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At least 1,531 records · Page 85Linked to original sources
PubMed2005

Cellular localization of human Rad51C and regulation of ubiquitin-mediated proteolysis of Rad51.

Rad51-catalyzed homologous recombination is an important pathway for repair of DNA double strand breaks and maintenance of genome integrity in vertebrate cells. Five proteins referred to as Rad51 paralogs promote Rad51 activity and are proposed to act at various, and in some cases, multiple stages in the recombination pathway. Imaging studies of native Rad51 have revealed its cellular response to DNA damage, yet visualization of the paralog proteins has met with limited success. In this study, we are able to detect endogenous Rad51C and Xrcc3 in human cells. In an effort to determine how Rad51, Rad51C, and Xrcc3 influence the pattern of localization of each other over the time course of DNA damage and repair, we have made the unexpected observation that Rad51 degradation via the ubiquitin-mediated proteasome pathway occurs as a natural part of recombinational DNA repair. Additionally, we find that Rad51C plays an important role in regulating this process. This article contains supplementary material, which may be viewed at the Journal of Cellular Biochemistry website at http://www.interscience.wiley.com/jpages/0730-2312/suppmat/index.html.

Animals↗
PubMed2026

Multi-omics panorama of glaucoma: Pathogenesis, biomarkers, and novel therapeutic strategies.

Glaucoma is a group of irreversible, blinding eye diseases characterized by progressive loss of retinal ganglion cells, leading to gradual visual field defects that severely impact patients' quality of life. Its complex pathophysiological mechanisms remain incompletely understood, limiting the development of early diagnostic and effective therapeutic strategies. Advances in omics technologies have provided new insights into elucidating the pathophysiology of glaucoma. We summarize specific alterations in genomics, transcriptomics, proteomics, metabolomics, epigenomics, and microbiomics associated with glaucoma. We emphasize the systematic analysis of disease mechanisms, identification of clinically applicable biomarkers, and discovery of novel therapeutic targets through the integration of these data. This approach paves new pathways for glaucoma subtype diagnosis and personalized treatment, while also outlining future research directions and challenges.

Humans↗
PubMed1973

Structure and development of neuronal connections in isogenic organisms: variations and similarities in the optic system of Daphnia magna.

It is readily apparent upon examination and comparison of organisms of the same and related species that to a large extent genes control morphological features. One means to ascertain the role and degree of genetic control is to study in detail the anatomy and development of a particular structure, say an identifiable neuron, in a population with a fixed genome, and at different stages of morphogenesis. The small crustacean, Daphnia, is well suited for this type of study, since it reproduces parthenogenically, its development is easily staged, and its nervous system is reasonably simple. In this paper comparisons of detailed morphology of neurons in the visual system of adult Daphnia magna are considered. Results indicate that gross features of the system are reproduced within the clone, but some of the finer details are not reproduced.

Animals↗
PubMedDate not supplied

Postnatal refractive development in the Brown Norway rat: limitations of standard refractive and ocular component dimension measurement techniques.

PURPOSE: The genetic tractability of the rat and its larger eye size as compared to the mouse make it an attractive model for studies of ocular development and emmetropisation. This study aimed to provide normative data in the strain of rat being used for the rat genome sequencing project whilst also evaluating standard measurement techniques. METHODS: Ocular refraction (retinoscopy, Hartinger coincidence optometry) and ocular component dimensions (keratometry, A-scan ultrasonography, calliper measures, eye weight) were measured at intervals from eye-opening to adulthood. RESULTS: There was no convincing evidence of visually guided emmetropisation during normal development. Key measurement techniques such as high-resolution A-scan ultrasonography, which work effectively in several other animal species, were unusable or inaccurate in the rat. CONCLUSIONS: This study found no evidence of emmetropisation during normal development in rat. As in mice, technical difficulties prevent accurate measurement of ocular refraction and vitreous chamber depth and may complicate tests of emmetropisation to imposed blur.

Aging↗
PubMed2026

ssHiCstuff: a package for the design and analysis of ssDNA-specific Hi-C experiments.

