MemO: a consensus approach to the annotation of a protein's membrane organization

Membrane organization describes the relationship of proteins to the membrane, that is, whether the protein crosses the membrane or is integral to the membrane and its orientation with respect to the membrane. Membrane organization is determined primarily by the presence of two features which target proteins to the secretory pathway: the endoplasmic reticulum signal peptide and the ?-helical transmembrane domain. In order to generate membrane organization annotation of high quality, confidence and throughput, the Membrane Organization (MemO) pipeline was developed, incorporating consensus feature prediction modules with integration and annotation rules derived from biological observations. The pipeline classifies proteins into six categories based on the presence or absence of predicted features: Soluble, intracellular proteins; Soluble, secreted proteins; Type I membrane proteins; Type II membrane proteins; Multi-span membrane proteins and Glycosylphosphatidylinositol anchored membrane proteins. The MemO pipeline represents an integrated strategy for the application of state-of-the-art bioinformatics tools to the annotation of protein membrane organization, a property which adds biological context to the large quantities of protein sequence information available.     

Structure-guided consensus approach to create a more thermostable penicillin G acylase

The thermostabilization of penicillin G acylase (PGA) is a difficult problem due to the large size of the protein and its complex maturation process. We developed a data-driven protein design method that requires fewer homologous sequences than the traditional consensus approach and utilizes structural information to limit the number of variants created. Approximately 50% of our 21 single-point mutants were found experimentally to be more thermostable than the wild-type PGA, two had almost threefold longer half-life at 50 degrees C, with very little effect on activity. An analysis of four programs that predict the thermostability conferred by point mutations shows little agreement between the programs and with the experimental data, emphasizing that the chosen stabilizing mutations are very difficult to predict, but that our data-driven design method should prove useful.     

Two unique cyanobacteria lead to a traceable approach of the first appearance of oxygenic photosynthesis

The evolutionary route from anoxygenic photosynthetic bacteria to oxygenic cyanobacteria is discontinuous in terms of photochemical/photophysical reaction systems. It is difficult to describe this transition process simply because there are no recognized intermediary organisms between the two bacterial groups. Gloeobacter violaceus PCC 7421 might be a model organism that is suitable for analysis because it still possesses primordial characteristics such as the absence of thylakoid membranes. Whole genome analysis and biochemical and biophysical surveys of G. violaceus have favored the hypothesis that it is an intermediary organism. On the other hand, species differentiation is an evolutionary process that could be driven by changes in a small number of genes, and this process might give fair information more in details by monitoring of those genes. Comparative studies of genes, including those in Acaryochloris marina MBIC 11017, have provided information relevant to species differentiation; in particular, the acquisition of a new pigment, chlorophyll d, and changes in amino acid sequences have been informative. Here, based on experimental evidence from these two species, we discuss some of the evolutionary pathways for the appearance and differentiation of cyanobacteria.     

A proteomic approach to iron and copper homeostasis in cyanobacteria.

Cyanobacteria, which are considered to be the chloroplast precursors, are significant contributors to global photosynthetic productivity. The ample variety of membrane and soluble proteins containing different metals (mainly, iron and copper) has made these organisms develop a complex homeostasis with different mechanisms and tight regulation processes to fulfil their metal requirements in a changing environment. Cell metabolism is so adapted as to synthesize alternative proteins depending on the relative metal availabilities. In particular, plastocyanin, a copper protein, and cytochrome c(6), a haem protein, can replace each other to play the same physiological role as electron carriers in photosynthesis and respiration, with the synthesis of one protein or another being regulated by copper concentration in the medium. The unicellular cyanobacterium Synechocystis sp. PCC 6803 has been widely used as a model system because of completion of its genome sequence and the ease of its genetic manipulation, with a lot of proteomic work being done. In this review article, we focus on the functional characterization of knockout Synechocystis mutants for plastocyanin and cytochrome c(6), and discuss the ongoing proteomic analyses performed at varying copper concentrations to investigate the cyanobacterial metal homeostasis and cell response to changing environmental conditions.     

