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Genes Encoding Proteins (gene + encoding_protein)
Selected AbstractsAssociation analysis of genes in the renin-angiotensin system with subclinical cardiovascular disease in families with Type 2 diabetes mellitus: The Diabetes Heart StudyDIABETIC MEDICINE, Issue 3 2006K. P. Burdon Abstract Aims Cardiovascular disease (CVD) is a major complication of Type 2 diabetes mellitus. The renin-angiotensin system (RAS) and nitric oxide production are both important regulators of vascular function and blood pressure. Genes encoding proteins involved in these pathways are candidates for a contribution to CVD in diabetic patients. We have investigated variants of the angiotensinogen (AGT), angiotensin converting enzyme (ACE), angiotensin type 1 receptor (AT1R) and endothelial nitric oxide synthase (NOS3) genes for association with subclinical measures of CVD in families with Type 2 diabetes mellitus (T2DM). Methods Atherosclerosis was measured by carotid intima-media thickness and calcification of the carotid and coronary arteries in 620 European Americans and 117 African Americans in the Diabetes Heart Study. Because of the role of these systems in blood pressure regulation, blood pressure was also investigated. Results Compelling evidence of association was not detected with any of the SNPs with any outcome measures after adjustments for covariates despite sufficient power to detect relatively small differences in traits for specific genotype combinations. Conclusions Genetic variation of the RAS and NOS3 genes do not appear to strongly influence subclinical cardiovascular disease or blood pressure in this diabetic population. [source] In GERD patients, mucosal repair associated genes are upregulated in non-inflamed oesophageal epitheliumJOURNAL OF CELLULAR AND MOLECULAR MEDICINE, Issue 5 2009D. R. De Vries Abstract Previous studies addressing the effects of acid reflux and PPI therapy on gene expression in oesophageal epithelium concentrated on inflamed tissue. We aimed to determine changes in gene expression in non-inflamed oesophageal epithelium of GERD patients. Therefore, we included 20 GERD patients with pathological total 24-hr acid exposure of 6,12% and SAP , 95%. Ten patients discontinued PPI treatment (PPI-), 10 took pantoprazole 40 mg bid (PPI+). Ten age/sex-matched healthy controls were recruited. Biopsies were taken from non-inflamed mucosa 6 cm and 16 cm proximal to the squamocolumnar junction (SCJ). Gene expression profiling of biopsies from 6 cm was performed on Human Genome U133 Plus 2.0 arrays (Affymetrix). Genes exhibiting a fold change >1.4 (t-test P -value < 1E, 4) were considered differentially expressed. Results were confirmed by real-time RT-PCR. In PPI- patients, 92 microarray probesets were deregulated. The majority of the corresponding genes were associated with cell,cell contacts, cytoskeletal reorganization and cellular motility, suggesting facilitation of a migratory phenotype. Genes encoding proteins with anti-apoptotic or anti-proliferative functions or stress-protective functions were also deregulated. No probesets were deregulated in PPI+ patients. QPCR analysis of 20 selected genes confirmed most of the deregulations in PPI- patients, and showed several deregulated genes in PPI+ patients as well. In the biopsies taken at 16 cm QPCR revealed no deregulations of the selected genes. We conclude that upon acid exposure, oesophageal epithelial cells activate a process globally known as epithelial restitution: up-regulation of anti-apoptotic, anti-oxidant and migration associated genes. Possibly this process helps maintaining barrier function. [source] Dopamine receptor gene polymorphisms in Parkinson's disease patients reporting "sleep attacks"MOVEMENT DISORDERS, Issue 11 2004Ida Rissling MD Abstract Genes encoding proteins involved in dopaminergic transmission are potential candidate genes for the induction of somnolence in Parkinson's disease (PD) because dopaminergic agents have been shown to be associated with sudden onset of sleep (SOS) in PD. We conducted an association study on dopamine D2, D3, and D4 receptor gene polymorphisms comparing 137 PD patients with SOS and 137 PD patients without SOS matched according to drug therapy, disease duration, sex, and age. Our results show a significant association between the dopamine D2 receptor gene