The Proteomic Code: a molecular recognition code for proteins

<p>Abstract</p> <p>Background</p> <p>The Proteomic Code is a set of rules by which information in genetic material is transferred into the physico-chemical properties of amino acids. It determines how individual amino acids interact with each other during folding and in specific protein-protein interactions. The Proteomic Code is part of the redundant Genetic Code.</p> <p>Review</p> <p>The 25-year-old history of this concept is reviewed from the first independent suggestions by Biro and Mekler, through the works of Blalock, Root-Bernstein, Siemion, Miller and others, followed by the discovery of a Common Periodic Table of Codons and Nucleic Acids in 2003 and culminating in the recent conceptualization of partial complementary coding of interacting amino acids as well as the theory of the nucleic acid-assisted protein folding.</p> <p>Methods and conclusions</p> <p>A novel cloning method for the design and production of specific, high-affinity-reacting proteins (SHARP) is presented. This method is based on the concept of proteomic codes and is suitable for large-scale, industrial production of specifically interacting peptides.</p

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Ectopic calcification in diabetic vascular disease.

INTRODUCTION: Cardiovascular diseases represent over one-half of all deaths in both type 1 and type 2 diabetes mellitus. In diabetic patients, vascular calcifications are more frequently observed than in people without diabetes. In particular, elevated degrees of coronary artery and valvular calcifications are reported in populations with diabetes. AREAS COVERED: We will present and discuss findings from clinical and basic science studies that investigate the pathophysiological processes leading to exaggerated arterial/valve calcification in diabetic patients. We will also illustrate the likely effects of the current therapies on vascular calcification progression in diabetic patients. A special focus will be dedicated to the contribution of resident/circulating calcifying cells to the calcific processes observed under diabetic conditions. EXPERT OPINION: Interest in the topic of ectopic calcification in diabetic vascular disease is expanding and more knowledge is adding on its mechanisms and consequences. Importantly, new therapeutic targets are emerging, implying possible future chances to modulate vascular calcification for cardiovascular protection

Search for new resonances decaying to a WW or ZZ boson and a Higgs boson in the ℓ+ℓ−bbˉ\ell^+ \ell^- b\bar b, ℓνbbˉ\ell \nu b\bar b, and ννˉbbˉ\nu\bar{\nu} b\bar b channels with pppp collisions at s=13\sqrt s = 13 TeV with the ATLAS detector

See paper for full list of authors, 18 pages (plus author list + cover pages: 36 pages total), 13 figures, 1 table. Submitted to PLB. All figures including auxiliary figures are available at https://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/EXOT-2015-18/International audienceA search is presented for new resonances decaying to a $W$ or $Z$ boson and a Higgs boson in the $\ell^+ \ell^- b\bar b$, $\ell\nu b\bar b$, and $\nu\bar{\nu} b\bar b$ channels in $pp$ collisions at $\sqrt s = 13$ TeV with the ATLAS detector at the Large Hadron Collider using a total integrated luminosity of 3.2 fb$^{-1}$. The search is conducted by looking for a localized excess in the $WH$/$ZH$ invariant or transverse mass distribution. No significant excess is observed, and the results are interpreted in terms of constraints on a simplified model based on a phenomenological Lagrangian of heavy vector triplets