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At least 937 records · Page 52Linked to original sources
PubMed2002

Cold stress decreases the capacity for respiratory NADH oxidation in potato leaves.

Cold stress effects on the expression of genes for respiratory chain enzymes were investigated in potato (Solanum tuberosum L., cv. Desiree) leaves. The nda1 and ndb1 genes, homologues to genes encoding the non-proton-pumping respiratory chain NADH dehydrogenases of Escherichia coli and yeast, were compared to genes encoding catalytic subunits of the proton-pumping NADH dehydrogenase (complex I). Using a real-time PCR system, we demonstrate a specific and gradual decrease of the NDA1 transcript after exposing the plants to 5 degrees C. After 6 days of cold treatment the NDA1 transcript abundance is 10% of the original level. This decrease is accompanied by specific decreases of immunodetected NDA protein and internal rotenone-insensitive NADH oxidation in mitochondria isolated from cold-treated plants. The alternative oxidase is not cold-induced neither at the protein nor at the activity level. The results are discussed in relation to the recent finding that the nda1 gene expression is completely light-dependent.

Cold Temperature↗
PubMed1998

Identification and functional characterization of DR6, a novel death domain-containing TNF receptor.

Tumor nectosis factor (TNF) receptors are key players in inflammation and immune regulation. A new member of this family, termed death receptor-6 (DR6), has been identified. Like other death receptors, DR6 is a type I transmembrane receptor, possesses four extracellular cysteine-rich motifs and a cytoplasmic death domain. DR6 is expressed in most human tissues and abundant transcript was detected in heart, brain, placenta, pancreas, thymus, lymph node and several non-lymphoid cancer cell lines. DR6 interacts with TRADD, which has previously been shown to associate with TNFR1. Furthermore, ectopic expression of DR6 in mammalian cells induces apoptosis and activation of both NF-kappaB and JNK.

Amino Acid Sequence↗
PubMed1998

Quantification of cytokine mRNA in peripheral blood mononuclear cells using branched DNA (bDNA) technology.

Changes in the patterns of cytokine expression are thought to be of central importance in human infectious and inflammatory diseases. As such, there is a need for precise, reproducible assays for quantification of cytokine mRNA that are amenable to routine use in a clinical setting. In this report, we describe the design and performance of a branched DNA (bDNA) assay for the direct quantification of multiple cytokine mRNA levels in peripheral blood mononuclear cells (PBMCs). Oligonucleotide target probe sets were designed for several human cytokines, including TNFalpha, IL-2, IL-4, IL-6, IL-10, and IFNgamma. The bDNA assay yielded highly reproducible quantification of cytokine mRNAs, exhibited a broad linear dynamic range of over 3-log10, and showed a sensitivity sufficient to measure at least 3000 molecules. The potential clinical utility of the bDNA assay was explored by measuring cytokine mRNA levels in PBMCs from healthy and immunocompromised individuals. Cytokine expression levels in PBMCs from healthy blood donors were found to remain relatively stable over a one-month period of time. Elevated levels of IFNgamma mRNA were detected in PBMCs from HIV-1 seropositive individuals, but no differences in mean levels of TNFalpha or IL-6 mRNA were detected between seropositive and seronegative individuals. By providing a reproducible method for quantification of low abundance transcripts in clinical specimens, the bDNA assay may be useful for studies addressing the role of cytokine expression in disease.

Cytokines↗
PubMed2003

Functional expression of cinnamate 4-hydroxylase from Ammi majus L.