polymorphism Taq IA and SOS in PD. No significant association between two other investigated polymorphisms and the phenomenon of "sleep attacks" in PD was observed. © 2004 Movement Disorder Society [source] The plant pathogenic fungus Gaeumannomyces graminis var. tritici improves bacterial growth and triggers early gene regulations in the biocontrol strain Pseudomonas fluorescens Pf29ArpNEW PHYTOLOGIST, Issue 2 2009M. Barret Summary ,,In soil, some antagonistic rhizobacteria contribute to reduce root diseases caused by phytopathogenic fungi. Direct modes of action of these bacteria have been largely explored; however, commensal interaction also takes place between these microorganisms and little is known about the influence of filamentous fungi on bacteria. ,,An in vitro confrontation bioassay between the pathogenic fungus Gaeumannomyces graminis var. tritici (Ggt) and the biocontrol bacterial strain Pseudomonas fluorescens Pf29Arp was set up to analyse bacterial transcriptional changes induced by the fungal mycelium at three time-points of the interaction before cell contact and up until contact. For this, a Pf29Arp shotgun DNA microarray was constructed. Specifity of Ggt effect was assessed in comparison with one of two other filamentous fungi, Laccaria bicolor and Magnaporthe grisea. ,,During a commensal interaction, Ggt increased the growth rate of Pf29Arp. Before contact, Ggt induced bacterial genes involved in mycelium colonization. At contact, genes encoding protein of stress response and a patatin-like protein were up-regulated. Among all the bacterial genes identified, xseB was specifically up-regulated at contact by Ggt but down-regulated by the other fungi. ,,Data showed that the bacterium sensed the presence of the fungus early, but the main gene alteration occurred during bacterial,fungal cell contact. [source] Increased fat oxidation and regulation of metabolic genes with ultraendurance exerciseACTA PHYSIOLOGICA, Issue 1 2007J. W. Helge Abstract Aim:, Regular endurance exercise stimulates muscle metabolic capacity, but effects of very prolonged endurance exercise are largely unknown. This study examined muscle substrate availability and utilization during prolonged endurance exercise, and associated metabolic genes. Methods:, Data were obtained from 11 competitors of a 4- to 5-day, almost continuous ultraendurance race (seven males, four females; age: 36 ± 11 years; cycling o2peak: males 57.4 ± 5.9, females 48.1 ± 4.0 mL kg,1 min,1). Before and after the race muscle biopsies were obtained from vastus lateralis, respiratory gases were sampled during cycling at 25 and 50% peak aerobic power output, venous samples were obtained, and fat mass was estimated by bioimpedance under standardized conditions. Results:, After the race fat mass was decreased by 1.6 ± 0.4 kg (11%; P < 0.01). Respiratory exchange ratio at the 25 and 50% workloads decreased (P < 0.01) from 0.83 ± 0.06 and 0.93 ± 0.03 before, to 0.71 ± 0.01 and 0.85 ± 0.02, respectively, after the race. Plasma fatty acids were 3.5 times higher (from 298 ± 74 to 1407 ± 118 ,mol L,1; P < 0.01). Muscle glycogen content fell 50% (from 554 ± 28 to 270 ± 25 nmol kg,1 d.w.; n = 7, P < 0.01), whereas the decline in muscle triacylglycerol (from 32 ± 5 to 22 ± 3 mmol kg,1 d.w.; P = 0.14) was not statistically significant. After the race, muscle mRNA content of lipoprotein lipase and glycogen synthase increased (P < 0.05) 3.9- and 1.7-fold, respectively, while forkhead homolog in rhabdomyosarcoma, pyruvate dehydrogenase kinase 4 and vascular endothelial growth factor mRNA tended (P < 0.10) to be higher, whereas muscle peroxisome proliferator-activated receptor , co-activator-1, mRNA tended to be lower (P = 0.06). Conclusion:, Very prolonged exercise markedly increases plasma fatty acid availability and fat utilization during exercise. Exercise-induced regulation of genes encoding proteins involved in fatty acid recruitment and oxidation may contribute to these changes. [source] Genetic and functional properties of uncultivated thermophilic crenarchaeotes from a subsurface gold mine as revealed by analysis of genome fragmentsENVIRONMENTAL MICROBIOLOGY, Issue 12 2005Takuro Nunoura Summary Within a phylum Crenarchaeota, only some members of the hyperthermophilic class Thermoprotei, have been cultivated and characterized. In this study, we have constructed a metagenomic