11.4% and 13.4% of DLBCL and FL cases, respectively, had mutations in MEF2B, a calcium-regulated gene that cooperates with CREBBP and EP300 in acetylating histones. Our analysis suggests a previously unappreciated disruption of chromatin biology in lymphomagenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210554/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210554/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Morin, Ryan D -- Mendez-Lago, Maria -- Mungall, Andrew J -- Goya, Rodrigo -- Mungall, Karen L -- Corbett, Richard D -- Johnson, Nathalie A -- Severson, Tesa M -- Chiu, Readman -- Field, Matthew -- Jackman, Shaun -- Krzywinski, Martin -- Scott, David W -- Trinh, Diane L -- Tamura-Wells, Jessica -- Li, Sa -- Firme, Marlo R -- Rogic, Sanja -- Griffith, Malachi -- Chan, Susanna -- Yakovenko, Oleksandr -- Meyer, Irmtraud M -- Zhao, Eric Y -- Smailus, Duane -- Moksa, Michelle -- Chittaranjan, Suganthi -- Rimsza, Lisa -- Brooks-Wilson, Angela -- Spinelli, John J -- Ben-Neriah, Susana -- Meissner, Barbara -- Woolcock, Bruce -- Boyle, Merrill -- McDonald, Helen -- Tam, Angela -- Zhao, Yongjun -- Delaney, Allen -- Zeng, Thomas -- Tse, Kane -- Butterfield, Yaron -- Birol, Inanc -- Holt, Rob -- Schein, Jacqueline -- Horsman, Douglas E -- Moore, Richard -- Jones, Steven J M -- Connors, Joseph M -- Hirst, Martin -- Gascoyne, Randy D -- Marra, Marco A -- 1U01CA114778/CA/NCI NIH HHS/ -- HHSN261200800001E/PHS HHS/ -- P50CA130805-01/CA/NCI NIH HHS/ -- TGT-53912/Canadian Institutes of Health Research/Canada -- U24 CA143866/CA/NCI NIH HHS/ -- U24 CA143866-01/CA/NCI NIH HHS/ -- U24 CA143866-02/CA/NCI NIH HHS/ -- U24 CA143866-03/CA/NCI NIH HHS/ -- England -- Nature. 2011 Jul 27;476(7360):298-303. doi: 10.1038/nature10351.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21796119" target="_blank"〉PubMed〈/a〉
    Keywords: Chromatin/genetics/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Genome, Human/genetics ; Histone Acetyltransferases/genetics/metabolism ; Histone-Lysine N-Methyltransferase/genetics/metabolism ; Histones/*metabolism ; Humans ; Loss of Heterozygosity/genetics ; Lymphoma, Follicular/enzymology/genetics ; Lymphoma, Large B-Cell, Diffuse/enzymology/genetics ; Lymphoma, Non-Hodgkin/enzymology/*genetics ; MADS Domain Proteins/genetics/metabolism ; MEF2 Transcription Factors ; Mutation/*genetics ; Myogenic Regulatory Factors/genetics/metabolism ; Neoplasm Proteins/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    De novo mutations revealed by whole-exome sequencing are strongly associated with autism (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-04-13
    Description: Multiple studies have confirmed the contribution of rare de novo copy number variations to the risk for autism spectrum disorders. But whereas de novo single nucleotide variants have been identified in affected individuals, their contribution to risk has yet to be clarified. Specifically, the frequency and distribution of these mutations have not been well characterized in matched unaffected controls, and such data are vital to the interpretation of de novo coding mutations observed in probands. Here we show, using whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with autism spectrum disorders and carry large effects. On the basis of mutation rates in unaffected individuals, we demonstrate that multiple independent de novo single nucleotide variants in the same gene among unrelated probands reliably identifies risk alleles, providing a clear path forward for gene discovery. Among a total of 279 identified de novo coding mutations, there is a single instance in probands, and none in siblings, in which two independent nonsense variants disrupt the same gene, SCN2A (sodium channel, voltage-gated, type II, alpha subunit), a result that is highly unlikely by chance.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667984/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667984/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanders, Stephan J -- Murtha, Michael T -- Gupta, Abha R -- Murdoch, John D -- Raubeson, Melanie J -- Willsey, A Jeremy -- Ercan-Sencicek, A Gulhan -- DiLullo, Nicholas M -- Parikshak, Neelroop N -- Stein, Jason L -- Walker, Michael F -- Ober, Gordon T -- Teran, Nicole A -- Song, Youeun -- El-Fishawy, Paul -- Murtha, Ryan C -- Choi, Murim -- Overton, John D -- Bjornson, Robert D -- Carriero, Nicholas J -- Meyer, Kyle A -- Bilguvar, Kaya -- Mane, Shrikant M -- Sestan, Nenad -- Lifton, Richard P -- Gunel, Murat -- Roeder, Kathryn -- Geschwind, Daniel H -- Devlin, Bernie -- State, Matthew W -- K08 MH087639/MH/NIMH NIH HHS/ -- R25 MH077823/MH/NIMH NIH HHS/ -- T32 GM008042/GM/NIGMS NIH HHS/ -- U01 MH081896/MH/NIMH NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2012 Apr 4;485(7397):237-41. doi: 10.1038/nature10945.