Restoration of the inflammatory gene expression by horse oil in DNCB-treated mice skin

Effects of Litsea cubeba oil on gene expression profile of Candida albicans / 中国感染与化疗杂志

Objective To analyze the effects of Litsea cubeba oil on gene expression profile of Candida albicans by comparing the differential gene expression profile after exposure to Litsea cubeba oil using genome-wide gene expression array.Methods Candida albicans ATCC90028 was exposed to Litsea cubeba oil for 90 min.Then RNA was isolated and gene expression profiles were compared to identify the differential gene expression profile using cDNA microarray analysis.Results A total of 491 geneswerefoundtoberesponsivetoLitseacubebaoil,accountingforabout11% ofthetotalnumberofgenesinCandida albicans (491/4 634),of which 216 genes were up-regulated and 275 down-regulated.These differentially expressed genes included genes encoding the key target enzyme in ergosterol biosynthesis pathway,genes in stress response,DNA replication and repair,molecular transport,and energy metabolism.Conclusions Litsea cubeba oil has significant effect on the expression of about 1 1% genes of Candida albicans genome.We presume that the genes encoding the key target enzyme in ergosterol biosynthesis pathway may contribute to the action of Litseacubeba oil on Candidaalbicans,which is similar to azole antifungal drugs.However,the role of other differentially expressed genes in the action of Litseacubeba oil on Candidaalbicans remains unclear,which deserves further study to characterize their potential association with the antifungal effect of Litsea cubeba oil.

Análise da expressão de RNAs não codificadores longos em adenocarcinoma de pâncreas / Expression analysis of long noncoding RNAs in pancreatic adecarcinoma

RNAs não codificadores longos (lncRNAs) compõem uma fração significativa do transcriptoma. Alterações na expressão de lncRNAs já foram observadas em vários cânceres humanos, mas ainda não foram exploradas no adenocarcinoma pancreático ductal (PDAC), uma doença devastadora e agressiva para a qual faltam métodos para diagnóstico precoce e tratamentos efetivos. Utilizando uma plataforma de microarranjo de cDNA com sondas para 984 lncRNAs e 2371 mRNAs, o presente estudo identificou conjuntos de lncRNAs expressos em 38 amostras clínicas pancreáticas. O enriquecimento de (i) elementos regulatórios associados às regiões promotoras (H3K4me3); (ii) possíveis inícios de transcrição (CAGE-tags); (iii) presença de elementos conservados sugere que ao menos uma fração desses RNAs seja originada a partir de unidades transcricionais independentes, reguladas e possivelmente funcionais. Foram identificadas assinaturas de expressão gênica compostas por mRNA e lncRNAs associadas ao tumor primário e à metástase pancreática. A assinatura gIenica associada à metástase apresentou enriquecimento RNAs intrônicos de loci gênicos associados à via MAPK quinase. O aumento de expressão dos transcritos intrônicos dos loci PPP3CB, MAP3K14 e DAPK1 foi confirmado por qPCR em metástases. Em conjunto, este trabalho aponta para a importância de lncRNAs intrônicos no PDAC e para a necessidade de estudos mais aprofundados para uma melhor compreensão do papel dessa classe de transcritos na biologia da doença

Long noncoding RNAs (lncRNAs) compose a significant fraction of transcriptome. Altered expression of lncRNAs has been observed in diverse human cancers, but has not being investigated in pancreatic ductal adenocarcinoma (PDAC), a devastating and aggressive disease that lack early diagnosis methods and effective treatments. Using a cDNA microarray platform with probes interrogating 984 lncRNAs and 2371 mRNA, the present study identified subsets of lncRNAs expressed in 38 pancreatic clinical samples. Enrichment of (i) regulatory elements associated to promoter region (H3K4me3); (ii) putative transcription start site (CAGEtags) and (iii) conserved elements, suggest that at least a fraction of these RNAs could be independent transcriptional unit, regulated, an possibly functional. Gene expression signatures comprised of mRNAs and lncRNAs and associated to primary or metastatic tumors were found. A gene signature associated to metastasis was enriched in intronic ncRNAs mapping to gene loci associated to the MAPK pathway. Over expression of intronic RNAs from PPP3CB, MAP3K14 and DAPK1 was confirmed by qPCR in metastatic samples. Taken together, this study points to the importance of intronic lncRNAs in PDAC and for the need to study this class of ncRNAs in greater detail to better understand its role in the biology of PDAC

