MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Briefings in Functional Genomics and Proteomics' source. Sat, 20 Mar 2010 15:46:57 +0100 http://www.medworm.com/index.php?rid=3351300&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20211968%26dopt%3DAbstract Authors: Wimmers K, Murani E, Ponsuksili S The benefit of functional genomics is to identify key pathways and functional networks of genes and candidate genes underlying the genetic control of phenotypes. Genetical genomics, i.e. the integration of genetic analysis and expression phenotypes, has the potential to uncover regulatory networks controlling the coordinated expression of genes and to map variation on the level of DNA affecting the mRNA expression. Here we illustrate our own attempts to apply functional genomics and genetical genomics approaches in order to identify functional networks of genes relevant to traits related to meat performance. Expression data of 74 M longissimus dorsi samples obtained using Affymetrix GeneChips were correlated with drip loss and principal compon... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3351300 Mon, 08 Mar 2010 00:00:00 +0100 3351300 http://www.medworm.com/index.php?rid=3284208&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20156985%26dopt%3DAbstract The objectives of this article are to review essential aspects of GS and summarize the important take-home messages from recent theoretical, simulation and empirical studies. We then look forward and consider research needs surrounding methodological questions and the implications of GS for long-term selection. PMID: 20156985 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3284208 Mon, 15 Feb 2010 00:00:00 +0100 3284208 http://www.medworm.com/index.php?rid=3244252&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20130067%26dopt%3DAbstract Authors: Wang L, Li P, Brutnell TP Ultra high-throughput sequencing (UHTS) technologies offer the potential to interrogate transcriptomes in detail that has traditionally been restricted to single gene surveys. For instance, it is now possible to globally define transcription start sites, polyadenylation signals, alternative splice sites and generate quantitative data on gene transcript accumulation in single tissues or cell types. These technologies are thus paving the way for whole genome transcriptomics and will undoubtedly lead to novel insights into plant development and biotic and abiotic stress responses. However, several challenges exist to making this technology broadly accessible to the plant research community. These include the current need for a computationally intensive a... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3244252 Wed, 03 Feb 2010 00:00:00 +0100 3244252 http://www.medworm.com/index.php?rid=3223740&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20110271%26dopt%3DAbstract Authors: Figueroa DM, Bass HW Plant cytogenetics has continued to flourish and make essential contributions to genomics projects by delineating marker order, defining contig gaps and revealing genome rearrangements. Here we review the field of plant cytogenetics from its conception through the eras of molecular biology and genomics. Significant advances in chromosome preparation, such as extended fiber-FISH, have greatly increased the axial resolution limits, while imaging and signal amplification technologies have improved our ability to detect small gene-sized probes. Combinations of traditional FISH technologies with chromatin immunocytochemistry serve to broaden the ability of plant cytogenetics to shed light on genome structure and organization. These advances are described, toget... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3223740 Wed, 27 Jan 2010 00:00:00 +0100 3223740 http://www.medworm.com/index.php?rid=3200753&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20093306%26dopt%3DAbstract Authors: Deblasio SL, Sylvester AW, Jackson D First discovered in jellyfish, fluorescent proteins (FPs) have been successfully optimized for use as effective biomarkers within living plant cells. When exposed to light, FPs fused to a protein or regulatory element will fluoresce, and non-invasively mark expression and protein localization, which allows for the in vivo monitoring of diverse cellular processes. In this review, we discuss how FP technology has evolved from small-scale analysis of individual genes to more high-throughput techniques for global expression and functional profiling in plants. PMID: 20093306 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3200753 Thu, 21 Jan 2010 00:00:00 +0100 3200753 http://www.medworm.com/index.php?rid=3186042&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20081216%26dopt%3DAbstract Authors: Baxter I Ionomics is the study of elemental accumulation in living systems using high-throughput elemental profiling. This approach has been applied extensively in plants for forward and reverse genetics, screening diversity panels, and modeling of physiological states. In this review, I will discuss some of the advantages and limitations of the ionomics approach as well as the important parameters to consider when designing ionomics experiments, and how to evaluate ionomics data. PMID: 20081216 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3186042 Sat, 16 Jan 2010 00:00:00 +0100 3186042 http://www.medworm.com/index.php?rid=3186040&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20081217%26dopt%3DAbstract Authors: Nowick K, Stubbs L Nature is replete with examples of diverse cell types, tissues and body plans, forming very different creatures from genomes with similar gene complements. However, while the genes and the structures of proteins they encode can be highly conserved, the production of those proteins in specific cell types and at specific developmental time points might differ considerably between species. A full understanding of the factors that orchestrate gene expression will be essential to fully understand evolutionary variety. Transcription factor (TF) proteins, which form gene regulatory networks (GRNs) to act in cooperative or competitive partnerships to regulate gene expression, are key components of these unique regulatory programs. Although many TFs are conserved in ... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3186040 Sat, 16 Jan 2010 00:00:00 +0100 3186040 http://www.medworm.com/index.php?rid=3186035&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20081218%26dopt%3DAbstract Authors: Gilchrist E, Haughn G Genetic analysis represents a powerful tool that establishes a direct link between the biochemical function of a gene product and its role in vivo. Genome sequencing projects have identified large numbers of plant genes for which no role has yet been defined. To address this problem a number of techniques have been developed, over the last 15 years, to enable researchers to identify plants with mutations in genes of known sequence. These reverse genetic approaches include RNAi and related technologies and screening of populations mutagenised by insertion (PCR), deletion (PCR) and point mutation (TILLING), each with its own strengths and weaknesses. The development of next-generation sequencing techniques now allows such screening to be done by sequencing.... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3186035 Sat, 16 Jan 2010 00:00:00 +0100 3186035 http://www.medworm.com/index.php?rid=3168249&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20064859%26dopt%3DAbstract Authors: Hegeman AD Plant metabolomics has benefited from a rich array of pre-existing methodological approaches and bioanalytical knowledge for the characterization of the many chemically diverse classes of metabolites. While the field has pushed the implementation of unbiased and generally applicable strategies for metabolite extraction, fractionation and detection, significant challenges in fundamental activities such as compound identification and quantification still exist. This review provides an introduction to metabolomics terminology, methods and resources and discusses analytical limitations. Progress in the application of stable isotope dilution and stable isotopic metabolic labeling to metabolite identification and quantification are discussed. New strategies to address spa... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3168249 Mon, 11 Jan 2010 00:00:00 +0100 3168249 http://www.medworm.com/index.php?rid=3157716&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20056723%26dopt%3DAbstract This article gives an overview of experimental and computational techniques for identifying and analyzing protein phosphorylation on a systems level. PMID: 20056723 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3157716 Thu, 07 Jan 2010 00:00:00 +0100 3157716 http://www.medworm.com/index.php?rid=3153831&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20053813%26dopt%3DAbstract Authors: Savas JN, Tanese N While initiation of transcription has attracted the most attention in the field of gene regulation, it has become clear that additional stages in the gene expression cascade including post-transcriptional events are under equally exquisite control. The seminal discovery that short RNAs (microRNA, small interfering RNA, Piwi-interacting RNA), play important roles in repressing gene expression has spurred a rush of new interest in post-transcriptional gene silencing mechanisms. The development of affinity tags and high-resolution tandem mass spectrometry (MS/MS) has greatly simplified the analysis of proteins that regulate gene expression. Further, the use of DNA microarrays and 'second generation' nucleic acid sequencing ('deep sequencing') technologies has f... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3153831 Wed, 06 Jan 2010 00:00:00 +0100 3153831 http://www.medworm.com/index.php?rid=3153830&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20053814%26dopt%3DAbstract Authors: Ni Z, Lee SS Our understanding of the genetic mechanisms of organismal aging has advanced dramatically during the past two decades. With the development of large-scale RNAi screens, the last few years saw the remarkable identifications of hundreds of new longevity genes in the roundworm Caenorhabditis elegans. The various RNAi screens revealed many biological pathways previously unknown to be related to aging. In this review, we focus on findings from the recent large-scale RNAi longevity screens, and discuss insights they have provided into the complex biological process of aging and considerations of the RNAi technology will continue to have on the future development of the aging field. PMID: 20053814 [PubMed - as supplied by publisher] (Source: Briefings in Functional G... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3153830 Wed, 06 Jan 2010 00:00:00 +0100 3153830 http://www.medworm.com/index.php?rid=3153829&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20053815%26dopt%3DAbstract Authors: Hall D, Tegström C, Ingvarsson PK Association or linkage disequilibrium mapping has become a very popular method for dissecting the genetic basis of complex traits in plants. The benefits of association mapping, compared with traditional quantitative trait locus mapping, is, for example, a relatively detailed mapping resolution and that it is far less time consuming since no mapping populations need to be generated. The surge of interest in association mapping has been fueled by recent developments in genomics that allows for rapid identification and scoring of genetic markers which has traditionally limited mapping experiments. With the decreasing cost of genotyping future emphasis will likely focus on phenotyping, which can be both costly and time consuming but which is... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3153829 Wed, 06 Jan 2010 00:00:00 +0100 3153829 http://www.medworm.com/index.php?rid=3153828&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20053816%26dopt%3DAbstract Authors: McGinnis KM RNAi refers to several different types of gene silencing mediated by small, dsRNA molecules. Over the course of 20 years, the scientific understanding of RNAi has developed from the initial observation of unexpected expression patterns to a sophisticated understanding of a multi-faceted, evolutionarily conserved network of mechanisms that regulate gene expression in many organisms. It has also been developed as a genetic tool that can be exploited in a wide range of species. Because transgene-induced RNAi has been effective at silencing one or more genes in a wide range of plants, this technology also bears potential as a powerful functional genomics tool across the plant kingdom. Transgene-induced RNAi has indeed been shown to be an effective mechanism for silenci... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3153828 Wed, 06 Jan 2010 00:00:00 +0100 3153828 http://www.medworm.com/index.php?rid=3102416&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20008400%26dopt%3DAbstract Authors: Arda HE, Walhout AJ Differential gene expression plays a critical role in the development and physiology of multicellular organisms. At a 'systems level' (e.g. at the level of a tissue, organ or whole organism), this process can be studied using gene regulatory network (GRN) models that capture physical and regulatory interactions between genes and their regulators. In the past years, significant progress has been made toward the mapping of GRNs using a variety of experimental and computational approaches. Here, we will discuss gene-centered approaches that we employed to characterize GRNs and describe insights that we have obtained into the global design principles of gene regulation in complex metazoan systems. PMID: 20008400 [PubMed - as supplied by publisher] (Source: ... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3102416 Sun, 13 Dec 2009 00:00:00 +0100 3102416 http://www.medworm.com/index.php?rid=3056023&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19952073%26dopt%3DAbstract Authors: Mattila J, Puig O RNA interference (RNAi) is a powerful method to unravel the role of a given gene in eukaryotic cells. The development of high throughput assay platforms such as fluorescence plate readers and high throughput microscopy has allowed the design of genome wide RNAi screens to systemically discern members of regulatory networks around various cellular processes. Here we summarize the different strategies employed in RNAi screens to reveal regulators of transcriptional networks. We focus our discussion in experimental approaches designed to uncover regulatory interactions modulating transcription factor activity. PMID: 19952073 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3056023 Tue, 01 Dec 2009 00:00:00 +0100 3056023 http://www.medworm.com/index.php?rid=3056022&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19952074%26dopt%3DAbstract Authors: Kainth P, Andrews B In the last decade or so, advances in genome-scale technologies have allowed systematic and detailed analysis of gene function. The experimental accessibility of budding yeast makes it a test-bed for technology development and application of new functional genomic tools and resources that pave the way for comparable efforts in higher eukaryotes. In this article, we review advances in reporter screening technology to discover trans-acting regulators of promoters (or cis-elements) of interest in the context of a novel functional genomics approach called Reporter Synthetic Genetic Array (R-SGA) analysis. We anticipate that this methodology will enable researchers to collect quantitative data on hundreds of gene expression pathways in an effort to better unders... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=3056022 Tue, 01 Dec 2009 00:00:00 +0100 3056022 http://www.medworm.com/index.php?rid=2900221&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19833697%26dopt%3DAbstract Authors: Griffiths-Jones S PMID: 19833697 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2900221 Sat, 17 Oct 2009 12:46:15 +0100 2900221 http://www.medworm.com/index.php?rid=2900220&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19833698%26dopt%3DAbstract Authors: van Bakel H, Hughes TR The last decade has seen an explosion of interest in new classes of non-coding RNA. While some are now firmly established as new categories of legitimate functional RNAs, the purpose and even existence of others remain to be solidified. Here, we discuss the challenges associated with discovery and characterization of non-traditional categories of non-coding RNA. PMID: 19833698 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2900220 Sat, 17 Oct 2009 12:46:12 +0100 2900220 http://www.medworm.com/index.php?rid=2900219&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19833699%26dopt%3DAbstract Authors: Forrest AR, Abdelhamid RF, Carninci P Non-coding RNA (ncRNA) transcripts are RNA molecules that do not code for proteins, but elicit function by other mechanisms. The vast majority of RNA produced in a cell is non-coding ribosomal RNA, produced from relatively few loci, however more recently complementary DNA (cDNA) cloning, tag sequencing, and genome tiling array studies suggest that ncRNAs also account for the majority of RNA species produced by a cell. ncRNA based regulation has been referred to as a 'hidden layer' of signals or 'dark matter' that control gene expression in cellular processes by poorly described mechanisms. These terms have appeared as ncRNAs until recently have been ignored by expression profiling and cDNA annotation projects and their mode of action is di... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2900219 Sat, 17 Oct 2009 12:46:10 +0100 2900219 http://www.medworm.com/index.php?rid=2900218&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19833700%26dopt%3DAbstract Authors: Gardner PP In this review we discuss bioinformatic issues in non-coding RNA analysis, in particular the annotation of genome sequences using covariance models. Some recent innovations for improving the speed and accuracy of covariance models is discussed. PMID: 19833700 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2900218 Sat, 17 Oct 2009 12:46:07 +0100 2900218 http://www.medworm.com/index.php?rid=2900213&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19833701%26dopt%3DAbstract Authors: Bernhart SH, Hofacker IL Reliable structure prediction is a prerequisite for most types of bioinformatical analysis of RNA. Since the accuracy of structure prediction from single sequences is limited, one often resorts to computing the consensus structure for a set of related RNA sequences. Since functionally important RNA structures are expected to evolve much more slowly than the underlying sequences, the pattern of sequence (co-)variation can be exploited to dramatically improve structure prediction. Since a conserved common structure is only expected when the RNA structure is under selective pressure, consensus structure prediction also provides an ideal starting point for the de novo detection of structured non-coding RNAs. Here, we review different strategies for the pre... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2900213 Sat, 17 Oct 2009 12:46:05 +0100 2900213 http://www.medworm.com/index.php?rid=2834707&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19779009%26dopt%3DAbstract Authors: Mosig A, Zhu L, Stadler PF A large fraction of non-coding RNAs is short and/or poorly conserved in sequence. Most of the longer examples, furthermore, consist of a collection of conserved structural motifs rather than a coherent globally conserved secondary structure. As a consequence, the conceptually simple problem of homology search becomes a complex and technically demanding task. Despite the best efforts of databases such as Rfam, the situation is complicated further by the sparsity of information in many-in particular prokaryotic-RNA families. In this contribution, we review recent efforts to customize sequence-based search tools for ncRNA applications. In particular, semi-global alignments and the development of methods for fragmented pattern search have brought signifi... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2834707 Wed, 23 Sep 2009 23:00:00 +0100 2834707 http://www.medworm.com/index.php?rid=2828825&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19770204%26dopt%3DAbstract Authors: Dinger ME, Amaral PP, Mercer TR, Mattick JS Genome-wide analyses of the eukaryotic transcriptome have revealed that the majority of the genome is transcribed, producing large numbers of non-protein-coding RNAs (ncRNAs). This surprising observation challenges many assumptions about the genetic programming of higher organisms and how information is stored and organized within the genome. Moreover, the rapid advances in genomics have given little opportunity for biologists to integrate these emerging findings into their intellectual and experimental frameworks. This problem has been compounded by the perception that genome-wide studies often generate more questions than answers, which in turn has led to confusion and controversy. In this article, we address common questions assoc... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2828825 Sun, 20 Sep 2009 23:00:00 +0100 2828825 http://www.medworm.com/index.php?rid=2779389&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19737800%26dopt%3DAbstract We describe the use of several statistical models in copy number detection in germline samples. We also present a comparison of data using these methods to assess accuracy of prediction and detection of changes in copy number. PMID: 19737800 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2779389 Mon, 07 Sep 2009 23:00:00 +0100 2779389 http://www.medworm.com/index.php?rid=2770325&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19729447%26dopt%3DAbstract Authors: Mourier T, Willerslev E Retrotransposons constitute a significant fraction of mammalian genomes. Considering the finding of widespread transcriptional activity across entire genomes, it is not surprising that retrotransposons contribute to the collective RNA pool. However, the transcriptional output from retrotransposons does not merely represent spurious transcription. We review examples of functional RNAs transcribed from retrotransposons, and address the collection of non-protein coding RNAs derived from transposable element sequences, including numerous human microRNAs and the neuronal BC RNAs. Finally, we review the emerging understanding of how retrotransposons themselves are regulated by small RNAs. PMID: 19729447 [PubMed - as supplied by publisher] (Source: Briefin... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2770325 Wed, 02 Sep 2009 23:00:00 +0100 2770325 http://www.medworm.com/index.php?rid=2674602&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19651703%26dopt%3DAbstract Authors: Chopra VS, Levine M The classical concept of the morphogen gradient proposes that small differences in the levels of a signalling molecule or transcription factor are responsible for producing a continuous spectrum of distinctive cellular identities across a naïve field of cells. In this review, we discuss how the Dorsal gradient controls the dorsal-ventral patterning of the early Drosophila embryo. This gradient extends from the ventral midline of the embryo into dorso-lateral regions, encompassing a cross-sectional field of approximately 20 cells. There is no evidence that these cells acquire distinctive identities due to subtle changes in the nuclear concentrations of the Dorsal protein. Rather, a variety of evidence suggests that the Dorsal gradient generates just thr... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2674602 Sun, 02 Aug 2009 23:00:00 +0100 2674602 http://www.medworm.com/index.php?rid=2674601&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19651704%26dopt%3DAbstract Authors: Naville M, Gautheret D Premature termination of transcription, or attenuation, is an efficient RNA-based regulatory strategy that is commonly used in bacterial organisms. Attenuators are generally located in the 5' untranslated regions of genes or operons and combine a Rho-independent terminator, controlling transcription, with an RNA element that senses specific environmental signals. A striking diversity of sensing elements enable regulation of gene expression in response to multiple environmental conditions, including temperature changes, availability of small metabolites (such as ions, amino acids, nucleobases or vitamins), or availability of macromolecules such as tRNAs and regulatory proteins. The wide distribution of attenuators suggests an early emergence among bacteri... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2674601 Sun, 02 Aug 2009 23:00:00 +0100 2674601 http://www.medworm.com/index.php?rid=2674600&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19651705%26dopt%3DAbstract Authors: Jiménez-Delgado S, Pascual-Anaya J, Garcia-Fernàndez J The discovery that most regulatory genes were conserved among animals from distant phyla challenged the ideas that gene duplication and divergence of homologous coding sequences were the basis for major morphological changes in metazoan evolution. In recent years, however, the interest for the roles, conservation and changes of non-coding sequences grew-up in parallel with genome sequencing projects. Presently, many independent studies are highlighting the importance that subtle changes in cis-regulatory regions had in the evolution of morphology trough the Animal Kingdom. Here we will show and discuss some of these studies, and underscore the future of cis-Evo-Devo research. Nevertheless, we would also explore h... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2674600 Sun, 02 Aug 2009 23:00:00 +0100 2674600 http://www.medworm.com/index.php?rid=2658433&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19641088%26dopt%3DAbstract Authors: Schwach F, Moxon S, Moulton V, Dalmay T RNA silencing is a complex and highly conserved regulatory mechanism that is now known to be involved in such diverse processes as development, pathogen control, genome maintenance and response to environmental changes. Since its recent discovery, RNA silencing has become a fast moving key area of research in plant and animal molecular biology. Research in this field has greatly profited from recent developments in novel sequencing technologies that allow massive parallel sequencing of small RNA (sRNA) molecules, the key players of all RNA silencing phenomena. As researchers are beginning to decipher the complexity of RNA silencing, novel methodologies have to be developed to make sense of the large amounts of data that are currently bei... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2658433 Tue, 28 Jul 2009 23:00:00 +0100 2658433 http://www.medworm.com/index.php?rid=2658432&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19641089%26dopt%3DAbstract Authors: Epstein DJ Cis-acting regulatory sequences are required for the proper temporal and spatial control of gene expression. Variation in gene expression is highly heritable and a significant determinant of human disease susceptibility. The diversity of human genetic diseases attributed, in whole or in part, to mutations in non-coding regulatory sequences is on the rise. Improvements in genome-wide methods of associating genetic variation with human disease and predicting DNA with cis-regulatory potential are two of the major reasons for these recent advances. This review will highlight select examples from the literature that have successfully integrated genetic and genomic approaches to uncover the molecular basis by which cis-regulatory mutations alter gene expression and contri... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2658432 Tue, 28 Jul 2009 23:00:00 +0100 2658432 http://www.medworm.com/index.php?rid=2614484&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19605518%26dopt%3DAbstract Authors: Fredman D, Engström PG, Lenhard B Regulatory elements can affect specific genes from megabase distances, often from within or beyond unrelated neighbouring genes. The task of computational charting of regulatory inputs in the genome can be approached from several directions. Typically, computational identification of putative regulatory elements for a gene of interest requires tools that will aid in estimating the extent of the (potentially vast) genomic region around the gene that is likely to contain regulatory elements, as well as tools for the identification and characterization of individual elements. Conversely, starting from a putative regulatory element or a regulatory variation in a non-coding region, one often wants to associate the regulatory element with the c... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2614484 Tue, 14 Jul 2009 23:00:00 +0100 2614484 http://www.medworm.com/index.php?rid=2607048&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19596743%26dopt%3DAbstract Authors: Kleinjan DJ, Coutinho P The spatiotemporally and quantitatively correct activity of a gene requires the presence of intact coding sequence as well as properly functioning regulatory control. One of the great challenges of the post-genome era is to gain a better understanding of the mechanisms of gene control. Proper gene regulation depends not only on the required transcription factors and associated complexes being present (in the correct dosage), but also on the integrity, chromatin conformation and nuclear positioning of the gene's chromosomal segment. Thus, when either the cis-trans regulatory system of a gene or the normal context of its chromatin structure are disrupted, gene expression may be adversely affected, potentially leading to disease. As transcriptional regulat... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2607048 Sun, 12 Jul 2009 23:00:00 +0100 2607048 http://www.medworm.com/index.php?rid=2571881&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19571035%26dopt%3DAbstract Authors: Panoutsopoulou K, Zeggini E The identification of complex disease susceptibility loci has been accelerated considerably by advances in high-throughput genotyping technologies, improved insight into correlation patterns of common variants and the availability of large-scale sample sets. Linkage scans and small-scale candidate gene studies have now given way to genome-wide association scans. In this review, we summarize insights gained from the past, highlight practical issues relating to the design and analysis of current state-of-the-art GWA studies and look into future trends in the field of human complex trait genetics. PMID: 19571035 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2571881 Tue, 30 Jun 2009 23:00:00 +0100 2571881 http://www.medworm.com/index.php?rid=2556519&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19561171%26dopt%3DAbstract Authors: Navratilova P, Becker TS Despite a recent explosion in the production of vertebrate genome sequence data and large-scale efforts to completely annotate the human genome, we still have scant knowledge of the principles that built vertebrate genomes in evolution, and of genome architecture and its functional significance. We review approaches using bioinformatics, zebrafish transgenesis, and recent findings in the molecular basis of gene regulation and tie these in with mechanisms for the maintenance of long-range conserved synteny across all vertebrate genomes. Specifically, we discuss the recently discovered genomic regulatory blocks which we argue are principal units of vertebrate genome evolution and serve as the foundations onto which evolutionary innovations are built thro... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2556519 Thu, 25 Jun 2009 23:00:00 +0100 2556519 http://www.medworm.com/index.php?rid=2542727&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19535508%26dopt%3DAbstract Authors: Hurd PJ, Nelson CJ Several recent studies from the field of epigenetics have combined chromatin-immunoprecipitation (ChIP) with next-generation high-throughput sequencing technologies to describe the locations of histone post-translational modifications (PTM) and DNA methylation genome-wide. While these reports begin to quench the chromatin biologists thirst for visualizing where in the genome epigenetic marks are placed, they also illustrate several advantages of sequencing based genomics compared to microarray analysis. Accordingly, next-generation sequencing (NGS) technologies are now challenging microarrays as the tool of choice for genome analysis. The increased affordability of comprehensive sequence-based genomic analysis will enable new questions to be addressed in man... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2542727 Wed, 24 Jun 2009 23:00:00 +0100 2542727 http://www.medworm.com/index.php?rid=2542730&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19535505%26dopt%3DAbstract Authors: Theo Sijtse Palstra RJ The transcriptional output of genes in higher eukaryotes is frequently modulated by cis-regulatory DNA elements like enhancers. On the linear chromatin template these elements can be located hundreds of kilobases away from their target gene and for a long time it was a mystery how these elements communicate. For example, in the beta-globin locus the main regulatory element, the Locus Control Region (LCR), is located up to 40-60 kb away from the beta-globin genes. Recently it was demonstrated that the LCR resides in close proximity to the active beta-globin genes while the intervening inactive chromatin loops out. Thus the chromatin fibre of the beta-globin locus adopts an erythroid-specific spatial organization referred to as the Active Chromatin Hub (AC... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2542730 Tue, 16 Jun 2009 23:00:00 +0100 2542730 http://www.medworm.com/index.php?rid=2542729&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19535506%26dopt%3DAbstract Authors: Kubo A, Imai KS, Satou Y Ascidians belong to the subphylum Urochordata or Tunicata, which is the sister group of the vertebrates. The simple architecture of the ascidian larva represents the basic chordate body plan. Recent analyses have shown many instances of developmental mechanisms conserved during evolution, while these studies have also revealed a much larger number of instances of divergence. However, to precisely determine the degree of conservation and divergence, that is, how many ways are used to make tadpole-like larvae, we need a systems-level understanding of development. Because animal development is organized by the genome and the minimal functional unit of development is a cell, comprehensiveness and single-cell resolution are necessary for a systems-biologica... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2542729 Tue, 16 Jun 2009 23:00:00 +0100 2542729 http://www.medworm.com/index.php?rid=2542728&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19535507%26dopt%3DAbstract We present a historical overview of the genetic studies carried out on populations from this region in order to understand the influence of geographic, linguistic and religious factors on population diversity in this region, and discuss future prospects in light of developments in high throughput genotyping and next generation sequencing technologies. PMID: 19535507 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2542728 Tue, 16 Jun 2009 23:00:00 +0100 2542728 http://www.medworm.com/index.php?rid=2542731&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19498043%26dopt%3DAbstract Authors: Narlikar L, Ovcharenko I Proper development and functioning of an organism depends on precise spatial and temporal expression of all its genes. These coordinated expression-patterns are maintained primarily through the process of transcriptional regulation. Transcriptional regulation is mediated by proteins binding to regulatory elements on the DNA in a combinatorial manner, where particular combinations of transcription factor binding sites establish specific regulatory codes. In this review, we survey experimental and computational approaches geared towards the identification of proximal and distal gene regulatory elements in the genomes of complex eukaryotes. Available approaches that decipher the genetic structure and function of regulatory elements by exploiting various s... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2542731 Wed, 03 Jun 2009 23:00:00 +0100 2542731 http://www.medworm.com/index.php?rid=2542733&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19474126%26dopt%3DAbstract Authors: Bacher U, Kohlmann A, Haferlach T Considering the heterogeneity of leukaemias and the widening spectrum of therapeutic strategies, novel diagnostic methods are urgently needed for haematological malignancies. For a decade, gene expression profiling (GEP) has been applied in leukaemia research. Thus, various studies demonstrated worldwide that the majority of genetically defined leukaemia subtypes are accurately predictable by GEP, for example, with respect to reciprocal rearrangements in acute myeloid leukaemia (AML). Moreover, novel prognostically relevant gene classifiers were developed as, for example, in normal karyotype AML. Considering the lymphatic malignancies, GEP studies defined novel clinically relevant subtypes in diffuse large B cell lymphoma (DLBCL), and improved... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2542733 Tue, 26 May 2009 23:00:00 +0100 2542733 http://www.medworm.com/index.php?rid=2542732&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19474127%26dopt%3DAbstract Authors: Hey Y, Pepper SD The last 10 years have seen microarrays go from being a nascent technology available only in a limited range of research facilities to becoming a ubiquitous approach to expression profiling. Developments in microarray technology have allowed the content of arrays to increase to the point that complete transcriptomes can be assayed on a single array, whilst developments in RNA labelling technology have reduced the amount of RNA needed down to the point where single cell profiling is technically possible. Recently it has also become possible to generate expression data from formalin-fixed paraffin-embedded archival samples. With the range of samples that can now be successfully profiled by microarray analysis this should be a good time to be running a microarray... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2542732 Tue, 26 May 2009 23:00:00 +0100 2542732 http://www.medworm.com/index.php?rid=2542734&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19468039%26dopt%3DAbstract Authors: Vandiedonck C, Knight JC Since its discovery more than 50 years ago, the human Major Histocompatibility Complex (MHC) on chromosome 6p21.3 has been at the forefront of human genetic research. Here, we review from a historical perspective the major advances in our understanding of the nature and consequences of genetic variation which have involved the MHC, as well as highlighting likely future directions. As a consequence of its particular genomic structure, its remarkable polymorphism and its early implication in numerous diseases, the MHC has been considered as a model region for genomics, being the first substantial region to be sequenced and establishing fundamental concepts of linkage disequilibrium, haplotypic structure and meiotic recombination. Recently, the MHC became... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2542734 Sun, 24 May 2009 23:00:00 +0100 2542734 http://www.medworm.com/index.php?rid=2320621&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19351682%26dopt%3DAbstract Authors: Gao Y, Holland RD, Yu LR The emerging field of toxicoproteomics has been greatly advanced by quantitative proteomic technologies and their increasing applications in toxicology. The discipline is focused on the proteomic study of toxicity caused by toxic substances, including but not limited to drugs, toxins, environmental stressors, chemicals and any other materials that induce significant pathological responses. Drug safety is a major point of concern during the development phase and clinical application. Identification of toxicity biomarkers, potential drug targets and characterization of toxicity mechanisms represent major research areas for quantitative toxicoproteomics during drug development and evaluation. Further development and application of quantitative proteomic a... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2320621 Tue, 07 Apr 2009 04:00:00 +0100 2320621 http://www.medworm.com/index.php?rid=2267288&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19282470%26dopt%3DAbstract Authors: Sanderson CM One of the greatest challenges of the post-genomic era is the construction of a more comprehensive human protein interaction map. While this process may take many years to complete, the development of stringent high throughput techniques and the emergence of complementary assays mean that the aim of building a detailed binary map of the human interactome is now a very realistic goal. In particular, methods which facilitate the analysis of large numbers of membrane-protein interactions mean that it will be possible to construct more extensive networks, which in turn provide new insights into the functional connectivity between intra- and extra-cellular processes. This is important as many therapeutic strategies are designed to elicit effects via 'tractable' cell-su... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2267288 Thu, 12 Mar 2009 04:00:00 +0100 2267288 http://www.medworm.com/index.php?rid=2267356&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19279070%26dopt%3DAbstract We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses. PMID: 19279070 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2267356 Wed, 11 Mar 2009 04:00:00 +0100 2267356 http://www.medworm.com/index.php?rid=2267338&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19279071%26dopt%3DAbstract Authors: Yocum AK, Chinnaiyan AM Quantitative targeted proteomics has recently taken front stage in the proteomics community. Centered on multiple reaction monitoring-mass spectrometry (MRM-MS) methodologies, quantitative targeted proteomics is being used in the verification of global proteomics data, the discovery of lower abundance proteins, protein post-translational modifications, discrimination of select highly homologous protein isoforms and as the final step in biomarker discovery. An older methodology utilized with small molecule analysis, the proteomics community is making great technological strides to develop MRM-MS as the next method to address previously challenging issues in global proteomics experimentation, namely dynamic range, identification of post-translational modi... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2267338 Wed, 11 Mar 2009 04:00:00 +0100 2267338 http://www.medworm.com/index.php?rid=2267311&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19279072%26dopt%3DAbstract Authors: Meyer M, Vilardell J Removal of introns during pre-mRNA splicing is a critical process in gene expression, and understanding its control at both single-gene and genomic levels is one of the great challenges in Biology. Splicing takes place in a dynamic, large ribonucleoprotein complex known as the spliceosome. Combining Genetics and Biochemistry, Saccharomyces cerevisiae provides insights into its mechanisms, including its regulation by RNA-protein interactions. Recent genome-wide analyses indicate that regulated splicing is broad and biologically relevant even in organisms with a relatively simple intronic structure, such as yeast. Furthermore, the possibility of coordination in splicing regulation at genomic level is becoming clear in this model organism. This should provide... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2267311 Wed, 11 Mar 2009 04:00:00 +0100 2267311 http://www.medworm.com/index.php?rid=2255564&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19273537%26dopt%3DAbstract This article provides a summary of technologies, potential clinical applications, and challenges of omics in head and neck cancer. PMID: 19273537 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2255564 Mon, 09 Mar 2009 04:00:00 +0100 2255564 http://www.medworm.com/index.php?rid=2117182&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19151093%26dopt%3DAbstract Authors: Ye X, Luke B, Andresson T, Blonder J A variety of stable isotope labeling techniques have been developed and used in mass spectrometry (MS)-based proteomics, primarily for relative quantitation of changes in protein abundances between two compared samples, but also for qualitative characterization of differentially labeled proteomes. Differential (16)O/(18)O coding relies on the (18)O exchange that takes place at the C-terminal carboxyl group of proteolytic fragments, where two (16)O atoms are typically replaced by two (18)O atoms by enzyme-catalyzed oxygen-exchange in the presence of H(2)(18)O. The resulting mass shift between differentially labeled peptide ions permits identification, characterization and quantitation of proteins from which the peptides are proteolytically g... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2117182 Fri, 16 Jan 2009 05:00:00 +0100 2117182 http://www.medworm.com/index.php?rid=2066113&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19109305%26dopt%3DAbstract Authors: Ye X, Blonder J, Veenstra TD The rapid rise and application of proteomic technologies has resulted in an exponential increase in the number of proteins that have been discovered and presented as 'potential' biomarkers for specific diseases. Unfortunately, the number of biomarkers approved for use by the Food and Drug Administration has not risen in likewise manner. While there are a number of reasons for this discrepancy, this glut of 'potential' biomarkers also indicates the need for validation methods to confirm or refute their utility in clinical diagnostics. For this reason, the emphasis on developing methods to target and measure the absolute quantity of specific proteins and peptides in complex proteomic samples has grown. PMID: 19109305 [PubMed - as supplied by publ... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2066113 Wed, 24 Dec 2008 05:00:00 +0100 2066113 http://www.medworm.com/index.php?rid=2066112&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19109306%26dopt%3DAbstract Authors: Blackburn K, Goshe MB Despite its importance, the 'ultimate' method to identify and quantify site-specific protein phosphorylation using mass spectrometry (MS) has yet to be established. This is as much a function of the dynamic range of instrumentation as it is the complexities surrounding the isolation and behavior of phosphopeptides. Phosphorylation site analysis using MS can be quite challenging when analyzing just one protein and quickly becomes a daunting task when attempting to perform proteome-wide measurements. Data-dependent tandem MS-based methods which are useful for the discovery and characterization of novel phosphorylation sites often lack the dynamic range and quantitative aspect required for studying the temporal phases of phosphorylation. While targeted metho... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2066112 Wed, 24 Dec 2008 05:00:00 +0100 2066112 http://www.medworm.com/index.php?rid=2054445&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19091783%26dopt%3DAbstract Authors: Wei X, Li L Glycosylation plays fundamental roles in controlling various biological processes. Therefore, glycosylation analysis has become an important target for proteomic research and has great potential for clinical applications. With the continuous development and refinement of glycoprotein isolation methods, increasing attention has been directed to the quantitative and comparative aspects. This review describes the mass spectrometry (MS)-based techniques for the comparative analysis of glycoproteins and their applications to answer a wide range of interesting biological questions. PMID: 19091783 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2054445 Wed, 17 Dec 2008 05:00:00 +0100 2054445 http://www.medworm.com/index.php?rid=2042291&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19074495%26dopt%3DAbstract Authors: Tautz D The classical textbook assumption for the structure of an eukaryotic gene is that it codes for a single polypeptide of more than 100 amino acids in length. This is also the implicit assumption in most gene annotation pipelines. A gene family has now been discovered in insects that shows that an eukaryotic mRNA can code for peptides as short as eleven amino acids and that a single mRNA can code for several such peptides. This raises the question whether short open reading frames might also have a functional potential in other mRNAs, in particular those that occur in the 5'-UTR of many mRNAs. A number of these have been shown to act in cis to regulate the translation of the main open reading frame of the mRNA. But there may be others that could act in trans on other biol... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2042291 Fri, 12 Dec 2008 05:00:00 +0100 2042291 http://www.medworm.com/index.php?rid=2042290&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19074496%26dopt%3DAbstract Authors: Kamleh MA, Dow JA, Watson DG Metabolomics provides rich datasets for systems biology. Mass spectrometric (MS) techniques are rapidly gaining in importance for untargeted metabolic profiling. In this review, we survey the various techniques for sample preparation and analysis relating to the various MS techniques and illustrate the potential of these techniques for both observing complete metabolomes and detecting changes in the metabolism resulting from genetic mutation of other perturbations. The use of some of these techniques in the study of model organisms including rodent and various invertebrate models is described. The invertebrate systems are of particular interest since such organisms have valuable mutant resources, such as RNAi panels directed against nearly all the ... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=2042290 Fri, 12 Dec 2008 05:00:00 +0100 2042290 http://www.medworm.com/index.php?rid=1993258&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19028802%26dopt%3DAbstract Authors: Moens CB, Donn TM, Wolf-Saxon ER, Ma TP TILLING, for Targeting Induced Local Lesions in Genomes, is a reverse genetics strategy that identifies mutations in specific genes of interest in chemically mutagenized populations. First described in 2000 for mutation detection in Arabidopsis, TILLING is now used in a wide range of plants including soybean, rice, barley and maize as well as for animal model systems, including Arabidopsis, Drosophila, Caenorhabditis elegans, rat, medaka and zebrafish and for the discovery of naturally occurring polymorphisms in humans. This review summarizes current TILLING methodologies as they have been applied to the zebrafish, ongoing TILLING projects and resources in the zebrafish community, and the future of zebrafish TILLING. PMID: 19028802 [... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1993258 Fri, 21 Nov 2008 05:00:00 +0100 1993258 http://www.medworm.com/index.php?rid=1931250&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18977782%26dopt%3DAbstract Authors: Jao LE, Maddison L, Chen W, Burgess SM We review different uses of the retroviral mutagenesis technology as the tool to manipulate the zebrafish genome. In addition to serving as a mutagen in a phenotype-driven forward mutagenesis screen as it was originally adapted for, retroviral insertional mutagenesis can also be exploited in reverse genetic approaches, delivering enhancer- and gene-trap vectors for the purpose of examining gene expression patterns and mutagenesis, making sensitized mutants amenable for chemical and genetic modifier screens, and producing gain-of-function mutations by epigenetically overexpressing the retroviral-inserted genes. From a technology point of view, we also summarize the recent advances in the high-throughput cloning of retroviral integration si... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1931250 Fri, 31 Oct 2008 04:00:00 +0100 1931250 http://www.medworm.com/index.php?rid=1857211&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18836205%26dopt%3DAbstract Authors: Kobayashi D, Takeda H The medaka Oryzias latipes is a small egg-laying freshwater teleost, and has become an excellent model system for ecotoxicology, developmental genetics, genomics and evolutionary biology studies. A high-quality draft genome sequence (700 Mb) of the medaka inbred strain, Hd-rR, has now been completed. In this review, we present an overview of the medaka genome project and describe the substantial genomic resources and genome browsers through which researchers can now freely access these resources. We also present specific findings that have been obtained using these tools, such as sex chromosome differentiation, gene prediction and gene evolution. PMID: 18836205 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomic... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1857211 Sat, 04 Oct 2008 04:00:00 +0100 1857211 http://www.medworm.com/index.php?rid=1857210&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18836206%26dopt%3DAbstract Authors: Burgess HA, Granato M One of the central questions in neuroscience is how refined patterns of connectivity in the brain generate and monitor behavior. Genetic mutations can influence neural circuits by disrupting differentiation or maintenance of component neuronal cells or by altering functional patterns of nervous system connectivity. Mutagenesis screens therefore have the potential to reveal not only the molecular underpinnings of brain development and function, but to illuminate the cellular basis of behavior. Practical considerations make the zebrafish an organism of choice for undertaking forward genetic analysis of behavior. The powerful array of experimental tools at the disposal of the zebrafish researcher makes it possible to link molecular function to neuronal prope... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1857210 Sat, 04 Oct 2008 04:00:00 +0100 1857210 http://www.medworm.com/index.php?rid=1857209&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18836207%26dopt%3DAbstract Authors: Tedford NC, White FM, Radding JA Advances in protein phosphorylation analysis by mass spectrometry (MS) are enabling the generation of high quality, quantitative datasets of protein phosphorylation with a breadth of coverage and reproducibility not previously attainable. Comparisons of signaling responses in cells at a network level are now feasible and studies looking at cellular response to ligand stimulation, drug treatment or genetic modification are transforming our understanding of how cellular decision processes are encoded through the signaling network. The large and dynamic datasets acquired through MS-based phosphoproteomics can be combined with other types of biological data for computational modeling of cellular decision processes with direct biological relevance t... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1857209 Sat, 04 Oct 2008 04:00:00 +0100 1857209 http://www.medworm.com/index.php?rid=1838460&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18820318%26dopt%3DAbstract Authors: Pashos EE, Kague E, Fisher S As increasing numbers of vertebrate genomes are sequenced, comparative genomics offers tremendous promise to unveil mechanisms of transcriptional gene regulation on a large scale. However, the challenge of analysing immense amounts of sequence data and relating primary sequence to function is daunting. Several teleost species occupy crucial niches in the world of comparative genomics, as experimental model organisms of wide utility and living roadmaps of molecular evolution. Extant species have evolved after a teleost-specific genome duplication, and offer the opportunity to examine the evolution of thousands of duplicate gene pairs. Transgenesis in zebrafish is being increasingly employed to functionally examine non-coding sequences, from fish and... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1838460 Sat, 27 Sep 2008 04:00:00 +0100 1838460 http://www.medworm.com/index.php?rid=1816595&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18805902%26dopt%3DAbstract Authors: Hou W, Zhou H, Elisma F, Bennett SA, Figeys D Lipid analysis is a well-established field of research that focuses on one lipid or a few lipids. The recent developments in mass spectrometry technologies have enabled more comprehensive studies to be performed on lipids present in a sample. The move towards extensive lipid research has led to the coining of the term lipidomics, which is defined as the ensemble of lipids present in a sample. In this review, we will discuss the technical developments in the field of lipidomics and the current limitations of this nascent field. PMID: 18805902 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1816595 Fri, 19 Sep 2008 04:00:00 +0100 1816595 http://www.medworm.com/index.php?rid=1786706&cid=s_37631_50_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18784194%26dopt%3DAbstract Authors: Kokel D, Peterson RT Despite their ubiquity and impact, psychiatric illnesses and other disorders of the central nervous system remain among the most poorly treated diseases. Most psychiatric medicines were discovered due to serendipitous observations of behavioural phenotypes in humans, rodents and other mammals. Extensive behaviour-based chemical screens would likely identify novel psychiatric drugs. However, large-scale chemical screens in mammals are inefficient and impractical. In contrast, zebrafish are very well suited for high-throughput behaviour-based drug discovery. Furthermore, the vast amounts of data generated from large-scale behavioural screens in zebrafish will facilitate a systems-level analysis of how chemicals affect behaviour. Unlike serendipitous discover... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1786706 Wed, 10 Sep 2008 04:00:00 +0100 1786706 http://www.medworm.com/index.php?rid=1643487&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18641417%26dopt%3DAbstract Authors: Pawlowski K Many 'omics' studies, gene expression microarray experiments in particular, aim at charting the molecular mechanisms of physiology, disease and drug response. This short review discusses the bias present in many such studies whereas the focus is set on the well understood and established molecular scenarios. The under-reporting rate of 'hypothetical' or uncharacterized genes and proteins, differentially regulated in disease context, is assessed here. Reasons for this bias are discussed. Particular examples from the genomics studies on respiratory diseases are presented. This review aims at increasing awareness of the unexplored genomics data and proposes remedies in order to refocus genomics studies on the less-charted territories of the genome, transcriptome and p... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1643487 Sat, 19 Jul 2008 04:00:00 +0100 1643487 http://www.medworm.com/index.php?rid=1635914&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18632743%26dopt%3DAbstract Authors: Krishnan A, Pereira A Challenges in modern biology demand shifting focus from components-genes and proteins-to their interacting whole. Integrating information from multiple genomic datasets is seen as a means to this end, capable of providing robust and accurate ways to unravel these functional associations. Integrative strategies, both novel and adapted from other well-studied organisms, are being employed in the model plant Arabidopsis thaliana to interpret genome-wide expression, metabolic profiling and protein interaction studies. Exciting inroads are being made in mining and interpretation of developmental, physiological and environmental-response 'programs' using sequence and functional information. The fundamental transcriptional regulatory logic is emerging in Arabido... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1635914 Wed, 16 Jul 2008 04:00:00 +0100 1635914 http://www.medworm.com/index.php?rid=1635913&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18632744%26dopt%3DAbstract Authors: Negrete A, Kotin RM The development of recombinant adeno-associated virus (rAAV) gene therapy applications is hampered by the inability to produce rAAV in sufficient quantities to support pre-clinical and clinical trials. Contrasting with adherent cell cultures, suspension cultures provide a straightforward means for expansion, however, transiently expressing the necessary, but cytotoxic virus proteins remains the challenge for rAAV production. Both the expansion and expression issues are resolved by using the baculovirus expression vector (bev) and insect cell culture system. This review addresses strategies for the production of rAAV exploiting baculovirus technology at different scales using different configurations of bioreactors as well as processing and product character... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1635913 Wed, 16 Jul 2008 04:00:00 +0100 1635913 http://www.medworm.com/index.php?rid=1628017&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18621799%26dopt%3DAbstract Authors: Elgar G PMID: 18621799 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1628017 Fri, 11 Jul 2008 04:00:00 +0100 1628017 http://www.medworm.com/index.php?rid=1598813&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18599513%26dopt%3DAbstract Authors: Gherardini PF, Helmer-Citterich M The ever increasing number of protein structures determined by structural genomic projects has spurred much interest in the development of methods for structure-based function prediction. Existing methods can be roughly classified in two groups: some use a comparative approach looking for the presence of structural motifs possibly associated with a known biochemical function. Other methods try to identify functional patches on the surface of a protein using only its physicochemical characteristics. This review will cover both kinds of approaches to structure-based function prediction as well as their use in real-world cases. The main issues and limitations in using protein structure to predict function will also be discussed. These are mainly:... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598813 Thu, 03 Jul 2008 04:00:00 +0100 1598813 http://www.medworm.com/index.php?rid=1598814&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18586755%26dopt%3DAbstract Authors: Saerens D, Ghassabeh GH, Muyldermans S Today's proteomic analyses are generating increasing numbers of biomarkers, making it essential to possess highly specific probes able to recognize those targets. Antibodies are considered to be the first choice as molecular recognition units due to their target specificity and affinity, which make them excellent probes in proteomics. In the post-genomic era and with high-throughput techniques available, the goal is to discriminate between all individual proteins from the proteome including their splice variants and post-translationally modified derivatives. Aided by advances in generation, selection and engineering of antibody-based recognition units, antibody fragments provide tools for detection of high- as well as low-abundant analyte... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598814 Fri, 27 Jun 2008 04:00:00 +0100 1598814 http://www.medworm.com/index.php?rid=1598818&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18579614%26dopt%3DAbstract This report provides guidelines for rapidly developing an MRM assay using the same mass spectrometry platform used for profiling experiments (typically ion traps) and reviews methodological and analytical validation considerations. The analytical validation guidelines presented are drawn from existing practices on immunological assays and are applicable to any mass spectrometry platform technology. PMID: 18579614 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598818 Wed, 25 Jun 2008 04:00:00 +0100 1598818 http://www.medworm.com/index.php?rid=1598817&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18579615%26dopt%3DAbstract Authors: Wang M, You J, Bemis KG, Tegeler TJ, Brown DP Major technological advances have made proteomics an extremely active field for biomarker discovery and validation in recent years. These improvements have lead to an increased emphasis on larger scale, faster and more efficient methods for protein biomarker discoveries in human tissues, cells and biofluids. However, most current proteomic methodologies for biomarker discovery and validation are not highly automated and generally labour intensive and expensive. Improved automation as well as software programs capable of handling a large amount of data are essential in order to reduce the cost of discovery and increase the throughput. In this review, we will discuss and describe the label-free mass spectrometry-based protein quantif... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598817 Wed, 25 Jun 2008 04:00:00 +0100 1598817 http://www.medworm.com/index.php?rid=1598816&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18579616%26dopt%3DAbstract Authors: Hood L, Rowen L, Galas DJ, Aitchison JD Systems biology represents an experimental approach to biology that attempts to study biological systems in a holistic rather than an atomistic manner. Ideally this involves gathering dynamic and global data sets as well as phenotypic data from different levels of the biological information hierarchy, integrating them and modeling them graphically and/or mathematically to generate mechanistic explanations for the emergent systems properties. This requires that the biological frontiers drive the development of new measurement and visualization technologies and the pioneering of new computational and mathematical tools-all of which requires a cross-disciplinary environment composed of biologists, chemists, computer scientists, engineers, m... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598816 Wed, 25 Jun 2008 04:00:00 +0100 1598816 http://www.medworm.com/index.php?rid=1598815&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18579617%26dopt%3DAbstract Authors: Pisabarro AG, Pérez G, Lavín JL, Ramírez L The high-throughput analytical techniques used in genome, proteome and metabolome studies produce large sets of data that must be studied using appropriate tools. The construction of networks linking different genetic elements and/or functions makes it possible to obtain an integrated view of the cell molecular biology and will eventually help us to predict complex phenotypes from molecular data. Genetic networks can be constructed using different types of data such as genes involved in the control of complex phenotypic traits, genes controlling global gene expression, genetic elements involved in the same metabolic process, gene products interacting physically between them. The connections linking these genetic element... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598815 Wed, 25 Jun 2008 04:00:00 +0100 1598815 http://www.medworm.com/index.php?rid=1598822&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18511486%26dopt%3DAbstract Authors: Martins de Souza D, Oliveira BM, Castro-Dias E, Winck FV, Horiuchi RS, Baldasso PA, Caetano HT, Pires NK, Marangoni S, Novello JC Proteomic research has proved valuable for understanding the molecular mechanisms of biological processes, as well as in the search for biomarkers for a variety of diseases which lack a molecular diagnostic. While several new approaches are being developed, two-dimensional (2-DE) gel electrophoresis is still one of the most commonly used techniques, despite its many limitations. However, for biomarker research, 2-DE gel electrophoresis alone does not fulfill the necessary pre-requisites. If such a technique is utilized exclusively, a great part of a given proteome remains unseen. Therefore, very precise and sensitive techniques are needed. Here, we ... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598822 Fri, 13 Jun 2008 04:00:00 +0100 1598822 http://www.medworm.com/index.php?rid=1598823&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18467351%26dopt%3DAbstract Authors: Ye X, Lotan R High throughput genomic and proteomic methods are often used for comparisons between expression of genes and proteins, respectively in normal cells and malignant counterparts for the identification of potential tumor markers for diagnosis and prognosis. Some experiments use normal and malignant cells cultured in vitro as a source of the mRNA or proteins for analysis. The conditions used for cell culture can exert major effects on the expression of genes and proteins. The interpretation of results of some such studies can be erroneous if normal cells and cancer cells are cultured in serum-free medium (SFM) and serum-supplemented media, respectively as recommended for their optimal growth. The reason for potential complications in the data interpretation is that se... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598823 Thu, 08 May 2008 04:00:00 +0100 1598823 http://www.medworm.com/index.php?rid=1598833&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18332038%26dopt%3DAbstract Authors: Bamps S, Hope IA Observation of gene expression in situ provides a direct connection between the genetic information in the genome sequence and the fully determined developmental cell lineage of Caenorhabditis elegans. Green Fluorescent Protein (GFP) reporters have been fused with many C. elegans genes, in large-scale projects, by conventional DNA ligation, PCR stitching, Gateway recombination and recombineering. These reporter gene fusions have then been used in C. elegans transformation either by microinjection or microprojectile bombardment. So far, the developmental distributions of GFP, as driven by the C. elegans DNA to which the reporter gene has been attached, have been determined simply from direct examination of the transgenic strains by epifluorescence microscopy. A... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598833 Thu, 01 May 2008 04:00:00 +0100 1598833 http://www.medworm.com/index.php?rid=1598831&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18372286%26dopt%3DAbstract Authors: Audhya A, Desai A Proteomic approaches are increasingly being used to complement genetic and RNA interference-based studies of gene function in Caenorhabditis elegans. Several strategies to isolate protein complexes from whole worms and individual differentiated cell types have been described. In vivo labelling methods have also been developed to quantitatively assess proteome-wide changes depending on genetic composition or developmental stage. Here, we review proteomic approaches that are becoming part of the essential toolbox for studies of gene function in C. elegans and highlight specific examples where their application has led to important new insights. PMID: 18372286 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598831 Thu, 01 May 2008 04:00:00 +0100 1598831 http://www.medworm.com/index.php?rid=1598828&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18417533%26dopt%3DAbstract Authors: Moerman DG, Barstead RJ The combined efforts of the Caenorhabditis elegans Knockout Consortium and individuals within the worm community are moving us closer to the goal of identifying mutations in every gene in the nematode C. elegans. At present, we count about 7000 deletion alleles that fall within 5500 genes. The principal method used to detect deletion mutations in the nematode utilizes polymerase chain reaction (PCR). More recently, the Moerman group has incorporated array comparative genome hybridization (aCGH) to detect deletions across the entire coding genome. Other methods used to detect mutant alleles in C. elegans include targeting induced local lesion in genomes (TILLING), transposon tagging, using either Tc1 or Mos1 and resequencing. These combined strategies ha... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598828 Thu, 01 May 2008 04:00:00 +0100 1598828 http://www.medworm.com/index.php?rid=1598826&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18443013%26dopt%3DAbstract Authors: Maine EM The RNA interference (RNAi) method for targeted gene silencing is widely used in Caenorhabditis elegans for large-scale functional genomic studies, analysis of limited gene sets and detailed analysis of individual gene function. The application of RNAi has identified genes that participate in various aspects of development, physiology and cell biology. In addition, RNAi has been used to identify interacting genes and to study functionally redundant genes. This review discusses the various applications of RNAi in C. elegans, focusing particularly on the analysis of developmental processes. PMID: 18443013 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598826 Thu, 01 May 2008 04:00:00 +0100 1598826 http://www.medworm.com/index.php?rid=1598824&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18445637%26dopt%3DAbstract Authors: Lehner B, Lee I A challenge facing nearly all biologists is to identify the complete set of genes that are important for a process or disease. This applies to scientists investigating fundamental pathways in model organisms, but also to clinicians trying to understand human disease. There are many different types of experimental data that can be used to predict the genes that are important for a process, but these data are normally dispersed across numerous publications and databases, and are of varying and unknown quality. Integrated functional gene networks aim to gather functional information from all of these data into a single intuitive graph model that can be used to predict gene functions. In this approach, the ability of each data set to predict functional associations... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598824 Thu, 01 May 2008 04:00:00 +0100 1598824 http://www.medworm.com/index.php?rid=1598821&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18541540%26dopt%3DAbstract Authors: Kuwabara P PMID: 18541540 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598821 Thu, 01 May 2008 04:00:00 +0100 1598821 http://www.medworm.com/index.php?rid=1598820&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18565984%26dopt%3DAbstract Authors: Lehrbach NJ, Miska EA MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression in many eukaryotes. miRNAs were first discovered in Caenorhabditis elegans by Victor Ambros' laboratory in 1993. At the same time Gary Ruvkun's laboratory identified the first miRNA target gene. Together, these two seminal discoveries identified a novel mechanism of post-transcriptional gene regulation that has been recognized as important for development, physiology and pathology of many organisms. Here we discuss how functional genomic, computational and proteomic approaches complement classical genetic analyses to unravel miRNA biology in C. elegans. PMID: 18565984 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598820 Thu, 01 May 2008 04:00:00 +0100 1598820 http://www.medworm.com/index.php?rid=1598819&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18573804%26dopt%3DAbstract Authors: Thomas JH Since the completion of the Caenorhabditis elegans genome sequence 10 years ago, efforts of the large community of C. elegans geneticists have resulted in a high-quality annotation of the structures and sequence relatedness of nearly all the protein encoding and RNA genes. Based on increasingly accurate gene counts in other species, it now appears that C. elegans has more functional genes than most insects and approximately the same number as most mammals. In the last few years, draft genome sequences for several other nematodes have been published (C. briggsae and Brugia malayi) or publicly released (C. remanei, C. brenneri, C. japonica, Pristionchus pacificus, Trichinella spiralis and Haemonchus contortus). Comparisons of gene content within the phylum and to other... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598819 Thu, 01 May 2008 04:00:00 +0100 1598819 http://www.medworm.com/index.php?rid=1598852&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18187513%26dopt%3DAbstract Authors: Kim Y, Nandakumar MP, Marten MR Aspergilli are an important genus of filamentous fungi that contribute to a multibillion dollar industry. Since many fungal genome sequencing were recently completed, it would be advantageous to profile their proteome to better understand the fungal cell factory. Here, we review proteomic data generated for the Aspergilli in recent years. Thus far, a combined total of 28 cell surface, 102 secreted and 139 intracellular proteins have been identified based on 10 different studies on Aspergillus proteomics. A summary proteome map highlighting identified proteins in major metabolic pathway is presented. PMID: 18187513 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598852 Sat, 01 Mar 2008 05:00:00 +0100 1598852 http://www.medworm.com/index.php?rid=1598842&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18270217%26dopt%3DAbstract Authors: Fazeli A, Pewsey E Maternal communication with gametes and embryos influences a broad range of events crucial to pregnancy. Events such as final maturation of gametes, gamete transport, fertilization, early embryonic development and development of foetus to term, are all dependant upon the relay of appropriate molecular signals between the mother, gametes and embryos. This signalling is temporally and spatially regulated, involving complex interactions. Disturbances in maternal communication with gametes and embryos can influence the outcome of pregnancy. Effects range from those that are immediately obvious, such as spontaneous miscarriage (due to inappropriate hormonal signalling), to more subtle consequences that may not become apparent until offspring reach adulthood ('foe... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598842 Sat, 01 Mar 2008 05:00:00 +0100 1598842 http://www.medworm.com/index.php?rid=1598840&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18272547%26dopt%3DAbstract In this report, we describe iTRAQPak, a free software package developed in the R statistical and visualization environment that can be applied to the analysis of 8-plex expression data. The utility of this package is demonstrated through its application to the analysis of 8-plex iTRAQ protein expression data obtained from cerebrospinal fluid samples from Alzheimer's disease subjects involved in a Phase I drug trial. PMID: 18272547 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598840 Sat, 01 Mar 2008 05:00:00 +0100 1598840 http://www.medworm.com/index.php?rid=1598836&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18326543%26dopt%3DAbstract Authors: O'Callaghan PM, James DC The increasing demand for recombinant therapeutic proteins has placed significant pressure on the biopharmaceutical industry to develop high-yielding, mammalian cell-based production systems. Current efforts to increase the production of recombinant proteins by mammalian host cells largely proceed by the lengthy screening of clonal derivatives rather than by directed genetic or metabolic engineering. However, the advent of systems biology has created a new set of tools that will ensure that future engineering strategies will be informed by an understanding of the genetic/regulatory and metabolic networks that determine the functional competence of mammalian cell factories in vitro. In this review we summarize recent systems-level studies that utilize g... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598836 Sat, 01 Mar 2008 05:00:00 +0100 1598836 http://www.medworm.com/index.php?rid=1598835&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18326544%26dopt%3DAbstract Authors: Noirel J, Ow SY, Sanguinetti G, Jaramillo A, Wright PC Technological developments in the life sciences have resulted in an ever-accelerating pace of data production. Systems Biology tries to shed light upon these data by building complex models describing the interactions between biological components. However, extracting information from this morass of data requires the use of sophisticated computational techniques. Here, we propose a method suitable to integrate data drawn from quantitative proteomics into a metabolic scaffold and identify the metabolic pathways which are collectively up-regulated or down-regulated. The availability of such a tool is highly desirable as the extracted information could then be taken as a starting point for in-depth analyses, in particular in ... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598835 Sat, 01 Mar 2008 05:00:00 +0100 1598835 http://www.medworm.com/index.php?rid=1598830&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18372287%26dopt%3DAbstract Authors: Singh R Disulfide bonds play an important role in understanding protein folding, evolution, and in studies related to determining structural and functional properties of specific proteins. At the state-of-the-art, a large number of computational techniques have been proposed for determining disulfide bonds. Operating across the gamut of input data, from pure sequence-based information to spectra from mass spectrometry, these techniques provide researchers with a variety of methodological choices and trade-offs. Techniques for disulfide-bond determination are also underpinned by a rich variety of algorithmic formulations. Analysis of these algorithms can provide valuable cues towards choosing a particular technique and understanding its results. Further, their study is critical... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598830 Sat, 01 Mar 2008 05:00:00 +0100 1598830 http://www.medworm.com/index.php?rid=1598829&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18390580%26dopt%3DAbstract In this study, we compare two software packages, Mascot and Peaks, for the analysis of iTRAQ data from ESI-Q/TOF mass spectrometry. In the case of a six-protein mixture combined in a known proportion, the output of the Peaks algorithm deviated from the correct result by 14% on average, while the error of the Mascot quantification was nearly 200%. When the software were used to analyse iTRAQ data from a complex protein sample, the quantification results agreed within 20% for only 26% of the quantified proteins, showing significant differences in the two quantification algorithms. This comparison and analysis revealed major intricacies in peptide and protein quantification that must be taken into consideration for software development. PMID: 18390580 [PubMed - in process] (Source: Briefi... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598829 Sat, 01 Mar 2008 05:00:00 +0100 1598829 http://www.medworm.com/index.php?rid=1598827&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18440985%26dopt%3DAbstract Authors: Wright PC PMID: 18440985 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598827 Sat, 01 Mar 2008 05:00:00 +0100 1598827 http://www.medworm.com/index.php?rid=1598825&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18443014%26dopt%3DAbstract Authors: Ciriello G, Guerra C Several algorithms have been recently designed to identify motifs in biological networks, particularly in protein-protein interaction networks. Motifs correspond to repeated modules in the network that may be of biological interest. The approaches proposed in the literature often differ in the definition of a motif, the way the occurrences of a motif are counted and the way their statistical significance is assessed. This has strong implications on the computational complexity of the discovery process and on the type of results that can be expected. This review presents in a systematic way the different computational settings outlining their main features and limitations. PMID: 18443014 [PubMed - in process] (Source: Briefings in Functional Genomics an... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598825 Sat, 01 Mar 2008 05:00:00 +0100 1598825 http://www.medworm.com/index.php?rid=1598849&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18208863%26dopt%3DAbstract Authors: Scott GB, Meade JL, Cook GP Natural killer (NK) cells are lymphocytes with an innate ability to recognize and kill infected cells and tumour cells. Unlike B and T cells, NK cells do not express an antigen receptor. Instead, NK cells detect changes in the phenotype of the target cell surface; malignant transformation or infection resulting in the loss or gain of particular molecules that are detected by inhibitory or activating receptors on the NK cell surface. The identification and characterization of NK cells and their receptors was made possible by monoclonal antibody technology. The ease with which genes and gene products can now be identified and manipulated has accelerated our understanding of NK cell function. Furthermore, gene and protein profiling studies are beginnin... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598849 Tue, 01 Jan 2008 05:00:00 +0100 1598849 http://www.medworm.com/index.php?rid=1598843&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18270216%26dopt%3DAbstract Authors: Jørgensen C, Linding R Directionality in protein signalling networks is due to modulated protein-protein interactions and is fundamental for proper signal progression and response to external and internal cues. This property is in part enabled by linear motifs embedding post-translational modification sites. These serve as recognition sites, guiding phosphorylation by kinases and subsequent binding of modular domains (e.g. SH2 and BRCT). Characterization of such modification-modulated interactions on a proteome-wide scale requires extensive computational and experimental analysis. Here, we review the latest advances in methods for unravelling phosphorylation-mediated cellular interaction networks. In particular, we will discuss how the combination of new quantitative mass... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598843 Tue, 01 Jan 2008 05:00:00 +0100 1598843 http://www.medworm.com/index.php?rid=1598841&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18270218%26dopt%3DAbstract Authors: Merrick BA Toxicoproteomics uses the discovery potential of proteomics in toxicology research by applying global protein measurement technologies to biofluids and tissues after host exposure to injurious agents. Toxicoproteomic studies thus far have focused on protein profiling of major organs and biofluids such as liver and blood in preclinical species exposed to model toxicants. The slow pace of discovery for new biomarkers, toxicity signatures and mechanistic insights is partially due to the limited proteome coverage derived from analysis of native organs, tissues and body fluids by traditional proteomic platforms. Improved toxicoproteomic analysis would result by combining higher data density LC-MS/MS platforms with stable isotope labelled peptides and parallel use of comp... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598841 Tue, 01 Jan 2008 05:00:00 +0100 1598841 http://www.medworm.com/index.php?rid=1598839&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18283051%26dopt%3DAbstract Authors: Casadio R, Martelli PL, Pierleoni A Automated sequence annotation is a major goal of post-genomic era with hundreds of genomes in the databases, from both prokaryotes and eukaryotes. While the number of fully sequenced chromosomes from microbial organisms exponentially increased in the last decade above 600, presently we know the whole DNA content of only 25 eukaryotic organisms, including Homo sapiens. However, the process of genome annotation is far from being completed. This is particularly relevant in eukaryotes, whose cells contain several subcellular compartments, or organelles, enclosed by membranes, where different relevant functions are performed. Translocation across the membrane into the organelles is a highly regulated and complex cellular process. Indeed different... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598839 Tue, 01 Jan 2008 05:00:00 +0100 1598839 http://www.medworm.com/index.php?rid=1598838&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18283052%26dopt%3DAbstract Authors: Gul O, Basaga H, Kutuk O Acquired or innate resistance to chemotherapy is a major drawback of cancer therapeutics, which is frequently seen in epithelial cancers. However, the molecular mechanisms underlying chemotherapy resistance remain poorly understood. The mitochondrial pathway is a critical death pathway common to many different types of chemotherapy. Aberrations in this pathway can result in resistance to chemotherapy. The Bcl-2 family of proteins control commitment to programmed cell death by mitochondrial apoptosis. In this review, we will summarize the strategies in determining the components of apoptotic defects responsible for chemotherapy resistance, mainly focused on Bcl-2 protein network. PMID: 18283052 [PubMed - indexed for MEDLINE] (Source: Briefings in Fu... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598838 Tue, 01 Jan 2008 05:00:00 +0100 1598838 http://www.medworm.com/index.php?rid=1598837&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18308835%26dopt%3DAbstract Authors: McGuire JN, Overgaard J, Pociot F Biomarker discovery in clinical proteomics is being performed on relatively large patient cohorts by utilizing the high throughput of laser desorption/ionization mass spectrometry (MALDI- and SELDI-TOF-MS). Dealing directly with patient samples as opposed to working in cell or animal systems requires a host of considerations both before and after mass spectrometric analysis to obtain robust biomarker candidates. The challenges associated with the heterogeneity of typical samples are amplified by the ability to detect hundreds to thousands of proteins simultaneously. Adherence to protocols and consistency, however, can ensure optimal results. A study starts necessarily with a relevant clinical question and proceeds to a planning phase where sam... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598837 Tue, 01 Jan 2008 05:00:00 +0100 1598837 http://www.medworm.com/index.php?rid=1598834&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18326545%26dopt%3DAbstract Authors: Yulug IG, Gur-Dedeoglu B Conventional molecular and genetic methods for studying cancer are limited to the analysis of one locus at a time. A cluster of genes that are regulated together can be identified by DNA microarray, and the functional relationships can uncover new aspects of cancer biology. Breast cancer can be used to provide a model to demonstrate the current approaches to the molecular analysis of cancer. Meta-analysis is an important tool for the identification and validation of differentially expressed genes to increase power in clinical and biological studies across different sets of data. Recently, meta-analysis approaches have been applied to large collections of microarray datasets to investigate molecular commonalities of multiple cancer types not only to fin... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598834 Tue, 01 Jan 2008 05:00:00 +0100 1598834 http://www.medworm.com/index.php?rid=1598832&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18334489%26dopt%3DAbstract Authors: Ansong C, Purvine SO, Adkins JN, Lipton MS, Smith RD While genome sequencing efforts reveal the basic building blocks of life, a genome sequence alone is insufficient for elucidating biological function. Genome annotation--the process of identifying genes and assigning function to each gene in a genome sequence--provides the means to elucidate biological function from sequence. Current state-of-the-art high-throughput genome annotation uses a combination of comparative (sequence similarity data) and non-comparative (ab initio gene prediction algorithms) methods to identify protein-coding genes in genome sequences. Because approaches used to validate the presence of predicted protein-coding genes are typically based on expressed RNA sequences, they cannot independently and uneq... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598832 Tue, 01 Jan 2008 05:00:00 +0100 1598832 http://www.medworm.com/index.php?rid=1598851&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18192320%26dopt%3DAbstract Authors: Hancock JM, Mallon AM An essential aspect to understanding the functional significance of individual genes in the mouse genome is an understanding of the phenotypic consequences of gene mutations. A wide variety of online sites exist that provide different types of phenotypic information on the laboratory mouse. In this review, we describe the major resources that are currently available and discuss some of the bioinformatics requirements that will be necessary to make more seamless searching, comparison and analysis of these various data types possible. PMID: 18192320 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598851 Sat, 01 Dec 2007 05:00:00 +0100 1598851 http://www.medworm.com/index.php?rid=1598850&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18192321%26dopt%3DAbstract Authors: De la Cerda B, Castielli O, Durán RV, Navarro JA, Hervás M, De la Rosa MA Cyanobacteria, which are considered to be the chloroplast precursors, are significant contributors to global photosynthetic productivity. The ample variety of membrane and soluble proteins containing different metals (mainly, iron and copper) has made these organisms develop a complex homeostasis with different mechanisms and tight regulation processes to fulfil their metal requirements in a changing environment. Cell metabolism is so adapted as to synthesize alternative proteins depending on the relative metal availabilities. In particular, plastocyanin, a copper protein, and cytochrome c(6), a haem protein, can replace each other to play the same physiological role as electron carriers in pho... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598850 Sat, 01 Dec 2007 05:00:00 +0100 1598850 http://www.medworm.com/index.php?rid=1598848&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18208864%26dopt%3DAbstract This article reviews the advances in molecular genetics that have led to the identification of genes and markers associated with meat quality in pig. The development of a considerable number of annotated livestock genome sequences represents an incredibly rich source of information that can be used to identify candidate genes responsible for complex traits and quantitative trait loci effects. In pig, the huge amount of information emerging from the study of the genome has helped in the acquisition of new knowledge concerning biological systems and it is opening new opportunities for the genetic selection of this specie. Among the new fields of genomics recently developed, functional genomics and proteomics that allow considering many genes and proteins at the same time are very useful tool... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598848 Sat, 01 Dec 2007 05:00:00 +0100 1598848 http://www.medworm.com/index.php?rid=1598847&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18208865%26dopt%3DAbstract Authors: Kaas Q, Ehrenmann F, Lefranc MP The immunoglobulin superfamily (IgSF) comprises the immunoglobulins (IG), T cell receptors (TR) and proteins that have the common feature of having at least one Ig-like domain. The major histocompatibility complex (MHC) superfamily (MhcSF) comprises, in addition to the MHC, proteins which share the common feature of having Mhc-like domains. IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr) has set up a unique numbering system and standardized 2D graphical representations, or IMGT Colliers de Perles, which take into account the structural features of the Ig-like and Mhc-like domains. In this article, we review the IMGT Scientific chart rules for the description of the IgSF (V and C types) and of the MhcSF (G type) d... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598847 Sat, 01 Dec 2007 05:00:00 +0100 1598847 http://www.medworm.com/index.php?rid=1598846&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18216026%26dopt%3DAbstract Authors: Cordero F, Botta M, Calogero RA Microarray based transcription profiling is now a consolidated methodology and has widespread use in areas such as pharmacogenomics, diagnostics and drug target identification. Large-scale microarray studies are also becoming crucial to a new way of conceiving experimental biology. A main issue in microarray transcription profiling is data analysis and mining. When microarrays became a methodology of general use, considerable effort was made to produce algorithms and methods for the identification of differentially expressed genes. More recently, the focus has switched to algorithms and database development for microarray data mining. Furthermore, the evolution of microarray technology is allowing researchers to grasp the regulative nature of tr... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598846 Sat, 01 Dec 2007 05:00:00 +0100 1598846 http://www.medworm.com/index.php?rid=1598845&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18216027%26dopt%3DAbstract Authors: Pérez-Ortín JE Most studies on eukaryotic gene regulation have focused on mature mRNA levels. Nevertheless, the steady-state mRNA level is the result of two opposing biological processes: transcription and degradation, both of which can be important points to regulate gene expression. It is now possible to determine the transcription and degradation rates (TR and DR), as well as the mRNA amount, for each gene using DNA chip technologies. In this way, each individual contribution to gene expression can be analysed. This review will deal with the techniques used for the genomic evaluation of TR and DR developed for the yeast Saccharomyces cerevisiae. They will be described in detail and their potential drawbacks discussed. I will also discuss the integration of the dat... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598845 Sat, 01 Dec 2007 05:00:00 +0100 1598845 http://www.medworm.com/index.php?rid=1598844&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18218650%26dopt%3DAbstract Authors: Koegl M, Uetz P Yeast two-hybrid (Y2H) screening methods are an effective means for the detection of protein-protein interactions. Optimisation and automation has increased the throughput of the method to an extent that allows the systematic mapping of protein-protein interactions on a proteome-wide scale. Since two-hybrid screens fail to detect a great number of interactions, parallel high-throughput approaches are needed for proteome-wide interaction screens. In this review, we discuss and compare different approaches for adaptation of Y2H screening to high-throughput, the limits of the method and possible alternative approaches to complement the mapping of organism-wide protein-protein interactions. PMID: 18218650 [PubMed - in process] (Source: Briefings in Functional G... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598844 Sat, 01 Dec 2007 05:00:00 +0100 1598844 http://www.medworm.com/index.php?rid=1598859&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17709347%26dopt%3DAbstract Authors: Hagn M, Marschall S, Hrabè de Angelis M The European Mouse Mutant Archive (EMMA) offers the worldwide scientific community a free archiving service for its mutant mouse lines and access to a wide range of disease models and other research tools. EMMA is currently comprised of seven partners who operate as the primary mouse repository in Europe. EMMA' s primary objectives are to establish and manage a unified repository for maintaining mouse mutations and to make them available to the scientific community. In addition to these core services, the consortium can generate germ-free (axenic) mice for its customers and also hosts courses in cryopreservation. EMMA is a founder member of the Federation of International Mouse Resources (FIMRe). The EMMA network is funded by the pa... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598859 Sat, 01 Sep 2007 04:00:00 +0100 1598859 http://www.medworm.com/index.php?rid=1598858&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17916592%26dopt%3DAbstract Authors: Asslaber M, Zatloukal K Biobanks contain biological samples and associated information that are essential raw materials for advancement of biotechnology, human health, and research and development in life sciences. Population-based and disease-oriented biobanks are major biobank formats to establish the disease relevance of human genes and provide opportunities to elucidate their interaction with environment and lifestyle. The developments in personalized medicine require molecular definition of new disease subentities and biomarkers for identification of relevant patient subgroups for drug development. These emerging demands can only be met if biobanks cooperate at the transnational or even global scale. Establishment of common standards and strategies to cope with the hetero... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598858 Sat, 01 Sep 2007 04:00:00 +0100 1598858 http://www.medworm.com/index.php?rid=1598857&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17942476%26dopt%3DAbstract Authors: Wierling C, Herwig R, Lehrach H Modelling and simulation techniques are valuable tools for the understanding of complex biological systems. The design of a computer model necessarily has many diverse inputs, such as information on the model topology, reaction kinetics and experimental data, derived either from the literature, databases or direct experimental investigation. In this review, we describe different data resources, standards and modelling and simulation tools that are relevant to integrative systems biology. PMID: 17942476 [PubMed - indexed for MEDLINE] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598857 Sat, 01 Sep 2007 04:00:00 +0100 1598857 http://www.medworm.com/index.php?rid=1598856&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17967806%26dopt%3DAbstract Authors: Wagner F, Heidtke KR, Drescher B, Radelof U A number of fundamental technical developments like the evolvement of oligonucleotide microarrays, new sequencing technologies and gene synthesis have considerably changed the character of genomic biological resource centres in recent years. While genomic biological resource centres traditionally served mainly as providers of sparsely characterized cDNA clones and clone sets, there is nowadays a clear tendency towards well-characterized, high-quality clones. In addition, major new service units like microarray services have developed, which are completely independent of clone collections, reflecting the co-evolution of data generation and technology development. The new technologies require an increasingly higher degree of specializa... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598856 Sat, 01 Sep 2007 04:00:00 +0100 1598856 http://www.medworm.com/index.php?rid=1598855&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17967807%26dopt%3DAbstract Authors: Spudich G, Fernández-Suárez XM, Birney E A wealth of gene information is accruing in public databases. Genome browsers such as Ensembl are needed to organize and depict this information in the context of the genome. Ensembl provides an open source gene set based on experimental evidence for over 30 species, the majority of which are vertebrates. Genes and annotation are accessible through the Ensembl browser (http://www.ensembl.org), and through direct queries of its databases using the Perl API (Application Programme Interface), MySQL or BioMart. PMID: 17967807 [PubMed - indexed for MEDLINE] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598855 Sat, 01 Sep 2007 04:00:00 +0100 1598855 http://www.medworm.com/index.php?rid=1598854&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17967808%26dopt%3DAbstract Authors: Friedel RH, Seisenberger C, Kaloff C, Wurst W Functional analysis of the mammalian genome is an enormous challenge for biomedical scientists. To facilitate this endeavour, the European Conditional Mouse Mutagenesis Program (EUCOMM) aims at generating up to 12 000 mutations by gene trapping and up to 8000 mutations by gene targeting in mouse embryonic stem (ES) cells. These mutations can be rendered into conditional alleles, allowing Cre recombinase-mediated disruption of gene function in a time- and tissue-specific manner. Furthermore, the EUCOMM program will generate up to 320 mouse lines from the EUCOMM resource and up to 20 new Cre driver mouse lines. The EUCOMM resource of vectors, mutant ES cell lines and mutant mice will be openly available to the scientific community. E... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598854 Sat, 01 Sep 2007 04:00:00 +0100 1598854 http://www.medworm.com/index.php?rid=1598853&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D18029381%26dopt%3DAbstract Authors: Kawai J, Carninci P, Hayashizaki Y For the past decade, extensive efforts have been made for establishing cDNA clone resources for various species. The most striking breakthrough has been full-length cDNA technology allowing cloning of intact RNA molecules as cDNA. These transcriptomics resources are providing researchers with essential tools for studies of functional genomics. Here, the importance of quality and availability of these resources is discussed. PMID: 18029381 [PubMed - indexed for MEDLINE] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598853 Sat, 01 Sep 2007 04:00:00 +0100 1598853 http://www.medworm.com/index.php?rid=1598867&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17584761%26dopt%3DAbstract Authors: Barbaric I, Miller G, Dear TN In the field of mammalian functional genomics, one of the main aims in the post-genomic era is to elucidate the function of all genes in the genome. The powerful technology of gene targeting in embryonic stem cells has enabled the simple generation of mice lacking a specific gene. However, it is evident that in a proportion of such knockout mice no deviation in phenotype could be detected. Advancements in the field of mouse phenotyping and use of extensive phenotyping tests on each knockout showed that abnormal phenotypes were sometimes detected in physiological areas where they were not initially anticipated, or only manifested under certain conditions, emphasizing the need for careful phenotypic investigation. Nevertheless, the effect of some ge... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598867 Fri, 01 Jun 2007 04:00:00 +0100 1598867 http://www.medworm.com/index.php?rid=1598866&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17584762%26dopt%3DAbstract Authors: Gelfanova V, Higgs RE, Dean RA, Holtzman DM, Farlow MR, Siemers ER, Boodhoo A, Qian YW, He X, Jin Z, Fisher DL, Cox KL, Hale JE Immunoprecipitation (IP) combined with matrix-assisted laser desorption ionization (MALDI) time of flight (Tof) mass spectrometry has been used to develop quantitative assays for amyloid-beta (Abeta) peptides in cerebrospinal fluid (CSF). Inclusion of (15)N labelled standard peptides allows for absolute quantification of multiple Abeta isoforms in individual samples. Characterization of variability associated with all steps of the assay indicated that the IP step is the single largest contributor to overall variability. Optimization of the assay resulted in overall coefficient of variation <or=8% with high agreement to an Abeta(1-40) and Abeta(1-42... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598866 Fri, 01 Jun 2007 04:00:00 +0100 1598866 http://www.medworm.com/index.php?rid=1598865&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17611236%26dopt%3DAbstract Authors: Nolan JP, Yang L Biomedical research is evolving to address biological systems as molecular pathways integrated into complex networks. Tools for molecular and cell analysis are also evolving to address the new challenges and opportunities of this approach. Flow cytometry is a versatile analytical platform, capable of high speed quantitative measurements of cells and other particles. These capabilities are being exploited and extended in a range of new applications stemming from opportunities presented by the advances of genomics, proteomics and systems biology, which are in turn impacting clinical diagnosis, vaccine development and drug discovery. In this review, we highlight some of these advances and consider the future evolution of flow cytometry technology. PMID: 17611... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598865 Fri, 01 Jun 2007 04:00:00 +0100 1598865 http://www.medworm.com/index.php?rid=1598864&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17644526%26dopt%3DAbstract Authors: Pozhitkov AE, Tautz D, Noble PA Microarray technology, which has been around for almost two decades, now provides an indispensable service to the biomedical research community. Soaring demand for high-throughput screening of genes potentially associated with cancer and other diseases, as well as the increased need for identifying microorganisms, have substantially opened up the application of this technology to many fields of science, including new ones such as array-based comparisons of whole genomes. Yet, despite this significant progress, the fundamental understanding of the pillars of this technology, have been largely unexplored, in particular for oligonucleotide-based microarrays. In fact, most of the current approaches for the design of microarrays are based on 'common-... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598864 Fri, 01 Jun 2007 04:00:00 +0100 1598864 http://www.medworm.com/index.php?rid=1598863&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17652104%26dopt%3DAbstract Authors: Southall TD, Brand AH The correct control of gene expression is essential for the proper development of organisms. Abnormal expression of genes can lead to cancerous growth and certain diseases. To understand how gene expression is controlled on a genome-wide scale, methods for assaying transcription factor binding sites are required. There are two prevailing techniques for mapping protein-chromatin interactions, ChIP (chromatin immunoprecipitation) and DamID (DNA adenine methyltransferase identification). Both of these methods, when combined with microarray technology, can provide powerful insights into transcription factor function, higher order chromatin structure and gene regulatory networks. In vivo chromatin profiling studies are now being performed on model organisms, t... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598863 Fri, 01 Jun 2007 04:00:00 +0100 1598863 http://www.medworm.com/index.php?rid=1598862&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17670766%26dopt%3DAbstract Authors: Liu B A major challenge to the development of therapeutic small interfering RNAs (siRNAs) is specific and efficient in vivo delivery to target cells. Recent studies suggest that cell type-specific gene silencing in vivo can be achieved by combining siRNAs with cell type-specific affinity ligands such as monoclonal antibodies. The antibody-directed siRNA complex enters target cells through receptor endocytosis and is subsequently released to the cytosol to specifically silence target gene expression through biologically conserved RNA interference (RNAi) pathways. Antibody fragments fused with a small basic nucleic-acid-binding protein and antibody fragment-directed nanoimmunoliposomes are two examples of effective delivery vehicles in vivo. The demonstrated specificity of in vi... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598862 Fri, 01 Jun 2007 04:00:00 +0100 1598862 http://www.medworm.com/index.php?rid=1598861&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17670767%26dopt%3DAbstract Authors: Sudheer S, Adjaye J Early mammalian embryogenesis is currently the focus of intense interest because of the potential of inner cell mass-derived embryonic stem cell lines in new therapeutic strategies. As such, creating molecular profiles of gene expression during pre-implantation development will provide a framework for understanding the biological properties of these cells and also establish a tool set for subsequent functional studies. However, a major obstacle impeding progress in this area are moral issues regarding their use, the scarcity of these cells and the ability to successfully isolate and amplify enough mRNA from the minute amounts of total RNA present in these cells. The elucidation, unravelling and understanding the molecular basis of transcriptional control du... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598861 Fri, 01 Jun 2007 04:00:00 +0100 1598861 http://www.medworm.com/index.php?rid=1598860&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17698857%26dopt%3DAbstract Authors: Osborn MJ, Miller JR The fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae have, in addition to being extensively studied themselves, both been utilized for the last quarter century as experimental systems for the isolation of genes from other organisms. Mutations conferring growth defects in either of the two yeast strains have frequently been complemented by expression of cDNA libraries from heterologous species, often human. Many successful experiments have utilized available yeast mutations to allow successful complementation by a human gene, which can thus be deduced to have the same, or an overlapping function as the mutated yeast gene. However complementation in yeast has also been used with success to study two fields, apoptosis and... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598860 Fri, 01 Jun 2007 04:00:00 +0100 1598860 http://www.medworm.com/index.php?rid=1598874&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17353200%26dopt%3DAbstract Authors: Grant KJ, Wu CC Proteomic investigation of normal and diseased brain states has the potential to reveal novel molecular therapeutic and diagnostic targets for a multitude of pathological central nervous system conditions. Due to their unique properties, integral membrane proteins are likely to play a central role in the aetiology of these disorders. These properties, however, have prevented comprehensive analysis of this important class of proteins. Recent advances in sample preparation and proteomic quantification platforms, specifically focused on recovery and enrichment of integral membrane proteins, are discussed. PMID: 17353200 [PubMed - indexed for MEDLINE] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598874 Thu, 01 Mar 2007 05:00:00 +0100 1598874 http://www.medworm.com/index.php?rid=1598873&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17384421%26dopt%3DAbstract Authors: Costoya JA Transcription factors (TF) play a key role in certain mechanisms by which specific genes are expressed in a temporal and tissue-specific manner. Understanding those mechanisms is still a challenging question in biology. Their modular organization allows the possibility of classifying them based on the structure of the domains that bind DNA or interact with other proteins. Those domains not only define the different TF families but also provide insights into the biological functions played by them. Among these, the POK (Poxviruses and Zinc-finger (POZ) and Krüppel) family of transcription repressors is characterized by the presence in their structures of an amino-terminal POZ/Broad Complex, Tramtrack, and Bric à brac (BTB) domain and several Krüppel-ty... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598873 Thu, 01 Mar 2007 05:00:00 +0100 1598873 http://www.medworm.com/index.php?rid=1598872&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17401136%26dopt%3DAbstract Authors: Armstrong J, Bone N, Dodgson J, Beck T FYSSION is a resource for researchers working on the fission yeast Schizosaccharomyces pombe. It currently comprises libraries of temperature-sensitive mutants in essential genes, and insertional mutants in non-essential genes, available for screening by visiting workers. Here we outline methods for constructing and using the libraries, and describe future prospects for functional genomics of this organism, here and elsewhere. PMID: 17401136 [PubMed - indexed for MEDLINE] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598872 Thu, 01 Mar 2007 05:00:00 +0100 1598872 http://www.medworm.com/index.php?rid=1598871&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17478451%26dopt%3DAbstract Authors: Jagannath A, Wood M Neurodegenerative disorders represent a major class of disorders for which thus far any effective small molecule drug therapy has failed to emerge. RNA interference (RNAi), by which disease genes such as those identified for spino-cerebellar ataxia and Huntington's disease can be specifically silenced, has great potential in becoming a successful therapeutic strategy for these diseases. RNAi has shown therapeutic value in vitro and in animal disease models and clinical trials are currently on their way. However, there are problems, such as toxicity due to non-specific silencing, generation of immune responses and over-saturation of RNAi pathway components that must be overcome in order to establish RNAi as a safe and effective therapy. Current research on t... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598871 Thu, 01 Mar 2007 05:00:00 +0100 1598871 http://www.medworm.com/index.php?rid=1598870&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17525073%26dopt%3DAbstract Authors: Angeloni D Epithelial cancers inflict a heavy human and social burden. It was estimated [Tyczynski JE, Bray F, Parkin DM. Lung cancer in Europe in 2000: epidemiology, prevention, and early detection. Lancet Oncol 2003;4:45-55 (Review)] that in Europe, in the year 2000, 347 000 persons died of lung cancer alone, the deadliest cancer disease. Loss of heterozygosity and large homozygous deletions of the human chromosome region 3p21 are especially frequent in epithelial cancers of several organs. In fact, 3p21 is a very peculiar region of the genome harbouring, tightly clustered, several types of cancer-causing genes (CCG) (Lerman MI, Minna JD. The 630 kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumo... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598870 Thu, 01 Mar 2007 05:00:00 +0100 1598870 http://www.medworm.com/index.php?rid=1598869&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17525074%26dopt%3DAbstract Authors: Curtis RH This review focuses on the proteins and secretions of sedentary plant parasitic nematodes potentially important for plant-nematode interactions. These nematodes are well equipped for parasitism of plants. Having acquired the ability to manipulate fundamental aspects of plant biology, they are able to hijack host-cell development to make their feeding site. They feed exclusively from feeding sites as they complete their life cycle, satisfying their nutritional demands for development and reproduction. Biochemical and genomic approaches have been used successfully to identify a number of nematode parasitism genes. So far, 65 204 expressed sequence tags (ESTs) have been generated for six Meloidogyne species and sequencing projects, currently in progress, will underpin g... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598869 Thu, 01 Mar 2007 05:00:00 +0100 1598869 http://www.medworm.com/index.php?rid=1598868&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17556486%26dopt%3DAbstract Authors: Martins D, Menezes de Oliveira B, dos Santos Farias A, Horiuchi RS, Crepaldi Domingues C, de Paula E, Marangoni S, Gattaz WF, Dias-Neto E, Camillo Novello J Protein extraction is the most important step to reveal a proteome by Two-Dimensional Gel Electrophoresis. Usually, the urea/thiourea based standard protein extraction buffer (SB) is combined with detergents with the aim of achieving better resolution and solubilization of different classes of proteins. In order to produce better gels and achieve the greatest spot resolution of Human Brain Proteins, comparisons using 2-DE of extracted proteins from Human Brain Frontal Cortex with SB constituents (7M Urea, 2M Thiourea and 100mM DTT) were made, using different detergent compositions in the buffer. SB preparations in combinat... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598868 Thu, 01 Mar 2007 05:00:00 +0100 1598868 http://www.medworm.com/index.php?rid=1598895&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16772273%26dopt%3DAbstract Authors: Waters KM, Pounds JG, Thrall BD The functioning of even a simple biological system is much more complicated than the sum of its genes, proteins and metabolites. A premise of systems biology is that molecular profiling will facilitate the discovery and characterization of important disease pathways. However, as multiple levels of effector pathway regulation appear to be the norm rather than the exception, a significant challenge presented by high-throughput genomics and proteomics technologies is the extraction of the biological implications of complex data. Thus, integration of heterogeneous types of data generated from diverse global technology platforms represents the first challenge in developing the necessary foundational databases needed for predictive modelling of cell a... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598895 Fri, 01 Dec 2006 05:00:00 +0100 1598895 http://www.medworm.com/index.php?rid=1598884&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17035357%26dopt%3DAbstract Authors: Allen MJ, Wilson WH The Coccolithoviridae is a recently discovered family of giant algal viruses. Here, we review the genomic and transcriptomic characterization of this family based on the results generated from a coccolithovirus microarray. The microarray has been used to aid the annotation of the genome, to investigate the infection process at the transcriptional level and to assess the diversity in genomic content within the family. PMID: 17035357 [PubMed - indexed for MEDLINE] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598884 Fri, 01 Dec 2006 05:00:00 +0100 1598884 http://www.medworm.com/index.php?rid=1598883&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17082210%26dopt%3DAbstract Authors: Gao L, Gross DS Silent chromatin in budding yeast is characterized by the presence of a specialized chromatin modification complex consisting of silent information regulator (Sir) proteins, closely packed pairs of nucleosomes, and hypoacetylated and hypomethylated histones. How this specialized chromatin is established, maintained and inherited has been extensively studied. Less investigated are the determinants that constrain its linear spread along the chromatin fibre and the manner by which it represses gene transcription. Here we review the essential features of SIR-mediated heterochromatin, and discuss genomic and proteomic approaches for discerning the composition of its boundaries and for elucidating the mechanisms by which it silences transcription. PMID: 17082210 ... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598883 Fri, 01 Dec 2006 05:00:00 +0100 1598883 http://www.medworm.com/index.php?rid=1598882&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17124183%26dopt%3DAbstract Authors: Mitulovic G, Mechtler K Due to the complex nature of the proteome, instrumentation and methods development for sample cleanup, fractionation, preconcentration, chromatographic separation and detection becomes urgent for the identification of peptides and proteins. Newly developed techniques and equipment for separation and detection, such as nano-HPLC and multidimensional HPLC for protein and peptide separation, enabled proteomics to experience dynamic growth during the past few years. In any proteomic analysis the most important and sometimes most difficult task is the separation of the complex mixture of proteins or peptides. This review describes some aspects and limitations of HPLC, both multidimensional and one-dimensional, in proteomics research without attempting to dis... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598882 Fri, 01 Dec 2006 05:00:00 +0100 1598882 http://www.medworm.com/index.php?rid=1598881&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D17170013%26dopt%3DAbstract Authors: Heintzmann R, Ficz G Fluorescent imaging microscopy has been an essential tool for biologists over many years, especially after the discovery of the green fluorescent protein and the possibility of tagging virtually every protein with it. In recent years dramatic enhancement of the level of detail at which a fluorescing structure of interest can be imaged have been achieved. We review classical and new developments in high-resolution microscopy, and describe how these methods have been used in biological research. Classical methods include widefield and confocal microscopy whereas novel approaches range from linear methods such as 4Pi, I(5) and structured illumination microscopy to non-linear schemes such as stimulated emission depletion and saturated structured illumination. ... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598881 Fri, 01 Dec 2006 05:00:00 +0100 1598881 http://www.medworm.com/index.php?rid=1598894&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16772274%26dopt%3DAbstract Authors: Ausió J In recent years, the chromatin field has witnessed a renewed interest in histone variants as pertaining to their structural role, but mainly because of the functional specificity they impart to chromatin. In this review, I am going to discuss several of the most recent structural studies on core histone (H2A.Bbd, H2A.Z, H2A.X, macroH2A, H3.3, CENP-A) and linker histone variants (histone H1 microheterogeneity) focusing on their role in nucleosome stability and chromatin fibre dynamics with special emphasis on their possible functional implications. The data accumulated to date indicates that histone variability plays an important role in the histone-mediated regulation of chromatin metabolism. Understanding and deciphering the underlying structural amino acid code ... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598894 Fri, 01 Sep 2006 04:00:00 +0100 1598894 http://www.medworm.com/index.php?rid=1598891&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16772277%26dopt%3DAbstract Authors: Osley MA Histone ubiquitylation has emerged as an important chromatin modification with roles in transcription and trans-histone methylation. In the past several years, there has been dramatic progress in the identification of factors that control ubiquitin attachment to the core histones H2A and H2B. Recent advances in this area will be reviewed, and outstanding questions relating to the cellular functions of these modified histones will be discussed. PMID: 16772277 [PubMed - indexed for MEDLINE] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598891 Fri, 01 Sep 2006 04:00:00 +0100 1598891 http://www.medworm.com/index.php?rid=1598887&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16877467%26dopt%3DAbstract Authors: Verdone L, Agricola E, Caserta M, Di Mauro E Genetic information is packaged in the highly dynamic nucleoprotein structure called chromatin. Many biological processes are regulated via post-translational modifications of key proteins. Acetylation of lysine residues at the N-terminal histone tails is one of the most studied covalent modifications influencing gene regulation in eukaryotic cells. This review focuses on the role of enzymes involved in controlling both histone and non-histone proteins acetylation levels in the cell, with particular emphasis on their effects on cancer. PMID: 16877467 [PubMed - indexed for MEDLINE] (Source: Briefings in Functional Genomics and Proteomics) Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598887 Fri, 01 Sep 2006 04:00:00 +0100 1598887 http://www.medworm.com/index.php?rid=1598886&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16951415%26dopt%3DAbstract Authors: Imhof A Epigenetic inheritance is a key element in the adaptation of organisms to a rapidly changing environment without stably changing their DNA sequence. The necessary changes in its gene expression profiles are frequently associated with variations in chromatin structure. The conformation of chromatin is profoundly influenced by the post-translational modification of the histone proteins, the incorporation of histone variants, the activity of nucleosome remodelling factors and the association of non-histone chromatin proteins. Although the hierarchy of these factors is still not fully understood, genetic experiments suggest that histone-modifying enzymes play a major causal role in setting up a particular chromatin structure. In this article, the recent progress that was m... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598886 Fri, 01 Sep 2006 04:00:00 +0100 1598886 http://www.medworm.com/index.php?rid=1598885&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16980317%26dopt%3DAbstract Authors: Fukuda H, Sano N, Muto S, Horikoshi M Eukaryotic DNA is packaged into chromatin by histone proteins, which assemble the DNA into an organized, higher-order structure. The precise organization of chromatin is essential for faithful execution of DNA-mediated reactions such as transcription, DNA replication, DNA repair and DNA recombination. The organization of chromatin is considered to be regulated by a variety of post-translational modifications of histones, such as acetylation, methylation, phosphorylation, ubiquitination, SUMOylation and poly-ADP-ribosylation. The relationship between histone acetylation and gene expression was first observed in 1964. Since then, a great deal of evidence has accumulated showing that not only transcription but other DNA-mediated reactions als... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598885 Fri, 01 Sep 2006 04:00:00 +0100 1598885 http://www.medworm.com/index.php?rid=1598897&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16772271%26dopt%3DAbstract Authors: Hood BL, Conrads TP, Veenstra TD Biofluid detectable biomarkers that originate at the site of diseased tissues would be advantageous, in that, they may provide mechanistic information concerning the manifestation and progression of the disease. Unfortunately, tissue biopsies are precious samples that can generally be acquired in small amounts due to the invasive nature of the sample collection. One of the foundations of pathological diagnosis for decades has been from formalin-fixed paraffin-embedded (FFPE) tissues, of which a vast archive exists worldwide. These tissues have also been widely used for immunohistochemistry and in situ hybridization studies examining for expression of specific proteins or transcripts. Unfortunately, the ability to analyse FFPE tissues using mass... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598897 Thu, 01 Jun 2006 04:00:00 +0100 1598897 http://www.medworm.com/index.php?rid=1598896&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16772272%26dopt%3DAbstract Authors: Aggarwal K, Choe LH, Lee KH Shotgun proteomic methods involving isobaric tagging of peptides enable high-throughput proteomic analysis. iTRAQ reagents allow simultaneous identification and quantitation of proteins in four different samples using tandem mass spectrometry (MS). In this article, we provide a brief description of proteome analysis using iTRAQ reagents and review the current applications of these reagents in proteomic studies. We also compare different aspects of protein identification including protein sequence coverage and proteome coverage obtained using iTRAQ reagents with those using other shotgun proteomic techniques. We briefly discuss the issue of isotope purity correction in measured peak areas during protein quantitation using iTRAQ reagents. Finally, we ... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598896 Thu, 01 Jun 2006 04:00:00 +0100 1598896 http://www.medworm.com/index.php?rid=1598893&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16772275%26dopt%3DAbstract This study assesses progress in cyanobacterial shotgun proteomics to date, and adds a new perspective by developing a protocol for the shotgun proteomic analysis of the filamentous cyanobacterium Anabaena variabilis ATCC 29413, a model for N(2) fixation. Using approaches for enhanced protein extraction, 646 proteins were identified, which is more than double the previous results obtained using 2DE. Notably, the improved extraction method and shotgun approach resulted in a significantly higher representation of basic and hydrophobic proteins. The use of protein bioinformatics tools to further mine these shotgun data is illustrated through the application of PSORTb for localization, the grand average hydropathy (GRAVY) index for hydrophobicity, LipoP for lipoproteins and the exponentially mo... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598893 Thu, 01 Jun 2006 04:00:00 +0100 1598893 http://www.medworm.com/index.php?rid=1598892&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16772276%26dopt%3DAbstract Authors: Khalsa-Moyers G, McDonald WH State-of-the-art proteomics workflows involve multiple interdependent steps: sample preparation, protein-peptide separation, mass spectrometry and data analysis. While improvements in any of these steps can increase the depth and breadth of analysis, advances in mass spectrometry have catalysed many of the most important developments. We discuss common classes of mass analysers and how these analysers are put together to produce some of the most popular mass spectrometry platforms. The capabilities of these platforms determine how they can be used in a variety of common proteomic strategies and, in turn, what types of biological questions can be addressed. Moving forward, powerful new hybrid mass spectrometers and application of emerging types of t... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598892 Thu, 01 Jun 2006 04:00:00 +0100 1598892 http://www.medworm.com/index.php?rid=1598890&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16772278%26dopt%3DAbstract Authors: Redding AM, Mukhopadhyay A, Joyner DC, Hazen TC, Keasling JD The response of Desulfovibrio vulgaris Hildenborough (DvH), a sulphate-reducing bacterium, to nitrate stress was examined using quantitative proteomic analysis. DvH was stressed with 105 mM sodium nitrate (NaNO(3)), a level that caused a 50% inhibition in growth. The protein profile of stressed cells was compared with that of cells grown in the absence of nitrate using the iTRAQ peptide labelling strategy and tandem liquid chromatography separation coupled with mass spectrometry (quadrupole time-of-flight) detection. A total of 737 unique proteins were identified by two or more peptides, representing 22% of the total DvH proteome and spanning every functional category. The results indicate that this was a mild stress... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598890 Thu, 01 Jun 2006 04:00:00 +0100 1598890 http://www.medworm.com/index.php?rid=1598889&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16772279%26dopt%3DAbstract Authors: Biringer RG, Amato H, Harrington MG, Fonteh AN, Riggins JN, Hühmer AF The cerebrospinal fluid (CSF) provides a ready access into the health state of the central nervous system, and alterations in some CSF proteins have been documented in brain disease. However, the complete variety of proteins is not known and methods to identify protein components are still being developed. The goal of this study was to examine the sequence coverage obtained from human CSF digests produced with different proteases. Enzymatic digests of CSF proteins were obtained with arginine-C endopeptidase (ArgC), glutamic acid endopeptidase (GluC), chymotrypsin, trypsin and their combinations, and then examined using reverse phase chromatography and a Finnigan LTQ linear ion trap mass spectrometer. Pe... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598889 Thu, 01 Jun 2006 04:00:00 +0100 1598889 http://www.medworm.com/index.php?rid=1598888&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16798750%26dopt%3DAbstract Authors: Nunn BL, Shaffer SA, Scherl A, Gallis B, Wu M, Miller SI, Goodlett DR Shotgun proteomics is rapidly becoming one of the most efficient and popular tools to examine protein expression in cells. Numerous laboratories now have a wide array of low- and high-performance mass spectrometry instrumentation necessary to complete proteome-wide projects. Often these laboratories have time and financial constraints that prohibit all projects from being conducted on high-performance state-of-the-art mass spectrometers. Here, we compare shotgun proteomic results using a direct 'lyse, digest and analyse' approach on a high-performance mass spectrometer (i.e. the LTQ-FT) with the results from a much lower-performance instrument (i.e. the LCQ-DUO) where, for the latter, various traditional pro... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598888 Thu, 01 Jun 2006 04:00:00 +0100 1598888 http://www.medworm.com/index.php?rid=1598911&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16769671%26dopt%3DAbstract Authors: Law WJ, Cann KL, Hicks GG Multifunctional proteins are demonstrating that gene expression is not a series of compartmentalized events beginning with transcription and culminating in delivery of mature mRNA into the cytoplasm, but an integrated pathway of transcription, splicing, RNA metabolism and subcellular targeting of translation. One such multifunctional family is made up of the RNA-binding proteins TLS, EWS and TAF15. These three proteins each contribute a potent transcriptional activation domain to oncogenic fusion proteins, and the formation of these fusion genes are thought to be the primary causes of their associated cancers. Wild-type TLS, EWS and TAF15 can function as classical transcription factors in addition to their better-known functions in splicing and mRNA t... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598911 Wed, 01 Mar 2006 05:00:00 +0100 1598911 http://www.medworm.com/index.php?rid=1598910&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16769672%26dopt%3DAbstract Authors: Schnütgen F A novel generation of retroviral gene-trap vectors has been developed with the ability to induce conditional mutations in most genes expressed in mouse embryonic stem (ES) cells. The vectors rely on directional site-specific recombination systems, which can repair and re-induce the gene-trap mutations when activated in succession. After the gene-trap insertions are passaged into mice, this system enables the induction of temporally and spatially restricted mutations in somatic cells. In addition to their conditional features, the vectors create multipurpose alleles amenable to a wide range of post-insertional modifications. These vectors have been used to assemble the largest library of ES cell lines with conditional mutations in single genes, presently totall... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598910 Wed, 01 Mar 2006 05:00:00 +0100 1598910 http://www.medworm.com/index.php?rid=1598909&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16769673%26dopt%3DAbstract Authors: Amsterdam A In order to rapidly identify a substantial fraction of the genes with a unique and essential role in vertebrate development, the laboratory of Nancy Hopkins at MIT has performed a large insertional mutagenesis screen in zebrafish using a pseudotyped retroviral vector as the mutagen. We have recovered mutations in about one-quarter of the embryonic essential genes in this organism, and have identified the mutated genes in nearly all of these (333). As the ease of gene identification allowed us to clone the mutated genes for nearly all of the mutants rather than prioritizing based upon the initially observed phenotypes, this has provided an unbiased view of the diversity of genes required for vertebrate development as well as a large collection of mutants to be scree... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598909 Wed, 01 Mar 2006 05:00:00 +0100 1598909 http://www.medworm.com/index.php?rid=1598908&cid=s_37631_176_f&fid=37631&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D16769674%26dopt%3DAbstract Authors: Winkelmann S, Klar M, Benham C, Prashanth A, Goetze S, Gluch A, Bode J The conventional string-based bioinformatic methods of genomic sequence analysis are often insufficient to identify DNA regulatory elements, since many of these do not have a recognizable motif. Even in case a sequence pattern is known to be associated with an element it may only partially mediate its function. This suggests that properties not correlated with the details of base sequence contribute to regulation. One of these attributes is the DNA strand-separation potential, known as SIDD (stress-induced duplex destabilization) which facilitates the access of tracking proteins and the formation of local secondary structures. Using the type 1 interferon gene cluster as a paradigm, we demonstrate that the i... Briefings in Functional Genomics and Proteomics journals http://www.medworm.com/rss/comments.php?id=1598908 Wed, 01 Mar 2006 05:00:00 +0100 1598908