Fluorescent differential display: arbitrarily primed RT-PCR fingerprinting on an automated DNA sequencer

Primary and Secondary Abscission in Pisum sativum and Euphorbia pulcherrima-How Do They Compare and How Do They Differ?

Abscission is a highly regulated and coordinated developmental process in plants. It is important to understand the processes leading up to the event, in order to better control abscission in crop plants. This has the potential to reduce yield losses in the field and increase the ornamental value of flowers and potted plants. A reliable method of abscission induction in poinsettia (Euphorbia pulcherrima) flowers has been established to study the process in a comprehensive manner. By correctly decapitating buds of the third order, abscission can be induced in 1 week. AFLP differential display (DD) was used to search for genes regulating abscission. Through validation using qRT-PCR, more information of the genes involved during induced secondary abscission have been obtained. A study using two pea (Pisum sativum) mutants in the def (Developmental funiculus) gene, which was compared with wild type peas (tall and dwarf in both cases) was performed. The def mutant results in a deformed, abscission-less zone instead of normal primary abscission at the funiculus. RNA in situ hybridization studies using gene sequences from the poinsettia differential display, resulted in six genes differentially expressed for abscission specific genes in both poinsettia and pea. Two of these genes are associated with gene up- or down-regulation during the first 2 days after decapitation in poinsettia. Present and previous results in poinsettia (biochemically and gene expressions), enables a more detailed division of the secondary abscission phases in poinsettia than what has previously been described from primary abscission in Arabidopsis. This study compares the inducible secondary abscission in poinsettia and the non-abscising mutants/wild types in pea demonstrating primary abscission zones. The results may have wide implications on the understanding of abscission, since pea and poinsettia have been separated for 94-98 million years in evolution, hence any genes or processes in common are bound to be widespread in the plant kingdom.

Screening of upregulated genes induced by high density in the vetch aphid Megoura crassicauda

Aphids exhibit several polyphenisms in which discontinuous, alternative phenotypes are produced depending on environmental conditions. One representative example is the wing polyphenism, where winged and wingless females are produced through parthenogenesis. Previous work has shown that, in some aphid species, the density condition sensed by the mother aphid determines the developmental fate of embryos in her ovary, with high densities leading to winged progeny and low densities to wingless progeny. However, little is known about the molecular and physiological mechanisms underlying the wing polyphenism. To identify genes involved in the wing-morph determination in the vetch aphid, Megoura crassicauda, we compared maternal and embryonic transcripts between high- and low-density conditions using differential display, followed by quantitative real-time PCR (qRT-PCR). Under the high-density condition, two genes (Uba1 and Naca) were found to be upregulated in maternal tissues without ovaries, while one gene (ClpP) was upregulated in ovaries containing embryos. Uba1 and Naca encode factors that function in protein modification or transcriptional/translational regulation, respectively. In addition to differential display, candidate gene approaches focusing on morphogenetic and endocrine genes, i.e., wg, dpp, ap, hh, InR, IRS, Foxo, EcR, and USP, were also carried out. We found that wg was upregulated in maternal tissues under the high-density condition. The identified genes from both approaches are candidates for further study of their involvement in the transduction of density signals in mother aphids and/or the initial process of wing differentiation in embryos.

Receptor activator of NF-κB ligand-dependent expression of caveolin-1 in osteoclast precursors, and high dependency of osteoclastogenesis on exogenous lipoprotein

Although extensive studies have done much to clarify the molecular mechanisms of osteoclastogenesis during the last ten years, there may still be unknown molecules associated with osteoclast differentiation. Thus, we used fluorescent differential display to screen for genes whose expression is induced by receptor activator of NF-κB ligand (RANKL), a crucial molecule for osteoclast formation. We identified caveolin-1 (Cav-1) as a RANKL-induced gene. Cav-1 is a major structural protein of caveolae and lipid rafts, cholesterol-enriched microdomains in the plasma membrane (PM). The RANKL-induced Cav-1 was immediately conveyed to lipid rafts. Conversely, expression of flotillin-1 (Flot-1), another scaffolding protein of lipid rafts, was reduced during osteoclastogenesis, indicating conversion of Flot-1-predominant rafts into Cav-1-enriched rafts. However, in vitro osteoclastogenesis of precursor cells from Cav-1-null mice was comparable to that of wild-type mice, while Cav-2 expression in the knockout osteoclasts was maintained. Conversely, Cav-2 gene silencing in Cav-1-null osteoclast precursors using siRNA for Cav-2 increased osteoclast formation, suggesting that the Cav-1/Cav-2 complex may act as a negative regulator for osteoclastogenesis. On the other hand, destruction of lipid rafts by removal of cholesterol from the PM by methyl-ß-cyclodextrin (MCD) treatment caused disordered signal transductions for osteoclastogenesis, such as hyperactivation of Erk1/2 and insensitivity of Akt to RANKL stimulus. The abnormal signaling was reproduced by deleting exogenous lipoproteins from the culture medium, which also resulted in reduced osteoclast formation. In addition, the deletion caused delayed expression of nuclear factor of activated T cells c1 (NFATc1), and depressed its activation in the cytosol and inhibited its translocation into nuclei. Simultaneously, the deletion reduced the level of FcRγ, a trigger protein for initiating the calcium signaling needed to activate NFATc1, and decreased Cav-1 in lipid rafts. These findings indicate that the molecular mechanisms of osteoclastogenesis are highly dependent on extracellular lipoprotein and the integrity of lipid rafts, and suggest possible involvement of cholesterol.

Identification of a reproductive-specific, putative lipid transport protein gene in a queenless ponerine ant Diacamma sp

Of the various characteristics of social insects, communication for reproductive differentiation is one of the most important and basic social interactions among colony members. To elucidate the molecular basis underlying this process, genes responsible for reproductive differentiation in Diacamma were screened using fluorescent differential display. Differential display, together with real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR), revealed that a gene belonging to the family of cellular retinaldehyde-binding proteins was specifically expressed in the epidermis of the head, legs, and thorax in reproductives. The deduced protein sequence in the coding region, obtained by rapid amplification of cDNA ends (RACE)-PCR, was found to include cellular retinaldehyde-binding domain (CRAL-TRIO domain), suggesting that DiaCRALDCP functions in transportation of lipids, such as cuticular hydrocarbons. DiaCRALDCP transcript levels immediately decreased 1 day after the gemma mutilation, suggesting that DiaCRALDCP is involved in the physiological changes provoked by the behavioral regulation. Considering these results, the social functions of DiaCRALDCP in Diacamma are discussed.

