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At least 1,783 records · Page 99Linked to original sources
PubMed1998

Serotonin receptor variants in disease: new therapeutic opportunities?

This review describes a novel genetic approach to the assessment of receptor function that is based on association studies of polymorphisms within human genes. The realization that variations within human genes may significantly affect gene function has led to increased use of this approach in recent years. Analysis of polymorphisms within the human 5-HT2A receptor is used as a specific example of the application of association genetics to elucidate gene function. The interaction of many neuroleptics and antidepressants with 5-HT2A receptors points up the potential importance of this receptor for understanding and treating neuropsychiatric disorders such as schizophrenia and depression.

Antipsychotic Agents↗
PubMed1994

Characterization of the complete genomic structure of the human versican gene and functional analysis of its promoter.

Versican is a modular proteoglycan involved in the control of cellular growth and differentiation. To understand versican gene regulation and transcriptional control, we have isolated genomic clones spanning the entire gene locus including 5'- and 3'-flanking sequences. Versican was encoded by 15 exons encompassing over 90 kilobase pairs of continuous DNA. The exon organization corresponded to the protein subdomains encoded by homologous proteins, with a remarkable conservation of exon size and intron phase. We discovered an additional exon just proximal to the glycosaminoglycan-binding region that was identical to a recently identified splice variant of versican (Dours-Zimmermann, M.T., and Zimmermann, D.R. (1994) J. Biol. Chem. 269, 32992-32998). The versican promoter harbored a typical TATA box located approximately 16 base pairs upstream of the transcription start site and binding sites for a number of transcription factors involved in regulated gene expression. This promoter was shown to be highly functional in transiently transfected cells of both mesenchymal and epithelial origin. Stepwise 5' deletions identified a strong enhancer element between -209 and -445 base pairs and a strong negative element between -445 and -632 base pairs. This study provides the molecular basis for discerning the transcriptional control of the versican gene and offers the opportunity to investigate genetic disorders linked to this important human gene.

Base Sequence↗
PubMed2005

Molecular genetic analysis of two functional candidate genes in the autosomal recessive retinitis pigmentosa, RP25, locus.

PURPOSE: To identify the disease gene in five Spanish families with autosomal recessive retinitis pigmentosa (arRP) linked to the RP25 locus. Two candidate genes, EEF1A1 and IMPG1, were selected from the region between D6S280 and D6S1644 markers where the families are linked. The genes were selected as good candidates on the basis of their function, tissue expression pattern, and/or genetic data. METHODS: A molecular genetic study was performed on DNA extracted from one parent and one affected member of each studied family. The coding exons, splice sites, and the 5' UTR of the genes were amplified by polymerase chain reaction (PCR). For mutation detection, direct sequence analysis was performed using the ABI 3100 automated sequencer. Segregation of an IMPG1 single nucleotide polymorphism (SNP) in all the families studied was analyzed by restriction enzyme digest of the amplified gene fragments. RESULTS: In total, 15 SNPs were identified of which 7 were novel. Of the identified SNPs, one was insertion, two were deletions, five were intronic, six were missense, and one was located in the 5' UTR. These changes, however, were also identified in unaffected members of the families and/or 50 control Caucasians. The examined known IMPG1 SNP was not segregating with the disease phenotype but was correlating with the genetic data in all families studied. CONCLUSIONS: Our results indicate that neither EEF1A1 nor IMPG1 could be responsible for RP25 in the studied families due to absence of any pathogenic variants. However, it is important to notice that the methodology used in this study cannot detect larger deletions that lie outside the screened regions or primer site mutations that exist in the heterozygous state. A role of both genes in other inherited forms of RP and/or retinal degenerations needs to be elucidated.

Chromosome Mapping↗
PubMed2004

Intronic polymorphism (1541-1542delGT) of the constitutive heat shock protein 70 gene has functional significance and shows evidence of association with lung cancer risk.

