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PubMed2002

yMGV: helping biologists with yeast microarray data mining.

yMGV (yeast Microarray Global Viewer) was designed to provide biologists with meaningful information from genome-wide yeast expression data. The database includes most of the available expression data published on yeast microarrays over the last 4 years. It provides customizable tools for the rapid visualization of expression profiles associated with a set of genes from all published experiments. It also allows users to compare the results from different publications so that they can identify genes with common expression profiles. We used yMGV to perform global analyses to find a gene expression profile specific for given biological conditions and to locate functional gene clusters on chromosomes. Other organisms will be added to this database. yMGV is accessible on the web at http://transcriptome.ens.fr/ymgv.

Computer Graphics↗
PubMed2004

Impact of mismatch repair deficiency on genomic stability in the maternal germline and during early embryonic development.

The effects of lack of the mismatch repair protein PMS2 on germline and maternal-effect mutations were studied in transgenic mice that allow mutant cells to be visualized in situ. Tg(betaA-G11PLAP) mice are transgenic for the G11 allele of a human placental alkaline phosphatase (PLAP) gene driven by a human beta-actin promoter. The G11 allele of the PLAP gene does not produce enzyme due to a frameshift induced by a mononucleotide repeat containing 11 G:C basepairs. Loss of one G:C basepair restores enzyme production. When the G11 PLAP allele was passed through the germline of female mice lacking PMS2, approximately 25% of the offspring that inherited the transgene exhibited the phenotype expected for germline mutation. The mice transmitted the germline-mutation phenotype normally and their offspring exhibited PLAP enzyme activity in at least 30% of the cells in each tissue examined. By contrast, only 1 of 32 mice that inherited the G11 PLAP transgene from a wild-type male crossed to a Pms2-/- female exhibited a high number of PLAP+ cells. Compared to germline revertants, approximately one half to one quarter as many cells were PLAP+, suggesting that a mutation occurred in one cell of an embryo containing two to four cells. These data suggest that the paternally derived Pms2 gene provided normal levels of PMS2 protein to embryos by the time they reached the eight-cell stage, but that smaller embryos formed from PMS2-deficient eggs lacked PMS2 function.

Alkaline Phosphatase↗
PubMed2004

Understanding the yeast proteome: a bioinformatics perspective.

Rapid development of genomic and proteomic methodologies has provided a wealth of data for deciphering the biomolecular circuitry of a living cell. The main areas of computational research of proteomes outlined in this review are: understanding the system, its features and parameters to help plan the experiments; data integration, to help produce more reliable data sets; visualization and other forms of data representation to simplify interpretation; modeling of the functional regulation; and systems biology. With false-positive rates reaching 50% even in the more reliable data sets, handling the experimental error remains one of the most challenging tasks. Integrative approaches, incorporating results of various genome- and proteome-wide experiments, allow for minimizing the error and bring with them significant predictive power.

Computational Biology↗
PubMed1995

High-resolution physical mapping of a 250-kb region of human chromosome 11q24 by genomic sequence sampling (GSS).

A physical map of the region of human chromosome 11q24 containing the FLI1 gene, disrupted by the t(11;22) translocation in Ewing sarcoma and primitive neuroectodermal tumors, was analyzed by genomic sequence sampling. Using a 4- to 5-fold coverage chromosome 11-specific library, 22 region-specific cosmid clones were identified by phenol emulsion reassociation hybridization, with a 245-kb yeast artificial chromosome clone containing the FLI1 gene, and by directed "walking" techniques. Cosmid contigs were constructed by individual clone fingerprinting using restriction enzyme digestion and assembly with the Genome Reconstruction and AsseMbly (GRAM) computer algorithm. The relative orientation and spacing of cosmid contigs with respect to the chromosome was determined by the structural analysis of cosmid clones and by direct visual in situ hybridization mapping. Each cosmid clone in the contig was subjected to "one-pass" end sequencing, and the resulting ordered sequence fragments represent approximately 5% of the complete DNA sequence, making the entire region accessible by PCR amplification. The sequence samples were analyzed for putative exons, repetitive DNAs, and simple sequence repeats using a variety of computer algorithms. Based upon the computer predictions, Southern and Northern blot experiments led to the independent identification and localization of the FLI1 gene as well as a previously unknown gene located in this region of chromosome 11q24. This approach to high-resolution physical analysis of human chromosomes allows the assembly of detailed sequence-based maps and provides a tool for further structural and functional analysis of the genome.

