A high throughput screening for rarely transcribed differentially expressed genes

Improved live-cell PCR method for detection of organophosphates degrading opd genes and applications

Organophosphates are becoming an emerging pollutant due to their various applications, particularly as pesticides. In this study, an improved Colony (Live-cell) PCR method was developed for the detection of opd genes from bacteria encoding the organophosphate hydrolase enzymes capable of degrading various organophosphates. The improved method does not require pre-heating or pre-lysis of bacterial cells as essential in the conventional colony PCR. The reaction volume was scaled down to 10 µl by optimizing the PCR buffer and amplification conditions. The improved method was used for Gram positive and negative bacteria, glycerol stocks, liquid cultures, recombinant and mutant strains. Also, 16S rRNA gene was amplified from unknown environmental isolates and known E. coli strains. The amplified opd and 16S rRNA genes from the improved colony PCR method and by conventional PCR were sequenced, and similar results were obtained from both techniques. Thus, the improved method can be further explored in molecular biology or during biomarker studies. KEY POINTS: • Improved colony PCR method was developed for screening of opd genes from bacteria. • Method was validated for Gram positive/negative bacteria from solid as well as liquid media. • The improved method was rapid, efficient, and can be applied under various conditions.

Ultra-High Efficient Colony PCR for High Throughput Screening of Bacterial Genes

Current colony PCR methods are not suitable for screening genes encoded in genomic DNA and are limited to E. coli host strains. Here, we describe an ultra-high efficient colony PCR method for high throughput screening of bacterial genes embedded in the genomic DNA of any bacterial species. This new technique expands colony PCR method to several hosts as well as offers a rapid, less expensive and reliable bacterial genomic DNA extraction.

Lung fibrosis: drug screening and disease biomarker identification with a lung slice culture model and subtracted cDNA Library

Pulmonary fibrosis is a progressive and irreversible disorder with no appropriate cure. A practical and effective experimental model that recapitulates the disease will greatly benefit the research community and, ultimately, patients. In this study, we tested the lung slice culture (LSC) system for its potential use in drug screening and disease biomarker identification. Fibrosis was induced by treating rat lung slices with 1ng/ml TGF-β1 and 2.5μM CdCl2, quantified by measuring the content of hydroxyproline, and confirmed by detecting the expression of collagen type III alpha 1 (Col3α1) and connective tissue growth factor (CTGF) genes. The anti-fibrotic effects of pirfenidone, spironolactone and eplerenone were assessed by their capability to reduce hydroxyproline content. A subtractive hybridisation technique was used to create two cDNA libraries (subtracted and unsubtracted) from lung slices. The housekeeping gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was employed to assess the subtraction efficiency of the subtracted cDNA library. Clones from the two libraries were sequenced and the genes were identified by performing a BLAST search on the NCBI GenBank database. Furthermore, the relevance of the genes to fibrosis formation was verified. The results presented here show that fibrosis was effectively induced in cultured lung slices, which exhibited significantly elevated levels of hydroxyproline and Col3α1/CTGF gene expression. Several inhibitors have demonstrated their anti-fibrotic effects by significantly reducing hydroxyproline content. The subtracted cDNA library, which was enriched for differentially expressed genes, was used to successfully identify genes associated with fibrosis. Collectively, the results indicate that our LSC system is an effective model for the screening of drug candidates and for disease biomarker identification.

Restricted neural epidermal growth factor-like like 2 (NELL2) expression during muscle and neuronal differentiation

We have identified a secreted glycoprotein, neural epidermal growth factor-like like 2 (NELL2), in a screen designed to isolate molecules regulating sensory neuron genesis and differentiation in the dorsal root ganglia (DRG). In investigating NELL2 expression during embryogenesis, we demonstrate here that NELL2 is highly regulated spatially and temporally, being only transiently expressed in discrete regions of the central (CNS) and peripheral nervous systems (PNS) and in a subset of mesoderm derived structures during their peak periods of development. In the CNS and PNS, NELL2 is maximally expressed as motor and sensory neurons differentiate. Interestingly, its expression is restricted to sublineages of the neural crest, being strongly expressed throughout the immature DRG, but excluded from sympathetic ganglia. Similarly during muscle development, NELL2 is specifically expressed by hypaxial muscle precursor cells in the differentiating somite and derivatives in the forelimbs and body wall, but not by epaxial muscle precursors. Furthermore, NELL2 is differentially regulated in the CNS and PNS; in the CNS, NELL2 is only expressed by nascent, post-mitotic neurons as they commence their differentiation, yet in the PNS, NELL2 is expressed by subsets of progenitor cells in addition to nascent neurons. Based on this restricted spatial and temporal expression pattern, functional studies are in progress to determine NELL2's role during neuronal differentiation in both the PNS and CNS.

Removing PCR for the elimination of undesired DNA fragments cycle by cycle

A novel removing polymerase chain reaction (R-PCR) technique was developed, which can eliminate undesired genes, cycle by cycle, with efficiencies of 60.9% (cDNAs), 73.6% (genomic DNAs), and ~ 100% (four DNA fragments were tested). Major components of the R-PCR include drivers, a thermostable restriction enzyme - ApeKI, and a poly(dA) adapter with mismatched restriction enzyme recognition sites. Drivers were generated from the undesired genes. In each cycle of R-PCR, drivers anneal to complementary sequences and allow extension by Taq DNA polymerase. Thus, ApeKI restriction sites in the undesired genes are recovered, and adapters of these undesired DNA fragments are removed. Using R-PCR, we isolated maize upregulated defense-responsive genes and Blumeria graminis specialized genes, including key pathogenesis-related effectors. Our results show that after the R-PCR reaction, most undesired genes, including very abundant genes, became undetectable. The R-PCR is an easy and cost-efficient method to eliminate undesired genes and clone desired genes.

Development of novel diagnostic and prognostic molecular markers for sporadic colon cancer

Gene expression studies are informative about changes in colon cancer, increase understanding of the biology of tumorigenesis and aid in developing diagnostic and prognostic markers. In this review, expression techniques used to examine the multistage process of colon cancer are discussed. Many genes have been found to differ in expression between normal and tumorigenic states, as early as the seemingly normal colonic crypts. The clinical usefulness of markers varies with stage, ethnicity and anatomic location of colon cancer. Thus, combinations of markers can be used to develop an approach to molecularly screen and follow the progression of this prevalent cancer.