Gene expression of MC3T3-E1 osteoblastic cells on titanium and zirconia surface

PURPOSE: This study was performed to define attachment and growth behavior of osteoblast-like cells and evaluate the gene expression on zirconia compared to titanium. MATERIALS AND METHODS: MC3T3-E1 cells were cultured on (1) titanium and (2) zirconia discs. The tetrazolium-based colorimetric assay (MTT test) was used for examining the attachment of cells. Cellular morphology was examined by scanning electron microscopy (SEM) and alkaline phosphatase (ALP) activity was measured to evaluate the cell differentiation rate. Mann-Whitney test was used to assess the significance level of the differences between the experimental groups. cDNA microarray was used for comparing the 20215 gene expressions on titanium and zirconia. RESULTS: From the MTT assay, there was no significant difference between titanium and zirconia (P>.05). From the SEM image, after 4 hours of culture, cells on both discs were triangular or elongated in shape with formation of filopodia. After 24 hours of culture, cells on both discs were more flattened and well spread compared to 4 hours of culture. From the ALP activity assay, the optical density of E1 cells on titanium was slightly higher than that of E1 cells on zirconia but there was no significant difference (P>.05). Most of the genes related to cell adhesion showed similar expression level between titanium and zirconia. CONCLUSION: Zirconia showed comparable biological responses of osteoblast-like cells to titanium for a short time during cell culture period. Most of the genes related to cell adhesion and signal showed similar expression level between titanium and zirconia.

Caracterización molecular de los genes pr1 y tpt1 en especies y variedades cubanas de tabaco (Nicotiana tabacum L. ) / Molecular characterization of pr1 and tpt1 proteins in cuban tobacco species and varieties (Nicoatiana tabacum L. )

La identificación de genes nuevos relacionados con la respuesta de Nicotiana tabacum L. al estrés biótico y abiótico contribuye al mejoramiento genético del cultivo del tabaco en todo el mundo. El objetivo de este trabajo fue detectar la presencia de los genes tpt1 y pr1 en el genoma de algunas especies y variedades cubanas de tabaco. Se identificaron 265 etiquetas de secuencias expresadas (ESTs-expressed sequences tags) que nunca se habían informado con anterioridad en especies vegetales, y el gen que codifica para la proteí­na tumoral controlada durante la transcripción (Transcriptional Controlled Tumor Protein) (tpt1) nunca se había informado en N. tabacum, pues los estudios del mismo se han centrado en su mayoría en animales y humanos. Los resultados del microarreglo se confirmaron utilizando la RT-PCR cuantitativa en tiempo real. Los genes tpt1 y proteí­na relacionada con la patogénesis (pr1) se utilizaron para diseñar cebadores para la caracterización molecular de algunas especies y variedades de tabaco cubano. El gen tpt1 solamente se expresó en dos especies (N. glutinosa y N. tomentosiformis) y el pr1, después de la digestión, mostró diferentes bandas entre las variedades susceptibles y resistentes. La presencia de estos genes en una parte del germoplasma analizado constituye un paso inicial para la utilización de este conocimiento en el mejoramiento genético del tabaco.

The identification of new genes related with Nicotiana tabacum L. response to biotic and abiotic stress contribute to the genetic improvement of tobacco plants around the world. The aim of this research was to identify tpt1 and pr1 genes in the genomic of some cuban tobacco varieties and species. The microarray technology has been used with ESTs for the construction of a cDNA library. 265 expressed sequences tags (ESTs) that have never been reported before in vegetables species were identified and the gene that codified for the Transcriptional Controlled Tumor Protein (tpt1), has never been reported before in N. tabacum, with the studies about this gene being focused on human and animals mostly. The microarray results were confirmed using quantitative RT- PCR. TCTP and pathogenesis-related protein 1 (PR-1) ESTs were used to design primers for the molecular characterization of some species and cuban tobacco varieties. The tpt1 gene was only expressed in two species (N. glutinosa y N. tomentosiformis) and pr1 gen, after a digestion, exhibited different bands for susceptible and resistant varieties. The detection of these genes in some species and cuban tobacco varieties represents one step to go deeply in the molecular characterization of cuban germoplasm.

