Advertisement | | APPLY TODAY for the 2014 ONCOLOGY RESEARCH GRANT. Together with Illumina, we're giving two deserving researchers the power to tap into the wealth of genomic data locked within FFPE samples using an innovative technique developed by EA | Quintiles using Illumina's RNA Access method. Unleash the power of your research with RNA-seq and DNA Methylation. expressionanalysis.com/grant | | | | | | TABLE OF CONTENTS | June 2014 Volume 46, Issue 6 | | | | | Editorial Correspondence News and Views Research Highlights Articles Letters Corrigenda Erratum
| | Advertisement | | | | Analyzing exome or targeted sequencing data for causal variants? The Human Gene Mutation Database (HGMD®) provides the most comprehensive data on human inherited disease mutations. Widely used in human genetics research, diagnostics and personal genomics, HGMD enables quick access to single mutation queries and advanced search applications. HGMD is now integrated into Ingenuity® Variant Analysis for the most comprehensive resource available for understanding your sequencing data.
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| | | | | Advertisement | | Genome Informatics 2014 (21-24 September 2014) Churchill College, Cambridge, UK The 14th Genome Informatics conference will focus on large-scale genome informatics with a new emphasis on microbial and medical informatics. Limited bursaries for PhD students are available. Abstract/Bursary Deadline: 2 July. Registration Deadline: 30 July | | | | | | Advertisement | | Scientific Data: Credit where credit's due
Get credit for sharing your data! Scientific Data is now accepting Data Descriptor submissions. The Data Descriptor is designed to provide detailed descriptions of datasets: focusing on how these have been produced, by whom, and how they could be reused. Submit yours today! | | | | | | Editorial | Top | | | | Nature Plants p523 doi:10.1038/ng.3005 We welcome our new sister journal Nature Plants and the increased commitment to the plant science community that it represents. This is an opportunity for Nature Genetics to emphasize the use of genetic and genomic tools and resources in discovering new plant biology and solving major agricultural challenges.
| | Correspondence | Top | | | | Turtle ghrelin pp524 - 525 Dan Larhammar & David Lagman doi:10.1038/ng.2960
| | | | Turtle ghrelin pp525 - 526 Inge Seim, Penny L Jeffery, Adrian C Herington & Lisa K Chopin doi:10.1038/ng.2964
| | | | Turtle ghrelin p526 Juan Pascual-Anaya, Amonida Zaddissa, Bronwen Aken, Guojie Zhang & Naoki Irie doi:10.1038/ng.2988
| | News and Views | Top | | | | | | Research Highlights | Top | | | | RPGRIP1L, FTO and obesity | RGS2 rescues LRRK2 pathogenicity | iPSC models of ALS | Immune cell-specific eQTLs | Polar bear genomics | Articles | Top | | | | Large-scale genetic study in East Asians identifies six new loci associated with colorectal cancer risk pp533 - 542 Ben Zhang, Wei-Hua Jia, Koichi Matsuda, Sun-Seog Kweon, Keitaro Matsuo, Yong-Bing Xiang, Aesun Shin, Sun Ha Jee, Dong-Hyun Kim, Qiuyin Cai, Jirong Long, Jiajun Shi, Wanqing Wen, Gong Yang, Yanfeng Zhang, Chun Li, Bingshan Li, Yan Guo, Zefang Ren, Bu-Tian Ji, Zhi-Zhong Pan, Atsushi Takahashi, Min-Ho Shin, Fumihiko Matsuda, Yu-Tang Gao, Jae Hwan Oh, Soriul Kim, Yoon-Ok Ahn, Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO), Andrew T Chan, Jenny Chang-Claude, Martha L Slattery, Colorectal Transdisciplinary (CORECT) Study, Stephen B Gruber, Fredrick R Schumacher, Stephanie L Stenzel, Colon Cancer Family Registry (CCFR), Graham Casey, Hyeong-Rok Kim, Jin-Young Jeong, Ji Won Park, Hong-Lan Li, Satoyo Hosono, Sang-Hee Cho, Michiaki Kubo, Xiao-Ou Shu, Yi-Xin Zeng & Wei Zheng doi:10.1038/ng.2985 Wei Zheng and colleagues report the results of a large-scale genome-wide association study of colorectal cancer in East Asians. They identify six new susceptibility loci, including variants near TCF7L2 and TGFB1.