Somatic mutations of 11q23.3-linked constitutive heat shock protein 70 gene (HSPA8 alias HSC70) are detected by others in breast carcinomas. To examine whether intragenic, somatic mutations of HSPA8 occur in lung carcinomas, we sequenced its exons 2-8, with adjacent intronic sequences, in a series of DNA samples from non-small-cell lung cancers (NSCLC). Twenty-one polymorphisms were detected, but no somatic mutation. However, we observed an association between the HSC70 1541-1542delGT genotype and the immunohistochemical staining pattern of HSC70 protein. Tumors with weak (+) HSC70 protein staining were more frequent in the carriers of the polymorphic 1541-1542delGT allele than in the homozygotes of the major allele (20% vs. 6%, P=0.05 by Fisher's exact test). This statistically significant association prompted us to test the polymorphism functionally. The method we developed for the functional evaluation of intronic sequence alterations showed that the HSPA8 intron 2 with the deleted GT dinucleotide was associated with noticeable (approximately 20%) and statistically significant (P=0.005) reduction of the reporter gene activity. Our case-control analysis showed that the 1541-1542delGT heterozygous genotype was associated with significantly decreased risk for lung cancer (crude odds ratio (OR)=0.44; 95% confidence interval (CI): 0.23-0.84). To the best of our knowledge, this is the first report on the association between a polymorphism of a gene coding for the chaperone protein and lung cancer risk. Moreover, the simple method reported here, based on the dual-luciferase reporter assay system, can be useful for testing functional significance of polymorphisms located in introns of other genes.

Alleles↗
PubMed2002

Functional genomics in the mouse.

The mouse is the premier genetic model organism for the study of human disease and development. With the recent advances in sequencing of the human and mouse genomes, there is strong interest now in large-scale approaches to decipher the function of mouse genes using various mutagenesis technologies. This review discusses what tools are currently available for manipulating and mutagenizing the mouse genome, such as ethylnitrosourea and gene trap mutagenesis, engineered inversions and deletions using the cre-lox system, and proviral insertional mutagenesis in somatic cells, and how these are being used to uncover gene function.

Alkylating Agents↗
PubMed1999

Large-scale analysis of the yeast genome by transposon tagging and gene disruption.

Economical methods by which gene function may be analysed on a genomic scale are relatively scarce. To fill this need, we have developed a transposon-tagging strategy for the genome-wide analysis of disruption phenotypes, gene expression and protein localization, and have applied this method to the large-scale analysis of gene function in the budding yeast Saccharomyces cerevisiae. Here we present the largest collection of defined yeast mutants ever generated within a single genetic background--a collection of over 11,000 strains, each carrying a transposon inserted within a region of the genome expressed during vegetative growth and/or sporulation. These insertions affect nearly 2,000 annotated genes, representing about one-third of the 6,200 predicted genes in the yeast genome. We have used this collection to determine disruption phenotypes for nearly 8,000 strains using 20 different growth conditions; the resulting data sets were clustered to identify groups of functionally related genes. We have also identified over 300 previously non-annotated open reading frames and analysed by indirect immunofluorescence over 1,300 transposon-tagged proteins. In total, our study encompasses over 260,000 data points, constituting the largest functional analysis of the yeast genome ever undertaken.

Algorithms↗
PubMed2002

Genetic analysis in human hypertension.

Hypertension is considered to be a complex trait to which genetic, environmental, and demographic factors contribute interactively. Recently, molecular genetic studies have achieved remarkable success in the elucidation of causative mutations in several Mendelian hypertensive disorders in which single nucleotide polymorphisms (SNPs) disrupt the function of single genes, thereby leading to unambiguous phenotypes. It seems unlikely, however, that such a simple base-substitution is the primary mechanism in cases of essential hypertension, even if SNPs modify the relevant gene function to some extent. Despite the enormous efforts made to date, no consistent association between any of the candidate genes and essential hypertension has been established. One plausible explanation is that because individual genes play a modest role in the pathogenesis of hypertension, confounding variables, whether individual (sex, ethnic origin, etc.) or environmental, may decrease the chance of identifying a causative relation between the genes and hypertension, depending on the populations studied. Several approaches can be proposed to overcome this problem, including long-term follow-up of clinical events collected to attain sufficient phenotypic information and statistical power. With the recent advances in high-throughput genotyping techniques and bioinformatic strategies, it has become possible to perform even SNP-based genome-wide screening. At present, however, the need for identification of susceptibility genes for hypertension still poses a great and unanswered challenge. Nonetheless, we believe that a precise understanding of the manner in which genetic variations affect hypertension can be achieved, and that clarification of the associated phenotypes will lead to the development of effective preventive and treatment strategies.