Research priorities for bat conservation in Southeast Asia: a consensus approach

Southeast Asia is a critical area for biodiversity conservation; levels of species richness and endemism are among the highest in the world, but rapid land-use changes endanger much of the region’s fauna. Bats are a critical component of this diversity, comprising nearly a third of Southeast Asia’s mammal species and providing vital ecological and economic services. However, nearly half the species are of conservation concern and as many as 40% of bat species are predicted to be extinct by the end of this century if current deforestation rates persist. Conservation efforts are urgently needed, and the taxonomic continuity of Southeast Asia and the prevalence of major threats throughout suggest that a region-wide initiative could be an effective approach. The Southeast Asian Bat Conservation Research Unit (SEABCRU) was established in 2007 to provide an organizational framework to both accelerate the advancement of bat research, and to coordinate conservation efforts. The SEABCRU is an informal collaboration among institutes, NGOs and individuals and provides a web-based forum for the growing number of researchers and outreach workers to interact and coordinate activities. It was launched at the 1st International Southeast Asian Bat Conference in Thailand (May 2007), during which a forum was held to derive conservation research priorities using a consensus approach. Four priorities were identified by participants: flying fox conservation and monitoring, taxonomy, conservation of cave-dependent bats, and conservation of forest-dependent bats. Here I provide an overview of the rationales behind these priorities and list the specific recommendations for the actions identified.     

Phylogenetic comparison among the heterocystous cyanobacteria based on a polyphasic approach

Phylogenetic comparison has been done among the selected heterocystous cyanobacteria belonging to the sections IV and V. The hierarchical cluster analysis based on antibiotics sensitivity showed a distant relationship between the members of Nostocales and Stigonematales. Thus, multiple antibiotic resistance pattern used as marker provide easy, fast, and reliable method for strain discrimination and genetic variability. However, morphological, physiological (both based on principal component analysis) and biochemical analysis grouped true branching cyanobacteria along with the members of section IV. Molecular analysis based on 16S rRNA gene sequences revealed that Hapalosiphon welwitschii and Westiellopsis sp. were grouped in cluster I whereas Scytonema bohnerii, a false branching genera showed a close proximity with Calothrix brevissima in cluster II. Cluster III of clade 2 included Nostoc calcicola and Anabaena oryzae which proved the heterogeneity at the generic level. Cluster IV the largest group of clade 2 based on 16S rRNA gene sequences includes six strains of the genera Nostoc, Anabaena, and Cylindrospermum showing ambiguous evolutionary relationship. In cluster IV, Anabaena sp. and Anabaena doliolum were phylogenetically linked by sharing 99% sequence similarity. Probably, they were of the same genetic makeup but appear differently under the diverse physiological conditions. Section IV showed polyphyletic origin whereas section V showed monophyletic origin. Results suggested that either morphological or physiological or biochemical or molecular attribute is not sufficient to provide true diversity and phylogeny of the cyanobacteria at the generic level and thus, a polyphasic approach would be more appropriate and reliable.     

Prediction of partial membrane protein topologies using a consensus approach

We have developed a method to reliably identify partial membrane protein topologies using the consensus of five topology prediction methods. When evaluated on a test set of experimentally characterized proteins, we find that approximately 90% of the partial consensus topologies are correctly predicted in membrane proteins from prokaryotic as well as eukaryotic organisms. Whole-genome analysis reveals that a reliable partial consensus topology can be predicted for approximately 70% of all membrane proteins in a typical bacterial genome and for approximately 55% of all membrane proteins in a typical eukaryotic genome. The average fraction of sequence length covered by a partial consensus topology is 44% for the prokaryotic proteins and 17% for the eukaryotic proteins in our test set, and similar numbers are found when the algorithm is applied to whole genomes. Reliably predicted partial topologies may simplify experimental determinations of membrane protein topology.     