Gene expression changes during caste-specific neuronal development in the damp-wood termite Hodotermopsis sjostedti

BACKGROUND

One of the key characters of social insects is the division of labor, in which different tasks are allocated to various castes. In termites, one of the representative groups of social insects, morphological differences as well as behavioral differences can be recognized among castes. However, very little is known about the neuronal and molecular bases of caste differentiation and caste-specific behavior. In almost all termite species, soldiers play defensive roles in their colonies, and their morphology and behavior are largely different from workers (or pseudergates). Therefore, we predicted that some genes linked to defensive behavior and/or those required for neuronal changes are differentially expressed between workers and soldiers, or during the soldier differentiation, respectively.

RESULTS

Using the brain and suboesophageal ganglion (SOG) of the damp-wood termite Hodotermopsis sjostedti, we first screened genes specifically expressed in soldiers or during soldier differentiation by the differential display method, followed by quantitative real-time polymerase chain reaction. No distinctive differences in expression patterns were detected between pseudergates and soldiers. In the course of soldier differentiation, however, five genes were found to be up-regulated in brain and/or SOG: 14-3-3 epsilon, fibrillin2, beta-tubulin, ciboulot, and a hypothetical protein containing a SAP motif. Some of these genes are thought to be associated with cytoskeletal structure or motor-associated proteins in neuronal tissues.

CONCLUSION

The identified five genes could be involved in soldier-specific neuronal modifications, resulting in defensive behaviors in termite soldiers. The temporal expression patterns of these genes were consistent with the neuronal changes during soldier differentiation, suggesting that molecular machineries, in which the identified factors would participate, play important roles in behavioral differentiation of termite soldiers.

Identification of differentially expressed genes in mandibular condylar and tibial growth cartilages using laser microdissection and fluorescent differential display: chondromodulin-I (ChM-1) and tenomodulin (TeM) are differentially expressed in mandibular condylar and other growth cartilages

Mandibular condylar cartilage can be distinguished from articular and growth cartilages of long bones based on several differences in morphology, physiology, and function between these structures. However, there is almost no information available on the types of genes that contribute to these differences. In this study, genes that were differentially expressed in mandibular condylar and growth cartilages in 1-week-old rats were investigated using fluorescent differential display (FDD) and laser microdissection (LMD). A number of genes were identified by FDD including chondromodulin-1 (ChM-1), which is known to be an angiogenesis inhibitor of endochondral ossification. ChM-1 expression was then compared with that of tenomodulin (TeM) in mandibular condylar and tibial cartilages of 1- and 5-week-old rats using real time PCR (RT-PCR), immunohistochemistry, and in situ hybridization. There was negligible detection of ChM-1 mRNA and protein in mandibular condylar cartilages compared to tibial cartilages of 1- and 5-week-old rats. On the other hand, TeM mRNA was more abundant in mandibular condylar cartilage than in tibial. These observations demonstrated that gene expression in mandibular condylar cartilage differed from other types of cartilage such as articular and growth ones.

Large-scale differential display analysis of T helper cell differentiation

We have developed a novel large-scale multicapillary fluorescent differential display (FDD) platform amenable to further automation. The power of the method is demonstrated by the analysis of T helper cell differentiation. Eight RNA samples from wild type, Stat4 knockout and Stat6 knockout mice were analyzed with 16 anchoring primers and 24 arbitrary primers, resulting in 285 294 sample peaks. Visually selected patterns of differential expression suggest two major regulatory mechanisms: activation and Stat4 genotype. A subset of the findings is reproduced in the confirmatory differential display (DD) that included technical and biological replicates. In a small fragment identification pilot study, we identify Ifi27 and Cct8 to be up-regulated by T cell activation. We present a method for the analysis of electropherogram similarity across large datasets, based on correlation of low-resolution representations of electrophoretic data. We show how it can be applied to analyze experimental and technical variables. Using this method, we demonstrate the effect of activation and genotype. In addition, agreement of our real experimental data to the theoretical basis of DD, as well as issues in anchoring primer selectivity, are studied.

Electroacupuncture suppresses myostatin gene expression: cell proliferative reaction in mouse skeletal muscle

Complementary and alternative medicine (CAM) may provide patients with an alternative to traditional medicine, but an assessment of its efficacy is required. One CAM method, electroacupuncture (EA) treatment, is a maneuver that utilizes stimulation of acupuncture needles with a low-frequency microcurrent. To study the effect of short-term EA, we evaluated the differential expression of genes induced by EA in mouse skeletal muscle for up to 24 h. We then used RT-PCR to confirm the expression patterns of six differentially expressed genes. Bioinformatics analysis of their transcription control regions showed that EA-inducible genes have numerous common binding motifs that are related to cell differentiation, cell proliferation, muscle repair, and hyperplasia. These results suggested that EA treatment may induce cell proliferation in skeletal muscle. To verify this possibility, we used EA to stimulate mouse skeletal muscle daily for up to 1 mo and examined the long-term effects. Immunohistochemical analysis showed that nuclei of muscle cells treated with EA for 1 mo, especially nuclei of satellite cells, reacted with anti-human PCNA. Also, expression of the gene encoding myostatin, which is a growth repressor in muscle satellite cells, was suppressed by daily EA treatment for 1 wk; EA treatment for 1 mo resulted in more marked suppression of the gene. These molecular findings constitute strong evidence that EA treatment suppresses myostatin expression, which leads to a satellite cell-related proliferative reaction and repair in skeletal muscle.

SAP discovery: the sword edges--beneficial and harmful

We cloned the SLAM associated protein (SAP) gene in 1995. In 1998, it was discovered that the SAP gene was defective in patients with X-linked lymphoproliferative disease. Subsequently, details on the key role of life-long immune memory (vaccination) and of life-long autoantibody production in patients suffering from autoimmune disease have been revealed. In this paper, we discuss the dual nature of SAP in humans: its beneficial effect on life-long immune memory (vaccination) and its harmful effect on life-long autoantibody production.

From differential display to DNA microarrays--a personal account

This article is a tribute to Dr. Arthur Pardee, one of the most innovative and brilliant scientists of our time, on the occasion of his 85th birthday. In this partially perspective and partially review piece, I look back how fate, by twist and turn, has led me eventually to his lab at Harvard where we worked out the Differential Display technology from scratch, how the method has revolutionized the field of gene expression analysis and where DD is taking us in the "era" of DNA microarrays.

Simple screening method for differentially methylated regions of the genome using a small number of cells

Genomic DNA methylation is a major epigenetic mechanism controlling the expression of genetic information. Therefore, identifying regions of the genome that are differentially methylated in different cells is a useful strategy for the study of biological phenomena. To date, several useful screening methods have been established for identifying differentially methylated genomic regions. However, it is impossible to use these methods in fields of study in which it is difficult to obtain a large number of uniform cells, because considerable amounts of genomic DNA are required. Given this situation, we developed a method for preparing large genomic DNA from a small number of cells, and a simple and highly sensitive method for screening for differentially methylated sites. Combined, these two methods comprise a simple screening method, which we named "Differential Methylation Site Scanning" (DMSS), for identifying differentially methylated regions of the genome from a small number of cells. Just 10 cells are sufficient for the method described here.

