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Results for “gene expression variability”

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At least 127 records · Page 7Linked to original sources
PubMed2001

Deciphering Campylobacter jejuni cell surface interactions from the genome sequence.

The completion of the Campylobacter jejuni genome sequence is a landmark in Campylobacter research. Discoveries directly arising from these data include the identification of a capsular polysaccharide, extensive capacity for phase variable gene expression and lipo-oligosaccharide structural phase variation. The recent identification of a unique system of general protein glycosylation in C. jejuni, a C. jejuni protein that is translocated into eukaryotic cells, and plasmid-encoded components of a putative type IV secretion system are likely to be significant in terms of the host-pathogen interaction.

Antigenic Variation↗
PubMedDate not supplied

Pharmacogenetics and pharmacogenomics: origin, status, and the hope for personalized medicine.

Pharmacogenetics arose with studies of single genes, which had major effects on the action of particular drugs. It turned into pharmacogenomics through realization that the controls of most drug responses are multifactorial. Then, variable gene expression posed new problems, for example what do drugs do to genes, or how useful is any genetic pretesting of a person? A common disease may be caused by different groups of genes in different people, who therefore require different drugs for treatment. Personalized medicine is currently represented by a physician's attention to a patients age, sex, or ethnic background, that is groups showing smaller genetic variation than is typical for general humanity. Occasionally, there is also the use of single-gene pretesting of a patient before drug administration. Over time, improvements in multigenic testing promise to increase the role of personalized medicine. However, the many pharmacogenomic complexities, and particularly time-dependent changes of gene expression, will never allow personalized medicine to become an error-free entity.

Biomarkers↗
PubMed2000

Embryonic, fetal, and neonatal tongue myoblasts exhibit molecular heterogeneity in vitro.

Variable gene expression patterns have been shown to exist between embryonic, fetal, and neonatal lineages of limb skeletal myoblasts in vitro and in vivo. In this study, we examined the molecular phenotype of embryonic, fetal, and neonatal tongue myoblasts in primary culture for comparison with in vivo developmental tongue myoblasts. Myogenic regulatory factor (MRF) and myosin heavy chain (MHC) gene expression were determined in culture during both growth and differentiation conditions by PCR, immunoblotting, and immunohistochemistry. Unlike their in vivo tongue myoblast equivalents, developmental tongue myoblast cultures featured the expression of MyoD when kept in growth conditions. Differentiation conditions in vitro induced myogenic tongue lineages to maintain characteristics of their in vivo morphologic and contractile gene phenotype. Both in vivo and in vitro, embryonic tongue lineages predominantly expressed MHC-embryonic isoforms, while fetal and neonatal tongue lineages predominantly expressed fast and perinatal isoforms of contractile genes. A notable difference from the in vivo condition that was observed in differentiated tongue myotubes in vitro was the presence of the MHC-slow protein. It was previously demonstrated that MHC-slow protein was undetectable during the in vivo development of the tongue musculature despite the abundance of slow isoform transcripts. The present characterization of primary tongue myogenic cultures indicates that murine myoblast heterogeneity exists primarily between developmental lineages at the level of contractile gene expression. Outside their native surroundings, developmental myogenic tongue populations are unable to recapitulate the determination and differentiation molecular profiles that occur in vivo.

Animals↗
PubMed2004

Genetic and epigenetic aspects of cloning and potential effects on offspring of cloned mammals.

Although the biological mechanisms by which host cytoplasm and donor nuclei interact to produce a developmentally competent reconstructed embryo remain largely unknown, some advances have been made to our understanding of the genetic and epigenetic factors involved in the of reprogramming of the donor nucleus. Genetic alterations, which comprise changes to the genetic information in both the nuclear and cytoplasm compartments, are passed on to subsequent generations at fertilization and are a potential source of variation among cloned animals and their offspring. Apart from the major chromosomal anomalies found in developmentally arrested embryos and fetuses, less detrimental rearrangements and/or mutations are likely to go unnoticed in most donor cell karyotypes, suggesting that such problems could lead to inheritable anomalies among clones and their offspring. Mitochondrial DNA is also relevant to cloning because most animals inherit most or all of their mitochondria from the host oocyte. Epigenetic alterations to the DNA or to the histone packaging proteins are independent of gene sequences. Aberrant epigenetic events may lead to variable gene expression or mitosis and consequent effects on development and phenotype. Although much of the epigenetic marking is reset during embryogenesis and development, the impact of epimutations on progeny remains unexplored.