Molecular characterization and expression analysis of NDUFS4 gene in m. longissimus dorsi of Laiwu pig (Sus scrofa)

To study the molecular basis of intramuscular fat (IMF) deposition, suppression subtractive hybridization was used to investigate the differences in gene expression between m. longissimus dorsi (LD) of high IMF Laiwu pig group and low IMF Laiwu pig group. From two specific subtractive cDNA libraries, the expression-upregulated clone HL-27 was selected by reverse Northern high-density blot, and then identified to be pig mitochondrial NADH dehydrogenase (ubiquinone) Fe-S protein 4 (NDUFS4). Pig NDUFS4 full-length cDNA was cloned by RACE, and contains a 528 bp-open reading frame (ORF) encoding 175 amino acid residues. The derived amino acid sequence of NDUFS4 is well conserved compared with NDUFS4 of various species with higher degree of sequence similarity with other mammalian (86.3-92.6 %) than amphibian, aves, and fishes (70.2-81.1 %), and contains one N-linked glycosylation site, one O-linked glycosylation site, seven Ser phosphorylation sites and five Thr phosphorylation sites. A-G mutation was found at nt 122 site of ORF between Laiwu pig and Large White, which results in the K-R mutation at 41 site of protein sequence. Real-time PCR analysis indicated that the level of NDUFS4 mRNA expression was higher in high IMF Laiwu pig group than in low IMF Laiwu pig group, and in Laiwu pig than in Large White. The tissue expression of the pig NDUFS4 gene showed a tissue-specific pattern: highly expressed in LD muscle, spleen and kidney, but hardly expressed in lung, stomach and large intestine. The possible role of NDUFS4 and its relation to IMF deposition are discussed.

Isolation and analysis of genes mainly expressed in adult mouse heart using subtractive hybridization cDNA library

Subtractive hybridization cDNA library (SHL) is one of the powerful approaches for isolating differentially expressed genes. Using this technique between mouse heart and skeletal muscle (skm) tissues, we aimed to construct a cDNA-library that was specific to heart tissue and to identify the potential candidate genes that might be responsible for the development of cardiac diseases or related pathophysiological conditions. In the first step of the study, we created a cDNA-library between mouse heart and skm tissues. The homologies of the randomly selected 215 clones were analyzed and then classified by function. A total of 146 genes were analyzed for their expression profiles in the heart and skm tissues in published mouse microarray dataset. In the second step, we analyzed the expression patterns of the selected genes by Northern blot and RNA in situ hybridization (RISH). In Northern blot analyses, the expression levels of Myl3, Myl2, Mfn2, Dcn, Pdlim4, mt-Co3, mt-Co1, Atpase6 and Tsc22d1 genes were higher in heart than skm. For first time with this study, expression patterns of Pdlim4 and Tsc22d1 genes in mouse heart and skm were shown by RISH. In the last step, 43 genes in this library were identified to have relationships mostly with cardiac diseases and/or related phenotypes. This is the first study reporting differentially expressed genes in healthy mouse heart using SHL technique. This study confirms our hypothesis that tissue-specific genes are most likely to have a disease association, if they possess mutations.

Discovery of a novel tumour metastasis-promoting gene, NVM-1

We have previously reported that over-expression of a panel of 119 genes correlates with the metastatic potential of pancreatic carcinoma cells. We sought to identify and functionally characterize candidate tumour metastasis promoting genes among this library using a secondary phenotype-assisted screen. Here we report the discovery of the metastasis-promoting function of a hitherto not characterized gene located on chromosome 14 (ORF138), which we have named 'novel metastasis-promoting gene 1' (NVM-1). The NVM-1 transcript is extensively alternatively spliced, is expressed endogenously in a number of different tissues, and is strongly over-expressed at the protein level in a variety of human tumour types. Importantly, NVM-1 expression stimulates the migratory and invasive behaviour of tumour cells and promotes metastasis formation in experimental animals in vivo. Up-regulation of FMNL2 and MT1E and down-regulation of TIMP4 and MHC-I is observed as a consequence of NVM-1 expression. Together these data identify NVM-1 as a gene that is functionally involved in tumour metastasis, and suggest that NVM-1 may constitute a promising therapeutic target for inhibition of tumour metastasis.

Studies of quinapyramine-resistance of Trypanosoma brucei evansi in China

In the present article, we summarize our studies of antrycide-resistance of Trypanosoma brucei evansi in four aspects in the last recent several years, the analysis of quinapyramine-sensitive situation of T. b. evansi in China, biological characteristics of T. b. evansi population in quinapyramine-resistance and biological materials of quinapyramine-resistance in T. b. evansi population. Firstly, the correlative assays of effective dosage of quinapyramine on T. b. evansi disease between in vivo and in vitro methods showed that their relationship was parabolic with positive correlation. On the other hand, the IC(50) and CD(100) values of 12 T. b. evansi isolates, AHB, GDB1, GDB2, HNB, JSB1, JSB2, YNB, ZJB, GDH, GXM, HBM and XJCA, collected from buffaloes, horses, mules and camels across nine provinces of China were examined using the two methods, respectively. Among them, the nine isolates, AHB, GDB1, GDB2, HNB, JSB1, JSB2, YNB, ZJB and GDH, became quinapyramine-sensitive T. b. evansi. Secondly, T. evansi populations could rapidly obtain antrycide-resistance when they were passed through immunosuppressed mice treated with low doses of the drug. But, the replication rate of trypanosomes with antrycide-resistance decreases as the level of drug-resistance increases. Thirdly, the analysis of the HK, G6PDH, ALAT and ASAT isoenzymes showed that they were not involved in the quinapyramine-resistance of T. b. evansi. But the protein bands of 15.79kDa and 19.76kDa might be involved in the antrycide-resistance of T. b. evansi population. At genetic level, the gene, TbTA1, could be amplified from the T. b. evansi isolate sensitive to quinapyramine-sensitivity but the T. b. evansi isolate with quinapyramine-resistance using not only the RT-PCR technique, but also PCR technique. We used the SSH (Suppression Subtractive Hybridization) to clone highly or low expressed cDNA fragments caused by production of antrycide-resistance in T. b. evansi. The 5 low and 9 high expressed new cDNA fragments were amplified. Among them, the 3 low expressed cDNA fragments had the same sequence of 65 amino acids and the 3 high expressed cDNA fragments were located in chromosome VI, like T. brucei. Lastly, more work needs to be done in order to elucidate the mechanism of quinapyramine-resistance of T. b. evansi.

Suppression subtractive hybridization as a tool to identify anthocyanin metabolism-related genes in apple skin

The pigmentation of anthocyanins is one of the important determinants for consumer preference and marketability in horticultural crops such as fruits and flowers. To elucidate the mechanisms underlying the physiological process leading to the pigmentation of anthocyanins, identification of the genes differentially expressed in response to anthocyanin accumulation is a useful strategy. Currently, microarrays have been widely used to isolate differentially expressed genes. However, the use of microarrays is limited by its high cost of special apparatus and materials. Therefore, availability of microarrays is limited and does not come into common use at present. Suppression subtractive hybridization (SSH) is an alternative tool that has been widely used to identify differentially expressed genes due to its easy handling and relatively low cost. This chapter describes the procedures for SSH, including RNA extraction from polysaccharides and polyphenol-rich samples, poly(A)+ RNA purification, evaluation of subtraction efficiency, and differential screening using reverse northern in apple skin.

Identification and expression analysis of the aldo-ketoreductase1-B10 gene in primary malignant liver tumours

BACKGROUND & AIMS

The aim of our study was to search for highly up-regulated genes in primary malignant liver tumours and to analyse their expression at the mRNA- and protein level.

