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.     

GenAlyzer: interactive visualization of sequence similarities between entire genomes

SUMMARY: Genalyzer is a software tool designed for the interactive visualization of sequence matches between DNA or protein sequences. It provides visualizations on different levels of granularity, from complete overviews via zoomed regions to alignments of particular matching substrings. Genalyzer can efficiently handle very large datasets, allowing to display tens of thousands of matches between sequences of tens of millions of bases. AVAILABILITY: Genalyzer is available free of charge for non-commercial research institutions. For more details, see http://www.genalyzer.de     

The Bioinformatics Template Library--generic components for biocomputing

MOTIVATION: The efficiency of bioinformatics programmers can be greatly increased through the provision of ready-made software components that can be rapidly combined, with additional bespoke components where necessary, to create finished programs. The new standard for C++ includes an efficient and easy to use library of generic algorithms and data-structures, designed to facilitate low-level component programming. The extension of this library to include functionality that is specifically useful in compute-intensive tasks in bioinformatics and molecular modelling could provide an effective standard for the design of reusable software components within the biocomputing community. RESULTS: A novel application of generic programming techniques in the form of a library of C++ components called the Bioinformatics Template Library (BTL) is presented. This library will facilitate the rapid development of efficient programs by providing efficient code for many algorithms and data-structures that are commonly used in biocomputing, in a generic form that allows them to be flexibly combined with application specific object-oriented class libraries. AVAILABILITY: The BTL is available free of charge from our web site http://www.cryst.bbk.ac.uk/~classlib/ and the EMBL file server http://www.embl-ebi.ac.uk/FTP/index.html     

IL-1beta-induced production of metalloproteinases by synovial cells depends on gap junction conductance

Synovial cells can form networksconnected by gap junctions. The purpose of this study was to obtainevidence for a necessary role of gap junction intercellularcommunication in protein secretion by synovial cells. We developed anovel assay to measure the enzymatic activity of metalloproteinases(MMPs) produced by synovial cells in response to interleukin-1(IL-1) and employed the assay to explore the biological function ofgap junctions. IL-1 produced a dose-dependent increase in MMPactivity that was blocked by exposure to the gap junction inhibitors18-glycyrrhetinic acid and octanol for as few as 50 min. Theinhibitors produced an immediate and marked reduction in intercellularcommunication, as assessed by transient current analysis using thenystatin perforated-patch method. These observations suggest thatcommunication through gap junctions early in IL-1 signaltransduction is critical to the process of cytokine-regulated secretionof MMPs by synovial cells.

     

LVB: parsimony and simulated annealing in the search for phylogenetic trees

The program LVB seeks parsimonious phylogenies from nucleotide alignments, using the simulated annealing heuristic. LVB runs fast and gives high quality results. AVAILABILITY: The software is available at http://www.rubic.reading.ac.uk/lvb/ Supplementary information: Supplementary information may be downloaded from http://www.rubic.reading.ac.uk/~daniel/     

Compressed suffix tree--a basis for genome-scale sequence analysis

Summary: Suffix tree is one of the most fundamental data structuresin string algorithms and biological sequence analysis. Unfortunately,when it comes to implementing those algorithms and applyingthem to real genomic sequences, often the main memory size becomesthe bottleneck. This is easily explained by the fact that whilea DNA sequence of length n from alphabet = {A, C, G, T } canbe stored in n log ||= 2n bits, its suffix tree occupies O(nlog n) bits. In practice, the size difference easily reachesfactor 50. We provide an implementation of the compressed suffix tree veryrecently proposed by Sadakane (Theory of Computing Systems,in press). The compressed suffix tree occupies space proportionalto the text size, i.e. O(n log} | |) bits, and supports alltypical suffix tree operations with at most log n factor slowdown.Our experiments show that, e.g. on a 10 MB DNA sequence, thecompressed suffix tree takes 10% of the space of normal suffixtree. Typical operations are slowed down by factor 60. Availability: The C++ implementation under GNU license is availableat http://www.cs.helsinki.fi/group/suds/cst/. An example programimplementing a typical pattern discovery task is included. Experimentalresults in this note correspond to version 0.95. Contact: vmakinen{at}cs.helsinki.fi     

ISFOLD: Structure Prediction of Base Pairs in Non-Helical RNA Motifs from Isostericity Signatures in Their Sequence Alignments

