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PubMed1978

A-T rich sequences in vertebrate DNA. A possible explanation of q-banding in metaphase chromosomes.

Partially denatured DNAs from mouse, cow, and chicken were visualized in the electron microscope by the basic protein film technique and the size and distribution of the denatured regions characterized. A-T rich sequences visualized at 15% denaturation average about 1500 bases in length for all three species and are arranged quite non-randomly in the genome. This arrangement is such that 30--50% of the entire genome contains no A-T rich DNA, and another 20% is composed about one-half of A-T rich sequences and one-half of other sequences. Comparison with DNA denaturation profiles indicates that for each organism these sequences are from 25--30% G+C and that there is very little if any DNA more A-T rich than these. Estimates from published studies of fluorescence enhancement of quinacrine bound to A-T rich DNAs suggest that the observed non-random organization of A-T rich sequences is sufficient to account for Q banding of metaphase chromosomes.

Adenine↗
PubMed2003

A review of primary hereditary optic neuropathies.

The primary inherited optic neuropathies are a heterogeneous group of disorders that result in loss of retinal ganglion cells, leading to the clinical appearance of optic atrophy. They affect between 1:10,000 to 1:50,000 people. The main clinical features are a reduction in visual acuity, colour vision abnormalities, centro-caecal visual field defects and pallor of the optic nerve head. Electrophysiological testing shows a normal flash electroretinogram, absent or delayed pattern visually evoked potentials suggestive of a conduction deficit and N95 waveform reduction on the pattern electroretinogram, consistent with a primary ganglion cell pathology. The primary inherited optic neuropathies may be sporadic or familial. The mode of inheritance may be autosomal dominant, autosomal recessive, X-linked recessive or mitochondrial. Within each of these groups, the phenotypic characteristics vary in such features as the mode and age of onset, the severity of the visual loss, the colour deficit and the overall prognosis. A number of different genes (most as yet unidentified) in both nuclear and mitochondrial genomes, underlie these disorders. The elucidation of the role of the encoded proteins will improve our understanding of basic mechanisms of ganglion cell development, physiology and metabolism and further our understanding of the pathophysiology of optic nerve disease. It will also improve diagnosis, counselling and management of patients, and eventually lead to the development of new therapeutic modalities.

Chromosomes, Human, X↗
PubMed2005

Dual hereditary jaundice: simultaneous occurrence of mutations causing Gilbert's and Dubin-Johnson syndrome.

BACKGROUND & AIMS: Dubin-Johnson syndrome is recessively inherited, conjugated hyperbilirubinemia induced by mutations in the ABCC2/MRP2 gene encoding the canalicular transporter for conjugated bilirubin. Gilbert's syndrome is recessively inherited, unconjugated hyperbilirubinemia caused by decreased conjugation rate of bilirubin associated mostly with homozygous A(TA) 7 TAA variant of the TATAA-box in the UGT1A1 gene promoter. Our aim was to establish the molecular diagnosis in a 3-year-old male with atypical, intermittent, predominantly unconjugated, hyperbilirubinemia. METHODS: 99m Tc-HIDA cholescintigraphy was used for imaging the biliary tree. Expression of ABCC2/MRP2 protein in hepatocytes was investigated immunohistochemically. UGT1A1 and ABCC2/MRP2 genes were sequenced from genomic DNA, and the mutations were verified by fragment analysis, sequencing the cloned exons, and restriction fragment length polymorphism. RESULTS: Cholescintigraphy revealed delayed visualization of the gallbladder. A brown granular lipopigment differing from melanin-like pigment reported in Dubin-Johnson syndrome was present in hepatocytes, but, otherwise, liver histology was normal. ABCC2/MRP2 protein was not detected on the canalicular membrane of hepatocytes, and 2 novel mutations were found in the ABCC2/MRP2 gene: a heterozygous in-frame insertion-deletion mutation 1256insCT/delAAACAGTGAACCTGATG in exon 10 inherited from the father and a heterozygous deletion 4292delCA in exon 30 inherited from the mother. In addition, the patient was homozygous for -3279T>G and A(TA) 7 TAA mutations in the UGT1A1 gene promoter. CONCLUSIONS: Our patient represents a case of digenic mixed hyperbilirubinemia-a distinct type of constitutive jaundice resulting from coinherited defects in ABCC2/MRP2 and UGT1A1 genes.