Base Sequence↗
PubMed2002

Retrovirus-mediated gene expression during chick visual system development.

The chick embryo is an excellent model for studying eye morphogenesis, retinal cell fate determination, and retinotectal projections due to its accessibility and the available molecular tools. Avian replication-competent retroviruses allow efficient infection of proliferating cells and stable integration of the viral genome, including up to 2.3kb of foreign cDNA, into the host chromosome. High-titer retroviruses are produced by transient transfection of avian DF-1 cells followed by centrifugation of the culture medium. Targeted infection of the optic vesicle, the lens vesicle, the retina and pigmented epithelium, the periocular mesenchyme, and the tectum can be performed at different developmental stages in ovo. In addition, retroviruses can be used to transduce genes of interest into various ocular tissue explants or cells in vitro. Virus-mediated gene expression can be detected within 12h of infection. Therefore, avian replication-competent retroviruses serve as powerful tools to misexpress wild-type and mutant gene products and to study molecular mechanisms underlying vertebrate visual system development.

Animals↗
PubMed1998

Assembly of a tailed bacterial virus and its genome release studied in three dimensions.

We present the first three-dimensional reconstruction of a prolate, tailed phage, and its empty prohead precursor by cryo-electron microscopy. The head-tail connector, the central component of the DNA packaging machine, is visualized for the first time in situ within the Bacillus subtilis dsDNA phage phi29. The connector, with 12- or 13-fold symmetry, appears to fit loosely into a pentameric vertex of the head, a symmetry mismatch that may be required to rotate the connector to package DNA. The prolate head of phi29 has 10 hexameric units in its cylindrical equatorial region, and 11 pentameric and 20 hexameric units comprise icosahedral end-caps with T=3 quasi-symmetry. Reconstruction of an emptied phage particle shows that the connector and neck/tail assembly undergo significant conformational changes upon ejection of DNA.

Bacillus Phages↗
PubMed2000

The quincunx of surgery.

From the earliest days of surgery the central and unifying theme of the discipline has been the mastery of technical proficiency with the view to not only management of the diseased or damaged part but the preservation of general health and well being. This central tenet of the discipline has been supported by four critical columns of knowledge, each of which has amplified over the passage of time. Initially anatomy was the cornerstone of surgical intervention and mastery of surgery to a large part depended upon a secure grasp of the intricacies and relationships of corporeal macro structure. The second column comprised functional anatomy or physiology and the appreciation of organ activity enabled the subsequent delineation of malfunction during disease. Regardless of the level of sophistication that could be brought to bear upon the disease a requisite for most successful technical intervention was the management of pain and the prevention of sepsis. As the quincunx of surgery embraces a new century it must continue to evolve to maintain the balance of growth in the four supporting columns. Thus anatomy has been expanded into subcellular structure and the elucidation of function has amplified into the role of individual organelles. Similarly pathology has moved beyond the organ and cell into the genome and deletion may be conceived of in terms of codons and sequences rather than colons and spleens. Indeed it is feasible that antisense strategies may become more sensible than antibiotics. Manual and digital techniques will be supplanted by robotic intervention and visualization will move beyond the visible into the non-visible world of spectroscopy. Millimetric dexterity will need to become nanometric and the mantra must become molecular and intervention directed not only at adults or neonates but the fetus. In order to achieve such goals teaching and training strategies need dramatic revision to produce individuals capable of transforming from tactile to telemetric skills and from gentle technique to genomic intervention.

Adult↗
PubMed2002

The methylenetetrahydrofolate reductase 677 C-->T polymorphism and preeclampsia in two populations.

OBJECTIVE: The C677T polymorphism of the 5,10 methylenetetrahydrofolate reductase (MTHFR) gene is associated with decreased MTHFR activity and elevated plasma homocysteine levels with the result of an increased risk for vascular disease. Because thrombosis of the maternal spiral arteries can be one of the causative events in the disease, it has been suggested that the C677T polymorphism may also play a role in the pathogenesis of preeclampsia. Our case-control study investigated the prevalence of the 677T allele in two ethnically different populations and the potential association of the 677T allele with preeclampsia. Special attention was paid to the potential contribution of the fetal genotype to disease risk. METHODS: Blood samples were collected from 81 mothers and 61 newborns after preeclampsia and 99 mothers and 61 newborns with normal pregnancies. Genomic DNA was amplified by polymerase chain reaction with locus-specific primers, and presence of the polymorphism was determined by enzymatic digestion with HinfI and visualization on polyacrylamide gels. RESULTS: Genotypes carrying the MTHFR 677T allele were significantly more frequent in German-Croatians than in Indonesians in both patients and controls (P =.0033 in controls). In contrast, the prevalence of genotypes with the 677T allele was not increased among patients with preeclampsia compared with controls in both ethnic groups (P >.5 in all groups). In Germans, the frequency of 677T homozygotes among controls even exceeded that observed in preeclamptic patients (677T/T genotype frequency 0.20 in controls and 0.07 in patients). We did not find an increased prevalence of paternally inherited 677T alleles in preeclamptic fetuses relative to controls or other signs of maternal-fetal transmission distortion. CONCLUSION: In our study, the MTHFR C677T polymorphism was not associated with an increased risk for preeclampsia on the level of the maternal or fetal genotype. However, significant differences of the frequency of genotypes carrying the 677T allele between Middle-Europeans and Indonesians were identified.

