ALBERT

Description: Motivation: It has been recently suggested that atomic burials, as expressed by molecular central distances, contain sufficient information to determine the tertiary structure of small globular proteins. A possible approach to structural determination from sequence could therefore involve a sequence-to-burial intermediate prediction step whose accuracy, however, is theoretically limited by the mutual information between these two variables. We use a non-redundant set of globular protein structures to estimate the mutual information between local amino acid sequence and atomic burials. Discretizing central distances of or atoms in equiprobable burial levels, we estimate relevant mutual information measures that are compared with actual predictions obtained from a Naive Bayesian Classifier (NBC) and a Hidden Markov Model (HMM). Results: Mutual information density for 20 amino acids and two or three burial levels were estimated to be roughly 15% of the unconditional burial entropy density. Lower estimates for the mutual information between local amino acid sequence and burial of a single residue indicated an increase in mutual information with the number of burial levels up to at least five or six levels. Prediction schemes were found to efficiently extract the available burial information from local sequence. Lower estimates for the mutual information involving single burials are consistently approached by predictions from the NBC and actually surpassed by predictions from the HMM. Near-optimal prediction for the HMM is indicated by the agreement between its density of prediction information and the corresponding density of mutual information between input and output representations. Availability: The dataset of protein structures and the prediction implementations are available at http://www.btc.unb.br/ (in ‘Software’). Contact: aaraujo@unb.br Supplementary information: Supplementary data are available at Bioinformatics online.

Description: E-cadherin (Ecad) is a well-known invasion suppressor and its loss of expression is common in invasive carcinomas. Germline Ecad mutations are the only known genetic cause of hereditary diffuse gastric cancer (HDGC), demonstrating the causative role of Ecad impairment in gastric cancer. HDGC-associated Ecad missense mutations can lead to folding defects and premature proteasome-dependent endoplasmic reticulum-associated degradation (ERAD), but the molecular determinants for this fate were unidentified. Using a Drosophila-based genetic screen, we found that Drosophila DnaJ-1 interacts with wild type (WT) and mutant human Ecad in vivo . DnaJ (Hsp40) homolog, subfamily B, member 4 (DNAJB4), the human homolog of DnaJ-1, influences Ecad localization and stability even in the absence of Ecad endogenous promoter, suggesting a post-transcriptional level of regulation. Increased expression of DNAJB4 leads to stabilization of WT Ecad in the plasma membrane, while it induces premature degradation of unfolded HDGC mutants in the proteasome. The interaction between DNAJB4 and Ecad is direct, and is increased in the context of the unfolded mutant E757K, especially when proteasome degradation is inhibited, suggesting that DNAJB4 is a molecular mediator of ERAD. Post-translational regulation of native Ecad by DNAJB4 molecular chaperone is sufficient to influence cell adhesion in vitro . Using a chick embryo chorioallantoic membrane assay with gastric cancer derived cells, we demonstrate that DNAJB4 stimulates the anti-invasive function of WT Ecad in vivo . Additionally, the expression of DNAJB4 and Ecad is concomitantly decreased in human gastric carcinomas. Altogether, we demonstrate that DNAJB4 is a sensor of Ecad structural features that might contribute to gastric cancer progression.

Description: Segerberg presented a general completeness proof for propositional logics. For this purpose, a deductive system was defined in a way that its rules were rules for an arbitrary k -place Boolean operator in a given propositional logic. Each of those rules corresponds to a row on the operator's truth-table. This article extends Segerberg's idea to finite-valued propositional logic. We maintain the idea of defining a deductive system whose rules correspond to rows of truth-tables, but instead of having n types of rules (one for each truth-value), we use a bivalent representation that makes use of the technique of separating formulas as defined by Carlos Caleiro and João Marcos.

