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Identified Genes (identified + gene)
Selected AbstractsScreening of chondrogenic factors with a real-time fluorescence-monitoring cell line ATDC5-C2ER: Identification of sorting nexin 19 as a novel factorARTHRITIS & RHEUMATISM, Issue 11 2009Akinori Kan Objective To establish a cell culture system for noninvasive and real-time monitoring of chondrogenic differentiation in order to screen for chondrogenic factors. Methods The optimum reporter construct transfected into chondrogenic ATDC5 cells was selected by a luciferase reporter assay and fluorescence analysis during cultures with insulin. The established cell line was validated according to its fluorescence following stimulation with SOX proteins, bone morphogenetic protein 2 (BMP-2), or transforming growth factor , (TGF,) and was compared with the level of messenger RNA for COL2A1 as well as with the degree of Alcian blue staining. Screening of chondrogenic factors was performed by expression cloning using a retroviral expression library prepared from human tracheal cartilage. The expression pattern of the identified molecule was examined by in situ hybridization and immunohistochemistry. Functional analysis was performed by transfection of the identified gene, the small interfering RNA, and the mutated gene. Results We established an ATDC5 cell line with 4 repeats of a highly conserved enhancer ligated to a COL2A1 basal promoter and the DsRed2 reporter (ATDC5-C2ER). Fluorescence was induced under the stimulations with SOX proteins, BMP-2, or TGF,, showing good correspondence to the chondrogenic markers. Screening using the ATDC5-C2ER system identified several chondrogenic factors, including sorting nexin 19 (SNX19). SNX19 was expressed in the limb cartilage of mouse embryos and in the degraded cartilage of adult mouse knee joints during osteoarthritis progression. The gain-of-function and loss-of-function analyses revealed a potent chondrogenic activity of SNX19. Conclusion We established the ATDC5-C2ER system for efficient monitoring of chondrogenic differentiation by fluorescence analysis, and we identified a novel chondrogenic factor (SNX19) using this system. This system will be useful for elucidating the molecular network of chondrogenic differentiation. [source] 3332: The new IC3D nomenclature of corneal dystrophiesACTA OPHTHALMOLOGICA, Issue 2010J WEISS Purpose Advances in genotyping have challenged the significance of the entities called the corneal dystrophies. Although the term corneal dystrophy typically refers to a group of inherited corneal disease that are bilateral, symmetric, slowly progressive and without relation to sytemic disease or environmental factors; exceptions to each part of the definition exist. Mutations in different genes can result in one phenotype and mutations in one gene can result in different allelic dystrophy phenotypes. The phenotypic classification system has become archaic. The International Committee on the Classification of Corneal Dystrophies (ICD3) was created in 2005 to revise the corneal dystrophy nomenclature. Methods A critical evaluation of the literature to remove inaccurate information and distil the facts was performed by an international panel of world experts including geneticists, pathologist and ophthalmologists. A template was created for each dystrophy which summarized the genetic, clinical and pathologic information with accompanying clinical photographs. Each dystrophy was reviewed to determine if there was an identified gene, gene locus and whether it was clinically well defined. Results The dystrophies were organized anatomically and each dystrophy was assigned a category from 1 to 4 indicating the level of evidence supporting the existence of a given dystrophy. Category 1- A well defined dystrophy with known gene locus and gene Category 2- A well defined dystrophy with known gene locus, unknown gene Category 3- A well defined dystrophy with unknown gene locus and gene Category 4- A poorly defined dystrophy with unknown gene locus and gene Conclusion The IC3D nomenclature system is available online at www.corneasociety.org in English and Spanish. A German translation has just been completed. [source] Microarray analysis of retinoid-dependent gene activity during rat embryogenesis: Increased collagen fibril production in a model of retinoid insufficiencyDEVELOPMENTAL DYNAMICS, Issue 4 2004George R. Flentke Abstract Retinoic acid (RA) is an essential mediator of embryogenesis. Some, but not all, of its targets have been identified. We previously developed a rat model of gestational retinoid deficiency (RAD; Power et al. [1999] Dev. Dyn. 216:469,480) and generated embryos with developmental impairments that closely resemble genetic and dietary models of retinoid insufficiency. Here, we used microarray analysis and expression profiling to identify 88 transcripts whose abundance was altered