Differential gene expression pattern in brains of acrylamide-administered mice / 대한수의학회지

The present study was performed to evaluate the relationship between the neurotoxicity of acrylamide and the differential gene expression pattern in mice. Both locomotor test and rota-rod test showed that the group treated with higher than 30 mg/kg/day of acrylamide caused impaired motor activity in mice. Based on cDNA microarray analysis of mouse brain, myelin basic protein gene, kinesin family member 5B gene, and fibroblast growth factor (FGF) 1 and its receptor genes were down-regulated by acrylamide. The genes are known to be essential for neurofilament synthesis, axonal transport, and neuro-protection, respectively. Interestingly, both FGF 1 and its receptor genes were down-regulated. Genes involved in nucleic acid binding such as AU RNA binding protein/enoyl-coA hydratase, translation initiation factor (TIF) 2 alpha kinase 4, activating transcription factor 2, and U2AF 1 related sequence 1 genes were down-regulated. More interesting finding was that genes of both catalytic and regulatory subunit of protein phosphatases which are important for signal transduction pathways were down-regulated. Here, we propose that acrylamide induces neurotoxicity by regulation of genes associated with neurofilament synthesis, axonal transport, neuro-protection, and signal transduction pathways.

Gene Expression Profile during Chondrogenesis in Human Bone Marrow derived Mesenchymal Stem Cells using a cDNA Microarray

Mesenchymal stem cells (MSCs) have the capacity to proliferate and differentiate into multiple connective tissue lineages, which include cartilage, bone, and fat. Cartilage differentiation and chondrocyte maturation are required for normal skeletal development, but the intracellular pathways regulating this process remain largely unclear. This study was designed to identify novel genes that might help clarify the molecular mechanisms of chondrogenesis. Chondrogenesis was induced by culturing human bone marrow (BM) derived MSCs in micromass pellets in the presence of defined medium for 3, 7, 14 or 21 days. Several genes regulated during chondrogenesis were then identified by reverse transcriptase-polymerase chain reaction (RT-PCR). Using an ABI microarray system, we determined the differential gene expression profiles of differentiated chondrocytes and BM-MSCs. Normalization of this data resulted in the identification of 1,486 differentially expressed genes. To verify gene expression profiles determined by microarray analysis, the expression levels of 10 genes with high fold changes were confirmed by RT-PCR. Gene expression patterns of 9 genes (Hrad6B, annexinA2, BMP-7, contactin-1, peroxiredoxin-1, heat shock transcription factor-2, synaptotagmin IV, serotonin receptor-7, Axl) in RT-PCR were similar to the microarray gene expression patterns. These findings provide novel information concerning genes involved in the chondrogenesis of human BM-MSCs.

Screening of differentially expressed genes in osteosarcoma cell lines with various metastatic potentialities / 中国肿瘤生物治疗杂志

Objective: To investigate the differentially expressed genes in osteosarcoma cell lines with various metastatic potentialities, and to screen for new candidate genes related to metastasis of osteosarcomas. Methods: The total RNAs of a lowly metastatic and a highly metastatic osteosarcoma cell lines (M6 and M8) were extracted. Differentially expressed genes in the two osteosarcoma cell lines were studied by cDNA microarray. The hybridization signals were scanned with a Generation Ⅲ array scanner and analyzed by Imagequant 5.0 software. Typical differentially expressed genes were further verified by real-time quantitative PCR. Results: There were 330 differentially expressed genes between M6 and M8 cells. In the high-metastasis M8 cells, 178 genes were up-regulated and 152 genes were down-regulated compared to the low-metastasis M6 cells, with 43 extremely up-regulated and 49 extremely down-regulated. The differentially expressed genes were mainly associated with cell proliferation, indicating these genes might be related to the inhibition of M6 cells. Other differentially expressed genes included those associated with the regulation of gene expression and signal transduction, indicating these genes might be correlated with tumor metastasis. Conclusion: cDNA microarray shows an advantage in identifying genes associated with metastasis of osteosarcoma. In M8 subset of MG63 osteosarcoma cells,43 genes are up-regulated and 49 genes are down-regulated, which may be related with metastasis of osteosarcoma.