METHODS

Using a random-based gene fishing approach (representational difference analysis coupled to array hybridisation) we identified 7 genes high abundantly expressed in hepatocellular carcinoma (HCC) as compared to non-neoplastic liver tissue, among them a gene fragment of the aldo-ketoreductase (AKR) superfamily. Full length cloning and sequencing of the gene fragment identified it as B10 gene of the AKR-family 1 (AKR1B10). For expression analysis on transcriptional level quantitative real-time RT-PCR was performed in 22 HCC and 22 non-neoplastic liver cirrhotic tissues.

RESULTS

Our data demonstrate significantly higher expression levels of AKR1B10-mRNA in HCC compared to non-tumourous cirrhotic liver tissue (p<0.0001). To evaluate its protein expression in primary malignant liver tumours, we investigated tissue arrays of 210 HCC and 51 cholangiocarcinomas (CC) by immunohistochemistry, using a monoclonal antibody against AKR1B10. Protein staining of AKR1B10 was significantly increased in well and moderately differentiated tumours compared to corresponding non-neoplastic liver tissue (p=0.023). However, AKR1B10-staining decreased in advanced, low differentiated tumours with a significant inverse correlation between AKR1B10-staining and tumour proliferation, indicated by Ki67 (MIB-1) staining (r=-0.89, p=0.02).

CONCLUSION

The over-expression of AKR1B10 in early stages of well and moderately differentiated tumours and its down-regulation in advanced tumour-stages with low grade of differentiation demonstrated that AKR1B10 may be a helpful marker for differentiation and proliferation of HCC and CC.

Isolation, Characterization and Expression Analysis of a Leaf-specific Phosphoenolpyruvate Carboxylase Gene inOryza sativa

Suppression subtractive hybridization was carried out to enrich gene fragments over-expressed in rice leaves by subtraction to rice roots, from which two identical cDNA fragments were identified to encode putative phosphoenolpyruvate carboxylase. Then the corresponding full-length cDNA (Osppc) is isolated by RT-PCR and sequenced, which indicates an open reading frame of 2895bp is contained. Its deduced protein is encoded in 10 exons and shows high similarity to many other plant PEPCs. Comparing with maize and bacterial PEPCs, it is revealed that OSPPC shares many conserved domains and active sites that responsible for the structure, activity and regulation of this enzyme. Phylogenetic analysis demonstrates that OSPPC is grouped with C3 form PEPCs of wheat, maize and sorghum, which is consistent with the classification of rice. And a putative promoter element is predicted with DOF binding box, CAAT box and TATA box in the 5'-flanking sequence of Osppc gene. Moreover, Quantitative RT-PCR analyses are performed in hybrid rice and its parents, which show that Osppc is specifically expressed in leaf including leaf vein and sheath.

Identification of a new WASP and FKBP-like (WAFL) protein in inflammatory bowel disease: a potential marker gene for ulcerative colitis

BACKGROUND AND AIMS

Inflammatory bowel disease (IBD) is a complex inflammatory disease of the gastrointestinal tract with unknown cause that lacks molecular markers for diagnosis. Crohn's disease (CD) and ulcerative colitis (UC) are the two major forms of IBD. The aim of this study was to investigate gene expression patterns in UC and characterize newly identified marker genes potentially linked to disease pathogenesis of UC.

MATERIALS AND METHODS

Biopsies were taken from eight UC patients, from inflamed and non-inflamed parts of the colon. Gene expression was investigated by subtractive suppression hybridization (SSH), and further study of a selected gene was performed by Northern blot, immunohistochemistry, immunocytochemistry, and in vitro monocyte differentiation.

RESULTS

Three hundred thirty-one differentially expressed genes were found and classified into functional groups. In this paper, we report one gene with unknown function to be differentially expressed in UC but not Crohn's disease by real-time reverse transcriptase polymerase chain reaction. Due to its predicted protein architecture, we call this gene Wiskott-Aldrich syndrome protein and FKBP-like (WAFL). Initial pilot experiments suggest WAFL to participate in innate immune functions.

CONCLUSION

The SSH result supports the current view of UC to be a chronic inflammatory disorder with aberrant expression of epithelial barrier proteins, cell fate-related factors, and disturbed metabolism. The new gene, WAFL, reported in this study, appears to be conditionally regulated in myeloid cells. This indicates that WAFL may be connected to innate immune-host responses. As such, it represents an interesting, hitherto unknown player in IBD where there is a need for further elucidation on the molecular and cellular level.

Multigene analysis can discriminate between ulcerative colitis, Crohn's disease, and irritable bowel syndrome

BACKGROUND & AIMS

Inflammatory bowel diseases (IBDs) and the irritable bowel syndrome (IBS) are heterogeneous disorders of the gastrointestinal tract and can profoundly affect the quality of life. Because many of the symptoms of IBD are similar to those of IBS, the former may be misdiagnosed. In addition, the 2 major forms of IBD, ulcerative colitis (UC) and Crohn's disease (CD), have overlapping nonspecific, pathologic features leading to difficulties in assessing colonic inflammation and hence the term IBD unclassified has been proposed. The aim of this study was to identify and assess the utility of a certain set of marker genes that could help to distinguish IBS from IBD, and further to discriminate between UC and CD.

METHODS

Subtractive suppression hybridization was used to identify IBD-specific genes in colonic mucosal biopsy specimens. In quantitative polymerase chain reaction experiments, the differential expressions of identified genes then were analyzed using a classification algorithm and the possible clinical value of these marker genes was evaluated in a total of 301 patients in 3 stepwise studies.

RESULTS

Seven marker genes were identified as differentially expressed in IBD, making it possible to discriminate between patients suffering from UC, CD, or IBS with area under the receiver-operating characteristic curves ranging from 0.915 to 0.999 (P < .0001) using the clinical diagnosis as gold standard.

CONCLUSIONS

Expression profiling of relevant marker genes in colonic biopsy specimens from patients with IBD/IBS-like symptoms may enable swift and reliable determination of diagnosis, ultimately improving disease management.

Identification of differentially expressed genes involved in the formation of multicellular tumor spheroids by HT-29 colon carcinoma cells

The multicellular tumor spheroid (MCTS) model represents a suitable in vitro model recreating in vivo tumor formation. The aim of this study was to identify differentially expressed genes that could potentially serve as predictive gene markers for MCTS and be involved in the formation of MCTS. Using the suppression subtractive hybridization (SSH) method, we identified ERBB2/HER2-interacting protein (Erbin), Tumor rejection gp96 (Tr-gp96), 12S ribosomal RNA (12S rRNA), ATP synthase, Kruppel-like transcription factor 5 (KLF5), transcription factor-like 5 (TCFL5), and the dual-specificity phosphatase 11 (DUSP11) to be overexpressed in 3-day-old HT-29 colon carcinoma MCTSs compared to HT-29 colon carcinoma cells grown in monolayer. We could also confirm overexpression of these genes in HT-29 MCTSs and in MCTSs formed by the human glioblastoma tumor cell lines U343 MG, U373 MG, and DBTRG 05 MG. Knockdown of KLF5, Erbin, DUSP11, and TCFL5 was effectively achieved after transfection of HT-29 cells with the appropriate short-interfering RNAs (siRNAs), and correlated with a significant inhibition of MCTS formation in the case of KLF5, Erbin, and TCFL5 siRNAs. We suggest that KLF5, Erbin, and TCFL5 are essential for MCTS formation and play a key role in the development of tumor diseases.

