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PubMed2006

Differentially expressed genes in hemocytes of Vibrio harveyi-challenged shrimp Penaeus monodon.

Differential Display PCR technique (DD-PCR) was used for the analysis of altered gene expression in hemocytes of Vibrio harveyi-infected Penaeus monodon. Forty-four combinations of arbitrary and oligo(dT) primers were used to screen for differentially expressed genes. A total of 79 differentially expressed bands could be identified from 33 primer combinations. These included 48 bands (61%) whose expression level increased and 31 bands (39%) decreased after V. harveyi challenge. Subsequently, forty-eight differential display fragments were successfully reamplified and cloned. A total of 267 clones were randomly selected and sequenced. The sequence analysis showed that 85 (31%) out of 267 clones were matched with sequences in the GenBank database which represented 24 different genes with known functions. Among the known genes, glucose transporter 1, interferon-related developmental regulator 1, lysozyme, profilin, SERPINB3, were selected for further confirmation of their differentially expression patterns by real-time PCR. The results showed increasing in expression level of the selected genes in shrimp hemocytes after microbial challenge suggesting the involvement of such genes in bacterial response in shrimp. The anti-lipopolysaccharide factor type 3 (ALFPm3) gene, previously reported in P. monodon (Supungul et al., 2002) was found among the up-regulated genes but diversity due to amino acid changes was observed. Increase in ALFPm3 transcripts upon V. harveyi injection is in accordance with that found in the previous study.

Amino Acid Sequence↗
PubMed2003

Identification and quantification of differentially expressed transcripts in in vitro-produced bovine preimplantation stage embryos.

In this study, we used mRNA differential display reverse transcription polymerase chain reaction (DDRT-PCR) to analyze the mRNA expression patterns in in vitro-produced bovine 8-cell, 16-cell, morula, and blastocyst stage embryos and isolate differentially expressed amplicons. Moreover, we have used a fluorescence monitored real time quantitative PCR to quantify and analyze the expression patterns of the target differentially expressed transcripts through out the preimplantation stages from oocytes to blastocyst. For this, total RNA isolated from bovine 8-cell (n = 188), 16-cell (n = 94), morula (n = 35), and blastocyst (n = 15) were reverse transcribed and subjected to DDRT-PCR. Target differentially expressed transcripts were quantified by real time quantitative PCR. The cDNA banding pattern analysis revealed that large number of cDNA bands were conserved at 8-cell and blastocyst stage with a slight decrease at the morula stage. A total of 16 amplicons were cloned and sequenced. All expressed sequence tags (ESTs), except 1C19, showed sequence similarity with known genes or ESTs in GenBank. Sixty-two percent (10/16) of cDNA bands representing differentially expressed genes originated from 8-cell stage and the rest derived from the 16-cell, morula, or blastocyst stage. The quantitative PCR analysis has validated the expression patterns of 75% (12/16) of our transcripts to be in agreement with the results of DDRT-PCR. However, the quantitative PCR results of four transcripts showed a deviation from the pattern seen in DDRT-PCR. In conclusion, we have successfully applied mRNA DDRT-PCR to identify and isolate stage-specific expressed genes in bovine preimplantation embryos. In addition to validating the results of DDRT-PCR, quantitative real time PCR provides quantitative data on the expression of target genes.

Animals↗
PubMed2005

cimp1, a novel astacin family metalloproteinase gene from East African cichlids, is differentially expressed between species during growth.

