Alignment of helical membrane protein sequences using AlignMe

Few sequence alignment methods have been designed specifically for integral membrane proteins, even though these important proteins have distinct evolutionary and structural properties that might affect their alignments. Existing approaches typically consider membrane-related information either by using membrane-specific substitution matrices or by assigning distinct penalties for gap creation in transmembrane and non-transmembrane regions. Here, we ask whether favoring matching of predicted transmembrane segments within a standard dynamic programming algorithm can improve the accuracy of pairwise membrane protein sequence alignments. We tested various strategies using a specifically designed program called AlignMe. An updated set of homologous membrane protein structures, called HOMEP2, was used as a reference for optimizing the gap penalties. The best of the membrane-protein optimized approaches were then tested on an independent reference set of membrane protein sequence alignments from the BAliBASE collection. When secondary structure (S) matching was combined with evolutionary information (using a position-specific substitution matrix (P)), in an approach we called AlignMePS, the resultant pairwise alignments were typically among the most accurate over a broad range of sequence similarities when compared to available methods. Matching transmembrane predictions (T), in addition to evolutionary information, and secondary-structure predictions, in an approach called AlignMePST, generally reduces the accuracy of the alignments of closely-related proteins in the BAliBASE set relative to AlignMePS, but may be useful in cases of extremely distantly related proteins for which sequence information is less informative. The open source AlignMe code is available at https://sourceforge.net/projects/alignme​/, and at http://www.forrestlab.org, along with an online server and the HOMEP2 data set

Interfaces in partly compatible polymer mixtures: A Monte Carlo simulation approach

The structure of polymer coils near interfaces between coexisting phases of symmetrical polymer mixtures (AB) is discussed, as well as the structure of symmetric diblock copolymers of the same chain length N adsorbed at the interface. The problem is studied by Monte Carlo simulations of the bond fluctuation model on the simple cubic lattice, using massively parallel computers (CRAY T3D). While homopolymer coils in the strong segregation limit are oriented parallel to the interface, the diblocks form ``dumbbells'' oriented perpendicular to the interface. However, in the dilute case (``mushroom regime'' rather than ``brush regime''), the diblocks are only weakly stretched. Distribution functions for monomers at the chain ends and in the center of the polymer are obtained, and a comparison to the self consistent field theory is made.Comment: to appear in Physica

Breaking paradigms in severe epistaxis: the importance of looking for the S-point

Introduction: Since the introduction of nasal endoscopy into the field of Otorhinolaryngology, the treatment paradigm for cases of severe epistaxis has shifted toward early and precise identification of the bleeding site. Although severe epistaxis is usually considered to arise from posterior bleeding, an arterial vascular pedicle in the superior portion of the nasal septum, around the axilla projection of the middle turbinate, posterior to the septal body, frequently has been observed. That vascular pedicle was named the Stamm's S-point. Objective: The aim of this study was to describe the S-point and report cases of severe epistaxis originating from it. Methods: A retrospective case series study was conducted. Nine patients with spontaneous severe epistaxis, where the S-point was identified as the source of bleeding, were treated between March 2016 and March 2017. Results: Male predominance (77.8%) with age average of 59.3 years old were reported. Most cases presented comorbidities (88.9%) and were not taking acetylsalicylic acid (66.7%). A predominance of left sided involvement (55.6%) and anteroposterior bleeding being the principal initial presentation (77.8%) was seen. Six patients (66.7%) presented with hemoglobin levels below 10g/dL, and four (44.4%) required blood transfusion. Cauterization of S-point was performed in all patients, with complete resolution of bleeding. No patient experienced recurrence of severe epistaxis. Conclusion: The Stamm's S-point, a novel source of spontaneous severe epistaxis, is reported, and its cauterization was effective and safe. Otolaryngologists must actively seek this site of bleeding in cases of severe epistaxis. (C) 2018 Associacao Brasileira de Otorrinolaringologia e Cirurgia Cervico-Facial. Published by Elsevier Editora Ltda. This is an open access article under the CC BY license.Introdução: Desde a introdução da endoscopia nasal no campo de otorrinolaringologia, o paradigma de tratamento para casos graves de epistaxe voltou-se para a identificação precoce e correta do local de sangramento. Embora a epistaxe grave seja geralmente considerada uma hemorragia posterior, um pedículo vascular arterial tem sido frequentemente observado na porção superior do septo nasal, ao redor da projeção da axila da concha média, posterior ao tubérculo septal. Esse pedículo vascular foi chamado de Stamm's S-point. Objetivo: Descrever o S-point e relatar casos graves de epistaxe que se originam nesse local. Método: Um estudo retrospectivo de série de casos foi conduzido. Nove pacientes com epistaxe grave espontânea, na qual o S-point foi identificado como a fonte do sangramento, foram tratados de março de 2016 a março de 2017. Resultados: Houve predominância do sexo masculino (77,8%) com média de 59,3 anos. A maioria dos casos apresentava comorbidades (88,9%), mas sem uso de ácido acetilsalicílico (66,7%). Observou-se predominância do lado esquerdo (55,6%) com sangramento anteroposterior como a principal apresentação inicial (77,8%). Seis pacientes (66,7%) apresentaram níveis de hemoglobina inferiores a 10 g/dL e quatro (44,4%) necessitaram de transfusão sanguínea. Cauterização do S-point foi feita em todos os pacientes, com resolução completa do sangramento. Nenhum paciente apresentou recorrência de epistaxe grave. Conclusão: O Stamm's S-point é relatado como uma nova região de origem de epistaxe grave espontânea e o tratamento feito com cauterização foi eficaz e seguro. Os otorrinolaringologistas devem buscar ativamente esse local de sangramento em casos de epistaxe grave.Univ Fed Sao Paulo, UNIFESP, Setor Rinol,Escola Paulista Med, Dept Otorrinolaringol & Cirurgia Cabeca & Pescoco, Sao Paulo, SP, BrazilComplexo Hosp Edmundo Vasconcelos, Ctr Otorrinolaringol & Fonoaudiol, Sao Paulo, SP, BrazilPoliclin Botafogo, Dept Otorrinolaringol, Rio De Janeiro, RJ, BrazilUniv Fed Sao Paulo, UNIFESP, Setor Rinol,Escola Paulista Med, Dept Otorrinolaringol & Cirurgia Cabeca & Pescoco, Sao Paulo, SP, BrazilSciEL

