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At least 1,135 records · Page 63Linked to original sources
PubMed2004

The 14-3-3 proteins in the teleost fish rainbow trout (Oncorhynchus mykiss).

We report studies of 14-3-3 genes in rainbow trout, adding to current understanding of the molecular evolution of this multigene family and its functional importance in fish. Ten genes were identified that are apparent duplicates of five ancestors. The duplicated 14-3-3 genes diverged rapidly and their cladogram is markedly different from the phylogenetic tree. The mean rate of nonsynonymous divergence of trout 14-3-3 genes is one order of magnitude greater than that of mammalian genes. An evolutionarily recent genome duplication in salmonid fish relaxed functional constraints, and selection favored establishment of novel isoforms. Differences in tissue distribution of 14-3-3 genes were minor; however, results of 31 microarray experiments showed divergence of expression profiles, which was related to structural divergence of the duplicates. We observed remarkable coordination of expression of all isoforms in our study of stress response in the brain. Profiles of the 14-3-3 genes correlated with a large group of chaperones and genes involved in cell communication and signal transduction. We studied embryonic expression of 14-3-3 genes and found abundant transcripts in the rapidly growing and differentiating parts of embryos such as eyes, tail bud and yolk syncytium during somitogenesis and in gills and pectoral fins after completion of somitogenesis. Consistent expression was observed in the neural crest, which is known to have high morphogenetic potential.

14-3-3 Proteins↗
PubMed2002

Branchial expression of an aquaporin 3 (AQP-3) homologue is downregulated in the European eel Anguilla anguilla following seawater acclimation.

A cDNA encoding the homologue of mammalian aquaporin 3 (AQP-3) was isolated by reverse transcription-polymerase chain reaction from the gill of the European eel. The derived amino acid sequence shares 67-70% homology with other vertebrate AQP-3 homologues. Northern blot analysis revealed two AQP-3-specific mRNA species of 2.4 kb and 7 kb. AQP-3 mRNA is expressed predominantly in the eye, oesophagus, intestine (as found in mammals) and the gill; no expression could be demonstrated in the stomach and only low and sporadic levels in the kidney. Quantitative studies demonstrated that, following the 3-week acclimation of freshwater (FW)-adapted yellow and silver eels to seawater (SW), transcript abundance in the gill was reduced by 76% and 97%, respectively. The half time of branchial AQP-3 mRNA downregulation in yellow eels was approximately 10 h, with a maximal 94% decrease in expression after 2 days in SW (compared to time-matched FW controls). However, in fish acclimated to SW for more than 4 days, the fall in AQP-3 mRNA abundance recovered slightly, such that after 3 weeks, expression was 16% of that in time-matched FW controls. The potential roles for this aquaporin isoform in water or solute transport in the eel gill are discussed.

Acclimatization↗
PubMed2006

[Cytogenetics and application in domesticated silkworm Bombyx mori].

Chromosome identification and karyotype analyses of Bombyx mori (Lepidoptera) have long been hampered by the high number and the absence of suitable markers, such as centromeric position and chromosome bands. Recently, the cytological map has been constructed using comparative genomic hybridization-genomic in situ hybridization and BAC-based fluorescence in situ hybridization. Dense cytogenetic maps are being constructed by integrating cytological map with molecular linkage maps. Molecular and cytogenetics will help us to reveal the structure and function of chromosome of Bombyx mori, the W chromosome is composed largely of dense nested retrotransposons, and telomeres are consist of the TTAGG motifs and two type of telomere-specific non-LTR retrotransposons (TRAS1 and SART1), the TRAS1 and SART1 with abundant transcription activity may be involved in the stabilization of chromosomal ends.

Animals↗
PubMed2024

A computational model for bacteriophage ϕX174 gene expression.