Lake Victoria cichlid fishes are excellent examples of explosive adaptive radiation. Although Lake Victoria cichlids are believed to have arisen during a short period (approximately 14,000 years), they have various species-specific phenotypes. One important phenotype that distinguishes each species is the shape of the jaw, which has diverged to adapt to the wide variety of trophic habitats present in the lake. Here we demonstrate a new approach to investigate the diversification of cichlid jaw morphology at the genetic level by examining differentially expressed genes. We used a DNA chip to compare gene expression levels between closely related cichlid fishes. This analysis indicated that the expression of some genes differed in the larvae of two cichlid species. One such clone encodes a new astacin family metalloproteinase. The expression level of the isolated gene, named cimp1, was analyzed in more detail by real-time quantitative reverse transcription-polymerase chain reaction. A significant difference in cimp1 expression was observed between two Haplochromis cichlid species during development. Using in situ hybridization, we found that this gene is expressed only in head and gill epithelia. Biochemical analysis showed that cichlid metalloproteinase 1 (CiMP1) has proteolytic activity, a common attribute of all astacin family proteins. Because some astacin family proteins contribute to morphogenesis in animals, CiMP1 is expected to participate in species-specific head morphogenesis in cichlids. This is the first study to demonstrate that differentially expressed genes among cichlids can be identified using a DNA chip.

Africa↗
PubMed2005

Identification of differentially expressed proteins in pancreatic cancer using a global proteomic approach.

Proteomics is the term used for the large-scale analysis of proteins in biological fluids or cells by biochemical methods. Two approaches are used for proteomics analysis: two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and a mass-spectrometry-based approach, such as surface-enhanced laser desorption ionization (SELDI). SELDI can be used for large protein profiling or peptide identification after enzymatic digestion. In pancreatic cancer, proteomics analysis can be performed with the aim to identify all differentially expressed proteins in cancer cells vs normal pancreatic cells. Protein profiling of pancreatic juice or serum may also identify biomarkers for pancreatic cancer that could be used as diagnostic markers or therapeutic targets. This chapter outlines the use of 2D-PAGE and SELDI for profiling the protein content of pancreatic juice samples and for identifying proteins differentially expressed in pancreatic cancer patient samples compared to control patient samples.

Electrophoresis, Gel, Two-Dimensional↗
PubMedDate not supplied

Application of isotope coded affinity tag (ICAT) analysis for the identification of differentially expressed proteins following infection of atlantic salmon (Salmo salar) with infectious hematopoietic necrosis virus (IHNV) or Renibacterium salmoninarum (BKD).

Aquaculture and commercial fisheries worldwide suffer from significant economic loss due to diseases of net-pen reared fish. In British Columbia, infectious hematopoietic necrosis (IHN) and bacterial kidney disease (BKD) epidemics occur because there are currently no commercially available drugs or fully licensed vaccines to treat these diseases. With a better understanding of the molecular mechanisms underlying these diseases, this circumstance might be significantly improved. In the present study, we have used a proteomics approach in an effort to identify and quantitate differentially expressed proteins in the liver and kidneys of diseased and healthy Atlantic salmon (Salmo salar). Isotope coded affinity tagging (ICAT), 2D gel electrophoresis, and multidimensional liquid chromatography coupled to tandem mass spectrometry (2D-LC MS/MS) were used to identify hundreds of differentially expressed proteins. While the direct significance of changes in expression levels of many proteins remains to be elucidated, others appear to be more clearly related to the infectious process. Examples of the latter are discussed here and include, a natural killer cell enhancement factor (NKEF), procathepsin L, superoxide-producing NADPH oxidase and interferon-induced viral resistance protein Mx (IFI-Mx).

Affinity Labels↗
PubMed2004

Identification of differentially expressed genes in mouse kidney after irradiation using microarray analysis.

