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Domain fishing: a first step in protein comparative modelling.

UNLABELLED: To optimize the search for structural templates in protein comparative modelling, the query sequence is split into domains. The initial list of templates for each domain, extracted from PFAM plus PDB and SCOP, is then ranked according to sequence identity (%ID), coverage and resolution. If %ID is less than 30, secondary structure matching is used to filter out false templates. AVAILABILITY: http://www.bmm.icnet.uk/~3djigsaw/dom_fish

Algorithms↗

Prospects for a vaccine against human papillomavirus.

OBJECTIVE: To summarize existing data regarding the feasibility of developing strategies for prophylactic and therapeutic vaccination against human papillomavirus (HPV) infection. DATA SOURCES: We used the Medline data base and reference lists of articles to identify English-language papers that evaluate strategies for prophylactic and therapeutic vaccination against HPV infection. METHODS OF STUDY SELECTION: Our search uncovered several reports of systems that produce recombinant HPV major capsid proteins as antigens for biochemical, molecular, and immunologic studies and investigations that evaluate cell-mediated immune responses to HPV-induced, tumor-associated peptides. DATA EXTRACTION AND SYNTHESIS: Recombinant HPV major capsid proteins, which self-assemble into virus-like particles, are produced in quantity, mimic the conformation of native virions, react with neutralizing antibodies, and are type-specific. Human papillomavirus early viral peptides induce cytotoxic T lymphocyte responses that retard tumor progression and protect against tumor development after challenge in animal models. CONCLUSIONS: Recombinant papillomavirus virus-like particles are highly antigenic, protective in animal models, lack potentially carcinogenic viral DNA, and are, therefore, ideal candidates for a prophylactic vaccine against HPV infection. Immunization with HPV tumor peptides may be beneficial in tumor prevention, regression, and rejection. Vaccines against HPV infection can be important in reducing the incidence of cervical dysplasia and carcinoma worldwide, particularly in developing countries.

Animals↗

The hematologic system as a marker of organ dysfunction in sepsis.

Sepsis with acute organ dysfunction (severe sepsis) results from a systemic proinflammatory and procoagulant response to infection. Organ dysfunction in the patient with sepsis is associated with increased mortality. Although most organs have discrete anatomical boundaries and carry out unified functions, the hematologic system is poorly circumscribed and serves several unrelated functions. This review addresses the hematologic changes associated with sepsis and provides a framework for prompt diagnosis and rational drug therapy. Data sources used include published research and review articles in the English language related to hematologic alterations in animal models of sepsis and in critically ill patients. Hematologic changes are present in virtually every patient with severe sepsis. Leukocytosis, anemia, thrombocytopenia, and activation of the coagulation cascade are the most common abnormalities. Despite theoretical advantages of using granulocyte colony-stimulating factor to enhance leukocyte function and/or circulating numbers, large clinical trials with these growth factors are lacking. Recent studies support a reduction in the red blood cell transfusion threshold and the use of erythropoietin treatment to reduce transfusion requirements. Treatment of thrombocytopenia depends on the cause and clinical context but may include platelet transfusions and discontinuation of heparin or other inciting drugs. The use of activated protein C may provide a survival benefit in subsets of patients with severe sepsis. The hematologic system should not be overlooked when assessing a patient with severe sepsis. A thorough clinical evaluation and panel of laboratory tests that relate to this organ system should be as much a part of the work-up as taking the patient's blood pressure, monitoring renal function, or measuring liver enzymes.

Blood Transfusion↗

Population genetic study among the Orange Asli (Semai Senoi) of Malaysia: Malayan aborigines.

