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Distinct Genes (distinct + gene)
Selected AbstractsMorphological irregularities and features of resistance to apoptosis in the dcp-1/pita double mutated egg chambers during Drosophila oogenesisCYTOSKELETON, Issue 1 2005Ioannis P. Nezis Abstract In the present study, we demonstrate the most novel characteristic morphological features of Drosophila egg chambers lacking both dcp-1 and pita functions in the germline cells. Dcp-1 is an effector caspase and it has been previously shown to play an important role during Drosophila oogenesis [McCall and Steller, 1998 : Science 279 : 230,234; Laundrie et al., 2003 : Genetics 165 : 1881,1888; Peterson et al., 2003 : Dev Biol 260 : 113,123]. The completion of sequencing and annotation of the Drosophila genome has revealed that the dcp-1 gene is nested within an intron of another distinct gene, called pita, a member of the C2H2 zinc finger protein family that regulates transcriptional initiation. The dcp-1,/,/pita,/, nurse cells exhibit euchromatic nuclei (delay of apoptosis) during the late stages of oogenesis, as revealed by conventional light and electron microscopy. The phalloidin-FITC staining discloses significant defects in actin cytoskeleton arrangement. The actin bundles fail to organize properly and the distribution of actin filaments in the ring canals is changed compared to the wild type. The oocyte and the chorion structures have been also modified. The oocyte nucleus is out of position and the chorion appears to contain irregular foldings, while the respiratory filaments obtain an altered morphology. The dcp-1,/,/pita,/, egg chambers do not exhibit the rare events of spontaneously induced apoptosis, observed for the wild type flies, during mid-oogenesis. Interestingly, the mutated egg chambers are protected by staurosporine-induced apoptosis in a percentage of 40%, strongly suggesting the essential role of dcp-1 and/or pita during mid-oogenesis. Cell Motil. Cytoskeleton 60:14,23, 2005. © 2004 Wiley-Liss, Inc. [source] Enzymatic control of anhydrobiosis-related accumulation of trehalose in the sleeping chironomid, Polypedilum vanderplankiFEBS JOURNAL, Issue 20 2010Kanako Mitsumasu Larvae of an anhydrobiotic insect, Polypedilum vanderplanki, accumulate very large amounts of trehalose as a compatible solute on desiccation, but the molecular mechanisms underlying this accumulation are unclear. We therefore isolated the genes coding for trehalose metabolism enzymes, i.e. trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP) for the synthesis step, and trehalase (TREH) for the degradation step. Although computational prediction indicated that the alternative splicing variants (PvTps,/,) obtained encoded probable functional motifs consisting of a typical consensus domain of TPS and a conserved sequence of TPP, PvTps, did not exert activity as TPP, but only as TPS. Instead, a distinct gene (PvTpp) obtained expressed TPP activity. Previous reports have suggested that insect TPS is, exceptionally, a bifunctional enzyme governing both TPS and TPP. In this article, we propose that TPS and TPP activities in insects can be attributed to discrete genes. The translated product of the TREH ortholog (PvTreh) certainly degraded trehalose to glucose. Trehalose was synthesized abundantly, consistent with increased activities of TPS and TPP and suppressed TREH activity. These results show that trehalose accumulation observed during anhydrobiosis induction in desiccating larvae can be attributed to the activation of the trehalose synthetic pathway and to the depression of trehalose hydrolysis. [source] Non-core subunit eIF3h of translation initiation factor eIF3 regulates zebrafish embryonic developmentDEVELOPMENTAL DYNAMICS, Issue 6 2010Avik Choudhuri Abstract Eukaryotic translation initiation factor eIF3, which plays a central role in translation initiation, consists of five core subunits that are present in both the budding yeast and higher eukaryotes. However, higher eukaryotic eIF3 contains additional (non-core) subunits that are absent in the budding yeast. We investigated the role of one such non-core eIF3 subunit eIF3h, encoded by two distinct genes,eif3ha and eif3hb, as a regulator of embryonic development in zebrafish. Both eif3h genes are expressed during early embryogenesis, and display overlapping yet distinct and highly dynamic spatial expression patterns. Loss of function analysis using specific morpholino oligomers indicates that each