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Certain Genes (certain + gene)
Selected AbstractsQSAR model for alignment-free prediction of human breast cancer biomarkers based on electrostatic potentials of protein pseudofolding HP-lattice networksJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2008Santiago Vilar Abstract Network theory allows relationships to be established between numerical parameters that describe the molecular structure of genes and proteins and their biological properties. These models can be considered as quantitative structure,activity relationships (QSAR) for biopolymers. The work described here concerns the first QSAR model for 122 proteins that are associated with human breast cancer (HBC), as identified experimentally by Sjöblom et al. (Science 2006, 314, 268) from over 10,000 human proteins. In this study, the 122 proteins related to HBC (HBCp) and a control group of 200 proteins that are not related to HBC (non-HBCp) were forced to fold in an HP lattice network. From these networks a series of electrostatic potential parameters (,k) was calculated to describe each protein numerically. The use of ,k as an entry point to linear discriminant analysis led to a QSAR model to discriminate between HBCp and non-HBCp, and this model could help to predict the involvement of a certain gene and/or protein in HBC. In addition, validation procedures were carried out on the model and these included an external prediction series and evaluation of an additional series of 1000 non-HBCp. In all cases good levels of classification were obtained with values above 80%. This study represents the first example of a QSAR model for the computational chemistry inspired search of potential HBC protein biomarkers. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008 [source] Induction of early murine cytomegalovirus infection by different reporter gene-associated recombinant virusesJOURNAL OF VIRAL HEPATITIS, Issue 6 2006U. Drebber Summary., Murine cytomegalovirus (MCMV) has provided useful models for acute, chronic and latent CMV infection because of its similarities in structure and biology with human CMV. We report the induction of acute MCMV hepatitis with different bacterial artificial chromosome (BAC)-cloned virus constructs [MCMV-SEAP which includes the gene for secreted alkaline phosphatase (SEAP) under Rous sarcoma virus (RSV)-promoter control, MCMV-GFP which includes the gene for enhanced green fluorescent protein (eGFP) under HCMV-ie promoter control, MCMV-HBs includes the gene for hepatitis B surface antigen (HBsAg) under simian virus (SV)40-promoter control and the DeltaMC95.21 virus in which the m152 gene was deleted and substituted by the reporter gene lacZ] in order to elucidate the histopathological changes together with different reporter-gene products in the liver tissue and the effect of the deletion of a certain gene. All the virus constructs induced a similar mild acute hepatitis which had its climax from days 3 to 5 post-infection in immunocompetent mice. In situ, the reporter-gene products beta-galactosidase and secreted alkaline phosphatase could be visualized in relation to the inflammatory changes. The composition of the invading cell populations did not change even in the absence of the m152 gene. Additionally discrete inflammatory changes were seen in kidney and serosa while the other organs were not involved. This model helps us understand the immunological and histopathological mechanisms of the CMV-induced hepatitis, which plays an important role especially in the immunocompromised patient. The morphological changes can be analysed while the respective reporter gene product is expressed by the virus construct. [source] Understanding heterologous protein overproduction under the T7 promoter: A practical exerciseBIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, Issue 3 2002Evangelos Christodoulou Abstract Because various genome projects have been advanced many genes are known, and large amounts of proteins are required to elucidate their function. Most biomolecular research laboratories have a need to overexpress a certain gene, or a part of it, in eukaryotic or prokaryotic expression systems. It is therefore important for young students to become familiar with the technology of heterologous gene expression systems. Gene expression in eukaryotic cells is rather complicated and costly and is therefore not ideally suited to exercises for students. The goal of this paper is to describe an experimental example of a well known and broadly used prokaryotic system, the pET system, that works under the