Gene expression profiles in human bladder epithelial cells stimulated with uropathogenic Escherichia coli / 中华微生物学和免疫学杂志

Objective To investigate the interaction between uropathogenic Escherichia coli (UPEC) and host uroepithelial cells, define the role uroepithelial cells play in initiating and modulating the host response to infection with UPEC strain. Methods The human bladder transitional epithelial EJ cells were evaluated for their capacities to allow the adherence and invasion by UPEC132, a clinical strain isolated from Tianjin, China, and a cDNA microarray for 22 000 human genes was used to identify the gene expression differences between EJ cells infected with UPEC132 and uninfected EJ cells. Results Microscope observation showed that UPEC132 could adhere to EJ cells with the adherence rate of (73.20 ± 5.26)%. And visualization by confocal microscope revealed that this microorganism could be seen within the cells. EJ cells infected with UPEC132 changed mRNA expression of a total of 29 genes, including 28 genes up-regulated and 1 gene down-regulated. Of these, regulators of growth and proliferation, cytokines, and modulators of apoptotic responses were the most prominent. Conclusion The gene expression profiling of EJ cells is affected by the infection of UPEC strain. The differentially expressed genes may contribute to further investigate the interaction of UPEC and uroepithelial cells.

Discovery of Diagnostic Biomarkers for Legionnaires' Disease: Virulence Gene Expression Profiling of Legionella pneumophila serogroup 1 in A/J Mouse Model

BACKGROUND: Legionella pneumophila is the causative agent of Legionnaires' disease, a severe form of pneumonia. After L. pneumophila is inhaled through contaminated aerosols, it is phagocytized by alveolar macrophages, multiplies in a specialized phagosome approximately 10 h postinfection, and eventually leads to the death of host cells. Currently available diagnostic tests for Legionella pneumonia have some limitations. This study was conducted to find diagnostic biomarkers for Legionella pneumonia using virulence gene expression profiling in a murine experimental model. MATERIALS AND METHODS: A/J mice were intranasally inoculated with L. pneumophila serogroup 1, and lungs were harvested 4, 8, 24, and 48 h postinfection. The strain grown in buffered yeast extract broth was used as reference samples. Cy-dye labeled cDNA samples were prepared with total RNA from lungs or broth culture, and hybridized on the oligo-microarray slide containing 2,895 genes of L. pneumophila serogroup 1. Virulence gene expression patterns were analyzed using a MIDAS software from TIGR (www.tigr.org). RESULTS: Among a total of 332 virulence genes examined, 17 genes including sidA, lepB, the genes related to flagella assembly (fliR and fliP), LPS lipid A biosynthesis, and the enhanced entry protein EnhA were up-regulated at all four time points. We further confirmed by quantitative real-time reverse transcription PCR that the expression of fliP gene was highly expressed in lung tissue as well as in bronchoalveolar lavage fluids from the mouse infected with L. pneumophila serogroup 1. CONCLUSIONS: Through gene expression analysis of L. pneumophila in a mouse model, several candidate biomarkers for diagnosing Legionnaires' disease could be identified.

