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At least 1,261 records · Page 70Linked to original sources
PubMed2006

In vitro study of nuclear assembly and nuclear import using Xenopus egg extracts.

Nuclear import is a critical process for the cell: molecules are selectively permitted into the nuclear interior where the sheltered genome resides. The process of nuclear import can be biochemically studied in vitro using nuclei reconstituted from Xenopus egg extract components and Xenopus sperm chromatin. This in vitro system allows for the visualization of nuclear import by monitoring the accumulation of fluorescent nuclear import substrates in the reconstituted nuclei. A powerful aspect of the system is that "biochemically mutant" nuclei can be readily generated, either by immunodepletion of proteins from or addition of proteins to the reaction. This ability allows ascertainment of the role of specific proteins in nuclear import.

Active Transport, Cell Nucleus↗
PubMed2006

Molecular characterization of a deep-sea methanotrophic mussel symbiont that carries a RuBisCO gene.

In our previous investigation on the genes of 1,5-ribulose bisphosphate carboxylase/oxygenase (RuBisCO; EC 4.1.1.39) in deep-sea chemoautotrophic and methanotrophic endosymbioses, the gene encoding the large subunit of RuBisCO form I (cbbL) had been detected in the gill of a mussel belonging to the genus Bathymodiolus from a western Pacific back-arc hydrothermal vent. This study further examined the symbiont source of the RuBisCO cbbL gene along with the genes of 16S ribosomal RNA (16S rDNA) and particulate methane monooxygenase (EC 1.14.13.25; pmoA) and probed for the presence of the ATP sulfurylase gene (EC 2.7.7.4; sopT). The 16S rDNA sequence analysis indicated that the mussel harbors a monospecific methanotrophic Gammaproteobacterium. This was confirmed by amplification and sequencing of the methanotrophic pmoA, while thiotrophic sopT was not amplified from the same symbiotic genome DNA. Fluorescence in situ hybridization demonstrated simultaneous occurrence of the symbiont-specific 16S rDNA, cbbL and pmoA, but not sopT, in the mussel gill. This is the first molecular and visual evidence for a methanotrophic bacterial endosymbiont that bears the RuBisCO cbbL gene relevant to autotrophic CO(2) fixation.

Animals↗
PubMed1996

Expression of the green fluorescent protein-encoding gene from a tobacco mosaic virus-based vector.

A cDNA fragment encompassing the Aequorea victoria green fluorescent protein-encoding gene (gfp) was introduced into a genomic cDNA clone of tobacco mosaic virus (TMV). Infectious RNA transcripts produced in vitro were used to inoculate tobacco (Nicotiana benthamiana) leaves. After 1-2 days, bright green fluorescent areas could be visualized upon illumination with a long-wave ultraviolet (UV) light source. The virus was capable of infecting and expressing gfp in plant tissues both locally (in the inoculated leaf) and systemically (throughout the entire plant). Continued observation of inoculated plants indicated that systemic infection resulted from a combination of two forms of virus movement: a slow, cell-to-cell spread with concomitant virus replication and gfp expression, and a rapid, vascular-mediated form of transport without gfp expression.

Animals↗
PubMed2005

Occurrence and characterization of multiple novel genotypes of Mycobacterium immunogenum and Mycobacterium chelonae in metalworking fluids.

