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At least 199 records · Page 11Linked to original sources

PubMed1996

p21/WAF1 cyclin-kinase inhibitor expression in non-Hodgkin's lymphomas: a potential marker of p53 tumor-suppressor gene function.

p21WAF1 (wild-type p53-activated fragment 1) is involved in the control of mammalian cell cycle through the binding and inhibition of cyclin-dependent kinases (Cdk). Because the product of WAF1 gene is a potent downstream effector of the p53 tumor-suppressor gene function, its pattern of cellular expression might correlate with nuclear accumulation of p53-encoded protein and/or p53 gene mutations occurring in malignant lymphomas. To investigate this issue, we analyzed immunohistochemically the expression of p53 and p21WAF1 proteins in tissue involved by non-Hodgkin's lymphomas (NHLs;253 cases) of various histologic types. In a proportion of them (80 cases), we also investigated the possible presence of p53 gene mutations using single-strand conformation polymorphism analysis and direct DNA sequencing. The absence of both p21WAF1 and p53 proteins was observed in 147 of 217 cases (67.7%) among CD30-NHL and in only 8 of 36 (22.2%) CD30+cases, which were mostly anaplastic large-cell lymphomas. A consistent number (> 10%) of p21WAF1-expressing cells was shown in 48 of 253 (18.9%) NHL cases, with a higher incidence in CD30+cases (25/36 [69.4%]), which mostly (21/36) coexpressed p53. These latter cases were characterized by a germline configuration of the p53 gene. In 50 of 253 NHL samples (19.7%), 47 of which (21.6%) belong to the CD30-group, neoplastic cells were p53+/p21-. In all of these cases, the p53+cells accounted for more than 50% of neoplastic cells, up to 100%. Point mutations of p53 gene were solely observed in all investigated cases with this latter phenotype. Our findings strongly suggest that the combined immunohistochemical evaluation of p53 and p21WAF1 is a valuable means of assessing the functional status of the p53 tumor-suppressor gene product in NHL with potential application in the monitorage and prognostication of individual cases.

Biomarkers↗

PubMed1993

Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila.

The origin of new genes includes both the initial molecular events and subsequent population dynamics. A processed Drosophila alcohol dehydrogenase (Adh) gene, previously thought to be a pseudogene, provided an opportunity to examine the two phases of the origin of a new gene. The sequence of the processed Adh messenger RNA became part of a new functional gene by capturing several upstream exons and introns of an unrelated gene. This novel chimeric gene, jingwei, differs from its parent Adh gene in both its pattern of expression and rate of molecular evolution. Natural selection participated in the origin and subsequent evolution of this gene.

Alcohol Dehydrogenase↗

PubMed1997

Muscles in the Drosophila second thoracic segment are patterned independently of autonomous homeotic gene function.

BACKGROUND: In Drosophila, segment-specific muscle pattern is thought to be determined by the autonomous function of homeotic selector genes in the mesoderm in combination with inductive cues from the developing epidermis and nervous system. Here, we have examined the roles of homeotic genes in the patterning of the somatic muscles of the thoracic segments of Drosophila. RESULTS: We determined the expression patterns of homeoproteins in the mesoderm of the thoracic segments during embryonic and adult development. We found that, unlike the mesoderm of the first and third thoracic segments which express Sex combs reduced and Antennapedia (Antp), respectively, the mesoderm of the second thoracic segment does not express any known homeotic selector gene of the Antp or bithorax complex. In animals homozygous for Antp null mutations, the muscles of the second thoracic segment were affected in the embryo, probably as an indirect consequence of its requirement in the ectoderm. Animals that specifically lacked Antp function in the mesoderm, but expressed the gene in the epidermis, developed with a normal muscle pattern in the second thoracic segment. Furthermore, specific ectopic expression of Antp and other homeotic selector genes in the mesoderm of the second thoracic segment respecified its muscle pattern, indicating that these genes are not required autonomously during muscle development in this segment. Finally, we showed that Antp continues to be expressed in the mesoderm of the homeotically transformed third thoracic segment in the 'four-winged fly', and suggest that this is a likely reason for the failure of flight muscle development in the transformed segment. CONCLUSIONS: We present a model for muscle development in the second thoracic segment whereby mesodermal properties are specified entirely by induction, in contrast to muscle development in other segments, where autonomous function for homeotic selector genes is also required.

Animals↗

PubMed1998

Molecular evolution of the Cecropin multigene family in Drosophila. functional genes vs. pseudogenes.