Bacteriophage ϕX174 has been widely used as a model organism to study fundamental processes in molecular biology. However, several aspects of ϕX174 gene regulation are not fully resolved. Here we construct a computational model for ϕX174 and use the model to study gene regulation during the phage infection cycle. We estimate the relative strengths of transcription regulatory elements (promoters and terminators) by fitting the model to transcriptomics data. We show that the specific arrangement of a promoter followed immediately by a terminator, which occurs naturally in the ϕX174 genome, poses a parameter identifiability problem for the model, since the activity of one element can be partially compensated for by the other. We also simulate ϕX174 gene expression with two additional, putative transcription regulatory elements that have been proposed in prior studies. We find that the activities of these putative elements are estimated to be weak, and that variation in ϕX174 transcript abundances can be adequately explained without them. Overall, our work demonstrates that ϕX174 gene regulation is well described by the canonical set of promoters and terminators widely used in the literature.

Gene Expression Regulation, Viral↗
PubMed2026

Rasputin/G3BP mediates subversion of antiviral immunity by o'nyong-nyong virus in Anopheles coluzzii.

Cellular G3BP proteins are essential for alphavirus infection in both vertebrate and mosquito hosts, but the underlying mechanism of their proviral activity is poorly understood in any host. Whether the mosquito G3BP ortholog, Rasputin (Rin), interacts with host immunity to influence alphavirus infection has not been investigated, and anopheline mosquito interactions with arboviruses have been little studied. Here, we find that Rin silencing in Anopheles mosquitoes results in decreased ONNV infection levels, indicating a proviral activity for Anopheles Rin. We find that Rin function is required to maintain basal activity of the antiviral Imd and JAK/STAT pathways in uninfected mosquitoes. However, during ONNV infection, the control of the Imd pathway by Rin activity appears corrupted because Rin silencing leads to overexpression of the Imd positive regulator, Rel2. Thus, silencing of Rin both augments Rel2 transcript abundance and decreases ONNV load. Co-silencing of Rel2 with Rin restores normal ONNV infection levels, indicating that Rin activity is required to inhibit Imd function during ONNV infection, and which explains most of the Rin proviral phenotype. In addition, we show that the ONNV non-structural protein 3 (nsP3), which binds to Rin, strongly alters the pattern of Anopheles cellular protein partners interacting with Rin. In the presence of ONNV nsP3, 48 Rin-binding host proteins are unchanged but seven binding proteins are excluded and eight new cellular proteins bind Rin. The altered cellular protein partners are candidate host factors involved in viral subversion of Rin control over Imd activity. Overall, these results reveal a molecular mechanism in which ONNV, probably through nsP3, co-opts the normal Rin function for basal cellular immune activity by subverting the Imd antiviral pathway to promote infection. These results may be generalizable for Rin function during alphavirus infection of other mosquitoes, as well as for G3BP function in the mammalian host, and could offer a target for development of vector-based genetic control tools against arbovirus transmission.

Animals↗
PubMed2005

Novel isothermal, linear nucleic acid amplification systems for highly multiplexed applications.

BACKGROUND: Global analysis of the genome, transcriptome, and proteome is facilitated by the recent development of tools for large-scale, highly parallel analysis. We describe a novel nucleic acid amplification system that generates products by several methods. 3'-Ribo-SPIA primes cDNA synthesis at the 3' polyA tail, and whole transcript (WT)-Ribo-SPIA primes cDNA synthesis across the full length of the transcripts and thus provides whole-transcriptome amplification, independent of the 3' polyA tail. METHODS: We developed isothermal linear nucleic acid amplification systems, which use a single chimeric primer, for amplification of DNA (SPIA) and RNA (Ribo-SPIA). The latter allows mRNA amplification from as little as 1 ng of total RNA. Amplification efficiency was calculated based on the delta threshold cycle between nonamplified cDNA targets and amplified cDNA. The amounts and quality of total RNA and amplification products were determined after purification of the amplification products. GeneChip array gene expression profiling and real-time PCR were used to test the accuracy and reproducibility of the method. Quantification of cDNA products (before and after amplification) at the 2 loci along the transcripts was used to assess product length (for evaluation of the 3'-initiated Ribo-SPIA) and equal representation throughout the length of the transcript (for evaluation of the whole transcript amplification system, WT-Ribo-SPIA). RESULTS: Ribo-SPIA-based global RNA amplification exhibited linearity over 6 orders of magnitude of transcript abundance and generated microgram amounts of amplified cDNA from as little as 1 ng of total RNA. CONCLUSIONS: The described methods enable comprehensive gene expression profiling and analysis from limiting biological samples. The WT-Ribo-SPIA procedure, which enables amplification of non-polyA-tailed RNA, is suitable for amplification and gene expression analysis of both eukaryotic and prokaryotic biological samples.