isoform has specific as well as redundant functions during early development. The morphant phenotypes correlate with their spatial expression patterns, indicating that eif3h regulates development of the brain, heart, vasculature, and lateral line. These results indicate that the non-core subunits of eIF3 regulate specific developmental programs during vertebrate embryogenesis. Developmental Dynamics 239:1632,1644, 2010. © 2010 Wiley-Liss, Inc. [source] Novel member of the mouse desmoglein gene family: Dsg1-,EXPERIMENTAL DERMATOLOGY, Issue 1 2003L. Pulkkinen Abstract: Desmosomes are major intercellular adhesion junctions that provide stable cell,cell contacts and mechanical strength to epithelial tissues by anchoring cytokeratin intermediate filaments of adjacent cells. Desmogleins (Dsg) are transmembrane core components of the desmosomes, and belong to the cadherin supergene family of calcium-dependent adhesion molecules. Currently, there are three known isoforms of Dsgs (Dsg1, Dsg2, and Dsg3), encoded by distinct genes that are differentially expressed to determine their tissue specificity and differentiation state of epithelial cells. In this study, we cloned a novel mouse desmoglein gene sharing high homology to both mouse and human Dsg1. We propose to designate the previously published mouse Dsg1 gene as Dsg1- , and the new gene as Dsg1-,. Analysis of intron/exon organization of the Dsg1-, and Dsg1-, genes revealed significant conservation. The full-length mouse Dsg1-, cDNA contains an open reading frame of 3180 bp encoding a precursor protein of 1060 amino acids. Dsg1-, protein shares 94% and 76% identity with mouse Dsg1-, and human DSG1, respectively. RT-PCR using a multitissue cDNA panel demonstrated that while Dsg1-, mRNA was expressed in 15- to 17-day-old embryos and adult spleen and testis, Dsg1-, mRNA was detected in 17-day-old embryos only. To assess subcellular localization, a FLAG-tagged expression construct of Dsg1-, was transiently expressed in epithelial HaCaT cells. Dsg1-,-FLAG was found at the cell,cell border and was recognized by the anti-Dsg1/Dsg2 antibody DG3.10. In summary, we have cloned and characterized a novel member of the mouse desmoglein gene family, Dsg1-,. [source] Integrative nuclear FGFR1 signaling (INFS) as a part of a universal "feed-forward-and-gate" signaling module that controls cell growth and differentiationJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 4 2003Michal K. Stachowiak Abstract A novel signaling mechanism is described through which extracellular signals and intracellular signaling pathways regulate proliferation, growth, differentiation, and other functions of cells in the nervous system. Upon cell stimulation, fibroblast growth factor receptor-1 (FGFR1), a typically plasma membrane-associated protein, is released from ER membranes into the cytosol and translocates to the cell nucleus by an importin-,-mediated transport pathway along with its ligand, FGF-2. The nuclear accumulation of FGFR1 is activated by changes in cell contacts and by stimulation of cells with growth factors, neurotransmitters and hormones as well as by a variety of different second messengers and thus was named integrative nuclear FGFR1 signaling (INFS). In the nucleus, FGFR1 localizes specifically within nuclear matrix-attached speckle-domains, which are known to be sites for RNA Pol II-mediated transcription and co-transcriptional pre-mRNA processing. In these domains, nuclear FGFR1 colocalizes with RNA transcription sites, splicing factors, modified histones, phosphorylated RNA Pol II, and signaling kinases. Within the nucleus, FGFR1 serves as a general transcriptional regulator, as indicated by its association with the majority of active nuclear centers of RNA synthesis and processing, by the ability of nuclear FGFR1 to activate structurally distinct genes located on different chromosomes and by its stimulation of multi-gene programs for cell growth and differentiation. We propose that FGFR1 is part of a universal "feed-forward-and-gate" signaling module in which classical signaling cascades initiated by specific membrane receptors transmit signals to sequence specific transcription factors (ssTFs), while INFS elicited by the same stimuli feeds the signal forward to the common coactivator, CREB-binding protein (CBP). Activation of CBP by INFS, along with the activation of ssTFs by classical signaling cascades brings about coordinated responses from structurally different genes located at different