Child, Preschool↗
PubMed1986

Introduction and expression of the bacterial PaeR7 methylase gene in mammalian cells.

An approach is devised for studying the role of DNA methylation in eukaryotic gene expression. The approach is based on the expression of site-specific bacterial methylase genes in animal cells. A model system using the cloned PaeR7 (an isoschizomer of Xho I) methylase gene was constructed to test the feasibility of this approach. Expression plasmids for the PaeR7 methylase gene were introduced into mouse Ltk- cells by cotransfection with the cloned chicken thymidine kinase (tk) gene. Several of the cell strains derived from Tk+ colonies were found to express the PaeR7 gene as judged by four criteria: the cellular DNA of these strains showed increased resistance to cleavage by Xho I; these strains contained cellular proteins that comigrated with pure PaeR7 methylase protein, as visualized by immunoblotting; PaeR7 methylase activity was found in vitro in crude extracts of total cellular protein from these strains; and murine adenovirus genomes grown on cells expressing PaeR7 methylase showed resistance to cleavage to PaeR7 endonuclease. The potential applications of this approach for the study of cellular and viral gene regulation, DNA repair, and restriction modification are discussed.

Animals↗
PubMed1994

Cell size predicts morphological complexity in the brains of frogs and salamanders.

The morphological organization of the brain of frogs and salamanders varies greatly in the degree to which it is subdivided and differentiated. Members of these taxa are visually oriented predators, but the morphological complexity of the visual centers in the brain varies interspecifically. We give evidence that the morphological complexity of the amphibian tectum mesencephali, the main visual center, can be predicted from knowledge of cell size, which varies greatly among these taxa. Further, cell size is highly correlated with genome size. Frogs with small cells have more complex morphologies of the tectum than do those with large cells independent of body and brain size. In contrast, in salamanders brain-body size relationships also are correlated with morphological complexity of the brain. Small salamanders with large cells have the simplest tecta, whereas large salamanders with small cells exhibit the most complex tectal morphologies. Increases in genome, and consequently cell size, are associated with a decrease in the differentiation rate of nervous tissue, which leads to the observed differences in brain morphology. On the basis of these findings we hypothesize that important features of the structure of the brain can arise independently of functional demands, from changes at a lower level of organismal organization--in this case increase in genome size, which induces simplification of brain morphology.

Animals↗
PubMed2001

Factors controlling embryo viability.

Many diverse factors affect embryo viability. The morphological measures routinely used to grade human embryos are of limited use as many of the factors influencing the longterm viability of embryos are genetic or molecular and are undetectable or inconclusive from visualization of living embryos by microscopy. This article presents examples of factors that are known to affect embryo viability, including gamete formation, embryonic genome activation, and im-printing. Aspects of both gamete and embryo development are addressed, and the possibility that various anomalies remain hidden for extended periods before impacting upon a later aspect of development is hypothesized. In future, more detailed and informative assessments of embryo viability before embryo transfer may require invasive approaches to study the composition of embryos at various stages of preimplantation development; however, indirect, non-invasive measures would be preferable.

Aging↗
PubMed2006

Molecular imaging: a primer for interventionalists and imagers.

The characterization of human diseases by their underlying molecular and genomic aberrations has been the hallmark of molecular medicine. From this, molecular imaging has emerged as a potentially revolutionary discipline that aims to visually characterize normal and pathologic processes at the cellular and molecular levels within the milieu of living organisms. Molecular imaging holds promise to provide earlier and more precise disease diagnosis, improved disease characterization, and timely assessment of therapeutic response. This primer is intended to provide a broad overview of molecular imaging with specific focus on future clinical applications relevant to interventional radiology.

Animals↗
PubMed2005

Distinct segregation dynamics of the two Vibrio cholerae chromosomes.

