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PubMed1983

Role of the major histocompatibility complex in T cell activation of B cell subpopulations. Ir gene regulation of the T cell-dependent activation of distinct B cell subpopulations.

Antibody responses to (T,G)-A--L and (H,G)-A--L or to the TNP conjugates of these polypeptides, are regulated in the mouse by Ir genes encoded in the I-A subregion of the mouse MHC. To study the mechanism by which Ir genes function, it is essential to identify the cell interactions that are regulated by these genes. In the present report, it was specifically determined whether Ir gene function is expressed differently in the activation of B cell subpopulations that participate in two different pathways of B cell activation for in vitro antibody responses to TNP-(T,G)-A--L and TNP- (H,G)-A--L. The results of these studies demonstrate that under conditions that activate the Lyb-5- b cell subpopulation via MHC-restricted TH cell-B cell and TH cell-APC interactions, Ir gene function regulates TH cell interactions with these B cells as well as with APC. In addition, under conditions that activate the Lyb-5+ B cell subpopulation via MHC-restricted TH cell-APC but not TH cell-B cell interaction, Ir gene function regulates only TH cell interactions with APC but not with B cells.

Animals↗

PubMed2004

A series of maturity onset diabetes of the young, type 2 (MODY2) mouse models generated by a large-scale ENU mutagenesis program.

Mutant mouse models are indispensable tools for clarifying the functions of genes and for elucidating the underlying pathogenic mechanisms of human diseases. Currently, several large-scale mutagenesis projects that employ the chemical mutagen N-ethyl-N-nitrosourea (ENU) are underway worldwide. One specific aim of our ENU mutagenesis project is to generate diabetic mouse models. We screened 9375 animals for dominant traits using a clinical biochemical test and thereby identified 11 mutations in the glucokinase (Gk) gene that were associated with hyperglycemia. GK is a key regulator of insulin secretion in the pancreatic beta-cell. Approximately 190 heterozygous mutations in the human GK gene have been reported to cause maturity onset diabetes of the young, type 2 (MODY2). In addition, five mutations have been reported to cause permanent neonatal diabetes mellitus (PNDM) when present on both alleles. The mutations in our 11 hyperglycemic mutants are located at different positions in Gk. Four have also been found in human MODY2 patients, and another mutant bears its mutation at the same location that is mutated in a PNDM patient. Thus, ENU mutagenesis is effective for developing mouse models for various human genetic diseases, including diabetes mellitus. Some of our Gk mutant lines displayed impaired glucose-responsive insulin secretion and the mutations had different effects on Gk mRNA levels and/or the stability of the GK protein. This collection of Gk mutants will be valuable for understanding GK gene function, for dissecting the function of the enzyme and as models of human MODY2 and PNDM.

Amino Acid Sequence↗

PubMed1981

The human beta-globin gene and a functional viral thymidine kinase gene in developing mice.

Two foreign cloned genes--one encoding a tissue-specific protein and one encoding a constitutive enzyme--were introduced into mouse eggs by microinjection into a pronucleus shortly after fertilization. They were the adult human genomic beta-globin gene and the thymidine kinase (TK; ATP:thymidine 5'-phosphotransferase, EC 2.7.1.21) gene of herpes simplex virus (HSV), ligated in the pBR322 plasmid. Thirty-three developing mice were autopsied in late fetal life; all appeared normal. Blot hybridization tests revealed that the DNA of as many as five (15%) of the fetuses (from separate litters), and of their corresponding placentas, contained copies of the human beta-globin gene and of the HSV tk gene that had been retained and replicated without significant loss or rearrangement. The estimated total numbers of copies per cell were 3-50 for the donor globin gene and 3-20 for the donor tk. In some of the fetuses, these totals included some copies of molecular weight higher than that of the intact sequence; the additional segments may have arisen through changes such as deletions or duplications. The foreign genes in the five positive fetuses appear to be present in high molecular weight DNA. Assays capable of distinguishing between foreign and native TK indicated that at least one of the fetuses with the HSV tk gene had some TK enzyme of the HSV type and, therefore, at least one gene copy that was being accurately transcribed and translated to produce a functional protein, despite the absence of selective pressure. Thus, pure recombinant genes introduced into mice at the onset of their development can remain intact and be stably incorporated and even expressed. These experiments provide a practical basis for novel investigations of the developmental control of normal gene expression in vivo of the causes and possible cures of genetic diseases.