Subtractive hybridization

Subtractive hybridization, like serial analysis of gene expression (SAGE), RNA arbitrarily primed polymerase chain reaction (RAP-PCR) and microarrays, is a screening method for differentially expressed genes. At first, poly-A+-RNA is isolated and reverse transcribed into cDNA. With the SMART technology, total RNA can be used. For subtractive hybridization, two adaptors are ligated to the tester cDNA. The tester cDNA is then mixed twice with cDNA of the reference sample. Sequences that are present in equal levels in the tester and in the reference cDNA hybridize to each other and are then removed. In contrast, differentially expressed genes are highly enriched and then amplified by PCR. Because subtractive hybridization is a complex multistep procedure, the results should be controlled at each level and positive controls are recommended. Because all screening methods produce a significant number of false positives, the differential expression has to be confirmed by independent methods.

Oncogenic signaling pathways and deregulated target genes

A limited number of somatic mutations are known to trigger malignancy via chronic activation of cellular signaling pathways. High-throughput analysis of gene expression in cancer cells has revealed a plethora of deregulated genes by far exceeding the number of known genetic alterations. Targeted tumor therapy takes advantage of deregulated signaling in cancer. However, cancer cells may evade successful therapy, e.g., targeting oncogenic kinases, due to mutation of the target protein or to resistance mechanisms acting downstream of or parallel to the therapeutic block. To improve therapy and molecular diagnostics, we need detailed information on the wiring of pathway components and targets that ultimately execute the malignant properties of advanced tumors. Here we review work on Ras-mediated signal transduction and Ras pathway-responsive targets. We introduce the concept of signal-regulated transcriptional modules comprising groups of target genes responding to individual branches of the pathway network. Furthermore, we discuss functional approaches based on RNA interference for elucidating critical nodes in oncogenic signaling and the targets essential for malignancy.

Gene expression profiles linked to the hormonal induction of male-effect pheromone synthesis in goats (Capra hircus)

The male effect is a well-known phenomenon in female sheep and goats whereby a pheromone-induced activation of reproductive function occurs. However, the molecule(s) involved in this phenomenon are unknown. We investigated gene expression profiles for the induction of male effect pheromone synthesis using a PCR-based cDNA subtraction strategy. We constructed two subtracted cDNA libraries using mRNA from the skin of the head or rump region of orchidectomized male goats with or without pheromone induction using testosterone or dihydrotestosterone (DHT). Both libraries were assumed to contain genes whose expression increases with pheromone induction. Clones (n = 480) from each library were sequenced and identified using BLAST to reveal 115 and 239 types of sequences in the libraries of the head and rump region, respectively. Among these, 12 genes were expressed in both libraries. We conducted real-time PCR to further analyze their expression using cDNA samples derived from pheromone-producing or nonproducing skin from the head of an ovariectomized female goat with or without DHT implantation, respectively. For nine genes, we observed significantly increased expression in samples following DHT implantation. Among these, stearoyl-CoA desaturase 1 (SCD1) and elongation of long chain fatty acids family member 5 (ELOVL5) genes showed more than 100-fold higher expression levels in pheromone-positive samples, suggesting that the products of these genes may be important in pheromone synthesis.

Transcriptional and metabolic profiles of stress-induced, embryogenic tobacco microspores

Higher plant microspores, when subjected to various stress treatments in vitro, are able to reprogram their regular gametophytic development towards the sporophytic pathway to form haploid embryos and plants. Suppression subtractive hybridization (SSH) and metabolic profiling were used to characterize this developmental switch. Following differential reverse Northern hybridizations 90 distinct up-regulated sequences were identified in stressed, embryogenic microspores (accessible at www.univie.ac.at/ntsm). Sequence analyses allowed the classification of these genes into functional clusters such as metabolism, chromosome remodeling, signaling, transcription and translation, while the putative functions of half of the sequences remained unknown. A comparison of metabolic profiles of non-stressed and stressed microspores using gas chromatography/mass spectrometry (GC/MS) identified 70 compounds, partly displaying significant changes in metabolite levels, e.g., highly elevated levels of isocitrate and isomaltose in stressed microspores compared to non-stressed microspores. The formation of embryogenic microspores is discussed on the basis of the identified transcriptional and metabolic profiles.

Gene cooption without duplication during the evolution of a male-pregnancy gene in pipefish

Comparative studies of developmental processes suggest that novel traits usually evolve through the cooption of preexisting genes and proteins, mainly via gene duplication and functional specialization of paralogs. However, an alternative hypothesis is that novel protein function can evolve without gene duplication, through changes in the spatiotemporal patterns of gene expression (e.g., via cis-regulatory elements), or functional modifications (e.g., addition of functional domains) of the proteins they encode, or both. Here we present an astacin metalloprotease, dubbed patristacin, which has been coopted without duplication, via alteration in the expression of a preexisting gene from the kidney and liver of bony fishes, for a novel role in the brood pouch of pregnant male pipefish. We examined the molecular evolution of patristacin and found conservation of astacin-specific motifs but also several positively selected amino acids that may represent functional modifications for male pregnancy. Overall, our results pinpoint a clear case in which gene cooption occurred without gene duplication during the genesis of an evolutionarily significant novel structure, the male brood pouch. These findings contribute to a growing understanding of morphological innovation, a critically important but poorly understood process in evolutionary biology.

Subtractive hybridization for differential gene expression in mechanically unloaded rat heart

The objective of this study was to identify differentially expressed genes in the mechanically unloaded rat heart by suppression subtractive hybridization. In male Wistar-Kyoto rats, mechanical unloading was achieved by infrarenal heterotopic heart transplantation. Differentially expressed genes were investigated systematically by suppression subtractive hybridization. Selected targets were validated by Northern blot analysis, real-time RT-PCR, and immunoblot analysis. Maximal ADP-stimulated oxygen consumption (state 3) was measured in isolated mitochondria. Transplantation caused atrophy (heart-to-body weight ratio: 1.6 ± 0.1 vs. 2.4 ± 0.1, P < 0.001). We selected 1,880 clones from the subtractive hybridization procedure (940 forward and 940 reverse runs assessing up- or downregulation). The first screen verified 465 forward and 140 reverse clones, and the second screen verified 67 forward and 30 reverse clones. On sequencing of 24 forward and 23 reverse clones, 9 forward and 14 reverse homologies to known genes were found. Specifically, we identified reduced mRNA expression of complex I (−49%, P < 0.05) and complex II (−61%, P < 0.001) of the respiratory chain. Significant reductions were also observed on the respiratory chain protein level: −42% for complex I ( P < 0.01), −57% for complex II ( P < 0.05), and −65% for complex IV ( P < 0.05). Consistent with changes in gene and protein expression, state 3 respiration was significantly decreased in isolated mitochondria of atrophied hearts, with glutamate and succinate as substrates: 85 ± 27 vs. 224 ± 32 natoms O·min−1·mg−1with glutamate ( P < 0.01) and 59 ± 18 vs. 154 ± 30 natoms O·min−1·mg−1with succinate ( P < 0.05). Subtractive hybridization indicates major changes in overall gene expression by mechanical unloading and specifically identified downregulation of respiratory chain genes. This observation is functionally relevant and provides a mechanism for the regulation of respiratory capacity in response to chronic mechanical unloading.