The study of prokaryotic chromosome segregation has focused primarily on bacteria with single circular chromosomes. Little is known about segregation in bacteria with multipartite genomes. The human diarrhoeal pathogen Vibrio cholerae has two circular chromosomes of unequal sizes. Using static and time-lapse fluorescence microscopy, we visualized the localization and segregation of the origins of replication of the V. cholerae chromosomes. In all stages of the cell cycle, the two origins localized to distinct subcellular locations. In newborn cells, the origin of chromosome I (oriCIvc) was located near the cell pole while the origin of chromosome II (oriCIIvc) was at the cell centre. Segregation of oriCIvc occurred asymmetrically from a polar position, with one duplicated origin traversing the length of the cell towards the opposite pole and the other remaining relatively fixed. In contrast, oriCIIvc segregated later in the cell cycle than oriCIvc and the two duplicated oriCIIvc regions repositioned to the new cell centres. DAPI staining of the nucleoid demonstrated that both origin regions were localized to the edge of the visible nucleoid and that oriCIvc foci were often associated with specific nucleoid substructures. The differences in localization and timing of segregation of oriCIvc and oriCIIvc suggest that distinct mechanisms govern the segregation of the two V. cholerae chromosomes.

Chromosome Segregation↗
PubMedDate not supplied

Adult-onset primary open angle glaucoma does not localize to chromosome 2cen-q13 in North American families.

Glaucoma is one of the leading causes of irreversible blindness in the world and is characterized by elevated intraocular pressure, optic nerve atrophy, and progressive visual field loss. Primary open angle glaucoma (POAG) is the most common subtype of glaucoma in the United States. Recently, Stoilova and coworkers [Genomics 1996;36:142-150] identified a locus for POAG on chromosome 2 (2cen-q13) in families primarily located in the United Kingdom. We examined families with POAG identified within the US for linkage to the 2cen-q13 locus. A total of 18 families with POAG were used in the analysis. Of 77 family members, 46 were classified as affected and 31 were either glaucoma suspects or considered normal. Eight highly polymorphic and informative markers flanking and distributed throughout the region were used. Parametric lod score analysis was performed using both a dominant and recessive low penetrance or 'affecteds-only' model. Multipoint affected sibpair exclusion mapping was also performed. Lod score (both models) and sibpair analysis excluded linkage of the POAG phenotype to the 2cen-q13 region in these families. These data suggest that the chromosome 2cen-q13 locus does not explain a substantial amount of genetic variation in familial POAG.

Adult↗
PubMedDate not supplied

Porcine repeat element DNA: in situ detection of xenotransplanted cells.

Using a digoxygenin-labelled DNA probe derived from the porcine repeat element PRE-1, we have developed a protocol for the detection of transplanted porcine islets and hepatocytes against a background of murine host tissue. Analysis of this probe by Southern blotting indicated that PRE-1 hybridizes to pig genomic DNA but not to human or mouse DNA. On tissue sections, hybridizing probe was detected using alkaline phosphatase-conjugated antidigoxygenin antibody visualized with 5-bromo-4-chloro-3-indolyl-phosphate/4-nitro-blue tetrazolium chloride (BCIP/NBT) substrate. We have demonstrated sensitive and highly specific staining of porcine nuclei in fixed, paraffin embedded tissue sections, and have applied the technique to detect porcine pancreatic islets and hepatocytes transplanted into murine kidney and spleen. Application of this technique include detection of transplanted cells or organs across the variety of xenogeneic barriers.

Animals↗
PubMed1996

PCR detection of acute Ehrlichia canis infection in dogs.

A polymerase chain reaction (PCR)-based detection assay that specifically detected Ehrlichia canis in dogs with acute infections was developed. A region of the 16S ribosomal RNA gene of E. canis was targeted for PCR amplification and chemiluminescent hybridization (CH) with a complementary internal 287-base pair (bp) oligonucleotide probe. The CH improved the PCR assay sensitivity 1,000-fold as compared with visualization on ethidium bromide-stained agarose gels. The PCR assay with CH (PCR/CH) detected as little as 30 fg of E. canis genomic DNA, the equivalent of approximately 150 E. canis organisms. The 495-bp product defined by the specific primers was not detected when genomic DNA from E. platys, E. chaffeensis, E. risticii, and E. equi were used in the PCR/CH assay. The PCR/CH assay was tested with unfractionated blood samples collected from 9 dogs experimentally infected with E. canis. The PCR/CH assay had greater detection sensitivity than did cell culture isolation (CCI) from infected blood. PCR/CH detected E. canis 7 days prior to CCI in 4 of 6 experimentally infected dogs. The results obtained with the PCR/CH assay otherwise consistently matched the results obtained by CCI. This PCR/CH assay is a rapid, sensitive, and specific method for E. canis detection with sensitivity comparable to or exceeding that of CCI. A diagnosis of E. canis using this PCR/CH assay can be made in 2 days as compared with 1-4 weeks for CCI. The PCR/CH assay appears to be an acceptable alternative or complement to current diagnostic techniques.