library from a microbial mat formation in a subsurface hot water stream of the Hishikari gold mine, Japan, and sequenced genome fragments of two different phylogroups of uncultivated thermophilic Crenarchaeota: (i) hot water crenarchaeotic group (HWCG) I (41.2 kb), and (ii) HWCG III (49.3 kb). The genome fragment of HWCG I contained a 16S rRNA gene, two tRNA genes and 35 genes encoding proteins but no 23S rRNA gene. Among the genes encoding proteins, several genes for putative aerobic-type carbon monoxide dehydrogenase represented a potential clue with regard to the yet unknown metabolism of HWCG I Archaea. The genome fragment of HWCG III contained a 16S/23S rRNA operon and 44 genes encoding proteins. In the 23S rRNA gene, we detected a homing-endonuclease encoding a group I intron similar to those detected in hyperthermophilic Crenarchaeota and Bacteria, as well as eukaryotic organelles. The reconstructed phylogenetic tree based on the 23S rRNA gene sequence reinforced the intermediate phylogenetic affiliation of HWCG III bridging the hyperthermophilic and non-thermophilic uncultivated Crenarchaeota. [source] The regulation of the endosomal compartment by p53 the tumor suppressor geneFEBS JOURNAL, Issue 8 2009Xin Yu The endosomal compartment of the cell is involved in a number of functions including: (a) internalizing membrane proteins to multivesicular bodies and lysosomes; (b) producing vesicles that are secreted from the cell (exosomes); and (c) generating autophagic vesicles that, especially in times of nutrient deprivation, supply cytoplasmic components to the lysosome for degradation and recycling of nutrients. The p53 protein responds to various stress signals by initiating a transcriptional program that restores cellular homeostasis and prevents the accumulation of errors in a cell. As part of this process, p53 regulates the transcription of a set of genes encoding proteins that populate the endosomal compartment and impact upon each of these endosomal functions. Here, we demonstrate that p53 regulates transcription of the genes TSAP6 and CHMP4C, which enhance exosome production, and CAV1 and CHMP4C, which produce a more rapid endosomal clearance of the epidermal growth factor receptor from the plasma membrane. Each of these p53-regulated endosomal functions results in the slowing of cell growth and division, the utilization of catabolic resources and cell-to-cell communication by exosomes after a stress signal is detected by the p53 protein. These processes avoid errors during stress and restore homeostasis once the stress is resolved. [source] Association of common genetic variation in the insulin/IGF1 signaling pathway with human longevityAGING CELL, Issue 4 2009Ludmila Pawlikowska Summary The insulin/IGF1 signaling pathways affect lifespan in several model organisms, including worms, flies and mice. To investigate whether common genetic variation in this pathway influences lifespan in humans, we genotyped 291 common variants in 30 genes encoding proteins in the insulin/IGF1 signaling pathway in a cohort of elderly Caucasian women selected from the Study of Osteoporotic Fractures (SOF). The cohort included 293 long-lived cases (lifespan , 92 years (y), mean ± standard deviation (SD) = 95.3 ± 2.2y) and 603 average-lifespan controls (lifespan , 79y, mean = 75.7 ± 2.6y). Variants were selected for genotyping using a haplotype-tagging approach. We found a modest excess of variants nominally associated with longevity. Nominally significant variants were then replicated in two additional Caucasian cohorts including both males and females: the Cardiovascular Health Study and Ashkenazi Jewish Centenarians. An intronic single nucleotide polymorphism in AKT1, rs3803304, was significantly associated with lifespan in a meta-analysis across the three cohorts (OR = 0.78 95%CI = 0.68,0.89, adjusted P = 0.043); two intronic single nucleotide polymorphisms in FOXO3A demonstrated a significant lifespan association among women only (rs1935949, OR = 1.35, 95%CI = 1.15,1.57, adjusted P = 0.0093). These results demonstrate that common variants in several genes in the insulin/IGF1 pathway are associated with human lifespan. [source] ANALYSIS OF EXPRESSED SEQUENCE TAGS (ESTS) FROM THE POLAR DIATOM FRAGILARIOPSIS CYLINDRUS,JOURNAL OF PHYCOLOGY, Issue 1 2006Thomas Mock Analysis of expressed sequence tags (ESTs) was performed to gain