A population genetic study was undertaken to provide gene frequency data on the additional blood genetic markers in the Semai and to estimate the genetic relations between the Semai and their neighboring and linguistically related populations by genetic distance and principal components analyses. Altogether 10 polymorphic and 7 monomorphic blood genetic markers (plasma proteins and red cell enzymes) were studied in a group of 349 Senoi Semai from 11 aboriginal settlements (villages) in the Pahang State of western Malaysia. Both the red cell glucose-6-phosphate dehydrogenase (G6PD) and 6-phosphogluconate dehydrogenase (PGD) loci reveal the presence of polymorphic frequencies of a nondeficient slow allele at the G6PD locus and a fast allele at the PGD locus. The Semai are characterized by high prevalences of ahaptoglobinemia and G6PD deficiency, high frequencies of HP*1, HB*E, RH*R1, ACP*C, GLO1*1, PGM1*2+, and GC*1F and corresponding low frequencies of ABO*A, HbCoSp, HB*B0, TF*D, CHI, and GC*2. Genetic distance analyses by both cluster and principal components models were performed between the Semai and 14 other populations (Malay; Javanese; Khmer; Veddah; Tamils of Malaysia, Sri Lanka, and India; Sinhalese; Oraon; Toda and Irula of India; Chinese; Japanese; Koreans) on the basis of 30 alleles at 7 polymorphic loci. A more detailed analysis using 53 alleles at 13 polymorphic loci with 10 populations was carried out. Both analyses give genetic evidence of a close relationship between the Semai and the Khmer of Cambodia. Furthermore, the Semai are more closely related to the Javanese than to their close neighbors--the Malay, Chinese, and Tamil Indians. There is no evidence for close genetic relationship between the Semai and the Veddah or other Indian tribes. The evidence fits well with the linguistic relationship of the Semai with the Mon-Khmer branch of the Austro-Asiatic language family.

Adolescent↗

Molecular dynamics simulation on a network of workstations using a machine-independent parallel programming language.

Molecular dynamics simulations investigate local and global motion in molecules. Several parallel computing approaches have been taken to attack the most computationally expensive phase of molecular simulations, the evaluation of long range interactions. This paper reviews these approaches and develops a straightforward but effective algorithm using the machine-independent parallel programming language, Linda. The algorithm was run both on a shared memory parallel computer and on a network of high performance Unix workstations. Performance benchmarks were performed on both systems using two proteins. This algorithm offers a portable cost-effective alternative for molecular dynamics simulations. In view of the increasing numbers of networked workstations, this approach could help make molecular dynamics simulations more easily accessible to the research community.

Algorithms↗

Knowledge representation of signal transduction pathways.

MOTIVATIONS: Signal transduction is the common term used to define a diverse topic that encompasses a large body of knowledge about the biochemical mechanisms. Since most of the knowledge of signal transduction resides in scientific articles and is represented by texts in natural language or by diagrams, there is the need of a knowledge representation model for signal transduction pathways that can be as readily processed by a computer as it is easily understood by humans. RESULTS: A signal transduction pathway representation model is presented. It is based on a compound graph structure and is designed to handle the diversity and hierarchical structure of pathways. A prototype knowledge base was implemented on a deductive database and a number of biological queries are demonstrated on it.

Amino Acid Motifs↗

[The aetiopathogenesis of auditory hallucinations in psychosis].

INTRODUCTION: Auditory hallucinations is one of the core symptoms of psychosis. Two main different approaches have been made in recent years in order to understand this perceptual abnormality. The psycho-social approaches is trying to explain auditory hallucinations as a common human phenomenon that only environmental factors cause them to be pathological. It propose psychotherapeutic techniques based on the cognitive model, paying special attention to the emotional component. The neurobiological approach, specially with neuroimaging techniques, is giving us new information about abnormal activation in specific neural networks, particularly in language areas. It propose biological treatments with antipsychotics and transcranial magnetic stimulation. Neither of these approaches are listening to each other. Neither of them look at the molecular genetic vulnerability to auditory hallucinations in psychosis. DEVELOPMENT: From a review of the literature and our own findings, we present a genetic-environmental model of auditory hallucinations in psychoses. We hypothesize two types of genetic vulnerability: vulnerability to hearing voices -that could be related with genes that are expressed in language areas and are related with language abnormalities (FOXP2)-, and vulnerability to abnormal emotional response to voices -that could be related with genes that are involved in the regulation of dopamine in the limbic system (5-HTT, CCK-AR)-. Finally, environmental and cultural factors explain the content and social adjustment to auditory hallucinations. CONCLUSION: Our model allow the integration of many data from epidemiology and neuroimaging, to psychopharmacology in the understanding of the aetiology of auditory hallucinations.

Brain↗

The language of covalent histone modifications.

Histone proteins and the nucleosomes they form with DNA are the fundamental building blocks of eukaryotic chromatin. A diverse array of post-translational modifications that often occur on tail domains of these proteins has been well documented. Although the function of these highly conserved modifications has remained elusive, converging biochemical and genetic evidence suggests functions in several chromatin-based processes. We propose that distinct histone modifications, on one or more tails, act sequentially or in combination to form a 'histone code' that is, read by other proteins to bring about distinct downstream events.