Animals↗
PubMed2006

Idiopathic pulmonary fibrosis: is it a familial disease?

PURPOSE OF REVIEW: Idiopathic pulmonary fibrosis is a progressively fatal interstitial lung disease associated with pathological findings of usual interstitial pneumonia. Its pathogenesis is unknown, and there are no proven effective therapies. Familial cases account for 0.5-2% of idiopathic pulmonary fibrosis. Familial idiopathic pulmonary fibrosis occurs as an autosomal dominant disorder with variable penetrance. The clinical characteristics of familial idiopathic pulmonary fibrosis are indistinguishable from sporadic idiopathic pulmonary fibrosis. These marked similarities support the hypothesis there may, in part, be a genetic basis for idiopathic pulmonary fibrosis. RECENT FINDINGS: Many investigations have evaluated genetic polymorphisms and idiopathic pulmonary fibrosis. Candidate genes include cytokines and surfactant protein genes. To date, no gene has been consistently identified to be associated with idiopathic pulmonary fibrosis. Recent studies in familial idiopathic pulmonary fibrosis have demonstrated a strong association with surfactant protein C gene mutations in one large kindred. SUMMARY: The pathogenesis of both idiopathic pulmonary fibrosis and familial idiopathic pulmonary fibrosis remains unclear. A consistent genetic basis has not yet been demonstrated in all cases. Other factors, including variable gene expression, co-carriage of other modifying genes and environmental stimuli, particularly cigarette smoke, significantly contribute to disease expression.

Humans↗
PubMed1996

A case of duplication of 13q32-->qter and deletion of 18p11.32-->pter with mild phenotype: Patau syndrome and duplications of 13q revisited.

A mild clinical phenotype is described in a patient with duplication of 13q32-->qter and a small deletion of 18p11.32-->pter. The 8 year old white male presented with psychomotor retardation, tethered cord, soft, fleshy ears, and normal facial features except for thin lips. The karyotype was found to be 46, XY, der(18)t(13;18) (q32;p11.32) pat confirmed by fluorescence in situ hybridisation (FISH). A review of earlier studies showed that features of trisomy 13 are found in cases of duplication of bands 13q14 to qter. None of the cardinal features of trisomy 13 was seen in this patient. The absence of polydactyly, hernias, urogenital abnormalities, and haemangiomas contrast this condition with both trisomy 13 and duplication of 13q14-22-->qter. Possible explanations for lack of Patau syndrome in this patient could include restriction of the critical region for Patau syndrome to duplication 13q14-->13q32 with variable expression, gene interactions, or interchromosomal effects.

Child↗
PubMed2001

Multiple intracranial aneurysms associated with branchio-oto-dysplasia.

Branchio-oto-dysplasia is characterized by abnormalities of embryonic branchial arch system and deafness inherited as autosomal dominant with variable gene expression. We present a rare case of multiple intracranial aneurysms associated with branchio-oto-dysplasia. A 40-yr-old man with severe headache presented as spontaneous subarachnoid hemorrhage on brain computed tomographic scan. The patient also manifested clinical features of branchio-oto-dysplasia and right hemifacial hypoplasia. Carotid angiogram confirmed an aneurysm in the anterior communicating artery. Intraoperative findings demonstrated multiple aneurysms in the anterior communicating artery and in the left posterior communicating artery, which were clipped successfully. Postoperative course was uneventful. This condition has not been reported previously. We also reviewed literatures to discuss whether the intracranial aneurysm was as a coincidental finding or a part of this malformation.

Adult↗
PubMed1988

Influence of flanking sequences on variability in expression levels of an introduced gene in transgenic tobacco plants.