| | | | An atlas of genetic influences on human blood metabolites pp543 - 550 So-Youn Shin, Eric B Fauman, Ann-Kristin Petersen, Jan Krumsiek, Rita Santos, Jie Huang, Matthias Arnold, Idil Erte, Vincenzo Forgetta, Tsun-Po Yang, Klaudia Walter, Cristina Menni, Lu Chen, Louella Vasquez, Ana M Valdes, Craig L Hyde, Vicky Wang, Daniel Ziemek, Phoebe Roberts, Li Xi, Elin Grundberg, The Multiple Tissue Human Expression Resource (MuTHER) Consortium, Melanie Waldenberger, J Brent Richards, Robert P Mohney, Michael V Milburn, Sally L John, Jeff Trimmer, Fabian J Theis, John P Overington, Karsten Suhre, M Julia Brosnan, Christian Gieger, Gabi Kastenmüller, Tim D Spector & Nicole Soranzo doi:10.1038/ng.2982 Nicole Soranzo, Tim Spector, Gabi Kastenmuller and colleagues report a large-scale analysis of genetic variants influencing human blood metabolite levels. They identify genome-wide significant associations at 145 loci, providing a framework for exploring relationships between genetic variation, metabolism and complex disease.
| | | | The noncoding RNA IPW regulates the imprinted DLK1-DIO3 locus in an induced pluripotent stem cell model of Prader-Willi syndrome pp551 - 557 Yonatan Stelzer, Ido Sagi, Ofra Yanuka, Rachel Eiges & Nissim Benvenisty doi:10.1038/ng.2968 Nissim Benvenisty and colleagues use induced pluripotent stem cells (iPSCs) derived from individuals with Prader-Willi syndrome (PWS) to model PWS in vitro. By comparison to parthenogenetic human iPSCs, they find that the PWS-associated noncoding RNA IPW regulates maternally expressed genes at the DLK1-DIO3 imprinted region through its effect on H3K9me3 histone marks in that region.
See also: News and Views by Murrell | | | | Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance pp558 - 566 Alexandre Fort, Kosuke Hashimoto, Daisuke Yamada, Md Salimullah, Chaman A Keya, Alka Saxena, Alessandro Bonetti, Irina Voineagu, Nicolas Bertin, Anton Kratz, Yukihiko Noro, Chee-Hong Wong, Michiel de Hoon, Robin Andersson, Albin Sandelin, Harukazu Suzuki, Chia-Lin Wei, Haruhiko Koseki, The FANTOM Consortium, Yuki Hasegawa, Alistair R R Forrest & Piero Carninci doi:10.1038/ng.2965 Piero Carninci and colleagues report the discovery of a large class of noncoding RNAs, non-annotated stem cell transcripts (NASTs), which are implicated in the regulation of stem cell properties. The authors identify 8,873 mouse and 3,042 human NASTs and functionally validate 4 as having an important role in the maintenance of pluripotency.
| | | | Genome sequence of the cultivated cotton Gossypium arboreum OPEN pp567 - 572 Fuguang Li, Guangyi Fan, Kunbo Wang, Fengming Sun, Youlu Yuan, Guoli Song, Qin Li, Zhiying Ma, Cairui Lu, Changsong Zou, Wenbin Chen, Xinming Liang, Haihong Shang, Weiqing Liu, Chengcheng Shi, Guanghui Xiao, Caiyun Gou, Wuwei Ye, Xun Xu, Xueyan Zhang, Hengling Wei, Zhifang Li, Guiyin Zhang, Junyi Wang, Kun Liu, Russell J Kohel, Richard G Percy, John Z Yu, Yu-Xian Zhu, Jun Wang & Shuxun Yu doi:10.1038/ng.2987 Yu-Xian Zhu, Jun Wang, Shuxun Yu and colleagues report sequencing and assembly of the genome of cultivated cotton, Gossypium arboreum. Comparison with the Gossypium raimondii genome sequence provides insights into genome evolution and speciation, and identifies two shared whole-genome duplication events occurring before the speciation event around 2-13 million years ago.
| | | | Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer pp573 - 582 Kai Wang, Siu Tsan Yuen, Jiangchun Xu, Siu Po Lee, Helen H N Yan, Stephanie T Shi, Hoi Cheong Siu, Shibing Deng, Kent Man Chu, Simon Law, Kok Hoe Chan, Annie S Y Chan, Wai Yin Tsui, Siu Lun Ho, Anthony K W Chan, Jonathan L K Man, Valentina Foglizzo, Man Kin Ng, April S Chan, Yick Pang Ching, Grace H W Cheng, Tao Xie, Julio Fernandez, Vivian S W Li, Hans Clevers, Paul A Rejto, Mao Mao & Suet Yi Leung doi:10.1038/ng.2983 Suet Yi Leung, Mao Mao and colleagues report whole-genome sequencing of 100 gastric cancers and DNA copy number, gene expression and methylation profiling of these tumors. They identify new recurrently mutated genes and find mutation of RHOA in 14% of diffuse-type gastric cancers.
| | Letters | Top | | | | Recurrent gain-of-function mutations of RHOA in diffuse-type gastric carcinoma pp583 - 587 Miwako Kakiuchi, Takashi Nishizawa, Hiroki Ueda, Kengo Gotoh, Atsushi Tanaka, Akimasa Hayashi, Shogo Yamamoto, Kenji Tatsuno, Hiroto Katoh, Yoshiaki Watanabe, Takashi Ichimura, Tetsuo Ushiku, Shinichi Funahashi, Keisuke Tateishi, Ikuo Wada, Nobuyuki Shimizu, Sachiyo Nomura, Kazuhiko Koike, Yasuyuki Seto, Masashi Fukayama, Hiroyuki Aburatani & Shumpei Ishikawa doi:10.1038/ng.2984 Shumpei Ishikawa and colleagues report the identification of recurrent gain-of-function mutations in RHOA in diffuse-type gastric carcinomas.
| | | | Pan-cancer genetic analysis identifies PARK2 as a master regulator of G1/S cyclins pp588 - 594 Yongxing Gong, Travis Ian Zack, Luc G T Morris, Kan Lin, Ellen Hukkelhoven, Radhika Raheja, I-Li Tan, Sevin Turcan, Selvaraju Veeriah, Shasha Meng, Agnes Viale, Steven E Schumacher, Perry Palmedo, Rameen Beroukhim & Timothy A Chan doi:10.1038/ng.2981 Timothy Chan and colleagues show that the PARK2 tumor suppressor is a master regulator of G1 and S phase cyclins and is critical for proper cell cycle regulation. PARK2 genetic alterations are common across many human cancers as well as in hereditary Parkinson's disease.
See also: News and Views by Bartek & Hodny | | | | A recurrent neomorphic mutation in MYOD1 defines a clinically aggressive subset of embryonal rhabdomyosarcoma associated with PI3K-AKT pathway mutations pp595 - 600 Shinji Kohsaka, Neerav Shukla, Nabahet Ameur, Tatsuo Ito, Charlotte K Y Ng, Lu Wang, Diana Lim, Angela Marchetti, Agnes Viale, Mono Pirun, Nicholas D Socci, Li-Xuan Qin, Raf Sciot, Julia Bridge, Samuel Singer, Paul Meyers, Leonard H Wexler, Frederic G Barr, Snjezana Dogan, Jonathan A Fletcher, Jorge S Reis-Filho & Marc Ladanyi doi:10.1038/ng.2969 Marc Ladanyi and colleagues identify a recurrent somatic mutation in MYOD1 in a subset of rhabdomyosarcomas with poor outcome. The mutation alters the DNA binding and transactivation properties of MYOD1 and promotes a switch from differentiation to proliferation.