Abstract

The existence and identity of non-Watson-Crick base pairs (bps) within RNA bulges, internal loops, and hairpin loops cannot reliably be predicted by existing algorithms. We have developed the Isfold (Isosteric Folding) program as a tool to examine patterns of nucleotide substitutions from sequence alignments or mutation experiments and identify plausible bp interactions. We infer these interactions based on the observation that each non-Watson-Crick bp has a signature pattern of isosteric substitutions where mutations can be made that preserve the 3D structure. Isfold produces a dynamic representation of predicted bps within defined motifs in order of their probabilities. The software was developed under Windows XP, and is capable of running on PC and MAC with Matlab 7.1 (SP3) or higher. A PC standalone version that does not require Matlab also is available. This software and a user manual are freely available at www.ucsf.edu/frankel/isfold.     

StrBioLib: a Java library for development of custom computational structural biology applications

SUMMARY: StrBioLib is a library of Java classes useful for developing software for computational structural biology research. StrBioLib contains classes to represent and manipulate protein structures, biopolymer sequences, sets of biopolymer sequences, and alignments between biopolymers based on either sequence or structure. Interfaces are provided to interact with commonly used bioinformatics applications, including (psi)-blast, modeller, muscle and Primer3, and tools are provided to read and write many file formats used to represent bioinformatic data. The library includes a general-purpose neural network object with multiple training algorithms, the Hooke and Jeeves non-linear optimization algorithm, and tools for efficient C-style string parsing and formatting. StrBioLib is the basis for the Pred2ary secondary structure prediction program, is used to build the astral compendium for sequence and structure analysis, and has been extensively tested through use in many smaller projects. Examples and documentation are available at the site below. AVAILABILITY: StrBioLib may be obtained under the terms of the GNU LGPL license from http://strbio.sourceforge.net/     

DBAli: a database of protein structure alignments

SUMMARY: The DBAli database includes approximately 35000 alignments of pairs of protein structures from SCOP (Lo Conte et al., Nucleic Acids Res., 28, 257-259, 2000) and CE (Shindyalov and Bourne, Protein Eng., 11, 739-747, 1998). DBAli is linked to several resources, including Compare3D (Shindyalov and Bourne, http://www.sdsc.edu/pb/software.htm, 1999) and ModView (Ilyin and Sali, http://guitar.rockefeller.edu/ModView/, 2001) for visualizing sequence alignments and structure superpositions. A flexible search of DBAli by protein sequence and structure properties allows construction of subsets of alignments suitable for a number of applications, such as benchmarking of sequence-sequence and sequence-structure alignment methods under a variety of conditions. AVAILABILITY: http://guitar.rockefeller.edu/DBAli/     

Statistical alignment based on fragment insertion and deletion models

Motivation: The topic of this paper is the estimation of alignments and mutation rates based on stochastic sequence-evolution models that allow insertions and deletions of subsequences ('fragments') and not just single bases. The model we propose is a variant of a model introduced by Thorne et al., (J. Mol. Evol., 34, 3-16, 1992). The computational tractability of the model depends on certain restrictions in the insertion/deletion process; possible effects we discuss. Results: The process of fragment insertion and deletion in the sequence-evolution model induces a hidden Markov structure at the level of alignments and thus makes possible efficient statistical alignment algorithms. As an example we apply a sampling procedure to assess the variability in alignment and mutation parameter estimates for HVR1 sequences of human and orangutan, improving results of previous work. Simulation studies give evidence that estimation methods based on the proposed model also give satisfactory results when applied to data for which the restrictions in the insertion/deletion process do not hold. Availability: The source code of the software for sampling alignments and mutation rates for a pair of DNA sequences according to the fragment insertion and deletion model is freely available from http://www.math.uni-frankfurt.de/~stoch/software/mcmcsalut under the terms of the GNU public license (GPL, 2000).     