Characteristics of CTX-M Type Extended Spectrum beta-lactamase Producing Non-typhoi dal Salmonella Isolates

BACKGROUND: Extended-spectrum beta-lactamase (ESBL)-producing Salmonella have been increasingly reported worldwide. ESBL-producing Salmonella is of particular concern since children cannot be treated with quinolones. This study was conducted to determine the phenotypic and genetic characteristics of ESBL-producing Salmonella in a tertiary hospital. MATERIALS AND METHODS: Four clinical ESBL-producing isolates of non-typhoidal Salmonella were collected during 2001 to 2009. Antimicrobial susceptibility was determined by disk diffusion test and VITEK-II system. ESBL production was tested by ESBL phenotypic confirmatory test. TEM, SHV, CTX-M1, CTX-M2, CTX-M8, and CTX-M9 type ESBL genes were detected by PCR amplification, and PCR products were subjected to direct sequencing. RESULTS: Phenotypic confirmatory test showed that 4 of the 300 non-typhoidal Salmonella isolates were ESBL-producing: 3 S. Enteritidis and 1 S. Typhimurium. All 4 isolates were recovered during the past 1 year period. All 3 S. Enteritidis harbored CTX-M-15, while the S. Typhimurium harbored CTX-M-14. All CTX-M-15-producing S. Enteritidis isolates showed resistance both to cefotaxime and ceftazidime, while the CTX-M-14-producing S. Enteritidis were resistant only to cefotaxime. CONCLUSIONS: ESBL-producing nontyphoidal Salmonella has emerged recently and the type of ESBL has switched from TEM and SHV to CTX-M.

Analysis of Gene Expression in Helicobacter pylori-associated Nodular Gastritis in Children Using Microarray / 대한소아소화기영양학회지

PURPOSE: Nodular gastritis is a characteristic finding of Helicobacter pylori infection in children. The aim of this study was to evaluate the difference in gene expression in the gastric mucosa of H. pylori-infected and non-infected children, and to analyze the difference in gene expression using cDNA microarray analysis of nodular gastritis caused by H. pylori infection. METHODS: Twelve children (6 boys and 6 girls; mean age 9.8 years) who underwent upper gastrointestinal endoscopy and biopsy at Seoul National University Bundang Hospital were included in the study. The subjects were divided into three groups according to the presence of H. pylori infection and nodular gastritis on endoscopic examination. Gastric mucosa tissue was kept at -70degrees C and RNA was extracted to perform cDNA microarray analysis in each patient. RESULTS: cDNA microarray analysis in children revealed a clear distinction between H. pylori-infected and non-infected gastric mucosa. Specifically, 182 over-expressed genes and 29 under-expressed genes were identified in H. pylori-infected gastric mucosa compared to non-infected mucosa. H. pylori-infected nodular gastritis revealed different gene expression patterns from H. pylori-infected normal gastric mucosa; five genes were over-expressed and five genes were under-expressed. CONCLUSION: In the presence of H. pylori infection, gastric mucosa shows distinct differences in gene expression, and nodular gastritis with H. pylori infection in children may be associated with over- or under-expression of some genes. Further studies are required to clarify the host response and the pathogenesis of nodular gastritis in children.

Stimulation of the Extracellular Matrix Production in Dermal Fibroblasts by Velvet Antler Extract

BACKGROUND: Fibroblasts produce many components of the extracellular matrix (ECM) and so they contribute to the maintenance of connective tissue integrity. OBJECTIVE: The aim of this study is to evaluate the effect of velvet antler extract (VAE) on the ECM production of dermal fibroblasts cultured in vitro. METHODS: Primary cultured human dermal fibroblasts were treated with VAE, and then the ECM production was determined by RT-PCR, ELISA and Western blot analysis. Furthermore, the change of gene expression according to VAE treatment was evaluated by cDNA microarray. RESULTS: VAE accelerated the growth of fibroblasts in a dose-dependent manner. VAE increased the production of several ECM components, including type 1 collagen, fibronectin and elastin. In line with these results, the phosphorylations of p42/44 ERK and p38 mitogen-activated protein kinase were markedly increased by VAE, suggesting that the enhancement of ECM production may be linked to the activation of intracellular signaling cascades. VAE also significantly increased cell migration on an in vitro scratch wound test. In cDNA microarray, many genes related with connective tissue integrity were identified to be up-regulated by VAE. CONCLUSION: These results suggest that VAE has a potential to stimulate ECM production, and VAE may be applicable for maintaining the skin's texture.