Identification of differentially expressed genes in mouse hepatocarcinoma ascites cell line with low potential of lymphogenous metastasis

AIM: To identify genes differentially expressed in mouse hepatocarcinoma ascites cell line with low potential of lymphogenous metastasis.

METHODS: A subtracted cDNA library of mouse hepatocarcinoma cell line with low potential of lympho-genous metastasis Hca-P and its synogenetic cell line Hca-F with high metastatic potential was constructed by suppression subtracted hybridization (SSH) method. The screened clones of the subtracted library were sequenced and GenBank homology search was performed.

RESULTS: Fifteen differentially expressed cDNA fragments of Hca-P were obtained which revealed 8 known genes, 4 expressed sequence tags (ESTs) and 3 cDNAs showed no homology.

CONCLUSION: Tumor metastasis is an incident involving multiple genes. SSH is a useful technique to detect differentially expressed genes and an effective method to clone novel genes.

Identification of a differentially expressed gene PPP1CB between porcine Longissimus dorsi of Meishan and Large WhitexMeishan hybrids

To study the molecular basis of heterosis, suppression subtractive hybridization was used to investigate the differences in gene expression between porcine Longissimus dorsi of F1 hybrids Large WhitexMeishan and their female parents Meishan. From two specific subtractive cDNA libraries, the clones selected by reverse Northern high-density blot screening were chosen to clone full-length cDNA by rapid amplification of cDNA ends. An expression-upregulated gene for Meishan skeletal muscle, designated protein phosphatase 1, catalytic subunit, beta isoform (PPP1CB), was identified. Porcine PPP1CB contains an open reading frame encoding 327 amino acid residues with 13 and 1763 nucleotides in the 5' and 3' untranslated regions, respectively. A DNA fragment of 721 nucleotides was amplified and a mutation that creates/disrupts a restriction site for endonuclease RsaI was found. The derived amino acid sequence of PPP1CB has high homology with the PPP1CB of three species, Mus musculus (99%), human (99%) and mouse (100%). The tissue expression analysis indicated that the swine PPP1CB gene is generally expressed in most tissues. The possible role of PPP1CB and its relation to porcine heterosis are discussed.

Genome-wide analysis of differentially expressed genes from Penicillium chrysogenum grown with a repressing or a non-repressing carbon source

Penicillium chrysogenum is an economically important ascomycete used as industrial producer of penicillin. However, with the exception of penicillin biosynthesis genes, little attention has been paid to the genetics of other aspects of the metabolism of this fungus. In this article we describe the first attempt of systematic analysis of expressed genes in P. chrysogenum, using a suppression subtractive hybridization approach to clone and identify sequences of genes differentially expressed in media with glucose or lactose as carbon source (penicillin-repressing or non-repressing conditions). A total of 167 clones were analysed, 95 from the glucose condition and 72 from the lactose condition. Genes differentially expressed in the glucose condition encode mainly proteins involved in the mitochondrial electron transport chain and primary metabolism. Genes expressed differentially in lactose-containing medium include genes for secondary metabolism (pcbC, isopenicillin N synthase), different hydrolases and a gene encoding a putative hexose transporter or sensor. The results provided information on how the metabolism of this fungus adapts to different carbon sources. The expression patterns of some of the genes support the hypothesis that glucose induces higher rates of respiration in P. chrysogenum while repressing secondary metabolism.

Brain slice invasion model reveals genes differentially regulated in glioma invasion

Invasion of tumor cells into adjacent brain areas is one of the major problems in treatment of glioma patients. To identify genes that might contribute to invasion, fluorescent F98 glioma cells were allowed to invade an organotypic brain slice. Gene expression analysis revealed 5 up-regulated and 14 down-regulated genes in invasive glioma cells as compared to non-invasive glioma cells. Two gene products, ferritin and cyclin B1, were verified in human gliomas by immunohistochemistry. Ferritin exhibited high mRNA levels in migratory F98 cells and also showed higher protein expression in the infiltrating edge of human gliomas. Cyclin B1 with high mRNA expression levels in stationary F98 cells showed marked protein expression in the central portions of gliomas. These findings are compatible with the concept of tumor cells either proliferating or migrating. Our study is the first to apply brain slice cultures for the identification of differentially regulated genes in glioma invasion.

Identification and characterization of genes differentially expressed in the resistance reaction in wheat infected with Tilletia tritici, the common bunt pathogen

The differentially virulent race T1 of common bunt (Tilletia tritici) was used to inoculate the wheat lines Neepawa (compatible) and its sib BW553 (incompatible) that are nearly isogenic for the Bt-10 resistance gene. Inoculated crown tissues were used to construct a suppression subtractive hybridization (SSH) cDNA library. Of the 1920 clones arrayed from the SSH cDNA library, approximately 10 % were differentially regulated. A total of 168 differentially up-regulated and 25 downregulated genes were identified and sequenced; 71 % sequences had significant homology to genes of known function, of which 59 % appeared to have roles in cellular metabolism and development, 24 % in abiotic/biotic stress responses, 3 % involved in transcription and signal transduction responses. Two putative resistance genes and a transcription factor were identified among the upregulated sequences. The expression of several candidate genes including a lipase, two non-specific lipid transfer proteins (ns-LTPs), and several wheat pathogenesis-related (PR)-proteins, was evaluated following 4 to 32 days postinoculation in compatible and incompatible interactions. Results confirmed the higher overall expression of these genes in resistant BW553 compared to susceptible Neepawa, and the differential up-regulation of wheat lipase, chitinase and PR-1 proteins in the expression of the incompatible interaction.