Angiotensinogen↗
PubMed2006

Cause and effect considerations in diagnostic pathology and pathology phenotyping of genetically engineered mice (GEM).

Over the next several decades, biology is embarking on its most ambitious project yet: to annotate the human genome functionally, prioritizing and focusing on those genes relevant to development and disease. Model systems are fundamental prerequisites for this task, and genetically engineered mice (GEM) are by far the most accessible mammalian system because of their anatomical, physiological, and genetic similarity to humans. The scientific utility of GEM has become commonplace since the technology to produce them was established in the early 1980s. Conceptually, however, an efficiently coordinated high-throughput approach that permits correlation between newly discovered genes, functional properties of their protein products, and biological relevance of these products as drug targets has yet to be established. The discipline of veterinary anatomical pathology (hereafter referred to as pathology) is not immune to this requirement for evolution and adaptation, and to address relationships and tissue consequences between tens of thousands of genes and their cognate proteins, novel interdisciplinary technologies and approaches must emerge. Although many of the techniques of pathology are well established, in the context of pathology's contribution to functional annotation of the genome, several conceptually important and unresolved issues remain to be addressed. While an ever-increasing arsenal of genetic and molecular tool-sets are available to evaluate and understand the function of genes and their pathophysiological mechanisms, pathology will continue to play an essential role in confirming cause and effect relationships of gene function in development and disease. This role will continue to be dependent on keen observation, a systematic but disciplined approach, expert knowledge of strain-dependent anatomical differences and incidental lesions, and relevant tissue-based evidence. Miniaturization and high-throughput adaptation of these methods must also continue so that they can complement parallel phenotyping efforts, provide pathology-based data in pace with concurrent phenotyping efforts, and continue to find new utility in the collective effort of functional annotation.

Animals↗
PubMed2025

Depth-dependent multi-kingdom microbial interactions and biogeochemical cycling genes in eutrophic shallow lake sediments.

Microorganisms are pivotal to lake ecosystem biogeochemical cycles, yet existing research often focuses on single microbial kingdoms or surface sediments, neglecting multi-kingdom interactions and depth-resolved dynamics. To address these gaps, we used metagenomic sequencing to characterize microbial communities and their functional associations across overlying water and 0-45 cm sediments in four shallow lakes of the middle Yangtze River basin, China. Despite increasing bacterial and fungal diversity with depth, the 0-9 cm surface sediments exhibited the strongest multi-kingdom network connectivity and the greatest microbial stability. Functional genes exhibited clear depth-dependent patterns: nitrogen cycling genes, including those involved in dissimilatory nitrate reduction to ammonium, were most enriched in the upper 0-9 cm of sediment; methane cycling genes were positively correlated with depth; phosphorus cycling genes and some sulfur cycling genes, such as assimilatory sulphate reduction, declined with depth. Sediment microbial assembly was dominated by deterministic processes, in which the vertical distribution of functional genes was primarily dictated by heavy metals and conventional environmental indicators. These findings highlight depth-specific multi-kingdom microbial interactions and their associations with biogeochemical cycling, advancing lacustrine microbial ecology understanding and providing references for lake conservation under environmental change.

Lakes↗
PubMed2025

Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.

Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.

Soil Microbiology↗
PubMed2004

LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.

Networks are proving to be central to the study of gene function, protein-protein interaction, and biochemical pathway data. Visualization of networks is important for their study, but visualization tools are often inadequate for working with very large biological networks. Here, we present an algorithm, called large graph layout (LGL), which can be used to dynamically visualize large networks on the order of hundreds of thousands of vertices and millions of edges. LGL applies a force-directed iterative layout guided by a minimal spanning tree of the network in order to generate coordinates for the vertices in two or three dimensions, which are subsequently visualized and interactively navigated with companion programs. We demonstrate the use of LGL in visualizing an extensive protein map summarizing the results of approximately 21 billion sequence comparisons between 145579 proteins from 50 genomes. Proteins are positioned in the map according to sequence homology and gene fusions, with the map ultimately serving as a theoretical framework that integrates inferences about gene function derived from sequence homology, remote homology, gene fusions, and higher-order fusions. We confirm that protein neighbors in the resulting map are functionally related, and that distinct map regions correspond to distinct cellular systems, enabling a computational strategy for discovering proteins' functions on the basis of the proteins' map positions. Using the map produced by LGL, we infer general functions for 23 uncharacterized protein families.