Approximately 4 kb of the Cecropin cluster region have been sequenced in nine lines of Drosophila melanogaster and one line of the sibling species D. simulans, D. mauritiana, and D. sechellia. This region includes three functional genes (CecA1, CecA2, and CecB), which are involved in the insect immune response, and two pseudogenes (CecPsi1 and CecPsi2). The level of silent polymorphism in the three Cec genes is rather high (0.028), and there is no excess of nonsynonymous polymorphism. There is no evidence of gene conversion in the history of these genes. The interspecific comparison has revealed that in the three species of the simulans cluster the CecA2 gene is partially deleted and has therefore lost its function and become a pseudogene; in each of the species, subsequent deletions have accumulated. Divergence estimates indicate that the CecPsi1 and CecPsi2 pseudogenes are highly diverged, both between themselves and relative to the other three Cec genes. However, both CecPsi1 and CecPsi2 have conserved transcriptional signals and splice sites, and they present an open reading frame; also, correctly spliced transcripts have been detected for both CecPsi1 and CecPsi2. The data support that these genes are either active genes with some null alleles or young pseudogenes.

Amino Acid Sequence↗

PubMed1981

Cloning of a functional gene responsible for the expression of a cell surface antigen correlated with human chronic lymphocytic leukemia.

A cell--cell hybrid of a Chinese hamster ovary (CHO) cell line and human peripheral blood lymphoblasts from a patient with B-cell chronic lymphocytic leukemia produces a surface antigen detectable by a monoclonal antibody. This surface antigen can be detected at significant levels on a fraction of chronic lymphocytic leukemia cells, but not on normal human lymphocytes from peripheral blood or bone marrow. Two different clones capable of transforming mouse cells to produce the surface antigen were isolated from a gene library of the hybrid cell by identification of small portions of the library containing functional genes, followed by detection of clones with human-specific reiterated sequences. Both clones also contain CHO-specific reiterated sequences and are therefore human--CHO recombinants. From the frequency of antigen-producing clones in the library, we estimate that they were present in the hybrid cell genome at a copy number of 100 to 1000.

Animals↗

PubMed1990

[Methods of studying genes and gene function].

In several fields, such as immunology, biochemistry, and structural biology, but particularly in molecular genetics, modern methods enable genes and their protein products to be analysed and described. The tools are now available to study any physiological process or disease at the molecular level. As a result, genetic diseases and viral infections can be better identified and understood. Basic cellular and physiological mechanisms are beginning to be elucidated, the disturbance of which is a factor involved in cancerogenesis, for instance, or the development of hypercholesterolaemia. The article is intended as a brief review of current methods of studying genes and their function. The isolation and characterisation of genes by means of recombinant DNA technology, the identification of defective genes, and the analysis of gene function, both in vitro and in vivo are presented.

Chromosome Mapping↗

PubMed1997

The evolution of Msx gene function: expression and regulation of a sea urchin Msx class homeobox gene.

Msx- class homeobox genes, characterized by a distinct and highly conserved homeodomain, have been identified in a wide variety of metazoans from vertebrates to coelenterates. Although there is evidence that they participate in inductive tissue interactions that underlie vertebrate organogenesis, including those that pattern the neural crest, there is little information about their function in simple deuterostomes. Both to learn more about the ancient function of Msx genes, and to shed light on the evolution of developmental mechanisms within the lineage that gave rise to vertebrates, we have isolated and characterized Msx genes from ascidians and echinoderms. Here we describe the sequence and expression of a sea urchin (Strongylocentrotus purpouratus) Msx gene whose homeodomain is very similar to that of vertebrate Msx2. This gene, designated SpMsx, is first expressed in blastula stage embryos, apparently in a non-localized manner. Subsequently, during the early phases of gastrulation, SpMsx transcripts are expressed intensely in the invaginating archenteron and secondary mesenchyme, and at reduced levels in the ectoderm. In the latter part of gastrulation, SpMsx transcripts are concentrated in the oral ectoderm and gut, and continue to be expressed at those sites through the remainder of embryonic development. That vertebrate Msx genes are regulated by inductive tissue interactions and growth factors suggested to us that the restriction of SpMsx gene expression to the oral ectoderm and derivatives of the vegetal plate might similarly be regulated by the series of signaling events that pattern these embryonic territories. As a first test of this hypothesis, we examined the influence of exogastrulation and cell-dissociation on SpMsx gene expression. In experimentally-induced exogastrulae, SpMsx transcripts were distributed normally in the oral ectoderm, evaginated gut, and secondary mesenchyme. However, when embryos were dissociated into their component cells, SpMsx transcripts failed to accumulate. These data show that the localization of SpMsx transcripts in gastrulae does not depend on interactions between germ layers, yet the activation and maintenance of SpMsx expression does require cell-cell or cell-matrix interactions.