Establishment of radioresistant human nasopharyngeal carcinoma cells and the differential gene expression by cDNA microarray analysis / 西安交通大学学报(医学版)

Objective To observe the differential gene expression in human nasopharyngeal carcinoma (NPC) cell line with different radiosensitivity by cDNA microarray analysis. Methods A radioresistant cell line, CNE-2R, was established from a human nasopharyngeal carcinoma cells line CNE-2 by repeated X-ray irradiation. The differential gene expression of CNE-2 and CNE-2R was screened with cDNA microarray by BioStarH-141s profile gene chip. Results There were expressed 308 genes to be screened out between CNE-2R cell line with different radiosensitivity and its parental CNE-2 cell line, while 176 up-regulated genes in CNE-2R cells and 132 down-regulated genes were found. In them, there were 40 up-regulated ones and 36 down-regulated ones whose ratios were higher than 6.0 or lower than 0.1. The different genes included DNA damage- and repair-related genes; cell cycle-related and cytoskeleton-related proteins; and apoptosis-related genes. Conclusion The radioresistant CNE-2R cells were isolated from the CNE-2 cell line by repeated X-ray irradiation. The stable radioresistance is the result of co-effect by polygene and multiple factors, which provide several gene targets to sensitize the radioresistant cells for improving the radiocurability of NPC.

Identification of Differently Expressed Genes in Chemical Carcinogen-induced Rat Bladder Cancers / 华中科技大学学报（医学）（英德文版）

Possible altered gene expression patterns in bladder turnout carcinogenesis in rat bladder cancers induced by BBN [N-butyl-N-(4-hydroxybutyl)nitrosamine] was examined by cDNA microarray analysis of gene expression profiles.Thirty Sprague-Dawley rats were given drinking water containing 0.05% BBN ad libitum for 24 to 28-weeks.Equal numbers of control rats were given tap water without BBN.After treatment,the rat bladders were excised for RNA extraction and histopathological examinations.Total RNAs were extracted from rat transitional cell carcinoma (TCC) tissues and micro-dissected normal rat bladder epithelia.The atlas glass rat microarray was used,which included oligonucleotides of 1081 rat genes.Some of the up-regulated genes in rat bladder TCCs were further confirmed by Northern blotting.Our results showed that the transcriptions of 30 genes were significantly elevated in the rat bladder TCCs,and these included fly proto-oncogene,Lipocortin 2,COX Ⅳ,COX Ⅴ a,and cathepsin D.Also,15 genes were significantly down-regulated in the rat bladder TCCs and they included B7.1,TNFrl,APOAI and VHL.The resuits of cDNA microarray analysis demonstrated that normal rat bladder epithelia and bladder TCC exhibited different and specific gene statement profiles.The increased expressions of the identified genes may play an important role in the chemically induced bladder carcinogenesis.

Regulação da expressão gênica por oxigênio no fungo aquático Blastocladiella emersonii / Regulation of gene expression by oxygen in the aquatic fungus Blastocladiella emersonii