Total RNA was isolated from dark-grown cell suspension cultures of Ammi majus L. that had been induced with fungal elicitor or treated with water for control and used as template with cytochrome P450-specific primers for DD-RT-PCR amplifications. A cDNA clone was generated from the elicited transcripts and assigned to cinnamate 4-monooxygenase based on sequence alignments and functional expression in yeast cells. Comparison of the translated polypeptide with database accessions of heterologous cytochrome P450 monooxygenases revealed a high degree of similarity (99.6%) with 98.6% identity to cinnamic acid 4-hydroxylase from parsley, documenting the close evolutionary relationship within the Apiaceae family. Maximal activity of the Ammi hydroxylase in yeast microsomes was determined at 25 degrees C and in the pH range of 6.5-7.0 reaching 2.5 pkat/mg on average. An apparent K(m) of 8.9 microM was determined for cinnamate. Preincubations with psoralen or 8-methoxypsoralen added up to 100 microM in the presence or absence of NADPH hardly affected the turnover rate. A. majus cell cultures accumulate sets of O-prenylated umbelliferones and linear furanocoumarins besides lignin-like compounds upon treatment with elicitor, and cinnamic acid 4-hydroxylase catalyzes the initial reaction leading from the general into the various phenylpropanoid branch pathways. Correspondingly, the hydroxylase transcript abundance was induced in the elicited cells.

Amino Acid Sequence↗
PubMed2003

SAGE surveys C. elegans carbohydrate metabolism: evidence for an anaerobic shift in the long-lived dauer larva.

The dauer larva, a non-feeding and developmentally arrested stage of the free-living nematode Caenorhabditis elegans, is morphologically and physiologically specialized for survival and dispersal during adverse growth conditions. The ability of dauer larvae to live several times longer than the continuous developmental life span has been attributed in part to a repressed metabolism. We used serial analysis of gene expression (SAGE) profiles from dauer larvae and mixed growing stages to compare expression patterns for genes with known or predicted roles in glycolysis, gluconeogenesis, glycogen metabolism, the Krebs and glyoxylate cycles, and selected fermentation pathways. Ratios of mixed:dauer transcripts indicated non-dauer enrichment that was consistent with previously determined adult:dauer enzyme activity ratios for hexokinase (glycolysis), phosphoenolpyruvate carboxykinase and fructose 1,6-bisphosphatase (gluconeogenesis), isocitrate dehydrogenase (NADP-dependent), and isocitrate lyase-malate synthase (glyoxylate cycle). Transcripts for the majority of Krebs cycle components were not differentially represented in the two profiles. Transcript abundance for pyruvate kinase, alcohol dehydrogenase, a putative cytosolic fumarate reductase, two pyruvate dehydrogenase components, and a succinyl CoA synthetase alpha subunit implied that anaerobic pathways were upregulated in dauer larvae. Generation of nutritive fermentation byproducts and the moderation of oxidative damage are potential benefits of a hypoxic dauer interior.

Alcohols↗
PubMed2001

Optimisation of methods for selecting candidate genes from cDNA array screens: application to rat brain punches and pineal.

DNA arrays are potentially powerful experimental tools within neuroscience but application of this technology to in vivo paradigms may, in practice, be limited by the sensitivity of transcript detection and inter-screen variation. Here we describe the use of brain punch micro-sampling, used in combination with commercially available cDNA arrays, for profiling brain gene expression in a mutant strain of rat (GAERS model of absence epilepsy). Furthermore, we describe a multi-step optimisation of analysis methods which provides for improved sensitivity and absence of bias in the selection of candidate genes which may be differentially expressed in the mutant. Our method has been validated through application to a second paradigm, rhythmic gene expression in the rat pineal gland. Our experimental design, and analysis method should therefore be generally applicable to subtle discriminations of transcript abundance within discrete brain areas.

Animals↗
PubMed2003

Genetic polymorphisms of osteopontin in association with multiple sclerosis in Japanese patients.

Osteopontin (OPN) exhibits pleiotropic functions and abundant transcripts for OPN are present in brains of patients with multiple sclerosis (MS). The aim of this study was to investigate the role of OPN genes in the pathogenesis of MS. Polymorphisms at the 8090th, 9250th and 9583rd positions in OPN were detected by PCR-RFLP from DNAs of 116 MS Japanese patients and 124 healthy controls. The C/C genotype at the 8090th position in exon 6 was more prevalent in MS than in control (p<0.0001), and C allele was more prevalent in MS than in control (p<0.0001, OR=2.57, 95% CI=1.65-4.00). For the 9583rd position polymorphism in exon 7, patients with G/G genotype (age; 32.1+/-12.5 years, mean+/-S.D.) showed a later disease onset than G/A (age; 25.9+/-7.8 years, p=0.01) and A/A (age; 25.2+/-8.9 years, p=0.01) genotypes. There were no significant correlations between OPN gene polymorphisms and disease progression. Our results suggest that the 8090th polymorphism might be associated with susceptibility to MS, while the 9583rd polymorphism might be associated with age of onset of MS.

