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At least 811 records · Page 45Linked to original sources
PubMed2006

Phase-specific gene expression underlying morphological adaptations of the dimorphic human pathogenic fungus, Coccidioides posadasii.

Coccidioides posadasii is a dimorphic fungal pathogen that grows as a filamentous saprobe in the soil and as endosporulating spherules within the host. To identify genes specific to the pathogenic phase of Co. posadasii, we carried out a large-scale study of gene expression in two isolates of the species. From the sequenced Co. posadasii genome, we chose 1,000 open reading frames to construct a 70-mer microarray. RNA was recovered from both isolates at three life-cycle phases: hyphae, presegmented spherules, and spherules releasing endospores. Comparative hybridizations were conducted in a circuit design, permitting comparison between both isolates at all three life-cycle phases, and among all life-cycle phases for each isolate. By using this approach, we identified 92 genes that were differentially expressed between pathogenic and saprobic phases in both fungal isolates, and 43 genes with consistent differential expression between the two parasitic developmental phases. Genes with elevated expression in the pathogenic phases of both isolates included a number of genes that were involved in the response to environmental stress as well as in the metabolism of lipids. The latter observation is in agreement with previous studies demonstrating that spherules contain a higher proportion of lipids than saprobic phase tissue. Intriguingly, we discovered statistically significant and divergent levels of gene expression between the two isolates profiled for 64 genes. The results suggest that incorporating more than one isolate in the experimental design offers a means of categorizing the large collection of candidate genes that transcriptional profiling typically identifies into those that are strain-specific and those that characterize the entire species.

Adaptation, Biological↗
PubMed2001

Allosteric modulation of estrogen receptor conformation by different estrogen response elements.

Estrogen-regulated gene expression is dependent on interaction of the estrogen receptor (ER) with the estrogen response element (ERE). We assessed the ability of the ER to activate transcription of reporter plasmids containing either the consensus vitellogenin A2 ERE or the imperfect pS2, vitellogenin B1, or oxytocin (OT) ERE. The A2 ERE was the most potent activator of transcription. The OT ERE was significantly more effective in activating transcription than either the pS2 or B1 ERE. In deoxyribonuclease I (DNase I) footprinting experiments, MCF-7 proteins protected A2 and OT EREs more effectively than the pS2 and B1 EREs. Limited protease digestion of the A2, pS2, B1, or OT ERE-bound receptor with V8 protease or proteinase K produced distinct cleavage products demonstrating that individual ERE sequences induce specific changes in ER conformation. Receptor interaction domains of glucocorticoid receptor interacting protein 1 and steroid receptor coactivator 1 bound effectively to the A2, pS2, B1, and OT ERE-bound receptor and significantly stabilized the receptor-DNA interaction. Similar levels of the full-length p160 protein amplified in breast cancer 1 were recruited from HeLa nuclear extracts by the A2, pS2, B1, and OT ERE-bound receptors. In contrast, significantly less transcriptional intermediary factor 2 was recruited by the B1 ERE-bound receptor than by the A2 ERE-bound receptor. These studies suggest that allosteric modulation of ER conformation by individual ERE sequences influences the recruitment of specific coactivator proteins and leads to differential expression of genes containing divergent ERE sequences.

Allosteric Regulation↗
PubMed1994

Spatial and temporal expression patterns of FGF receptor genes type 1 and type 2 in the developing chick retina.

Fibroblast growth factors are known to influence the growth and differentiation of cultured cells derived from the chick retina. The fibroblast growth factors can interact with a family of at least four closely related receptor kinases. To find a correlation between the presence of fibroblast growth factor receptors and eye development, the patterns of expression of transcripts encoding the type 1 (FGF-R1) and type 2 (FGF-R2) receptors in the developing chick retina have been studied. Northern blot analysis of RNA of the whole retina was used to observe that FGF-R1 transcripts are abundant at embryonic day 4 and then decrease until day 11. After this stage, the level of expression of FGF-R1 increases and its peak of expression at embryonic day 18 is concomitant with the detection of the opsin transcript. FGF-R2 transcript is also detected by Northern blots of RNA of the whole retina until embryonic day 6. However, the re-expression after embryonic day 11 of FGF-R2 could only be demonstrated by PCR studies. The same pattern of expression is observed with in situ hybridization of sagittal sections. The two genes are coexpressed in the pigmented epithelium and in the neural retina during embryonic development. The expression follows the retinal layering according to a gradient from the vitreous humor to the choroid. Quantification of the in situ hybridization signals demonstrates that the pattern of expression of both receptors diverges after embryonic day 6 between the pigmented epithelium and the neuronal cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2000

Muscle-specific transcriptional regulation of the slowpoke Ca(2+)-activated K(+) channel gene.