Neste trabalho realizamos a análise das variações na expressão gênica global do fungo aquático Blastocladiella emersonii submetido ao estresse de carência de oxigênio (hipóxia), utilizando a técnica de microarranjos de cDNA em lâminas contendo 3773 genes distintos. Nos experimentos de hipóxia gradual (diminuição gradual da concentração de oxigênio dissolvido, seguido de reoxigenação) e hipóxia direta (diminuição direta da concentração de oxigênio dissolvido, seguido de reoxigenação) observamos que 650 genes foram diferencialmente expressos em pelo menos uma das condições de estresse e que 534 deles mostraram-se afetados (direta ou indiretamente) pela disponibilidade de oxigênio, uma vez que apresentaram recuperação (ou tendência à recuperação) da sua expressão aos níveis normais, quando as células foram reoxigenadas. Além de modular a expressão de diversos genes sem função conhecida, B. emersonii responde à hipóxia reajustando a expressão de genes responsáveis pela produção e consumo de energia. Pelo menos transcricionalmente, este fungo favorece o metabolismo anaeróbico, através da indução de genes que codificam enzimas da via glicolítica e lactato desidrogenase, ao passo que no ciclo do ácido cítrico, a maioria dos genes encontram-se reprimidos ou não sofrem alteração na expressão. Processos dispendiosos em energia como síntese protéica, metabolismo de aminoácidos, enovelamento de proteínas e transporte por membrana apresentaram perfis predominantemente de repressão gênica quando em carência de oxigênio. Ainda utilizando a técnica de microarranjos, mostramos semelhanças entre os perfis transcricionais nos experimentos hipóxia e de carência de Fe2+ (tratamento com quelante de Fe2+ 2,2´-dipyridyl) sugerem que estes estresses estão de alguma forma relacionados, fornecendo bons indícios de que o íon Fe2+ possa ter um papel importante no mecanismo sensor de oxigênio e/ou de resposta a hipóxia em B. emersonii. Além disso, o tratamento prévio de células...

In this work we analyzed global gene expression changes in the aquatic fungus Blastocladiella emersonii submitted to oxygen deprivation (hypoxia), using cDNA microarrays containing 3,773 distinct genes. In gradual hypoxia (gradual decrease in dissolved oxygen concentration, followed by reoxygenation) and direct hypoxia (direct decrease of dissolved oxygen concentration, followed by reoxygenation) we observed 650 differentially expressed genes in at least one of the stress conditions tested, 534 of them being affected (directly or indirectly) by oxygen availability, since they showed recovery of normal expression levels or a tendency to recover, when cells were reoxygenated. Besides modulating many genes with no previously assigned function, B. emersonii responds to hypoxia by readjusting the expression levels of genes responsible for energy production and consumption. At least transcriptionally, this fungus seems to favour anaerobic metabolism through the induction of genes encoding glycolytic enzymes and lactate dehydrogenase, while in the TCA-cycle, most genes were repressed or unchanged. Energy-costly processes like protein synthesis, amino acid metabolism, protein folding and transport had their gene expression profiles predominantly repressed during oxygen deprivation. Microarray experiments also showed similarities between the transcriptional profile of genes in hypoxia and iron (II) deprivation (treatment with the iron (II) chelator 2,2/'-dipyridyl), suggesting that these stresses are somehow related, giving good evidence that Fe2+ ion could have a role in the mechanism of oxygen sensing and/or response to hypoxia in B. emersonii. Furthermore, pretreatment of cells subjected to hypoxia with the antibiotic geldanamycin, a known inhibitor of the heat shock protein HSP90, caused a significant decrease in the induction of certain hypoxic genes, indicating that this fungus could have a mechanism similar to that of the mammalian hypoxia transcription factor...

The comparison of gene expression from human dental pulp cells and periodontal ligament cells / 대한치과보존학회지

The purpose of this study was to characterize functional distinction between human dental pulp cells(PC) and periodontal ligament cells(PDLC) using cDNA microarray assay and to confirm the results of the microarray assay using RT-PCR. 3 genes out of 51 genes which were found to be more expressed(>2 fold) in PC were selected, and 3 genes out of 19 genes which were found to be more expressed(>2 fold) in PDLC were selected for RT-PCR as well. According to this study, the results were as follows: 1. From the microarray assay, 51 genes were more expressed (2 fold) from PC than PDLC. 2. RT-PCR confirmed that ITGA4 and TGF beta2 were more expressed in PC than in PDLC 3. From the microarray assay, 19 genes were more expressed (2 fold) from PDLC than PC. 4. RT-PCR confirmed that LUM, WISP1, and MMP1 were more expressed in PDLC than in PC. From the present study, different expression of the genes between the PC and PDLC were characterized to show the genes which play an important role in dentinogenesis were more expressed from PC than PDLC, while the genes which were related with collagen synthesis were more expressed from PDLC than PC.