genomic loci. © 2003 Wiley-Liss, Inc. [source] Cation/proton antiporter complements of bacteria: why so large and diverse?MOLECULAR MICROBIOLOGY, Issue 2 2009Terry A. Krulwich Summary Most bacterial genomes have five to nine distinct genes predicted to encode transporters that exchange cytoplasmic Na+ and/or K+ for H+ from outside the cell, i.e. monovalent cation/proton antiporters. By contrast, pathogens that live primarily inside host cells usually possess zero to one such antiporter while other stress-exposed bacteria exhibit even higher numbers. The monovalent cation/proton antiporters encoded by these diverse genes fall into at least eight different transporter protein families based on sequence similarity. They enable bacteria to meet challenges of high or fluctuating pH, salt, temperature or osmolarity, but we lack explanations for why so many antiporters are needed and for the value added by specific antiporter types in specific settings. In this issue of Molecular Microbiology, analyses of the pH dependence of cytoplasmic [Na+], [K+], pH and transmembrane electrical potential in the ,poly extremophile'Natranaerobius thermophilus are the context for assessment of the catalytic properties of 12 predicted monovalent cation/proton antiporters in the genome of this thermophilic haloalkaliphile. The results provide a profile of adaptations of the poly extremophilic anaerobe, including a proposed role of cytoplasmic buffering capacity. They also provide new perspectives on two large monovalent cation/proton antiporter families, the NhaC and the cation/proton antiporter-3 antiporter families. [source] Remodelling of the Escherichia coli outer membrane by two small regulatory RNAsMOLECULAR MICROBIOLOGY, Issue 1 2006Maude Guillier Summary Small non-coding RNAs that play important regulatory roles exist in numerous organisms. In Escherichia coli, about 60 small RNAs have been found and those that have been studied are involved in the response and adaptation to different stresses. RygA and RygB, two of these small RNAs, were identified on the basis of their conservation between different species and their ability to bind Hfq. They are adjacent on the chromosome and have sequence similarity at their 5, and 3, ends but distinct central regions, suggesting that they could regulate the expression of both common and distinct genes. A screen using a multicopy E. coli library led to identification of the response regulator OmpR and its associated sensor kinase EnvZ as positive regulators of rygA and rygB transcription. Therefore, RygA and RygB were renamed OmrA and OmrB respectively (for OmpR- regulated sRNAs A and B). When expressed at high levels, OmrA and OmrB RNAs negatively regulate the expression of several genes encoding multiple outer membrane proteins, including cirA, fecA, fepA and ompT. Taken together, these data suggest that OmrA and OmrB participate in the regulation of outer membrane composition in response to environmental conditions. [source] Plasma Proteome Database as a resource for proteomics researchPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 13 2005Babylakshmi Muthusamy Abstract Plasma is one of the best studied compartments in the human body and serves as an ideal body fluid for the diagnosis of diseases. This report provides a detailed functional annotation of all the plasma proteins identified to date. In all, gene products encoded by 3778,distinct genes were annotated based on proteins previously published in the literature as plasma proteins and the identification of multiple peptides from proteins under HUPO's Plasma Proteome Project. Our analysis revealed that 51% of these genes encoded more than one protein isoform. All single nucleotide polymorphisms involving protein-coding regions were mapped onto the protein sequences. We found a number of examples of isoform-specific subcellular localization as well as tissue expression. This database is an attempt at comprehensive annotation of a complex subproteome and is available on the web at http://www.plasmaproteomedatabase.org. [source] A catalogue of proteins released by colorectal cancer cells in vitro as an alternative source for biomarker discoveryPROTEOMICS - CLINICAL APPLICATIONS, Issue 1 2007Hanna C. Diehl Abstract Improved methods for the early diagnosis of colorectal cancer by way of sensitive and specific tumour markers are highly desirable. Therefore, efficient strategies for biomarker discovery are urgently needed. Here we present an approach that