under conditions of retinoid insufficiency, as compared with normal embryos. Among these, the induction by RAD of genes involved in collagen I synthesis (COL1A1, IA2 and VA2, prolyl-4-hydroxylase-,1) and protein galactosylation (galactokinase, ABO galactosyltransferase, UDP-galactose transporter-related protein) was especially noteworthy because extracellular matrix regulates many developmental events. We also identified several genes involved with stress responses (cathepsin H, UBC2E, IGFBP3, smoothelin). Real-time polymerase chain reaction analysis of selected candidates revealed excellent agreement with the array findings. Further validation came from the demonstration that these genes were similarly dysregulated in two genetic models of retinoid insufficiency, the retinol binding protein null-mutant embryo and the Raldh2 null-mutant embryo. In situ hybridization of RAD embryos found increased collagen IA1 and IGFBP3 mRNA within the connective mesenchyme and vasculature, respectively, and a failure to repress the growth factor midkine within the RAD neural tube. Many of the identified genes were not known previously to respond to retinoid status and will provide new insights to retinoid roles and to the consequences of retinoid insufficiency. Developmental Dynamics 229:886,898, 2004. © 2004 Wiley-Liss, Inc. [source] Expression profiling of IL-10-regulated genes in human monocytes and peripheral blood mononuclear cells from psoriatic patients during IL-10 therapyEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 2 2004Mechthild Jung Abstract Interleukin-10 (IL-10), originally identified as an inhibitor of pro-inflammatory cytokine production, exerts multiple immunomodulatory functions. Its ability to inhibit a Th1 response has been used in clinical trials for the treatment of inflammatory diseases including psoriasis. However, little is known about the molecular mechanisms of IL-10 functions. We aimed at identifying possiblemediators of in vitro IL-10 treatment in monocytes by gene chip technology using Hu95a Affymetrix mRNA arrays with,12,000 genes. To prove relevance of the identified genes for the clinicalsituation we compared these in vitro results with genes being regulated by IL-10 in peripheral blood mononuclear cells from psoriatic patients undergoing IL-10 therapy. A high proportion of the 1,600,genes up-regulated and 1,300 genes down-regulated in vitro was found to be similarly regulated in vivo. Some genes, which were previously unknown to be regulated by IL-10, can be assigned to known IL-10 functions like e.g. the increase of pathogen clearance. Other new potentially immunomodulating genes have been identified to be regulated by IL-10, but their impact needs to be experimentally evaluated. We could confirm a recently reported up-regulation of heme oxygenase-1 (HO-1). However, we demonstrate that the anti-inflammatory mechanisms of IL-10 remain functional even when HO-1 is irreversibly inhibited. [source] Schwann cells and the pathogenesis of inherited motor and sensory neuropathies (Charcot-Marie-Tooth disease)GLIA, Issue 4 2006Philipp Berger Abstract Over the last 15 years, a number of mutations in a variety of genes have been identified that lead to inherited motor and sensory neuropathies (HMSN), also called Charcot-Marie-Tooth disease (CMT). In this review we will focus on the molecular and cellular mechanisms that cause the Schwann cell pathologies observed in dysmyelinating and demyelinating forms of CMT. In most instances, the underlying gene defects alter primarily myelinating Schwann cells followed by secondary axonal degeneration. The first set of proteins affected by disease-causing mutations includes the myelin components PMP22, P0/MPZ, Cx32/GJB1, and periaxin. A second group contains the regulators of myelin gene transcription EGR2/Krox20 and SOX10. A third group is composed of intracellular Schwann cells proteins that are likely to be involved in the synthesis, transport and degradation of myelin components. These include the myotubularin-related lipid phosphatase MTMR2 and its regulatory binding partner MTMR13/SBF2, SIMPLE, and potentially also dynamin 2. Mutations affecting the mitochondrial fission factor GDAP1 may indicate an important contribution of mitochondria in myelination or myelin maintenance, whereas the functions of other identified genes, including NDRG1, KIAA1985, and the tyrosyl-tRNA synthase YARS, are not yet clear. Mutations in GDAP1, YARS, and the pleckstrin homology domain of dynamin 2 lead to an intermediate form of CMT that is characterized by moderately reduced nerve conduction velocity consistent with minor myelin deficits. Whether these phenotypes originate in Schwann cells or in neurons, or whether both cell types are directly affected, remains a challenging question. However, based on the advances in systematic gene identification in CMT and the analyses of the function and dysfunction of the affected