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.     

A polyphasic approach for the taxonomy of cyanobacteria: principles and applications

Taxonomic classification is the only method for understanding and exploring knowledge about organismal diversity. However, it is complicated in prokaryotic, phylogenetically old, phototrophic cyanobacteria, which contain very simple unicellular forms up to multicellular types with a differentiated and diversified thallus. Their cells are cytologically relatively simple, but variable in shape. Various genotypes are adaptable to various specialized ecosystems. The introduction and combination of modern molecular, cytomorphological and ecological methods in the taxonomy of cyanobacteria is necessary and should be accepted as the only method for the elaboration of their modern systematics. The combination of different methods should be based on molecular sequencing as the basic approach, to which must be added other criteria (morphological, ecological) if they are available and which are distinct and recognizable in cyanobacterial populations. The use of such characteristics is necessary and must be obligatorily included for the final characterization both of strains and natural populations. Application of this polyphasic, i.e. combined approach is considered as a unique, modern, unambiguous, unequivocal and a fully acceptable methodological procedure, but it is not yet commonly used, nor possible for all known cyanobacterial populations. The main principles and recent problems of this modern classification method are discussed in the following review and will be the basis of further discussion.     

Antifouling potential of cyanobacteria: a mini-review

Abstract

Cyanobacteria produce a variety of bioactive metabolites that may have allelochemical functions in the natural environment, such as in the prevention of fouling by colonising organisms. Chemical compounds from cyanobacteria are also of biotechnological interest, especially for clinical applications, because of their antibiotic, algicidal, cytotoxic, immunosupressive and enzyme inhibiting activities. Cyanobacterial metabolites have the potential for use in antifouling technology, since they show antibacterial, antialgal, antifungal and antimacrofouling properties which could be expoited in the prevention of biofouling on man-made substrata in the aquatic environment. Molecules with antifouling activity represent a number of types including fatty acids, lipopeptides, amides, alkaloids, terpenoids, lactones, pyrroles and steroids. The isolation of biogenic compounds and the determination of their structure may provide leads for future development of, for example, environmentally friendly antifouling paints. An advantage of exploring the efficacy of cyanobacterial products is that the organisms can be grown in mass culture, which can be manipulated to achieve optimal production of bioactive substances. Phycotoxins and related products from cyanobacteria may serve as materials for antimicro- and antimacrofouling applications. A survey of antibiotic compounds with antifouling potential revealed more than 21 different antifouling substances from 27 strains of cyanobacteria.     

Antifouling potential of cyanobacteria: a mini-review

Cyanobacteria produce a variety of bioactive metabolites that may have allelochemical functions in the natural environment, such as in the prevention of fouling by colonising organisms. Chemical compounds from cyanobacteria are also of biotechnological interest, especially for clinical applications, because of their antibiotic, algicidal, cytotoxic, immunosupressive and enzyme inhibiting activities. Cyanobacterial metabolites have the potential for use in antifouling technology, since they show antibacterial, antialgal, antifungal and antimacrofouling properties which could be expoited in the prevention of biofouling on man-made substrata in the aquatic environment. Molecules with antifouling activity represent a number of types including fatty acids, lipopeptides, amides, alkaloids, terpenoids, lactones, pyrroles and steroids. The isolation of biogenic compounds and the determination of their structure may provide leads for future development of, for example, environmentally friendly antifouling paints. An advantage of exploring the efficacy of cyanobacterial products is that the organisms can be grown in mass culture, which can be manipulated to achieve optimal production of bioactive substances. Phycotoxins and related products from cyanobacteria may serve as materials for antimicro- and antimacrofouling applications. A survey of antibiotic compounds with antifouling potential revealed more than 21 different antifouling substances from 27 strains of cyanobacteria.     