strong T7 promoter. The clones described in this paper are suitable for the practical exercise and are available upon request. [source] Villin: A marker for development of the epithelial pyloric borderDEVELOPMENTAL DYNAMICS, Issue 1 2002Evan M. Braunstein Abstract In the adult gastrointestinal tract, the morphologic borders between esophagus and stomach and between stomach and small intestine are literally one cell thick. The patterning mechanisms that underlie the development of these sharp regional divisions from a once continuous endodermal tube are still obscure. In the embryonic endoderm of the developing gut, region-specific expression of certain genes (e.g., intestine-specific expression of the actin bundling protein villin) can be detected as early as 9.0 days post coitum, although the morphologic differentiation of the gut epithelium proper does not begin until 4 to 5 days later. By using a mouse model in which a ,-galactosidase marker has been inserted into the endogenous villin locus, we examined the development of the stomach/intestinal (pyloric) border during gut organogenesis. The data indicate that the border is not sharp from the outset. Rather, the initial border region is characterized by a decreasing gradient of villin/,-galactosidase expression that extends into the distal stomach. A sharp epithelial border of villin/,-galactosidase expression appears abruptly at day 16 and is further refined over the next 3 weeks to form the distinct one-cell-thick border characteristic of the adult. These results indicate that an important previously unrecognized patterning event occurs in the gut epithelium at 16 days; this event may define an epithelial compartment boundary between the stomach and the intestine. The villin/,-galactosidase mouse model characterized here provides an excellent substrate with which to further dissect the mechanisms involved in this patterning process. © 2002 Wiley-Liss, Inc. [source] microRNAs in acute myeloid leukemia: Expression patterns, correlations with genetic and clinical parameters, and prognostic significanceGENES, CHROMOSOMES AND CANCER, Issue 3 2010Rotraud Wieser Acute myeloid leukemia (AML) is a malignant disease of hematopoietic cells whose emergence, course, and prognosis is affected by specific recurrent genetic alterations like chromosome aberrations and point mutations, as well as by changes in the expression of certain genes. In the past 2 years, microRNAs (miRNAs),a novel class of small RNA molecules involved in posttranscriptional gene regulation,have also been shown to be aberrantly expressed in AML. Furthermore, specific miRNA expression patterns were found to be associated with certain genetic and cytogenetic alterations in this disease, and two studies identified miRNAs whose expression levels were predictive of survival. Interestingly, the results of these analyses showed only very limited congruence. This review summarizes published reports on the expression patterns of miRNAs in AML, and discusses possible reasons for the differences in their results. © 2009 Wiley-Liss, Inc. [source] The human complement C9 gene: structural analysis of the 5, gene region and genetic polymorphism studiesINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 5 2001K. Witzel-Schlömp Summary C9 is the last of the human complement components creating the membrane attack complex. The single chain serum protein is encoded by a gene located on chromosome 5p13 that is composed of 11 exons. With the aid of inverse PCR, the hitherto unknown regions flanking exon 1 and the 3, part of exon 11 (3,UTR) have been sequenced. A computer-based analysis of the 300-bp region located just upstream of the AUG start codon showed homologies to known DNA modules which affect the transcriptional regulation of certain genes. The most striking of these is a sequence that may substitute the missing TATA box in initiating C9 transcription. In the 3,UTR, three successive polyadenylation signals were found. Although the C9 protein is invariant, four different single nucleotide polymorphisms (SNPs) have been observed at the DNA level by exon-specific PCR and direct sequencing. None of them changes the amino acid composition of the mature protein. Due to a C , T transition in exon 1 at cDNA position 17, the fifth amino acid of the leader peptide may be either an arginine or a tryptophane. Using either PCR/RFLP analysis (exons 1 and 11) or allele-specific PCR (intron 1 and exon 4), each polymorphism can be characterized without sequencing. All of the exon 1, intron 1 and exon 11 variants could be detected in small population samples of