The Candida Genome Database (CGD), a community resource for Candida albicans gene and protein information

The Candida Genome Database (CGD) is a new database that contains genomic information about the opportunistic fungal pathogen Candida albicans. CGD is a public resource for the research community that is interested in the molecular biology of this fungus. CGD curators are in the process of combing the scientific literature to collect all C.albicans gene names and aliases; to assign gene ontology terms that describe the molecular function, biological process, and subcellular localization of each gene product; to annotate mutant phenotypes; and to summarize the function and biological context of each gene product in free-text description lines. CGD also provides community resources, including a reservation system for gene names and a colleague registry through which Candida researchers can share contact information and research interests. CGD is publicly funded (by NIH grant R01 DE15873-01 from the NIDCR) and is freely available at http://www.candidagenome.org/

Sequence resources at the Candida Genome Database

The Candida Genome Database (CGD, ) contains a curated collection of genomic information and community resources for researchers who are interested in the molecular biology of the opportunistic pathogen Candida albicans. With the recent release of a new assembly of the C.albicans genome, Assembly 20, C.albicans genomics has entered a new era. Although the C.albicans genome assembly continues to undergo refinement, multiple assemblies and gene nomenclatures will remain in widespread use by the research community. CGD has now taken on the responsibility of maintaining the most up-to-date version of the genome sequence by providing the data from this new assembly alongside the data from the previous assemblies, as well as any future corrections and refinements. In this database update, we describe the sequence information available for C.albicans, the sequence information contained in CGD, and the tools for sequence retrieval, analysis and comparison that CGD provides. CGD is freely accessible at and CGD curators may be contacted by email at [email protected]

Investigation of initiation of gigantic jets connecting thunderclouds to the ionosphere

The initiation of giant electrical discharges called as "gigantic jets" connecting thunderclouds to the ionosphere is investigated by numerical simulation method in this paper. Using similarity relations, the triggering conditions of streamer formation in laboratory situations are extended to form a criterion of initiation of gigantic jets. The energy source causing a gigantic jet is considered due to the quasi-electrostatic field generated by thunderclouds. The electron dynamics from ionization threshold to streamer initiation are simulated by the Monte Carlo technique. It is found that gigantic jets are initiated at a height of ~18-24 km. This is in agreement with the observations. The method presented in this paper could be also applied to the analysis of the initiation of other discharges such as blue jets and red sprites.Comment: 12th International Congress on Plasma Physics, 25-29 October 2004, Nice (France

Anomalous Hall Effect in Ferromagnetic Metals: Role of Phonons at Finite Temperature

The anomalous Hall effect in a multiband tight-binding model is numerically studied taking into account both elastic scattering by disorder and inelastic scattering by the electron-phonon interaction. The Hall conductivity is obtained as a function of temperature $T$, inelastic scattering rate $\gamma$, chemical potential $\mu$, and impurity concentration $x_{\rm imp}$. We find that the new scaling law holds over a wide range of these parameters; $-\sigma_{xy}= (\alpha \sigma_{xx0}^{-1} + \beta \sigma_{xx0}^{-2}) \sigma_{xx}^2 + b$, with $\sigma_{\mu \nu}$ ($\sigma_{\mu \nu 0}$) being the conductivity tensor (with only elastic scattering), which corresponds to the recent experimental observation [Phys. Rev. Lett. {\bf 103} (2009) 087206]. The condition of this scaling is examined. Also, it is found that the intrinsic mechanism depends on temperature under a resonance condition.Comment: 5 figure

Saccharomyces Genome Database provides mutant phenotype data

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is a scientific database for the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker’s or budding yeast. The information in SGD includes functional annotations, mapping and sequence information, protein domains and structure, expression data, mutant phenotypes, physical and genetic interactions and the primary literature from which these data are derived. Here we describe how published phenotypes and genetic interaction data are annotated and displayed in SGD

New tools at the Candida Genome Database: biochemical pathways and full-text literature search

The Candida Genome Database (CGD, http://www.candidagenome.org/) provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. Herein, we describe two recently added features, Candida Biochemical Pathways and the Textpresso full-text literature search tool. The Biochemical Pathways tool provides visualization of metabolic pathways and analysis tools that facilitate interpretation of experimental data, including results of large-scale experiments, in the context of Candida metabolism. Textpresso for Candida allows searching through the full-text of Candida-specific literature, including clinical and epidemiological studies

Schistosoma mansoni Stomatin Like Protein-2 Is Located in the Tegument and Induces Partial Protection against Challenge Infection

Schistosomiasis is a parasitic disease causing serious chronic morbidity in tropical countries. Together with the publication of the transcriptome database, a series of new vaccine candidates were proposed based on their functional classification. However, the prediction of vaccine candidates from sequence information or even by proteomics or microarrays data is somewhat speculative and there remains the considerable task of functional analysis of each new gene/protein. In this study, we present the characterization of one of these molecules, a stomatin like protein 2 (SmStoLP-2). Sequence analysis predicts signals that could contribute to protein membrane association and mitochondrial targeting, which was confirmed by differential extractions of schistosome tegument membranes and mitochondria. Additionally, confocal microscope analysis showed SmStoLP-2 present in the tegument of 7-day-old schistosomula and adult worms. Studies in patients living in endemic areas for schistosomiasis revealed high levels of IgG1, IgG2, IgG3 and IgA anti-SmStoLP-2 antibodies in individuals resistant to reinfection. Recombinant SmStoLP-2 protein, when used as vaccine, induced significant levels of protection in mice. This reduction in worm burden was associated with a typical Th1-type immune response. These results indicate that SmStoLP-2 could be useful in association with other antigens for the composition of a vaccine against schistosomiasis