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program on Neurogenetics, Child Study Center, Department of Psychiatry, Yale University School of Medicine, 230 South Frontage Road, New Haven, Connecticut 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22495306" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Autistic Disorder/*genetics ; Codon, Nonsense/genetics ; Exome/*genetics ; Exons/*genetics ; Genetic Heterogeneity ; Genetic Predisposition to Disease/*genetics ; Humans ; Mutation/*genetics ; NAV1.2 Voltage-Gated Sodium Channel ; Nerve Tissue Proteins/*genetics ; RNA Splice Sites/genetics ; Siblings ; Sodium Channels/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    The clonal and mutational evolution spectrum of primary triple-negative breast cancers (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-04-13
    Description: Primary triple-negative breast cancers (TNBCs), a tumour type defined by lack of oestrogen receptor, progesterone receptor and ERBB2 gene amplification, represent approximately 16% of all breast cancers. Here we show in 104 TNBC cases that at the time of diagnosis these cancers exhibit a wide and continuous spectrum of genomic evolution, with some having only a handful of coding somatic aberrations in a few pathways, whereas others contain hundreds of coding somatic mutations. High-throughput RNA sequencing (RNA-seq) revealed that only approximately 36% of mutations are expressed. Using deep re-sequencing measurements of allelic abundance for 2,414 somatic mutations, we determine for the first time-to our knowledge-in an epithelial tumour subtype, the relative abundance of clonal frequencies among cases representative of the population. We show that TNBCs vary widely in their clonal frequencies at the time of diagnosis, with the basal subtype of TNBC showing more variation than non-basal TNBC. Although p53 (also known as TP53), PIK3CA and PTEN somatic mutations seem to be clonally dominant compared to other genes, in some tumours their clonal frequencies are incompatible with founder status. Mutations in cytoskeletal, cell shape and motility proteins occurred at lower clonal frequencies, suggesting that they occurred later during tumour progression. Taken together, our results show that understanding the biology and therapeutic responses of patients with TNBC will require the determination of individual tumour clonal genotypes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863681/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863681/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shah, Sohrab P -- Roth, Andrew -- Goya, Rodrigo -- Oloumi, Arusha -- Ha, Gavin -- Zhao, Yongjun -- Turashvili, Gulisa -- Ding, Jiarui -- Tse, Kane -- Haffari, Gholamreza -- Bashashati, Ali -- Prentice, Leah M -- Khattra, Jaswinder -- Burleigh, Angela -- Yap, Damian -- Bernard, Virginie -- McPherson, Andrew -- Shumansky, Karey -- Crisan, Anamaria -- Giuliany, Ryan -- Heravi-Moussavi, Alireza -- Rosner, Jamie -- Lai, Daniel -- Birol, Inanc -- Varhol, Richard -- Tam, Angela -- Dhalla, Noreen -- Zeng, Thomas -- Ma, Kevin -- Chan, Simon K -- Griffith, Malachi -- Moradian, Annie -- Cheng, S-W Grace -- Morin, Gregg B -- Watson, Peter -- Gelmon, Karen -- Chia, Stephen -- Chin, Suet-Feung -- Curtis, Christina -- Rueda, Oscar M -- Pharoah, Paul D -- Damaraju, Sambasivarao -- Mackey, John -- Hoon, Kelly -- Harkins, Timothy -- Tadigotla, Vasisht -- Sigaroudinia, Mahvash -- Gascard, Philippe -- Tlsty, Thea -- Costello, Joseph F -- Meyer, Irmtraud M -- Eaves, Connie J -- Wasserman, Wyeth W -- Jones, Steven -- Huntsman, David -- Hirst, Martin -- Caldas, Carlos -- Marra, Marco A -- Aparicio, Samuel -- 5U01ES017154-02/ES/NIEHS NIH HHS/ -- R01 GM084875/GM/NIGMS NIH HHS/ -- R01GM084875/GM/NIGMS NIH HHS/ -- Cancer Research UK/United Kingdom -- England -- Nature. 2012 Apr 4;486(7403):395-9. doi: 10.1038/nature10933.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada. sshah@bccrc.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22495314" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Breast Neoplasms/diagnosis/*genetics/*pathology ; Clone Cells/metabolism/pathology ; DNA Copy Number Variations/genetics ; DNA Mutational Analysis ; Disease Progression ; *Evolution, Molecular ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic/genetics ; Genotype ; High-Throughput Nucleotide Sequencing ; Humans ; INDEL Mutation/genetics ; Mutation/*genetics ; Point Mutation/genetics ; Precision Medicine ; Reproducibility of Results ; Sequence Analysis, RNA
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Spatio-temporal transcriptome of the human brain (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-10-28