Gene Expression Profiling↗
PubMed2000

High-copy cDNA amplification of minimal total RNA quantities for gene expression analyses.

This protocol describes a PCR-based cDNA amplification technique of small total RNA quantities, optimized for determination and verification of gene expression variations in cells or tissue specimen. A proportional amplification of rare and abundant transcripts is thereby achieved by initial random hexamer-primed reverse transcription of total RNA. Compared to established oligo(dT)-primed techniques, this approach generates shorter than full length copies of long RNAs which leads to a normalized cDNA pool for a more adequate PCR-amplification. Subsequent double oligo(dA) tailing of the synthesized total cDNA strands and the utilization of heteropolymeric primers allow a highly specific, up to 500-fold PCR-amplification of the total cellular RNA amount. Thus, obstacles in availability of RNA from limited sources, such as human biopsies or microdissected histological sections, can be overcome. The amplified total cDNA (atcDNA) is shown to be applicable for confirmation of differential gene expression, as demonstrated in this protocol by expression analysis of the multidrug resistance-associated genes mdr1, mrp1 and lrp, using human cell lines as well as microdissected human tissue sections.

Base Sequence↗
PubMed2006

Local synthesis of actin-binding protein beta-thymosin regulates neurite outgrowth.

Local protein synthesis plays an essential role in the regulation of various aspects of axonal and dendritic function in adult neurons. At present, however, there is no direct evidence that local protein translation is functionally contributing to neuronal outgrowth. Here, we identified the mRNA encoding the actin-binding protein beta-thymosin as one of the most abundant transcripts in neurites of outgrowing neurons in culture. Beta-thymosin mRNA is not evenly distributed in neurites, but appears to accumulate at distinct sites such as turning points and growth cones. Using double-stranded RNA knockdown, we show that reducing beta-thymosin mRNA levels results in a significant increase in neurite outgrowth, both in neurites of intact cells and in isolated neurites. Together, our data demonstrate that local synthesis of beta-thymosin is functionally involved in regulating neuronal outgrowth.

Amino Acid Sequence↗
PubMed2005

Diffusion, mixing, and associated dye effects in DNA-microarray hybridizations.

Typical DNA microarrays utilize diffusion of dye-labeled cDNA probes followed by sequence-specific hybridization to immobilized targets. Here we experimentally estimated the distance typical probes travel during static 16-h hybridizations. Probes labeled with Cy3 and Cy5 were individually introduced to opposite sides of a microarray with minimal convective mixing. Oppositely labeled probes diffused across the initial front separating the two solutions, generating a zone with both dyes present. Diffusion-distance estimates for Cy3- and Cy5-labeled cDNAs were 3.8 mm and 2.6 mm, respectively, despite having almost identical molecular masses. In separate 16-h hybridization experiments with oppositely labeled probes premixed, arrays that were continuously mixed had 15-20% higher signal intensities than arrays hybridized statically. However, no change was observed in the Cy3/Cy5 signal intensity ratio between continuously mixed and static hybridizations. This suggests that the observed dye bias in diffusion-distance estimates results from differences in the detection limits of Cy3 and Cy5-labeled cDNA, a potential concern for array data on low-abundance transcripts. Our conservative diffusion-distance estimates indicate that replicate targets >7.6 mm apart will not compete for scarce probes. Also, raising the microarray gap height would delay the onset of diffusion-limited hybridization by increasing the amount of available probe.

Algorithms↗
PubMed1997

Starvation-induced increase in the parathyroid hormone/PTH-related protein receptor mRNA of bone and kidney in sham-operated and thyroparathyroidectomized rats.