Animals↗
PubMed2004

Restriction endonuclease accessibility as a determinant of altered chromatin structure.

Active genes in eukaryotic genomes are typically found in open, nuclease-sensitive regions of chromatin. This chapter presents an overview of the techniques used to assay restriction endonuclease cleavage of chromosomal DNA as an approach to assess general accessibility at a genomic region of interest. We describe protocols to (1) prepare nuclei templates, (2) treat chromosomal DNA with a restriction enzyme(s), and (3) visualize and quantify chromosomal cleavage(s), with an emphasis on ligation-mediated (LM) PCR techniques.

Animals↗
PubMed2004

Novel paramagnetic contrast agents for molecular imaging and targeted drug delivery.

Molecular biology and genomic sciences are revealing the early biological signatures for many diseases. In response, the Molecular Imaging community is rapidly developing contrast agents to visualize the nascent pathological changes and to concomitantly deliver treatment directly to the site of disease. The evaluation, development and use of these new agents require a complementary understanding of contrast chemistry and imaging techniques. The fundamental issues surrounding magnetic contrast agent development, rational drug delivery, MR molecular imaging, and their interdependence are elucidated.

Animals↗
PubMed2002

[Molecular epidemiology of Mycobacterium tuberculosis: its accomplishment and future perspective].

In the traditional study of tuberculosis epidemiology, information about social contact of persons and patient's illness history used to be an only relevant basis for elucidating transmission of tuberculosis infection. Therefore, it was very difficult to give a clear conclusion of whether isolates from different patients derived from a common source of infection or not. Recently, the subspecies typing of M. tuberculosis strains has become possible, based on the visualization of multiple loci of an insertion sequence (IS6110) that is a relatively stable gene fragment existing in a specific region of the genome. The variability of the number of copies and locations of this IS6110 in a genome is the basis that enables this technique to be used for the above purpose, which is a unique tool applicable to the analysis of M. tuberculosis. Generally, this technique, i.e., restriction fragment length polymorphism (RFLP) analysis, depends on the diversity of pattern of any polymorphic marker found in a genome of a strain. Among various markers so far developed and examined, IS6110 has been proved most appropriate for the purpose of typing strains of M. tuberculosis complex, especially in such circumstances as in Japan where isolated strains' RFLP patterns are similar each with others so that finer subtyping is needed. In this lecture, I would like to review the following topics based on the world literature of molecular epidemiology and the findings of our own that we have achieved during 1992 through 2001 in our Institute; 1) typing of the isolates for the identification of the infection source, 2) pathogenesis of tuberculosis under low incidence situation, 3) predominance of certain genotypes endemic in an area, 4) cross-contamination of isolates in the laboratory, 5) the stability of IS6110 patterns, 6) phylogeny of M. tuberculosis complex, and 7) differentiation between M. tuberculosis and M. bovis BCG.

DNA Transposable Elements↗
PubMed1997

Disease expression in X-linked retinitis pigmentosa caused by a putative null mutation in the RPGR gene.