Adult↗
PubMed1999

Enhanced retinal longwave sensitivity using a chlorophyll-derived photosensitiser in Malacosteus niger, a deep-sea dragon fish with far red bioluminescence.

Through partial bleaching of both visual pigment extracts and cell suspensions we show that the deep-sea stomiid Malacosteus niger, which produces far red bioluminescence, has two visual pigments within its retina which form a rhodopsin/porphyropsin pigment pair with lambda max values around 520 and 540 nm, but lacks the very longwave sensitive visual pigments (lambda max > 550 nm) observed in two other red light producing stomiids. The presence of only a single opsin gene in the M. niger genome was confirmed by molecular and cladistic analysis. To compensate for its apparently reduced longwave sensitivity compared to related species, the outer segments of M. niger contain additional pigments, which we identify as a mixture of defarnesylated and demetallated derivatives of bacteriochlorophylls c and d, that are used as a photosensitiser to enhance its sensitivity to longwave radiation.

Animals↗
PubMed1998

A review of research to elucidate the causes of the generalized progressive retinal atrophies.

Progressive retinal atrophy (PRA) is a leading hereditary cause of blindness in pedigree dogs as is its counterpart retinitis pigmentosa (RP) in humans. PRA shows genetic heterogeneity, as does RP, with several distinct forms already recognized and several more remaining to be investigated. Progress in molecular genetics has allowed the identification of the gene mutation responsible for an early onset form of PRA in the Irish setter, classified as rod-cone dysplasia type 1. The gene involved is the beta-subunit of cyclic guanosine monophosphate phosphodiesterase which encodes a protein of the visual transduction cascade. Investigation of this gene in other breeds of dog with PRA has failed to find further breeds with the same mutation. Other genes that have been investigated include those encoding other proteins in the visual transduction cascade and for photoreceptor specific structural proteins. Further disease causing mutations have not yet been identified. Recently, developments in the mapping of the canine genome have produced sufficient markers to allow preliminary mapping of PRA genes. Already linkage to the most common form of PRA, progressive rod-cone degeneration (prcd), has been established. prcd occurs in poodles, cocker spaniels and Labrador retrievers and possibly other breeds. The prcd-linked marker should enable development of a DNA-based test for the disease locus and facilitate identification of the actual disease causing gene mutation. Over the next few years we can look forward to the identification of several more PRA-causing gene mutations. This article will review research that seeks to characterize PRA in the dog, identify the responsible gene mutations, and elucidate the disease processes involved.

Animals↗
PubMed2007

Genotyping of single-nucleotide polymorphisms by primer extension reaction in a dry-reagent dipstick format.

The primer extension (PEXT) reaction is the most widely used approach to genotyping of single-nucleotide polymorphisms (SNPs). Current methods for analysis of PEXT reaction products are based on electrophoresis, fluorescence resonance energy transfer, fluorescence polarization, pyrosequencing, mass spectrometry, microarrays, and spectrally encoded microspheres. We report the first dry-reagent dipstick method that enables rapid visual detection of PEXT products without instrumentation. The method is applied to the analysis of six SNPs in the mannose-binding lectin gene (MBL2). The genomic region that spans each SNP of interest is amplified by PCR. Two primer extension reactions are performed with allele-specific primers (for one or the other variant nucleotide), which contain an oligo(dA) segment at the 5'-end. Biotin-dUTP is incorporated in the extended strand. The product is applied to the strip followed by immersion in the appropriate buffer. As the DNA moves along the strip by capillary action, it hybridizes with oligo(dT)-functionalized gold nanoparticles, such that only extended products are captured by immobilized streptavidin at the test zone, generating a red line. A second red line is formed at the control zone of the strip by hybridization of the nanoparticles with immobilized oligo(dA). The dipstick test is complete within 10 min. We analyzed six SNPs of the mannose-binding lectin gene (MBL2) using genomic DNA from 27 patients, representing a total of 74 variant nucleotide positions. Patient genotypes showed 100% concordance with direct DNA sequencing data. The described PEXT-dipstick assay is rapid and highly accurate; it does not require specialized instrumentation or highly trained technical personnel. It is appropriate for a diagnostic laboratory where a few selected SNP markers are examined per patient with a low cost per assay.

