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Gene Array (gene + array)
Terms modified by Gene Array Selected AbstractsExpression of major vault protein gene in osteosarcoma patientsJOURNAL OF ORTHOPAEDIC RESEARCH, Issue 7 2007Cristiane Arruda Dalla-Torre Abstract Osteosarcoma (OS) is a primary malignant tumor of bone. Despite the successful use of multiple chemotherapeutic agents in the treatment of OS, more than 30% of OS tumors remain resistant to treatment. Elucidation of cellular resistance mechanisms may lead to better treatments for cancer patients. In this study, we used the low-density expression cDNA array, GEArray Q Series Human Cancer Drug Resistance and Metabolism Gene Array to screen genes related to drug resistance in 15 OS tumors. Expression patterns of the MPV gene were validated by real time PCR on 45 OS patient tumor samples and correlated with clinical and pathological data. Major vault protein (MVP) expression was present in 24 (53%) tumor samples and absent in 21 (47%). Samples from surgery showed correlation between the expression of MVP, metastatic disease at diagnosis and event free survival (EFS). The MVP gene expression correlates with metastatic disease at diagnosis after neoadjuvant chemotherapy (p,=,0.048), and is also associated with worse EFS (p,=,0.036). These findings suggest that MVP expression is involved in one of the mechanisms of drug resistance in OS and is induced by chemotherapy. © 2007 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 25:958,963, 2007 [source] Microbial functional structure of Montastraea faveolata, an important Caribbean reef-building coral, differs between healthy and yellow-band diseased coloniesENVIRONMENTAL MICROBIOLOGY, Issue 2 2010Nikole E. Kimes Summary A functional gene array (FGA), GeoChip 2.0, was used to assess the biogeochemical cycling potential of microbial communities associated with healthy and Caribbean yellow band diseased (YBD) Montastraea faveolata. Over 6700 genes were detected, providing evidence that the coral microbiome contains a diverse community of archaea, bacteria and fungi capable of fulfilling numerous functional niches. These included carbon, nitrogen and sulfur cycling, metal homeostasis and resistance, and xenobiotic contaminant degradation. A significant difference in functional structure was found between healthy and YBD M. faveolata colonies and those differences were specific to the physical niche examined. In the surface mucopolysaccharide layer (SML), only two of 31 functional categories investigated, cellulose degradation and nitrification, revealed significant differences, implying a very specific change in microbial functional potential. Coral tissue slurry, on the other hand, revealed significant changes in 10 of the 31 categories, suggesting a more generalized shift in functional potential involving various aspects of nutrient cycling, metal transformations and contaminant degradation. This study is the first broad screening of functional genes in coral-associated microbial communities and provides insights regarding their biogeochemical cycling capacity in healthy and diseased states. [source] GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquiferENVIRONMENTAL MICROBIOLOGY, Issue 10 2009Joy D. Van Nostrand Summary A pilot-scale system was established for in situ biostimulation of U(VI) reduction by ethanol addition at the US Department of Energy's (DOE's) Field Research Center (Oak Ridge, TN). After achieving U(VI) reduction, stability of the bioreduced U(IV) was evaluated under conditions of (i) resting (no ethanol injection), (ii) reoxidation by introducing dissolved oxygen (DO), and (iii) reinjection of ethanol. GeoChip, a functional gene array with probes for N, S and C cycling, metal resistance and contaminant degradation genes, was used for monitoring groundwater microbial communities. High diversity of all major functional groups was observed during all experimental phases. The microbial community was extremely responsive to ethanol, showing a substantial change in community structure with increased gene number and diversity after ethanol injections resumed. While gene numbers showed considerable variations, the relative abundance (i.e. percentage of each gene category) of most gene groups changed little. During the reoxidation period, U(VI) increased, suggesting reoxidation of reduced U(IV). However, when introduction of DO was stopped, U(VI) reduction resumed and returned to pre-reoxidation levels. These findings suggest that the community in this system can be stimulated and that the ability to reduce U(VI) can be maintained by the addition of electron donors. This biostimulation approach may potentially offer an effective means for the bioremediation of U(VI)-contaminated sites. [source] RNAi-mediated inhibition of MSP58 decreases tumour growth, migration and invasion in a human glioma cell lineJOURNAL OF CELLULAR AND MOLECULAR MEDICINE, Issue 11-12 2009Wei Lin Abstract MSP58, a 58-kD nuclear microspherule protein, is an evolutionarily conserved nuclear protein implicated in the regulation of gene transcription as well as in malignant transformation. An analysis of mRNA expression by real-time PCR revealed