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/api

Hidden breakpoints in genome alignments

During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain and loss occurs in addition to other types of rearrangement, breakpoints of rearrangement can exist that are only detectable by comparison of three or more genomes. An arbitrarily large number of these "hidden" breakpoints can exist among genomes that exhibit no rearrangements in pairwise comparisons. We present an extension of the multichromosomal breakpoint median problem to genomes that have undergone gene gain and loss. We then demonstrate that the median distance among three genomes can be used to calculate a lower bound on the number of hidden breakpoints present. We provide an implementation of this calculation including the median distance, along with some practical improvements on the time complexity of the underlying algorithm. We apply our approach to measure the abundance of hidden breakpoints in simulated data sets under a wide range of evolutionary scenarios. We demonstrate that in simulations the hidden breakpoint counts depend strongly on relative rates of inversion and gene gain/loss. Finally we apply current multiple genome aligners to the simulated genomes, and show that all aligners introduce a high degree of error in hidden breakpoint counts, and that this error grows with evolutionary distance in the simulation. Our results suggest that hidden breakpoint error may be pervasive in genome alignments.Comment: 13 pages, 4 figure

Small-scale spatial variability of soil CO2 flux: Implication for monitoring strategy

In recent decades, soil CO2 flux measurements have been often used in both volcanic and seismically active areas to investigate the interconnections between temporal and spatial anomalies in degassing and telluric activities. In this study, we focus on a narrow degassing area of the Piton de la Fournaise volcano, that has been chosen for its proximity and link with the frequently active volcanic area. Our aim is to constrain the degassing in this narrow area and identify the potential processes involved in both spatial and temporal soil CO2 variations in order to provide an enhanced monitoring strategy for soil CO2 flux. We performed a geophysical survey (self-potential measurements: SP; electrical resistivity tomography: ERT) to provide a high-resolution description of the subsurface. We identified one main SP negative anomaly dividing the area in two zones. Based on these results, we set ten control points, from the site of the main SP negative anomaly up to 230 m away, where soil CO2 fluxes were weekly measured during one year of intense eruptive activity at Piton de la Fournaise. Our findings show that lateral and vertical soil heterogeneities and structures exert a strong control on the degassing pattern. We find that temporal soil CO2 flux series at control points close to the main SP negative anomaly better record variations linked to the volcanic activity. We also show that the synchronicity between the increase of soil CO2 flux and deep seismicity can be best explained by a pulsed process pushing out the CO2 already stored and fractionated in the system. Importantly, our findings show that low soil CO2 fluxes and low carbon isotopic signature are able to track variations of volcanic activity in the same way as high fluxes and high carbon isotopic signature do. This result gives important insights in terms of monitoring strategy of volcanic and seismotectonic areas in geodynamics contexts characterized by difficult environmental operational conditions as commonly met in tropical areaPublished13-264A. Oceanografia e climaJCR Journa

The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP

CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes

BACKGROUND: The recent accumulation of closely related genomic sequences provides a valuable resource for the elucidation of the evolutionary histories of various organisms. However, although numerous alignment calculation and visualization tools have been developed to date, the analysis of complex genomic changes, such as large insertions, deletions, inversions, translocations and duplications, still presents certain difficulties. RESULTS: We have developed a comparative genome analysis tool, named CGAT, which allows detailed comparisons of closely related bacteria-sized genomes mainly through visualizing middle-to-large-scale changes to infer underlying mechanisms. CGAT displays precomputed pairwise genome alignments on both dotplot and alignment viewers with scrolling and zooming functions, and allows users to move along the pre-identified orthologous alignments. Users can place several types of information on this alignment, such as the presence of tandem repeats or interspersed repetitive sequences and changes in G+C contents or codon usage bias, thereby facilitating the interpretation of the observed genomic changes. In addition to displaying precomputed alignments, the viewer can dynamically calculate the alignments between specified regions; this feature is especially useful for examining the alignment boundaries, as these boundaries are often obscure and can vary between programs. Besides the alignment browser functionalities, CGAT also contains an alignment data construction module, which contains various procedures that are commonly used for pre- and post-processing for large-scale alignment calculation, such as the split-and-merge protocol for calculating long alignments, chaining adjacent alignments, and ortholog identification. Indeed, CGAT provides a general framework for the calculation of genome-scale alignments using various existing programs as alignment engines, which allows users to compare the outputs of different alignment programs. Earlier versions of this program have been used successfully in our research to infer the evolutionary history of apparently complex genome changes between closely related eubacteria and archaea. CONCLUSION: CGAT is a practical tool for analyzing complex genomic changes between closely related genomes using existing alignment programs and other sequence analysis tools combined with extensive manual inspection

Adventive hydrothermal circulation on Stromboli volcano (Aeolian Islands, Italy) revealed by geophysical and geochemical approaches: Implications for general fluid flow models on volcanoes