Animals↗

PubMed2003

Transgenic RNA interference in ES cell-derived embryos recapitulates a genetic null phenotype.

Gene targeting via homologous recombination in murine embryonic stem (ES) cells has been the method of choice for deciphering mammalian gene function in vivo. Despite improvements in this technology, it still remains a laborious method. Recent advances in RNA interference (RNAi) technology have provided a rapid loss-of-function method for assessing gene function in a number of organisms. Studies in mammalian cell lines have shown that introduction of small interfering RNA (siRNA) molecules mediates effective RNA silencing. Plasmid-based systems using RNA polymerase III (RNA pol III) promoters to drive short hairpin RNA (shRNA) molecules were established to stably produce siRNA. Here we report the generation of knockdown ES cell lines with transgenic shRNA. Because of the dominant nature of the knockdown, embryonic phenotypes could be directly assessed in embryos completely derived from ES cells by the tetraploid aggregation method. Such embryos, in which endogenous p120-Ras GTPase-activating protein (RasGAP), encoded by Rasa1 (also known as RasGAP), was silenced, had the same phenotype as did the previously reported Rasa1 null mutation.

Animals↗

PubMed2003

When negative is positive in functional genomics.

The post-genomic era has caused classical approaches to analyse gene function to be reviewed and refined. Conventional reverse genetic approaches to predict gene function have drawbacks in terms of genetic redundancy and being limited mainly to well-characterized genomes. The relatively recent use of dominant-negative transgenes has been successful in elaborating certain pathways and it is now possible to extend this technique to convert transcription factors into dominant repressor functions by fusion to repressor domains such as ENGRAILED from Drosophila. This methodology opens up new possibilities to overcome genetic redundancy, to identify novel gene functions and also to apply information on conserved protein domains between species to repress heterologous protein function.

Animals↗

PubMed1994

Cloning and sequence of REV7, a gene whose function is required for DNA damage-induced mutagenesis in Saccharomyces cerevisiae.

The function of the REV7 gene is required for DNA damage-induced mutagenesis in budding yeast, Saccharomyces cerevisiae, and is therefore thought to promote replication past sites of mutagen damage in the DNA template. We have cloned this gene by complementation of the rev7-2 mutant defect, and determined its sequence. REV7 encodes a predicted protein of M(r) 28,759 which is unlikely any other protein in the NCBI non-redundant protein sequence data base, and which is inessential for viability.

Amino Acid Sequence↗

PubMed2002

Cnidarian and bilaterian promoters can direct GFP expression in transfected hydra.

Complete sexual development is not easily amenable to experimentation in hydra. Therefore, the analysis of gene function and gene regulation requires the introduction of exogenous DNA in a large number of cells of the hydra polyps and the significant expression of reporter constructs in these cells. We present here the procedure whereby we coupled DNA injection into the gastric cavity to electroporation of the whole animal in order to efficiently transfect hydra polyps. We could detect GFP fluorescence in both endodermal and ectodermal cell layers of live animals and in epithelial as well as interstitial cell types of dissociated hydra. In addition, we could confirm GFP protein expression by showing colocalisation between GFP fluorescence and anti-GFP immunofluorescence. Finally, when a FLAG epitope was inserted in-frame with the GFP coding sequence, GFP fluorescence also colocalised with anti-FLAG immunofluorescence. This GFP expression in hydra cells was directed by various promoters, either homologous, like the hydra homeobox cnox-2 gene promoter, or heterologous, like the two nematode ribosomal protein S5 and L28 gene promoters, and the chicken beta-actin gene promoter. This strategy provides new tools for dissecting developmental molecular mechanisms in hydra; more specifically, the genetic regulations that take place in endodermal cells at the time budding or regeneration is initiated.

Animals↗

PubMed2001

The in vivo conformation of the plastid DNA of Toxoplasma gondii: implications for replication.

