Evaluation of Parkia pendula lectin mRNA differentially expressed in seedlings / Avaliação de mRNA da lectina de Parkia pendula diferencialmente expressa em plântulas

Parkia pendula (Willd.) Walp. (Fabaceae) is a neotropical species of the genus Parkia more abundantly distributed in Central to South America. From the seeds of P. pendula a glucose/mannose specific lectin (PpeL) was isolated that has been characterised and used as a biotechnological tool but until now this is the first manuscript to analyse P. pendula mRNA expression in seedlings. For this porpoise a Differential display reverse transcription polimerase chain reaction (DDRT-PCR) was used to evaluate the expression of P. pendula lectin mRNAs in non-rooted seedlings. No bands were observed in the agarose gel, indicating the absence of mRNA of PpeL seedlings. our findings confirm that lectins mRNAs are differently regulated among species even if they are grouped in the same class.

Parkia pendula (Willd.) Walp. (Fabaceae) é a espécie neotropical do gênero Parkia mais abundantemente distribuída na América Central a do Sul. Das sementes de P. pendula foi isolada uma lectina glicose/manose específica (Ppel) que foi caracterizada e usada como ferramenta biotecnológica, porém até o momento esse é o primeiro artigo a analisar a expressão do mRNA nas plântulas de P. pendula. Para esse propósito uma reação de PCR diferencial de transcriptase reversa (DDRT-PCR) foi utilizada para avaliar a expressão do mRNA da lectina de P. pendula em plântulas não enraizadas. Nenhuma banda foi observada no gel de agarose, indicando a ausência de mRNA das plântulas de PpeL. Nossos achados confirmam que os mRNAs de lectinas são regulados de forma diferentes entre as espécies, mesmo que sejam agrupadas na mesma classe.

Exequibility of differential gene expression analysis by DDRT-PCR in murine bone marrow cells / Exequibilidade do DDRT-PCR para análise da expressão gênica diferencial em células de medula óssea murina

Model of study: Experimental study. Introduction: Recently, stem cell research has generated great interest due to its applicability in regenerative medicine. Bone marrow is considered the most important source of adult stem cells and the establishment of new methods towards gene expression analysis regarding stem cells has become necessary. Thus Differential Display Reverse Transcription Polymerase Chain Reaction (DDRT-PCR) may be an accessible tool to investigate small differences in the gene expression of different stem cells in distinct situations. Aim: In the present study, we investigated the exequibility of DDRT-PCR to identify differences in global gene expression of mice bone marrow cells under two conditions. Methods: First, bone marrow cells were isolated fresh and a part was cultivated during one week without medium replacement. Afterwards, both bone marrow cells (fresh and cultivated) were submitted to gene expression analyses by DDRT-PCR...

Modelo do estudo: Estudo Experimental. Introdução: Atualmente a pesquisa com células-tronco tem gerado grande interesse devido a sua aplicabilidade no campo na medicina regenerativa. A medula óssea é considerada a maior fonte de células-tronco adultas e o estabelecimento de novos métodos para a análise da expressão gênica torna-se estritamente necessário. Desse modo, o "Differential Display Reverse Transcription Polymerase Chain Reaction (DDRT-PCR)", pode ser uma ferramenta acessível para investigação de pequenas diferenças no nível de expressão gênica em diferentes tipos celulares, sob distintas condições. Objetivo: Neste presente trabalho nós investigamos a exequibilidade do DDRT-PCR na identificação de diferenças no nível de expressão gênica global em células da medula óssea de camundongos sob duas condições. Métodos: Primeiramente, a medula óssea foi isolada frescamente e uma secunda parte foi cultivada por uma semana sem troca de meio. Posteriormente, as células da medula (fresca e cultivada) foram submetidas a análise da expressão gênica, seguindo a metodologia de DDRT-PCR...

Analysis of Gene Expression in Primary Hepatocellular Carcinoma Using Differentially Displayed Reverse Transcriptase Polymerase Chain Reaction / 대한소화기학회지

BACKGROUND/AIMS: The investigation of a specific tumor marker for hepatocellular carcinoma (HCC) is needed to examine the carcinogenesis and to select the patients for treatment options. The aim of this study was to find the genes related to HCC. We also examined the expression level of these genes in cancer cell lines and tissue specimens. METHODS: Three pairs of HCC tissue and non-neoplastic hepatic tissue around the HCC were collected from three patients who underwent resection for HCC. Differential display reverse transcriptase-PCR (DD RT-PCR) using GeneFishing (TM) PCR was used to detect the differences in the gene expression between in HCC tissue and non-neoplatic tissue. Up- or down-regulated genes in HCC tissue were identified through BLAST searches after cloning and sequencing assays. Real-time RT-PCR assay was employed to detect the expression rate in 11 HCC tissues and human cancer cell lines. RESULTS: Differentially expressed 21 genes were identified, and they were classified as genes involved in protein metabolism, ubiquitin-dependent protein catabolism, carbohydrate metabolism, lipid metabolism, DNA repair, and inflammatory response. CONCLUSIONS: We identified differentially expressed genes in HCC, and these genes may play an important role in the study of hepatocarcinogenesis, development of biomarker, and target therapy for HCC.