A cDNA macroarray approach to parasite-induced gene expression changes in a songbird host: genetic response of house finches to experimental infection by Mycoplasma gallisepticum

In 1994, the bacterial parasite Mycoplasma gallisepticum expanded its host range and swept through populations of a novel host--eastern US populations of the house finch (Carpodacus mexicanus). This epizootic caused a dramatic decline in finch population numbers, has been shown to have caused strong selection on house finch morphology, and presumably caused evolutionary change at the molecular level as finches evolved enhanced resistance. As a first step toward identifying finch genes that respond to infection by Mycoplasma and which may have experienced natural selection by this parasite, we used suppression subtractive hybridization (SSH) and cDNA macroarray approaches to identify differentially expressed genes regulated by the Mycoplasma parasite. Two subtractive cDNA libraries consisting of 16,512 clones were developed from spleen using an experimentally uninfected bird as the 'tester' and an infected bird as 'driver', and vice versa. Two hundred and twenty cDNA clones corresponding 34 genes with known vertebrate homologues and a large number of novel transcripts were found to be qualitatively up- or down-regulated genes by high-density filter hybridization. These gene expression changes were further confirmed by a high throughout reverse Northern blot approach and in specific cases by targeted Northern analysis. blast searches show that heat shock protein (HSP) 90, MHC II-associated invariant chain (CD74), T-cell immunoglobulin mucin 1 (TIM1), as well as numerous novel expressed genes not found in the databases were up- or down-regulated by the host in response to this parasite. Our results and macroarray resources provide a foundation for molecular co-evolutionary studies of the Mycoplasma parasite and its recently colonized avian host.

Pseudomonas fluorescens and Glomus mosseae trigger DMI3-dependent activation of genes related to a signal transduction pathway in roots of Medicago truncatula

Plant genes induced during early root colonization of Medicago truncatula Gaertn. J5 by a growth-promoting strain of Pseudomonas fluorescens (C7R12) have been identified by suppressive subtractive hybridization. Ten M. truncatula genes, coding proteins associated with a putative signal transduction pathway, showed an early and transient activation during initial interactions between M. truncatula and P. fluorescens, up to 8 d after root inoculation. Gene expression was not significantly enhanced, except for one gene, in P. fluorescens-inoculated roots of a Myc(-)Nod(-) genotype (TRV25) of M. truncatula mutated for the DMI3 (syn. MtSYM13) gene. This gene codes a Ca(2+) and calmodulin-dependent protein kinase, indicating a possible role of calcium in the cellular interactions between M. truncatula and P. fluorescens. When expression of the 10 plant genes was compared in early stages of root colonization by mycorrhizal and rhizobial microsymbionts, Glomus mosseae activated all 10 genes, whereas Sinorhizobium meliloti only activated one and inhibited four others. None of the genes responded to inoculation by either microsymbiont in roots of the TRV25 mutant. The similar response of the M. truncatula genes to P. fluorescens and G. mosseae points to common molecular pathways in the perception of the microbial signals by plant roots.

Be more specific! Laser-assisted microdissection of plant cells

Laser-assisted microdissection (LAM) is a powerful tool for isolating specific tissues, cell types and even organelles from sectioned biological specimen in a manner conducive to the extraction of RNA, DNA or protein. LAM, which is an established technique in many areas of biology, has now been successfully adapted for use with plant tissues. Here, we provide an overview of the processes involved in conducting a successful LAM study in plants and review recent developments that have made this technique even more desirable. We also discuss how the technology might be exploited to answer some pertinent questions in plant biology.

Modified representational difference analysis: isolation of differentially expressed mRNAs from rare cell populations

Representational difference analysis of cDNAs (cDNA-RDA) is a sensitive subtractive hybridization technique capable of isolating rare mRNAs differentially expressed in two cell populations. cDNA-RDA can detect sequences represented at 0.0001% in the starting mRNA. By using reverse transcriptase polymerase chain reaction (PCR), cDNA-RDA also lends itself to studies in which samples are derived from limited numbers of cells. Standard cDNA-RDA protocols depend upon the presence of specific restriction enzyme sites in each cDNA, typically enzymes with four base recognition sequences. These sites are used to reduce the cDNA size range and provide primer sites for subsequent PCR amplification. Consequently, transcripts containing fewer than two of the chosen restriction sites are undetectable by cDNA-RDA. We have developed a restriction enzyme site-independent cDNA-RDA protocol called modified RDA (MRDA). We constructed MRDA test sequences from random hexamer-primed cDNA, thereby increasing the representation of mRNAs which are excluded by cDNA-RDA protocols. MRDA is also more efficient than cDNA-RDA at removing highly expressed housekeeping genes during the subtractive hybridization process, thereby allowing more efficient isolation of preferentially expressed mRNAs. Using MRDA, we isolated cDNAs differentially expressed between limited numbers of human CD4(+) naive and memory T lymphocyte subsets and skin- and gut-homing memory T cell subsets.

Williams-Beuren syndrome critical region-5/non-T-cell activation linker: a novel target gene of AML1/ETO

The chromosomal translocation t(8;21) fuses the AML1 (RUNX1) gene on chromosome 21 and the ETO gene on chromosome 8 in human acute myeloid leukemias (AMLs), resulting in expression of the chimeric transcription factor AML1/ETO. AML1/ETO-mediated dysregulation of target genes critical for hematopoietic differentiation and proliferation is thought to contribute to the leukemic phenotype. Several mechanisms, including recruitment of histone deacetylases (HDACs) to AML1 target genes, may be responsible for altered gene expression. We used an ecdysone-inducible expression system in the human monoblastic U-937 cell line to isolate genes that were differentially expressed upon induction of AML1/ETO expression. By representational difference analysis (cDNA-RDA), we identified 26 genes whose expression levels were significantly modulated following AML1/ETO induction for 48 h. None of these genes has previously been described as a target of AML1, ETO or AML1/ETO. One gene downregulated by AML1/ETO in vitro, Williams Beuren syndrome critical region 5 (WBSCR5), was expressed in primary t(8;21)-negative AML blasts but not in primary t(8;21)-positive AML blasts, strongly implying a role of this gene in the phenotype of t(8;21)-positive AML. Four upregulated and four downregulated genes were further studied with all-trans-retinoic acid (ATRA), an inducer of differentiation of U-937 cells, and Trichostatin A (TSA), an HDAC inhibitor. Three out of eight genes including WBSCR5 were regulated during ATRA-induced monocytic differentiation of U-937 cells, however, none of them antagonistically, upon both ATRA treatment and AML1/ETO induction. AML1/ETO-associated dysregulation of gene expression was not mediated by a TSA-sensitive mechanism. The identified genes provide a useful model to study the mechanism by which the AML1/ETO fusion protein exerts its function in transcriptional dysregulation in AML. The possible role of WBSCR5 in normal and malignant hematopoiesis warrants further study.

Screening differentially expressed genes in mouse hepatocarcinoma ascites cell line with high potential of lymphatic metastasis

AIM: To screen genes differentially expressed in mouse hepatocarcinoma ascites cell line with high potential of lymphatic metastasis.

METHODS: A subtracted cDNA library of mouse hepatocarcinoma cell line with high potential of lymphatic metastatic Hca-F and its synogenetic cell line Hca-P with a low metastatic potential was constructed by suppression subtracted hybridization(SSH) method. The screened clones of the subtracted library were sequenced and GeneBank homology search was performed.

RESULTS: Fourteen differentially expressed cDNA fragments of Hca-F were obtained with two novel genes.

CONCLUSION: SSH is a useful technique to detect differentially expressed genes and an effective method to clone novel genes.