The petunia rbcS gene SSU301 was introduced into tobacco using Agrobacterium tumefaciens-mediated transformation. The time at which rbcS expression was maximal after transfer of the tobacco plants to the greenhouse was determined. The expression level of the SSU301 gene varied up to 9 fold between individual tobacco plants which had been standardized physiologically as much as possible. The presence of adjacent pUC plasmid sequences did not affect the expression of the SSU301 gene. In an attempt to reduce the between-transformant variability in expression, the SSU301 gene was introduced into tobacco surrounded by 10kb of 5' and 13 kb of 3' DNA sequences which normally flank SSU301 in petunia. The longer flanking regions did not reduce the between-transformant variability of SSU301 gene expression.

Blotting, Northern↗
PubMed2006

Bayesian variable selection for gene expression modeling with regulatory motif binding sites in neuroinflammatory events.

Multiple transcription factors (TFs) coordinately control transcriptional regulation of genes in eukaryotes. Although numerous computational methods focus on the identification of individual TF-binding sites (TFBSs), very few consider the interdependence among these sites. In this article, we studied the relationship between TFBSs and microarray gene expression levels using both family-wise and memberspecific motifs, under various combination of regression models with Bayesian variable selection, as well as motif scoring and sharing conditions, in order to account for the coordination complexity of transcription regulation. We proposed a three-step approach to model the relationship. In the first step, we preprocessed microarray data and used p-values and expression ratios to preselect upregulated and downregulated genes. The second step aimed to identify and score individual TFBSs within DNA sequence of each gene. A method based on the degree of similarity and the number of TFBSs was employed to calculate the score of each TFBS in each gene sequence. In the last step, linear regression and probit regression were used to build a predictive model of gene expression outcomes using these TFBSs as predictors. Given a certain number of predictors to be used, a full search of all possible predictor sets is usually combinatorially prohibitive. Therefore, this article considered the Bayesian variable selection for prediction using either of the regression models. The Bayesian variable selection has been applied in the context of gene selection, missing value estimation, and regulatory motif identification. In our modeling, the regressor was approximated as a linear combination of the TFBSs and a Gibbs sampler was employed to find the strongest TFBSs. We applied these regression models with the Bayesian variable selection on spinal cord injury gene expression data set. These TFs demonstrated intricate regulatory roles either as a family or as individual members in neuroinflammatory events. Our analysis can be applied to create plausible hypotheses for combinatorial regulation by TFBSs and avoiding false-positive candidates in the modeling process at the same time. Such a systematic approach provides the possibility to dissect transcription regulation, from a more comprehensive perspective, through which phenotypical events at cellular and tissue levels are moved forward by molecular events at gene transcription and translation levels.

Amino Acid Motifs↗
PubMed2006

Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables.

A fundamental step in the analysis of gene expression and other high-dimensional genomic data is the calculation of the similarity or distance between pairs of individual samples in a study. If one has collected N total samples and assayed the expression level of G genes on those samples, then an N x N similarity matrix can be formed that reflects the correlation or similarity of the samples with respect to the expression values over the G genes. This matrix can then be examined for patterns via standard data reduction and cluster analysis techniques. We consider an alternative to conventional data reduction and cluster analyses of similarity matrices that is rooted in traditional linear models. This analysis method allows predictor variables collected on the samples to be related to variation in the pairwise similarity/distance values reflected in the matrix. The proposed multivariate method avoids the need for reducing the dimensions of a similarity matrix, can be used to assess relationships between the genes used to construct the matrix and additional information collected on the samples under study, and can be used to analyze individual genes or groups of genes identified in different ways. The technique can be used with any high-dimensional assay or data type and is ideally suited for testing subsets of genes defined by their participation in a biochemical pathway or other a priori grouping. We showcase the methodology using three published gene expression data sets.

Animals↗
PubMed1983

Relationship between multiple copies of a T. brucei variable surface glycoprotein gene whose expression is not controlled by duplication.