True versus apparent malaria infection prevalence: the contribution of a Bayesian approach

Aims

To present a new approach for estimating the “true prevalence” of malaria and apply it to datasets from Peru, Vietnam, and Cambodia.

Methods

Bayesian models were developed for estimating both the malaria prevalence using different diagnostic tests (microscopy, PCR & ELISA), without the need of a gold standard, and the tests'' characteristics. Several sources of information, i.e. data, expert opinions and other sources of knowledge can be integrated into the model. This approach resulting in an optimal and harmonized estimate of malaria infection prevalence, with no conflict between the different sources of information, was tested on data from Peru, Vietnam and Cambodia.

Results

Malaria sero-prevalence was relatively low in all sites, with ELISA showing the highest estimates. The sensitivity of microscopy and ELISA were statistically lower in Vietnam than in the other sites. Similarly, the specificities of microscopy, ELISA and PCR were significantly lower in Vietnam than in the other sites. In Vietnam and Peru, microscopy was closer to the “true” estimate than the other 2 tests while as expected ELISA, with its lower specificity, usually overestimated the prevalence.

Conclusions

Bayesian methods are useful for analyzing prevalence results when no gold standard diagnostic test is available. Though some results are expected, e.g. PCR more sensitive than microscopy, a standardized and context-independent quantification of the diagnostic tests'' characteristics (sensitivity and specificity) and the underlying malaria prevalence may be useful for comparing different sites. Indeed, the use of a single diagnostic technique could strongly bias the prevalence estimation. This limitation can be circumvented by using a Bayesian framework taking into account the imperfect characteristics of the currently available diagnostic tests. As discussed in the paper, this approach may further support global malaria burden estimation initiatives.     

嗜盐古菌分类学研究进展

嗜盐古菌是一类需要高盐维持生长的古菌。到目前为止,已发现的嗜盐古菌都属于古菌域的广古菌门,主要包括:嗜盐甲烷古菌类群、嗜盐古菌纲的全部成员以及尚不能培养的纳米嗜盐古菌类群。嗜盐古菌是盐环境的土著类群,驱动着盐环境生态系统的生物地球化学循环。作为极端微生物,嗜盐古菌在理论研究和应用领域具有重要的研究价值。本文从嗜盐古菌分类学地位的变迁、分类学方法、分类学研究现状及我国的嗜盐古菌分类学研究等方面综述了嗜盐古菌分类学的最新研究进展。     

Domain assignment for protein structures using a consensus approach: characterization and analysis.

A consensus approach for the assignment of structural domains in proteins is presented. The approach combines a number of previously published algorithms, and takes advantage of the elevated accuracy obtained when assignments from the individual algorithms are in agreement. The consensus approach is tested on a data set of 55 protein chains, for which domain assignments from four automated methods were known, and for which crystallographers assignments had been reported in the literature. Accuracy was found to increase in this test from 72% using individual algorithms to 100% when all four methods were in agreement. However a consensus prediction using all four methods was only possible for 52% of the dataset. The consensus approach [using three publicly available domain assignment algorithms (PUU, DETECTIVE, DOMAK)] was then used to make domain assignments for a data set of 787 protein chains from the Protein Data Bank. Analysis of the assignments showed 55.7% of assignments could be made automatically, and of these, 13.5% were multi-domain proteins. Of the remaining 44.3% that could not be assigned by the consensus procedure 90.4% had their domain boundaries assigned correctly by at least one of the algorithms. Once identified, these domains were analyzed for trends in their size and secondary structure class. In addition, the discontinuity of each domain along the protein chain was considered.     