Algorithms↗
PubMed1998

Xiro3 encodes a Xenopus homolog of the Drosophila Iroquois genes and functions in neural specification.

We have identified in Xenopus and in the mouse two highly related genes, Xiro3 and Irx3 respectively, that encode a Drosophila Iroquois-related homeobox transcription factor. Xiro3 in Xenopus and Irx3 in the mouse are expressed early in the prospective neural plate in a subset of neural precursor cells. In Xenopus, injection of Xiro3 mRNA expands the neural tube and induces ectopic neural tissue in the epidermis, based on the ectopic expression of early neural markers such as Xsox3. In contrast, the differentiation of the early forming primary neurons, as revealed by the expression of the neuronal marker N-tubulin, is prevented by Xiro3 expression. Activation of Xiro3 expression itself requires the combination of a neural inducing (noggin) and a posteriorizing signal (basic fibroblast growth factor). These results suggest that Xiro3 activation constitutes one of the earliest steps in the development of the neural plate and that it functions in the specification of a neural precursor state.

Amino Acid Sequence↗
PubMed1997

CDC45, a novel yeast gene that functions with the origin recognition complex and Mcm proteins in initiation of DNA replication.

The CDC45 gene of Saccharomyces cerevisiae was isolated by complementation of the cold-sensitive cdc45-1 mutant and shown to be essential for cell viability. Although CDC45 genetically interacts with a group of MCM genes (CDC46, CDC47, and CDC54), the predicted sequence of its protein product reveals no significant sequence similarity to any known Mcm family member. Further genetic characterization of the cdc45-1 mutant demonstrated that it is synthetically lethal with orc2-1, mcm2-1, and mcm3-1. These results not only reveal a functional connection between the origin recognition complex (ORC) and Cdc45p but also extend the CDC45-MCM genetic interaction to all known MCM family members that were shown to be involved in replication initiation. Initiation of DNA replication in cdc45-1 cells was defective, causing a delayed entry into S phase at the nonpermissive temperature, as well as a high plasmid loss rate which could be suppressed by tandem copies of replication origins. Furthermore, two-dimensional gels directly showed that chromosomal origins fired less frequently in cdc45-1 cells at the nonpermissive temperature. These findings suggest that Cdc45p, ORC, and Mcm proteins act in concert for replication initiation throughout the genome.

Amino Acid Sequence↗
PubMed1999

Hypothesis: genes which function in a stochastic lineage commitment process are subject to monoallelic expression.

The collection of genes which are now known to be monoallelically expressed in mammals is a diverse set. In the case of the genes which encode transducing receptors, such as immunoglobulins or odoront receptors, monoallelic expression ensures that cell activity is related to encountering a unique ligand. However, some monoallelically expressed genes do not encode receptors, and in these cases the physiological purpose of monoallelic expression is uncertain. Even more puzzling are the cases of imprinted genes, where only the maternal or only the paternal allele is expressed. In this article we consider the hypothesis that some of these cases of monoallelic expression reflect the unusual instances in development in which lineage commitment results from a selective rather than an instructive mechanism. These mechanisms are distinguished by their reliance on either external signals (instructive) or internal, cell autonomous events (selective) to cause the changes in gene expression which correspond to lineage commitment. While the instructive mechanism predicts that lineage commitment genes will be expressed or silenced biallelically, the selective mechanism predicts that commitment genes will be subject to monoallelic expression. Specifically, for the cases in which lineage commitment results from activating gene expression, the selective mechanism predicts that commitment genes will be monoallelically expressed following commitment, such as observed recently for some cytokine and transcription factor genes. For the cases in which extinction of gene expression causes commitment, the selective mechanism predicts that the commitment genes will be monoallelically expressed prior to commitment, as for X-linked and imprinted genes.