DNA Primers↗
PubMed2001

RNA expression in the early characterization of hepatotoxicants in Wistar rats by high-density DNA microarrays.

High-density microarrays are useful tools to study gene expression for the purpose of characterizing functional tissue changes in response to the action of drugs and chemicals. To test whether high-density expression data can identify mechanisms of toxicity and to identify an unknown sample through its RNA expression pattern, groups of male Wistar rats were administered 6 hepatotoxicants. The compounds chosen for this study were microcystin-LR (MLR), phenobarbital (PB), lipopolysaccharide (LPS), carbon tetrachloride (CT), thioacetamide (THA), and cyproterone acetate (CPA). These hepatotoxicants are known to induce adverse liver effects through different mechanisms. Liver mRNA was isolated and used to generate biotinylated cRNA for hybridization to a custom 1,600-rat gene DNA microarray. Treatment correlation matrices analyzed hybridization data from a hepatotoxicant-blinded sample, with gene expression coefficients (GEC) evaluated by means of hierarchical cluster analysis and visual representation as dendrograms. The experimental liver toxicity from the different treatments was confirmed by means of concurrent histopathology, liver enzymes, and bilirubin assays. This toxico genomic analysis identified multiple genes and groups of genes that were affected by the hepatotoxicants on study, indicating that high-density microarray expression data are useful to identify groups of genes involved in toxicity. In addition, the mRNA expression profile of an unidentified sample can be accurately identified when compared with the expression profiles resident in the data set. This study supports the use of gene expression-profiling technology to determine or to predict toxic liver effects.

Animals↗
PubMed2005

A discordant sib-pair linkage analysis of age-related macular degeneration.

BACKGROUND: Age-related macular degeneration (AMD) is the leading cause of visual impairment and blindness among older adults in the United States and throughout the developed world. Etiological research implicates both genetic and environmental components. Our prior genome scan in 511 affected sib-pairs and other relative pairs identified significant or suggestive linkage signals on chromosomes 1, 2, 3, 6, 8, 10, 12, 16, and 22. PURPOSE: To search for genetic loci for AMD using the extremely discordant sib-pair (EDSP) method of linkage analysis, which until now has never been applied to the study of AMD. METHODS: The EDSP method is a more powerful approach than standard methods which rely on relative pairs selected at random or pairs concordant for the phenotype. The EDSP approach has also been characterized as the only design that is uniformly powerful in nearly all genetic situations. Thus, substantial reductions in sample size can be achieved. STUDY POPULATION: The study sample for analysis included 110 EDSPs from 40 families that comprise a subset of the 158 families studied in a prior genome-wide scan using affected relative pairs. RESULTS: Evidence for linkage was found on chromosomes 1q, 2q, 6q, 19p, and 20q. The regions identified on chromosomes 1q and 2q were the same regions identified in our prior analysis, whereas the identified region on 6q was approximately 80 cM distal to our previous signal. DISCUSSION: Within this study population, we have narrowed the focus to chromosomes 1q, 2q, 6q, 19p, and 20q in our search for AMD loci. However, given the fact that a gene was recently identified on chromosome 1q, future family- and population-based analyses should concentrate on testing for associations with candidate gene variants in the other identified chromosomal regions in searches for additional AMD loci.

Chromosome Mapping↗
PubMed2006

metaSHARK: a WWW platform for interactive exploration of metabolic networks.

The metaSHARK (metabolic search and reconstruction kit) web server offers users an intuitive, fully interactive way to explore the KEGG metabolic network via a WWW browser. Metabolic reconstruction information for specific organisms, produced by our automated SHARKhunt tool or from other programs or genome annotations, may be uploaded to the website and overlaid on the generic network. Additional data from gene expression experiments can also be incorporated, allowing the visualization of differential gene expression in the context of the predicted metabolic network. metaSHARK is available at http://bioinformatics.leeds.ac.uk/shark/.

Animals↗
PubMed2004

Measurement of refractive state and deprivation myopia in two strains of mice.