Acetylation↗

IPSA-Inductive Protein Structure Analysis.

The Inductive Structure Protein Analysis (IPSA) project presents a new method for investigating protein structure. IPSA includes the creation of a new database which was designed specifically for the analysis of protein structure by statistics and machine learning. The Protein Representation Language (PRL) database includes explicit and symbolic representations of geometrical, topological and chemophysical information about secondary structures and the relationships between secondary structures. The IPSA methodology consists of: the use of PRL information to produce a new database of examples of secondary structures which associate together (examples of possible super-secondary structures); then the use of a variety of clustering techniques to produce a consensus clustering of these examples (super-secondary structures); these super-secondary structures are finally examined to uncover any biological features of significance. We have applied this method to find simple super-secondary structures consisting of pairs of alpha-helices. We found four well-defined super-secondary structures, one formed exclusively by long range interactions, and another in association with an additional element of secondary structure (alpha t alpha-motif). Examinations were carried out using homologous pairs and conformational fits which confirm our clustering.

Cluster Analysis↗

A LuxS-dependent cell-to-cell language regulates social behavior and development in Bacillus subtilis.

Cell-to-cell communication in bacteria is mediated by quorum-sensing systems (QSS) that produce chemical signal molecules called autoinducers (AI). In particular, LuxS/AI-2-dependent QSS has been proposed to act as a universal lexicon that mediates intra- and interspecific bacterial behavior. Here we report that the model organism Bacillus subtilis operates a luxS-dependent QSS that regulates its morphogenesis and social behavior. We demonstrated that B. subtilis luxS is a growth-phase-regulated gene that produces active AI-2 able to mediate the interspecific activation of light production in Vibrio harveyi. We demonstrated that in B. subtilis, luxS expression was under the control of a novel AI-2-dependent negative regulatory feedback loop that indicated an important role for AI-2 as a signaling molecule. Even though luxS did not affect spore development, AI-2 production was negatively regulated by the master regulatory proteins of pluricellular behavior, SinR and Spo0A. Interestingly, wild B. subtilis cells, from the undomesticated and probiotic B. subtilis natto strain, required the LuxS-dependent QSS to form robust and differentiated biofilms and also to swarm on solid surfaces. Furthermore, LuxS activity was required for the formation of sophisticated aerial colonies that behaved as giant fruiting bodies where AI-2 production and spore morphogenesis were spatially regulated at different sites of the developing colony. We proposed that LuxS/AI-2 constitutes a novel form of quorum-sensing regulation where AI-2 behaves as a morphogen-like molecule that coordinates the social and pluricellular behavior of B. subtilis.

Bacillus subtilis↗

Design and application of PDBlib, a C++ macromolecular class library.

PDBlib is an extensible object-oriented class library written in C++ for representing the three-dimensional structure of biological macromolecules. The software design strategy, features of many of the 129 classes currently distributed with the library, and two sample applications which use the library are described. Version 1.0 of the library represents the structural features of proteins, DNA, RNA and complexes thereof, at a level of detail on a par with that which can be parsed from a Protein Data Bank (PDB) entry. However, the memory-resident representation of the macromolecule is independent of the PDB entry and can be obtained from other sources, e.g. relational and object-oriented databases. PDBlib classes are organized into four categories: (i) classes that model the macromolecule; (ii) classes that enhance the extensibility of the library; (iii) classes that provide navigation facilities of the object-oriented macromolecular structure representation; and (iv) a class that loads a PDB file into the memory-resident object-oriented representation. A number of general-purpose procedures that return features of this representation and that are relevant to all biological disciplines are included in (i). The library has been used to develop PDBtool, a prototype structure verification tool, and PDBview, a structure rendering tool that requires no specialized graphics hardware and software. Current work centers on making the macromolecular structures represented by PDBlib persistent using a commercial object-oriented database and providing an additional class library, MMQLlib, to query those structures.

Databases, Factual↗

Zebra finch CB1 cannabinoid receptor: pharmacology and in vivo and in vitro effects of activation.