Description: Sediments cored along the southwestern Iberian margin during Integrated Ocean Drilling Program Expedition 339 provide constraints on Mediterranean Outflow Water (MOW) circulation patterns from the Pliocene epoch to the present day. After the Strait of Gibraltar opened (5.33 million years ago), a limited volume of MOW entered the Atlantic. Depositional hiatuses indicate erosion by bottom currents related to higher volumes of MOW circulating into the North Atlantic, beginning in the late Pliocene. The hiatuses coincide with regional tectonic events and changes in global thermohaline circulation (THC). This suggests that MOW influenced Atlantic Meridional Overturning Circulation (AMOC), THC, and climatic shifts by contributing a component of warm, saline water to northern latitudes while in turn being influenced by plate tectonics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hernandez-Molina, F Javier -- Stow, Dorrik A V -- Alvarez-Zarikian, Carlos A -- Acton, Gary -- Bahr, Andre -- Balestra, Barbara -- Ducassou, Emmanuelle -- Flood, Roger -- Flores, Jose-Abel -- Furota, Satoshi -- Grunert, Patrick -- Hodell, David -- Jimenez-Espejo, Francisco -- Kim, Jin Kyoung -- Krissek, Lawrence -- Kuroda, Junichiro -- Li, Baohua -- Llave, Estefania -- Lofi, Johanna -- Lourens, Lucas -- Miller, Madeline -- Nanayama, Futoshi -- Nishida, Naohisa -- Richter, Carl -- Roque, Cristina -- Pereira, Helder -- Sanchez Goni, Maria Fernanda -- Sierro, Francisco J -- Singh, Arun Deo -- Sloss, Craig -- Takashimizu, Yasuhiro -- Tzanova, Alexandrina -- Voelker, Antje -- Williams, Trevor -- Xuan, Chuang -- New York, N.Y. -- Science. 2014 Jun 13;344(6189):1244-50. doi: 10.1126/science.1251306.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK. javier.hernandez-molina@rhul.ac.uk. ; Institute of Petroleum Engineering, Heriot-Watt University, Edinburgh EH14 4AS, Scotland, UK. ; International Ocean Discovery Program, Department of Oceanography, Texas A&M University, College Station, TX 77845, USA. ; Department of Geography and Geology, Sam Houston State University, Huntsville, TX 77341, USA. ; Institute of Geosciences, University of Frankfurt, 60438 Frankfurt, Germany. ; Institute of Marine Sciences, University of California, Santa Cruz, CA 95064, USA. ; EPOC, Universite de Bordeaux, 33615 Pessac Cedex, France. ; School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA. ; Departamento de Geologia, Universidad de Salamanca, 3008 Salamanca, Spain. ; Department of Natural History Sciences, Hokkaido University, N10W8, Kita-ku, Sapporo 060-0810, Japan. ; Institute for Earth Sciences, University of Graz, A-8010 Graz, Austria. ; Godwin Laboratory for Palaeoclimate Research, University of Cambridge, Cambridge CB2 3EQ, UK. ; Department of Biogeochemistry, JAMSTEC, 237-0061 Yokosuka, Japan. ; Korea Institute of Ocean Science & Technology, Ansan 426-744, Korea. ; School of Earth Sciences, Ohio State University, Columbus, OH 43210, USA. ; Institute for Frontier Research on Earth Evolution (IFREE), JAMSTEC, 2-15 Natsushima-Cho, Yokosuka-city, Kanagawa 237-0061, Japan. ; Department of Micropalaeontology, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, P.R. China. ; Instituto Geologico y Minero de Espana, Rios Rosas 23, 28003 Madrid, Spain. ; Geosciences Montpellier, Universite Montpellier II, 34090 Montpellier, France, and Department of Geology, University of Leicester, Leicester LE1 7RH, UK. ; Institute of Earth Sciences, Utrecht University, 3584 CD Utrecht, Netherlands. ; Department of Mechanical Engineering, California Institute of Technology, Pasadena, CA 91125, USA. ; Institute of Geology and Geoinformation, Geological Survey of Japan (AIST), Ibaraki 305-8567, Japan. ; School of Geosciences, University of Louisiana, Lafayette, LA 70504, USA. ; Divisao de Geologia e Georecursos Marinhos, IPMA, 1749-077 Lisboa, Portugal. ; Grupo de Biologia e Geologia, Escola Secundaria de Loule, 8100-740 Loule, Portugal. ; Ecole Pratique des Hautes Etudes, EPOC, Universite de Bordeaux, 33615 Pessac, France. ; Department of Geology, Banaras Hindu University, Varanasi 221005, India. ; School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland 4001, Australia. ; Department of Geology, Faculty of Education, Niigata University, Niigata 950-2181, Japan. ; Department of Geological Sciences, Brown University, Providence, RI 02912, USA. ; Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, USA. ; Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Waterfront Campus, Southampton SO14 3ZH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24926012" target="_blank"〉PubMed〈/a〉

Description: Pham, C. K., Canha, A., Diogo, H., Pereira, J. G., Prieto, R., and Morato, T. 2013. Total marine fishery catch for the Azores (1950–2010). – ICES Journal of Marine Science, 70: 564–577. Official fishery statistics often fail to report what has been truly extracted from the marine environment. Therefore, in this study, we estimated illegal, unreported, and unregulated (IUU) catch in the context of a small-scale fishery (the Azores) and provide an improved compilation of official catches, including whaling. Reconstructed removals during 1950–2010 total 1.10 million t (95% CI, 1.06–1.16 million t), a factor of 1.17 higher than the amount reported in Azorean official statistics. Unreported catches were attributed to foreign fishing activities (27%), recreational fishing (25%), discards from the demersal fishing fleet (21%), baitfish for the pole-and-line tuna fishery (11%), discards from pelagic longlining (7%), local pelagic fleet landing outside the Azores (3%), coastal invertebrate harvesting (6%), and big-game fishing (0.1%). The overall low level of unreported catches compared to other locations might reflect the small-scale nature of the fisheries, the geographic isolation of the islands, and the small size of its community.

Description: Sediments cored along the southwestern Iberian margin during Integrated Ocean Drilling Program Expedition 339 provide constraints on Mediterranean Outflow Water (MOW) circulation patterns from the Pliocene epoch to the present day. After the Strait of Gibraltar opened (5.33 million years ago), a limited volume of MOW entered the Atlantic. Depositional hiatuses indicate erosion by bottom currents related to higher volumes of MOW circulating into the North Atlantic, beginning in the late Pliocene. The hiatuses coincide with regional tectonic events and changes in global thermohaline circulation (THC). This suggests that MOW influenced Atlantic Meridional Overturning Circulation (AMOC), THC, and climatic shifts by contributing a component of warm, saline water to northern latitudes while in turn being influenced by plate tectonics.