Identification of differentially expressed cDNAs in Acanthamoeba culbertsoni after mouse brain passage

Free-living amoebae of the genus Acanthamoeba are causative agents of granulomatous amebic encephalitis and amebic keratitis. Because the virulence of Acanthamoeba culbertsoni cultured in the laboratory is restored by consecutive brain passages, we examined the genes induced in mouse brain-passaged A. culbertsoni by differential display reverse transcriptase polymerase chain reaction (DDRT-PCR). Enhanced A. culbertsoni virulence was observed during the second mouse brain passage, i.e., infected mouse mortality increased from 5% to 70%. Ten cDNAs induced during mouse brain passage were identified by DDRT-PCR and this was confirmed by northern blot analysis. BlastX searches of these cDNAs indicated the upregulations of genes encoding predictive NADH-dehydrogenase, proteasomal ATPase, and GDP-mannose pyrophosphorylase B, which have previously been reported to be associated with A. culbertsoni virulence factors.

Identification of Gene Expression and Gene Ontology Classification by Differential Display RT-PCR in Human Cervical Squamous Cell Carcinoma / 대한산부인과학회잡지

OBJECTIVE: The molecular pathology of cervical cancer associated with human papillomavirus infection is presently unclear. In an effort to clarify the multiple interactions of a number of genes involved in cervical carcinogenesis, the gene expression profiles and pathogenic cellular processes between human cervical squamous cell carcinoma and normal cervix were investigated by mRNA differential display and the Gene Ontology analysis. METHODS: Cervical cancer biopsies were obtained from patients at the Department of Obstetrics and Gynecology, The Catholic University of Korea. The disease status was assigned according to the International Federation of Gynecology and Obstetrics. The squamous cell carcinoma tissue samples of 3 patients invasive cancer stage II (1), IV (2) were investigated by mRNA differential display. As a control, we used a common reference that was mixed with equal amount of RNA obtained from 17 normal cervix to obtain variation- independent control. Also, we constructed hierarchical functional structures using gene ontology. Then, the specific function groups were correlated with differential gene expression profiles. In addition, specific gene expression patterns in several tissue samples were investigated by using DDRT-PCR analysis. RESULTS: Differentially expressed 191 genes were identified in tumor samples. Of these genes, 128 were up-regulated and 63 were down-regulated above 1.5-fold. The gene expression profiles were classified into 46 mutually dependent function sets and organized into sub-function sets depending on the cervical cancer pathway, suggesting the potentially significant genes of unknown function affected by carcinogenesis pathway. The genes related to metabolism, signal transduction, and chaperon activity were significantly up-regulated. In contrast, significant down-regulations were shown in nucleic acid binding activity, tumor suppressor and structural activity. Reliable gene expression data shows the validation of profiling method for studying the cervical cancer-specific pathway. CONCLUSION: The specific functions assigned to each expressed gene were correlated with gene ontology for the establishment of a powerful cervical carcinogenesis pathway. The results suggest that the differentially regulated cellular process profiles have an important impact on discovery of pathogenic pathway in human cervical squamous cell carcinoma and provide the potentially significant genes of unknown function. Also, the gene ontology analysis can overcome the complexity of the expression profiles of mRNA differential display via a cellular process level approach. Thereby, a valuable prognostic candidate gene with real relevance to disease-specific pathogenesis can be found at the cellular process levels.

Characterization of the Two Genes Differentially Expressed During Development in Human Fetal Astrocytes

Astrocytes are ubiquitous in the brain and have multiple functions. It is becoming clear that they play an important role in monitoring the neuromicroenvironment, information processing, and signaling in the central nervous system (CNS) in normal conditions and that they respond to CNS injuries. During the development of the CNS, astrocytes play a key role as a substrate for neuronal migration and axonal growth. To identify genes that could participate in astrocyte maturation, we used the differential display reverse transcription-PCR (DDRT-PCR) method. Human fetal astrocytes were cultured and total RNAs were isolated at intervals of 5 days for 50 days. Using 24 primer combinations, we identified a set of 18 candidate cDNAs deriving from the excised DDRT-PCR bands. DNA sequencing revealed 16 genes that have been described already. We found that RTP, TG, hTM-alpha, SPARC, TRIP7, and RPL7 genes were expressed increasingly, while HMGCR, RPL27a, NACA, NPM, and TARBP2 genes were expressed decreasingly, according to their culture stages. We also found two unidentified genes, A3 and C8, which were expressed differently in culture stages; the former was expressed decreasingly and the latter increasingly. These two genes were found in the same amount in genomic DNA from various human cells such as astrocytes, astrocytoma, trophoblasts and lymphocytes. The A3 gene was found only in human genomic DNA, but not in rat (ATr5), mouse (RAW264.7), or monkey (Vero) cells, whereas the C8 gene was found in human genomic DNA and monkey cells, but not in rat or mouse cells. We analysed these two genes for identification. There was > 92% nucleotide sequence identity between the A3 gene (3, 626 bp) and the Homo sapiens general transcription factor 3 (GTF3), and > 96% nucleotide sequence identity between the C8 gene (2, 401 bp) and the transmembrane receptor Unc5h2. These findings suggest that these two genes may participate in some functional roles within the cells.

