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News 578 Publications 12 Members

Comparative genomics reveals insights into avian genome evolution and adaptation.

Zhang, Guojie Li, Cai Li, Qiye Li, Bo Larkin, Denis M Lee, Chul Storz, Jay F Antunes, Agostinho Greenwold, Matthew J Meredith, Robert W ...

Published in Science (New York, N.Y.)

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific...

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Jarvis, Erich D Mirarab, Siavash Aberer, Andre J Li, Bo Houde, Peter Li, Cai Ho, Simon Y W Faircloth, Brant C Nabholz, Benoit Howard, Jason T ...

Published in Science (New York, N.Y.)

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergen...

The birds of Genome10K

OBrien, Stephen J Haussler, David Ryder, Oliver

Published in GigaScience

Everyone loves the birds of the world. From their haunting songs and majesty of flight to dazzling plumage and mating rituals, bird watchers – both amateurs and professionals - have marveled for centuries at their considerable adaptations. Now, we are offered a special treat with the publication of a series of papers in dedicated issues of Science,...

Visual circuit development requires patterned activity mediated by retinal acetylcholine receptors.

Burbridge, Timothy J Xu, Hong-Ping Ackman, James B Ge, Xinxin Zhang, Yueyi Ye, Mei-Jun Zhou, Z Jimmy Xu, Jian Contractor, Anis Crair, Michael C ...

Published in Neuron

The elaboration of nascent synaptic connections into highly ordered neural circuits is an integral feature of the developing vertebrate nervous system. In sensory systems, patterned spontaneous activity before the onset of sensation is thought to influence this process, but this conclusion remains controversial, largely due to the inherent difficul...

Neurofunctional dopaminergic impairment in elderly after lifetime exposure to manganese.

Lucchini, Roberto G Guazzetti, Stefano Zoni, Silvia Benedetti, Chiara Fedrighi, Chiara Peli, Marco Donna, Filippo Bontempi, Elza Borgese, Laura Micheletti, Serena ...

Published in Neurotoxicology

Lifelong exposure to Mn was significantly associated with changes in odor discrimination, motor coordination, cognitive abilities and serum PRL levels. These effects are consistent with the hypothesis of a specific mechanism of toxicity of Mn on the dopaminergic system. Lead co-exposure, even at very low levels, can further enhance Mn toxicity.

Copper–zinc cross-modulation in prion protein binding

Stellato, Francesco Minicozzi, Velia Millhauser, Glenn L. Pascucci, Marco Proux, Olivier Rossi, Giancarlo C. Spevacek, Ann Morante, Silvia

Published in European Biophysics Journal

In this paper we report a systematic XAS study of a set of samples in which Cu(II) was progressively added to complexes in which Zn(II) was bound to the tetra-octarepeat portion of the prion protein. This work extends previous EPR and XAS analysis in which, in contrast, the effect of adding Zn(II) to Cu(II)–tetra-octarepeat complexes was investigat...

Determinants of manganese levels in house dust samples from the CHAMACOS cohort.

Gunier, R B Jerrett, M Smith, D R Jursa, T Yousefi, P Camacho, J Hubbard, A Eskenazi, B Bradman, A

Published in The Science of the total environment

Manganese (Mn) is an essential nutrient, but at high exposure levels Mn is a neurotoxicant. The fungicides maneb and mancozeb are approximately 21% Mn by weight and more than 150,000 kg are applied each year to crops in the Salinas Valley, California. It is not clear, however, whether agricultural use of these fungicides increases Mn levels in home...

Tumor xenograft uptake of a pyrrole-imidazole (Py-Im) polyamide varies as a function of cell line grafted.

Raskatov, Jevgenij A Szablowski, Jerzy O Dervan, Peter B

Published in Journal of medicinal chemistry

Subcutaneous xenografts represent a popular approach to evaluate efficacy of prospective molecular therapeutics in vivo. In the present study, the C-14 labeled radioactive pyrrole-imidazole (Py-Im) polyamide 1, targeted to the 5'-WGWWCW-3' DNA sequence, was evaluated with regard to its uptake properties in subcutaneous xenografts, derived from the ...

Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin.

Hoadley, Katherine A Yau, Christina Wolf, Denise M Cherniack, Andrew D Tamborero, David Ng, Sam Leiserson, Max D M Niu, Beifang McLellan, Michael D Uzunangelov, Vladislav ...

Published in Cell

Recent genomic analyses of pathologically defined tumor types identify "within-a-tissue" disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a u...

Comprehensive molecular profiling of lung adenocarcinoma.

Published in Nature

Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen gene...

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