European, Thai or South American Indian origin. In contrast, the exon 4 C variant was observed only once in a European. The first three SNPs can be combined to designate eight different ,C9 alleles'. Of these, six have actually be found. These data provide strong evidence that several mutation and recombination events occurred in the course of C9 gene evolution. [source] Nuclear pore complex oxalate binding protein p62: Its expression on oxalate exposure to VERO cellsJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2004P. Sivakamasundari Abstract Oxalate rich stones are the most common among the various stones. Oxalate binding protein plays a vital role in the transport of oxalate. Nuclear pore complex (NPC) contains a protein of molecular weight 62 kDa and it has maximum oxalate binding activity. The physiological significance of the presence of oxalate binding protein in the NPC is not well understood. In order to study its function, the expression of this protein during oxalate stress condition and the morphological changes on oxalate exposure to synchronized VERO cells have been determined. VERO cells were synchronized at different stages of cell cycle using cell cycle blockers and expression of the NPC p62 was assessed using enzyme linked immunosorbent assay (ELISA) technique with p62 antibody (MAb 414). Expression of NPC p62 was more pronounced in 1.0 mM oxalate concentration in mitotic phase than in S phase, suggesting cell cycle dependency. During oxalate exposure there is cell aggregation and complete degeneration of cell morphology occurs, which in turn lead to the expression of certain genes, including the NPC oxalate binding protein p62. Thus, oxalate induces degeneration of cells (may be due to the lipid peroxidation) and leads to the expression of NPC oxalate binding protein and the expression is of cell cycle dependent manner. © 2004 Wiley-Liss, Inc. [source] Thyroid tumor marker genomics and proteomics: Diagnostic and clinical implicationsJOURNAL OF CELLULAR PHYSIOLOGY, Issue 3 2010Angelo Carpi Two systems biology concepts, genomics and proteomics, are highlighted in this review. These techniques are implemented to optimize the use of thyroid tumor markers (TTM). Tissue microarray studies can produce genetic maps and proteomics, patterns of protein expression of TTM derived from preoperative biopsies and specimens. For instance, papillary and medullary thyroid cancers harbor RAS, RET, and BRAF genetic mutations. Follicular thyroid cancers harbor translocations and fusions of certain genes (PAX 8 and PPAR-gamma). Proteomic analysis from various tissue sources can provide useful information regarding the overall state of a thyroid cancer cell. Understanding the molecular events related to these genetic and protein alterations can potentially clarify thyroid cancer pathogenesis and guide appropriate molecular targeted therapies. However, despite the realization that these emerging technologies hold great promise, there are still significant obstacles to the routine use of TTM. These include equivocal thyroid nodule tissue morphologic interpretations, inadequate standardization of methods, and monetary costs. Interpretative shortcomings are frequently due to the relative scarcity of cellular material from fine-needle aspiration biopsy (FNAB) specimens. This can be rectified with large needle aspiration biopsy (LNAB) techniques and is exemplified by the favorable performance of galectin-3 determinations on LNAB specimens. J. Cell. Physiol. 224: 612,619, 2010. © 2010 Wiley-Liss, Inc. [source] Solid emulsion gel as a vehicle for delivery of polyunsaturated fatty acids: implications for tissue repair, dermal angiogenesis and wound healingJOURNAL OF TISSUE ENGINEERING AND REGENERATIVE MEDICINE, Issue 7 2008Kirill I. Shingel Abstract The paper describes preparation and biological characterization of the solid hybrid biomaterial that was designed for cell-targeted lipid delivery in healing tissues. The material referred to as ,solid emulsion gel' combines a protein-stabilized lipid emulsion and a hydrogel structure in a single compartment. The potential of the omega-3 (n-3)-fatty acids rich solid emulsion gel for tissue repair applications was investigated at the macro-, micro-, molecular and gene expression levels, using human fibroblasts and endothelial cells and a porcine model of full-thickness wounds. Being non-cytotoxic in vitro and in vivo, the biomaterial was found to affect cell metabolism, modulate expression of certain genes, stimulate early angiogenesis and promote wound repair in vivo. The neovascular response in vivo was