Zebra finches (Taeniopygia guttata) learn vocal behavior during sensitive developmental periods, similar to the way in which human language is acquired. As adults, they recite the learned song pattern in a stereotyped manner. Previously, we demonstrated that central nervous system-associated cannabinoid receptors (CB1) are expressed in brain regions known to control both juvenile song learning and adult recitation of song. Here we extend these findings by establishing the zebra finch as a behavioral model to study cannabinoid pharmacology, showing that the cannabinoid agonist WIN55212-2 inhibits both adult song production and locomotor activity, effects that are antagonist-reversed. Through radioligand binding assays we investigated the pharmacology of a number of cannabinoid ligands representing all structural classes and established an affinity profile that can be compared with that of other species. To begin to characterize signal transduction mechanisms we isolated cDNA encoding the receptor protein. The zebra finch CB1 receptor (ZFCB1) is highly expressed in brain with amino acid sequence 92% identical to human CB1 receptor. Establishment of a Chinese hamster ovary cell line stably expressing ZFCB1 allowed demonstration that the cannabinoid agonist WIN55212-2 dose dependently and potently inhibits forskolin-stimulated adenylate cyclase activity (IC(50) = 9.0 nM, maximum inhibition = 49% at 100 nM WIN55212-2, reversed by 1 mM SR141716A). Cyclase inhibition indicates that ZFCB1-mediated signal transduction is consistent with that of mammalian CB1 receptors. Overall, cannabinoid inhibition of adult song production and conserved pharmacology render the zebra finch a promising model to investigate cannabinoid effects on learning by juveniles.

Adenine↗

AceTree: a tool for visual analysis of Caenorhabditis elegans embryogenesis.

BACKGROUND: The invariant lineage of the nematode Caenorhabditis elegans has potential as a powerful tool for the description of mutant phenotypes and gene expression patterns. We previously described procedures for the imaging and automatic extraction of the cell lineage from C. elegans embryos. That method uses time-lapse confocal imaging of a strain expressing histone-GFP fusions and a software package, StarryNite, processes the thousands of images and produces output files that describe the location and lineage relationship of each nucleus at each time point. RESULTS: We have developed a companion software package, AceTree, which links the images and the annotations using tree representations of the lineage. This facilitates curation and editing of the lineage. AceTree also contains powerful visualization and interpretive tools, such as space filling models and tree-based expression patterning, that can be used to extract biological significance from the data. CONCLUSION: By pairing a fast lineaging program written in C with a user interface program written in Java we have produced a powerful software suite for exploring embryonic development.

Animals↗

A greedy strategy for finding motifs from yes-no examples.

We define a motif as an expression Z1.Z2...Zn with sets Z1, Z2,..., Zn of strings in a specified family omega called the type. This notion can capture the most of the motifs in PROSITE as well as regular pattern languages. A greedy strategy is developed for finding such motifs with ambiguity just from positive and negative examples by exploiting the probabilistic argument. This paper concentrates on describing the idea of the greedy algorithm with its underlying theory. Its experimental results on splicing sites and E. coli promoters are also presented.

Algorithms↗

Recombinant human activated protein C for severe sepsis in neonates.