PicXAA: greedy probabilistic construction of maximum expected accuracy alignment of multiple sequences

Accurate tools for multiple sequence alignment (MSA) are essential for comparative studies of the function and structure of biological sequences. However, it is very challenging to develop a computationally efficient algorithm that can consistently predict accurate alignments for various types of sequence sets. In this article, we introduce PicXAA (Probabilistic Maximum Accuracy Alignment), a probabilistic non-progressive alignment algorithm that aims to find protein alignments with maximum expected accuracy. PicXAA greedily builds up the multiple alignment from sequence regions with high local similarities, thereby yielding an accurate global alignment that effectively grasps the local similarities among sequences. Evaluations on several widely used benchmark sets show that PicXAA constantly yields accurate alignment results on a wide range of reference sets, with especially remarkable improvements over other leading algorithms on sequence sets with local similarities. PicXAA source code is freely available at: http://www.ece.tamu.edu/∼bjyoon/picxaa/.     

Estrogen receptor-alpha predominantly mediates the salutary effects of 17beta-estradiol on splenic macrophages following trauma-hemorrhage

Although 17-estradiol administration following trauma-hemorrhage prevents the suppression in splenic macrophage cytokine production, it remains unknown whether the salutary effects are mediated via estrogen receptor (ER)- or ER- and which signaling pathways are involved in such 17-estradiol effects. Utilizing ER-- or ER--specific agonists, this study examined the role of ER- and ER- in 17-estradiol-mediated restoration of macrophage cytokine production following trauma-hemorrhage. In addition, since MAPK and NF-B are known to regulate macrophage cytokine production, we also examined the activation of those signaling molecules. Male rats underwent trauma-hemorrhage (mean arterial pressure of 40 mmHg for 90 min) and fluid resuscitation. The ER- agonist propyl pyrazole triol (PPT; 5 µg/kg), the ER- agonist diarylpropionitrile (DPN; 5 µg/kg), 17-estradiol (50 µg/kg), or vehicle (10% DMSO) was injected subcutaneously during resuscitation. Twenty-four hours thereafter, splenic macrophages were isolated, and their IL-6 and TNF- production and activation of MAPK and NF-B were measured. Macrophage IL-6 and TNF- production and MAPK activation were decreased, whereas NF-B activity was increased, following trauma-hemorrhage. PPT or 17-estradiol administration after trauma-hemorrhage normalized those parameters. DPN administration, on the other hand, did not normalize the above parameters. Since PPT but not DPN administration following trauma-hemorrhage was as effective as 17-estradiol in preventing the suppression in macrophage cytokine production, it appears that ER- plays the predominant role in mediating the salutary effects of 17-estradiol on macrophage cytokine production following trauma-hemorrhage and that such effects are likely mediated via normalization of MAPK but not NF-B signaling pathways. shock; mitogen-activated protein kinase; nuclear factor-B; propyl pyrazole triol; diarylpropionitrile     

Rfam: an RNA family database

Rfam is a collection of multiple sequence alignments and covariance models representing non-coding RNA families. Rfam is available on the web in the UK at http://www.sanger.ac.uk/Software/Rfam/ and in the US at http://rfam.wustl.edu/. These websites allow the user to search a query sequence against a library of covariance models, and view multiple sequence alignments and family annotation. The database can also be downloaded in flatfile form and searched locally using the INFERNAL package (http://infernal.wustl.edu/). The first release of Rfam (1.0) contains 25 families, which annotate over 50 000 non-coding RNA genes in the taxonomic divisions of the EMBL nucleotide database.     

alpha -Adrenergic receptors regulate human lymphocyte amiloride-sensitive sodium channels

Two independentsignal transduction pathways regulate lymphocyte amiloride-sensitivesodium channels (ASSCs), one utilizing cAMP as a second messenger andthe other utilizing a GTP-binding protein. This implies that two plasmamembrane receptors play a role in the regulation of lymphocyte ASSCs.In this study, we tested the hypothesis that₁- and₂-adrenergic receptorsindependently regulate lymphocyte ASSCs via the two previouslyidentified second messengers. Direct measurements indicated thatnorepinephrine increased lymphocyte cAMP and activated ASSCs. The₂-specific inhibitor,yohimbine, blocked this activation, thereby linking ₂-adrenergic receptors to ASSCregulation via cAMP. The₁-specific ligand, terazosin,acted as an agonist and activated lymphocyte ASSCs but inhibited ASSCcurrent that had been preactivated by norepinephrine or8-(4-chlorophenylthio) (CPT)-cAMP. Terazosin had no effect on thelymphocyte whole cell ASSC currents preactivated by treatment withpertussis toxin. This finding indirectly links ₁-adrenergic receptors tolymphocyte ASSC regulation via GTP-binding proteins. Terazosin had nodirect inhibitory or stimulatory effects on ,,-endothelialsodium channels reconstituted into planar lipid bilayers and expressedin Xenopus oocytes, ruling out a direct interaction between terazosin and the channels. These findings support the hypothesis that both₁- and₂-adrenergic receptors independently regulate lymphocyte ASSCs via GTP-binding proteins andcAMP, respectively.