Irradiation of the kidney induces dose-dependent, progressive renal functional impairment, which is partly mediated by vascular damage. The molecular mechanisms underlying the development of radiation-induced nephropathy are unclear. Given the complexity of radiation-induced responses, microarrays may offer new opportunities to identify a wider range of genes involved in the development of radiation injury. The aim of the present study was to determine whether microarrays are a useful tool for identifying time-related changes in gene expression and potential mechanisms of radiation-induced nephropathy. Microarray experiments were performed using amplified RNA from irradiated mouse kidneys (1 x 16 Gy) and from sham-irradiated control tissue at different intervals (1-30 weeks) after irradiation. After normalization procedures (using information from straight-color, color-reverse and self-self experiments), the differentially expressed genes were identified. Control and repeat experiments were done to confirm that the observations were not artifacts of the array procedure (RNA amplification, probe synthesis, hybridizations and data analysis). To provide independent confirmation of microarray data, semi-quantitative PCR was performed on a selection of genes. At 1 week after irradiation (before the onset of vascular and functional damage), 16 genes were significantly up-regulated and 9 genes were down-regulated. During the period of developing nephropathy (10 to 20 weeks), 31 and 42 genes were up-regulated and 9 and 4 genes were down-regulated. At the later time of 30 weeks, the vast majority of differentially expressed genes (191 out of 203) were down-regulated. Potential genes of interest included TSA-1 (also known as Ly6e) and Jagged 1 (Jag1). Increased expression of TSA-1, a member of the Ly-6 family, has previously been reported in response to proteinuria. Jagged 1, a ligand for the Notch receptor, is known to play a role in angiogenesis, and is particularly interesting in the context of radiation-induced vascular injury. The present study demonstrates the potential of microarrays to identify changing patterns of gene expression in irradiated kidney. Further studies will be required to evaluate functional involvement of these genes in vascular-mediated normal tissue injury.

Adaptation, Physiological↗
PubMed2002

Identification of differentially expressed genes by cDNA-AFLP technique during heat stress in cowpea nodules.

Legume nodules formed by diazotrophic microorganisms are active sites for biological nitrogen fixation (BNF). In tropical regions, a significant part of N supply for soybean, peanut and bean crops is derived from BNF, which is nevertheless often limited by high temperature stress. In contrast, cowpea nodules are very resistant to high temperatures. To understand the molecular bases of thermotolerance during BNF under heat stress, we have used cDNA-amplified fragment length polymorphism experiments to identify differentially expressed transcripts from cowpea nodules subjected to heat shock treatment. The expression profiles obtained showed approximately 600 bands, 55 up-regulated and nine corresponding to genes repressed by heat stress. Twenty transcript-derived fragments were isolated, cloned and sequenced. The Vigna unguiculata nodule and stress response transcripts present similarities to those that encode low molecular weight heat shock proteins, wound-induced proteins, disease resistance protein, and xylan endohydrolase isoenzyme, as well as different housekeeping genes. The differential expression of 15 genes was confirmed by using Northern blot or reverse Northern hybridization experiments.

Gene Expression Profiling↗
PubMed1999

Suppressive subtractive hybridisation reveals differential expression of serglycin, sorcin, bone marrow proteoglycan and prostate-tumour-inducing gene I (PTI-1) in drug-resistant and sensitive tumour cell lines of haematopoetic origin.

The development of therapy-induced drug resistance is still one of the most important therapeutic limitations. Nevertheless, an integrating view of the molecular mechanisms underlying resistance development in general is missing. In order to shed some light on the network of this resistance development, we established drug-resistant (doxorubicin (DX), methotrexate (MTX), cisplatin (cisPt), vincristine (Vin)) derivatives of six tumour cell lines (Jurkat, U937, HL60, DoHH-2, K562 and ARH77) of haematopoetic origin. Differential gene expression of drug-sensitive parental cell lines and the drug-resistant derivatives thereof was analysed by suppressive subtractive hybridisation. After dot blot screening for differential expression and sequencing of the cloned PCR fragments, differential expression was confirmed by Northern blot analysis. In an attempt to discriminate for differentially expressed genes only related to one or the other of the investigated drugs, the cDNAs of various resistant sublines (doxorubicin-, methotrexate-, cisplatin-resistant Jurkat cells) were pooled and compared with the sensitive parental cell line. In addition, cDNAs of the resistant derivatives of the different haematopoetic tumour cell lines were pooled and compared with the pooled cDNAs of the corresponding sensitive haematopoetic cell lines to eliminate cell line to cell line variations that were not related to drug resistance. As a result of this screening, the following genes showed a higher (at least 2-fold) or exclusive expression in the drug-resistant variants: serglycin, sorcin, BMPG (bone marrow proteoglycan gene) and PTI-1 (prostate-tumour-inducing gene 1). In addition, elevated expression of hsp90, previously found by our group to be upregulated in the drug-resistant colon carcinoma cell line LoVo H67P was found to be overexpressed in drug-resistant HL60 cells.

