Simultaneous alignment and folding of protein sequences

Accurate comparative analysis tools for low-homology proteins remains a difficult challenge in computational biology, especially sequence alignment and consensus folding problems. We presentpartiFold-Align, the first algorithm for simultaneous alignment and consensus folding of unaligned protein sequences; the algorithm’s complexity is polynomial in time and space. Algorithmically,partiFold-Align exploits sparsity in the set of super-secondary structure pairings and alignment candidates to achieve an effectively cubic running time for simultaneous pairwise alignment and folding. We demonstrate the efficacy of these techniques on transmembrane β-barrel proteins, an important yet difficult class of proteins with few known three-dimensional structures. Testing against structurally derived sequence alignments,partiFold-Align significantly outperforms state-of-the-art pairwise sequence alignment tools in the most difficult low sequence homology case and improves secondary structure prediction where current approaches fail. Importantly, partiFold-Align requires no prior training. These general techniques are widely applicable to many more protein families. partiFold-Align is available at http://partiFold.csail.mit.edu

PASTA: Ultra-Large Multiple Sequence Alignment

In this paper, we introduce a new and highly scalable algorithm, PASTA, for large-scale multiple sequence alignment estimation. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy of the leading alignment methods on large datasets, and is able to analyze much larger datasets than the current methods. We also show that trees estimated on PASTA alignments are highly accurate – slightly better than SATe ́ trees, but with substantial improvements rela-tive to other methods. Finally, PASTA is very fast, highly parallelizable, and requires relatively little memory

Alignment-Free Phylogenetic Reconstruction

14th Annual International Conference, RECOMB 2010, Lisbon, Portugal, April 25-28, 2010. ProceedingsWe introduce the first polynomial-time phylogenetic reconstruction algorithm under a model of sequence evolution allowing insertions and deletions (or indels). Given appropriate assumptions, our algorithm requires sequence lengths growing polynomially in the number of leaf taxa. Our techniques are distance-based and largely bypass the problem of multiple alignment

Disentangling the response of fishes to recreational fishing over 30 years within a fringing coral reef reserve network

Few studies assess the effects of recreational fishing in isolation from commercial fishing. We used meta-analysis to synthesise 4444 samples from 30 years (1987–2017) of fish surveys inside and outside a large network of highly protected reserves in the Ningaloo Marine Park, Western Australia, where the major fishing activity is recreational. Data were collected by different agencies, using varied survey designs and sampling methods. We contrasted the relative abundance and biomass of target and non-target fish groups between fished and reserve locations. We considered the influence of, and possible interactions between, seven additional variables: age and size of reserve, one of two reserve network configurations, reef habitat type, recreational fishing activity, shore-based fishing regulations and survey method. Taxa responded differently: the abundance and biomass inside reserves relative to outside was higher for targeted lethrinids, while other targeted (and non-targeted) fish groups were indistinguishable. Reef habitat was important for explaining lethrinid response to protection, and this factor interacted with reserve size, such that larger reserves were demonstrably more effective in the back reef and lagoon habitats. There was little evidence of changes in relative abundance and biomass of fishes with reserve age, or after rezoning and expansion of the reserve network. Our study demonstrates the complexities in quantifying fishing effects, highlighting some of the key factors and interactions that likely underlie the varied results in reserve assessments that should be considered in future reserve design and assessment

Saethre-Chotzen syndrome : cranofacial anomalies caused by genetic changes in the TWIST gene

In this thesis, one of the most frequently occurring and most variable craniosynostosis syndromes was investigated; Saethre-Chotzen syndrome. Craniosynostosis is the premature obliteration of cranial sutures in the developing embryo. It can also occur in the first few months of life. Saethre-Chotzen syndrome is, besides craniosynostosis, characterized by specific facial and limb abnormalities, of which the most frequently reported are ptosis, prominent crus helicis, cutaneous syndactyly of digit 2 and 3 on both hands and feet, and broad halluces. Saethre-Chotzen syndrome has been linked to the TWIST gene on chromosome 7p21.1. Mutations in and variably sized deletions of this gene can be found in patients with clinical features of Saethre-Chotzen syndrome. The latter, TWIST deletions, often also include part of the surrounding chromosome 7p and are reported to be associated with mental retardation. In Saethre-Chotzen patients, in whom neither a mutation nor a deletion of TWIST had been found, the FGFR3 P250R mutation was in some cases detected. This mutation has specifically been linked to Muenke syndrome that is characterized by unior bicoronal synostosis and slight facial dysmorphology. However, a Saethre-Chotzen like phenotype can also result from this mutation. Because of the possible overlap of Saethre-Chotzen with Muenke syndrome, these syndromes were studied in order to provide clinical criteria that discriminate between the two (chapter 4). Many phenotypic features occur in both syndromes. In addition, although unicoronal synostosis occurs slightly more frequently in Muenke syndrome, unicoronal and bicoronal synostosis are seen in both syndromes. The discrimination between Saethre-Chotzen and Muenke is often not made easily and the associated genes, TWIST and FGFR3, respectively, are simultaneously tested for pathogenic m