proteins, crucially interconnected pathways in Schwann cells in health and disease have started to emerge. These networks include the control of myelin formation and stability, membrane trafficking, intracellular protein sorting and quality control, and may extend to mitochondrial dynamics and basic protein biosynthesis. © 2006 Wiley-Liss, Inc. [source] Identification of genes up-regulated by retinoic-acid-induced differentiation of the human neuronal precursor cell line NTERA-2 cl.D1JOURNAL OF NEUROCHEMISTRY, Issue 3 2001Frank Leypoldt The human teratocarcinoma cell line NTERA-2 cl.D1 (NT2 cells) can be induced with retinoic acid and cell aggregation to yield postmitotic neurones. This seems to model the in vivo situation, as high concentrations of retinoic acid, retinoic acid binding proteins, and receptors have been detected in the embryonic CNS and the developing spinal cord suggesting a role for retinoic acid in neurogenesis. Suppression subtractive hybridization was used to detect genes up-regulated by this paradigm of neuronal differentiation. Microfibril-associated glycoprotein 2 was found to be drastically up-regulated and has not been implicated in neuronal differentiation before. Suppression subtractive hybridization also identified DYRK4, a homologue of the Drosophila gene minibrain. Minibrain mutations result in specific defects in the development of the fly central nervous system. In adult rats, DYRK4 is only expressed in testis, but our results suggest an additional role for DYRK4 in neuronal differentiation. We have shown that suppression subtractive hybridization in conjunction with an efficient screening procedure is a valuable tool to produce a repertoire of differentially expressed genes and propose a new physiological role for several identified genes and expressed sequence tags. [source] Genetic analysis of functions involved in the late stages of biofilm development in Burkholderia cepacia H111MOLECULAR MICROBIOLOGY, Issue 2 2002Birgit Huber Summary Burkholderia cepacia and Pseudomonas aeruginosa often co-exist as mixed biofilms in the lungs of patients suffering from cystic fibrosis (CF). Here, we report the isolation of 13 random mini-Tn 5 insertion mutants of B. cepacia H111 that are defective in biofilm formation on a polystyrene surface. We show that the screening procedure used in this study is biased towards mutants defective in the late stages of biofilm development. A detailed quantitative analysis of the biofilm structures formed by wild-type and mutant strains revealed that the isolated mutants are impaired in their abilities to develop a typical three-dimensional biofilm structure. Molecular investigations showed that the genes required for biofilm maturation fall into several classes: (i) genes encoding for surface proteins; (ii) genes involved in the biogenesis and maintenance of an integral outer membrane; and (iii) genes encoding regulatory factors. It is shown that three of the regulatory mutants produce greatly reduced amounts of N -octanoylhomoserine lactone (C8-HSL). This compound serves as the major signal molecule of the cep quorum-sensing system. As this density-dependent regulatory system is involved in the regulation of biofilm maturation, we investigated the interplay between the three regulatory genes and the quorum-sensing cascade. The results of these investigations show that the identified genes encode for regulatory elements that are positioned upstream of the cep system, indicating that the quorum-sensing system of B. cepacia is a major checkpoint for biofilm formation. [source] GeneChip® expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genesMOLECULAR MICROBIOLOGY, Issue 5 2002Urs A. Ochsner Summary Upon iron restriction, the opportunistic pathogen Pseudomonas aeruginosa produces various virulence factors, including siderophores, exotoxin, proteases and haemolysin. The ferric uptake regulator (Fur) plays a central role in this response and also controls other regulatory genes, such as pvdS, which encodes an alternative sigma factor. This circuit leads to a hierarchical cascade of direct and indirect iron regulation. We used the GeneChip® to analyse the global gene expression profiles in response to iron. In iron-starved cells, the expression of 118 genes was increased at least fivefold compared with that in iron-replete cells, whereas the expression of 87 genes was decreased at least fivefold. The GeneChip® data correlated well with results obtained using individual lacZ gene fusions. Strong iron regulation was observed for previously identified genes involved in biosynthesis or uptake of the siderophores pyoverdine and pyochelin, utilization of heterologous siderophores and haem and ferrous iron transport. A low-iron milieu led to increased expression of the genes encoding TonB, alkaline protease, PrpL protease, exotoxin A, as well as fumarase C, Mn-dependent superoxide dismutase SodA, a