insights into cold adaptation in the polar diatom Fragilariopsis cylindrus Grunow. The EST library was generated from RNA isolated 5 days after F. cylindrus cells were shifted from approximately +5° C to ,1.8°C. A total of 1376 ESTs were sequenced from a non-normalized cDNA library and assembled into 996 tentative unique sequences. About 27% of the ESTs displayed similarity (tBLASTX, e -value of ,10,4) to predicted proteins in the centric diatom Thalassiosira pseudonana Hasle & Heindal. Eleven additional algae and plant data bases were used for annotation of sequences not covered by Thalassiosira sequences (7%). Most of the ESTs were similar to genes encoding proteins responsible for translation, ribosomal structure, and biogenesis (3%), followed by genes encoding proteins for amino acid transport and metabolism and post-translational modifications. Interestingly, 66% of all the EST sequences from F. cylindrus displayed no similarity (e -value ,10,4) to sequences from the 12 non-redundant databases. Even 6 of the 10 strong to moderately expressed sequences in this EST library could not be identified. Adaptation of F. cylindrus to freezing temperatures of seawater may require a complex protein metabolism and possibly also genes, which were highly expressed but still unknown. However, it could also mean that due to low temperatures, there might have been a stronger pressure to adapt amino acid sequences, making it more difficult to identify these unknown sequences and/or that there are still few protist sequences available for comparison. [source] Molecular control of ethylene production by cyanide in Arabidopsis thalianaPHYSIOLOGIA PLANTARUM, Issue 2 2000Jennifer McMahon Smith Although cyanide has long been recognized as a co-product of ethylene synthesis, little attention has been given to its potential physiological and molecular roles. In the present work, the long-term effects of cyanide on growth and development were observed in Arabidopsis thaliana. Two days after a single 20-min application of cyanide, plants demonstrated visible signs of stress. Long-term detrimental effects on growth and photosynthetic capabilities were noted, including low chlorophyll accumulation and stunted growth. Because of the relationship between cyanide and ethylene production, we chose to evaluate the results of cyanide treatment on genes encoding proteins involved in ethylene synthesis. We have found that only the 1-aminocyclopropane-1-carboxylic acid (ACC) synthase gene, ACS6, is rapidly activated in response to cyanide treatment, while other ACS genes were unaffected. This same gene has previously been shown to be transcriptionally activated in response to touch and other environmental stimuli. Cyanide was capable of activating ACS6 transcription within 10 min of treatment, and the amount of transcript correlated positively with the cyanide dosage. Due to the toxic nature of cyanide, plant in vivo concentrations are generally maintained lower than 10 ,M, but can increase under certain stresses. In the present work, we observed that physiologically relevant concentrations as low as 1 ,M HCN, considered metabolically ,safe', were capable of initiating ACS6 transcription. ACS6 transcripts were not substantially reduced as a result of multiple cyanide treatments, which is in contrast with the effects of mechanical stimulation on transcription. Our results suggest a relationship between cyanide production during ethylene synthesis and the molecular control of ethylene synthesis. This work corresponds with earlier experiments that have demonstrated that ethylene and cyanide can elicit some similar physiological responses. It is possible that cyanide may play an active role in ethylene regulation under conditions where rapid cyanide accumulation occurs. Since cyanide can rapidly activate ethylene synthesis, it is possible that it is involved in the positive-feedback regulation of ethylene that occurs in some plant tissues. [source] Global transcript profiling of primary stems from Arabidopsis thaliana identifies candidate genes for missing links in lignin biosynthesis and transcriptional regulators of fiber differentiationTHE PLANT JOURNAL, Issue 5 2005Jürgen Ehlting Summary Different stages of vascular and interfascicular fiber differentiation can be identified along the axis of bolting stems in Arabidopsis. To gain insights into the