Transcriptional regulation of the Drosophila slowpoke calcium-activated potassium channel gene is complex. To date, five transcriptional promoters have been identified, which are responsible for slowpoke expression in neurons, midgut cells, tracheal cells, and muscle fibers. The slowpoke promoter called Promoter C2 is active in muscles and tracheal cells. To identify sequences that activate Promoter C2 in specific cell types, we introduced small deletions into the slowpoke transcriptional control region. Using transformed flies, we asked how these deletions affected the in situ tissue-specific pattern of expression. Sequence comparisons between evolutionarily divergent species helped guide the placement of these deletions. A section of DNA important for expression in all cell types was subdivided and reintroduced into the mutated control region, a piece at a time, to identify which portion was required for promoter activity. We identified 55-, 214-, and 20-nucleotide sequences that control promoter activity. Different combinations of these elements activate the promoter in adult muscle, larval muscle, and tracheal cells.

Animals↗
PubMed2003

Polycystin-1 distribution is modulated by polycystin-2 expression in mammalian cells.

Mutations in PKD1 and PKD2, the genes that encode polycystin-1 and polycystin-2 respectively, account for almost all cases of autosomal dominant polycystic kidney disease. Although the polycystins are believed to interact in vivo, the two proteins often display dissimilar patterns and gradients of expression during development. In an effort to understand this apparent discrepancy, we investigated how changes in polycystin-2 expression can affect the subcellular localization of polycystin-1. We show that, when polycystin-1 is expressed alone in a PKD2 null cell line, it localizes to the cell surface, as well as to the endoplasmic reticulum. When co-expressed with polycystin-2, however, polycystin-1 is not seen at the cell surface and co-localizes completely with polycystin-2 in the endoplasmic reticulum. The localization of a polycystin-1 fusion protein was similarly affected by changes in its level of expression relative to that of polycystin-2. This phenomenon was observed in populations as well as in individual COS-7 cells. Our data suggest that the localization of polycystin-1 can be regulated via the relative expression level of polycystin-2 in mammalian cells. This mechanism may help to explain the divergent patterns and levels of expression observed for the polycystins, and may provide clues as to how the function of these two proteins are regulated during development.

Animals↗
PubMed2002

Changes in connexin43 in early ocular surface development.

PURPOSE: In the limbo-corneal epithelium the stem and early precursor epithelial cell pool is confined to the limbal rim. Among the features associated with this spatial segregation is the general paucity of connexin43 (Cx43) within the limbal basal cell population and its complete absence in resident stem cells. The limbo-corneal epithelial lineage derives from a Cx43-positive (Cx43+) embryonic outer ectoderm. Accordingly, as a means of identifying the process through which limbal cell phenotypes emerge, we investigated the expression of Cx43 in the ocular surface of embryonic rats. METHODS: Ocular surface expression of Cx43 or K12 was determined in cryostat sections of rat embryos and eyes using immunohistological methods. RESULTS: Changes in Cx43 expression revealed the early phenotypic divergence of three main epithelial cell phenotypes of the ocular surface. An analysis of the level and distribution pattern of Cx43 puncta lead to the identification of two distinct domains by embryonic day 10 (E10), a stage that occurs soon after formation of the lens vesicle. Additionally, at E12, ectodermal cells directly adjacent to the edges of the developing retina no longer express connexin. A comparison of anatomical and expression changes throughout embryonic development demonstrated that the two early zones represent the rudiments for the epithelia of the central cornea and conjunctiva, respectively, and that the isolated Cx43-negative (Cx43-) cells represent the precursors of the basal and, putatively, stem cells of the limbal epithelium. CONCLUSIONS: Changes in Cx43 expression revealed that the phenotypic divergence of ocular surface epithelial cells and the generation of limbo-corneal stem cell precursors takes place at a very early stage in ocular development, ahead of the establishment of any identifiable anatomical or differentiation features for these domains.