Construction of a hepatic stellate cells subtracted cDNA library of differentially expressed genes in normal mice and mice with Schistosomiasis japonica

To construct a hepatic stellate cells (HSCs) subtracted cDNA library to find differentially expressed genes in normal mice and mice infected with Schistosoma japonicum (S. japonicum). Suppression subtractive hybridization (SSH) was used. The cDNA fragments of normal mouse were compared to those of schistosoma-infected mice to find differentially expressed genes. Then differentially expressed cDNA fragments were directly inserted into T/A cloning vector to set up the subtractive library. Amplification of the library was carried out with transformation of DH5alpha. The amplified library contained more than 400 positive bacterial clone, which were then hybridized with forward and backward subtracted probes for differential screening. One hundred positive bacterial clones were randomly selected for sequencing and BLAST analysis. Finally, virtual Northern Blot confirmed such differential expression. The subtracted cDNA library of differentially expressed genes of HSCs was constructed successfully, the library is efficient and lays foundation for screening and cloning new and specific genes of schistosomiasis.

Genes upregulated in a metastasizing human colon carcinoma cell line

Differential gene expression between the metastatic human colon cancer cell line HT29p and its nonmetastatic counterpart HT29-MTX was revealed by suppression subtractive hybridization. Fifty-eight individual genes showed increased mRNA levels in HT29p cells. Only 15 of these genes had been related to transformation in previous studies; the majority of genes are new candidates encoding proteins relevant for the metastatic process. Cancer profiling arrays as well as in situ hybridization study revealed that at least some of the genes obtained in the SSH screen are also differentially expressed in human tumors.

Identification of transcripts specific for physiological gene activation by platelet-derived growth factor (PDGF)-B in intact brain tissue

Platelet-derived growth factor-B (PDGF-B) and its receptors play essential roles in the complex process of blood vessel maturation and they therefore constitute promising targets for therapeutic strategies against blood vessel-related diseases. Additionally, they are involved in the autocrine stimulation of tumor cells and have been suggested to regulate tumor stroma fibroblasts. Our study aimed to identify genes that are regulated directly by PDGF-B, or indirectly via the recruitment of perivascular cells, in the context of an intact tissue. We used a subtractive cloning technique to compare gene transcription in the brains of wild-type (WT) mice and syngenic mice deficient of PDGF-B leading to a defect in the recruitment of perivascular cells. The resulting 147 differentially expressed sequences contained early and late PDGF-B target genes, and genes implicated in blood vessel maturation-related pathways. Additionally, gene clusters for specific biological processes such as cell migration and intracellular transport were identified. Of eight randomly selected sequences, six were found expressed in cultured cells of mesenchymal origin, two of them inducible by exogenous PDGF-BB. The collection of cDNA presented here provides insights into the changes provoked by the removal of one growth factor of a complete tissue and might be the basis for the identification of novel players in the complex process of blood vessel maturation.

Protein and mRNA characterization in high and low metastasis adenoid cystic carcinoma cell lines

Metastasis and invasion, the important characteristics of malignant tumors, are closely associated with a series of changes in the expression of genes and proteins. In this study, we compare mRNA and protein expression in high and low metastasis adenoid cystic carcinoma cell lines by mRNA suppression subtractive hybridization and two-dimensional electrophoresis combined with peptide mass fingerprint analysis. 34 differentially expressed genes were obtained using suppression subtractive hybridization experiments including 6 highly expressed gene sequences in the high metastasis cell line, and 28 in the low metastasis cell line. RNA dot blot hybridization further confirmed the results after excluding false positives. For protein analysis, ten significantly different protein spots were detected using two-dimensional gel electrophoresis technique combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometer (MALDI- TOF-MS). The results then compare with the SWISS PROT database. These results suggest that high tumor metastasis of adenoid cystic carcinoma is associated with multiple genes whose function include angiogenesis, protein synthesis, signal transduction, modulation of cell cycle, molecular chaperones, and immune co-stimulating molecule. Moreover, the results of the phenotypic function-related expression mapping analysis at the mRNA and protein level revealed obvious complementarities, providing important clues for further study of the molecular mechanism of metastasis, metastasis control and possible targets for cancer gene therapy.

Identification and characterization of a novel gene EOLA1 stimulating ECV304 cell proliferation

To study the changes in gene expression in endothelial cells stimulated by lipopolysaccharide (LPS) we performed subtraction hybridization on control human umbilical vein endothelial cells (HUVEC) versus HUVEC stimulated by LPS. A novel cDNA, named endothelial-overexpressed lipopolysaccharide-associated factor 1 (EOLA1), was cloned from our differentially expressed EST database of HUVEC cDNA library (GenBank Accession No. ). Computational analysis showed that EOLA1 is 1404bp long, encoding a 158aa, 17.8kDa protein, mapped to chromosome Xq27.4 with 5 exons, expressed in different human normal tissues and cancer cell lines. Using the EOLA1 cDNA as bait, we performed a yeast two-hybrid screening of a human liver cDNA library and identified metallothionein 2A (MT2A) as associated protein. Stable transfection of EOLA1 stimulates ECV304 cell proliferation. Our data suggest that the physical interaction of EOLA1 and MT2A may have an important role of cell protection in inflammation reaction.

Identification of genes regulating sensory neuron genesis and differentiation in the avian dorsal root ganglia

The dorsal root ganglia (DRG) derive from a population of migrating neural crest cells that coalesce laterally to the neural tube. As the DRG matures, discrete cell types emerge from a pool of differentiating progenitor cells. To identify genes that regulate sensory genesis and differentiation, we have designed screens to identify members from families of known regulatory molecules such as receptor tyrosine kinases, and generated full-length and subtractive cDNA libraries between immature and mature DRG for identifying novel genes not previously implicated in DRG development. Several genes were identified in these analyses that belong to important regulatory gene families. Quantitative PCR confirmed differential expression of candidate cDNAs identified from the subtraction/differential screening. In situ hybridization further validated dynamic expression of several cDNAs identified in our screens. Our results demonstrate the utility of combining specific and general screening approaches for isolating key regulatory genes involved in the genesis and differentiation of discrete cell types and tissues within the classic embryonic chick model system.

