DNA microarray data and contextual analysis of correlation graphs

BACKGROUND: DNA microarrays are used to produce large sets of expression measurements from which specific biological information is sought. Their analysis requires efficient and reliable algorithms for dimensional reduction, classification and annotation. RESULTS: We study networks of co-expressed genes obtained from DNA microarray experiments. The mathematical concept of curvature on graphs is used to group genes or samples into clusters to which relevant gene or sample annotations are automatically assigned. Application to publicly available yeast and human lymphoma data demonstrates the reliability of the method in spite of its simplicity, especially with respect to the small number of parameters involved. CONCLUSIONS: We provide a method for automatically determining relevant gene clusters among the many genes monitored with microarrays. The automatic annotations and the graphical interface improve the readability of the data. A C++ implementation, called Trixy, is available from

Studies of the ubiquitin conjugating (UBCv) enzyme encoded by African swine fever virus

Ubiquitin conjugating (UBC) enzymes play a key role in eukaryotes during the posttranslational modification of proteins by covalent attachment of ubiquitin. A gene was identified in the double stranded DNA genome of African swine fever virus (ASFV) which was predicted to encode a protein with high homology to eukaryotic UBC enzymes. This ASFV encoded enzyme (UBCv) was expressed in E. coli and was shown to have ubiquitin conjugating activity in vitro. Antisera against recombinant UBCv were used to detect UBCv in ASFV infected cells. UBCv was shown to be a cytosolic protein present throughout the early and late stages of ASFV replication and was packaged in ASPV virions. Attempts to inhibit UBCv activity during ASFV infection using antisense oligonucleotides were unsuccessful, and a recombinant ASPV mutant with the UBCv gene disrupted by the luciferase reporter could not be isolated. However, ASFV replication was impaired late in infection in TS20 cells at a temperature which inhibits the ubiquitin conjugating pathway. No novel ubiquitinated proteins could be detected in ASFV infected cells by immunoblotting, although an unspecific increase of cellular ubiquitin conjugation was observed in early infection. However, virus factories were intensely stained late in ASFV infection by immunofluorescence using anti-ubiquitin antisera. In addition, several ubiquitinated structural proteins were detected in purified ASFV extracellular particles by both immunoblotting and immunogold electron microscopy. An 18 kDa ubiquitinated structural protein, probably localized in the virion periphery, was purified to homogeneity and the sequence of its N-terminal 10 amino acids was determined. The N-terminal sequence of this protein matched exactly the product of a gene of unknown function encoded by the ASPV genome

Studies of the ubiquitin conjugating (UBCv) enzyme encoded by African swine fever virus

Ubiquitin conjugating (UBC) enzymes play a key role in eukaryotes during the posttranslational modification of proteins by covalent attachment of ubiquitin. A gene was identified in the double stranded DNA genome of African swine fever virus (ASFV) which was predicted to encode a protein with high homology to eukaryotic UBC enzymes. This ASFV encoded enzyme (UBCv) was expressed in E. coli and was shown to have ubiquitin conjugating activity in vitro. Antisera against recombinant UBCv were used to detect UBCv in ASFV infected cells. UBCv was shown to be a cytosolic protein present throughout the early and late stages of ASFV replication and was packaged in ASPV virions. Attempts to inhibit UBCv activity during ASFV infection using antisense oligonucleotides were unsuccessful, and a recombinant ASPV mutant with the UBCv gene disrupted by the luciferase reporter could not be isolated. However, ASFV replication was impaired late in infection in TS20 cells at a temperature which inhibits the ubiquitin conjugating pathway. No novel ubiquitinated proteins could be detected in ASFV infected cells by immunoblotting, although an unspecific increase of cellular ubiquitin conjugation was observed in early infection. However, virus factories were intensely stained late in ASFV infection by immunofluorescence using anti-ubiquitin antisera. In addition, several ubiquitinated structural proteins were detected in purified ASFV extracellular particles by both immunoblotting and immunogold electron microscopy. An 18 kDa ubiquitinated structural protein, probably localized in the virion periphery, was purified to homogeneity and the sequence of its N-terminal 10 amino acids was determined. The N-terminal sequence of this protein matched exactly the product of a gene of unknown function encoded by the ASPV genome

MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies

BACKGROUND: High throughput gene expression profiling (GEP) is becoming a routine technique in life science laboratories. With experimental designs that repeatedly span thousands of genes and hundreds of samples, relying on a dedicated database infrastructure is no longer an option. GEP technology is a fast moving target, with new approaches constantly broadening the field diversity. This technology heterogeneity, compounded by the informatics complexity of GEP databases, means that software developments have so far focused on mainstream techniques, leaving less typical yet established techniques such as Nylon microarrays at best partially supported. RESULTS: MAF (MicroArray Facility) is the laboratory database system we have developed for managing the design, production and hybridization of spotted microarrays. Although it can support the widely used glass microarrays and oligo-chips, MAF was designed with the specific idiosyncrasies of Nylon based microarrays in mind. Notably single channel radioactive probes, microarray stripping and reuse, vector control hybridizations and spike-in controls are all natively supported by the software suite. MicroArray Facility is MIAME supportive and dynamically provides feedback on missing annotations to help users estimate effective MIAME compliance. Genomic data such as clone identifiers and gene symbols are also directly annotated by MAF software using standard public resources. The MAGE-ML data format is implemented for full data export. Journalized database operations (audit tracking), data anonymization, material traceability and user/project level confidentiality policies are also managed by MAF. CONCLUSION: MicroArray Facility is a complete data management system for microarray producers and end-users. Particular care has been devoted to adequately model Nylon based microarrays. The MAF system, developed and implemented in both private and academic environments, has proved a robust solution for shared facilities and industry service providers alike

Locality and diel cycling of viral production revealed by a 24 h time course cross-omics analysis in a coastal region of Japan

International audienceViruses infecting microorganisms are ubiquitous and abundant in the ocean. However, it is unclear when and where the numerous viral particles we observe in the sea are produced and whether they are active. To address these questions, we performed time-series analyses of viral metagenomes and microbial metatranscriptomes collected over a period of 24 h at a Japanese coastal site. Through mapping the metatranscriptomic reads on three sets of viral genomes ((i) 878 contigs of Osaka Bay viromes (OBV), (ii) 1766 environmental viral genomes from marine viromes, and (iii) 2429 reference viral genomes), we revealed that all the local OBV contigs were transcribed in the host fraction. This indicates that the majority of viral populations detected in viromes are active, and suggests that virions are rapidly diluted as a result of diffusion, currents, and mixing. Our data further revealed a peak of cyanophage gene expression in the afternoon/dusk followed by an increase of genomes from their virions at night and less-coherent infectious patterns for viruses putatively infecting various groups of heterotrophs. This suggests that cyanophages drive the diel release of cyanobacteria-derived organic matter into the environment and viruses of heterotrophic bacteria might have adapted to the population-specific life cycles of hosts

Deep sequencing of amplified Prasinovirus and host green algal genes from an Indian Ocean transect reveals interacting trophic dependencies and new genotypes

International audienceHigh-throughput sequencing of Prasinovirus DNA polymerase and host green algal (Mamiellophyceae) ribosomal RNA genes was used to analyse the diversity and distribution of these taxa over a ∼10 000 km latitudinal section of the Indian Ocean. New viral and host groups were identified among the different trophic conditions observed, and highlighted that although unknown prasinoviruses are diverse, the cosmopolitan algal genera Bathycoccus, Micromonas and Ostreococcus represent a large proportion of the host diversity. While Prasinovirus communities were correlated to both the geography and the environment, host communities were not, perhaps because the genetic marker used lacked sufficient resolution. Nevertheless, analysis of single environmental variables showed that eutrophic conditions strongly influence the distributions of both hosts and viruses. Moreover, these communities were not correlated, in their composition or specific richness. These observations could result from antagonistic dynamics, such as that illustrated in a prey–predator model, and/or because hosts might be under a complex set of selective pressures. Both of these reasons must be considered to interpret environmental surveys of viruses and hosts, because covariation does not always imply interaction

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2–1.6 μm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104–105 genomes ml−1 for the samples from the photic zone and 102–103 genomes ml−1 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts

Submission of Microarray Data to Public Repositories

The Microarray Gene Expression Data Society believe that the time is right for journals to require that microarray data be deposited in public repositories, as a condition for publicatio

A Holistic Approach to Marine Eco-Systems Biology

With biology becoming quantitative, systems-level studies can now be performed at spatial scales ranging from molecules to ecosystems. Biological data generated consistently across scales can be integrated with physico-chemical contextual data for a truly holistic approach, with a profound impact on our understanding of life [1]–[5]. Marine ecosystems are crucial in the regulation of Earth's biogeochemical cycles and climate [6],[7]. Yet their organization, evolution, and dynamics remain poorly understood [8],[9]. The Tara Oceans project was launched in September 2009 for a 3-year study of the global ocean ecosystem aboard the ship Tara. A unique sampling programme encompassing optical and genomic methods to describe viruses, bacteria, archaea, protists, and metazoans in their physico-chemical environment has been implemented. Starting as a grassroots initiative of a few scientists, the project has grown into a global consortium of over 100 specialists from diverse disciplines, including oceanography, microbial ecology, genomics, molecular, cellular, and systems biology, taxonomy, bioinformatics, data management, and ecosystem modeling. This multidisciplinary community aims to generate systematic, open access datasets usable for probing the morphological and molecular makeup, diversity, evolution, ecology, and global impacts of plankton on the Earth system