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Editorial.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 19833697 [PubMed - in process] (Source: Briefings in Functional Genomics and Proteomics)
Source: Briefings in Functional Genomics and Proteomics - October 17, 2009 Category: Genetics & Stem Cells Authors: Griffiths-Jones S Tags: Brief Funct Genomic Proteomic Source Type: journals

Establishing legitimacy and function in the new transcriptome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Briefings in Functional Genomics and Proteomics - October 17, 2009 Category: Genetics & Stem Cells Authors: van Bakel H, Hughes TR Tags: Brief Funct Genomic Proteomic Source Type: journals

Annotating non-coding transcription using functional genomics strategies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - October 17, 2009 Category: Genetics & Stem Cells Authors: Forrest AR, Abdelhamid RF, Carninci P Tags: Brief Funct Genomic Proteomic Source Type: journals

The use of covariance models to annotate RNAs in whole genomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Briefings in Functional Genomics and Proteomics - October 17, 2009 Category: Genetics & Stem Cells Authors: Gardner PP Tags: Brief Funct Genomic Proteomic Source Type: journals

From consensus structure prediction to RNA gene finding.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 pr...
Source: Briefings in Functional Genomics and Proteomics - October 17, 2009 Category: Genetics & Stem Cells Authors: Bernhart SH, Hofacker IL Tags: Brief Funct Genomic Proteomic Source Type: journals

Customized strategies for discovering distant ncRNA homologs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Briefings in Functional Genomics and Proteomics - September 23, 2009 Category: Genetics & Stem Cells Authors: Mosig A, Zhu L, Stadler PF Tags: Brief Funct Genomic Proteomic Source Type: journals

Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Briefings in Functional Genomics and Proteomics - September 20, 2009 Category: Genetics & Stem Cells Authors: Dinger ME, Amaral PP, Mercer TR, Mattick JS Tags: Brief Funct Genomic Proteomic Source Type: journals

Comparing CNV detection methods for SNP arrays.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Briefings in Functional Genomics and Proteomics - September 7, 2009 Category: Genetics & Stem Cells Authors: Winchester L, Yau C, Ragoussis J Tags: Brief Funct Genomic Proteomic Source Type: journals

Retrotransposons and non-protein coding RNAs.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 understandin...
Source: Briefings in Functional Genomics and Proteomics - September 2, 2009 Category: Genetics & Stem Cells Authors: Mourier T, Willerslev E Tags: Brief Funct Genomic Proteomic Source Type: journals

Combinatorial patterning mechanisms in the Drosophila embryo.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ch...
Source: Briefings in Functional Genomics and Proteomics - August 2, 2009 Category: Genetics & Stem Cells Authors: Chopra VS, Levine M Tags: Brief Funct Genomic Proteomic Source Type: journals

Transcription attenuation in bacteria: theme and variations.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 availabili...
Source: Briefings in Functional Genomics and Proteomics - August 2, 2009 Category: Genetics & Stem Cells Authors: Naville M, Gautheret D Tags: Brief Funct Genomic Proteomic Source Type: journals

Implications of duplicated cis-regulatory elements in the evolution of metazoans: the DDI model or how simplicity begets novelty.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 st...
Source: Briefings in Functional Genomics and Proteomics - August 2, 2009 Category: Genetics & Stem Cells Authors: Jiménez-Delgado S, Pascual-Anaya J, Garcia-Fernàndez J Tags: Brief Funct Genomic Proteomic Source Type: journals

Deciphering the diversity of small RNAs in plants: the long and short of it.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - July 28, 2009 Category: Genetics & Stem Cells Authors: Schwach F, Moxon S, Moulton V, Dalmay T Tags: Brief Funct Genomic Proteomic Source Type: journals

Cis-regulatory mutations in human disease.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 su...
Source: Briefings in Functional Genomics and Proteomics - July 28, 2009 Category: Genetics & Stem Cells Authors: Epstein DJ Tags: Brief Funct Genomic Proteomic Source Type: journals

Web-based tools and approaches to study long-range gene regulation in Metazoa.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 regulator...
Source: Briefings in Functional Genomics and Proteomics - July 14, 2009 Category: Genetics & Stem Cells Authors: Fredman D, Engström PG, Lenhard B Tags: Brief Funct Genomic Proteomic Source Type: journals

Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Briefings in Functional Genomics and Proteomics - July 12, 2009 Category: Genetics & Stem Cells Authors: Kleinjan DJ, Coutinho P Tags: Brief Funct Genomic Proteomic Source Type: journals

Finding common susceptibility variants for complex disease: past, present and future.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 [PubM...
Source: Briefings in Functional Genomics and Proteomics - June 30, 2009 Category: Genetics & Stem Cells Authors: Panoutsopoulou K, Zeggini E Tags: Brief Funct Genomic Proteomic Source Type: journals