Differential-display analysis of gene expression in livers from normal and partially hepatectomized mice

Partial hepatectomy, resulting in the removal of approximately 70% of the liver, is widely utilized for studies of liver growth in experimental animals. The regenerative response is proportional to the amount of liver removed. Knowing when and where genes are expressed provides a strong clue as to its biological role. The RNA differential-display (DD) technique facilitates monitoring the differential expression of a large number of activated or suppressed genes under various biological conditions. To reveal mechanisms of liver regeneration, we performed a comparative analysis of gene expression during liver regeneration using DD. We sacrificed male Balb/c mice, aged 10 to 12 weeks, at 0, 24, 48, and 72 hours, and 1 and 2 weeks after PHx. The livers were weighed, and the amount of glutamic-oxaloacetate transaminase in serum measured. We extracted the total RNA from frozen liver tissue and confirmed the RNA quality using a lab-chip system. DD analysis was performed essentially as described by Liang and Pardee. Semiquantitative reverse-transcription polymerase chain reaction was performed to confirm the results of DD analysis. Of the 56 fragments that exhibited changed expression levels during PHx, 39 were cloned and sequenced. There were 31 known genes, 13 unknown genes, and 9 expressed-sequence tags. These results indicated that DD is a powerful approach for monitoring molecular events in the regenerating liver.

The application of differential display as a gene profiling tool

Differential display is an effective expression profiling tool which was first introduced in 1992. The original technique is discussed along with modifications that have been described over the last several years. A highly reproducible, semihigh-throughput differential display protocol used in our laboratories is described along with an example of its successful application using pancreatic cancer cells. In addition to the work performed in our laboratories, several examples of successful applications of differential display under a number of scenarios are reviewed. Differential display is one of several expression profiling technologies available and is compared with some of them. The future of differential display remains bright and is as applicable today as it was in 1992.

The NR4A nuclear receptor family in eosinophils

It is well-known that many members of the family of nuclear receptors have been implicated in human diseases, and metabolic disorders in particular. The NR4A nuclear receptor family consists of three members, Nur77, Nurr1, and NOR1. All of these are orphan receptors, and Nur77 and NOR1 exert possible pathological roles in immune diseases through the modulation of leukocyte functions. CD30 stimulation, which induces eosinophil-specific apoptosis, markedly enhances expression of Nur77 and NOR1 in eosinophils. This suggests the possibility of pharmacological modulation of Nur77- or NOR1-specific apoptotic pathways via receptor-dependent transactivation. In this review, we discuss treatment of allergic diseases by low molecular weight compounds acting through the NR4A receptor family to cause eosinophil apoptosis. NR4A nuclear receptor genes were selected following comprehensive analysis of differentially expressed genes in eosinophils of atopic dermatitis patients compared with healthy volunteers.

Antioxidant and Antibacterial Genes Are Upregulated in Early Involution of the Mouse Mammary Gland: Sharp Increase of Ceruloplasmin and Lactoferrin in Accumulating Breast Milk

The mammary gland develops mainly after birth, and shows a repeated cycle of pregnancy-triggered proliferation, differentiation for lactation, and a regressive phase after weaning known as involution. Compared to the proliferation and differentiation phases, the molecular mechanisms of involution are largely unknown. In the present study we screened genes that could play a potential role in early involution of the mouse mammary gland using fluorescent differential display followed by gene-specific reverse transcription-polymerase chain reaction. We found that five genes were upregulated more than twofold 48 h after weaning: ceruloplasmin, chemokine (CXC motif) ligand 4, epoxide hydrolase 1, lactoferrin, and properdin P factor. The products of these genes can be linked to defense against oxidative stress and/or infectious bacteria. Electrophoretic analysis and mass spectrometry of milk proteins showed that the concentrations of ceruloplasmin and lactoferrin in milk were increased fivefold and more than 38-fold, respectively, within 48 h after weaning. These increases were in contrast to the constant presence of other major proteins including albumin, caseins, transferrin, and whey acidic protein. Ceruloplasmin and lactoferrin may cooperate in the defense of the mammary gland in the postlactation period.

Altered gene expression in Opisthorchis viverrini-associated cholangiocarcinoma in hamster model

Cholangiocarcinoma (CCA) induced by liver fluke (Opisthorchis viverrini, Ov) infection is one of the most common and serious disease in northeast Thailand. To elucidate the molecular mechanism of cholangiocarcinogenesis induced by Ov infection, we employed a hamster model of CCA induced by Ov and N-nitrosodimethylamine and analyzed candidate genes involved in CCA using fluorescence differential display-PCR. Of 149 differentially amplified bands we identified, the upregulation of 23 transcripts and downregulation of 1 transcript related to CCA hamsters were confirmed by a reverse northern macroarray blot. The upregulated genes include signal transduction protein kinase A regulatory subunit Ialpha (Prkar1a), myristoylated alanine-rich protein kinase C substrate, transcriptional factor LIM-4-only domain, oxysterol-binding protein involved in lipid metabolism, splicing regulatory protein 9, ubiquitin conjugating enzyme involved in protein degradation, beta tubulin, beta actin, and collagen type VI. Quantitative real-time PCR confirmed that the expression of Prkar1a was significantly higher in CCA and its precursor lesion when compared with normal liver and normal gall bladder epithelia (P<0.05). Prkar1a expression tended to increase along with the progression of biliary transformation from hyperplasia and precancerous lesions to carcinoma. These findings contribute to our understanding of the processes involved in the molecular carcinogenesis of CCA in order to provide a unique perspective on the development of new chemotherapeutics in future.

Noise yields order--auxin, actin, and polar patterning

Plant patterns have to integrate environmental cues and to cope with a high level of noise in the sensory outputs of individual cells. In the first part of this review, we demonstrate that local self-amplification linked to lateral inhibition can meet this requirement. In the second part, we describe the search for candidates for such self-amplification loops in the context of auxin-dependent cell growth using Graminean coleoptiles as a model. Auxin-dependent reorganization of actin microfilaments interfered with the auxin sensitivity of growth. Auxin might control the intracellular transport of factors important for auxin sensing via the actomyosin system. By means of a rice mutant with elevated auxin responsiveness, we identified an auxin response factor (OSARF1), whose expression is upregulated by auxin as a second candidate for a self-amplification loop. We studied the cross-talk between auxin signalling and environmental cues in the rice mutant hebiba, where the photoinhibition of growth is impaired. We found that jasmonate plays a central role in this cross-talk correlated to a downregulation of auxin responsiveness. To obtain an insight into auxin-dependent coordination, we analyzed a tobacco cell line with axial cell divisions. By a combination of modelling and physiological manipulation, we could demonstrate that auxin synchronizes the divisions of adjacent cells on the background of strong heterogeneity of individual cells. We conclude that self-amplification of auxin signalling coupled to mutual competition for available auxin provides a versatile tool to fulfill the special requirements posed by patterning in plants.