Rapidly growing mycobacteria colonize metalworking fluids, leading to contamination of occupational environments and exposure-related respiratory illnesses in machine workers. Lately, it has been emphasized that these fluids are colonizable by a single genotype of a rapidly growing mycobacterium species, Mycobacterium immunogenum. Here, we report on the genotypic diversity of mycobacteria in these fluids, including isolation and characterization of multiple novel genotypes of two distinct species, Mycobacterium chelonae and M. immunogenum. Using agar culturing and Mycobacterium-specific PCR, 13 mycobacterial isolates were recovered from 100 geographically diverse in-use metalworking fluid samples. Based on restriction fragment length polymorphism of PCR products, DNA sequencing (hsp65 gene segment), and phylogenetic analysis of 16S-23S rDNA internal transcribed spacer (ITS) sequences, six isolates were identified as M. immunogenum and seven as M. chelonae; an additional isolate from metalworking fluid diluent water was identified as M. diernhoferi. Genomic DNA macro-restriction fragment pattern analysis, using pulsed-field gel electrophoresis with XbaI and SpeI restriction digestions, showed intraspecies variation among the isolates of M. immunogenum and M. chelonae. Visual and computer-assisted dendrogram analysis of the XbaI macro-restriction patterns revealed three novel genotypes of M. immunogenum and two of M. chelonae, whereas SpeI macro-restriction patterns revealed only two genotypes for each isolate. None of the identified genotypes matched the reportedly dominant one of M. immunogenum from metalworking fluids. Both mycobacterial species are prevalent in metalworking fluids and there is a considerable strain-level genetic diversity within them.

Bacterial Proteins↗
PubMed2005

Cooperative transitions of isolated Escherichia coli nucleoids: implications for the nucleoid as a cellular phase.

The genomic DNA of Escherichia coli occurs in compact bodies known as nucleoids. Organization and structure of nucleoids are poorly understood. Compact, characteristically shaped, nucleoids isolated by the polylysine-spermidine procedure were visualized by DNA fluorescence microscopy. Treatment with urea or trypsin converted compact nucleoids to partially expanded forms. The transition in urea solutions was accompanied by release of most DNA-associated proteins; the transition point between compact and partially expanded forms was not changed by the loss of the proteins nor was it changed in nucleoids isolated from cells after exposure to chloramphenicol or from cells in which Dps, Fis, or H-NS and StpA had been deleted. Partially expanded forms became dispersed upon RNase exposure, indicating a role of RNA in maintaining the partial expansion. Partially expanded forms that had been stripped of most DNA-associated proteins were recompacted by polyethylene glycol 8,000, a macromolecular crowding agent, in a cooperative transition. DNA-associated proteins are suggested to have relatively little effect on the phase-like behavior of the cellular nucleoid. Changes in the urea transition indicate that a previously described procedure for compaction of polylysine-spermidine nucleoids may have an artifactual basis, and raise questions about reports of repetitive local structures involving the DNA of lysed cells.

Chloramphenicol↗
PubMed1999

Pigmentary retinal dystrophy and the syndrome of maternally inherited diabetes and deafness caused by the mitochondrial DNA 3243 tRNA(Leu) A to G mutation.

OBJECTIVE: To study the association of retinal disease and the syndrome of maternally inherited diabetes and deafness caused by an A to G mutation in the tRNA leucine gene at base pair 3243 (A3243G) of the mitochondrial genome. DESIGN: Observational study of a genetically defined subject group. PARTICIPANTS: Thirteen subjects with the mitochondrial DNA A3243G mutation from seven different pedigrees with maternally inherited diabetes and deafness. INTERVENTION: Assessment of visual symptoms and visual acuity, dilated indirect ophthalmoscopy, retinal photography, and retinal electrophysiology. MAIN OUTCOME MEASURES: Loss of vision, funduscopic evidence of pigmentary retinal disease or diabetic retinopathy, and electrophysiologic evidence of defective functioning of the retinal pigment epithelium/photoreceptor complex. RESULTS: Funduscopic examination revealed abnormalities of retinal pigmentation in ten subjects (77%). Defects included speckled and patchy hyperpigmentation at the posterior pole of the fundus, particularly in the macular area, and varying degrees of loss of retinal pigmentation. Three subjects (23%) had visual symptoms, which included night blindness, visual loss, and photophobia. Electrophysiologic studies revealed impaired electro-oculogram responses in four of nine subjects with defects of retinal pigmentation (44%), two of whom also had much reduced scotopic and, to a lesser extent, flicker electroretinogram b wave potentials. Two subjects had diabetic retinopathy, including one with retinal depigmentation and impaired electro-oculogram activity. Both subjects with diabetic retinopathy had unilateral reduced electroretinogram responses, especially oscillatory potentials. CONCLUSIONS: Abnormalities of retinal pigmentation are common in subjects with maternally inherited diabetes and deafness caused by the mitochondrial DNA A3243G mutation. Visual symptoms, in particular loss of visual acuity, appear to be infrequent. The combination of deficits in the electro-oculogram and scotopic and flicker electroretinograms suggests that the retinal dystrophy includes defective functioning of retinal pigment epithelial cells and of both rod and cone photoreceptors. The pigmentary retinopathy does not prevent diabetic retinopathy; a single subject had funduscopic and electrophysiologic evidence of both diseases. Current evidence suggests that the mitochondrial DNA A3243G mutation accounts for 0.5% to 2.8% of diabetes. Most ophthalmic and diabetic clinics are therefore likely to contain such patients, who may benefit from identification of the genetic defect causing their disease and from genetic counseling.

