Report concludes that a fungal genome database is of “the highest priority”.
This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom.
Report concludes that a fungal genome database is of “the highest priority”.
This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom.
Categories: opinion
Tags: bioinformatics, bioinformatics support, comparative, curation, database, funding, fungal, fungal genome database, fungi, gene, genes, genome, genomes, gmod, maps, news, pathogen, pathogens, protein, pubmed, reporting, reports, research, sequences, sequencing, species, strain, systematics, transcription, transcripts
This month’s Genetics has a series of articles exploring the genome (published last year & freely available at Science) of the green algae [[Chlamydomonas reinhardtii]]. These manuscripts are primarily genome analyses making for a very bioinformatics focused issue of Genetics. Some of the highlights include:
Categories: bioinformatics · comparative · evolution · gene family · genome · genome annotation
Tags: algae, bioinformatics, chlamydamonas, genome, genomes, intron, multicellularity, transcription
Researchers from Technical University of Denmark published some interesting results from comparing expression across the very distinct Aspergillus species.
Kudos also goes to making it Open Access. I am posting a few key figures below the fold because I can! They grew the fungi in bioreactors fermenting glucose or xylose. After calibrating the growth curves they were able to sample the appropriate time points for comparison of gene expression across these three species. They found a set of genes commonly expressed.
Categories: aspergillus · evolution · gene regulation · microarray
Tags: aspergillus, candida, cerevisiae, comparative, development, evolution, fermentation, filamentous, fungi, gene, genes, genome, microarray, saccharomyces, sequencing, solexa, transcription, yeast
The following is an announcement to the B.dendrobatidis and fungal community at large from Alan Kuo at JGI. This is the JAM81 strain (Jess Morgan collected from a frog in the California Sierra Nevada). The JEL423 (Joyce Longcore, collected in Panama) strain genome sequence and annotation is available from the Broad Institute.
Categories: chytridomycota · genome · news
Tags: functional, gene, genes, genome, intron, JGI, methods, news, sequencing, transcription
A paper in PLoS Biology from Sandy Johnson’s lab entitled “Interlocking Transcriptional Feedback Loops Control White-Opaque Switching in Candida albicans” discusses phenotype switching in the human pathogenic fungus Candida albicans. Why is the important?
Categories: candida · development · human pathogen
Tags: candida, cell divisions, differential expression, feedback loops, fungi, fungus candida, master regulator, opaque, pathogen, pathogenic fungus, pathogens, phenotype, transcription
I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.
If there was any theme in the conference it was “Hey we are all using these genome sequences”.
Categories: Fungal Genetics · bioinformatics · chytridomycota · cryptococcus · dothideomycetes · euriotiomycetes · filamentous · glomeromycota · homobasidiomycota · horizontal gene transfer · neurospora · news · sordariomycetes · zygomycete
Tags: annotation, annotations, asilomar, aspergillus, basidiomycete, batrachochytrium, bioinforics, biology, candida, chytrid, clone, comparative, conferences & courses, coprinus, cryptococcus, definitions, development, diversity, ecology, endophyte, enzymes, evolution, experimental, frog, fungal, fungi, fungus, gene, genes, genome, genomes, horizontaltransfer, infection, JGI, maps, MAT, meetings, methods, microarray, microbes, multicellularity, mycological, neurospora, news, NRPS, organisms, pathogen, pathogens, phenotype, philosophy, phylogenetics, plant, plants, podospora, pombe, protein, repeats, rhizopus, RIP, s, saccharomyces, seminar, sequences, sequencing, SOLiD, speciation, species, strain, taxa, transcription, transcripts, wheat, yeast, zygomycete, zygomycetes
Your eye contains the same genetic content as your fingernail, but these two tissues look nothing alike. One significant cause of this difference is the tissue specific regulation of the genes in the genome. In some tissues in your body, a gene may be expressed (transcribed) while that same gene may be silent in another tissue type.
Categories: fungi · gene regulation · genome · journal club · magnaporthe · methods · transcription
Tags: fungi, gene regulation, genome, journal club, magnaporthe, methods, transcription
A recent paper describes the discovery of 9 new introns in Saccharomyces cerevisiae by Ron Davis’s group at Stanford, using high density tiling arrays from Affymetrix. The arrays are designed for both strands allow the detection of transcripts transcribed from both strands. The arrays were also put to work by the Davis and [...]
Categories: microarray · saccharomyces · tiling array · transcription
Tags: algorithm, annotation, annotations, cerevisiae, clone, cryptococcus, fungi, gene, genes, genome, genomes, hybrid, hybridization, intron, maps, microarray, news, parents, polymorphism, qtl, sequence, sequences, sequencing, species, tiling array, transcription, transcripts, yeast