MN-cadherin and its novel variant are transiently expressed in chick embryo spinal cord

To isolate cDNAs that are involved in limb-motoneuron development, we compared mRNAs of lumbar and thoracic motoneurons purified from spinal cord of E4 chick embryo by differential display. In situ hybridization demonstrated that one of cDNAs is expressed exclusively in lateral motor column in spinal cord from E4 to E10. We identified two mRNA variants for the cDNA by library screening. The long form (788 amino acids) was identical to chick MN-cadherin. The short variant (543 amino acids) lacks the first two of five extracellular domains of MN-cadherin, which commonly exist in classical cadherins. The amino acid sequence of the short form is identical to that of the carboxyl terminal MN-cadherin, except for the distinct signal sequence. The ratio of mRNA of short form to long form was 1-20. cDNA transfection study revealed that the long form but not the short form MN-cadherin had cell adhesion activity.

Differential display analysis reveals the expression of glutathione S-transferase ω and novel genes through an ITAM-containing receptor in ascidian immunocytes

The immunoreceptor tyrosine-based activation motif (ITAM) plays an important role in signal transduction through antigen receptors in mammalian lymphocytes. We previously reported that an ITAM-containing receptor, ascidian hemocyte ITAM-containing receptor 1 (AhITAMR1), exists on the hemocyte surfaces of the ascidian Halocynthia roretzi, and is involved in both phagocytosis and hemocyte aggregation. In this study, we carried out differential display screening of upregulated genes during H. roretzi hemocyte aggregation and found that at least three genes are upregulated. One encodes glutathione S-transferase omega (GSTomega), while the other two encode novel proteins. The expression of all three genes was induced by treatment with a specific monoclonal antibody against AhITAMR1, while their expression was inhibited by wortmannin, BAPTA-AM, and cyclosporin A. We also found that the expression of GSTomega was induced by treatment with anti-T cell receptor antibody in mouse peripheral T cells. We propose that signal transduction pathways mediated by ITAM-containing receptors are conserved from ascidian hemocytes to mammalian T cells.

An ascidian homologue of the gonadotropin-releasing hormone receptor is a retinoic acid target gene

Transdifferentiation of the multipotent atrial epithelium is a key event during budding of the ascidian Polyandrocarpa misakiensis. The transdifferentiation is induced by mesenchyme cells that were stimulated by retinoic acid. The fluorescent differential display identified a few cDNA fragments for retinoic acid-inducible genes. One of the cDNA clones, named Pm-GnRHR, encoded a seven-pass transmembrane receptor similar to gonadotropin-releasing hormone receptors. Putative amino acid sequence showed high similarity to Ciona intestinalis GnRHRs and formed a cluster with other GnRHR proteins in a phylogenetic tree. The level of expression of the Pm-GnRHR mRNA increased during the early stage of bud development, suggesting that the Pm-GnRHR function is involved in some aspects of bud development.

NR4A orphan nuclear receptor family in peripheral blood eosinophils from patients with atopic dermatitis and apoptotic eosinophils in vitro

To identify novel genes related to the clinical signs of atopic dermatitis (AD), differentially expressed genes were sought in peripheral blood eosinophils from both AD patients and healthy volunteers. RNA was prepared from eosinophils, expression of various genes was monitored using the Affymetrix GeneChip, and expression was quantified by real-time RT-PCR. Two genes, Nur77 and NOR1, members of NR4A orphan nuclear receptor family, were expressed at a significantly higher level in AD patients than in healthy volunteers. Expression of another gene in the NR4A receptor family, Nurr1, was also higher in AD patients than in healthy volunteers. When peripheral blood leukocytes from healthy volunteers were fractionated, NOR1 expression was highest in eosinophils, but expression of Nur77 and Nurr1 genes was not eosinophil-specific. Extremely intense apoptosis was induced in both eosinophils and an eosinophil cell line, AML14.3D10, by treatment with antibody (Ab) to both CD30 and Fas. Rapid expression of the genes for the NR4A receptor family was observed with anti-CD30 Ab treatment but not with anti-Fas Ab. The NR4A orphan nuclear receptor family gene expression and the subsequent eosinophil apoptosis were downregulated by the MAPK inhibitor, U0126. These results suggest that the expression of the NR4A receptor family genes through CD30 signaling may regulate eosinophil apoptosis in allergic conditions such as AD.

Conversion of cDNA differential display results (DDRT-PCR) into quantitative transcription profiles

BACKGROUND

Gene expression studies on non-model organisms require open-end strategies for transcription profiling. Gel-based analysis of cDNA fragments allows to detect alterations in gene expression for genes which have neither been sequenced yet nor are available in cDNA libraries. Commonly used protocols for gel-based transcript profiling are cDNA differential display (DDRT-PCR) and cDNA-AFLP. Both methods have been used merely as qualitative gene discovery tools so far.

RESULTS

We developed procedures for the conversion of cDNA Differential Display data into quantitative transcription profiles. Amplified cDNA fragments are separated on a DNA sequencer and detector signals are converted into virtual gel images suitable for semi-automatic analysis. Data processing consists of four steps: (i) cDNA bands in lanes corresponding to samples treated with the same primer combination are matched in order to identify fragments originating from the same transcript, (ii) intensity of bands is determined by densitometry, (iii) densitometric values are normalized, and (iv) intensity ratio is calculated for each pair of corresponding bands. Transcription profiles are represented by sets of intensity ratios (control vs. treatment) for cDNA fragments defined by primer combination and DNA mobility. We demonstrated the procedure by analyzing DDRT-PCR data on the effect of secondary metabolites of oilseed rape Brassica napus on the transcriptome of the pathogenic fungus Leptosphaeria maculans.

CONCLUSION

We developed a data processing procedure for the quantitative analysis of amplified cDNA fragments separated by electrophoresis. The system utilizes common software and provides an open-end alternative to DNA microarray analysis of the transcriptome. It is expected to work equally well with DDRT-PCR and cDNA-AFLP data and be useful particularly in research on organisms for which microarray analysis is not available or economical.

Screening of genes expressed in developing mandibles during soldier differentiation in the termite Hodotermopsis sjostedti

We investigated the morphological changes accompanying soldier differentiation in the damp-wood termite Hodotermopsis sjostedti. Genes expressed in the developing mandibles, which undergo the most remarkable morphological changes during soldier differentiation, were screened using fluorescent differential display. Database searches for sequence similarities were conducted and the relative expression levels were then quantified by real-time polymerase chain reaction. Among the identified candidate genes, 12 genes were upregulated during soldier differentiation. These included genes for cuticle proteins, nucleic acid binding proteins, ribosomal proteins and actin-binding protein, which were inferred to be involved in caste-specific morphogenesis in termites.