Synthetic Amorphous Silicon Dioxide (NM-200, NM-201, NM-202, NM-203, NM-204): Characterisation and Physico-Chemical Properties

The European Commission's Joint Research Centre (JRC) provides scientific support to European Union policy including nanotechnology. Within this context, the JRC launched, in February 2011, a repository for Representative Test Materials (RTMs), based on preparatory work started in 2008. It supports both EU and international research projects, and especially the OECD Working Party on Manufactured Nanomaterials (WPMN). The WPMN leads an exploratory testing programme "Testing a Representative set of Manufactured Nanomaterials" for the development and collection of data on characterisation, toxicological and ecotoxicological properties, as well as risk assessment and safety evaluation of nanomaterials. The purpose is to understand the applicability of the OECD Test Guidelines for the testing of nanomaterials as well as end-points relevant for such materials. The Repository responds to a need for nanosafety research purposes: availability of nanomaterial from a single production batch to enhance the comparability of results between different research laboratories and projects. The availability of representative nanomaterials to the international scientific community furthermore enhances and enables development of safe materials and products. The present report presents the physico-chemical characterisation of the synthetic amorphous silicon dioxide (SiO2, SAS) from the JRC repository: NM-200, NM-201, NM-202, NM-203 and NM-204. NM-200 was selected as principal material for the OECD test programme "Testing a representative set of manufactured nanomaterials". NM-200, NM-201 and NM-204 (precipitated SAS) are produced via the precipitation process, whereas NM-202 and NM-203 (fumed or pyrogenic SAS) are produced via a high temperature process. Each of these NMs originates from one respective batch of commercially manufactured SAS. They are nanostructured, i.e. they consist of aggregated primary particles. The SAS NMs may be used as a representative material in the measurement and testing with regard to hazard identification, risk and exposure assessment studies. The results for more than 15 endpoints are addressed in the present report, including physical-chemical properties, such as size and size distribution, crystallite size and electron microscopy images. Sample and test item preparation procedures are addressed. The results are based on studies by several European laboratories participating to the NANOGENOTOX Joint Action, as well as the JRC.JRC.I.4-Nanobioscience

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Comparison of membrane proteins using computational programs