     

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins.

Pfam is a collection of multiple alignments and profile hidden Markov models of protein domain families. Release 3.1 is a major update of the Pfam database and contains 1313 families which are available on the World Wide Web in Europe at http://www.sanger.ac.uk/Software/Pfam/ and http://www.cgr.ki.se/Pfam/, and in the US at http://pfam.wustl.edu/. Over 54% of proteins in SWISS-PROT-35 and SP-TrEMBL-5 match a Pfam family. The primary changes of Pfam since release 2.1 are that we now use the more advanced version 2 of the HMMER software, which is more sensitive and provides expectation values for matches, and that it now includes proteins from both SP-TrEMBL and SWISS-PROT.     

IL-1 and IL-6 induce hepatocyte plasminogen activator inhibitor-1 expression through independent signaling pathways converging on C/EBPdelta

To elucidate signaling pathways activated by IL-1 and IL-6 that contribute to increased expression of plasminogen activator inhibitor-1 (PAI-1), we studied human hepatoma (HepG2) cells and primary mouse hepatocytes. HepG2 cell PAI-1 mRNA increased in response to IL-1, IL-6, and IL-1 plus IL-6 as shown by real-time PCR. Activity of the transiently transfected PAI-1 promoter (–829 to +36 bp) increased as well. Systematic promoter deletion assays showed that the region from –239 to –210 bp containing a putative CCAAT-enhancer binding protein (C/EBP) binding site was critical. Point mutations in this region abolished the IL-1 and IL-6 responses. Antibody interference electrophoretic mobility shift assays showed that C/EBP (but not C/EBP or C/EBP) binding and protein were increased by IL-1, IL-6, and IL-1 plus IL-6 in HepG2 cells. IL-1 and IL-6 increased expression of both PAI-1 mRNA and C/EBP mRNA in mouse primary hepatocytes as well. Downregulation of C/EBP induced with small interfering RNA (siRNA) decreased secretion of PAI-1. As judged from results obtained with inhibitors, signal transduction in all three of the mitogen-activated protein kinase pathways was involved in IL-1-inducible PAI-1 expression. By contrast, JAK signaling was responsible for the IL-6-induced inducible expression. Thus IL-1 and IL-6 exert directionally similar effects on PAI-1 expression, but the induction involves distinct signaling pathways with a final common mediator, C/EBP. CCAAT-enhancer binding protein; interleukin-1; interleukin-6; statins; thrombosis     

Two new species of Cololejeunea (Spruce) Schiffn. from Western Ghats,India

Introduction. During a recent floristic survey of liverworts from Western Ghats, India, two interesting liverworts of genus Cololejeunea were collected from forests in Mahabaleshwar in the state of Maharashtra.

Methods. After critical investigation, they have been described as new to science and both species, C. ghatensis G.Asthana & A.Srivastava sp. nov. and C. mehrana G.Asthana & A.Srivastava sp. nov. are illustrated and described here.

Key results. Cololejeunea ghatensis is an epiphyllous species growing on angiosperm leaves and has been collected near Chinaman Waterfall, Robbers Cave, Connaught Peak and Polo Ground area. Cololejeunea mehrana has been collected near Monkey point and the latter has an interesting habitat as it was found growing on moss leaves. Cololejeunea ghatensis is monoicous and C. mehrana is dioicous.     

Prediction of linear B-cell epitopes

The use of antigenicity scales based on physicochemical properties and the sliding window method in combination with an averaging algorithm and subsequent search for the maximum value is the classical method for B-cell epitope prediction. However, recent studies have demonstrated that the best classical methods provide a poor correlation with experimental data. We review both classical and novel algorithms and present our own implementation of the algorithms. The AAPPred software is available at http://www.bioinf.ru/aappred/.