Adenine↗
PubMed2003

Colocalization of multiple DNA double-strand breaks at a single Rad52 repair centre.

DNA double-strand break repair (DSBR) is an essential process for preserving genomic integrity in all organisms. To investigate this process at the cellular level, we engineered a system of fluorescently marked DNA double-strand breaks (DSBs) in the yeast Saccharomyces cerevisiae to visualize in vivo DSBR in single cells. Using this system, we demonstrate for the first time that Rad52 DNA repair foci and DSBs colocalize. Time-lapse microscopy reveals that the relocalization of Rad52 protein into a focal assembly is a rapid and reversible process. In addition, analysis of DNA damage checkpoint-deficient cells provides direct evidence for coordination between DNA repair and subsequent release from checkpoint arrest. Finally, analyses of cells experiencing multiple DSBs demonstrate that Rad52 foci are centres of DNA repair capable of simultaneously recruiting more than one DSB.

Bacterial Proteins↗
PubMed2005

Inheritance of a novel COL8A2 mutation defines a distinct early-onset subtype of fuchs corneal dystrophy.

PURPOSE: To characterize the genetic basis and phenotype of inherited Fuchs corneal dystrophy (FCD). METHODS: DNA from blood was used for genome-wide linkage scans with tandem repeat polymorphisms. Mutation detection involved sequencing PCR-amplified exons. Families with FCD were clinically evaluated and graded on the Krachmer severity scale. Confocal specular microscopy visualized the morphology of endothelial guttae, small protrusions of Descemet's membrane that are characteristic of FCD. RESULTS: Linkage was obtained to 1p34.3-p32 for the autosomal dominant kindred originally reported by Magovern in 1979. All 21 cases with FCD and one with posterior polymorphous dystrophy were heterozygous for L450W, a novel point mutation in the COL8A2 gene. Of 62 independent cases of familial FCD, none had the previously reported mutations in COL8A2. Corneal guttae in COL8A2 patients were small, rounded, and associated with the endothelial cell center. This contrasts with common FCD, in which guttae were larger, sharply peaked, and initially positioned at edges of endothelial cells. The profile of age and disease severity for the L450W FCD kindred suggested that disease onset occurred in infancy, compared with an average age of onset of 50 years estimated for 201 familial FCD patients in 62 other families. CONCLUSIONS: A novel pathogenic L450W COL8A2 mutation was identified and its highly distinctive pathology characterized. This indicates that COL8A2 mutations give rise to a rare subtype of FCD. This study also provides the first direct evidence that COL8A2-FCD progresses from early to late stages in 25 years, a rate similar to that estimated for late-onset FCD.

Adolescent↗
PubMed2005

FACT--a framework for the functional interpretation of high-throughput experiments.

BACKGROUND: Interpreting the results of high-throughput experiments, such as those obtained from DNA-microarrays, is an often time-consuming task due to the high number of data-points that need to be analyzed in parallel. It is usually a matter of extensive testing and unknown beforehand, which of the possible approaches for the functional analysis will be the most informative. RESULTS: To address this problem, we have developed the Flexible Annotation and Correlation Tool (FACT). FACT allows for detection of important patterns in large data sets by simplifying the integration of heterogeneous data sources and the subsequent application of different algorithms for statistical evaluation or visualization of the annotated data. The system is constantly extended to include additional annotation data and comparison methods. CONCLUSION: FACT serves as a highly flexible framework for the explorative analysis of large genomic and proteomic result sets. The program can be used online; open source code and supplementary information are available at http://www.factweb.de.