Animals↗

PubMed1980

DNA methylation and gene function.

In most higher organisms, DNA is modified after synthesis by the enzymatic conversion of many cytosine residues to 5-methylcytosine. For several years, control of gene activity by DNA methylation has been recognized as a logically attractive possibility, but experimental support has proved elusive. However, there is now reason to believe, from recent studies, that DNA methylation is a key element in the hierarchy of control mechanisms that govern vertebrate gene function and differentiation.

Animals↗

PubMed2003

Use of RNA interference to investigate gene function in the human filarial nematode parasite Brugia malayi.

We describe the successful use of the reverse genetic technique RNA interference (RNAi) to investigate gene function in the human filarial nematode parasite Brugia malayi. We used fluorescently labelled double stranded RNA (dsRNA) to demonstrate that 300 bp molecules are able to enter adult females in culture while they remain excluded from microfilariae (mf). We have developed an optimised microvolume culture system to allow the exposure of parasites to high concentrations of dsRNA for extended periods. Culturing of adult female parasites in this system for 24h does not significantly reduce parasite lifespan or mf release in culture. Three B. malayi genes, beta-tubulin (Bm-tub-1), RNA polymerase II large subunit (Bm-ama-1) and B. malayi mf sheath protein 1/mf22 (Bm-shp-1) were targeted by soaking adult female B. malayi in dsRNA complementary to these transcripts in the optimised culture system. Targeting of the two housekeeping genes Bm-tub-1 and Bm-ama-1 led to a reduction in the levels of their transcripts, as assessed by reverse transcriptase coupled PCR (RT-PCR), and resulted in parasite death in culture. In contrast, targeting of the Bm-shp-1 gene was not lethal to adult females in culture. A marked reduction in mf release was observed for shp-1 RNAi parasites compared to controls and in addition 50% of mf released did not have fully elongated sheaths. This "short" phenotype correlated with the loss of the stockpiled shp-1 transcript from developing mf in treated adult female gonads. From these data we conclude that RNAi may be a useful method for assessment of drug target potential of genes identified in filarial gene discovery projects.

Alternative Splicing↗

PubMed1999

Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis.

We describe a genetic mosaic system in Drosophila, in which a dominant repressor of a cell marker is placed in trans to a mutant gene of interest. Mitotic recombination events between homologous chromosomes generate homozygous mutant cells, which are exclusively labeled due to loss of the repressor. Using this system, we are able to visualize axonal projections and dendritic elaboration in large neuroblast clones and single neuron clones with a membrane-targeted GFP marker. This new method allows for the study of gene functions in neuroblast proliferation, axon guidance, and dendritic elaboration in the complex central nervous system. As an example, we show that the short stop gene is required in mushroom body neurons for the extension and guidance of their axons.

Animals↗

PubMed1986

An estrogen-responsive element derived from the 5' flanking region of the Xenopus vitellogenin A2 gene functions in transfected human cells.

In the human breast cancer cell line MCF-7, we observe estrogen induction of the stable transfected Xenopus vitellogenin A2 gene. An estrogen-responsive element (ERE) could be defined by using a vitellogenin-chloramphenicol acetyltransferase hybrid gene in transient transfection experiments. The ERE is located in the 5' flanking region and is able to confer estrogen inducibility to the thymidine kinase gene promoter. By 5' and 3' deletions we have determined a 35 bp sequence sufficient for high stimulation by estradiol. Even 18 bp give a small estrogen response. The 35 bp ERE contains the palindromic sequence 5'GGTCACAGTGACC-3' as an essential element. The fact that the ERE of a frog gene functions in human cells demonstrates that signals and factors involved in the control have been conserved during evolution.

Acetyltransferases↗

PubMed2002

In silico approaches to microarray-based disease classification and gene function discovery.

The automated analysis of transcriptional profiling data promises a wealth of information that may be used to develop a more complete understanding of gene function and interactions. Moreover, it may improve the effectiveness of complex diagnostic tasks. This article discusses important data mining and management techniques to analyse genome-wide expression data. It reviews some of the major discovery goals, methods and applications in a number of biomedical domains. Finally, this paper highlights key problems that need to be approached by a new generation of computational solutions.

Algorithms↗

PubMed2002

Analysis of gene function in the zebrafish retina.

Mutagenesis screens in zebrafish have uncovered several hundred mutant alleles affecting the development of the retina and established the zebrafish as one of the leading models of vertebrate eye development. In addition to forward genetic mutagenesis approaches, gene function in the zebrafish embryo is being studied using several reverse genetic techniques. Some of these rely on the overexpression of a gene product, others take advantage of antisense oligonucleotides to block function of selected loci. Here we describe these methods in the context of the developing eye.