Upregulation of the transcript level of GTPase activating protein KIAA0603 in T cells from patients with atopic dermatitis

We have analyzed transcription profiles in peripheral blood CD3(+) cells from patients with allergic diseases to better understand the genes that are involved. Transcription levels of the gene KIAA0603/AS160 in CD3(+) cells from patients with atopic dermatitis (AD) were significantly higher than in normal individuals. The KIAA0603 gene encodes a 1299 amino acid protein with two phosphotyrosine interaction domains at the N-terminal region and a TBC domain at the C-terminal region. The region containing the TBC domain has a 31% homology to human rab6 GTPase activating protein (GAP). When human primary CD3(+) cells were stimulated with anti-CD3 or calcium ionophore, the KIAA0603 transcript level was upregulated. The marked upregulation of KIAA0607 was accompanied by activation induced cell death of primary CD3+ cells. KIAA0603 is likely to be a Rab GAP that participates in the regulation of activated T cells, especially helper memory T cells. Expression of KIAA0603 in T cells may be involved in pathogenesis of AD.

Potential role for heat shock protein 72 in antagonizing cerebral vasospasm after rat subarachnoid hemorrhage

BACKGROUND

Cerebral vasospasm can be defined as delayed-onset narrowing of the cerebral arteries that can occur after a spontaneous aneurysmal subarachnoid hemorrhage (SAH). Despite a large number of experimental and clinical investigations, the exact pathophysiology of vasospasm remains unknown. Using a fluorescence differential-display system, we have identified the gene encoding heat shock protein 72 (HSP72) as being highly upregulated by cerebral vasospasm. We therefore elucidated the role of the HSP72 gene in cerebral vasospasm in a rat experimental SAH model.

METHODS AND RESULTS

By angiography, cerebral vasospasm was detected from day 1, with maximal narrowing detected on day 2. Intracisternal injection of antisense HSP72 oligodeoxynucleotide led to specific inhibition of HSP72 gene expression and significantly aggravated cerebral vasospasm on days 2 and 3 of the angiographic studies. Oral administration of geranylgeranylacetone (GGA), an antiulcer drug, enhanced HSP72 induction and reduced cerebral vasospasm.

CONCLUSIONS

These results suggest HSP72 plays a novel role in antagonizing delayed cerebral vasospasm after SAH and that GGA provides protective effects against delayed cerebral vasospasm, at least partly via induction of HSP72.

Rice cDNA microarray-based gene expression profiling of the response to flagellin perception in cultured rice cells

Incompatible strains of Acidovorax avenae elicit an immune response in cultured rice cells, with immunity specifically induced by the flagellin of the incompatible strain. To identify genes regulated by flagellin perception signaling in cultured rice cells, gene expression patterns were analyzed with rice cDNA microarrays, including 3,353 independent rice cDNA clones. In all, 131 genes were differentially expressed between incompatible and compatible interactions. K-means clustering showed that 94 genes were upregulated and 32 genes were downregulated during incompatible interactions, whereas only 5 genes were upregulated during compatible interactions. Among the 126 genes that were up- or downregulated during incompatible interactions, expression of 46 genes was decreased when cultured rice cells were inoculated with a flagellin-deficient incompatible strain (delta fla1141-2), indicating that approximately 37% of the 126 genes were directly controlled by flagellin perception. Real-time reverse-transcription polymerase chain reaction analysis using flagellins purified from incompatible or compatible strains was performed to confirm flagellin-regulated expression of candidate genes selected by microarray analysis. Results showed that induction of some genes involved in the immune response is regulated not only by the flagellin perception pathway, but also by another recognition molecule-perception pathway.

Involvement of IL-1 family proteins in p38 linked cellular senescence of mouse embryonic fibroblasts

Senescence of mammalian cultured cells is essentially organized by a machinery of cell division and cellular stresses induced by various extracellular stimuli. Here, we show that in mouse embryonic fibroblasts (MEFs) culture in vitro, expression of an inflammatory cytokine, interleukin-1beta (IL-1beta) and its antagonist, IL-1 receptor antagonist (IL-1Ra) are induced by senescence. The kinetics of IL-1beta-expression was similar to that of p38 activation during MEFs culture. We also found a distinguishable accelerated senescence in cell growth in IL-1Ra deficient MEFs culture. Our results suggest that IL-1beta signaling pathway is involved in activation of p38 linked cellular senescence.

Expression of a Human SOCS Protein, HSOCP-1, in Peripheral Blood Eosinophils from Patients with Atopic Dermatitis

To identify new genes related to atopic dermatitis (AD), we screened for differentially expressed genes in peripheral blood eosinophils derived from AD patients and healthy volunteers. RNA was prepared from peripheral blood eosinophils obtained from both AD patients and healthy volunteers, and the expression of various genes was monitored using fluorescent differential display and real-time RT-PCR. One of the expressed sequence tags (ESTs) was expressed at a significantly higher level in AD patients than in healthy volunteers. A full-length cDNA was identified that encoded a human suppressor of cytokine signaling (SOCS) protein, HSOCP-1, also named hASB-8. The expression of HSOCP-1 was increased in cultured peripheral blood eosinophils after IL-4 stimulation, and overexpression of HSOCP-1 caused cell death in an eosinophil cell line, AML14.3D10. p34(SEI-1) was identified as a HSOCP-1-interacting protein by a yeast two-hybrid system. It is a protein that also interacts with the cyclin-dependent kinase inhibitor p16(INK4), suggesting that HSOCP-1 is involved in cell cycle control and apoptosis.

Target validation in hypoxia-induced vascular remodeling using transcriptome/metabolome analysis

The present study describes combined transcriptome and metabolome analysis for therapeutic target validation in hypoxia-induced vascular remodeling. Exposure to hypoxic conditions resulted in the upregulation of S100C mRNA and increased taurine (2-aminoethanesulfonic acid) content in the rat lung, as demonstrated by differential display and amino-acid content analysis. Hypoxia resulted in transcriptional activation of the S100C promoter through hypoxia-inducible factor-1 (HIF-1). Taurine suppressed HIF-1-mediated increases in S100C transcription. Moreover, oral taurine administration attenuated vascular remodeling in hypoxic rat lung, whereas depletion of endogenous taurine by administration of beta-alanine resulted in increased vascular remodeling. Inhibition of HIF transcription by taurine may be of therapeutic benefit in preventing hypoxia-induced vascular remodeling. In conclusion, we used transcriptome and metabolome analysis to identify a therapeutic low-molecular-weight ligand that plays a critical role in hypoxia-induced vascular remodeling. These techniques provided an excellent strategy for screening and validation of targets.

