MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'gene regulation'. Sat, 03 Sep 2011 02:36:36 +0100 http://www.medworm.com/index.php?rid=3585219&cid=t_104862_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2Ffiles%2Fhistone-like-hu-proteins.html%23unique-entry-id-75 Bacterial histone-like HU proteins are critical to maintenance of the nucleoid structure. In addition, they participate in all DNA-dependent functions, including replication, repair, recombination and gene regulation. Their function is typically architectural, inducing a specific DNA topology that promotes assembly of higher-order nucleo-protein structures. Although HU proteins are highly conserved, individual homologs have been shown to exhibit a wide range of different DNA binding specificities and affinities. The existence of such distinct specificities indicates functional evolution and predicts distinct in vivo roles. Emerging evidence suggests that HU proteins discriminate between DNA target sites based on intrinsic flexure, and that two primary features of protein binding contribute... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=3585219 Wed, 19 May 2010 23:00:00 +0100 3585219 http://www.medworm.com/index.php?rid=3487291&cid=t_104862_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FSJN6vdlBV3U%2F A new paper from the Zilberman lab at UC Berkeley shows the application of high throughput sequencing to the study of DNA methylation in eukaryotes.  They generate an huge data set of whole genome methylation patterns in several plants, animals, and five fungi including early diverging Zygomycete. The work was performed using Bisulfite sequencing (Illumina) to capture methylated DNA, RNA-Seq of mRNA. The also performed some ChIP-Seq of H2A.Z on pufferfish to look at the nucleosome positioning in that species. For aligning the reads, they used BowTie to align the bisulfite sequences (though I’d be curious how a new aligner, BRAT, designed for Bisulfite seq reads would perform) to the genome.  They also sequenced mRNA via RNA-Seq to assay gene expression for some of the species. They... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3487291 Tue, 20 Apr 2010 13:00:05 +0100 3487291 http://www.medworm.com/index.php?rid=3460323&cid=t_104862_131_f&fid=34995&url=http%3A%2F%2Fblogs.discovermagazine.com%2Fgnxp%2F2010%2F04%2Fwhen-a-trait-isnt-a-trait-isnt-a-trait%2F One of the great things about evolutionary theory is that it is a formal abstraction of specific concrete aspects of reality and dynamics. It allows us to squeeze inferential juice from incomplete prior knowledge of the state of nature. In other words, you can make predictions and models instead of having to observe every last detail of the natural world. But abstractions, models and formalisms often leave out extraneous details. Sometimes those details turn out not to be so extraneous. Charles Darwin’s original theory of evolution had no coherent or plausible mechanism of inheritance. R. A. Fisher and others imported the empirical reality of Mendelism into the logic of evolutionary theory, to produce the framework of 20th century population genetics. Though accepting the genetic inh... Gene Expression blogs http://www.medworm.com/rss/comments.php?id=3460323 Mon, 12 Apr 2010 13:15:19 +0100 3460323 http://www.medworm.com/index.php?rid=3408573&cid=t_104862_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FGNOX5BmVgp0%2F I spy a picture of Neurospora growing on the cover of Genetics this month.  The cover highlights the results from the work of the lab of Luis Corrochano who works on  light regulation in a variety of systems like Neurospora and Phycomyces.  This work describes their work on the fluffy gene which regulates conidiation (production of conidia or asexual spores). They show that an important interplay between an inducer of light response, the White Collar Complex (WCC), and the FLD protein on fluffy.  The data from indicate hat FLD represses fluffy as a response to dark but that this repression is removed in response to light through the action of WCC. Olmedo, M., Ruger-Herreros, C., & Corrochano, L. (2009). Regulation by Blue Light of the fluffy Gene Encoding a Major Regulator of Co... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3408573 Thu, 25 Mar 2010 21:49:41 +0100 3408573 http://www.medworm.com/index.php?rid=2868676&cid=t_104862_77_f&fid=37259&url=http%3A%2F%2Fwww.horizonpress.com%2Fblogger%2F2009%2F10%2Frnai-gene-therapy-to-control-hiv-1.html RNA interference (RNAi) was discovered as cellular gene regulation mechanism in 1998, but several RNAi-based applications for gene silencing have already made it into clinical trials. RNAi approaches have targeted pathogenic human viruses causing acute or chronic infections. HIV-1 infection has been considered for RNAi-based gene therapy. Viruses like HIV-1 are particularly difficult targets for RNAi-attack because they are escape-prone, which requires combinatorial RNAi strategies to prevent viral escape. The future of antiviral RNAi therapeutics is very promising, but it remains of critical importance to include many controls in pre-clinical test models to unequivocally demonstrate sequence-specific action of the RNAi inducers.Further reading: RNA Interference and Viruses: Current Innova... Microbiology Blog: The weblog for microbiologists. blogs http://www.medworm.com/rss/comments.php?id=2868676 Wed, 07 Oct 2009 15:25:00 +0100 2868676 http://www.medworm.com/index.php?rid=2008505&cid=t_104862_117_f&fid=38158&url=http%3A%2F%2Famericanacupuncture.blogspot.com%2F2008%2F12%2Fgene-regulation-in-cancer.html CANCER GENE REGULATION BY MICRO RNA MicroRNAs  in cancer medicine is a hot field of endeavor today.  Genes are regulated by micro RNAs  (miRNA).   If the microRNA is poorly regulated, it can cause cancer and other diseases.  This advance is useful to make early diagnoses of disease and get new targets for antiviral drugs. MicroRNA is a small noncoding RNA found in eukaryotes.  It has a unique compartment, is rapidly reversible and evolvable.  It is linked to cancer heart disease, diabetes, viral disease and a growing list of other ailments.  Human defects are caused by their deficiency. Five hundred of the 25,000 human genes have microRNAs.  