Algorithms↗
PubMed2003

Diagnosis of Fasciola gigantica in snail using the polymerase chain reaction (PCR) assay.

The 124-bp repetitive and highly abundant DNA sequence--used as a specific probe for the detection of Fasciola hepatica infection in snails--was tested in the detection of F. gigantica infection in Lymnaea natalensis. The probe did not show any positive PCR results with Lymnaea natalensis, Physa acuta, Biomphalaria alexandrina and Bulinus trucatus or with Schistosoma mansoni, S. haematobium and Echinostoma liei. However, the probe was found capable to detect F. gigantica infection within L. natalensis at very early stages of the prepatent period and at very low concentrations. Thus, the present assay is specific and sensitive for the detection of F. gigantica within its intermediate host. It confirmed the idea that 124-bp repetitive and highly abundant DNA sequence in Fasciola sp. genome could be used as an epidmiological tool for examination of fasciolosis intermediate host. The nucleic acid-based assay could eliminate both inherent uncertainties and lengthy periods of time required for visual examination of the snails. Also, the assay is valuable in epizootiology of F. gigantica, vector suitability and host-parasite relationship.

Animals↗
PubMed2001

[A mutation detection in a transcription factor for adipocyte development in children with severe obesity.].

OBJECTIVE: A substantial proportion of human obesity may be explained by genetic variability. Researchers have tried to identify the important genes in obesity with little sucsess. PPARg2 (peroxisome proliferator activated receptor g 2) is a transcription factor of the nuclear hormone receptor superfamily. It plays a key role in the developement and differentiation of adipocytes. Recently the mutation Pro115Gln in the PPARg2 gene was identified and shown to have a significant correlation with severe obesity. The actual prevalence and distribution of this mutation is not known. The aim of this study was to look for this mutation among Icelandic children suffering from severe obesity. MATERIAL AND METHODS: Thirty-five children and adolescents, aged 4-18, who have been diagnosed with severe obesity participated in the study. Eight parents and siblings aged 19-41 also participated. All study subjects had been obese since early childhood. Body mass index (BMI) was used to describe the phenotype of the subjects. The participants had a BMI of 28.0 to 52.2 kg/m(2). Genomic DNA was extracted from leucocytes. A 131 bp segment was amplified using polymerase chain reaction. The amplified product was digested with the restriction enzyme Hinc II, resolved on agarose gel and visualized under ultraviolet illumination after staining with ethidium bromide. To examine other mutations on the same 131 bp segment enzymatic mutation detection (EMD) was used. Finally the segments giving variable results using EMD were sequenced using the classic Sanger s method. RESULTS: The mutation Pro115Gln was not found in any of the specimens after analysis of the restriction fragment length polymorphism. The results of EMD indicated mutations or polymorphisms in three of the subjects but DNA sequencing failed to confirm these results. CONCLUSIONS: The mutation Pro115Gln or other genetic alternations within the exon examined do not appear to have a significant role in severe early - onset obesity in Icelandic children.

English Abstract↗
PubMed1995

[Searching for hepatitis C virus by immunoelectron microscopy and its morphology].

Many investigators have searched for the causative agent(s) of blood-borne non-A, non-B hepatitis in sera and liver from patients and experimental animals, and have reported various virus-like particles, morphologically resembling parvovirus, togavirus, picornavirus, hepadnavirus, paramyxovirus, papovavirus, retrovirus or bunyavirus. Despite extensive effort, none of these virus-like particles has been confirmed universally as an etiologic virus because of the absence of immunological identification. The frustration was solved by the success in cloning cDNA of the genome of hepatitis C virus (HCV), a major etiologic agent of human non-A, non-B hepatitis, in 1989, but the morphology of HCV remained in riddles. We attempted to visualize HCV by indirect immunogold electron microscopy, using specific antibodies to the putative HCV envelope 1 protein and succeeded in identifying HCV particle in HCV-RNA-rich plasma. Our study showed that HCV particles are 55-65 nm spherical particles with 6 nm fine surface spike-like projections, and have a 30-35 nm inner core.