Identification of genes associated with morphology in Aspergillus niger by using suppression subtractive hybridization

The morphology of citric acid production strains of Aspergillus niger is sensitive to a variety of factors, including the concentration of manganese (Mn(2+)). Upon increasing the Mn(2+) concentration in A. niger (ATCC 11414) cultures to 14 ppb or higher, the morphology switches from pelleted to filamentous, accompanied by a rapid decline in citric acid production. The molecular mechanisms through which Mn(2+) exerts effects on morphology and citric acid production in A. niger cultures have not been well defined, but our use of suppression subtractive hybridization has identified 22 genes responsive to Mn(2+). Fifteen genes were differentially expressed when A. niger was grown in media containing 1,000 ppb of Mn(2+) (filamentous form), and seven genes were expressed in 10 ppb of Mn(2+) (pelleted form). Of the 15 filament-associated genes, seven are novel and eight share 47 to 100% identity with genes from other organisms. Five of the pellet-associated genes are novel, and the other two genes encode a pepsin-type protease and polyubiquitin. All 10 genes with deduced functions are either involved in amino acid metabolism-protein catabolism or cell regulatory processes. Northern blot analysis showed that the transcripts of all 22 genes were rapidly enhanced or suppressed by Mn(2+). Steady-state mRNA levels of six selected filament-associated genes remained high during 5 days of culture in a filamentous state and remained low under pelleted growth conditions. The opposite behavior was observed for four selected pellet-associated genes. The full-length cDNA of the filament-associated clone, Brsa-25, was isolated. Antisense expression of Brsa-25 permitted pelleted growth and increased citrate production at concentrations of Mn(2+) that were higher than the parent strain could tolerate. These results suggest the involvement of the newly isolated genes in the regulation of A. niger morphology.

Construction and selection of subtracted cDNA library of mouse hepatocarcinoma cell lines with different lymphatic metastasis potential

AIM: In order to elucidate the molecular mechanism of lymphatic metastasis of hepatocarcinoma, we detected the difference of gene expression between mouse hepatocarcinoma cell lines Hca-F and Hca-P with different lymphatic metastasis potential.

METHODS: cDNA of Hca-F cells was used as a tester and cDNA of Hca-P cells was used as a driver. cDNAs highly expressed in Hca-F cells were isolated by the suppression subtractive hybridization (SSH) method. The isolated cDNA was cloned into T/A cloning vector. The ligation products were transformed into DH5 α competent cells. Individual clones were randomly selected and used for PCR amplification. Vector DNA from positive clones was isolated for sequencing.

RESULTS: There were 800 positive clones in amplified subtracted cDNA library. Random analysis of 160 clones with PCR showed that 95% of the clones contained 100-700 bp inserts. Analysis of 20 sequenced cDNA clones randomly picked from the SSH library revealed 4 known genes (mouse heat shock protein 84 ku, DNA helicase, ribosomal protein S13 ,ethanol induced 6 gene) and 3 expressed sequence tags (ESTs). Four cDNAs showed no homology and presumably represent novel genes.

CONCLUSION: A subtracted cDNA library of differentially expressed genes in mouse heptocarcinoma cell lines with different lymphatic metastasis potential was successfully constructed with SSH and T/A cloning techniques. The library is efficient and lays a solid foundation for searching new lymphatic metastasis related genes. The expression of mouse heat shock protein gene, DNA helicase and other 4 novel gene may be different between mouse heptocarcinoma cell lines with different lymphatic metastasis potential.

CD44 variant isoforms associate with tetraspanins and EpCAM

The metastasizing subline of the rat pancreatic adenocarcinoma BSp73 expresses a set of membrane molecules, the combination of which has not been detected on non-metastasizing tumor lines. Hence, it became of interest whether these molecules function independently or may associate and exert specialized functions as membrane complexes. Separation of CD44v4-v7 containing membrane complexes in mild detergent revealed an association with the alpha3 integrin, annexin I, EpCAM, and the tetraspanins D6.1A and CD9. EpCAM and the tetraspanins associate selectively with CD44 variant (CD44v), but not with the CD44 standard (CD44s) isoform. The complexes are found in glycolipid-enriched membrane (GEM) microdomains, which are dissolved by stringent detergents, but the complexes are not destroyed by methyl-beta-cyclodextrin (MbetaCD) treatment, which implies that complex formation does not depend on a lipid-rich microenvironment. However, a complex-associated impact on cell-matrix and cell-cell adhesion as well as on resistance towards apoptosis essentially depended on the location in GEMs. Thus, CD44v-specific functions may well be brought about by complex formation of CD44v with EpCAM, the tetraspanins, and the alpha3 integrin. Because CD44v4-v7-EpCAM complex-specific functions strictly depended on the GEM localization, linker or signal-transducing molecules associating with the complex are likely located in GEMs.

Two genes encoding Arabidopsis halleri MTP1 metal transport proteins co-segregate with zinc tolerance and account for high MTP1 transcript levels

The zinc hyperaccumulator plant Arabidopsis halleri is able to naturally accumulate 100-fold higher leaf zinc concentrations when compared with non-accumulator species such as the closely related A. lyrata and A. thaliana, without showing toxicity symptoms. A novel member of the cation diffusion facilitator (CDF) protein family, an A. halleri metal tolerance protein 1 (MTP1), and the homologous A. thaliana Zn transporter (ZAT)/AtMTP1 metal-specifically complement the zinc hypersensitivity of a Saccharomyces cerevisiae zrc1 cot1 mutant strain. A fusion of the AhMTP1 protein to green fluorescent protein (GFP) localizes to the vacuolar membrane of A. thaliana protoplasts. When compared with A. lyrata and A. thaliana, the total MTP1 transcript levels are substantially higher in the leaves and upregulated upon exposure to high zinc concentrations in the roots of A. halleri. The high MTP1 transcript levels in A. halleri can be primarily attributed to two genetically unlinked genomic AhMTP1 gene copies. The two corresponding loci co-segregate with zinc tolerance in the back-cross 1 generation of a cross between the zinc-tolerant species A. halleri and the zinc-sensitive species A. lyrata. In contrast, a third MTP1 gene in the genome of A. halleri generates only minor amounts of MTP1 transcripts and does not co-segregate with zinc tolerance. Our data suggests that zinc tolerance in A. halleri involves an expanded copy number of an ancestral MTP1 gene, encoding functional proteins that mediate the detoxification of zinc in the cell vacuole. At the transcript level, MTP1 gene copies of A. halleri are regulated differentially and in response to changes in zinc supply.

Overexpression of genes in the CA1 hippocampus region of adult rat following episodes of global ischemia

Ischemic stress is associated with marked changes in gene expression in the hippocampus--albeit little information exists on the activation of nonabundant genes. We have examined the expression of several known genes and identified novel ones in the adult rat hippocampus after a mild, transient, hypovolemic and hypotensive, global ischemic stress. An initial differential screening using a prototype array to assess gene expression after stress followed by a suppression subtractive hybridization protocol and cDNA microarray revealed 124 nonoverlapped transcripts predominantly expressed in the CA1 rat hippocampus region in response to ischemic stress. About 78% of these genes were not detected with nonsubtracted probes. Reverse transcription polymerase chain reaction (RT-PCR) and in situ hybridization on these 124 transcripts confirmed the differential expression of at least 83. Most robustly expressed were gene sequences NFI-B, ATP1B1, RHOGAP, PLA2G4A, BAX, CASP3, P53, MAO-A, FRA1, HSP70.2, and NR4A1 (NUR77), as well as sequence tags of unknown function. New stress-related genes of similar functional motifs were identified, reemphasizing the importance of functional grouping in the analysis of multiple gene expression profiles. These data indicate that ischemia elicits expression of an array of functional gene clusters that may be used as an index for stress severity and a template for target therapy design.