They are the regulators of the master regulator and control the entire pathway of genes. Some diseases have too much micronRNA and their expr... Dr. Needles Medical Blogs blogs http://www.medworm.com/rss/comments.php?id=2008505 Wed, 03 Dec 2008 16:02:00 +0100 2008505 http://www.medworm.com/index.php?rid=1296097&cid=t_104862_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F249938009%2F 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. (more...) © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under aspergillus, evolution, ge... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1296097 Wed, 12 Mar 2008 05:36:25 +0100 1296097 http://www.medworm.com/index.php?rid=1131712&cid=t_104862_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F211799560%2F A study shows how Caffeine regulates alternative splicing in a subset cancer-associated genes including the transcription factor and tumor suppressor KLF6 through the splicing factor SC35.  There is a necessary "caffeine response element" in the intron of KLF6 which plays a role in the splice-site choice, although caffeine induces up-regulation of SC35 and over-expression of SC35 is sufficient to mimic the caffeine response. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under alternative splicing, gene regulation. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1131712 Sat, 05 Jan 2008 22:54:29 +0100 1131712 http://www.medworm.com/index.php?rid=936857&cid=t_104862_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F167287968%2F A recent PLoS One article "A Genetic Code Alteration Is a Phenotype Diversity Generator in the Human Pathogen Candida albicans" finds some pretty dramatic changes in gene expression and phenotypes by replacing the tRNAs for CUG back to Leucine (Leu; in the standard genetic code) from their meaning of Serine (Ser) in these Candida species. The CUG codon transition in some Candida spp has been of interest since it is an example of a recent change in the genetic code and provides a comparative system to study the mechanism and genome changes of how a genetic code shift is manifested. Cite this... (more...) tags: genetic code, genome evolution, candida © Jason Stajich for Fungal Genomes and Comparative Genomics, 2007. | Permalink | No comment Add to del.icio.us Search blogs lin... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=936857 Tue, 09 Oct 2007 05:42:32 +0100 936857 http://www.medworm.com/index.php?rid=769000&cid=t_104862_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F139027077%2F Back from ISMB/ECCB and a mountain of things left undone that somehow still need doing ... including a quick entry about what was interesting at the conference. I heard many good talks and only a few bad ones - maybe I guessed properly in darting between the multiple sessions. The meeting itsself was much better than past ones I had attended. The combination of Special Interest Groups meeting (BOSC, AFP, and Microbial Comparative Genomics being the ones I spent my time in). I got to give my talks and tutorial during the first few days and was able to just try and soak up the rest of the meeting (when my brain wasn't melting from the heat). Particularly good was Carole Goble's presentation on 7-deadly sins of bioinformatics software development. Some general evolutionary talks that I found ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=769000 Tue, 31 Jul 2007 01:03:59 +0100 769000 http://www.medworm.com/index.php?rid=694218&cid=t_104862_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F127716937%2F When first discovered, the gene LaeA was thought to be a master switch for silencing of several NRPS secondary metabolite gene clusters in Aspergillus. NRPS and PKS are important genes in filamentous fungi as they produce many compounds that likely help fungi compete in the ecological niche mycotoxins (e.g. aflatoxin, gliotoxin), plant hormone (e.g. Gibberellin), and a potential wealth of additional undiscovered activities. A recent paper from Nancy Keller’s lab entitled Transcriptional Regulation of Chemical Diversity in Aspergillus fumigatus by LaeA has followed up previous studies with whole genome expression profiling of a LaeA knockout strain to explore the breadth of the genome that is regulated by this transcriptional regulator. (more…) aspergillus, gene cluster, gene fu... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=694218 Mon, 25 Jun 2007 10:41:35 +0100 694218 http://www.medworm.com/index.php?rid=486613&cid=t_104862_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F02%2Fdeeper-and-deeper-down-the-transcriptome-hole-we-fall%2F 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. A great deal of modern biological research explores the regulation of expression of all the genes in a genome, collectively known as the transcriptome. Such studies are, for example, aimed at understanding which genetic regulation events account for the differences between an eye and a fingernail. However, the effectiveness of this research is predicated upon actually knowing which parts of the genome are capable of being expressed and, subsequently, regulated.... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=486613 Tue, 06 Feb 2007 18:42:32 +0100 486613 http://www.medworm.com/index.php?rid=486615&cid=t_104862_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F02%2Fsplicing-machinery-and-introns%2F Splicing of pre-messenger RNA is necessary to remove introns and create well formed and translateable mRNA, but the purpose of introns still remains a mystery. One idea is they provide a role in the error checking machinery, or Nonsense Mediated Decay (NMD), by providing way-points during translation. A protein is deposited at the exon junction complex (EJC) which indicates a splicing event has occurred. During translation, if the ribosome encounters a premature stop (or termination) codon (PTC) and then sees one of these EJC way-points, it signals the corrupted message for degradation. Several predictions come out of these models including the lack of introns in the 3′ UTR and that the average length of exons should be correlated with the window that the proofreading mechanism can ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=486615 Tue, 06 Feb 2007 01:31:35 +0100 486615