Changes in Global Gene Expression Induced by NOR1 Over-expression in HepG2 Cells / 生物化学与生物物理进展

Previous work from this laboratory has cloned a novel gene NOR1 and showed its extensive expression in normal tissues and down-regulation in carcinomas. To further investigate its downstream target genes and better understand its function, NOR1 was over-expressed in HepG2 hepatoma cells and global changes in gene expressions from a stable line were identified by cDNA microarrays. The results discovered 59 genes up-regulated in these cells compared with the original cells, including Grb2, HBP17,TNFRSF11B genes that have been implicated in tumorigenesis and cancer development. In addition, 103 down-regalated genes were also identified, including genes encoding Bik, MAP2K6 and ZFP95 proteins. The expression patterns of certain genes identified by microarrays were validated by quantitative real-time PCR and the results showed that expression difference were statistically significant (P< 0.05). These data suggest that NOR1 may influence the biology and cancerous behaviors of HepG2 cells by regulating expression of a set of genes involved in signal traasduction, cell cycle regulation, transcription and Wanslation controls.

Effect of Leukapheresis on Gene Expression Profiles of Donor's Peripheral Blood Mononuclear Cells / 대한진단검사의학회지

BACKGROUND: Leukapheresis has commonly been used to obtain the cell products intended for clinical cell therapy. Hypocalcemia related to citrate toxicity and some circulatory effects such as hypovolemia and hypotension are well-known complications of leukapheresis. In this study, we analyzed the gene expression profiles of peripheral blood mononuclear cells (PBMCs) obtained before and after leukapheresis to determine if the hemodynamic changes can affect the gene expression profiles of leukocytes. METHODS: PBMCs were isolated from EDTA blood from 5 healthy donors collected before and immediately after apheresis. RNA was isolated, amplified, and analyzed using a cDNA microarray with 17,500 genes. Hierarchical clustering analysis was performed to evaluate the differences of gene expression profiling. RESULTS: Hierarchical clustering separated PBMCs from different donors with each other, but did not separate PBMCs collected before and after leukapheresis. Comparison of gene expression by PBMCs collected before and after leukapheresis found only 25 genes were differentially expressed (15 were up-regulated and 10 were down-regulated after leukapheresis) (F-test, P<0.005). Stress induced apoptosis-related genes, ANXA3, DEDD, and ATXN2L, and cytokine-related genes, IL13RA1 and IK, which were also related to stress, were up-regulated after leukapheresis. Genes involved in DNA and protein binding, such as CLSTN3, LRBA, SATB2, and HSPA8, were down-regulated. CONCLUSIONS: Leukapheresis had little effect on gene expression of PBMCs. Some genes showing differences between before and after leukapheresis were mainly involved in stress-related reactions.

DNA microarray analysis of gene expression of MC3T3-E1 osteoblast cell cultured on anodized- or machined titanium surface / 대한치주과학회지

PURPOSE: The aim of this study was to evaluate adhesion and gene expression of the MC3T3-E1 cells cultured on machined titanium surface (MS) and anodized titanium surface (AS) using MTT test, Scanning electron micrograph and cDNA microarray. MATERIALS AND METHODS: The MTT test assay was used for examining the proliferation of MC3T3-E1 cells, osteoblast like cells from Rat calvaria, on MS and AS for 24 hours and 48 hours. Cell cultures were incubated for 24 hours to evaluate the influence of the substrate geometry on both surfaces using a Scanning Electron Micrograph (SEM). The cDNA microarray Agilent Rat 22K chip was used to monitor expressions of genes. RESULTS: After 24 hours of adhesion, the cell density on AS was higher than MS (p0.05). AS had the irregular, rough and porous surface texture. After 48 hours incubation of the MC3T3-E1 cells, connective tissue growth factor (CTGF) was up-regulated on AS than MS (more than 2 fold) and the insulin-like growth factor 1 receptor was down-regulated (more than 2 fold) on AS than MS. CONCLUSION: Microarray assay at 48 hours after culturing the cells on both surfaces revealed that osteoinductive molecules appeared more prominent on AS, whereas the adhesion molecules on the biomaterial were higher on MS than AS, which will affect the phenotype of the plated cells depending on the surface morphology.