The Phylum Apicomplexa comprises thousands of obligate intracellular parasites, some of which cause serious disease in man and other animals. Though not photosynthetic, some of them, including the malaria parasites (Plasmodium spp.) and the causative organism of Toxoplasmosis, Toxoplasma gondii, possess a remnant plastid partially determined by a highly derived residual genome encoded in 35 kb DNA. The genetic maps of the plastid genomes of these two organisms are extremely similar in nucleotide sequence, gene function and gene order. However, a study using pulsed field gel electrophoresis and electron microscopy has shown that in contrast to the malarial version, only a minority of the plastid DNA of Toxoplasma occurs as circular 35 kb molecules. The majority consists of a precise oligomeric series of linear tandem arrays of the genome, each oligomer terminating at the same site in the genetic map, i.e. in the centre of a large inverted repeat (IR) which encodes duplicated tRNA and rRNA genes. This overall topology strongly suggests that replication occurs by a rolling circle mechanism initiating at the centre of the IR, which is also the site at which the linear tails of the rolling circles are processed to yield the oligomers. A model is proposed which accounts for the quantitative structure of the molecular population. It is relevant that a somewhat similar structure has been reported for at least three land plant chloroplast genomes.

Animals↗

PubMed1996

Molecular cloning of the mouse gene coding for carbonic anhydrase IV.

Carbonic anhydrase IV (CA IV) is expressed on apical surfaces of renal tubular epithelium and endothelium of specialized capillary beds. It plays a key role in bicarbonate reabsorption in kidney and in CO2 transport in other tissues. The human cDNA and genomic sequences have been cloned and characterized. Here we report the cloning and characterization of the entire mouse CA IV gene (contained in two overlapping lambda clones), which should enable generation of targeting constructs for disrupting the mouse CA IV gene to produce mouse models for in vivo analysis of CA IV gene function. The gene is approximately 8.2 kb long and contains eight exons ranging from 54 to 434 bp in length. The first exon (exon 1a) encodes the signal sequence. Exons 1b through 7 encode the remaining coding sequences. Exon 7 encodes the C terminus of the membrane-associated protein, as well as the 242-bp 3' untranslated sequence. The nucleotide sequence alignment between mouse and rat CA IV cDNAs reveals 84% identity. The nucleotide sequence alignment between mouse and human CA IV shows 69% identity in the coding region and all of the exon-intron boundaries are conserved, as are the sizes of the introns. The corresponding mouse and human exons are similar, except for the length of the untranslated regions in exons 1a and 7 and two small insertion/deletion events in exons 1a and 4. The 5' flanking region of the mouse gene (-300 to -1) is GC rich and contains 16 CpG dinucleotides. A TATA box sequence and several transcription factor binding sequences are identified upstream of exon 1a. Comparison of the nucleotide sequences surrounding the TATA box (-300 to -1) between mouse and human CA IV genes revealed 70% identity, indicating that regulatory sequences are as highly conserved as coding sequences between mouse and human CA IV genes.

Animals↗

PubMed2006

A synchrotron FTIR microspectroscopy investigation of fungal hyphae grown under optimal and stressed conditions.

Synchrotron FTIR can provide high spatial resolution (<10 microm pixel size) in situ biochemical analyses of intact biotissues, an area of increasing importance in the post-genomic era, as gene functions and gene networks are coming under direct scrutiny. With this technique, we can simultaneously assess multiple aspects of cell biochemistry and cytoplasmic composition. In this paper, we report the first results of our synchrotron FTIR examination of hyphae of three important fungal model systems, each with sequenced genomes and a wealth of research: Aspergillus, Neurospora, and Rhizopus. We have analyzed the FTIR maps of Aspergillus nidulans cells containing the hypA1 allele, a well-characterized single-gene temperature-sensitive morphogenetic mutation. The hypA1 cells resemble wildtype at 28 degrees C but have growth defects at 42 degrees C. We have also investigated Neurospora and Rhizopus cultures grown in media with optimal or elevated pH. Significant differences between the spectra of the three fungi are likely related to differences in composition and structure. In addition, high spatial resolution synchrotron FTIR spectroscopy provides an outstanding method for monitoring subtle subcellular changes that accompany environmental stress.

Colony Count, Microbial↗

PubMed2004

Towards a mutant map of the mouse--new models of neurological, behavioural, deafness, bone, renal and blood disorders.

With the completion of the first draft of the human genome sequence, the next major challenge is assigning function to genes. One approach is genome-wide random chemical mutagenesis, followed by screening for mutant phenotypes of interest and subsequent mapping and identification of the mutated genes in question. We (a consortium made up of GlaxoSmithKline, the MRC Mammalian Genetics Unit and Mouse Genome Centre, Harwell, Imperial College, London, and the Royal London Hospital) have used ENU mutagenesis in the mouse for the rapid generation of novel mutant phenotypes for use as animal models of human disease and for gene function assignment (Nolan et al., 2000). As of 2003, 35,000 mice have been produced to date in a genome-wide screen for dominant mutations and screened using a variety of screening protocols. Nearly 200 mutants have been confirmed as heritable and added to the mouse mutant catalogue and, overall, we can extrapolate that we have recovered over 700 mutants from the screening programme. For further information on the project and details of the data, see http://www.mgu.har.mrc.ac.uk/mutabase.