Membrane proteins are biological macromolecules that are located in a cell’s membrane and are responsible for essential functions within an organism, which makes them to prominent drug targets. The extraction of membrane proteins from the hydrophobic membrane bilayer to determine high-resolution crystal structures is a difficult task and only 2% of all solved proteins structures are membrane proteins. Computational methods may help to gain deeper insights into membrane protein structures and their functions. This study will give an overview of such computational methods on a representative set of membrane proteins and will provide ideas for future computational and experimental research on membrane proteins. In a first step (chapter 2), I updated an earlier, manually-curated data set of homologous membrane proteins (HOMEP) to more recent versions in 2010 (HOMEP2) and 2013 (HOMEP3) using an automated clustering approach. High-resolution structures of membrane proteins listed in the PDB_TM database were structurally aligned and subsequently clustered using structural similarity scores. Both data sets were used as a standard gold reference set for subsequent work. Subsequently, I have updated and applied the sequence alignment program AlignMe to determine protein descriptors that are suitable for detecting evolutionary relationship between homologous a-helical membrane proteins. Single input descriptors were tested alone and in combination with each other in different modes of AlignMe by optimizing gap penalties on the HOMEP2 data set. Most accurate alignments and homology models on the HOMEP2 data set were observed when using position-specific substitution information (P), secondary structure propensities (S) and transmembrane propensities (T) in the AlignMe PST mode. An evaluation on an independent reference set of membrane protein sequence alignments from the BAliBASE collection showed that different modes of AlignMe are suitable for different sequence similarity levels. The AlignMe PST mode improved the alignment accuracy significantly for distantly related proteins, whereas for closely-related proteins from the BAliBASE set the AlignMe PS mode was more suitable. This work was published in March 2013 in PLOS ONE. In order to allow also an easier usage of the AlignMe program, I have implemented a web server of AlignMe (chapter 4) that provides the optimized settings and gap penalties for the AlignMe P, PS and PST modes. A comparison to other recent alignment web server shows that the alignments of AlignMe are similar or even more accurate than those of other methods, especially for very distantly related proteins for which the inclusion of membrane protein information has been shown to be suitable. This work was published in the NAR web server issue in July 2014. Although membrane-specific information has been shown to be suitable for aligning distantly related membrane proteins on a sequence level, such information was not incorporated into structural alignment programs making it unclear which method is the most suitable for aligning membrane proteins. Thus, I compared 13 widely-used pairwise structural alignment methods on an updated reference set of homologous membrane protein structures (HOMEP3) and evaluated their accuracy by building models based on the underlying sequence alignments and used scoring functions (e.g., AL4 or CAD-score) to rate the model accuracy (chapter 5). The analysis showed that fragment-based approaches such as FR-TM-align are the most useful for aligning structures of membrane proteins that have undergone large conformational changes whereas rigid approaches were more suitable for proteins that were solved in the same or a similar state. However, no method showed a significant higher accuracy than any other. Additionally, all methods lack a measure to rate the reliability of the accuracy for a specific position within a structure alignment. In order to solve these problems, I propose a consensus-type approach that combines alignments from four different methods, namely FR-TM-align, DaliLite, MATT and FATCAT and assigns a confidence value to each position of the alignment that describes the agreement between the methods. This work has been published 2015 in the journal “PROTEINS: structure, function and bioinformatics”. Consensus alignments were then generated for each pair of proteins of the HOMEP3 data set and subsequently analyzed for single evolutionary events within membrane spanning segments and for irregular structures (e.g., 310- and p-helices) (chapter 6). Interestingly, single insertions and deletions could be observed with the help of consensus alignments in the conserved membrane-spanning segments of membrane proteins in four protein families. The detection of such single InDels might help to identify crucial residues for a proteins function

Modulare Weltmodellierung und Kommunikation in heterogenen Robotersystemen

Das Fachgebiet Simulation, Systemoptimierung und Robotik (SIM) der Technischen Universität Darmstadt beschäftigt sich mit der Forschung an mobilen autonomen Robotersystemen. Damit sich unterschiedliche autonome Robotersysteme in ihrer Umwelt zurechtfinden und miteinander kommunizieren können, wird eine Weltmodellierung mit heterogener Teamkommunikation benötigt. Ziel dieser Arbeit ist es, basierend auf dem Framework RoboFrame eine möglichst modulare Weltmodellierung zu entwickeln, die eine solche Kommunikation ermöglicht. Die Implementierung der Arbeit wird als Teil des DD-RoboCup-Softwarepakets im Frühjahr 2007 bei den Internationalen RoboCup GermanOpen, Internationalen RoboCup JapanOpen und im Sommer 2007 bei der RoboCup Weltmeisterschaft in der Humanoid League eingesetzt