metabolic, developmental, and regulatory events that control this pattern, we applied global transcript profiling employing an Arabidopsis full-genome longmer microarray. More than 5000 genes were differentially expressed, among which more than 3000 changed more than twofold, and were placed into eight expression clusters based on polynomial regression models. Within these, 182 upregulated transcription factors represent candidate regulators of fiber development. A subset of these candidates has been associated with fiber development and/or secondary wall formation and lignification in the literature, making them targets for functional studies and comparative genomic analyses with woody plants. Analysis of differentially expressed phenylpropanoid genes identified a set known to be involved in lignin biosynthesis. These were used to anchor co-expression analyses that allowed us to identify candidate genes encoding proteins involved in monolignol transport and monolignol dehydrogenation and polymerization. Similar analyses revealed candidate genes encoding enzymes that catalyze missing links in the shikimate pathway, namely arogenate dehydrogenase and prephenate aminotransferase. [source] Phenotypic interactions of spinster with the genes encoding proteins for cell death control in Drosophila melanogasterARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 3 2010Akira Sakurai Abstract The spin gene was first identified by its mutant phenotype, which is characterized by extremely strong mate refusal by females in response to male courtship in Drosophila. Spin mutants are also known to be accompanied by a remarkable reduction in programmed cell death in the reproductive and nervous systems. To better understand the molecular functions of spin, we searched for its genetic modifiers. Forced expression of spin+ in somatic cells as driven by ptc-Gal4 in the testis resulted in the invasion of mature sperm into the anterior testes tip, which is otherwise occupied only by immature germ cells. To obtain genes that modulate spin's effect, the gain-of-function spin phenotype was observed in the presence of a chromosome harboring an EP or GS P-element insertion, which initiates transcription of the genomic sequence neighboring the insertion site. We isolated th and emc as suppressors of spin and atg8a as a gene that reproduces the spin phenotype on its own. th encodes Inhibitor of apoptosis-1, and mammalian Id genes homologous to emc are known to inhibit apoptosis. atg8a encodes a protein essential for autophagy. These results suggest that spin promotes cell death mechanisms that are regulated negatively by th and emc and positively by atg8a. © 2010 Wiley Periodicals, Inc. [source] Developmental microRNA expression profiling of murine embryonic orofacial tissueBIRTH DEFECTS RESEARCH, Issue 7 2010Partha Mukhopadhyay Abstract BACKGROUND: Orofacial development is a multifaceted process involving precise, spatio-temporal expression of a panoply of genes. MicroRNAs (miRNAs), the largest family of noncoding RNAs involved in gene silencing, represent critical regulators of cell and tissue differentiation. MicroRNA gene expression profiling is an effective means of acquiring novel and valuable information regarding the expression and regulation of genes, under the control of miRNA, involved in mammalian orofacial development. METHODS: To identify differentially expressed miRNAs during mammalian orofacial ontogenesis, miRNA expression profiles from gestation day (GD) -12, -13 and -14 murine orofacial tissue were compared utilizing miRXplore microarrays from Miltenyi Biotech. Quantitative real-time PCR was utilized for validation of gene expression changes. Cluster analysis of the microarray data was conducted with the clValid R package and the UPGMA clustering method. Functional relationships between selected miRNAs were investigated using Ingenuity Pathway Analysis. RESULTS: Expression of over 26% of the 588 murine miRNA genes examined was detected in murine orofacial tissues from GD-12,GD-14. Among these expressed genes, several clusters were seen to be developmentally regulated. Differential expression of miRNAs within such clusters wereshown to target genes encoding proteins involved in cell proliferation, cell adhesion, differentiation, apoptosis and epithelial-mesenchymal transformation, all processes critical for normal orofacial