Animals↗
PubMed1986

Autoregulation of adenovirus E1A gene expression.

We examined E1A gene expression by two evolutionarily divergent human adenoviruses, type 5 (subgroup C) and type 3 (subgroup B). Adenovirus type 3 (Ad3)-infected A549 cells contained much larger amounts of E1A-specific RNA than adenovirus type 5 (Ad5)-infected cells, from very early (3 h) through the late stages (20 h) after infection. The appearance of such abundant Ad3 E1A transcripts was delayed after infection of Ad5 E1A-expressing 293 cells, suggesting a down regulation of the Ad3 E1A gene by Ad5 E1A gene products. In a reciprocal manner, coinfection of A549 cells led to typically early and intense Ad3 E1A transcription and strongly inhibited transcription of the Ad5 E1A gene. Transient expression assays were developed so that the autoregulation of the E1A gene could be studied apart from the more complex background of infected cells. The DNA sequence surrounding the transcription start site of the Ad3 E1A gene was placed 5' to the sequence which encodes the bacterial chloramphenicol acetyltransferase gene. Cotransfection of HeLa cells with Ad3 or Ad5 E1A-expression plasmids increased the expression of the Ad3 E1A promoter-driven chloramphenicol acetyltransferase gene. Taken together, these results suggest dual autoregulatory features of adenovirus E1A gene expression. The positive and negative effects appear to be temporally distinguished under different conditions, both in viral infection and in transient assays with plasmid-cloned genes.

Acetyltransferases↗
PubMedDate not supplied

Regulatory elements controlling chorion gene expression are conserved between flies and moths.

Flies and moths are approximately as distant phylogenetically as are mammals and birds. In terms of morphology, physiology and biochemistry, the complex proteinaceous eggshell or chorion differs substantially in these two insect groups, which are typified by Drosophila melanogaster and Bombyx mori. The major chorion proteins of moths are encoded by two families of genes, A and B, which have no obvious homologues in flies. Unlike Drosophila, where chorion genes are oriented in tandem, moths show mostly chorion gene pairs (A plus B) that are divergently transcribed and coordinately expressed. The 5' ends of the paired genes are separated by a DNA segment of only 300 +/- 50 base pairs, which may well include at least some of the cis-regulatory elements necessary for gene expression. Despite these differences, we have tested whether moth chorion genes might be expressed in flies. Cloned DNA fragments bearing moth chorion genes were introduced into the Drosophila germ line by P-element-mediated transformation. Analysis of RNAs from transformed lines revealed that the genes are expressed with correct sex, tissue and temporal specificity, resulting in the accumulation of abundant moth chorion transcripts in late fly follicles.

Animals↗
PubMed1990

Evolution of the glucose dehydrogenase gene in Drosophila.

The glucose dehydrogenase genes (Gld) of Drosophila melanogaster, of D. pseudoobscura, and of D. virilis have been isolated and compared with each other in order to identify conserved and divergent aspects of their structure and expression. The exon/intron structure of Gld is conserved. The Gld mRNAs are similar, with a range of 2.6-2.8 kb among the three species. All three species exhibit peaks of Gld expression during every major developmental stage, although considerable variation in the precise timing of these peaks exists between species. Interspecific gene transfer experiments demonstrate that the regulation and function of the D. pseudoobscura Gld is similar enough to the homologous gene in D. melanogaster to substitute for its essential role in the eclosion process. Comparison of the putative promoter sequences has identified both shared and divergent sequence elements which are likely responsible, respectively, for the conserved and divergent patterns of expression observed. The entire coding sequences of the pseudoobscura and melanogaster Gld genes are presented and shown to encode a 612-amino-acid pre-protein. The inferred amino acid sequences are 92% conserved between the two species. In general the intronic regions of Gld are unusually well conserved.

Amino Acid Sequence↗
PubMed2003

Cross-platform comparison and visualisation of gene expression data using co-inertia analysis.