    Description: Brain development and function depend on the precise regulation of gene expression. However, our understanding of the complexity and dynamics of the transcriptome of the human brain is incomplete. Here we report the generation and analysis of exon-level transcriptome and associated genotyping data, representing males and females of different ethnicities, from multiple brain regions and neocortical areas of developing and adult post-mortem human brains. We found that 86 per cent of the genes analysed were expressed, and that 90 per cent of these were differentially regulated at the whole-transcript or exon level across brain regions and/or time. The majority of these spatio-temporal differences were detected before birth, with subsequent increases in the similarity among regional transcriptomes. The transcriptome is organized into distinct co-expression networks, and shows sex-biased gene expression and exon usage. We also profiled trajectories of genes associated with neurobiological categories and diseases, and identified associations between single nucleotide polymorphisms and gene expression. This study provides a comprehensive data set on the human brain transcriptome and insights into the transcriptional foundations of human neurodevelopment.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566780/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566780/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, Hyo Jung -- Kawasawa, Yuka Imamura -- Cheng, Feng -- Zhu, Ying -- Xu, Xuming -- Li, Mingfeng -- Sousa, Andre M M -- Pletikos, Mihovil -- Meyer, Kyle A -- Sedmak, Goran -- Guennel, Tobias -- Shin, Yurae -- Johnson, Matthew B -- Krsnik, Zeljka -- Mayer, Simone -- Fertuzinhos, Sofia -- Umlauf, Sheila -- Lisgo, Steven N -- Vortmeyer, Alexander -- Weinberger, Daniel R -- Mane, Shrikant -- Hyde, Thomas M -- Huttner, Anita -- Reimers, Mark -- Kleinman, Joel E -- Sestan, Nenad -- DA026119/DA/NIDA NIH HHS/ -- G0700089/Medical Research Council/United Kingdom -- G9900837/Medical Research Council/United Kingdom -- GR082557/Wellcome Trust/United Kingdom -- HD000836/HD/NICHD NIH HHS/ -- MH081896/MH/NIMH NIH HHS/ -- MH089929/MH/NIMH NIH HHS/ -- NS054273/NS/NINDS NIH HHS/ -- R01 NS054273/NS/NINDS NIH HHS/ -- R01 NS054273-07/NS/NINDS NIH HHS/ -- RC2 MH089929/MH/NIMH NIH HHS/ -- RC2 MH089929-02/MH/NIMH NIH HHS/ -- U01 MH081896/MH/NIMH NIH HHS/ -- U01 MH081896-03/MH/NIMH NIH HHS/ -- England -- Nature. 2011 Oct 26;478(7370):483-9. doi: 10.1038/nature10523.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology and Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, Connecticut 06510, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22031440" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Aged ; Aged, 80 and over ; Aging/*genetics ; Brain/embryology/*growth & development/*metabolism ; Child ; Child, Preschool ; Exons/genetics ; Female ; Fetus/metabolism ; *Gene Expression Profiling ; Gene Expression Regulation, Developmental/*genetics ; Gene Regulatory Networks/genetics ; Humans ; Infant ; Male ; Middle Aged ; Quality Control ; Quantitative Trait Loci/genetics ; Sex Characteristics ; Time Factors ; Transcriptome/*genetics ; Young Adult
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    A draft genome of Yersinia pestis from victims of the Black Death (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-10-14
    Description: Technological advances in DNA recovery and sequencing have drastically expanded the scope of genetic analyses of ancient specimens to the extent that full genomic investigations are now feasible and are quickly becoming standard. This trend has important implications for infectious disease research because genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections. Here we report a reconstructed ancient genome of Yersinia pestis at 30-fold average coverage from Black Death victims securely dated to episodes of pestilence-associated mortality in London, England, 1348-1350. Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347-1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans, and further indicates that contemporary Y. pestis epidemics have their origins in the medieval era. Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690193/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690193/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bos, Kirsten I -- Schuenemann, Verena J -- Golding, G Brian -- Burbano, Hernan A -- Waglechner, Nicholas -- Coombes, Brian K -- McPhee, Joseph B -- DeWitte, Sharon N -- Meyer, Matthias -- Schmedes, Sarah -- Wood, James -- Earn, David J D -- Herring, D Ann -- Bauer, Peter -- Poinar, Hendrik N -- Krause, Johannes -- R24 HD044943/HD/NICHD NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2011 Oct 12;478(7370):506-10. doi: 10.1038/nature10549.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L8, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21993626" target="_blank"〉PubMed〈/a〉