that MSP58 was significantly up-regulated in 29% of high-grade glioblastoma tissues as well as in four glioblastoma cell lines. In the present study, we further evaluated the biological functions of MSP58 in U251 glioma cell proliferation, migration, invasion and tumour growth in vivo by specific MSP58 knockdown using short hairpin RNA (shRNA). We found that MSP58 depletion inhibited glioma cell growth, primarily by inducing cell cycle arrest rather than apoptosis. MSP58 depletion also decreased the invasive capability of glioma cells and anchorage-independent colony formation in soft agar. Moreover, suppression of MSP58 expression significantly impaired the growth of glioma xenografts in nude mice. Finally, a cell cycle-associated gene array revealed potential molecular mechanisms contributing to cell cycle arrest in MSP58-depleted glioma cells. In summary, our data highlight the importance of MSP58 in glioma progression and provided a biological basis for MSP58 as a novel candidate target for treatment of glioma. [source] The role of inflammatory mediators in the pathophysiology of X-ALD diseaseJOURNAL OF NEUROCHEMISTRY, Issue 2002A. S. Paintlia CER is the most frequent clinical phenotype of the defective X-ALD (ALD; ABCD1) gene, which results in accumulation of VLCFAs (in plasma, brain, adrenal glands and testis), inflammatory demyelination and subsequent death in children. To understand the inflammatory mediators that play a role in the neuropathology of CER, we studied mRNA expressions of inflammatory mediators in CER brain by using super gene array. Total of nine tissue slices were taken from three different locations from CER brain starting with plaque, demyelinating edge (Plaque shadow) and normal looking area. Histopathological examinations showed intensive demyelination in plaque region and accumulation of infiltrates (Macrophages and T lymphocytes) in plaque and plaque shadow as compared to normal looking area. Biochemical studies indicated significant increase in the levels of VLCFAs (26 : 0) in plaque and plaque shadow regions in comparison to normal looking area. There was significant increase in the levels of inflammatory cytokines (IL-1,, TNF-, and IL-6) in plaque shadow as compared with normal looking area and control brain tissue region. Other cytokines like IL-2, IL-3, GM-CSF, IL-11, IL-12A were found to be increased significantly (p < 0.01) in plaque shadow. There was significant (p < 0.01) increase in the expression chemokines; MCP-1, MCP-3, MIP-1, and MIP-2 in the plaque shadow in comparison with normal looking area of CER brain. Chemokines; Fractalkine, Eotaxin, SDF-2, MDC-2, HCC-4 were also observed to be higher in plaque shadow. Data was further evaluated using RT,PCR for MCP-1 and CCR-2, which showed elevated levels in plaque and plaque shadow. This study identified a group of inflammatory mediators that may play a role in pathophysiology of X-ALD disease. Acknowledgements:, Supported by grants; NS-22526, NS-34741, NS-37766 and NS-40810. [source] Neutralization of the chemokine CXCL10 reduces apoptosis and increases axon sprouting after spinal cord injuryJOURNAL OF NEUROSCIENCE RESEARCH, Issue 4 2006Janette Glaser Abstract Spinal cord injury (SCI) is followed by a secondary degenerative process that includes cell death. We have previously demonstrated that the chemokine CXCL10 is up-regulated following SCI and plays a critical role in T-lymphocyte recruitment to sites of injury and inhibition of angiogenesis; antibody-mediated functional blockade of CXCL10 reduced inflammation while enhancing angiogenesis. We hypothesized, based on these findings, that the injury environment established by anti-CXCL10 antibody treatment would support greater survival of neurons and enhance axon sprouting compared with the untreated, injured spinal cord. Here, we document gene array and histopathological data to support our hypothesis. Gene array analysis of treated and untreated tissue from spinal cord-injured animals revealed eight apoptosis-related genes with significant expression changes at 3 days postinjury. In support of these data, quantification of TUNEL-positive cells at 3 days postinjury indicated a 75% reduction in the number of dying cells in treated animals compared with untreated animals. Gene array analysis of treated and untreated tissue also revealed six central nervous system growth-related genes with significant expression changes in the brainstem at 14 days postinjury. In support of these data, quantification of anterograde-labeled corticospinal tract fibers indicated a 60,70% increase in axon sprouting caudal to the injury site in treated animals compared with untreated animals. These findings indicate that anti-CXCL10 antibody treatment provides an environment that reduces apoptosis and increases axon sprouting following injury to the adult spinal cord. © 2006 Wiley-Liss, Inc. [source] Varying ratios of wavelengths in dual wavelength LED photomodulation alters gene expression profiles in human skin fibroblastsLASERS IN SURGERY AND MEDICINE, Issue 6 2010D.H. McDaniel MD Abstract Background and Objective LED photomodulation has been shown to profoundly influence cellular behavior. A variety of parameters with