BACKGROUND: Rapid development of DNA microarray technology has resulted in different laboratories adopting numerous different protocols and technological platforms, which has severely impacted on the comparability of array data. Current cross-platform comparison of microarray gene expression data are usually based on cross-referencing the annotation of each gene transcript represented on the arrays, extracting a list of genes common to all arrays and comparing expression data of this gene subset. Unfortunately, filtering of genes to a subset represented across all arrays often excludes many thousands of genes, because different subsets of genes from the genome are represented on different arrays. We wish to describe the application of a powerful yet simple method for cross-platform comparison of gene expression data. Co-inertia analysis (CIA) is a multivariate method that identifies trends or co-relationships in multiple datasets which contain the same samples. CIA simultaneously finds ordinations (dimension reduction diagrams) from the datasets that are most similar. It does this by finding successive axes from the two datasets with maximum covariance. CIA can be applied to datasets where the number of variables (genes) far exceeds the number of samples (arrays) such is the case with microarray analyses. RESULTS: We illustrate the power of CIA for cross-platform analysis of gene expression data by using it to identify the main common relationships in expression profiles on a panel of 60 tumour cell lines from the National Cancer Institute (NCI) which have been subjected to microarray studies using both Affymetrix and spotted cDNA array technology. The co-ordinates of the CIA projections of the cell lines from each dataset are graphed in a bi-plot and are connected by a line, the length of which indicates the divergence between the two datasets. Thus, CIA provides graphical representation of consensus and divergence between the gene expression profiles from different microarray platforms. Secondly, the genes that define the main trends in the analysis can be easily identified. CONCLUSIONS: CIA is a robust, efficient approach to coupling of gene expression datasets. CIA provides simple graphical representations of the results making it a particularly attractive method for the identification of relationships between large datasets.

Breast Neoplasms↗
PubMed1998

Modulation of angiogenesis by human glioma xenograft models that differentially express vascular endothelial growth factor.

To evaluate the potential actions of vascular endothelial growth factor (VEGF) on capillary permeability and drug transport, tumorigenic human glioma cell lines were developed that expressed different levels of VEGF. Three human glioma cell lines (i.e. U373, SF126, SF188) were screened for VEGF under normoxic and hypoxic (i.e. induced by CoCl2) conditions by Western blot analysis. Subsequent to these results, sense and antisense VEGF164 cDNA transfections were conducted. It was found that parental SF188 (SF188/V-) and SF188/V+ (sense transfected) cells could serve as an appropriate in vivo model based on their divergent levels of VEGF expression. Media derived from SF188/V+ cells stimulated endothelial cell growth by 30-60%, and enhanced endothelial cell clonogenicity by 5-10-fold compared to SF188/V- or empty vector transfected cells. Nude rats implanted with either SF188/V- or SF188/V+ cells subcutaneously and intracerebrally formed tumors, with those derived from SF188/V+ cells growing at a faster rate. Immunohistochemistry analysis indicated that the expression of VEGF and number of capillaries (factor VIII assay) were approximately 3-fold greater in SF188/V+ tumors compared to SF188/V- tumors. Pharmacological assays, such as measurements of cytotoxicity and DNA adducts, in SF188/V- and SF188/V+ cells treated with carmustine or temozolomide were similar. Therefore, other than differences in VEGF expression and growth in vivo, SF188/V- and SF188/V+ cells possess a similar phenotype, and can serve as models to evaluate the influence of VEGF on drug transport.

Animals↗
PubMed1993

Concerted circadian oscillations in transcript levels of nineteen Lha/b (cab) genes in Lycopersicon esculentum (tomato).

Steady-state mRNA levels of nineteen members of the Lha/b (cab) gene family of Lycopersicon esculentum, encoding nine different types of light-harvesting complex (LHC) polypeptides, were determined by primer extension analysis. Each Lha/b gene is expressed and individual mRNAs accumulate to distinct levels. The relative contribution of each Lha/b mRNA to the total Lha/b mRNA levels is very similar in different green organs (leaves, stems, fruits, sepals) and after light treatment of etiolated seedlings. Detailed analysis of Lha/b mRNA accumulation in leaves under light/dark conditions, continuous darkness and continuous light revealed diurnal and circadian oscillations of Lha/b mRNAs for all genes. Only minor instances of divergence from a general expression pattern are apparent. Together these results indicate a concerted expression of all genes, suggesting that similar or identical molecular mechanisms and signal transduction chain control the expression of all Lha/b genes.