Antineoplastic Agents↗
PubMed1994

Identification of differentially expressed members of tobacco homeobox families by differential PCR.

As a first step to investigate the functions of homeobox genes in tobacco genetic tumorigenesis, we have used polymerase chain reaction to identify Hot (Homeobox in tobacco) genes that are expressed in tobacco genetic tumors. Five Hot genes that are actively expressed in tobacco genetic tumors are identified. Particularly, Hot1 is profoundly abundant in tumorous tissues, suggesting that it acts as a positive regulator of cell growth and differentiation during genetic tumorigenesis.

Amino Acid Sequence↗
PubMed2005

Staphylococcus aureus lipotechoic acid induces differential expression of bovine serum amyloid A3 (SAA3) by mammary epithelial cells: Implications for early diagnosis of mastitis.

Mastitis is one of the most costly diseases of agriculturally important animals and is a common problem for lactating cows. Current methods used to detect clinical and especially subclinical mastitis are either inadequate or problematic. Pathogens such as the gram-positive bacterium Staphylococcus aureus or the gram-negative bacterium Escherichia coli typically cause mastitis. E. coli induces clinical mastitis, whereas, S. aureus causes a subclinical, chronic infection of the mammary gland. In this study we report the differential expression and secretion of mammary-derived serum amyloid A3 (SAA3) by bovine mammary epithelial cells following stimulation with the S. aureus cell wall component, lipotechoic acid (LTA). Two-dimensional immunoblot analyses confirmed that bovine SAA3 is the predominant SAA isoform produced by LTA stimulated mammary epithelial cells. Our previous study showed that bovine SAA3 is also differentially expressed in response to the gram-negative bacterial endotoxin lipopolysaccharide. Collectively, these data indicate that the local production of SAA3 by mammary epithelial cells in response to either gram-positive or gram-negative bacterial components may provide a sensitive indicator for early detection and treatment of mastitis in vivo, minimizing chronic cases of infection, the spread of mastitis to other animals, and economic losses.

Animals↗
PubMed1992

Differential expression of acidic cytokeratins 18 and 19 during sexual differentiation of the rat gonad.

The expression of cytokeratins (CKs) 8, 18 and 19 was analyzed in male and female rat gonads from the undifferentiated stage (12.5 days of gestation) until two weeks after birth by indirect immunofluorescence, using specific monoclonal antibodies anti-CK 8 (LE41), anti-CK 19 (LP2K) and anti-CK 18 (LE65 and RGE53). In the undifferentiated blastema, the somatic cells were stained for CK 8 and CK 19, whereas no detectable immunoreactivity for CK 18 was obtained. The same staining CK pattern was observed in ovaries, in the somatic cells of ovigerous cords and in primary follicles. The staining was progressively decreasing in growing follicles after one week after birth. At the onset of testicular differentiation, when the first Sertoli cells differentiate in the gonad of 13.5-day old male fetuses, positive staining for CK 18 became evident, in addition to CK 8 and CK 19 expression. In the following days, CK 8, CK 18 and CK 19 were detected in Sertoli cells in the differentiating seminiferous cords, but progressively the reactivity for CK 19 decreased and was no longer observed after 18.5-19.5 days of gestation. In all cases, CKs were found to be coexpressed with vimentin, and germ cells were negative for both vimentin and CKs. The results reported here show first, that CKs are expressed before sexual differentiation in gonadal blastema in which no epithelial organization is observed, and second, that there is a CK 18/CK 19 shift in expression during morphogenesis of the testis which is not observed in the differentiating ovary. Future studies will have to determine whether these differences in CK expression are due to epitope-masking phenomena or to the regulation of CK synthesis.