| | | | Dystrophin is a tumor suppressor in human cancers with myogenic programs pp601 - 606 Yuexiang Wang, Adrian Marino-Enriquez, Richard R Bennett, Meijun Zhu, Yiping Shen, Grant Eilers, Jen-Chieh Lee, Joern Henze, Benjamin S Fletcher, Zhizhan Gu, Edward A Fox, Cristina R Antonescu, Christopher D M Fletcher, Xiangqian Guo, Chandrajit P Raut, George D Demetri, Matt van de Rijn, Tamas Ordog, Louis M Kunkel & Jonathan A Fletcher doi:10.1038/ng.2974 Jonathan Fletcher and colleagues describe highly recurrent deletions of the large muscular dystrophy-associated gene DMD in gastrointestinal stromal tumors, rhabdomyosarcomas and leiomyosarcomas, all cancers with muscle differentiation. Re-expression of DMD in these tumor cells inhibits aspects of their metastatic phenotypes.
| | | | Integrated genomic characterization of adrenocortical carcinoma pp607 - 612 Guillaume Assié, Eric Letouzé, Martin Fassnacht, Anne Jouinot, Windy Luscap, Olivia Barreau, Hanin Omeiri, Stéphanie Rodriguez, Karine Perlemoine, Fernande René-Corail, Nabila Elarouci, Silviu Sbiera, Matthias Kroiss, Bruno Allolio, Jens Waldmann, Marcus Quinkler, Massimo Mannelli, Franco Mantero, Thomas Papathomas, Ronald De Krijger, Antoine Tabarin, Véronique Kerlan, Eric Baudin, Frédérique Tissier, Bertrand Dousset, Lionel Groussin, Laurence Amar, Eric Clauser, Xavier Bertagna, Bruno Ragazzon, Felix Beuschlein, Rossella Libé, Aurélien de Reyniès & Jérôme Bertherat doi:10.1038/ng.2953 Jérôme Bertherat, Aurélien de Reyniès and colleagues perform integrated genomic analyses of adrenocortical carcinomas. They discover recurrent alterations in several new driver genes, including ZNRF3, DAXX, TERT and MED12, and identify two distinct molecular subgroups with opposite clinical outcomes.
| | | | Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors pp613 - 617 Gerald Goh, Ute I Scholl, James M Healy, Murim Choi, Manju L Prasad, Carol Nelson-Williams, John W Kuntsman, Reju Korah, Anna-Carinna Suttorp, Dimo Dietrich, Matthias Haase, Holger S Willenberg, Peter Stålberg, Per Hellman, Göran Åkerström, Peyman Björklund, Tobias Carling & Richard P Lifton doi:10.1038/ng.2956 Richard Lifton and colleagues identify a recurrent activating mutation in PRKACA, which encodes the catalytic subunit of protein kinase A, in cortisol-producing adrenal tumors. They further show that the mutation results in loss of binding by the regulatory subunit PRKAR1A, leading to increased phosphorylation of downstream targets.
| | | | Triplication of a 21q22 region contributes to B cell transformation through HMGN1 overexpression and loss of histone H3 Lys27 trimethylation pp618 - 623 Andrew A Lane, Bjoern Chapuy, Charles Y Lin, Trevor Tivey, Hubo Li, Elizabeth C Townsend, Diederik van Bodegom, Tovah A Day, Shuo-Chieh Wu, Huiyun Liu, Akinori Yoda, Gabriela Alexe, Anna C Schinzel, Timothy J Sullivan, Sébastien Malinge, Jordan E Taylor, Kimberly Stegmaier, Jacob D Jaffe, Michael Bustin, Geertruy te Kronnie, Shai Izraeli, Marian H Harris, Kristen E Stevenson, Donna Neuberg, Lewis B Silverman, Stephen E Sallan, James E Bradner, William C Hahn, John D Crispino, David Pellman & David M Weinstock doi:10.1038/ng.2949 David Weinstock and colleagues identify a triplication at chromosome 21q22 that is associated with development of B cell acute lymphoblastic leukemia (B-ALL) that causes B cell self renewal in vitro. They further demonstrate that this triplication leads to overexpression of the nucleosome remodeling protein HMGN1 and loss of H3K27me3, implicating these changes in B-ALL.
| | | | Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer pp624 - 628 Lars A Forsberg, Chiara Rasi, Niklas Malmqvist, Hanna Davies, Saichand Pasupulati, Geeta Pakalapati, Johanna Sandgren, Teresita Diaz de Ståhl, Ammar Zaghlool, Vilmantas Giedraitis, Lars Lannfelt, Joannah Score, Nicholas C P Cross, Devin Absher, Eva Tiensuu Janson, Cecilia M Lindgren, Andrew P Morris, Erik Ingelsson, Lars Lind & Jan P Dumanski doi:10.1038/ng.2966 Lars Forsberg, Jan Dumanski and colleagues report that age-related loss of chromosome Y in peripheral blood is associated with increased risks of all-cause mortality, cancer mortality and non-hematological cancer mortality.
| | | | Rare and low-frequency coding variants in CXCR2 and other genes are associated with hematological traits pp629 - 634 Paul L Auer, Alexander Teumer, Ursula Schick, Andrew O'Shaughnessy, Ken Sin Lo, Nathalie Chami, Chris Carlson, Simon de Denus, Marie-Pierre Dubé, Jeff Haessler, Rebecca D Jackson, Charles Kooperberg, Louis-Philippe Lemieux Perreault, Matthias Nauck, Ulrike Peters, John D Rioux, Frank Schmidt, Valérie Turcot, Uwe Völker, Henry Völzke, Andreas Greinacher, Li Hsu, Jean-Claude Tardif, George A Diaz, Alexander P Reiner & Guillaume Lettre doi:10.1038/ng.2962 Guillaume Lettre, Alexander Reiner, George Diaz and colleagues use an exome array to identify rare and low-frequency coding variants influencing hematological traits. They find several missense variants in CXCR2 associated with reduced white blood cell counts, and, in a separate family-based study, they identify a homozygous CXCR2 frameshift mutation in two siblings with congenital neutropenia.
| | | | RAF1 mutations in childhood-onset dilated cardiomyopathy pp635 - 639 Perundurai S Dhandapany, Md Abdur Razzaque, Uthiralingam Muthusami, Sreejith Kunnoth, Jonathan J Edwards, Sonia Mulero-Navarro, Ilan Riess, Sherly Pardo, Jipo Sheng, Deepa Selvi Rani, Bindu Rani, Periyasamy Govindaraj, Elisabetta Flex, Tomohiro Yokota, Michiko Furutani, Tsutomu Nishizawa, Toshio Nakanishi, Jeffrey Robbins, Giuseppe Limongelli, Roger J Hajjar, Djamel Lebeche, Ajay Bahl, Madhu Khullar, Andiappan Rathinavel, Kirsten C Sadler, Marco Tartaglia, Rumiko Matsuoka, Kumarasamy Thangaraj & Bruce D Gelb doi:10.1038/ng.2963 Bruce Gelb and colleagues identify rare RAF1 mutations in individuals with childhood-onset dilated cardiomyopathy in three cohorts from South India, North India and Japan. Variant RAF1 proteins show altered kinase activity that causes AKT hyperactivation.
| | | | De novo mutations in HCN1 cause early infantile epileptic encephalopathy pp640 - 645 Caroline Nava, Carine Dalle, Agnès Rastetter, Pasquale Striano, Carolien G F de Kovel, Rima Nabbout, Claude Cancès, Dorothée Ville, Eva H Brilstra, Giuseppe Gobbi, Emmanuel Raffo, Delphine Bouteiller, Yannick Marie, Oriane Trouillard, Angela Robbiano, Boris Keren, Dahbia Agher, Emmanuel Roze, Suzanne Lesage, Aude Nicolas, Alexis Brice, Michel Baulac, Cornelia Vogt, Nady El Hajj, Eberhard Schneider, Arvid Suls, Sarah Weckhuysen, Padhraig Gormley, Anna-Elina Lehesjoki, Peter De Jonghe, Ingo Helbig, Stéphanie Baulac, Federico Zara, Bobby P C Koeleman, EuroEPINOMICS RES Consortium, Thomas Haaf, Eric LeGuern & Christel Depienne doi:10.1038/ng.2952 Christel Depienne, Eric LeGuern and colleagues report the identification of 5 de novo missense mutations in HCN1 in individuals with early-onset epileptic encephalopathy. Functional studies confirmed the pathogenic nature of these mutations.