    Keywords: Chromosomes, Bacterial/genetics ; Contig Mapping ; Dental Pulp/microbiology ; Evolution, Molecular ; Genome, Bacterial/*genetics ; History, Medieval ; Humans ; London/epidemiology ; Molecular Sequence Data ; Phylogeny ; Plague/epidemiology/*microbiology/transmission ; Plasmids/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Virulence/genetics ; Yersinia pestis/classification/*genetics/*isolation & purification
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Finding the true value of US climate science (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-02-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Meyer, Ryan -- England -- Nature. 2012 Feb 8;482(7384):133. doi: 10.1038/482133a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉California Ocean Science Trust, Oakland, USA. ryan.meyer@calost.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22318567" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate ; Global Warming/economics/*prevention & control ; Human Genome Project ; Humans ; *Public Policy ; Research/*economics/*organization & administration ; United States
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
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    City living and urban upbringing affect neural social stress processing in humans (2011)
    Nature Publishing Group (NPG)
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    Publication Date: 2011-06-24
    Description: More than half of the world's population now lives in cities, making the creation of a healthy urban environment a major policy priority. Cities have both health risks and benefits, but mental health is negatively affected: mood and anxiety disorders are more prevalent in city dwellers and the incidence of schizophrenia is strongly increased in people born and raised in cities. Although these findings have been widely attributed to the urban social environment, the neural processes that could mediate such associations are unknown. Here we show, using functional magnetic resonance imaging in three independent experiments, that urban upbringing and city living have dissociable impacts on social evaluative stress processing in humans. Current city living was associated with increased amygdala activity, whereas urban upbringing affected the perigenual anterior cingulate cortex, a key region for regulation of amygdala activity, negative affect and stress. These findings were regionally and behaviourally specific, as no other brain structures were affected and no urbanicity effect was seen during control experiments invoking cognitive processing without stress. Our results identify distinct neural mechanisms for an established environmental risk factor, link the urban environment for the first time to social stress processing, suggest that brain regions differ in vulnerability to this risk factor across the lifespan, and indicate that experimental interrogation of epidemiological associations is a promising strategy in social neuroscience.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lederbogen, Florian -- Kirsch, Peter -- Haddad, Leila -- Streit, Fabian -- Tost, Heike -- Schuch, Philipp -- Wust, Stefan -- Pruessner, Jens C -- Rietschel, Marcella -- Deuschle, Michael -- Meyer-Lindenberg, Andreas -- England -- Nature. 2011 Jun 22;474(7352):498-501. doi: 10.1038/nature10190.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Central Institute of Mental Health, University of Heidelberg/Medical Faculty Mannheim, 68159 Mannheim, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21697947" target="_blank"〉PubMed〈/a〉
    Keywords: Amygdala/*physiology ; Anxiety Disorders/epidemiology ; *Cities/epidemiology ; Gyrus Cinguli/*physiology ; Humans ; Hydrocortisone/blood ; *Life Style ; Magnetic Resonance Imaging ; Mental Health/statistics & numerical data ; Models, Neurological ; Mood Disorders/epidemiology ; Rural Health/statistics & numerical data ; Sample Size ; Schizophrenia/epidemiology ; Stress, Psychological/blood/epidemiology/*physiopathology ; Time Factors ; Urban Health/statistics & numerical data ; Urbanization
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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    Genome-wide association study indicates two novel resistance loci for severe malaria (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-08-17