is based on the direct experimental access to proteins released by SW620 human colorectal cancer cells in vitro. A 2-D map and a catalogue of this subproteome , here termed the secretome , were established comprising more than 320 identified proteins which translate into approximately 220 distinct genes. As the majority of the secretome constituents were nominally cellular proteins, we directly compared the secretome and the total proteome by 2-D-DIGE analysis. We provide evidence that unspecific release through cell death, classical secretion, ectodomain shedding, and exosomal release contribute to the secretome in vitro, presumably reflecting the mechanisms in vivo which lead to the occurrence of tumour-specific proteins in the circulation. These data together with the fact that the SW620 secretome catalogue, as presented here, does comprise a large number of known and novel biomarker candidates, validates our approach to isolate and characterize the tumour cell secretome in vitro as a rich source for tumour biomarkers. [source] Gene therapy clinical trials worldwide 1989,2004,an overviewTHE JOURNAL OF GENE MEDICINE, Issue 6 2004Michael L. Edelstein Abstract In 1989, Rosenberg et al. performed the first human gene therapy trial when they used a retrovirus to introduce the gene coding for resistance to neomycin into human tumor-infiltrating lymphocytes before infusing them into five patients with advanced melanoma. This study demonstrated the feasibility of using retroviral gene transduction in humans and set the stage for further studies. Since then, over 900 clinical trials have been completed, are ongoing or have been approved worldwide. These trials have been designed to establish feasibility and safety, to demonstrate the reality of expression of therapeutic protein(s) in vivo by the genes transferred and, in some cases, to show therapeutic benefit. There is no single source of information that presents an overview of all the clinical trials undertaken worldwide. In 1997 we set up a database to bring all the information on clinical trials together as comprehensively and as globally as possible. The data were compiled and are regularly updated from official agency sources, the published literature, presentations at conferences and from information kindly provided by investigators or trial sponsors themselves. As of January 31, 2004, we have identified 918 trials in 24 countries. The USA accounts for two-thirds of these trials. Cancer is by far the most common disease indication, followed by inherited monogenic diseases, and cardiovascular diseases. Viral vectors have been the most frequently used vehicles for transferring genes into human cells, with retroviruses and adenoviruses representing the vast majority. Plasmid (naked) DNA and other non-viral vectors have been used in one-quarter of the trials. Over 100 distinct genes have been transferred. This article aims to provide a descriptive overview of the clinical trials that, to the best of our knowledge, have been or are being performed worldwide. Details of the data presented, including an interactive, searchable database that currently holds information on 918 trials, can be found on The Journal of Gene Medicine clinical trials website 1. Copyright © 2004 John Wiley & Sons, Ltd. [source] Construction of a ,unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genesTHE PLANT JOURNAL, Issue 5 2002Ralf Herwig Summary Access to the complete gene inventory of an organism is crucial to understanding physiological processes like development, differentiation, pathogenesis, or adaptation to the environment. Transcripts from many active genes are present at low copy numbers. Therefore, procedures that rely on random EST sequencing or on normalisation and subtraction methods have to produce massively redundant data to get access to low-abundance genes. Here, we present an improved oligonucleotide fingerprinting (ofp) approach to the genome of sugar beet (Beta vulgaris), a plant for which practically no molecular information has been available. To identify distinct genes and to provide a representative ,unigene' cDNA set for sugar beet, 159 936 cDNA clones were processed utilizing large-scale, high-throughput data generation and analysis methods. Data analysis yielded 30 444 ofp clusters reflecting the number of different genes in the original cDNA sample. A sample of 10 961 cDNA clones, each representing a different cluster, were selected for sequencing. Standard sequence analysis