Base Sequence↗
PubMed2006

Biologic pathways associated with relapse in childhood acute lymphoblastic leukemia: a Children's Oncology Group study.

Outcome for children with childhood acute lymphoblastic leukemia (ALL) who relapse is poor. To gain insight into the mechanisms of relapse, we analyzed gene-expression profiles in 35 matched diagnosis/relapse pairs as well as 60 uniformly treated children at relapse using the Affymetrix platform. Matched-pair analyses revealed significant differences in the expression of genes involved in cell-cycle regulation, DNA repair, and apoptosis between diagnostic and early-relapse samples. Many of these pathways have been implicated in tumorigenesis previously and are attractive targets for intervention strategies. In contrast, no common pattern of changes was observed among late-relapse pairs. Early-relapse samples were more likely to be similar to their respective diagnostic sample while we noted greater divergence in gene-expression patterns among late-relapse pairs. Comparison of expression profiles of early- versus late-relapse samples indicated that early-relapse clones were characterized by overexpression of biologic pathways associated with cell-cycle regulation. These results suggest that early-relapse results from the emergence of a related clone, characterized by the up-regulation of genes mediating cell proliferation. In contrast, late relapse appears to be mediated by diverse pathways.

Apoptosis↗
PubMed2003

Medulloblastoma tumorigenesis diverges from cerebellar granule cell differentiation in patched heterozygous mice.

Medulloblastoma is a cerebellar tumor that can arise through aberrant activation of Sonic hedgehog (Shh) signaling, which normally regulates cerebellar granule cell proliferation. Mutations of the Shh receptor PATCHED (PTCH) are associated with medulloblastomas, which have not been found to have loss of PTCH heterozygosity. We address whether patched (Ptc) heterozygosity fundamentally alters granule cell differentiation and contributes to tumorigenesis by increasing proliferation and/or decreasing apoptosis in Ptc+/- mice. Our data show that postnatal Ptc+/- mouse granule cell precursor growth is not globally altered. However, many older Ptc+/- mice display abnormal cerebellar regions containing persistently proliferating granule cell precursors. Since fewer Ptc+/- mice form medulloblastomas, these granule cell rests represent a developmentally disrupted, but uncommitted stage of tumorigenesis. Although Ptc+/- mouse medulloblastomas express neurodevelopmental genes, they diverge from granule cell differentiation in their discordant coexpression of postmitotic markers despite their ongoing growth. Like human medulloblastomas, mouse tumors with reduced levels of the neurotrophin-3 receptor, trkC/Ntrk3, display decreased apoptosis in vivo, illustrating the role of TrkC in regulating tumor cell survival. These results indicate that Ptc heterozygosity contributes to tumorigenesis by predisposing a subset of granule cell precursors to the formation of proliferative rests and subsequent dysregulation of developmental gene expression.

Animals↗
PubMed2002

Serial analysis of gene expression: technical considerations and applications to cardiovascular biology.

It has been 7 years since serial analysis of gene expression (SAGE) and microarray hybridization techniques were simultaneously introduced to allow the screening of thousands of expressed genes. Both techniques have stood up to the test of time as evidenced by their widespread use, and both have been used for studying cardiovascular diseases. SAGE has been used more extensively to study cancer cells, but it has also been used to examine gene expression in systems as divergent as rice seedlings, yeast, and Caenorhabditis elegans. In this review, a summary of the advances in SAGE technology and its unique attributes and potential applications to the cardiovascular system will be presented.

Cardiology↗
PubMed2000

Cortical and subcortical contributions to activity-dependent plasticity in primate somatosensory cortex.