Hepacivirus↗
PubMed1994

Generation of recombinant herpes simplex virus type 1 to be used for automatic tract tracing.

We generated two insertional beta-galactosidase (lacZ) expressing herpes simplex virus type 1 (HSV-1) with putative mutations in the UL41 or US5 open reading frames. Purified recombinants or wild-type HSV-1 were injected into the left adrenal gland of hamsters. Three days later, virus-infected neurons were visualized with immunohistochemistry in spinal cord sections from all infected hamsters. Neurons were also visualized with X-Gal histochemistry in spinal cord sections from hamsters infected with either of the recombinants but not with the wild-type virus. Insertional mutagenesis of the HSV-1 genome by lacZ did not disrupt the neurotropic properties of the virus. Both recombinant viruses transneuronally labelled the central nervous system (CNS) sympathoadrenal preganglionic neurons and may be useful for the study of synaptic organization of neural circuits. Successful transynaptic transmission of this marker gene into CNS neurons from a peripheral organ suggests that other foreign genes may also be delivered into CNS neurons using HSV-1.

Adrenal Glands↗
PubMed1997

Phylogenetic affinity of mitochondria of Euglena gracilis and kinetoplastids using cytochrome oxidase I and hsp60.

The mitochondrial DNA-encoded cytochrome oxidase subunit I (COI) gene and the nuclear DNA-encoded hsp60 gene from the euglenoid protozoan Euglena gracilis were cloned and sequenced. The COI sequence represents the first example of a mitochondrial genome-encoded gene from this organism. This gene contains seven TGG tryptophan codons and no TGA tryptophan codons, suggesting the use of the universal genetic code. This differs from the situation in the mitochondrion of the related kinetoplastid protozoa, in which TGA codes for tryptophan. In addition, a complete absence of CGN triplets may imply the lack of the corresponding tRNA species. COI cDNAs from E. gracilis possess short 5' and 3' untranslated transcribed sequences and lack a 3' poly[A] tail. The COI gene does not require uridine insertion/ deletion RNA editing, as occurs in kinetoplastid mitochondria, to be functional, and no short guide RNA-like molecules could be visualized by labeling total mitochondrial RNA with [alpha-32P]GTP and guanylyl transferase. In spite of the differences in codon usage and the 3' end structures of mRNAs, phylogenetic analysis using the COI and hsp60 protein sequences suggests a monophyletic relationship between the mitochondrial genomes of E. gracilis and of the kinetoplastids, which is consistent with the phylogenetic relationship of these groups previously obtained using nuclear ribosomal RNA sequences.

Animals↗
PubMed2000

Factor analysis of confocal image sequences of human papillomavirus DNA revealed with fast red in cervical tissue sections stained with TOTO-iodide.

OBJECTIVE: To visualize and localize specific DNA sequences by fluorescence in situ hybridization, confocal laser scanning microscopy (CLSM) and factor analysis of biomedical image sequences (FAMIS). STUDY DESIGN: Human papillomavirus (HPV) DNA was identified in cervical tissue sections with biotinylated DNA probes recognizing the whole genome of HPV DNA types 18 and 16, and DNA-DNA hybrids were revealed by streptavidin-alkaline phosphatase and Fast Red (FR). Cell nuclei were counterstained with TOTO-iodide. Image sequences were obtained using successive dynamic or spectral sequences of images on different optical slices from CLSM. The location of fluorescent signals inside tissue preparations was determined by FAMIS and/or selection of filters at emission. Image sequences were summarized into a reduced number of images, called "factor images," and curves, called "factors." Factors estimate spectral patterns and depth emission profiles. Factor images correspond to spatial distributions of the different factors. RESULTS: We distinguished between FR and nucleus staining in HPV DNA hybridization signals by taking into account differences in their spectral patterns and improved visualization by taking into account differences in their focus (depth emission profiles). CONCLUSION: FAMIS, together with CLSM, made possible the detection and characterization of HPV DNA sequences in cells of cervical tissue sections.