Animals↗

PubMed2003

Adenovirus-mediated functional gene transfer into parathyroid cells in vivo and in vitro.

Chronic renal failure patients usually develop secondary hyperparathyroidism and, as the disease progresses, there is a decrease in the number of vitamin D and calcium-sensing receptors (CaRs) in the parathyroid glands. Parathyroid cell function can be controlled if a functional gene is transferred into these cells using an adenovirus vector. Vitamin D or CaR genes transferred by the infected adenovirus vector induced a reduction in parathyroid hormone secretion. These results suggest that adenovirus-mediated gene transfer is a useful technique for control of parathyroid cell function.

Adenoviridae↗

PubMed2000

Chemical genetics: ligand-based discovery of gene function.

Chemical genetics is the study of gene-product function in a cellular or organismal context using exogenous ligands. In this approach, small molecules that bind directly to proteins are used to alter protein function, enabling a kinetic analysis of the in vivo consequences of these changes. Recent advances have strongly enhanced the power of exogenous ligands such that they can resemble genetic mutations in terms of their general applicability and target specificity. The growing sophistication of this approach raises the possibility of its application to any biological process.

Animals↗

PubMed2003

Screening for functional genes related to a novel gene, AngRem104, in human mesangial cells by cDNA microarray.

AngRem104 is a novel gene recently identified in human mesangial cells induced by angiotensin II. cDNA microarray was performed to screen the functional genes related to AngRem104. Thirty-one genes were up-regulated while 2 genes were down-regulated. Of all the up-regulated genes, fibronectin, one of the major extracellular matrixes, was up-regulated with over-expression of AngRem104.

Fibronectins↗

PubMed1983

Physical location of a herpes simplex virus type-1 gene function(s) specifically associated with a 10 million-fold increase in HSV neurovirulence.

In this paper we present a technique developed to physically locate the HSV-1 gene(s) which restore neurovirulence to a non-neurovirulent HSV intertypic recombinant described in the preceding report. In brief, tissue culture cells are co-transfected with unit length RE6 DNA and restriction endonuclease fragmented HSV-1 (strain 17 Syn+) DNA. In this way, random recombinations between RE6 and 17 Syn+ are produced. An in vivo enrichment in mouse brains is then employed to select recombinants which have incorporated the HSV-1 gene(s) associated with neurovirulence. In each of five cases where neurovirulent recombinants were isolated by this procedure, restriction enzyme and Southern DNA transfer analysis revealed that HSV-1 information from 0.71 to 0.83 map units had been incorporated into the RE6 genome. Confirmation of the role of this portion of the genome for HSV neurovirulence was obtained by similar cotransfection and in vivo rescue experiments performed with an electrophoretically purified HSV-1 DNA fragment which encompasses this region. Subsequent genome structure analysis of neurovirulent recombinants generated by this procedure revealed that only type-1 information from 0.71 to 0.83 map units had been incorporated into RE6. Thus an HSV-1 gene function(s) which resides in this region of the viral DNA is associated with a 10 million-fold increase in the neurovirulence of the virus. Potential applications of this in vivo selection technique are discussed.

Animals↗

PubMed1999

The maize tha4 gene functions in sec-independent protein transport in chloroplasts and is related to hcf106, tatA, and tatB.

Proteins are translocated across the chloroplast thylakoid membrane by a variety of mechanisms. Some proteins engage a translocation machinery that is derived from the bacterial Sec export system and require an interaction with a chloroplast-localized SecA homologue. Other proteins engage a machinery that is SecA-independent, but requires a transmembrane pH gradient. Recently, a counterpart to this Delta pH mechanism was discovered in bacteria. Genetic studies revealed that one maize protein involved in this mechanism, HCF106, is related in both structure and function to the bacterial tatA and tatB gene products. We describe here the mutant phenotype and molecular cloning of a second maize gene that functions in the Delta pH mechanism. This gene, thylakoid assembly 4 (tha4), is required specifically for the translocation of proteins that engage the Delta pH pathway. The sequence of the tha4 gene product resembles those of the maize hcf106 gene and the bacterial tatA and tatB genes. Sequence comparisons suggest that tha4 more closely resembles tatA, and hcf106 more closely resembles tatB. These findings support the notion that this sec-independent translocation mechanism has been highly conserved during the evolution of eucaryotic organelles from bacterial endosymbionts.

Amino Acid Sequence↗