Annealing control primer system for identification of differentially expressed genes on agarose gels

We developed GeneFishing technology, an improved method for the identification of differentially expressed genes (DEGs) using our novel annealing control primer (ACP) system. Because of high annealing specificity during PCR using the ACP system, the application of the ACP to DEG discovery generates reproducible, authentic, and long (100 bp to 2 kb) PCR products that are detectable on agarose gels. To demonstrate this method for gene expression profiling, Gene-Fishing technology was used to detect genes that are differentially expressed during development using total RNAs isolated from mouse conceptus tissues at 4.5-18.5 days of gestation. Ten DEGs (DEG1-10) were isolated and confirmed by Northern blot hybridization. The sequence analysis of these DEGs showed that DEG6 and DEG10 are unknown genes.

Aryl hydrocarbon receptor-mediated suppression of GH receptor and Janus kinase 2 expression in mice

Differential mRNA display revealed that a cDNA encoding the major urinary protein 2 (MUP2) that belongs to the lipocalin superfamily was absent in livers of mice treated with 3-methylcholanthrene (MC). The expression of MUP2 is known to be stimulated by growth hormone (GH), through the GH receptor (GHR), Janus kinase 2 (JAK2) and signal transducer and activator of transcription 5 (STAT5) signal transduction pathway. Since MC is an aryl hydrocarbon receptor (AhR) ligand, the effects of MC treatment on the expression of GHR, JAK2 or STAT5 in the livers of wild-type or AhR-null mice were examined. The result indicated that the expression of GHR and JAK2 mRNA was greatly decreased by MC in wild-type mice but not in AhR-null mice. In addition, the binding activity of STAT5 bound to STAT5-binding element was reduced after MC treatment in wild-type mice but not in AhR-null mice. Based on these results, we conclude that the suppression of MUP2 mRNA expression by MC is caused by the AhR-mediated disruption of the GH signaling pathway. Possible mechanism(s) by which exposure to aromatic hydrocarbons causes a decrease in the body weight of mice, which has been referred to as wasting syndrome, will also be discussed.

Novel insect picorna-like virus identified in the brains of aggressive worker honeybees

To identify candidate genes involved in the aggressive behavior of worker honeybees, we used the differential display method to search for RNAs exclusively detected in the brains of aggressive workers that had attacked a hornet. We identified a novel, 10,152-nucleotide RNA, termed Kakugo RNA. Kakugo RNA encodes a protein of 2,893 amino acid residues that shares structural features and sequence similarities with various picorna-like virus polyproteins, especially those from sacbrood virus, which infects honeybees. The Kakugo protein contains several domains that correspond to the virion protein, helicase, protease, and RNA-dependent RNA polymerase domains of various picorna-like virus polyproteins. When the worker bee tissue lysate was subjected to sucrose density gradient centrifugation, Kakugo RNA, except for the material at the bottom, was separated into two major peaks. One of the peaks corresponded to the position of Kakugo mRNA, and the other corresponded to the position of the poliovirus virion. These results suggest that the Kakugo RNA exists as an mRNA-like free RNA and virion RNA in the honeybee. Furthermore, injection of the lysate supernatant from the attacker heads into the heads of noninfected bees resulted in a marked increase in Kakugo RNA. These results demonstrate that Kakugo RNA is a plus-strand RNA of a novel picorna-like virus and that the brains of aggressive workers are infected by this novel virus. Kakugo RNA was detected in aggressive workers but not in nurse bees or foragers. In aggressive workers, Kakugo RNA was detected in the brain but not in the thorax or abdomen, indicating a close relation between viral infection in the brain and aggressive worker behaviors.

Quantitative Analysis of Nucleic Acids - the Last Few Years of Progress

DNA and RNA quantifications are widely used in biological and biomedical research. In the last ten years, many technologies have been developed to enable automated and high-throughput analyses. In this review, we first give a brief overview of how DNA and RNA quantifications are carried out. Then, five technologies (microarrays, SAGE, differential display, real time PCR and real competitive PCR) are introduced, with an emphasis on how these technologies can be applied and what their limitations are. The technologies are also evaluated in terms of a few key aspects of nucleic acids quantification such as accuracy, sensitivity, specificity, cost and throughput.

A novel marker for terminal Schwann cells, homocysteine-responsive ER-resident protein, as isolated by a single cell PCR-differential display

Terminal Schwann cells (TSCs) that cover motor neuron terminals are known to play important roles in maintaining neuromuscular junctions, as well as in the repair process after nerve injury. However, molecular characteristics of TSCs remain unknown, because of the difficulties in analyzing them due to their paucity. We have established a method of selectively and efficiently collecting TSCs so that cDNA analysis can be done properly. The expression of 1-2% of whole mRNAs was compared between myelinating Schwann cells (MSCs) and TSCs, and it turned out that approximately one-third of the bands could be categorized as cell-type-specific bands. TSCs thus constitute a distinct entity from the viewpoint of gene expression. As one of the cDNA clones belonging to TSC-specific bands was identified homocysteine-responsive ER-resident protein (Herp), and in situ hybridization confirmed that Herp mRNA is expressed in TSCs on motor nerve terminals but not in MSCs, both in developing and adult rats. In conclusion, we have been able to identify Herp as a novel molecular marker for TSCs.

Analysis of gene expression in peripheral blood eosinophils from patients with atopic dermatitis by differential display

To identify the genes related to atopic dermatitis (AD), we compared gene expression in eosinophils from AD patients and healthy volunteers. RNA was prepared from peripheral blood eosinophils. Gene expression was monitored by fluorescent differential display (DD) and real-time RT-PCR. Eighteen new sequences, including expressed sequence tags (ESTs), were expressed at higher levels in eosinophils from AD patients than in those from healthy volunteers. The functions of most of these genes are unknown. We found no correlation between the expression of a particular gene and clinical markers such as the number of eosinophils and the amount of IgE. Multivariate analysis of the gene expression data in each sample showed a very high coefficient of correlation among the copy numbers of each gene. The genes under investigation were also expressed in cultured blood eosinophils after IL-4, IL-5 and IFN-gamma stimulation. We were able to predict the function of some of the sequences by scanning for homologies within either the human or mouse genome databases. The mouse counterpart of one of these genes, intersectin 2, was expressed dramatically, as measured by ear edema, in 1-fluoro-2,4-dinitrobenzene-induced mouse contact dermatitis and in NC/Nga mouse dermatitis.