Azo Compounds↗
PubMed2005

InSNP: a tool for automated detection and visualization of SNPs and InDels.

Availability of high quality SNP data is a rate-limiting factor in understanding the impact of genetic variability on gene function and phenotype. Although global projects like HAPMAP generate large numbers of SNPs in an even spacing throughout the human genome, many variation studies have a more focused approach: in the follow-up of positional association findings, candidate gene studies, and functional genomics experiments, knowledge of all variations in a limited amount of sequence (e.g., a gene) is needed. This leads to a large number of resequencing experiments, for which there is a surprising lack of analysis software. We have thus developed specialized software (InSNP) for targeted mutation detection and compared its performance to Polyphred and Mutation Surveyor using 28 amplicons. Out of a total of 579 (InSNP), 644 (Polyphred), and 526 (Mutation Surveyor) SNP predictions, 39 SNPs were confirmed by human expert inspection, with five SNPs missed by Polyphred and one missed by InSNP using the default settings. For InDel detection, out of 70 (InSNP), 28 (Polyphred), and 693 (Mutation Surveyor) InDel predictions, two InDels were confirmed by human expert inspection, with one InDel missed by Polyphred. InSNP provides a user-friendly interface with better functionality for mutation detection than general-purpose sequence handling software. It provides similar SNP detection sensitivity and specificity as the public domain and commercial alternatives in the investigated dataset. We hope that InSNP lowers the barriers to the use of automated mutation detection software and aids in the improvement of the efficiency of such experiments. The Windows installer (setup) program and sample datasets are available at www.mucosa.de/insnp/.

Algorithms↗
PubMed1998

Tools for visualization and integration of intermediate sequencing results in large disease gene discovery projects.

We describe two Java applets which are useful for insightful presentation of intermediate experimental data in gene discovery projects involving large scale sequencing. One of these applets provides a physical map of a genomic region and provides easy access to the second applet, which furnishes a detailed map of sequence contigs associated with clones on the physical map. In particular, the second applet displays all the known information about each contig, including the presence of exons, database homology 'hits', repetitive elements and other features; the graphics are linked to other World Wide Web pages, providing detailed information on each feature. These applets should be useful to other research groups working on large sequencing projects.

Chromosome Mapping↗
PubMed2006

Detection and quantification of Erysiphe necator DNA in wine grapes and resultant must and juice.

Powdery mildew of grapevines is difficult to assess visually at the weighbridge, particularly in large consignments of machine-harvested fruit. To facilitate accurate methods for the detection and quantification of the disease in grape samples obtained from both the vineyard and winery, we developed a DNA probe for the pathogen Erysiphe necator. The E. necator-specific 450 bp DNA fragment pEnA1, targets highly repetitive sequences and was isolated from a partial genomic library. In screening for species specificity, clone pEnA1 was used in slot-blot hybridization and detected E. necator DNA from grapes and resultant must and juice, but not from clarified juice and wine. The detection threshold was approximately 50 pg of E. necator DNA per 100 ng total DNA of grape sample and was equivalent to 1-5% of a grape bunch visually affected by powdery mildew. Disease severity, expressed as the percentage of surface area of a bunch with powdery mildew, and E. necator DNA content were highly correlated, r2=0.955, P<0.001. The DNA-based hybridization assay has the potential to predict the severity of powdery mildew in grape samples from the vineyard and in must and juice samples at the winery. The DNA sequence of clone pEnA1 was used to design species-specific primers, the results maintaining the same specificity patterns observed in the initial hybridization assays. The PCR-based assay was sensitive enough to detect approximately 1 pg DNA, being equivalent to 1 conidium per sample. This is the first report to date of the detection of all known phenetic groups of E. necator DNA and of the quantification of DNA from grape samples at the winery. Accurate information on the extent of powdery mildew contamination of grape lots would enable wineries to make more informed decisions about the use of fruit and must.

Ascomycota↗