Unlike many other T. brucei variable surface glycoprotein (VSG) genes, the IITat 1.3 gene is not duplicated when it is expressed. Analysis of the multiple copies of this gene present in all IITaR 1 trypanosome clones by restriction enzyme mapping and sequencing shows that the expressed copy may have arisen by duplication and transposition to a telomeric site, as is observed for those VSG genes whose expression is linked to duplication. The existence of a mechanism selecting between a number of complete telomeric VSG gene copies for expression is implied by these results. Comparisons of the nontelomeric copies of the IITat 1.3 gene are consistent with involvement of gene duplication and mutational drift in the evolution of new VSG genes.

Animals↗
PubMed2000

Phenotypic heterogeneity of growth and psychometric intelligence in Prader-Willi syndrome: variable expression of a contiguous gene syndrome or parent-child resemblance?

Phenotypic variability in children with Prader-Willi syndrome (PWS) was investigated with respect to variable expression of the contiguous gene syndrome and trait variance. In a prospective study, parent/child resemblance of anthropometric and psychometric measures was analyzed in 22 children with PWS (11 females and 11 males; 18 deletions, 4 uniparental disomy (UPD)) and in a control group (88 females and 88 males). The average child-midparent Z-score difference for height in females was -1.9 and in males -0.9, head circumference -1.7 and -1.0, and body mass index (BMI) 2.3 and 2.7, respectively. Intellectual performance of females and males was, on average, -2.7 and -2.6 below maternal performance. Range and standard deviation were moderately increased for height and head circumference, doubled for BMI, and unchanged for IQ. Parent/child correlations for anthropometric and psychometric measurements in the study group did not significantly differ from those of the control group. Exceptions were higher correlations between mothers and daughters for height (P < 0.05) and BMI (P < 0.01), and lower correlations for head circumference between midparent values and daughters (P < 0.05) than in the control group. In conclusion, parent-child resemblance in growth and intellectual development among children with PWS was found to be comparable to that noted in the normal population, indicating a strong determination by trait variance. Children with PWS differed significantly with respect to a lower trait level and-with the exception of IQ-a larger variability. The latter may indicate a variable expression of the contiguous gene syndrome.

Adolescent↗
PubMed1991

T-cell receptor variable beta genes show differential expression in CD4 and CD8 T cells.

Studies in transgenic and inbred strains of mice have shown that the critical molecular interactions controlling positive selection involve major histocompatibility complex (MHC), T-cell receptor (TCR), and CD4 or CD8 coreceptor molecules. Correlations have been established between MHC gene products and the percentage of CD4 or CD8 T cells that express specific variable (V) beta-gene products as part of the alpha beta heterodimer. These studies have important implications regarding potential mechanisms of HLA-linked autoimmune diseases in humans. If similar interactions are required for positive selection in humans, one would predict that the TCR repertoire expressed by mature, peripheral blood CD4 and CD8 T cells would vary. To test this hypothesis the expression of specific TCR V beta-region genes by CD4 and CD8 T cells from healthy individuals was compared using both triple-color flow cytometry and polymerase chain reaction based experimental approaches. The results show that the TCR repertoire does vary as a function of CD4 and CD8 T-cell subsets. Among unrelated individuals certain V beta genes were consistently overrepresented in the CD4 population (V beta-5.1, -6.7a, and -18); some were skewed to the CD8 population (V beta-14) while others showed variable patterns (V beta-12 and -17). Deletion of entire V beta gene families was not observed suggesting that this is a rare event in humans. Attempts to correlate the expressed TCR repertoire in humans with HLA alleles will require consideration of these differences in expression as a function of subset.

Antibodies, Monoclonal↗
PubMed1992

Characteristics of murine monoclonal anti-CD4. Epitope recognition, idiotype expression, and variable region gene sequence.