ferredoxin and ferredoxin reductase and several oxidoreductases and dehydrogenases. Iron-controlled regulatory genes included seven alternative sigma factors and five other transcriptional regulators. Roughly 20% of the iron-regulated genes encoded proteins of unknown function and lacked any conclusive homologies. Under low-iron conditions, expression of 26 genes or operons was reduced in a ,pvdS mutant compared with wild type, including numerous novel pyoverdine biosynthetic genes. The GeneChip® proved to be a very useful tool for rapid gene expression analysis and identification of novel genes controlled by Fur or PvdS. [source] Ustilago maydis, model system for analysis of the molecular basis of fungal pathogenicityMOLECULAR PLANT PATHOLOGY, Issue 2 2004Christoph W. Basse SUMMARY Ustilago maydis, a facultative biotrophic basidiomycete fungus, causes smut disease in maize. A hallmark of this disease is the induction of large plant tumours that are filled with masses of black-pigmented teliospores. During the last 15 years U. maydis has become an important model system to unravel molecular mechanisms of fungal phytopathogenicity. This review highlights recent insights into molecular mechanisms of complex signalling pathways that are involved in the transition from budding to filamentous growth and operate during the pathogenic growth phase. In addition, we describe recent progress in understanding the structural basis of morphogenesis and polar growth in different stages of U. maydis development. Finally, we present an overview of recently identified genes related to pathogenic development and summarize novel molecular and genomic approaches that are powerful tools to explore the genetic base of pathogenicity. Taxonomy: Ustilago maydis (DC) Corda (synonymous with Ustilago zeae Ung.)-Kingdom Eukaryota, Phylum Fungi, Order Basidiomycota, Family Ustilaginomycetes, Genus Ustilago. Host range: Infects aerial parts of corn plants (Zea mays) and its progenitor teosinte (Zea mays ssp. parviglumis). Maize smut is distributed throughout the world. Disease symptoms: U. maydis causes chlorotic lesions in infected areas, the formation of anthocyanin pigments, necrosis, hyperplasia and hypertrophy of infected organs. Infection by U. maydis can inhibit development and lead to stunting of infected plants. A few days after infection plant tumours develop in which massive fungal proliferation and the formation of the black-pigmented, diploid teliospores occurs. Under natural conditions tumours predominantly develop on sexual organs (tassels and ears), stems and nodal shoots. Tumours may vary in size from minute pustules to several centimetres in diameter and contain up to 200 billion spores. Useful web site: http://www-genome.wi.mit.edu/annotation/fungi/ustilago_maydis/ [source] Ageing in Plants: Conserved Strategies and Novel PathwaysPLANT BIOLOGY, Issue 5 2003H.-C. Jing Abstract: Ageing increases chaos and entropy and ultimately leads to the death of living organisms. Nevertheless, single gene mutations substantially alter lifespan, revealing that ageing is subject to genetic control. In higher plants, ageing is most obviously manifested by the senescence of leaves, and recent molecular genetic studies, in particular the isolation of Arabidopsis mutants with altered leaf senescence, have greatly advanced our understanding of ageing regulation in plants. This paper provides an overview of the identified genes and their respective molecular pathways. Hormones, metabolic flux, reactive oxygen species and protein degradation are prominent strategies employed by plants to control leaf senescence. Plants predominantly use similar ageing-regulating strategies as yeast and animals but have evolved different molecular pathways. The senescence window concept is proposed to describe the age-dependent actions of the regulatory genes. It is concluded that the similarities and differences in ageing between plants and other organisms are deeply rooted in the evolution of ageing and we hope to stimulate discussion and research in the fascinating field of leaf senescence. [source] Proteome characterization of human T helper 1 and 2 cellsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 1 2004Kirsi Rautajoki Abstract T helper (Th) cells can be polarized into two different main subtypes, Th1 and Th2 cells. Their activation is linked to the eradication of different pathogens and to dissimilar immunological dysfunctions, which implies differences also in their protein expression patterns. To identify these differences, CD4+ T cells were isolated from human cord blood, polarized in vitro to Th1 and Th2 and activated via CD3 and CD28. Cells were lysed, soluble proteins were separated with two-dimensional electrophoresis and differing protein spots were identified with peptide mass fingerprinting. The expression of 14 proteins differed in Th1 and Th2 cells after both 7 and 14 days of