LED photomodulation can alter cellular response in vitro. The effects of one visible and one infrared wavelength were evaluated to determine the optimal ratio to produce a net increase in dermal collagen by altering the ratio of total energy output of each wavelength. The ratio between the two wavelengths (590 and 870,nm) was shifted in 25% increments. Study Design/Materials and Methods Human skin fibroblasts in culture were exposed to a 590/870,nm LED array with total combined energy density fixed at 4.0,mW/cm.. The ratio of 590/870,nm tested parameters were: 100/0%, 75/25%, 50/50%, 25/75%, and 0/100%. These ratios were delivered using pulsed duty cycle of exposure (250,milliseconds "on" time/100,milliseconds "off" time/100,pulses) for a total energy fluence of 0.1,J/cm.. Gene expression was examined using commercially available extra cellular matrix and adhesion molecule RT PCR Arrays (SA Biosciences, Fredrick, MD) at 24,hours post-exposure. Results Different expression profiles were noticed for each of the ratios studied. Overall, there was an average (in an 80 gene array) of 6% expression difference in up or downregulation between the arrays. The greatest increase in collagen I and decrease in collagenase (MMP-1) was observed with 75/25% ratio of 590/870,nm. The addition of increasing proportions of IR wavelengths causes alteration in gene expression profile. The ratios of the wavelengths caused variation in magnitude of expression. Conclusions Cell metabolism and gene expression can be altered by simultaneous exposure to multiple wavelengths of low energy light. Varying the ratios of specific wavelength intensity in both visible and near infrared light therapy can strongly influence resulting fibroblast gene expression patterns. Lasers Surg. Med. 42:540,545, 2010. © 2010 Wiley,Liss, Inc. [source] Flufenacet herbicide treatment phenocopies the fiddlehead mutant in Arabidopsis thalianaPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 8 2003Christa Lechelt-Kunze Abstract In order to study the mode of action of herbicides we conducted a pilot study analysing phenotype and gene expression of flufenacet- and benfuresate-treated Arabidopsis thaliana (L) Heynhoe plants. Treatments with either herbicide caused phenocopies of the known Arabidopsis mutant fiddlehead, displaying fused organs and the typical fiddlehead-like inflorescence. Herbicide treatments of other plant species, including monocots, also gave rise to analogous organ fusions, indicating the presence of the target in a broad range of plants. Furthermore, many other herbicides with a proposed similar mode of action, eg chloroacetanilides, produced comparable fusion phenotypes in plants. The fiddlehead gene encodes a putative very-long-chain fatty acid elongase (VLCFAE), which corroborates earlier biochemical results pointing to the inhibition of VLCFA synthesis as mode of action of flufenacet. Gene expression profiles of herbicide-treated plants using the first 8247 gene Arabidopsis gene array of Affymetrix provided additional clues in support of inhibition of VLCFA synthesis. We discuss fiddlehead -like elongases as plant specific targets for flufenacet and many other herbicides. Copyright © 2003 Society of Chemical Industry [source] MODULATION OF SIGNAL TRANSDUCERS AND ACTIVATORS OF TRANSCRIPTION (STAT) FACTOR PATHWAYS DURING FOCAL CEREBRAL ISCHAEMIA: A GENE EXPRESSION ARRAY STUDY IN RAT HIPPOCAMPUS AFTER MIDDLE CEREBRAL ARTERY OCCLUSIONCLINICAL AND EXPERIMENTAL PHARMACOLOGY AND PHYSIOLOGY, Issue 11 2007Sheng-Li Sun SUMMARY 1Signal transducers and activators of transcription (STAT) factors are a family of transcription factors that mediate intracellular signalling initiated at cytokine cell surface receptors and transmitted to the nucleus. In the present study, we determined the global changes in STAT gene expression in the hippocampus of rats after focal cerebral ischaemia and reperfusion using microarray analysis. 2The present study used middle cerebral artery occlusion (MCAO) to induce ischaemia and reperfusion in Sprague-Dawley rats. Using superarray Q series Janus tyrosine kinases (Jak)/STAT signalling pathway gene array, a total of 96 genes was screened in adult male rat hippocampus after transient focal cerebral ischaemia. 3The results showed that 23 genes were upregulated at least twofold by ischaemia treatment and that 12 genes were downregulated at least threefold by ischaemia treatment compared with controls. 4After confirmation by quantitative real-time polymerase chain reaction, the data suggest that the gene expression of STAT2, 5a, 5b, 6 and suppressor of cytokine signalling (SOCS) 4 was increased by ischaemia, probably due to a compensatory response of the brain, which may play a protective role in damaged brain tissue. 