Animals↗
PubMed2003

Differential expression of P450 aromatase during gonadal sex differentiation and sex reversal of the newt Pleurodeles waltl.

A better understanding of vertebrate sexual differentiation could be provided by a study of models in which genetic sex determination (GSD) of gonads can be reversed by temperature. In the newt Pleurodeles waltl, a P450 aromatase cDNA was isolated from adult gonads, and the nucleotide or deduced amino acid sequences showed a high level of identity with various vertebrate species. In adults, aromatase expression was found in gonads and brain. In developing gonads, the expression was found to fit with the thermo-sensitive period (TSP) and was detected in both ZZ and ZW larvae, as well as in ZW submitted during the whole TSP to a masculinizing temperature. In the latter individuals, in situ hybridization and semi quantitative RT-PCR showed that, at the end of TSP, aromatase expression was at the same level than in normal ZZ larvae and was significantly lower than in normal ZW ones. Furthermore, temperature-induced down regulation did not occur when heating was performed at the end of TSP. Our results confirm the importance of aromatase regulation in female versus male differentiation and demonstrate that a down regulation of aromatase expression is involved in the process of sex reversal.

Amino Acid Sequence↗
PubMed2006

Polymorphic and differential expression of the Trypanosoma cruzi alleles containing universal minicircle binding protein.

DNA replication mechanisms are poorly understood in most of trypanosomatids, in particular the replication of the peculiar mitochondrial DNA, the kinetoplast DNA (kDNA). To contribute to the knowledge on the mechanism of kDNA replication in Trypanosoma cruzi, we have previously characterized the Universal Minicircle Sequence Binding Protein of this parasite (TcUMSBP), which was first called PDZ5 [E.R. Coelho, T.P. Urmenyi, J. Franco da Silveira, E. Rondinelli, R. Silva, Identification of PDZ5, a candidate universal minicircle sequence binding protein of Trypanosoma cruzi, Int. J. Parasitol. 33 (2003) 853-858]. In this work, we describe two highly polymorphic alleles of the TcUMSBP locus in the T. cruzi reference clone CL Brener and the differential expression pattern of these alleles. A 62 bp sequence in the TcUMSBP upstream intergenic region in one of its alleles affects the efficiency of polycistronic RNA processing and the polyadenylation sites, and therefore regulates the differential expression of TcUMSBP alleles of this locus.

Alleles↗
PubMed1994

Differential expression of five sialyltransferase genes in human tissues.

Cell type-specific expression of specific carbohydrate structures on cell surface glycoproteins and glycolipids is increasingly recognized for providing information relevant to cell-cell interactions in developing and adult organisms. Sialyltransferases contribute to the diversity in carbohydrate structure through their attachment of sialic acid in various terminal positions on glycolipid and on glycoprotein (N-linked and O-linked) carbohydrate groups. In this report, differential expression of five sialyltransferase genes in human tissues is evaluated as a potential mechanism to account for cell type-specific variation in terminal sialoside structures produced by a cell. For this analysis, the complete cDNA of the human Gal beta 1,3GalNAc alpha 2,3-sialyltransferase and a partial cDNA of the developmentally regulated STX gene were cloned. Northern analysis was performed using these cDNAs and those of three previously cloned human sialyltransferase genes as probes. Each of the five sialyltransferase genes exhibits dramatic differential expression in the 16 adult and 5 fetal human tissues examined, and expression of each gene appears to be independently regulated. Comparison with fragmentary earlier studies of the expression of several of the same enzymes in rat tissues suggests that the overall pattern of expression is largely conserved.

Adult↗
PubMed2001

Identification of cyclosporine A and tacrolimus glucuronidation in human liver and the gastrointestinal tract by a differentially expressed UDP-glucuronosyltransferase: UGT2B7.