correlated with upregulated expression of the genes involved in lipid transport (e.g. adipophilin), anti-apoptosis (e.g. heat shock proteins, haem oxygenase 1) and angiogenesis (vascular endothelial growth factor, placental growth factor). Collectively, the results of this study provide first evidence that the angiogenic response provided by solid emulsion gel-mediated delivery of n-3 fatty acids is an alternative to the topical administration of exogenous growth factors or gene therapy, and can be advantageously used for the stimulation of tissue repair in complex wounds. Copyright © 2008 John Wiley & Sons, Ltd. [source] Von Hippel-Lindau diseaseMICROSCOPY RESEARCH AND TECHNIQUE, Issue 2 2003Toshiaki Sano Abstract Von Hippel-Lindau (VHL) disease is an uncommon, autosomal dominant hereditary multitumor syndrome caused by germline alterations of the VHL gene, which has been cloned recently and identified as a tumor suppressor gene. The major lesions in VHL disease include hemangioblastomas in the central nervous system and retina, clear cell renal cell carcinomas, pheochromocytomas, pancreatic tumors, epididymal cystadenomas, endolymphatic sac tumors, carcinoid tumors, and multiple cysts of the kidney, pancreas, and epididymis. Compared with sporadic ones, the tumors in VHL disease develop at an earlier age and often multifocally. Histologic features of VHL tumors are characterized by their high degree of vascularization and the presence of a clear cell component. Hypervascularization is induced by overexpression of vascular endothelial growth factor (VEGF), and because the principal function of VHL protein is the negative regulation of hypoxia-inducible mRNAs including VEGF mRNA, inactivation of VHL gene plays critical roles in angiogenesis of the VHL tumors. In addition, since VHL protein is also required for the down-regulation of transcription activity of certain genes for the cell growth and cell cycle, inactivation of VHL gene may contribute to tumorigenesis of the VHL tumors. A significant difference in the frequency of types of VHL gene mutation has been noted among the affected families, known as the genotype-phenotype correlations. Microsc. Res. Tech. 60:159,164, 2003. © 2003 Wiley-Liss, Inc. [source] Chaperones of the type III secretion pathway: jacks of all tradesMOLECULAR MICROBIOLOGY, Issue 1 2002Anne-Laure Page Summary The type III secretion (TTS) pathway is used by many Gram-negative bacteria to inject virulence proteins into cells of their host. The activity of the TTS apparatus is controlled by external signals and, in certain conditions, production and secretion are not coupled. Storage of some proteins before secretion involves their association with specific chaperones. Three classes of TTS chaperones have been distinguished according to whether they associate with: (i) one; (ii) several effector proteins; or (iii) the two translocators that allow passage of effectors across the membrane of eukaryotic cells. These chaperones are required for stabilization of their substrate(s) and prevention of their premature interactions with other partners during storage. They also play a role in secretion of their substrate(s). Some chaperones are also involved in transcriptional regulation of certain genes in response to the activity of secretion. The flagellar export apparatus is closely related to the TTS apparatus and some proteins of the flagellar export system have also been proposed to be chaperones that prevent premature interactions between the flagellum subunits. [source] An illustrated gardener's guide to transgenic Arabidopsis field experimentsNEW PHYTOLOGIST, Issue 2 2008Martin Frenkel Summary ,,Field studies with transgenic Arabidopsis lines have been performed over 8 yr, to better understand the influence that certain genes have on plant performance. Many (if not most) plant phenotypes cannot be observed under the near constant, low-stress conditions in growth chambers, making field experiments necessary. However, there are challenges in performing such experiments: permission must be obtained and regulations obeyed, the profound influence of uncontrollable biotic and abiotic factors has to be considered, and experimental design has to be strictly controlled. ,,The aim here is to provide inspiration and guidelines for researchers who are not used to setting up such experiments, allowing others to learn from our mistakes. ,, This is believed to be the first example of a ,manual' for field experiments with transgenic Arabidopsis plants. Many of the challenges encountered are common for all field experiments, and many researchers from