JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture

BACKGROUND: Whole-genome sequencing projects are rapidly producing an enormous number of new sequences. Consequently almost every family of proteins now contains hundreds of members. It has thus become necessary to develop tools, which classify protein sequences automatically and also quickly and reliably. The difficulty of this task is intimately linked to the mechanism by which protein sequences diverge, i.e. by simultaneous residue substitutions, insertions and/or deletions and whole domain reorganisations (duplications/swapping/fusion). RESULTS: Here we present a novel approach, which is based on random sampling of sub-sequences (probes) out of a set of input sequences. The probes are compared to the input sequences, after a normalisation step; the results are used to partition the input sequences into homogeneous groups of proteins. In addition, this method provides information on diagnostic parts of the proteins. The performance of this method is challenged by two data sets. The first one contains the sequences of prokaryotic lyases that could be arranged as a multiple sequence alignment. The second one contains all proteins from Swiss-Prot Release 36 with at least one Src homology 2 (SH2) domain – a classical example for proteins with modular architecture. CONCLUSION: The outcome of our method is robust, highly reproducible as shown using bootstrap and resampling validation procedures. The results are essentially coherent with the biology. This method depends solely on well-established publicly available software and algorithms

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks

Summary: MetaNetX.org is a website for accessing, analysing and manipulating genome-scale metabolic networks (GSMs) as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Currently, it provides access to hundreds of GSMs and pathways that can be interactively compared (two or more), analysed (e.g. detection of dead-end metabolites and reactions, flux balance analysis or simulation of reaction and gene knockouts), manipulated and exported. Users can also upload their own metabolic models, choose to automatically map them into the common namespace and subsequently make use of the website's functionality. Availability and implementation: MetaNetX.org is available at http://metanetx.org. Contact: [email protected]

Swiss EMBnet node web server

EMBnet is a consortium of collaborating bioinformatics groups located mainly within Europe (http://www.embnet.org). Each member country is represented by a ‘node', a group responsible for the maintenance of local services for their users (e.g. education, training, software, database distribution, technical support, helpdesk). Among these services a web portal with links and access to locally developed and maintained software is essential and different for each node. Our web portal targets biomedical scientists in Switzerland and elsewhere, offering them access to a collection of important sequence analysis tools mirrored from other sites or developed locally. We describe here the Swiss EMBnet node web site (http://www.ch.embnet.org), which presents a number of original services not available anywhere els

IL CARNICO DI LIERNA (COMO): STRATIGRAFIA E PALEOGEOGRAFIA

The Carnian sedimentary succession of the Lierna area, more than 4OO m thick and belonging to the Coltignone tectonic unit (Grigne Group), has considerable paleogeographic significance, for it documents the western termination of the deltalagoon-carbonate platform depositional system of the Lombard Prealps. The Carnian succession, directly overlying basinal (Perledo-Varenna Formation) to shallow-marine (Lierna Formation) carbonates of Ladinian age, is characterized by deltaic terrigenous deposits (Val Sabbia Sandstone), progressively replaced by lagoonal (Gorno Formation) to peritidal (Breno Formation) limestones. In the studied stratigraphic sections these three lithofacies alternate vertically at decametric scale, and are each characterized by different types of cyclothems at metric scale. High-frequency "punctuated aggradational cycles" (PAC) are best recognized at the top of the Val Sabbia clastic body, where the final transition to the Gorno lagoon is marked by arenite layers containing ferruginous ooids. Grains of this type have nor been previously reported from Southalpine arenites. The petrographic composition of the Val Sabbia Sandstone points to provenance from an active volcanic chain, but abundance of quartzose detritus and occurrence of perthitic K-feldspar and sedimentary rock fragments suggest extensive erosion of the Hercynian basement and Upper Carboniferous to Ladinian sedimentary cover. These peculiar characteristics confirm the existence of a small "Lierna lobe" separated from the deltaic systems of central Lombardy, and fed by a basement- high located southwest of Como lake

pfsearchV3: a code acceleration and heuristic to search PROSITE profiles

Summary: The PROSITE resource provides a rich and well annotated source of signatures in the form of generalized profiles that allow protein domain detection and functional annotation. One of the major limiting factors in the application of PROSITE in genome and metagenome annotation pipelines is the time required to search protein sequence databases for putative matches. We describe an improved and optimized implementation of the PROSITE search tool pfsearch that, combined with a newly developed heuristic, addresses this limitation. On a modern x86_64 hyper-threaded quad-core desktop computer, the new pfsearchV3 is two orders of magnitude faster than the original algorithm. Availability and implementation: Source code and binaries of pfsearchV3 are freely available for download at http://web.expasy.org/pftools/#pfsearchV3, implemented in C and supported on Linux. PROSITE generalized profiles including the heuristic cut-off scores are available at the same address. Contact: [email protected]

The Microbe browser for comparative genomics

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene predictions from five software packages. The Microbe browser is daily updated from the source databases and includes all completely sequenced bacterial and archaeal genomes. The data are displayed in an easy-to-use, interactive website based on Ensembl software. The Microbe browser is available at http://microbe.vital-it.ch/. Programmatic access is available through the OMA application programming interface (API) at http://microbe.vital-it.ch/ap

Dual Effect of Methylprednsolone Pulses on Apoptosis of Peripheral Leukocytes in Patients with Renal Diseases

It is well known that change in apoptosis may modulate the natural story of illness, and that many drugs may act through modulation of apoptosis, but the role of steroids in acting through apoptosis in different settings, including renal diseases, has still to be elucidated. We studied the in vivo effects of steroids by oral assumption (10 to 25 mg/deltacortene) or by intravenous pulses (300 to 1000 mg/dose) on apoptosis and cellular subsets of peripheral lymphocytes, by evaluating DNA-fragmentation and lymphocyte subsets in 79 subjects: 22 controls and 57 patients with various renal diseases (25 Lupus-GN, 19 membranous-GN (MGN), 6 rapidly progressive-GN (RPGN), 2 acute interstitial nephritis (AIN), 5 on chronic dialysis. Baseline apoptosis was present in 1/22 (4.5%) of controls, 3/25 (12%) SLE, 2/6 (33.3%) RPGN and 10/19 (52.6%) MGN. A significant decrease in CD3+CD8+ cell count and a significant increase of the CD3+CD4/CD3+CD8+ ratio were found in apoptosis-positive subjects. DNA fragmentation did not change after oral steroids, paralleling a 22 to 32% decrease in total lymphocytes. Following intravenous methylprednisolone pulses, a deeper drop of all lymphocyte subsets was observed, while DNA fragmentation turned from present to absent in 2 MGN, but not in 2 RPGN, and from absent to present in 1 ARF and 1 SLE, independently of the dosage. We demonstrated that the presence of apoptosis in renal diseases is associated with decreased CD3+CD8+ cell count. Furthermore, steroid intravenous pulses, besides inducing a profound decrease in lymphocyte subsets, do exert a dual effect on baseline leukocyte apoptosis, eventually leading to a reversal of baseline patterns, either turning from negative to positive or from positive to negative. Oral steroid therapy did not influence baseline apoptosis