confirmed that 89% of these EST sequences did represent different genes. These results indicate that the full set of 30 444 ofp clusters represent up to 25 000 genes. We conclude that the ofp analysis pipeline is an accurate and effective way to construct large representative ,unigene' sets for any plant of interest with no requirement for prior molecular sequence data. [source] Review article Male breast cancer , an andrological disease: risk factors and diagnosisANDROLOGIA, Issue 6 2004W. Krause Summary. Gynaecomastia, the enlargement of the male breast, is considered as an andrological disease. To date, a review on male breast cancer (MBC) has not been published in an andrological journal. The papers underlying this review were published from authors of different institutions: Clinical Genetics, Dermatology, Gynaecology, Internal Medicine, Oncology, Pathology, Psychiatry, Radiology and Surgery. MBC accounts for approximately 1% of breast cancer patients. A total of 182 men died of breast cancer in 1999, in Germany. In the US, 1500 new cases per year occur. MBC accounts for <5% of surgically removed breast lumps. Diseases with increased oestrogen action increase the risk of MBC. Mutations of distinct genes are estimated to account for up to roughly 10% of MBC. BRCA1 and BRCA2 gene mutations are responsible for approximately 80% of the families with hereditary breast cancer. The diagnosis of MBC is not possible without histological examination. Different diagnostic procedures such as clinical diagnosis, sonography, mammography, fine-needle biopsy and core needle facilitate the decision whether a biopsy is necessary. [source] Mapping of expressed sequence tags from a porcine early embryonic cDNA libraryANIMAL GENETICS, Issue 2 2001T. P. L. Smith The goal of this study was to identify and map genes expressed during the elongation phase of embryogenesis in swine. Expressed sequence tags were analysed from a previously described porcine cDNA library prepared from elongating swine embryos. Average insert length of randomly selected clones was approximately 600 bp, with a range from <100 to >2500 bp. Single-pass, coding strand sequences from 1132 independent clones were compared with the GenBank non-redundant (nr) database via BLASTN analysis to identify potential porcine homologous of known genes. Among these sequences, 781 (69%) showed significant (score >300) homology to non- mitochondrial sequences previously deposited in GenBank. Sequences matching interleucin 1 , and thymosin , 10 were most frequently observed (24 and 18 clones, respectively), in addition to matches with 310 other distinct genes. No significant match in the GenBank nr database was obtained for 303 sequences. Analysis demonstrated that 151 (50%) had open reading frames (ORF) extending at least 50 codons from the first base of the clone insert. Genetic markers were developed and used to map a subset of 17 genes, selected on the basis of function or of the ability to design primers that successfully amplified porcine genomic DNA, to 10 different porcine chromosomes, providing a set of mapped markers corresponding to genes expressed during conceptus elongation. [source] Screen for genes differentially expressed during regeneration of the zebrafish caudal finDEVELOPMENTAL DYNAMICS, Issue 3 2004Bhaja K. Padhi Abstract The zebrafish caudal fin constitutes an important model for studying the molecular basis of tissue regeneration. The cascade of genes induced after amputation or injury, leading to restoration of the lost fin structures, include those responsible for wound healing, blastema formation, tissue outgrowth, and patterning. We carried out a systematic study to identify genes that are up-regulated during "initiation" (1 day) and "outgrowth and differentiation" (4 days) of fin regeneration by using two complementary methods, suppression subtraction hybridization (SSH) and differential display reverse transcriptase polymerase chain reaction (DDRT-PCR). We obtained 298 distinct genes/sequences from SSH libraries and 24 distinct genes/sequences by DDRT-PCR. We determined the expression of 54 of these genes using in situ hybridization. In parallel, gene expression analyses were done in zebrafish embryos and early larvae. The information gathered from the present study provides resources for further investigations into the molecular mechanisms of fin development and regeneration. Developmental Dynamics 231:527,541, 2004. © 2004 Wiley-Liss, Inc. [source] | ||||||||||||||||