Genomic regulatory blocks in vertebrates and implications in human disease.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - June 25, 2009 Category: Genetics & Stem Cells Authors: Navratilova P, Becker TS Tags: Brief Funct Genomic Proteomic Source Type: journals

Advantages of next-generation sequencing versus the microarray in epigenetic research.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - June 24, 2009 Category: Genetics & Stem Cells Authors: Hurd PJ, Nelson CJ Tags: Brief Funct Genomic Proteomic Source Type: journals

Close encounters of the 3C kind: long-range chromatin interactions and transcriptional regulation.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - June 16, 2009 Category: Genetics & Stem Cells Authors: Theo Sijtse Palstra RJ Tags: Brief Funct Genomic Proteomic Source Type: journals

Gene-regulatory networks in the Ciona embryos.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - June 16, 2009 Category: Genetics & Stem Cells Authors: Kubo A, Imai KS, Satou Y Tags: Brief Funct Genomic Proteomic Source Type: journals

Genetic variation in South Asia: assessing the influences of geography, language and ethnicity for understanding history and disease risk.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Briefings in Functional Genomics and Proteomics - June 16, 2009 Category: Genetics & Stem Cells Authors: Ayub Q, Tyler-Smith C Tags: Brief Funct Genomic Proteomic Source Type: journals

Identifying regulatory elements in eukaryotic genomes.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - June 3, 2009 Category: Genetics & Stem Cells Authors: Narlikar L, Ovcharenko I Tags: Brief Funct Genomic Proteomic Source Type: journals

Perspectives of gene expression profiling for diagnosis and therapy in haematological malignancies.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 lympha...
Source: Briefings in Functional Genomics and Proteomics - May 26, 2009 Category: Genetics & Stem Cells Authors: Bacher U, Kohlmann A, Haferlach T Tags: Brief Funct Genomic Proteomic Source Type: journals

Interesting times for microarray expression profiling.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 sampl...
Source: Briefings in Functional Genomics and Proteomics - May 26, 2009 Category: Genetics & Stem Cells Authors: Hey Y, Pepper SD Tags: Brief Funct Genomic Proteomic Source Type: journals

The human Major Histocompatibility Complex as a paradigm in genomics research.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 a...
Source: Briefings in Functional Genomics and Proteomics - May 24, 2009 Category: Genetics & Stem Cells Authors: Vandiedonck C, Knight JC Tags: Brief Funct Genomic Proteomic Source Type: journals

Quantitative proteomics for drug toxicity.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 f...
Source: Briefings in Functional Genomics and Proteomics - April 7, 2009 Category: Genetics & Stem Cells Authors: Gao Y, Holland RD, Yu LR Tags: Brief Funct Genomic Proteomic Source Type: journals

The Cartographers toolbox: building bigger and better human protein interaction networks.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - March 12, 2009 Category: Genetics & Stem Cells Authors: Sanderson CM Tags: Brief Funct Genomic Proteomic Source Type: journals

Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Briefings in Functional Genomics and Proteomics - March 11, 2009 Category: Genetics & Stem Cells Authors: Lacerda CM, Reardon KF Tags: Brief Funct Genomic Proteomic Source Type: journals

Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ad...
Source: Briefings in Functional Genomics and Proteomics - March 11, 2009 Category: Genetics & Stem Cells Authors: Yocum AK, Chinnaiyan AM Tags: Brief Funct Genomic Proteomic Source Type: journals

The quest for a message: budding yeast, a model organism to study the control of pre-mRNA splicing.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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. Furthe...
Source: Briefings in Functional Genomics and Proteomics - March 11, 2009 Category: Genetics & Stem Cells Authors: Meyer M, Vilardell J Tags: Brief Funct Genomic Proteomic Source Type: journals

Evolving 'omics' technologies for diagnostics of head and neck cancer.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Briefings in Functional Genomics and Proteomics - March 9, 2009 Category: Genetics & Stem Cells Authors: Nagaraj NS Tags: Brief Funct Genomic Proteomic Source Type: journals

18O Stable Isotope Labeling in MS-based Proteomics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 pept...
Source: Briefings in Functional Genomics and Proteomics - January 16, 2009 Category: Genetics & Stem Cells Authors: Ye X, Luke B, Andresson T, Blonder J Tags: Brief Funct Genomic Proteomic Source Type: journals

Targeted proteomics for validation of biomarkers in clinical samples.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Briefings in Functional Genomics and Proteomics - December 24, 2008 Category: Genetics & Stem Cells Authors: Ye X, Blonder J, Veenstra TD Tags: Brief Funct Genomic Proteomic Source Type: journals