Search for Genes Potentially Related to Germ Tube Formation in Candida albicans by Differential-Display Reverse Transcription Polymerase Chain Reaction

Candida albicans exhibits the ability to grow in either a yeast or a mycelia form in response to different environmental factors. The mycelia form, found in infected tissues, is important as a virulence factor in the adherence of the organism to the host epithelium. In vitro, the morphological transition can be induced by environmental shifts in the growing conditions, or by a variety of exogenous factors, including ambient pH, nutritional status and temperature. The differential-display reverse transcription polymerase chain reaction (DDRT-PCR) is a powerful technique for comparing gene expression between cell types, stages of development or differentiation. Hyphae related genes were identified and characterized using a PCR-based differential display. Candida albicans formed a germ tube when cultured in rabbit serum, RPMI 1640 medium or 39degrees C-YPD medium. We gained 21 cDNA bands showing a different expression pattern from that of the uninduced culture. DNA was extracted from the same location of the isolated bands, and PCR was performed under the same conditions, which reamplified the PCR product, showing the specific expression patterns according to the culture conditions. We cloned 18 germ tube-related cDNA clones (inserts average size is 80 - 700 bp) and sequenced them. The nucleotide sequences of the 18 clones were identified through in the present study from GenBank, and were found to have the accession number (AF405213-AF405230). We could not find any nucleotide sequence having a high homology with these clones. This study could form a part of the projects in the search for genes related to the germ tube formation of C. albicans.

Several Genes Expressed During Morphogenesis of Lentinus edodes (ImHyup-1)

Differential display of reverse transcription (DDRT)-PCR was conducted to have a profile of the differentially expressed genes during the formation of fruiting body of Lentinus edodes. The lines of L. edodes (ImHyup-1) employed were cultivated in the artificial blocks of sawdust, and the fruiting body was induced from the mycelia or the mass protruded from the brown surface of the sawdust blocks. RNAs were prepared from the four different developmental stages; mycelial, primordial, and stipes and pileus of fruiting body. The fragments of cDNA were synthesized from the combinations of the arbitrary primers and 3' one anchored Oligo-dT primer. Twelve combinations using the primers have been tested, and among them nineteen bands were identified as differentially expressed. Those genes were further analyzed by DNA sequencing and followed by homology search. Characterization of one clone was conducted as a preliminary data and more are under investigation.

The alteration of gene expression in cortex tissue following BALB/c rat aging / 中华老年医学杂志

Objective To identify and clone rat aging-related genes to provide clues for human aging mechanism. Methods Improved different display reverse transcript-PCR method was applied to identify differentially expressed genes in cortex tissues of 4-month and 24-month old BALB/c mouse. Results Forty-two cDNA fragments with differential expression were identified, and 21 with increase and 21 with decrease of expression in old mice. Among them, 17 represented genes with known protein function, 12 represented known gene sequences but their protein function was unknown, and the other 13 probably belonged to new cDNAs. Among the genes with known protein function, 2 genes were associated with oxidative stress, 3 with energy production, and 4 with protein metabolism, respectively. Additionally, gene expression alterations were also found in those related to cell apoptosis, neurodegenerative disorder, and growth and development regulation. Conclusions Rat aging might be related with the alteration of oxidative stress status, energy production and protein metabolism.

Cloning aged-related gene of mouse thymus / 中国免疫学杂志

Objective:Differential expression analysis and cloning aged related genes of mouse thymus Methods:Different expressions of thymus mRNAs from 1 and 10 month old mouse were analyzed by DDRT PCR and different expression sequence tags (ESTs) were obtained One EST that represented high expressed level in one month mouse thymus was probed to screen mouse thymus cDNA library One 827 bp cDNA fragment was obtained and was extended to 1 406 bp by PCR Results:Homology analysis showed that mt22 1406 contained one 438AA coding region and showed high similarity with human elongation factor1?(EF1?) The Genbank accession number is BE241062 Conclusion:Cloning one gene related with mouse thymus aging