International audienceOn March 15th 2007 a paroxysmal explosion occurred at the Stromboli volcano. This event generated a large amount of products, mostly lithic blocks, some of which impacted the ground as far as down to 200 m a.s.l., about 1.5 km far away from the active vents. Two days after the explosion, a new vapour emission was discovered on the north-eastern flank of the volcanic edifice, at 560 m a.s.l., just above the area called "Nel Cannestrà". This new vapour emission was due to a block impact. In order to investigate the block impact area to understand the appearance of the vapour emission, we conducted on May 2008 a multidisciplinary study involving Electrical Resistivity Tomography (ERT), Ground Penetrating Radar (GPR), Self-Potential (SP), CO2 soil diffuse degassing and soil temperature surveys. This complementary data set revealed the presence of an anomalous conductive body, probably related to a shallow hydrothermal level, at about 10-15 m depth, more or less parallel to the topography. It is the first time that such a hydrothermal fluid flow, with a temperature close to the water boiling point (76 °C) has been evidenced at Stromboli at this low elevation on the flank of the edifice. The ERT results suggest a possible link between (1) the main central hydrothermal system of Stromboli, located just above the plumbing system feeding the active vents, with a maximum of subsurface soil temperature close to 90 °C and limited by the NeoStromboli summit crater boundary and (2) the investigated area of Nel Cannestrà, at ~ 500 m a.s.l., a buried eruptive fissure active 9 ka ago. In parallel, SP and CO2 soil diffuse degassing measurements suggest in this sector at slightly lower elevation from the block impact crater a magmatic and hydrothermal fluid rising system along the N41° regional fault. A complementary ERT profile, on May 2009, carried out from the NeoStromboli crater boundary down to the block impact crater displayed a flank fluid flow apparently connected to a deeper system. The concept of shallow hydrothermal level have been compared to similar ERT results recently obtained on Mount Etna and La Fossa cone of Vulcano. This information needs to be taken into account in general fluid flow models on volcanoes. In particular, peripheral thermal waters (as those bordering the north-eastern coast of Stromboli) could be contaminated by hydrothermal and magmatic fluids coming from regional faults but also from the summit

Differences in genotype and virulence among four multidrug-resistant <i>Streptococcus pneumoniae</i> isolates belonging to the PMEN1 clone

We report on the comparative genomics and characterization of the virulence phenotypes of four &lt;i&gt;S. pneumoniae&lt;/i&gt; strains that belong to the multidrug resistant clone PMEN1 (Spain&lt;sup&gt;23F&lt;/sup&gt; ST81). Strains SV35-T23 and SV36-T3 were recovered in 1996 from the nasopharynx of patients at an AIDS hospice in New York. Strain SV36-T3 expressed capsule type 3 which is unusual for this clone and represents the product of an in vivo capsular switch event. A third PMEN1 isolate - PN4595-T23 - was recovered in 1996 from the nasopharynx of a child attending day care in Portugal, and a fourth strain - ATCC700669 - was originally isolated from a patient with pneumococcal disease in Spain in 1984. We compared the genomes among four PMEN1 strains and 47 previously sequenced pneumococcal isolates for gene possession differences and allelic variations within core genes. In contrast to the 47 strains - representing a variety of clonal types - the four PMEN1 strains grouped closely together, demonstrating high genomic conservation within this lineage relative to the rest of the species. In the four PMEN1 strains allelic and gene possession differences were clustered into 18 genomic regions including the capsule, the blp bacteriocins, erythromycin resistance, the MM1-2008 prophage and multiple cell wall anchored proteins. In spite of their genomic similarity, the high resolution chinchilla model was able to detect variations in virulence properties of the PMEN1 strains highlighting how small genic or allelic variation can lead to significant changes in pathogenicity and making this set of strains ideal for the identification of novel virulence determinant

Four Competing Definitions of Morphine Equivalence Insidiously Inhibit Evidence Synthesis

Analysis of opioid milligrams of morphine equivalents (MME) per day definitions. Presented virtually at the 37th annual International Conference on Pharmacoepidemiology and Therapeutic Risk Management

Practical methods for constructing suffix trees

Sequence datasets are ubiquitous in modern life-science applications, and querying sequences is a common and critical operation in many of these applications. The suffix tree is a versatile data structure that can be used to evaluate a wide variety of queries on sequence datasets, including evaluating exact and approximate string matches, and finding repeat patterns. However, methods for constructing suffix trees are often very time-consuming, especially for suffix trees that are large and do not fit in the available main memory. Even when the suffix tree fits in memory, it turns out that the processor cache behavior of theoretically optimal suffix tree construction methods is poor, resulting in poor performance. Currently, there are a large number of algorithms for constructing suffix trees, but the practical tradeoffs in using these algorithms for different scenarios are not well characterized.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47869/1/778_2005_Article_154.pd