O-MACS, a novel member of the medium-chain acyl-CoA synthetase family, specifically expressed in the olfactory epithelium in a zone-specific manner

In rodents, the olfactory epithelium (OE) can be divided into four topographically distinct zones, and each member of the odorant receptor (OR) gene family is expressed only in one particular zone. To study the functional significance of the zonal structure of the OE, we searched for genes expressed in a zone-specific manner by using the differential display method. Among the clones isolated from the rat OE, we characterized a novel olfactory protein termed O-MACS, a member of the medium-chain acyl-CoA synthetase family. The o-macs gene encodes a protein of 580 amino acids, sharing 56-63% identity with other MACS family proteins. RT-PCR analysis demonstrated that the o-macs gene is expressed only in the OE, unlike other MACS family genes. In situ hybridization revealed that the o-macs transcripts are present in the neuronal cell layer of olfactory sensory neurons (OSNs) as well as in the supporting and basal cell layers in the most dorso-medial area (zone 1) of the OE. Developmental analysis revealed that the o-macs gene is already expressed on embryonic day 11.5, before the onset of the OR gene expression, in a restricted area within the rat olfactory placode. Recombinant O-MACS protein tagged with c-Myc and His6 demonstrated an acyl-CoA synthetase activity for fatty acid activation, and protein localization to mitochondria like other MACS family proteins. The present study indicates that this novel protein may play important roles in processing odorants in a zone-specific manner, or the zonal patterning of the OE during development.

Human T-cell leukemia virus type 1 Tax protein stimulates the interferon-responsive enhancer element via NF-kappaB activity

Gene expression in Rat-1 fibroblast cells transformed by Tax from human T-cell leukemia virus type 1 was studied using the reverse transcriptase polymerase chain reaction differential display technique. The analysis revealed eight genes that were upregulated and one gene that was suppressed in Tax-transformed cells. Interestingly, at least four of the upregulated genes were interferon-stimulated genes. Promoter analysis of the 2',5'-oligoadenylate synthetase gene, which was activated in both Tax-transformed Rat-1 cells and primary adult T-cell leukemia cells, demonstrated that Tax indirectly activates its interferon-responsive enhancer element in a nuclear factor-kappaB pathway-dependent manner, indicating a close association of interferon signaling with the transformation by Tax.

Differentially expressed genes associated with CIS-diamminedichloroplatinum (II) resistance in head and neck cancer using differential display and CDNA microarray

BACKGROUND

The mechanism by which cancer cells become resistant to cis-Diamminedichloroplatinum (II) (cDDP) is not completely understood. To investigate the molecular markers involved in the cDDP resistance, we compared the gene expression profiles between a head and neck squamous cell carcinoma (HNSCC) line sensitive to cDDP and its cDDP-resistant variant.

METHODS

Both a fluorescent differential display and a cDNA microarray analysis were applied to distinguish the gene profiles between KB, a human HNSCC line, and its cDDP-resistant variant (KB/cDDP). These results were confirmed by Northern blot analysis.

RESULTS

One up-regulated gene, glycoprotein hormone alpha-subunit, and two down-regulated genes coding membrane proteins, human folate receptor and tumor-associated antigen L6, were identified in KB/cDDP cells.

CONCLUSIONS

Our findings suggest that development of the cDDP-resistant phenotype is accompanied by alternations of gene expression including a glycoprotein hormone and membrane proteins. These gene products could be new molecular markers for resistance to cDDP.

Overexpression of NP95 mRNA by tumor promoters in the promotion phase of a two-stage BALB/3T3 cell transformation assay

We studied altered gene expressions in BALB/3T3 cells treated by different tumor promoters in the promotion phase of a transformation assay, an in vitro model of a two-stage carcinogenicity test, using fluorescent mRNA differential display analysis. Expression of the NP95 gene, which was previously found to be the gene of a murine nuclear protein associated with cell proliferation, was increased in the cultures treated by 12-O-tetradecanoylphorbol-13-acetate (TPA), okadaic acid, and orthovanadate. The upregulation of NP95 mRNA was confirmed by reverse transcription-PCR, and Northern blot. TPA, okadaic acid, and orthovanadate enhanced cell proliferation as measured by a 5-bromo-2'-deoxyuridine incorporation assay. The expression level of NP95 mRNA was not affected by the treatment with typical carcinogens benzo[a]pyrene and 3-methylcholanthrene at concentrations at which they act as initiators of cell transformation. These facts may imply that the enhancement of cell transformation by these tumor promoters is due, at least in part, to the acceleration of cell proliferation. NP95 mRNA was also increased in the transformed BALB/3T3 cells. Overexpression of NP95 may also participate in the maintenance of the transformed phenotype.

Identification of genes induced in regenerating Xenopus tadpole tails by using the differential display method

To identify candidate gene(s) involved in the tail regeneration of Xenopus laevis tadpoles, we used the differential display method to isolate four genes (clones 1, 2, 13a, and 13b) whose expression is induced in regenerating tadpole tails. Among them, clones 13a and 13b were found to encode the Xenopus homologues of the alpha1 chain of type XVIII collagen and neuronal pentraxin I, respectively. Expression of clone 2 and neuronal pentraxin I genes increased dramatically in the blastema 3 days after amputation, whereas that for the clone 1 and type XVIII collagen genes was induced gradually after amputation. In situ hybridization revealed that the neuronal pentraxin I gene is expressed specifically in the regenerating tail epidermis but not in the normal tail epidermis or the most distal margin of the tail blastema, suggesting that it has a tissue-inductive role in tail regeneration. Expression of the four genes was induced in the limb and in the tail blastema, suggesting that they are involved in the regeneration of both organs. Finally, expression of clone 2 and neuronal pentraxin I genes was scarce during embryonic stages in comparison to the tail blastema, suggesting that their main functions are in organ regeneration. Our results demonstrate unique features of spatial and temporal gene expression patterns during Xenopus tadpole tail regeneration.

Identification of highly expressed genes in peripheral blood T cells from patients with atopic dermatitis

BACKGROUND

Analysis of genes that are differentially expressed in patients with atopic dermatitis (AD) and normal individuals will provide important information on the underlying molecular pathogenetic mechanisms of AD.

METHODS

Transcript of freshly isolated peripheral blood T cells from 59 individuals were analyzed with a fluorescent differential display (FDD) method. Ninety-two differentially expressed genes were identified in this manner. Additionally, real-time quantitative RT-PCR was employed to investigate the expression of the FDD-selected genes and also genes related to T cell function.

RESULTS

A number of genes, including CC chemokine receptor 4, T cell-specific tyrosine kinase (Emt/Itk), integrin beta1, integrin alpha6, IQGAP1 and MAR/SAR DNA-binding protein (SATB1), were shown to be more highly expressed in patients with moderate and/or severe AD than in controls or patients with mild AD. Because the products of these upregulated genes influence chemotaxis, adhesion, migration and Th2 polarization, it is suggested that in more severe AD, circulating T cells may function differently in this regard. Several other genes, the role of which in T cell function is currently unknown, were also found to be differentially expressed in AD. These included the heat shock protein 40 and vasopressin-activated calcium-mobilizing receptor 1.