Parathyroid hormone (PTH) acts on bone and kidneys by binding to PTH/PTH-related protein (PTHrP) receptors and regulating calcium (Ca) and phosphorus (P) homeostasis. PTH/PTHrP receptor mRNA was expressed at high levels in PTH target tissues such as the kidneys and bone including the calvaria, femur, and tibia. Because short-term starvation influences Ca and P ion homeostasis, we measured changes in PTH/PTHrP receptor mRNA expression in the bone and kidneys. Food deprivation for 3 days decreased the serum Ca and P concentrations, and reinstitution of feeding for 2 days normalized the serum Ca level and significantly increased the serum P level. Concomitantly, rat immunoreactive PTH (riPTH) was increased during starvation and returned to the control level after 2 days of subsequent feeding. Serum 1 alpha, 25-dihydroxyvitamin D3 (1,25(OH)2D3) concentrations did not significantly change during starvation and subsequent feeding. Starvation up-regulated PTH/PTHrP receptor mRNA expression in both bone and kidney. The effects of food deprivation on the receptor transcript abundance were greater in bone (threefold increase compared with control) than in the kidney (1.8-fold increase), whereas the mRNA level increase by food deprivation was more rapid in the kidneys than in bone. The PTH-induced adenylyl cyclase activity of renal membranes increased in starvation. Feeding after starvation normalized the mRNA levels in both tissues. Serum PTH depression, initiated by thyroparathyroidectomy, did not affect PTH/PTHrP receptor mRNA levels in bone and kidney in rats that were fed or starved for 3 days. The abundance of receptor mRNA in bone and kidney was significantly lower in fed rats given either corticosterone or vehicle than in starved rats. These data indicate that starvation induces PTH/PTHrP receptor mRNA expression in bone and kidney, independently of serum PTH and corticosterone concentrations. The factors leading to up-regulated receptor mRNA induced by starvation remain unknown.

Adenylyl Cyclases↗
PubMed2006

A bovine oviduct epithelial cell suspension culture system suitable for studying embryo-maternal interactions: morphological and functional characterization.

We established a short-term (24 h) culture system for bovine oviduct epithelial cells (BOECs), obtained on day 3.5 of the estrous cycle and evaluated the cells with respect to morphological criteria, marker gene expression, and hormone responsiveness. BOEC sheets were isolated mechanically from the ampulla with similar yields from oviducts ipsi- and contralateral to the ovulation site (57.9 +/- 4.6 and 56.4 +/- 8.0 x 10(6) cells). BOECs showed > 95% purity and cells cultured for 24 h maintained morphological characteristics present in vivo, as determined by light microscopy, scanning electron microscopy, and transmission electron microscopy. Both secretory cells with numerous secretory granules and ciliated cells with long, well-developed, and vigorously beating kinocilia were visible. Quantitative real-time PCR failed to detect significant differences in transcript levels between ipsi-and contralateral BOECs for the majority of marker genes (estrogen receptors alpha and beta (ESR1 and ESR2), 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR), oviductal glycoprotein 1 (OVGP1), progesterone receptor (PGR), and tumor rejection antigen 1 (TRA1)) throughout the 24 h culture period. However, the combined data of all time points for glutathione peroxidase 4 (GPX4), a gene previously shown to be expressed at higher levels in the ipsilateral oviduct in vivo, also indicated significantly different mRNA levels in vitro. The expression of marker genes remained stable after 6 h cell culture, indicating only a short adaptation period. Western blot analysis confirmed ESR1 and PGR protein expression throughout the culture period. In agreement with cyclic differences in vivo, estradiol-17beta stimulation increased PGR transcript abundance in BOECs. Our novel culture system provides functional BOECs in sufficient quantities for holistic transcriptome and proteome studies, e.g. for deciphering early embryo-maternal communication.

Animals↗
PubMed2004

Quantifying the relationship between gene expressions and trait values in general pedigrees.

Treating mRNA transcript abundances as quantitative traits and examining their relationships with clinical traits have been pursued by using an analytical approach of quantitative genetics. Recently, Kraft et al. presented a family expression association test (FEXAT) for correlation between gene expressions and trait values with a family-based (sibships) design. This statistic did not account for biological relationships of related subjects, which may inflate type I error rate and/or decrease power of statistical tests. In this article, we propose two new test statistics based on a variance-components approach for analyses of microarray data obtained from general pedigrees. Our methods accommodate covariance between relatives for unmeasured genetic effects and directly model covariates of clinical importance. The efficacy and validity of our methods are investigated by using simulated data under different sample sizes, family sizes, and family structures. The proposed LR method has correct type I error rate with moderate to large sample sizes regardless of family structure and family sizes. It has higher power with complex pedigrees and similar power to the FEXAT with sibships. The other proposed FEXAT(R) method is favorable with large family sizes, regardless of sample sizes and family structure. Our methods, robust to population stratification, are complementary to the FEXAT in expression-trait association studies.