Adult↗
PubMed2000

Genotyping of Plasmodium falciparum gametocytes by reverse transcriptase polymerase chain reaction.

A molecular assay has been developed for the specific detection and genetic characterisation of Plasmodium falciparum gametocytes in the blood of malaria infected individuals. The assay is based on the reverse transcription and polymerase chain reaction (RT-PCR) amplification of the messenger RNA of gene pfg377, a sexual-stage specific transcript abundantly produced in maturing gametocytes. The gene contains four regions of repetitive sequences, of which region 3 was shown to be the most polymorphic in laboratory clones and field isolates of the parasite. Analysis of samples of malaria infected blood by RT-PCR specific for region 3 has enabled identification of multiple gametocyte-producing clones within single infections. The assay is able to detect gametocytes below the threshold of microscopic detection, and is highly specific for its gametocyte targets also in the presence of a vast excess of asexual forms.

Alleles↗
PubMed1998

Biochemical and molecular properties of the Trypanosoma brucei alternative oxidase.

The protozoal parasite Trypanosoma brucei depends on a mitochondrial non-cytochrome terminal oxidase known as the trypanosome alternative oxidase (TAO) in its mammalian host. We have recently cloned the cDNA from T. brucei bloodstream form and have characterized a 33 kDa mitochondrial protein as TAO. Here we report that the TAO is a single copy gene in T. brucei and its expression is down regulated at the level of transcript abundance during differentiation from the bloodstream to the procyclic trypanosomes. Like other alternative oxidases (AOXs) cloned from different plants and fungi, TAO possesses the conserved sequences at the centrally located predicted membrane spanning domains and the signature sequence at the C-terminal hydrophilic domain for a pair of putative iron binding motifs (E-X-X-H). Phylogenetic analysis of the deduced protein sequences of eight different alternative oxidases cloned from different plants and fungi revealed that TAO is more closely related to the alternative oxidases of the fungi clade than that of plants. TAO has been functionally expressed in Escherichia coli. In the first of the two putative iron binding motifs, site-directed mutagenesis of E215 to A, L, N and Q resulted in the loss of the ability of the TAO gene to complement the heme deficiency of the E. coli mutants (SASX41B and GE1387) by conferring on them a CN-insensitive pathway of respiration. The conservative substitution of E215 by aspartate and histidine reduced the growth of the E. coli auxotrophs by approximately 80%. The mutations apparently did not have any effect on the stability of the expressed protein as revealed by the immunoblot analysis of the bacterial protein using TAO monoclonal antibody, which we have developed. Together, these points suggest that E215 plays an important role in the function of TAO. The steady state level of TAO mRNA is down-regulated in the procyclic stage presumably accounting for the low levels of TAO protein in these forms.

Aldehyde Oxidoreductases↗
PubMed1999

The mRNA-binding ribosomal protein S26 as a molecular marker in plants: molecular cloning, sequencing and differential gene expression during environmental stress.

One condition for using a gene as a transcriptional marker for environmental stress is its specific and differential expression. In order to be used as such a marker, the ribosomal protein S26 cDNA from pea (Pisum sativum L.) was cloned and fully sequenced. The gene (PsRPS26) was shown to be differentially regulated by ozone and UV-B radiation in opposite ways. Ozone gave rise to increased mRNA levels, whereas UV-B led to a decrease in S26 transcript abundance. Thus, the expression of PsRPS26 can be used as a molecular marker to differentiate between these two environmental stresses.

Amino Acid Sequence↗
PubMed2003

The new role of SAGE in gene discovery.