ecological backgrounds are skilled in such methods. ,,There is huge potential in combining the detailed mechanistic understanding of molecular biologists with ecologists' expertise in examining plant performance under field conditions, and it is suggested that more interdisciplinary collaborations will open up new scientific avenues to aid analyses of the roles of genetic and physiological variation in natural systems. [source] The rice Mybleu transcription factor increases tolerance to oxygen deprivation in Arabidopsis plantsPHYSIOLOGIA PLANTARUM, Issue 1 2007Monica Mattana Mybleu is a natural incomplete transcription factor of rice (Oryza sativa), consisting of a partial Myb repeat followed by a short leucine zipper. We previously showed its localization to the apical region of rice roots and coleoptiles. Specifically, in coleoptiles, Mybleu is expressed under both aerobic and anaerobic conditions, whereas in roots, it is expressed only under aerobic conditions. Mybleu is able to dimerize with canonical leucine zippers and to activate transcription selectively. To investigate Mybleu function in vivo, we transformed Arabidopsis thaliana and evaluated several morphological, physiological and biochemical parameters. In agreement with a hypothesized role of Mybleu in cell elongation in the differentiation zone, we found that the constitutive expression of this transcription factor in Arabidopsis induced elongation in the primary roots and in the internodal region of the floral stem; we also observed a modification of the root apex morphology in transformed lines. Based on the high expression of Mybleu in anaerobic rice coleoptiles, we studied the role of this transcription factor in transgenic plants grown under low-oxygen conditions. We found that overexpression of this transcription factor increased tolerance to oxygen deficit. In transgenic plants, this effect may depend both on the maintenance of a higher metabolism during stress and on the higher expression levels of certain genes involved in the anaerobic response. [source] Nonparametric Testing for DNA Copy Number Induced Differential mRNA Gene ExpressionBIOMETRICS, Issue 1 2009Wessel N. Van Wieringen Summary The central dogma of molecular biology relates DNA with mRNA. Array CGH measures DNA copy number and gene expression microarrays measure the amount of mRNA. Methods that integrate data from these two platforms may uncover meaningful biological relationships that further our understanding of cancer. We develop nonparametric tests for the detection of copy number induced differential gene expression. The tests incorporate the uncertainty of the calling of genomic aberrations. The test is preceded by a "tuning algorithm" that discards certain genes to improve the overall power of the false discovery rate selection procedure. Moreover, the test statistics are "shrunken" to borrow information across neighboring genes that share the same array CGH signature. For each gene we also estimate its effect, its amount of differential expression due to copy number changes, and calculate the coefficient of determination. The method is illustrated on breast cancer data, in which it confirms previously reported findings, now with a more profound statistical underpinning. [source] Dermal fibroblast-associated gene induction by asiaticoside shown in vitro by DNA microarray analysisBRITISH JOURNAL OF DERMATOLOGY, Issue 3 2004L. Lu Summary Background, Asiaticoside, isolated from Centella asiatica, promotes fibroblast proliferation and extracellular matrix (ECM) synthesis in wound healing. The precise mechanism, however, in molecular and gene expression levels is still unclear. Objective, Using cDNA microarray technology, the alteration of gene expression profiles was determined for human dermal fibroblasts in vitro in the presence of asiaticoside (30 ,g mL,1). Fifty-four genes, with known functions for cell proliferation, cell cycle progression and synthesis of ECM, were significantly upregulated in our ,genome-nest' expression profile at various time points. Furthermore, the mRNA levels and protein production of certain genes responsible for ECM synthesis (e.g. encoding type I and type III collagen proteins) were evaluated by Northern blot and radioimmunoassay, respectively. Results, We found that there is a close correlation between the gene profile, mRNA and protein production in the response of the cells to asiaticoside stimulation. Conclusions, This information could be used for exploring the response of the target genes to asiaticoside in fibroblasts. 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