Aguas del Iténez o Guaporé

Bolivia y Brasil comparten una de las cuencas más atractivas y preservadas de la te-giuri amazônica: la cuenca del rio llénez o Guaporé, que escurre tanto sobre el lecho rocoso del Escudo Precámbrico Brasilefto como sobre las Hanuras del Beni. Estas influencias hacen que la cuenca del iténez tenga una elevada heterogeneidad de habitats, una fauna acuálica peculiar y un alto valor de conservation. Este patrimo­nio binacional posée un potencial importante para la conservación de la diversidad regional y cl dcsar rollo sostcniblc participativo de las comunidades locales. El libro contiene un resumen del conotimìento de la cuenca y sus recursos, generado en los últimos 10 anos por un equipo de investigadores bolivianos, brasilefios y de otras nacionalidades. Se presenta una descripeión del medio fisico, así como resultados relevantes sobre la biodiversidad acuática, con énfasis en algas, peces, reptiles y mamíferos. El aporte más notable del libro, adernas de la descripeión ecológica del ecosistema, son las lecciones aprendidas que surgieron de experiências locales sobre la élaboration participativa de herramientas para la gestion de los recursos hidrobiológicos.A Bolívia e o Brasil compartilham uma das bacias hidrográficas mais atrativas e preservadas da região amazônica: a bacia do Rio Iténez ou Guaporé. A combinação das influências do escudo pré-cambriano brasileiro e da planícies do Beni é uma das razões pela qual existem na região elevada heterogeneidade de habitats, fauna aquática peculiar e alto grau valor dc conservação. Eslc patrimônio binacional possui potencial significativo para a conservação da diversidade regional e desenvolvimento sustentável participativo das comunidades locais. O livro contém um resumo do conhecimento da bacia e seus recursos, gerado nos últimos dez anos por uma equipe de pesquisadores bolivianos, brasileiros e de outras nacionalidades. Apresentamos uma descrição do meio físico, bem como resultados relevantes da biodiversidade aquática, com ênfase em algas, peixes, répteis e mamíferos. A contribuição mais notável do livro, além da descrição ecológica do ecossistema, é a descrição das lições aprendidas que surgiram a partir de experiências locais sobre elaboração participativa de ferramentas para a gestão dos recursos aquáticos presentes nesta bacia

The performance of the jet trigger for the ATLAS detector during 2011 data taking

The performance of the jet trigger for the ATLAS detector at the LHC during the 2011 data taking period is described. During 2011 the LHC provided proton–proton collisions with a centre-of-mass energy of 7 TeV and heavy ion collisions with a 2.76 TeV per nucleon–nucleon collision energy. The ATLAS trigger is a three level system designed to reduce the rate of events from the 40 MHz nominal maximum bunch crossing rate to the approximate 400 Hz which can be written to offline storage. The ATLAS jet trigger is the primary means for the online selection of events containing jets. Events are accepted by the trigger if they contain one or more jets above some transverse energy threshold. During 2011 data taking the jet trigger was fully efficient for jets with transverse energy above 25 GeV for triggers seeded randomly at Level 1. For triggers which require a jet to be identified at each of the three trigger levels, full efficiency is reached for offline jets with transverse energy above 60 GeV. Jets reconstructed in the final trigger level and corresponding to offline jets with transverse energy greater than 60 GeV, are reconstructed with a resolution in transverse energy with respect to offline jets, of better than 4 % in the central region and better than 2.5 % in the forward direction