We have characterized a series of mouse monoclonal anti-CD4 and describe both their CD4 epitope recognition and Id expression. We also determined the V region gene sequences of these antibodies in an attempt to correlate epitope recognition and Id expression with V region sequence. All of these preparations recognize epitopes that cluster around the HIV gp120 binding site on the human CD4 molecule. However, we observed differences in epitope recognition among the anti-CD4 preparations, based on either competitive inhibition assays or functional assays, such as syncytium inhibition. Analysis of Id specificities using a polyclonal anti-Id generated against anti-Leu 3a indicated that five of the seven monoclonal anti-CD4 expressed a shared Id. Based on V region gene sequences, the V region kappa-chain (V[kappa]) from each of the seven antibodies was encoded by the V[kappa]21 gene family and expressed the J[kappa]4 gene segment. Those preparations that expressed the shared Id with anti-Leu 3a have virtually identical V[kappa] sequences, with a high degree of homology in the CDR. The VH region gene sequences of six of the seven antibodies also shared overall homology and appeared to be encoded by the J558 VH gene family. The seventh anti-CD4 VH region is encoded for by the VHGAM gene family. The majority of these antibodies used JH3 gene segment, although the JH2 and JH4 gene segments were also represented. In addition, several of these antibodies share a common sequence organization within their V-D-J joining regions that appears to involve N and P sequences to generate unique D segments. Together, these data suggest that differences in epitope recognition among the monoclonal anti-CD4 may reflect sequence variability primarily within the CDR3 region of both V[kappa] and VH. The basis for the detection of a shared Id most likely reflects the high degree of homology within the V[kappa] region sequences. In addition, these data, which are based on a limited analysis, suggest the possible restricted use of V region germ-line gene families in the secondary antibody response of BALB/c mice to specific epitopes on the human CD4 molecule.

Amino Acid Sequence↗
PubMedDate not supplied

Nonrandom features of the human immunoglobulin variable region gene repertoire expressed in response to HIV-1.

Characterization of the immune response toward HIV is important for understanding the basic mechanisms of the disease and may give essential information for development of an anti-HIV vaccine. Paradoxically, although HIV infection is associated with a strong antibody response to structural and nonstructural HIV proteins, this immune response does not seem to halt disease progression. Both quantitative and qualitative B-cell abnormalities are associated with disease progression. The immunological abnormalities in HIV-1 infection include abnormal cytokine production and expansion of HIV-1-specific B-cell precursors that may reach 40%. There is also evidence that gp120 exerts a B-cell superantigen-like activity on human B-cells through binding to gene products of the third heavy-chain variable region family (VH3). This property of gp120 may induce abnormal mechanisms of selection of the antibody repertoire. It may also account for the apparent paucity of anti-gp120 antibodies expressing VH3 genes and for the polyclonal activation seen in the early stages of HIV infection. This expansion would reflect specific stimulation of VH3 B-cells, but not all B-cells. It would then be followed by a significant deletion of this B-cell subset. Finally, autoimmune phenomena have been described in HIV infection, and several hypotheses have been put forward to account for such associations. On the basis of the superantigen concept discussed above, one may suggest that gp120 may trigger B-cell subsets bearing receptors with specificities for self-components. This would explain the multiplicity of autoantibody specificities seen in this disease.

B-Lymphocytes↗
PubMed1985

Molecular analysis of T cell receptor (Ti) variable region (V) gene expression. Evidence that a single Ti beta V gene family can be used in formation of V domains on phenotypically and functionally diverse T cell populations.

We examine the rules governing Ti beta variable (V) gene segment usage in the formation of T cell antigen-MHC receptors in diverse regulatory and effector T lymphoid subpopulations. To this end, a single Ti beta V gene family and its products were analyzed. A monoclonal antibody, termed anti-Ti3A, which was shown to be reactive with an epitope encoded by members of the REX cell line Ti beta V gene family, and which was expressed on 2% of human T lymphocytes was used in selection of clones from unprimed peripheral T lymphocytes. Both T4+, as well as T8+ T cell clones with inducer, suppressor, and/or cytotoxic function were defined. Southern analysis, isoelectric focusing and two-dimensional peptide mapping indicated that individual members of the REX V gene family were linked to different Ti beta diversity and/or joining and constant region segments. Moreover, the Ti alpha chains of such clones were distinct. These results imply that Ti beta V gene usage is not restricted to any functionally or phenotypically defined T cell subsets, and there is presumably little, if any, restriction on the mechanisms that generate combinational, junctional or chain association-mediated diversity.

Antibodies, Monoclonal↗