| | | | Mutations in CCNO result in congenital mucociliary clearance disorder with reduced generation of multiple motile cilia pp646 - 651 Julia Wallmeier, Dalal A Al-Mutairi, Chun-Ting Chen, Niki Tomas Loges, Petra Pennekamp, Tabea Menchen, Lina Ma, Hanan E Shamseldin, Heike Olbrich, Gerard W Dougherty, Claudius Werner, Basel H Alsabah, Gabriele Köhler, Martine Jaspers, Mieke Boon, Matthias Griese, Sabina Schmitt-Grohé, Theodor Zimmermann, Cordula Koerner-Rettberg, Elisabeth Horak, Chris Kintner, Fowzan S Alkuraya & Heymut Omran doi:10.1038/ng.2961 Heymut Omran and colleagues show that biallelic mutations in CCNO cause a chronic destructive lung disease resulting from loss of multiple motile cilia from the surface of respiratory epithelial cells. Subcellular analyses suggest that CCNO deficiency leads to defective centriole amplification and migration, leading to reduced ciliogenesis.
| | | | Heterotrimeric G proteins regulate nitrogen-use efficiency in rice pp652 - 656 Hongying Sun, Qian Qian, Kun Wu, Jijing Luo, Shuansuo Wang, Chengwei Zhang, Yanfei Ma, Qian Liu, Xianzhong Huang, Qingbo Yuan, Ruixi Han, Meng Zhao, Guojun Dong, Longbiao Guo, Xudong Zhu, Zhiheng Gou, Wen Wang, Yuejin Wu, Hongxuan Lin & Xiangdong Fu doi:10.1038/ng.2958 Xiangdong Fu and colleagues show that variation in DEP1, which encodes a G protein subunit known to influence rice panicle architecture, underlies a major quantitative trait locus for nitrogen-use efficiency. These findings suggest that modulating heterotrimeric G protein activity could contribute to environmentally sustainable increases in rice grain yield.
| | Corrigenda | Top | | | | Corrigendum: The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan p657 Zhuo Wang, Juan Pascual-Anaya, Amonida Zadissa, Wenqi Li, Yoshihito Niimura, Zhiyong Huang, Chunyi Li, Simon White, Zhiqiang Xiong, Dongming Fang, Bo Wang, Yao Ming, Yan Chen, Yuan Zheng, Shigehiro Kuraku, Miguel Pignatelli, Javier Herrero, Kathryn Beal, Masafumi Nozawa, Qiye Li, Juan Wang, Hongyan Zhang, Lili Yu, Shuji Shigenobu, Junyi Wang, Jiannan Liu, Paul Flicek, Steve Searle, Jun Wang, Shigeru Kuratani, Ye Yin, Bronwen Aken, Guojie Zhang & Naoki Irie doi:10.1038/ng0614-657a
| | | | Corrigendum: Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability p657 Katrina Tatton-Brown, Sheila Seal, Elise Ruark, Jenny Harmer, Emma Ramsay, Silvana del Vecchio Duarte, Anna Zachariou, Sandra Hanks, Eleanor O'Brien, Lise Aksglaede, Diana Baralle, Tabib Dabir, Blanca Gener, David Goudie, Tessa Homfray, Ajith Kumar, Daniela T Pilz, Angelo Selicorni, I Karen Temple, Lionel Van Maldergem, Naomi Yachelevich, Childhood Overgrowth Consortium, Robert van Montfort & Nazneen Rahman doi:10.1038/ng0614-657c
| | Erratum | Top | | | | Erratum: Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice p657 Yibo Li, Chuchuan Fan, Yongzhong Xing, Peng Yun, Lijun Luo, Bao Yan, Bo Peng, Weibo Xie, Gongwei Wang, Xianghua Li, Jinghua Xiao, Caiguo Xu & Yuqing He doi:10.1038/ng0614-657b
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