The relative contribution of local habitat and landscape context to metapopulation processes: a dynamic occupancy modeling approach

Changes in site occupancy across habitat patches have often been attributed to landscape features in fragmented systems, particularly when considering metapopulations. However, failure to include habitat quality of individual patches can mask the relative importance of local scale features in determining distributional changes. We employed dynamic occupancy modeling to compare the strength of local habitat variables and metrics of landscape patterns as drivers of metapopulation dynamics for a vulnerable, high‐elevation species in a naturally fragmented landscape. Repeat surveys of Bicknell's thrush Catharus bicknelli presence/non‐detection were conducted at 88 sites across Vermont, USA in 2006 and 2007. We used an organism‐based approach, such that at each site we measured important local‐scale habitat characteristics and quantified landscape‐scale features using a predictive habitat model for this species. We performed a principal component analysis on both the local and landscape features to reduce dimensionality. We estimated site occupancy, colonization, and extinction probabilities while accounting for imperfect detection. Univariate, additive, and interaction models of local habitat and landscape context were ranked using AICc scores. Both local and landscape scales were important in determining changes in occupancy patterns. An interaction between scales was detected for occupancy dynamics indicating that the relationship of the parameters to local‐scale habitat conditions can change depending on the landscape context and vice versa. An increase in both landscape‐ and local‐scale habitat quality increased occupancy and colonization probability while decreasing extinction risk. Colonization and extinction were both more strongly influenced by local habitat quality relative to landscape patterns. We also identified clear, qualitative thresholds for landscape‐scale features. Conservation of large habitat patches in high‐cover landscapes will help ensure persistence of Bicknell's thrushes, but only if local scale habitat quality is maintained. Our results highlight the importance of incorporating information beyond landscape characteristics when investigating patch occupancy patterns in metapopulations.     

An evidence-based approach to prescribing NSAIDs in musculoskeletal disease: a Canadian consensus. Canadian NSAID Consensus Participants.

OBJECTIVE. To make recommendations for the long-term use of nonsteroidal anti-inflammatory drugs (NSAIDs) in primary care practice, particularly for patients at high risk for NSAID-induced complications. OPTIONS. The use of misoprostol to prevent gastrointestinal ulceration and other unwanted NSAIDs effects was considered. The role of cyclooxygenase-2 (COX-2) versus COX-1 inhibiting agents was also examined. OUTCOMES. Reduction of complications associated with long-term use of NSAIDs. EVIDENCE. Evidence was gathered in late 1995 from published research studies and reviews. Position papers were prepared by faculty and advisory board members and discussed at the Canadian NSAID Consensus Symposium in Cambridge, Ont., Jan. 26 and 27, 1996. VALUES. Recommendations were based on randomized, placebo-controlled clinical trials (level I evidence) and case-control studies (level II evidence) involving NSAID use when such evidence was available. When the scientific literature was incomplete or inconsistent in a particular area, recommendations reflect the consensus of the participants at the symposium (level III evidence). Physicians were recruited from across Canada for their expertise in rheumatology, gastroenterology, epidemiology, gerontology, family practice, and clinical and basic scientific research. BENEFITS, HARMS AND COSTS. Although a reduction in complications due to inappropriate NSAID use should reduce costs of additional investigations, admissions to hospital and time lost from work, definitive cost analysis studies are not yet available. RECOMMENDATIONS. Currently, no NSAID is available that lacks potential for serious toxicity; therefore, long-term use of NSAIDs should be avoided whenever possible, particularly in high-risk patients (e.g., those who are elderly, suffer from hypertension, congestive heart failure, renal or hepatic impairment or volume depletion, take certain concomitant medications or have a history of peptic ulcer disease) (level I evidence). If NSAIDs are to be used in patients with gastric or nephrotoxic risk factors, the lowest effective dose of NSAID should be used (level III evidence); NSAIDs that are weak COX-1 inhibitors may be preferred (level II evidence). In addition, concomitant administration of misoprostol is recommended in patients at increased risk for upper gastrointestinal complications (level I evidence). However, the clinical judgement of the practising clinician must always be part of any therapeutic decision. VALIDATION. These recommendations are based on the consensus of Canadian experts in rheumatology, gastroenterology and epidemiology, and have been subjected to external peer review.