PURPOSE: To determine the disease expression in X-linked retinitis pigmentosa (XLRP) caused by a putative null mutation in the RPGR (retinitis pigmentosa GTPase regulator) gene. METHODS: In a family with XLRP, haplotype analysis was performed with polymorphic microsatellite markers from the Xp chromosomal region, and genomic polymerase chain reaction sequencing was used to identify sequence variations in the RPGR gene. Hemizygotes and heterozygotes were evaluated clinically and with visual function tests. Optical coherence tomography (OCT) was performed on heterozygotes. Postmortem donor retinas from a heterozygote were examined by microscopy and immunocytochemistry. RESULTS: X-linked inheritance was confirmed by haplotype analysis using Xp markers. Sequence analysis of the RPGR gene identified a single base pair change, a G-->T transversion, that converts codon 52 GGA (Gly) to TGA (stop codon); the mutation segregates with the disease. A hemizygote in the third decade of life had barely measurable rod function and severely impaired cone function that diminished further over a 7-year interval. Heterozygotes varied in degree of disease expression from mild to severe. Perimetry showed loci with normal rod and cone sensitivity interspersed with loci having either equal rod and cone dysfunction or rod > cone dysfunction. Electroretinographic photoreceptor responses had equal reductions in rod and cone maximal amplitude. OCT cross sectional reflectance images of retinal regions with severe dysfunction showed reduced thickness of the retina and retinal pigment epithelium-choriocapillaris (RPE-CC) complex and increased reflections posteriorly. Regions with mild dysfunction showed similar OCT findings but with preserved retinal thickness. Retinal histopathology in a heterozygote revealed loss of photoreceptors throughout, with retention of only a few islands of cones with tiny or absent outer segments and rods lacking outer segments. CONCLUSIONS: This RPGR gene mutation, in its mildest expression in heterozygotes, causes a relatively equal disturbance of rod and cone photoreceptor function. Detectable structural change by OCT at the level of the RPE-CC can be present in patches of retina with minimal functional disturbance. More advanced disease stages in heterozygotes show greater rod than cone dysfunction, and the end stage in hemizygotes and heterozygotes is that of typical RP, with only barely detectable cone function from residual cones in a thinned retina with abnormal RPE and choriocapillaris.

Adult↗
PubMed2003

Development of gene ontology tool for biological interpretation of genomic and proteomic data.

We have designed and developed a Gene Ontology based navigation tool, GoMiner, which organizes lists of interesting genes from a microarray or a protein array experiment for biological interpretation. It provides quantitative and statistical output files and useful visualization (e.g., a tree-like structure) to map the list of genes to its biological functional categories. It also provides links to other resources such as pubmed, locuslink, and biological molecular interaction map and signaling pathway packages.

Computational Biology↗
PubMed1993

Infectious virus replication in papillomas induced by molecularly cloned cottontail rabbit papillomavirus DNA.

The ability to obtain infectious papillomavirus virions from molecularly cloned DNA has not been previously reported. We demonstrate here that viral genomes isolated from a recombinant++ DNA clone of cottontail rabbit papillomavirus (CRPV) gave rise to infectious virus when inoculated into cottontail rabbit skin. Replication occurred in papillomas that formed at inoculation sites. Extract of a DNA-induced papilloma was serially passaged to naive rabbits with high efficiency. Complete virus was fractionated on cesium chloride density gradients, and papillomavirus particles were visualized by electron microscopy. CRPV DNA isolated from virions contained DNA sequence polymorphisms that are characteristic of the input CRPV-WA strain of virus, thereby proving that the newly generated virus originated from the molecularly cloned viral genome. These findings indicate that this will be a useful system in which to perform genetic analysis of viral gene functions involved in replication.

Animals↗
PubMed1989

Detection of point mutations in amplified single copy genes by biotin-labelled oligonucleotides: diagnosis of variants of alpha-1-antitrypsin.

Specific analysis for point mutations in genomic DNA has until recently been a difficult and time-consuming task, using large amounts of unstable, hazardous and expensive 32P. By enzymatically amplifying the mutation-bearing sequence of the DNA the sensitivity of the analysis is increased several 100-fold, making the detection possible with stable, non-radioactive and inexpensive biotinylated oligonucleotides. We have applied this method (polymerase chain reaction (PCR] to the detection of the Z-mutation in the alpha-1-antitrypsin gene. After amplification, dot-blots of amplified DNA were subjected to hybridization with allele specific biotinylated oligonucleotide probes and washed at temperatures giving allele specificity. The bound biotin was visualized with avidin conjugated alkaline phosphatase using 5-bromo-4-chloro-3-indolylphosphate and nitro blue tetrazolium as colour reagents. The detection can be performed on less than 1 microgram genomic DNA, and is therefore applicable on small amounts of blood, fibroblasts and chorionic villus biopsies.

Base Sequence↗