Animals↗

PubMed1992

The Rhizobium meliloti pmi gene encodes a new type of phosphomannose isomerase.

Interspecific complementation of a Xanthomonas campestris pv. campestris phosphomannose isomerase (PMI) mutant was used to isolate a cosmid from a genomic library of Rhizobium meliloti 2011 carrying the pmi gene of this strain. Subcloning experiments localized the coding region to a 2.0-kb SalI-ClaI fragment. Nucleotide sequence analysis of this fragment indicated the presence of two open reading frames (ORFs), coding for 18- and 43-kDa polypeptides. The analysis of the gene function by gene disruption experiments showed that ORF2 codes for pmi. A comparison of the deduced amino acid sequence with the corresponding sequences of the Pseudomonas aeruginosa and Escherichia coli PMIs revealed no significant homology, indicating that the isolated gene encodes a new type of PMI. The construction of a pmi-deficient mutant of R. meliloti using the sacB-sacR cassette technique showed that the loss of PMI activity does not affect the symbiotic properties of this strain.

Amino Acid Sequence↗

PubMed2005

Expression profiling of the estrogen responsive genes in response to phytoestrogens using a customized DNA microarray.

Here, we examined phytoestrogens, isoflavones (genistein, daidzein, glycitein, biochanin A and ipriflavone), flavones (chrysin, luteolin and apigenin), flavonols (kaempferol and quercetin), and a coumestan, a flavanone and a chalcone (coumestrol, naringenin and phloretin, respectively) by means of a DNA microarray assay. A total of 172 estrogen responsive genes were monitored with a customized DNA microarray and their expression profiles for the above phytoestrogens were compared with that for 17beta-estradiol (E2) using correlation coefficients, or R values, after a correlation analysis by linear regression. While R values indicate the similarity of the response by the genes, we also examined the genes by cluster analysis and by their specificity to phytoestrogens (specific to genistein, daidzein or glycitein) or gene functions. Several genes were selected from p53-related genes (CDKN1A, TP53I11 and CDC14), Akt2-related genes (PRKCD, BRCA1, TRIB3 and APPL), mitogen-activated protein kinase-related genes (RSK and SH3BP5), Ras superfamily genes (RAP1GA1, RHOC and ARHGDIA) and AP-1 family and related genes (RIP140, FOS, ATF3, JUN and FRA2). We further examined the extracts from two local crops of soy beans (Kuro-daizu or Mochi-daizu) by comparing the gene expression profiles with those of E2 or phytoestrogens as a first step in utilizing the expression profiles for various applications.

Cell Line, Tumor↗

PubMed2005

RNAi-hTERT inhibition hepatocellular carcinoma cell proliferation via decreasing telomerase activity.

BACKGROUND: RNA interference (RNAi), which has been demonstrated as having great potentional in the fields of gene function and gene therapy, was applied to inhibit the expression of some endogenous genes. Human telomerase reverse transcriptase (hTERT) is highly expressed in hepatocellular carcinoma cells. MATERIALS AND METHODS: In combination with DNA vector-based RNAi, quantitative real-time reverse transcription polymerase chain reaction, telomeric repeat amplification protocol-enzyme-linked immunosorbent assay, 3-(4,5 dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide assay, and xenograft tumor animal techniques, we first constructed three pTZU6 + 1-shRNA-hTERT vectors and their corresponding site-mutated vectors, then transfected them into hepatocarcinoma HepG2, SMMC-7721 cells, and normal liver L02 cells, respectively, injected them into xenograft hepatocarcinoma tumor tissues to induce RNAi, and then detected the alteration of cell and tumor proliferation, telomerase activity, hTERT, and c-myc expression in each treatment. RESULTS: The cell proliferation of hepatocellular carcinoma cells both in vitro and in vivo was significantly inhibited by ph1-shRNA, the most effective segment targeted hTERT gene. ph1-shRNA could inhibit telomerase activity, hTERT, and c-myc expression in hepatocarcinoma cells and xenograft tumor tissues compare with the cells treated with empty vector pTZU6 + 1. However, there were no obvious effects on normal liver L02 cells. Moreover, even a single base mutation in siRNAs transcription template would significantly reduce the ability of siRNAs to induce RNA silencing. CONCLUSIONS: RNAi-hTERT could inhibit the proliferation of hepatocarcinoma cells specifically via the suppression of telomease activity, hTERT, and c-myc expression. Therefore, hTERT and c-myc play key roles in hepatocarcinoma tumorgenesis, and an RNAi-targeted hTERT strategy would be a potential approach for hepatocarcinoma therapy.