Alleles↗
PubMed1995

An autoregulated dual-function antitat gene for human immunodeficiency virus type 1 gene therapy.

One approach to gene therapy for AIDS is to block the replication of human immunodeficiency virus type 1 (HIV-1) by inhibiting that tat gene, whose product activates the expression of all HIV-1 genes. To accomplish this, we constructed an antitat gene expressing an RNA with dual (polymeric TAR and antisense-tat) function in an attempt to both sequester Tat protein and block its translation from mRNA. A minigene consisting of the antitat gene driven by the HIV-1 long terminal repeat was inserted into a double-copy retrovirus vector, such that antitat expression would be upregulated only in HIV-1-infected cells. After transduction of a T-lymphocytic cell line (Molt-3) the antitat gene inhibited HIV-1 replication. This inhibition was inversely correlated with the virus infections dose. Virus replication was also inhibited for 5 months in two different T-cell lines after they had been infected at a high multiplicity of infection, suggesting that the antitat gene may be effective over long periods. Importantly, antitat blocked the replication and the cytopathic effect of HIV-1 in human peripheral blood mononuclear cells and led to as much as 4,000-fold inhibition of the replication of an HIV-1 field isolate as well as HIV-1 prototypes maintained in culture. These results suggest that antitat gene therapy has potential use for blocking HIV-1 replication in infected individuals.

Acquired Immunodeficiency Syndrome↗
PubMed2001

Cloning and Expression of SpltMNPV Sl136 Gene and Functions of the Expressed Product.

By computer-assisted analysis, it was revealed that ORF136 gene product in SpltMNPV genome had the basic properties of membrane protein. A putative signal peptide was present at the N-terminal and a transmembrane region near the C-terminal of SL136 protein. In the N-terminal half region, there was a coiled-coil domain, which is a typical feature of a number of viral fusion proteins. After PCR amplification, a recombinant plasmid pBVSl136 and a recombinant AcMNPV containing Sl 136 were constructed, in order to express Sl136 gene in E.coli and insect Hi5 cells, respectively. The SDS-PAGE results showed that both expression levels were high. Cell membrane fusion was induced in the Sl-zsu-1 cells, which had been transfected with Sl136 gene alone, by lowering pH of the medium. These results suggested that SL136 protein may be an envelope fusion protein.

Journal Article↗
PubMed1996

Receptor-mediated gene transfer into macrophages.

Gene transfer systems targeting various receptors have been developed to introduce functional genes into cells in culture and into intact animals. A synthetic molecular conjugate, consisting of mannosylated polylysine that exploits endocytosis via the macrophage mannose receptor, was constructed and complexed to expression plasmids containing either the Photinus pyralis luciferase or Escherichia coli beta-galactosidase (lacZ) reporter genes. The DNA complexes were used to transfect murine macrophages isolated from peritoneal exudates in vitro. Luciferase and beta-galactosidase activity was found in transfected cells in culture, whereas complexes consisting of an irrelevant plasmid bound to mannosylated polylysine or the expression plasmid bound to galactosylated polylysine resulted in no detectable transgene expression. Gene transfer was inhibited by the addition of excess mannosylated bovine serum albumin to the culture medium before transfection. Reporter genes were also transferred into macrophages residing in the spleen and liver of adult animals using this system. Luciferase activity was maximal at 4 days after transfection and decreased to lower levels by 16 days. Transgene expression conformed to the distribution of cells that had nonspecific esterase, a cytochemical marker for macrophages. Thus, this system can be used to introduce functional genes into macrophages and may be an approach to the treatment of storage diseases that affect the reticuloendothelial system.

Animals↗
PubMed2005

[Research on gene expression data based on clustering/classification technology].

As the work of sequencing the genome of the human and many model organisms has been partially or fully finished, the "postgenomic era" has begun. Scientists are turning their focus toward identifying gene function from sequencing. Clustering technology, as one of the important tools of analyzing gene expression data and identifying gene function, has been used widely. In this paper we discuss main clustering technology about gene expression data at present, analyze their advantages and disadvantages, present the methods to solve the problems and give new approaches to study gene expression data.

Algorithms↗