Challenges and strategies for targeted phosphorylation site identification and quantification using mass spectrometry analysis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 si...
Source: Briefings in Functional Genomics and Proteomics - December 24, 2008 Category: Genetics & Stem Cells Authors: Blackburn K, Goshe MB Tags: Brief Funct Genomic Proteomic Source Type: journals

Comparative glycoproteomics: approaches and applications.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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...
Source: Briefings in Functional Genomics and Proteomics - December 17, 2008 Category: Genetics & Stem Cells Authors: Wei X, Li L Tags: Brief Funct Genomic Proteomic Source Type: journals

Polycistronic peptide coding genes in eukaryotes--how widespread are they?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - December 12, 2008 Category: Genetics & Stem Cells Authors: Tautz D Tags: Brief Funct Genomic Proteomic Source Type: journals

Applications of mass spectrometry in metabolomic studies of animal model and invertebrate systems.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - December 12, 2008 Category: Genetics & Stem Cells Authors: Kamleh MA, Dow JA, Watson DG Tags: Brief Funct Genomic Proteomic Source Type: journals

Reverse genetics in zebrafish by TILLING.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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, ong...
Source: Briefings in Functional Genomics and Proteomics - November 21, 2008 Category: Genetics & Stem Cells Authors: Moens CB, Donn TM, Wolf-Saxon ER, Ma TP Tags: Brief Funct Genomic Proteomic Source Type: journals

Using retroviruses as a mutagenesis tool to explore the zebrafish genome.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 t...
Source: Briefings in Functional Genomics and Proteomics - October 31, 2008 Category: Genetics & Stem Cells Authors: Jao LE, Maddison L, Chen W, Burgess SM Tags: Brief Funct Genomic Proteomic Source Type: journals

Medaka genome project.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 pr...
Source: Briefings in Functional Genomics and Proteomics - October 4, 2008 Category: Genetics & Stem Cells Authors: Kobayashi D, Takeda H Tags: Brief Funct Genomic Proteomic Source Type: journals

The neurogenetic frontier--lessons from misbehaving zebrafish.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 powe...
Source: Briefings in Functional Genomics and Proteomics - October 4, 2008 Category: Genetics & Stem Cells Authors: Burgess HA, Granato M Tags: Brief Funct Genomic Proteomic Source Type: journals

Illuminating signaling network functional biology through quantitative phosphoproteomic mass spectrometry.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ...
Source: Briefings in Functional Genomics and Proteomics - October 4, 2008 Category: Genetics & Stem Cells Authors: Tedford NC, White FM, Radding JA Tags: Brief Funct Genomic Proteomic Source Type: journals

Evaluation of cis-regulatory function in zebrafish.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 duplic...
Source: Briefings in Functional Genomics and Proteomics - September 27, 2008 Category: Genetics & Stem Cells Authors: Pashos EE, Kague E, Fisher S Tags: Brief Funct Genomic Proteomic Source Type: journals

Technological developments in lipidomics.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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)
Source: Briefings in Functional Genomics and Proteomics - September 19, 2008 Category: Genetics & Stem Cells Authors: Hou W, Zhou H, Elisma F, Bennett SA, Figeys D Tags: Brief Funct Genomic Proteomic Source Type: journals

Chemobehavioural phenomics and behaviour-based psychiatric drug discovery in the zebrafish.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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-scal...
Source: Briefings in Functional Genomics and Proteomics - September 10, 2008 Category: Genetics & Stem Cells Authors: Kokel D, Peterson RT Tags: Brief Funct Genomic Proteomic Source Type: journals

Uncharacterized/hypothetical proteins in biomedical 'omics' experiments: is novelty being swept under the carpet?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 u...
Source: Briefings in Functional Genomics and Proteomics - July 19, 2008 Category: Stem Cells Authors: Pawlowski K Tags: Brief Funct Genomic Proteomic Source Type: journals

Integrative approaches for mining transcriptional regulatory programs in Arabidopsis.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 environme...
Source: Briefings in Functional Genomics and Proteomics - July 16, 2008 Category: Stem Cells Authors: Krishnan A, Pereira A Tags: Brief Funct Genomic Proteomic Source Type: journals

Strategies for manufacturing recombinant adeno-associated virus vectors for gene therapy applications exploiting baculovirus technology.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
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 ex...
Source: Briefings in Functional Genomics and Proteomics - July 16, 2008 Category: Stem Cells Authors: Negrete A, Kotin RM Tags: Brief Funct Genomic Proteomic Source Type: journals

Editorial.Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
PMID: 18621799 [PubMed - as supplied by publisher] (Source: Briefings in Functional Genomics and Proteomics)
Source: Briefings in Functional Genomics and Proteomics - July 11, 2008 Category: Stem Cells Authors: Elgar G Tags: Brief Funct Genomic Proteomic Source Type: journals