After manipulations of the periphery that reduce or enhance input to the somatosensory cortex, affected parts of the body representation will contract or expand, often over many millimeters. Various mechanisms, including divergence of preexisting connections, expression of latent synapses, and sprouting of new synapses, have been proposed to explain such phenomena, which probably underlie altered sensory experiences associated with limb amputation and peripheral nerve injury in humans. Putative cortical mechanisms have received the greatest emphasis but there is increasing evidence for substantial reorganization in subcortical structures, including the brainstem and thalamus, that may be of sufficient extent to account for or play a large part in representational plasticity in somatosensory cortex. Recent studies show that divergence of ascending connections is considerable and sufficient to ensure that small alterations in map topography at brainstem and thalamic levels will be amplified in the projection to the cortex. In the long term, slow, deafferentation-dependent transneuronal atrophy at brainstem, thalamic, and even cortical levels are operational in promoting reorganizational changes, and the extent to which surviving connections can maintain a map is a key to understanding differences between central and peripheral deafferentation.

Afferent Pathways↗
PubMed1990

Pseudomonas cepacia 2,2-dialkylglycine decarboxylase. Sequence and expression in Escherichia coli of structural and repressor genes.

A 3969-base pair PstI-PstI fragment of Pseudomonas cepacia DNA containing the gene for the pyridoxal 5'-phosphate dependent 2,2-dialkylglycine decarboxylase (pyruvate) (EC 4.1.1.64) was cloned in Escherichia coli. The insert was sequenced by the dideoxy method using nested deletions from both ends, revealing a central 1302-base pair region that codes for the decarboxylase subunit. The recombinant enzyme was expressed in E. coli, purified to homogeneity, and sequenced at the amino terminus. Also, a cofactor-labeled active site peptide was sequenced. The carboxyl terminus of the deduced amino acid sequence is homologous with the carboxyl terminus of mammalian ornithine aminotransferase; the active site sequence is similar to the active site sequences of several other aminotransferases. No homologies with known decarboxylase sequences could be found. Expression of the decarboxylase gene is negatively controlled by a 687-nucleotide sequence upstream of and diverging from the structural gene. Expression is induced by S-isovaline, 2-methylalanine, and D-2-aminobutanoic acid, but not by glycine, D- or L-alanine, L-2-aminobutanoic acid, R-isovaline, or other alkyl amino acids.

Amino Acid Sequence↗
PubMed2001

The dystrophin / utrophin homologues in Drosophila and in sea urchin.

The gene which is defective in Duchenne muscular dystrophy (DMD) is the largest known gene containing at least 79 introns, some of which are extremely large. The product of the gene in muscle, dystrophin, is a 427 kDa protein. The same gene encodes at least two additional non-muscle full length dystrophin isoforms transcribed from different promoters located in the 5'-end region of the gene, and four smaller proteins transcribed from internal promoters located further downstream, and lack important domains of dystrophin. Several other genes, encoding evolutionarily related proteins, have been identified. To study the evolution of the DMD gene and the significance of its various products, we have searched for genes encoding dystrophin-like proteins in sea urchin and in Drosophila. We previously reported on the characterization of a sea urchin gene encoding a protein which is an evolutionary homologue of Dp116, one of the small products of the mammalian DMD gene, and on the partial sequencing of a large product of the same gene. Here we describe the full-length product which shows strong structural similarity and sequence identity to human dystrophin and utrophin. We also describe a Drosophila gene closely related to the human dystrophin gene. Like the human gene, the Drosophila gene encodes at least three isoforms of full length dystrophin-like proteins (dmDLP1, dmDLP2 and dmDLP3,), regulated by different promoters located at the 5' end of the gene, and a smaller product regulated by an internal promoter (dmDp186). As in mammals, dmDp186 and the dmDLPs share the same C-terminal and cysteine-rich domains which are very similar to the corresponding domains in human dystrophin and utrophin. In addition, dmDp186 contains four of the spectrin-like repeats of the dmDLPs and a unique N-terminal region of 512 amino acids encoded by a single exon. The full length products and the small product have distinct patterns of expression. Thus, the complex structure of the dystrophin gene, encoding several large dystrophin-like isoforms and smaller truncated products with different patterns of expression, existed before the divergence between the protostomes and deuterostomes. The conservation of this gene structure in such distantly related organisms, points to important distinct functions of the multiple products.

Alternative Splicing↗