The sequencing of the human genome has led to in silico predictions of far fewer genes than anticipated. Recent studies using serial analysis of gene expression have cast doubt on this finding. One study predicts the presence of many unidentified low abundance transcripts, whereas two others have mapped unique tags to previously unpredicted exons. Genome and transcriptome complexity is thus greater than predicted and many of the missing genes are probably expressed in low copy numbers or only in early embryonic tissues.

Animals↗
PubMed2001

Effects of conditioned medium on activities of PAL, CHS, DAHP synthase (DS-Co and DS-Mn) and anthocyanin production in suspension cultures of Fragaria ananassa.

A conditioned medium (CM) prepared from cell suspension cultures of strawberry stimulated anthocyanin synthesis. The effect was significantly (P<0.05) greater than that of synthetic medium (SM), with macronutrient concentrations, carbohydrate concentrations and pH adjusted to those of CM. The activity of 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase (EC 4.1.2.15) (DS-Mn, DS-Co), phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) and chalcone synthase (CHS, EC 2.3.1.74) were monitored in the CM- and SM-cultured cells. PAL and CHS activities were found to increase significantly (P<0.05) in the CM-cultured cells. CHS transcript levels were higher in the CM-cultured cells compared to transcript abundance in SM-cultured cells. There was no significant difference in the DS-Mn and DS-Co activities of cells grown in conditioned or synthetic media.

Journal Article↗
PubMed1999

Discovery of a putative heme-binding protein family (SOUL/HBP) by two-tissue suppression subtractive hybridization and database searches.

In the domestic chicken, Gallus gallus, the retina and pineal gland contain circadian clocks that are directly entrained by environmental light-dark cycles. To identify novel genes that are expressed in the retina and pineal gland, we performed two-tissue suppression subtractive hybridization (SSH). Two-tissue SSH is designed to identify genes expressed in common between two RNA samples while at the same time subtracting out abundant transcripts. Using this method, we identified a novel chicken gene, named ckSoul, that is strongly expressed in the retina and pineal gland. The protein product of ckSoul is similar to a novel heme-binding protein (p22 HBP) and to an uncharacterized mammalian gene in the expressed sequence tag (EST) database. The mouse transcript of this new gene is expressed in the retina and may represent the mammalian ortholog of ckSoul. Molecular analysis of the mammalian and chicken proteins suggests SOUL and HBP are members of a new family of heme-binding proteins.

3T3 Cells↗
PubMed2002

Growth hormone regulation of rat liver gene expression assessed by SSH and microarray.

The sexually dimorphic secretion of growth hormone (GH) that prevails in the rat leads to a sex-differentiated expression of GH target genes, particularly in the liver. We have used subtractive suppressive hybridization (SSH) to search for new target genes induced by the female-characteristic, near continuous, pattern of GH secretion. Microarrays and dot-blot hybridizations were used in an attempt to confirm differential ratios of expression of obtained SSH clones. Out of 173 unique SSH clones, 41 could be verified as differentially expressed. Among these, we identified 17 known genes not previously recognized as differentially regulated by the sex-specific GH pattern. Additional SSH clones may also represent genes subjected to sex-specific GH regulation since only transcripts abundantly expressed could be verified. Optimized analyses, specific for each gene, are required to fully characterize the degree of differential expression.

Animals↗
PubMed2003

TSRC1, a widely expressed gene containing seven thrombospondin type I repeats.

The thrombospondin type 1 repeat domain is found in nearly 100 mammalian proteins with diverse biological functions that include cellular adhesion, angiogenesis, and patterning of the developing nervous system. We have characterized a novel thrombospondin type 1 repeat containing gene, TSRC1, encoding a predicted protein with seven thrombospondin repeats, six of which are clustered at the C-terminus. The 17 coding exons and two nontranslated exons of TSRC1 span 10 kb of genomic DNA. The human and mouse genes encode proteins of 1074 and 1036 amino acids, respectively, with 76% amino acid sequence identity. Thirty of the extra amino acids in the human protein are encoded by exon 6. Mouse Tsrc1 is expressed in all fetal and adult tissues tested. Three conserved noncoding sequence elements with potential regulatory function are located in intron 1. Mouse Tsrc1 was genetically mapped to chromosome 3 within the nonrecombinant region for the sodium channel modifier locus Scnm1. The sensitive and resistant alleles of Scnm1 did not differ in Tsrc1 protein sequence, transcript length, or transcript abundance. Human TSRC1 is located on chromosome 1q21 within an 11.7 Mb segment of conserved synteny. TSRC1 and the closely linked gene ADAM15 appear to be derived by a chromosomal inversion that interrupted an ancestral ADAMTS gene.