BACKGROUND: Sepsis is a common problem in both preterm and term infants. Although the overall incidence of neonatal sepsis has declined over the past decade, mortality remains high. Recombinant human activated protein C (rhAPC) has been shown to possess a broad spectrum of activity modulating coagulation and has been shown in septic adults to reduce mortality. In septic children, an open label study has shown similar pharmacokinetics, adverse reaction profile and frequency as in adults with severe sepsis. OBJECTIVES: To determine whether treatment with rhAPC will reduce mortality and/or morbidity in neonates with severe sepsis. SEARCH STRATEGY: Searches were carried out in July 2005 by the review authors independently of MEDLINE (1966 to July 2005), EMBASE (1980 to July 2005), CINAHL (1982 to July 2005), the Cochrane Central Register of Controlled Trials (CENTRAL, The Cochrane Library, Issue 3, 2005), abstracts of annual meetings of the Pediatric Academic Societies and Society for Pediatric Research which were published in Pediatric Research from 1980, and contacts were made with subject experts. Doctoral dissertations, theses and the Science Citation Index for articles on activated protein C were searched from 1980. No language restriction was applied. SELECTION CRITERIA: Studies were included if they were randomized or quasi-randomized trials, assessing the efficacy of rhAPC compared to placebo or no intervention as an adjunct to antibiotic therapy of suspected or confirmed severe sepsis in term and preterm infants less than 28 days old. Eligible trials were required to report treatment effects on at least one of the following outcomes: all cause mortality during initial hospital stay, neurological development and neurodevelopmental assessment at two years of age or later, length of hospital stay, duration of ventilation, chronic lung disease in survivors, periventricular leukomalacia, intraventricular hemorrhage, necrotizing enterocolitis, bleeding, and any other adverse events. DATA COLLECTION AND ANALYSIS: Both review authors independently evaluated the papers for inclusion criteria and quality, and abstracted information for the outcomes of interest. Differences were resolved by mutual discussion. The statistical methods were to include relative risk, risk difference, number needed to treat to benefit or number needed to treat to harm for dichotomous and weighed mean difference for continuous outcomes reported with 95% confidence intervals. A fixed effects model was to be used for meta-analysis. Heterogeneity tests, including the I(2) statistic, were to be performed to assess the appropriateness of pooling the data. MAIN RESULTS: No eligible trials were identified. AUTHORS' CONCLUSIONS: Despite the scientific rationale for its use, there are insufficient data to support the use of rhAPC for the management of severe sepsis in newborn infants. There is a need for large well-designed trials to elucidate the effectiveness of rhAPC to reduce mortality and adverse outcomes in neonates with severe sepsis. The results of such trials would guide clinical practice. Currently, a cautious approach to the use of rhAPC is warranted due to the high incidence of bleeding with its use; especially as severe sepsis in preterm infants is commonly associated with bleeding problems and intraventricular hemorrhage. Its use is not recommended outside of randomized controlled trials.

Humans↗

A plant dialect of the histone language.

The genome contains all the information needed to build an organism. However, during differentiation and development, additional epigenetic information determines the functional state of cells and tissues. This epigenetic information can be introduced by cytosine methylation and by marking nucleosomal histones. The code written on histones consists of post-translational modifications, including acetylation and methylation. In contrast to the universal nature of the DNA code, the histone language and its decoding machinery differ among animals, plants and fungi. Plant cells have retained totipotency to generate the entire plant and maintained the ability to dedifferentiate, which suggests that the establishment and maintenance of epigenetic information differs from animals. Here, I aim to summarize the histone code and plant-specific aspects of setting and translating the code.

Acetylation↗

Quantifying kinetic paths of protein folding.

We propose a new approach to activated protein folding dynamics via a diffusive path integral framework. The important issues of kinetic paths in this situation can be directly addressed. This leads to the identification of the kinetic paths of the activated folding process, and provides a direct tool and language for the theoretical and experimental community to understand the problem better. The kinetic paths giving the dominant contributions to the long-time folding activation dynamics can be quantitatively determined. These are shown to be the instanton paths. The contributions of these instanton paths to the kinetics lead to the "bell-like" shape folding rate dependence on temperature, which is in good agreement with folding kinetic experiments and simulations. The connections to other approaches as well as the experiments of the protein folding kinetics are discussed.

Algorithms↗

An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.

BACKGROUND: Many proteomics initiatives require a seamless bioinformatics integration of a range of analytical steps between sample collection and systems modeling immediately assessable to the participants involved in the process. Proteomics profiling by 2D gel electrophoresis to the putative identification of differentially expressed proteins by comparison of mass spectrometry results with reference databases, includes many components of sample processing, not just analysis and interpretation, are regularly revisited and updated. In order for such updates and dissemination of data, a suitable data structure is needed. However, there are no such data structures currently available for the storing of data for multiple gels generated through a single proteomic experiments in a single XML file. This paper proposes a data structure based on XML standards to fill the void that exists between data generated by proteomics experiments and storing of data. RESULTS: In order to address the resulting procedural fluidity we have adopted and implemented a data model centered on the concept of annotated gel (AG) as the format for delivery and management of 2D Gel electrophoresis results. An eXtensible Markup Language (XML) schema is proposed to manage, analyze and disseminate annotated 2D Gel electrophoresis results. The structure of AG objects is formally represented using XML, resulting in the definition of the AGML syntax presented here. CONCLUSION: The proposed schema accommodates data on the electrophoresis results as well as the mass-spectrometry analysis of selected gel spots. A web-based software library is being developed to handle data storage, analysis and graphic representation. Computational tools described will be made available at http://bioinformatics.musc.edu/agml. Our development of AGML provides a simple data structure for storing 2D gel electrophoresis data.

Computational Biology↗