development. CONCLUSIONS: Using miRNA microarray technology, unique gene expression signatures of hundreds of miRNAs in embryonic orofacial tissue were defined. Gene targeting and functional analysis revealed that the expression of numerous protein-encoding genes, crucial to normal orofacial ontogeny, may be regulated by specific miRNAs. Birth Defects Research (Part A), 2010. © 2010 Wiley-Liss, Inc. [source] Developmental gene expression profiling of mammalian, fetal orofacial tissueBIRTH DEFECTS RESEARCH, Issue 12 2004Partha Mukhopadhyay Abstract BACKGROUND The embryonic orofacial region is an excellent developmental paradigm that has revealed the centrality of numerous genes encoding proteins with diverse and important biological functions in embryonic growth and morphogenesis. DNA microarray technology presents an efficient means of acquiring novel and valuable information regarding the expression, regulation, and function of a panoply of genes involved in mammalian orofacial development. METHODS To identify differentially expressed genes during mammalian orofacial ontogenesis, the transcript profiles of GD-12, GD-13, and GD-14 murine orofacial tissue were compared utilizing GeneChip arrays from Affymetrix. Changes in gene expression were verified by TaqMan quantitative real-time PCR. Cluster analysis of the microarray data was done with the GeneCluster 2.0 Data Mining Tool and the GeneSpring software. RESULTS Expression of >50% of the ,12,000 genes and expressed sequence tags examined in this study was detected in GD-12, GD-13, and GD-14 murine orofacial tissues and the expression of several hundred genes was up- and downregulated in the developing orofacial tissue from GD-12 to GD-13, as well as from GD-13 to GD-14. Such differential gene expression represents changes in the expression of genes encoding growth factors and signaling molecules; transcription factors; and proteins involved in epithelial-mesenchymal interactions, extracellular matrix synthesis, cell adhesion, proliferation, differentiation, and apoptosis. Following cluster analysis of the microarray data, eight distinct patterns of gene expression during murine orofacial ontogenesis were selected for graphic presentation of gene expression patterns. CONCLUSIONS This gene expression profiling study identifies a number of potentially unique developmental participants and serves as a valuable aid in deciphering the complex molecular mechanisms crucial for mammalian orofacial development. Supplementary material for this article can be found at http://www.mrw.interscience.wiley.com/suppmat/1542-0752/suppmat/2004/70/v70.mukhopadhyay.html Birth Defects Research (Part A), 2004. © 2004 Wiley-Liss, Inc. [source] Chemotaxis of Entamoeba histolytica towards the pro-inflammatory cytokine TNF is based on PI3K signalling, cytoskeleton reorganization and the Galactose/N-acetylgalactosamine lectin activityCELLULAR MICROBIOLOGY, Issue 8 2008Samantha Blazquez Summary Entamoeba histolytica is the protozoan parasite responsible for human amoebiasis. During invasive amoebiasis, migration is an essential process and it has previously been shown that the pro-inflammatory compound tumour necrosis factor (TNF) is produced and that it has a migratory effect on E. histolytica. This paper focuses on the analysis of parasite signalling and cytoskeleton changes leading to directional motility. TNF-induced signalling was PI3K-dependent and could lead to modifications in the polarization of certain cytoskeleton-related proteins. To analyse the effect of TNF signalling on gene expression, we used microarray analysis to screen for genes encoding proteins that were potentially important during chemotaxis towards TNF. Interestingly, we found that elements of the galactose/N-acetylgalactosamine lectin (Gal/GalNAc lectin) were upregulated during chemotaxis as well as genes encoding proteins involved in cytoskeleton dynamics. The ,-actinin protein appeared to be an important candidate to link the Gal/GalNAc lectin to the cytoskeleton during chemotaxis signalling. Dominant negative parasites blocked for Gal/GalNAc lectin signalling were no longer able to chemotax towards TNF. These results have given us an insight on how E. histolytica changes its cytoskeleton dynamics during chemotaxis and revealed the capital role of PI3K and Gal/GalNAc lectin signalling in chemotaxis. [source] | ||||||||||||||||