ADAMTS Proteins↗
PubMed1997

Molecular cloning of a rod opsin cDNA from the skate retina.

Skates (Raja erinacea and R. ocellata) are among the few animals that have an exclusively rod retina. However, skate rods are unusual in that they are capable of adapting to extremely high levels of illumination that initially saturate the rod photocurrent. This adaptive process restores the ability of the visual cells to respond to incremental photic stimuli and enables them to function under ambient conditions that are subserved by the cone mechanism in mixed (rod/cone) retinae. As a first step towards exploring the molecular basis of visual adaptation in the skate retina, we have cloned and analyzed the opsin cDNA from a skate retina library. The cDNA codes for a protein 354 amino acids (aa) long and 39.7 kDa predicted molecular mass, and labels a single abundant transcript of 1.7 kb in retinal RNA. Amino acid alignments and a parsimony analysis of nucleotide alignments show the skate opsin to be homologous to other rod opsins. An analysis of the aa sequence reveals a high degree of conservation of those residues thought to be important for most aspects of rhodopsin function. However, a few critical aa replacements may indicate alterations in the interactions of skate rhodopsin with other proteins in the phototransduction cascade. In particular, replacements of Glu150 with serine and Cys323 with leucine are in cytoplasmic domains thought to interact with transducin and rhodopsin kinase. The latter change eliminates one of the conserved acylation sites in the carboxyl terminal tail. These substitutions increase the similarity of the cytoplasmic domains of skate opsin to those of blue-sensitive visual pigments.

Amino Acid Sequence↗
PubMed1998

A novel SCG10-related gene uniquely expressed in the nervous system.

We have isolated a novel cDNA (HiAT3: hippocampus abundant transcript 3) in the course of screening for genes that are preferentially expressed in neonatal mouse hippocampus using random 3'-directed cDNA sequencing approach. It encodes a 180-aa protein that has high similarity to SCG10, a neuron-specific negative regulator of microtubule dynamics during neurite outgrowth. The expression of HiAT3 is limited to neurons and peaks about 1 week after birth. The identification of HiAT3 suggests that there may be an elaborate destabilizing regulation for microtubule dynamics in neurons in addition to the stabilizing effect of multiple microtubule-associated proteins (MAPs).

Amino Acid Sequence↗
PubMed1999

Analysis of expressed sequence tags of porcine skeletal muscle.

Porcine skeletal muscle genes play a major role in determining muscle growth and meat quality. Therefore, to progress towards a better understanding of the genetic factors influencing these traits, the first step is to characterize the genes expressed in skeletal muscle tissue in pig. To this aim, we constructed a porcine biceps femoris muscle cDNA library and sequenced 111 randomly isolated clones. By FASTA analysis, we identified 72 unique clones: 47 showed homology to previously identified genes in human or other mammals, 20 matched uncharacterized expressed sequence tags (ESTs), two showed no significant matches to sequences already present in DNA databases, and three other clones containing only repetitive elements were excluded from further analysis. Mitochondrial genes (16.2%), myosin heavy chain genes (9%) and the actin alpha skeletal muscle gene (9%) were the most abundant transcripts. Among the 47 identified genes several muscle-specific or predominant sequences expressed in skeletal muscle were found. The sequences of the clones matching uncharacterized human, mouse or porcine ESTs were tested by GRAIL in order to identify putative coding regions. The results of our analysis allowed the establishment of a first list of genes expressed in porcine skeletal muscle.

Amino Acid Sequence↗