5The results of the present study provide evidence on global changes in STAT gene expression in the hippocampus of rats after focal cerebral ischaemia and reperfusion, in which STAT2, 5a, 5b, 6 and SOCS4 were confirmed to be significantly modulated during focal cerebral ischaemia. [source] Low-intensity microwave irradiation does not substantially alter gene expression in late larval and adult Caenorhabditis elegansBIOELECTROMAGNETICS, Issue 8 2009Adam S. Dawe Abstract Reports that low-intensity microwave radiation induces heat-shock reporter gene expression in the nematode, Caenorhabditis elegans, have recently been reinterpreted as a subtle thermal effect caused by slight heating. This study used a microwave exposure system (1.0,GHz, 0.5,W power input; SAR 0.9,3,mW,kg,1 for 6-well plates) that minimises temperature differentials between sham and exposed conditions (,0.1 °C). Parallel measurement and simulation studies of SAR distribution within this exposure system are presented. We compared five Affymetrix gene arrays of pooled triplicate RNA populations from sham-exposed L4/adult worms against five gene arrays of pooled RNA from microwave-exposed worms (taken from the same source population in each run). No genes showed consistent expression changes across all five comparisons, and all expression changes appeared modest after normalisation (,40% up- or down-regulated). The number of statistically significant differences in gene expression (846) was less than the false-positive rate expected by chance (1131). We conclude that the pattern of gene expression in L4/adult C. elegans is substantially unaffected by low-intensity microwave radiation; the minor changes observed in this study could well be false positives. As a positive control, we compared RNA samples from N2 worms subjected to a mild heat-shock treatment (30 °C) against controls at 26 °C (two gene arrays per condition). As expected, heat-shock genes are strongly up-regulated at 30 °C, particularly an hsp -70 family member (C12C8.1) and hsp -16.2. Under these heat-shock conditions, we confirmed that an hsp -16.2::GFP transgene was strongly up-regulated, whereas two non-heat-inducible transgenes (daf- 16::GFP; cyp -34A9::GFP) showed little change in expression. Bioelectromagnetics 30:602,612, 2009. © 2009 Wiley-Liss, Inc. [source] Global Gene Expression Differences Associated with Changes in Glycolytic Flux and Growth Rate in Escherichia coli during the Fermentation of Glucose and XyloseBIOTECHNOLOGY PROGRESS, Issue 1 2002Ramon Gonzalez The simplicity of the fermentation process (anaerobic with pH, temperature, and agitation control) in ethanologenic Escherichia coli KO11 and LY01 makes this an attractive system to investigate the utility of gene arrays for biotechnology applications. By using this system, gene expression, glycolytic flux, and growth rate have been compared in glucose-grown and xylose-grown cells. Although the initial metabolic steps differ, ethanol yields from both sugars were essentially identical on a weight basis, and little carbon was diverted to biosynthesis. Expression of only 27 genes changed by more than 2-fold in both strains. These included induction of xylose-specific operons ( xylE, xylFGHR, and xylAB) regulated by XylR and the cyclic AMP,CRP system and repression of Mlc-regulated genes encoding glucose uptake ( ptsHIcrr, ptsG) and mannose uptake ( manXYZ) during growth on xylose. However, expression of genes encoding central carbon metabolism and biosynthesis differed by less than 2-fold. Simple statistical methods were used to investigate these more subtle changes. The reproducibility (coefficient of variation of 12%) of expression measurements (mRNA as cDNA) was found to be similar to that typically observed for in vitro measurements of enzyme activities. Using Studentapos;s t test, many smaller but significant sugar-dependent changes were identified ( p < 0.05 in both strains). A total of 276 genes were more highly expressed during growth on xylose; 307 genes were more highly expressed with glucose. Slower growth (lower ATP yield) on xylose was accompanied by decreased expression of 62 genes concerned with the biosynthesis of small molecules (amino acids, nucleotides, cofactors, and lipids), transcription, and translation; 5 such genes were expressed at a higher level. In xylose-grown cells, 90 genes associated with the transport, catabolism, and regulation of pathways for alternative carbon sources were expressed at higher levels than in glucose-grown cells, consistent with a relaxation of control by the cyclic AMP,CRP regulatory system. Changes in expression of genes encoding the Embden,Meyerhof,Parnas (EMP) pathway were in excellent agreement with calculated changes in flux for individual metabolites. Flux through all but one step, pyruvate kinase, was predicted to be higher during glucose fermentation. Expression levels (glucose/xylose) were higher in glucose-grown cells for all EMP genes except the isoenzymes encoding pyruvate kinase ( pykA and pykF). Expression of both isoenzymes was generally higher during xylose fermentation but statistically higher in both strains only for pykF encoding the isoenzyme activated by fructose-6-phosphate, a key metabolite connecting pentose metabolism to the EMP pathway. The coordinated changes in expression of genes encoding the EMP pathway suggest the presence of a common regulatory system and that flux control within the EMP pathway may be broadly distributed. In contrast, expression levels for genes encoding the Pentose,Phosphate pathway did not differ significantly between glucose-grown and xylose-grown cells. [source] | |||||||||||||