Animals↗

PubMed2005

Comprehensive post-genomic data analysis approaches integrating biochemical pathway maps.

Post-genomic era research is focusing on studies to attribute functions to genes and their encoded proteins, and to describe the regulatory networks controlling metabolic, protein synthesis and signal transduction pathways. To facilitate the analysis of experiments using post-genomic technologies, new concepts for linking the vast amount of raw data to a biological context have to be developed. Visual representations of pathways help biologists to understand the complex relationships between components of metabolic networks, and provide an invaluable resource for the integration of transcriptomics, proteomics and metabolomics data sets. Besides providing an overview of currently available bioinformatic tools for plant scientists, we introduce BioPathAt, a newly developed visual interface that allows the knowledge-based analysis of genome-scale data by integrating biochemical pathway maps (BioPathAtMAPS module) with a manually scrutinized gene-function database (BioPathAtDB) for the model plant Arabidopsis thaliana. In addition, we discuss approaches for generating a biochemical pathway knowledge database for A. thaliana that includes, in addition to accurate annotation, condensed experimental information regarding in vitro and in vivo gene/protein function.

Computational Biology↗

PubMed2005

Transgenic mice.

For the past 20 years researchers have used transgenic mice to help understand the basic mechanisms associated with inherited human and animal diseases. The ability to integrate exogenous genetic information into the mouse genome has revolutionised the analysis of gene function. Both gene addition and gene replacement can be performed and the capability exists to create 'conditional' mutations and to study gene dosage effects. The aim of the present review is to provide a framework of information on transgenic mouse methodologies that can be applied to any area of research. A basic understanding of transgenic technology, recognising its advantages and disadvantages, is essential knowledge for the scientist in the 21st century.

Animals↗

PubMed1997

Molecular approaches to diagnosis and management of ovarian cancer.

The recent advances in the understanding of the pathogenesis of ovarian cancer have been helpful in addressing issues in diagnosis, prognosis and management. The study of ovarian tumours by novel techniques such as immunohistochemistry, fluorescent in situ hybridisation, comparative genomic hybridisation, polymerase chain reaction and new tumour markers have aided the evaluation and application of new concepts into clinical practice. The correlation of novel surrogate tumour specific features with response to treatment and outcome in patients has defined prognostic factors which may allow the future design of tailored therapy based on a molecular profile of the tumour. These have also been used to design new approaches to therapy such as antibody targeting and gene therapy. The delineation of roles of c-erbB2, c-fms and other novel receptor kinases in the pathogenesis of ovarian cancer has led initially to the development of anti-c-erbB2 monoclonal antibody therapy. The discovery of BRCA1 and BRCA2 genes will have an impact in the diagnosis and the prevention of familial ovarian cancer. The important role played by recessive genes such as p53 in cancer has raised the possibility of restoration of gene function by gene therapy. Although the pathological diagnosis of ovarian cancer is still confirmed principally on morphological features, addition of newer investigations will increasingly be useful in addressing difficult diagnostic problems. The increasingly rapid pace of discovery of genes important in disease, makes it imperative that the evaluation of their contribution in the pathogenesis of ovarian cancer is undertaken swiftly, thus improving the overall management of patients and their outcome.

Biomarkers, Tumor↗

PubMed2001

The art and design of genetic screens: zebrafish.

Inventive genetic screens in zebrafish are revealing new genetic pathways that control vertebrate development, disease and behaviour. By exploiting the versatility of zebrafish, biological processes that had been previously obscured can be visualized and many of the responsible genes can be isolated. Coupled with gene knockdown and overexpression technologies, and small-molecule-induced phenotypes, genetic screens in zebrafish provide a powerful system by which to dissect vertebrate gene function and gene networks.

Animals↗