    Description: Malaria causes approximately one million fatalities per year, mostly among African children. Although highlighted by the strong protective effect of the sickle-cell trait, the full impact of human genetics on resistance to the disease remains largely unexplored. Genome-wide association (GWA) studies are designed to unravel relevant genetic variants comprehensively; however, in malaria, as in other infectious diseases, these studies have been only partly successful. Here we identify two previously unknown loci associated with severe falciparum malaria in patients and controls from Ghana, West Africa. We applied the GWA approach to the diverse clinical syndromes of severe falciparum malaria, thereby targeting human genetic variants influencing any step in the complex pathogenesis of the disease. One of the loci was identified on chromosome 1q32 within the ATP2B4 gene, which encodes the main calcium pump of erythrocytes, the host cells of the pathogenic stage of malaria parasites. The second was indicated by an intergenic single nucleotide polymorphism on chromosome 16q22.2, possibly linked to a neighbouring gene encoding the tight-junction protein MARVELD3. The protein is expressed on endothelial cells and might therefore have a role in microvascular damage caused by endothelial adherence of parasitized erythrocytes. We also confirmed previous reports on protective effects of the sickle-cell trait and blood group O. Our findings underline the potential of the GWA approach to provide candidates for the development of control measures against infectious diseases in humans.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Timmann, Christian -- Thye, Thorsten -- Vens, Maren -- Evans, Jennifer -- May, Jurgen -- Ehmen, Christa -- Sievertsen, Jurgen -- Muntau, Birgit -- Ruge, Gerd -- Loag, Wibke -- Ansong, Daniel -- Antwi, Sampson -- Asafo-Adjei, Emanuel -- Nguah, Samuel Blay -- Kwakye, Kingsley Osei -- Akoto, Alex Osei Yaw -- Sylverken, Justice -- Brendel, Michael -- Schuldt, Kathrin -- Loley, Christina -- Franke, Andre -- Meyer, Christian G -- Agbenyega, Tsiri -- Ziegler, Andreas -- Horstmann, Rolf D -- WT077383/Z/05/Z/Wellcome Trust/United Kingdom -- England -- Nature. 2012 Sep 20;489(7416):443-6. doi: 10.1038/nature11334. Epub 2012 Aug 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Medicine, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany. timmann@bnitm.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22895189" target="_blank"〉PubMed〈/a〉
    Keywords: ABO Blood-Group System ; Anemia, Sickle Cell ; Case-Control Studies ; Chromosomes, Human, Pair 1/genetics ; Chromosomes, Human, Pair 16/genetics ; Disease Resistance/*genetics ; Genetic Loci/*genetics ; *Genome-Wide Association Study ; Ghana ; Humans ; Malaria, Falciparum/*genetics/parasitology/pathology ; Membrane Proteins/genetics ; Plasma Membrane Calcium-Transporting ATPases/genetics ; Polymorphism, Single Nucleotide/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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    Filamentous bacteria transport electrons over centimetre distances (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-10-30
    Description: Oxygen consumption in marine sediments is often coupled to the oxidation of sulphide generated by degradation of organic matter in deeper, oxygen-free layers. Geochemical observations have shown that this coupling can be mediated by electric currents carried by unidentified electron transporters across centimetre-wide zones. Here we present evidence that the native conductors are long, filamentous bacteria. They abounded in sediment zones with electric currents and along their length they contained strings with distinct properties in accordance with a function as electron transporters. Living, electrical cables add a new dimension to the understanding of interactions in nature and may find use in technology development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pfeffer, Christian -- Larsen, Steffen -- Song, Jie -- Dong, Mingdong -- Besenbacher, Flemming -- Meyer, Rikke Louise -- Kjeldsen, Kasper Urup -- Schreiber, Lars -- Gorby, Yuri A -- El-Naggar, Mohamed Y -- Leung, Kar Man -- Schramm, Andreas -- Risgaard-Petersen, Nils -- Nielsen, Lars Peter -- England -- Nature. 2012 Nov 8;491(7423):218-21. doi: 10.1038/nature11586. Epub 2012 Oct 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Geomicrobiology, Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23103872" target="_blank"〉PubMed〈/a〉
    Keywords: Aquatic Organisms/cytology/metabolism/ultrastructure ; Deltaproteobacteria/cytology/*metabolism/ultrastructure ; Denmark ; *Electric Conductivity ; Electron Transport ; Geologic Sediments/microbiology ; Glass ; Microspheres ; Molecular Sequence Data ; Molecular Typing ; Oceans and Seas ; Oxygen/metabolism ; Porosity ; RNA, Ribosomal, 16S/analysis/genetics ; Sulfides/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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