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Postgenomic Era (postgenomic + era)
Selected AbstractsRedefining Personalized Medicine in the Postgenomic EraBJU INTERNATIONAL, Issue 2 2010Developing bladder cancer therapeutics with proteomics First page of article [source] A Graphene Oxide,Streptavidin Complex for Biorecognition , Towards Affinity PurificationADVANCED FUNCTIONAL MATERIALS, Issue 17 2010Zunfeng Liu Abstract In our postgenomic era, understanding of protein-protein interactions by characterizing the structure of the corresponding protein complex is becoming increasingly important. An important problem is that many protein complexes are only stable for a few minutes. Dissociation will occur when using the typical, time-consuming purification methods such as tandem affinity purification and multiple chromatographic separations. Therefore, there is an urgent need for a quick and efficient protein-complex purification method for 3D structure characterization. The graphene oxide (GO)·streptavidin complex is prepared via a GO·biotin·streptavidin strategy and used for affinity purification. The complex shows a strong biotin recognition capability and an excellent loading capacity. Capturing biotinylated DNA, fluorophores and Au nanoparticles on the GO·streptavidin complexes demonstrates the usefulness of the GO·streptavidin complex as a docking matrix for affinity purification. GO shows a high transparency towards electron beams, making it specifically well suited for direct imaging by electron microscopy. The captured protein complex can be separated via a filtration process or even via on-grid purification and used directly for single-particle analysis via cryo-electron microscopy. Therefore, the purification, sample preparation, and characterization are rolled into one single step. [source] A new molecular tool for transgenic diatomsFEBS JOURNAL, Issue 13 2005Control of mRNA, protein biosynthesis by an inducible promoter, terminator cassette Research in diatom biology has entered the postgenomic era since the recent completion of the Thalassiosira pseudonana genome project. However, the molecular tools available for genetic manipulation of diatoms are still sparse, impeding the functional analysis of diatom genes in vivo. Here we describe the first method for inducible gene expression in transgenic diatoms. This method uses a DNA cassette containing both promoter (Pnr) and terminator (Tnr) elements derived from the nitrate reductase gene of the diatom Cylindrotheca fusiformis. By using green fluorescent protein (gfp) cDNA as a reporter gene, it is demonstrated that gene expression under the control of the Pnr/Tnr cassette is switched off when cells are grown in the presence of ammonium ions and becomes switched on within 4 h when cells are transferred to medium containing nitrate. Incubating cells in nitrogen-free medium switches on transcription of the gfp gene, yet gfp mRNA does not become translated into protein. This block on translation is released by the addition of nitrate, resulting in rapid onset of GFP production with a drastically reduced delay time of only 1 h. Altogether we have demonstrated that the Pnr/Tnr cassette enables inducible gene expression and control of both the level and timing of mRNA and protein expression in transgenic diatoms. [source] Identifying infection-associated genes of Candida albicans in the postgenomic eraFEMS YEAST RESEARCH, Issue 5 2009Duncan Wilson Abstract The human pathogenic yeast Candida albicans can cause an unusually broad range of infections reflecting a remarkable potential to adapt to various microniches within the human host. The exceptional adaptability of C. albicans is mediated by rapid alterations in gene expression in response to various environmental stimuli and this transcriptional flexibility can be monitored with tools such as microarrays. Using such technology it is possible to (1) capture a genome-wide portrait of the transcriptome that mirrors the environmental conditions, (2) identify known genes, signalling pathways and transcription factors involved in pathogenesis, (3) identify new patterns of gene expression and (4) identify previously uncharacterized genes that may be associated with infection. In this review, we describe the molecular dissection of three distinct stages of infections, covering both superficial and invasive disease, using in vitro, ex vivo and in vivo infection models and microarrays. [source] Capillary electrophoresis applied to proteomic analysisJOURNAL OF SEPARATION SCIENCE, JSS, Issue 8 2009Bryan R. Fonslow Abstract In the postgenomic era, proteomics has become a dominant field for identifying and quantifying the complex protein machinery of the cell. The expression levels, posttranslational modifications, and specific interactions of proteins control the biology of such processes as development, differentiation, and signal transduction. Studies of the proteins involved in these processes often lead to a better understanding of biology and of human disease. Powerful separation techniques and sensitive detection methods enable researchers to untangle these complicated networks of processes. CE coupled with either MS or LIF are two of the techniques that make this possible. This review will cover proven CE-based methods for proteomics on the cell and tissue level and their application in biological and clinical studies, relevant new developments in enabling technology such as microfluidic CE-MS demonstrated on model systems, and comment on the future of CE in proteomics. [source] Gene trap mutagenesis in mice: New perspectives and tools in cancer researchCANCER SCIENCE, Issue 1 2008Ken-ichi Yamamura The complete human DNA sequence of the human genome was published in 2004 and we entered the postgenomic era. However, many studies showed that gene function is much more complex than we expected, and that mutation of disease genes does not give any clue for molecular mechanisms for disease development. Since the first report on gene knockout mice in 1989, knockout mice have been shown to be a powerful tool for functional genomics and for the dissection of developmental processes in human diseases. In accordance with this successful application of knockout mice, three major mouse knockout programs are now underway worldwide, to mutate all protein-encoding genes in mouse embryonic stem cells using a combination of gene trapping and gene targeting. We developed the exchangeable gene trap method suitable for large scale mutagenesis in mice. In this method we can produce null mutation and post-insertional modification, enabling replacement of the marker gene with a gene of interest and conditional knockout. We herein discuss the effect of this gene-driven type approach for cancer research, especially for finding the genes that are related to cancer, but are paid little attention in hypothesis-driven cancer research. (Cancer Sci 2008; 99: 1,6) [source] Synthesis of S -Adenosyl- L -homocysteine Capture Compounds for Selective Photoinduced Isolation of MethyltransferasesCHEMBIOCHEM, Issue 2 2010Christian Dalhoff Dr. Abstract Understanding the interplay of different cellular proteins and their substrates is of major interest in the postgenomic era. For this purpose, selective isolation and identification of proteins from complex biological samples is necessary and targeted isolation of enzyme families is a challenging task. Over the last years, methods like activity-based protein profiling (ABPP) and capture compound mass spectrometry (CCMS) have been developed to reduce the complexity of the proteome by means of protein function in contrast to standard approaches, which utilize differences in physical properties for protein separation. To isolate and identify the subproteome consisting of S -adenosyl- L -methionine (SAM or AdoMet)-dependent methyltransferases (methylome), we developed and synthesized trifunctional capture compounds containing the chemically stable cofactor product S -adenosyl- L -homocysteine (SAH or AdoHcy) as selectivity function. SAH analogues with amino linkers at the N6 or C8 positions were synthesized and attached to scaffolds containing different photocrosslinking groups for covalent protein modification and biotin for affinity isolation. The utility of these SAH capture compounds for selective photoinduced protein isolation is demonstrated for various methyltransferases (MTases) acting on DNA, RNA and proteins as well as with Escherichia coli cell lysate. In addition, they can be used to determine dissociation constants for MTase,cofactor complexes. [source] | |||||||||||||