Animals↗
PubMed2005

Genetic analysis of variation in gene expression in Arabidopsis thaliana.

In Arabidopsis thaliana, significant efforts to determine the extent of genomic variation between phenotypically divergent accessions are under way, but virtually nothing is known about variation at the transcription level. We used microarrays to examine variation in transcript abundance among three inbred lines and two pairs of reciprocal F1 hybrids of the highly self-fertilizing species Arabidopsis. Composite additive genetic effects for gene expression were estimated from pairwise comparisons of the three accessions Columbia (Col), Landsberg erecta (Ler), and Cape Verde Islands (Cvi). For the pair Col and Ler, 27.0% of the 4876 genes exhibited additive genetic effects in their expression (alpha = 0.001) vs. 32.2 and 37.5% for Cvi with Ler and Col, respectively. Significant differential expression ranged from 32.45 down to 1.10 in fold change and typically differed by a factor of 1.56. Maternal or paternal transmission affected only a few genes, suggesting that the reciprocal effects observed in the two crosses analyzed were minimal. Dominance effects were estimated from the comparisons of hybrids with the corresponding midparent value. The percentage of genes showing dominance at the expression level in the F1 hybrids ranged from 6.4 to 21.1% (alpha = 0.001). Breakdown of these numbers of genes according to the magnitude of the dominance ratio revealed heterosis for expression for on average 9% of the genes. Further advances in the genetic analysis of gene expression variation may contribute to a better understanding of its role in affecting quantitative trait variation at the phenotypic level.

Arabidopsis↗
PubMed2003

The profile of gene expression of human marrow mesenchymal stem cells.

Mesenchymal stem cells (MSCs) are multipotent precursors present in adult bone marrow, that differentiate into osteoblasts, adipocytes and myoblasts, and play important roles in hematopoiesis. We examined gene expression of these cells by serial analysis of gene expression, and found that collagen I, secreted protein acidic and rich in cysteine (osteonectin), transforming growth factor beta- (TGF-beta) induced, cofilin, galectin-1, laminin-receptor 1, cyclophilin A, and matrix metalloproteinase-2 are among the most abundantly expressed genes. Comparison with a library of CD34(+) cells revealed that MSCs had a larger number of expressed genes in the categories of cell adhesion molecule, extracellular and development. The two types of cells share abundant transcripts of many genes, some of which are highly expressed in myeloid progenitors (thymosin-beta 4 and beta 10, fos and jun). Interleukin-11 (IL-11), IL-15, IL-27 and IL-10R, IL-13R and IL-17R were the most expressed genes among the cytokines and their receptors in MSCs, and various interactions can be predicted with the CD34(+) cells. MSCs express several transcripts for various growth factors and genes suggested to be enriched in stem cells. This study reports the profile of gene expression in MSCs and identifies the important contribution of extracellular protein products, adhesion molecules, cell motility, TGF-beta signaling, growth factor receptors, DNA repair, protein folding, and ubiquination as part of their transcriptome.

Adult↗
PubMed2004

Gene expression profiling in human insulinoma tissue: genes involved in the insulin secretion pathway and cloning of novel full-length cDNAs.