PURPOSE: The mouse eye has a bright retinal image (f/number <1) but low optical quality (visual acuity about 0.5 cpd) that may render emmetropization unnecessary. However, this species is potentially a powerful model to study eye growth and myopia because its genome can be readily manipulated and has been completely sequenced. We have investigated how precisely eyes of mice can be refracted and tested whether deprivation myopia can be induced by frosted diffusers. METHODS: An automated eccentric infrared photorefractor was adapted to refract eyes of two mouse strains--C57BL/6 (B6) and DBA/2 (D2)--during Tropicamide cycloplegia without anesthesia. Axial lengths were measured in highly magnified video images of freshly excised eyes. Plastic hemispherical diffusers were applied between postnatal days and 29 and left attached for 7 or 14 days. RESULTS: (1) Trial lenses ranging from +10 to -10 D produced high correlations between the brightness slope in the pupil and applied lens power (r = 0.81 and r = 0.87), demonstrating reliable refraction. Five repeated measures in 12 eyes showed an average standard deviation of 3.0 D, equivalent to an axial length change <10 microm (derived from schematic eye modeling). (2) Deprivation produced a significant shift toward myopia, relative to untreated eyes, but only after 14 days and only in B6 mice (p = 0.02 with or p = 0.00038 without one outlier; N = 9). In contrast, DBA/2J were unaffected by occlusion, perhaps due to mutations that target eye, lens, or anterior segment. (3) Both eyes of untreated animals often had axial lengths that differed markedly. Surprisingly, we detected no significant correlation between refractive error and axial length after treatment. CONCLUSIONS: The infrared refraction technique is sufficiently sensitive to resolve equivalent changes in axial length of only +/- 10 microm in alert mice. Prolonged occlusion produces a significant myopic shift in B6 mice, but not in D2 mice. Even among isogenic B6 mice, the response is variable for reasons that presumably trace back to subtle developmental, environmental, and technical factors.

Animals↗
PubMed2003

Penetrance and phenotype of the Cys433Arg myocilin mutation in a family pedigree with primary open-angle glaucoma.

PURPOSE: To evaluate the penetrance and the clinical characteristics of the Cys433Arg myocilin mutation in a family pedigree with primary open-angle glaucoma. PATIENTS AND METHODS: Primary open-angle glaucoma was defined as untreated intraocular pressure (IOP) over 24 mmHg, with characteristic optic nerve and visual field glaucomatous damage. Patients with IOP <24 mm Hg who were currently being treated for primary open-angle glaucoma were included as affected individuals. Genomic DNA was collected from peripheral blood. PCR, single-strand conformation polymorphism, and sequencing analyses were performed to identify the presence of the Cys433Arg mutation in family members. RESULTS: Of the 48 members of this family evaluated, 17 (35%) were found to harbor the Cys433Arg mutation, 9 (53%) of whom were glaucomatous. None of the 31 individuals without the mutation had glaucoma. Among the 9 patients with glaucoma, 5 had undergone surgical procedure to improve IOP control, including all patients older than 40 years of age. The mutation's penetrance was 0% in persons younger than 10 years (0/4), 40% in those 11 to 30 years (2/5), 75% in persons 30 to 40 years (3/4), and 100% in those older than 40 years (4/4). CONCLUSION: The Cys433Arg mutation in this pedigree was associated with a phenotype characterized by early-onset open-angle glaucoma, which frequently requires surgical intervention and is associated with a high penetrance

Adolescent↗
PubMed2005

ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data.

ChIPOTle (Chromatin ImmunoPrecipitation On Tiled arrays) takes advantage of two unique properties of ChIP-chip data: the single-tailed nature of the data, caused by specific enrichment but not specific depletion of genomic fragments; and the predictable enrichment of DNA fragments adjacent to sites of direct protein-DNA interaction. Implemented as a Microsoft Excel macro written in Visual Basic, ChIPOTle uses a sliding window approach that yields improvements in the identification of bona fide sites of protein-DNA interaction.

Algorithms↗
PubMed1992

Recent advances in fluorescence in situ hybridization.

Fluorescence in situ hybridization (FISH) procedures that directly couple molecular and cytological information allow precise visualization of DNA sequences on metaphase chromosomes and interphase nuclei. These techniques can be used to identify chromosomes, detect chromosomal aberrations, and analyze linear and spatial genome organization. FISH procedures are also used to clinical fields for diagnosis of disease-related chromosome changes and tumor biology.

Animals↗