polarization. Twelve of the proteins could be identified, most of which are new in this context. Two proteins were differentially modified in the two cell types. Especially, N -terminal acetylation of cyclophilin A was stronger in Th1 than in Th2 cells. To compare the RNA and the protein levels of the identified genes, mRNA expression was measured with Affymetrix oligonucleotide microarrays (HG-U133A). The mRNA and protein expression level correlated only in six cases out of eleven, which highlights the complementary roles that proteomics and transcriptomics have in the elucidation of biological phenomena. [source] Characterisation of gene expression in bovine adipose tissue before and after fatteningANIMAL GENETICS, Issue 3 2000M Oishi Summary It has been reported that fattening causes bovine adipose tissue development associated with an enlargement in adipocyte cell size. As a first study to elucidate mechanisms of bovine adipose tissue development during fattening, our experiment was designed to characterise gene expression in bovine adipose tissue before and after fattening. We randomly isolated a large number of cDNA clones derived from bovine adipose tissue before and after fattening. Sequence analysis of the isolated clones showed that 3 and 10 clones from before and after fattening, respectively, correspond to genes related to adipocyte development and/or function in the adipose tissue. In addition, we isolated cDNA clones that possess negative signal by hybridising the cDNA population from the adipose tissue after fattening with that before fattening as a probe. As a result, we identified five types of transcripts observed in the adipose tissue after fattening but not before fattening. Two of the five are likely to encode bovine orthologs of phospholipase A2 and RNA helicase p68, while the other three represent unknown genes. Further functional investigation of the identified genes might lead to elucidation of mechanisms of bovine adipose tissue development during fattening. [source] Genetic connections of the actin cytoskeleton and beyond,BIOESSAYS, Issue 5 2007Piergiorgio Percipalle Actin is a key protein in numerous cellular functions. One recent study has identified a large set of genes, associated with the actin cytoskeleton, which could be grouped into a wide spectrum of cytoplasmic and nuclear functions, such as protein biosynthesis and gene transcription.1 Deletions of many of the identified genes affected cellular actin organization,1 suggesting a functional link between different actin fractions probably regulated through changes in actin dynamics. The data are very exciting; speculations on the crosstalk between cytoplasmic and nuclear actin fractions in different cellular contexts may help placing the results in perspective to further understand how actin-mediated signalling affects cellular functions, such as gene expression. BioEssays 29:407,411, 2007. © 2007 Wiley Periodicals, Inc. [source] SEREX identification of new tumour-associated antigens in cutaneous T-cell lymphomaBRITISH JOURNAL OF DERMATOLOGY, Issue 2 2004T.B. Hartmann Summary Background Cutaneous T-cell lymphoma (CTCL) is a clonal lymphoproliferative disorder of mainly CD4+ T cells, with primary manifestation in the skin. Objectives To detect new CTCL-associated antigens for immunological therapies and to define their specificity in terms of RNA expression and seroreactivity. Methods A newly constructed CTCL cDNA phage library was screened and cross-reactivities against the detected clones were tested using 15 mycosis fungoides and six Sézary syndrome sera. The mRNA expression of the identified genes was analysed by reverse transcription,polymerase chain reaction (RT,PCR) using 22 tumour tissues, nine cell lines and up to 29 different types of normal tissue. Results We identified nine different tumour antigens (HD-CL-01 to HD-CL-09) of which seven clones had high homology to genes with known functions. Several of these genes had previously been associated with cancer, namely inositol 1,4,5-triphosphate 5-phosphatase, vimentin, aldose reductase and elongation factor-1,. Variations in the deduced protein sequences were observed in three cases, mostly due to variations in protein length. The individual clones were recognized by up to 56% of patients' sera, while control sera were negative except in one case. Using RT,PCR, we found a frequent expression of these new tumour antigens in tumour specimens (26,100%). In contrast to humoral specificity, specific mRNA was also detected in selected normal tissues (29,89%). Conclusions SEREX (serological identification of antigens by recombinant expression cloning) identified multiple tumour-associated antigens in CTCL. The serological specificity and the high percentage of reactive sera of CTCL patients against several clones suggest these genes as potential targets for diagnostic and prognostic purposes. [source] | ||||||||||||||||||||||