BACKGROUND/AIMS: The oral administration of the major transplant immunosuppressants cyclosporine A and tacrolimus leads to unpredictable drug levels requiring drug monitoring. Hepatic and extrahepatic metabolism of cyclosporine A and tacrolimus by cytochrome P450 proteins has been analyzed but metabolism and inactivation by glucuronidation has not been investigated. METHODS: Cyclosporine A and tacrolimus glucuronidation was measured in hepatic and gastrointestinal microsomal protein, and with 11 recombinant hepatic and extrahepatic family 1 and 2 UDP-glucuronosyltransferases. UDP-glucuronosyltransferase transcripts were determined by polymerase chain reaction. RESULTS: Significant cyclosporine and tacrolimus glucuronidation activity was present in endoplasmic reticulum from liver, duodenum, jejunum, ileum and colon, but was absent in stomach. Specific cyclosporine A glucuronidation activity was highest in liver and colon, tacrolimus glucuronidation was highest in liver. Analyses using recombinant UDPglucuronosyltransferases identified UGT2B7 as a human UDP-glucuronosyltransferase with specific activity toward cyclosporine A and tacrolimus. The hepato-gastrointestinal distribution of immunosuppressant glucuronidation activity corresponded to the differential expression pattern of UGT2B7 mRNA. CONCLUSIONS: This study provides conclusive evidence of hepatic and extrahepatic immunosuppressant glucuronidation by human UGT2B7 which was identified to be differentially expressed in the human hepatogastrointestinal tract. Hepatic and extrahepatic glucuronidation may influence the therapeutic efficacy of transplant immunosuppressants.

Administration, Oral↗
PubMed1999

Differentially expressed genes in activin-induced apoptotic LNCaP cells.

Gene transcripts differentially expressed in activin-induced human prostatic LNCaP apoptotic cells have been discovered by an improved subtractive hybridization method, uracil-DNA subtraction assay (USA), which involves digestion with uracil-DNA glycosylase and mung-bean nuclease. Among the five up-regulated and seven down-regulated genes, we have identified six known (>95% homology and similar size; p16, p53, Siva, RHAMM, Pax2, and eIF-4a1), three homologues (>95% homology but different size; myosin, a helicase motif, and a kinase motif), and three novel genes (no homology). In addition, anti-sense knock-out of a resulting novel kinase-like gene was found to abolish the apoptotic DNA fragmentation in activin-treated LNCaP cells. These findings indicate a new potential mechanism in DNA fragmentation of activin-induced cell-cycle arresting and apoptosis.

Activins↗
PubMed1996

Differential expression of AF4/FEL mRNA in human tissues.

This manuscript reports the differential expression of the AF4 gene among human tissues. AF4 mRNA is highly expressed in normal placental tissue which correlates with the newborn age of patients presenting with leukemia characterized by the MLL/AF4 gene rearrangement.

Base Sequence↗
PubMed2000

Cloning of differentially expressed sequence tags from nickel-transformed human embryonic lung cells.

Differential display polymerase chain reaction (DD-PCR) was used to analyze the differentially expressed genes from nickel-transformed human embryonic lung (HEL) cells (MRC-9 and IMR-90) and their control counterparts (non-treated). Two genes, MS515 and IC82, were confirmed by Northern blot analysis. MS515 was detected in control and nickel oxide (NiO)-transformed MRC-9 cells, as well as in non-small cell lung cancer (NSCLC) EBC-1 cells, while very weak expression was observed in nickel subsulfide (Ni(3)S(2))-transformed MRC-9 cells and small cell lung cancer (SCLC) SBC-2 cells. IC82 could not be detected in control IMR-90 cells, while it was expressed in EBC-1 cells and NiO- and Ni(3)S(2)-transformed IMR-90 cells. These findings indicate that individual nickel compounds have their own target gene(s) in inducing lung cancer. Sequencing analyses showed that the MS515 gene shared a high degree of homology (over 80%) with the gene Mena, which is involved in actin polymerization. IC82 showed 99% homology with human chromosome 4 clone C0440E08 and a coding sequence in the brain. The roles of these two genes in nickel carcinogenesis will be discussed.

Base Sequence↗