Insulinoma is a clinically common cause of organic hypoglycemia. The prominent characteristic of insulinoma is endogenous hyperinsulinism. Until now, the molecular biology of human insulinoma has been little understood. In this study, gene expression profiling of human insulinoma was established by expressed sequence tag (EST) sequencing and cDNA array. A total of 2063 clones were obtained, of these, 1589 clones were derived from EST sequencing, 975 clones were derived from cDNA array and 501 clones were shared by the two methods. G protein alpha-stimulating activity polypeptide (Gsalpha) and carboxypeptidase E (CPE) were the most highly expressed genes in human insulinoma, as derived by EST sequencing and cDNA array respectively. The genes involved in the protein/insulin secretion pathway were strongly expressed in human insulinoma tissue. Meanwhile, eight full-length cDNAs of novel genes were cloned and sequenced. The results demonstrated the molecular biology of human insulinoma tissue at the level of transcript abundance and validated the efficacy of EST sequencing combined with cDNA array in the construction of gene expression profiling. In conclusion, the predominance of the genes participating in the secretory pathway suggested that regulation of secretion might be a major mechanism by which insulin release is abnormally increased in patients with insulinomas. It was also concluded that overexpression of the Gsalpha gene played an important role in the pathogenesis of insulinoma.

Cloning, Molecular↗
PubMed1993

Growth hormone receptor gene expression in sex-linked dwarf Leghorn chickens: evidence against a gene deletion.

GH receptor (GHR) mRNA has been identified in peripheral (liver and muscle) and central (brain and hypothalamus) tissues of sex-linked dwarf (SLD) Leghorn chickens. Total RNA was extracted from the tissues of immature (1 week, 4 week), pubertal (16 week) and adult (> 24 weeks) SLD and K (the normally growing strain) Leghorn chickens. In both groups and all tissues, an mRNA moiety of 4.4 kb hybridized with cRNA probes derived from the rabbit hepatic GHR sequence. An additional low-abundance transcript of 2.8 kb was also identified in some tissues. An age-related increase in expression was observed in K and SLD hepatic GHR mRNA, suggesting normal regulation of SLD GHR gene transcription. Amplification of cDNA from K and SLD tissues in the presence of oligonucleotide primers coding for the intracellular or extracellular domains of the chicken GHR generated electrophoretically separable fragments of expected size. Restriction enzyme digestion of the products with EcoRI, BstNI, HaeIII, NcoI or BamHI produced smaller moieties of expected sizes in both strains. These results demonstrate that, in contrast to broiler SLDs, a GHR gene deletion is not responsible for the GHR dysfunction in Leghorn SLDs. Although the actual defect in GHR gene expression in SLD Leghorns remains to be identified, this study demonstrates that sex-linked dwarfism, like Laron dwarfism, is due to a heterogeneity of lesions.

Animals↗
PubMed2000

Nonspecific, nested suppression PCR method for isolation of unknown flanking DNA.

We report the development of a simple, sensitive and robust two-step PCR method for the isolation of unknown sequences flanking characterized regions of genomic DNA or cDNA. The method requires 100 bp or less of a known sequence upstream of an oligonucleotide primer binding site. A first round of suppression PCR is conducted at low stringency with a polymerase lacking exonuclease activity to generate a mixture of products including fragments of the desired flanking sequence that are often greater than 1 kb in length. The desired fragments are then amplified from the mixture in a second round of suppression PCR using an extended oligonucleotide in combination with a polymerase exhibiting exonuclease activity. These fragments are subsequently identified by hybridization with the 100 bp of known sequence or simply by cloning and sequencing. The method is widely applicable and allows isolation of novel cDNA from very low abundance transcripts.

Alkalies↗
PubMed2002

Correcting for signal saturation errors in the analysis of microarray data.

A variety of technical errors have arisen in data analysis when using cDNA or oligonucleotide microarrays. One of the most insidious problems is the saturation of the hybridization signal of high-abundant transcripts. This problem arises from the truncation of the laser fluorescence signal. When the hybridization signal on the microarray is very strong, this truncation can result in serious consequences that may not be readily apparent to the user. As an illustration of this problem, two subclasses of normal human tissue samples (six liver and six lung samples) were analyzed with GeneChip probe arrays to evaluate the patterns of expression for approximately 7000 human genes. Five of these data sets were found to suffer from signal truncation. This caused several tissues to be incorrectly classified using hierarchical clustering. To rectify this problem so that the gene expression data could be properly compared and clustered, we developed a "filtering" procedure that identifies a subset of genes least affected by the signal saturation. This filtering procedure can be obtained at www.hugeindex.org.

Aged↗