CONCLUSION

The upregulated genes identified in this work may serve as useful markers for moderate to severe AD as opposed to normal or mild AD and also as markers indicating progression to more severe AD. Further functional characterization will provide a better understanding of the pathophysiology of circulating T cells in AD.

Stomatin-related olfactory protein, SRO, specifically expressed in the murine olfactory sensory neurons

We identified a stomatin-related olfactory protein (SRO) that is specifically expressed in olfactory sensory neurons (OSNs). The mouse sro gene encodes a polypeptide of 287 amino acids with a calculated molecular weight of 32 kDa. SRO shares 82% sequence similarity with the murine stomatin, 78% with Caenorhabditis elegans MEC-2, and 77% with C. elegans UNC-1. Unlike other stomatin-family genes, the sro transcript was present only in OSNs of the main olfactory epithelium. No sro expression was seen in vomeronasal neurons. SRO was abundant in most apical dendrites of OSNs, including olfactory cilia. Immunoprecipitation revealed that SRO associates with adenylyl cyclase type III and caveolin-1 in the low-density membrane fraction of olfactory cilia. Furthermore, anti-SRO antibodies stimulated cAMP production in fractionated cilia membrane. SRO may play a crucial role in modulating odorant signals in the lipid rafts of olfactory cilia.

Dendritic cell appearance and differentiation during early and late stages of rat stomach carcinogenesis

Dendritic cell appearance and differentiation during early and late stages of rat stomach carcinogenesis were studied in the pyloric mucosa. Young male rats were given drinking water with or without N-methyl-N'-nitro-N-nitrosoguanidine (MNNG; 100 mg/liter) for 14 days. Use of competitive RT-PCR and northern blotting showed that MNNG exposure induced 3- to 4-fold greater expression of the genes for integrin beta7 and integrin alphaE2 (identical with antigen OX-62, a dendritic cell marker), as well as three cytokines, IL-4, GM-CSF and TNFalpha, in the stomach pyloric mucosa of resistant Buffalo rats compared to sensitive ACI rats. These genes were minimally expressed in control animals. The results confirm the appearance of dendritic cells in the target pyloric mucosa and suggest the possibility that dendritic cell differentiation and maturation are induced by various cytokines, at least in Buffalo rats. Competitive RT-PCR showed expression of integrin alphaE2 and beta7, MHC class II-associated invariant chain (Ii), MHC class II, B7-1, CD28, GM-CSF and TNFalpha genes in all 12 examined stomach adenocarcinomas and adenomas induced in male Lewis and WKY rats with 30 weeks' MNNG exposure, suggesting the presence of dendritic cells in tumors. OX-62 staining and western blotting for OX-62 also confirmed the presence of dendritic cells in tumors. However, the population of dendritic cells in tumors was less than that in the pyloric mucosa after 14 days' MNNG exposure. The present results suggest that immune defense involving dendritic cells is marshaled from the very early initiation stage during rat stomach cancer development, but is downgraded in developed tumors.

Male specific genes from dioecious white campion identified by fluorescent differential display

Fluorescent differential display (FDD) has been used to screen for cDNAs that are differentially up-regulated in male flowers of the dioecious plant Silene latifolia in which an X/Y chromosome system of sex determination operates. To adapt FDD to the cloning of large numbers of differential cDNAs, a novel method of confirming the differential expression of these has been devised. FDD gels were Southern electro-blotted and probed with mixtures of individual cDNA clones derived from different FDD product ligation reactions. These Southern blots were then stripped and re-probed with further mixtures of individual cloned FDD products to identify the maximum number of recombinant clones carrying the true differential amplification products. Of 135 differential bands identified by FDD, 56 differential amplification products were confirmed; these represent 23 unique differentially expressed genes as determined by virtual Northern analysis and two genes expressed at or below the level of detection by virtual Northern analysis. These two low expressed genes show bands of hybridization on genomic Southern blots that are specific to male plants, indicating that they are derived from, or closely related to, Y chromosome genes.

Molecular cloning of novel mouse and human putative citrate lyase beta-subunit

Using a fluorescent differential display (FDD) technique, a novel cDNA was identified by screening for gene expressed differentially between the Dunn osteosarcoma cell line and the LM8 cell line, an isolated variant of the Dunn cell line that has high metastatic potential to the lung. Molecular cloning of the cDNA revealed the clone has similarity to a bacterial fermentation enzyme, the citrate lyase beta-subunit (CL-beta). Northern blot and competitive reverse transcription-PCR (RT-PCR) analysis revealed up-regulation of the gene in the LM8 cell line. An RNA Master blot indicated that the mRNA encoding CL-beta is expressed abundantly in murine heart, liver, and kidney. A human expressed sequence tag (EST) database search suggested that a similar cDNA is expressed in humans. A gene with identical sequence is located on chromosome 13 in the genome database (Sanger centre, UK). These data suggest that a citrate fermentation pathway may exist in eukaryotes including mammals.

Aryl hydrocarbon receptor-mediated suppression of expression of the low-molecular-weight prekininogen gene in mice

Differential mRNA display showed that a cDNA band disappeared after treatment of mice with 3-methylcholanthrene (MC). The cDNA encoded low-molecular-weight (LMW) prekininogen, known to be the precursor of a potent vasodilator, bradykinin. MC is generally known to bind to aryl hydrocarbon receptor (AhR) as an initial event to cause effects in vivo. In accordance with the results, Northern blot analysis for LMW prekininogen mRNA using total RNAs from wild-type and AhR-null mice indicated that the suppression of the mRNA expression by MC was seen in wild-type mice but not in AhR-null mice. The expression of LMW prekininogen mRNA was almost completely lost within 1 h after treatment of mice with MC, while a clear increase of CYP1A2 mRNA, as a positive control, was noted 4 h after the treatment. The plasma concentration of bradykinin released from LMW prekininogen was decreased by MC in wild-type mice, but not in AhR-null mice. Based on these results, we conclude that AhR inhibits bradykinin synthesis in mice via suppression of the expression of LMW prekininogen. Possible mechanism(s) responsible for hypertension caused by treatment of mice with MC is also discussed.

Differential display analysis of mutants for the transcription factor Pdr1p regulating multidrug resistance in the budding yeast

The transcription factor Pdr1p recognizes Pdr1p/Pdr3p-response element (PDRE) to activate genes involved in multidrug resistance of the budding yeast. To identify novel targets of Pdr1p, we compared transcriptomes among the yeast cells bearing wild, disrupted and gain-of-function alleles of PDR1 using a high-throughput fluorescent differential display PCR. Consequently, we identified 20 transcripts apparently regulated by Pdr1p, which are derived from well-known target genes as well as those that have never been described in the context of drug resistance. Intriguingly, among the latter, a previously unrecognized gene bearing a small putative open reading frame preceded by a functional PDRE was found.