MOTIVATION: Single-strand DNA-specific Hi-C (ssHi-C) is a recently developed technique enabling the capture of chromatin interactions involving single-stranded DNA (ssDNA), an intermediate of various DNA metabolic processes. ssHi-C entails the restoration of restriction sites in ssDNA regions of interest upon introduction of designer, internally barcoded "annealing oligonucleotides" prior to the restriction digestion step of Hi-C. The design of these "annealing oligonucleotides," as well as the analysis of the resulting ssHi-C data presents specific challenges, such as (i) differentiating ssDNA from dsDNA-derived contacts, (ii) tracking probe-specific interactions, and (iii) calibrating the amount of ssDNA contacts across biological samples. Dedicated computational tools are therefore needed to facilitate the design of, and extract biological information from, ssHi-C experiments. RESULTS: We present ssHiCstuff, a Rust- and Python-based package for the design of key reagents for ssHi-C experiments and for the analysis of ssHi-C data. ssHiCstuff provides (i) an automated annealing oligonucleotides design module, (ii) an end-to-end analyses pipeline, and (iii) a graphical user interface. ssHiCstuff simplifies the high-resolution analysis of ssDNA interactions at genome-wide scale. A graphical user interface (GUI) implemented in Python is also available for biologists without coding skills. AVAILABILITY: ssHiCstuff is freely available at https://github.com/Piazzalab/ssHiCstuff and https://zenodo.org/records/19677479 (https://doi.org/10.5281/zenodo.19677479) under the GPL 3.0 license. The annealing oligonucleotides design and the visualization modules are additionally freely available on a web browser at https://bioshiny.ens-lyon.fr/public/app/sshicstuff. A test dataset is available at https://zenodo.org/records/20035366 (https://doi.org/10.5281/zenodo.20035366).

DNA, Single-Stranded↗
PubMed2005

DIG--a system for gene annotation and functional discovery.

SUMMARY: We describe a database and information discovery system named DIG (Duke Integrated Genomics) designed to facilitate the process of gene annotation and the discovery of functional context. The DIG system collects and organizes gene annotation and functional information, and includes tools that support an understanding of genes in a functional context by providing a framework for integrating and visualizing gene expression, protein interaction and literature-based interaction networks.

Chromosome Mapping↗
PubMed1999

Ribotyping of Vibrio parahaemolyticus isolates obtained from food poisoning outbreaks in Taiwan.

Vibrio parahaemolyticus is a prevalent food-borne pathogen in Taiwan, Japan and other Asian countries. This work presents a novel ribotyping method for the molecular epidemiological examination of this pathogen. Genomic DNA was fragmented by HindIII digestion and hybridized with cDNA probe for Escherichia coli 16S and 23S RNA genes. A total of 121 isolates obtained from outbreaks during 1992 and 1994 in Taiwan were characterized by this ribotyping method. Four to seventeen restricted fragments were visualized in these isolates. After hierarchical cluster analysis, these isolates were grouped into thirty different ribotypes. In addition, A3, A7, E3 and F1 were the major ribotypes, consisting of 22.3, 13.2, 9.1, and 8.3% of the isolates, respectively. A, E, F, G and B were the major groups, consisting of 46.2, 14.0, 9.1, 6.7, and 6.7% of the isolates, respectively. The discriminatory ability of this ribotyping method, as determined by Simpson's index of diversity, was 0.93, which closely resembled that of a previously reported pulsed-field gel electrophoresis method.

Bacterial Typing Techniques↗
PubMed2004

Application of genotypic and phenotypic analyses to commercial probiotic strain identity and relatedness.

AIMS: The objective of this study was to generate strain-specific genomic patterns of a bank of 67 commercial and reference probiotic strains, with a focus on probiotic lactobacilli. METHODS AND RESULTS: Pulsed-field gel electrophoresis (PFGE) was used as the primary method for strain differentiation. This method was compared with carbohydrate fermentation analysis. To supplement visual comparison, PFGE patterns were analysed quantitatively by cluster analysis using unweighted pair group method with arithmetic averages. SmaI, NotI and XbaI were found to effectively generate clear and easy-to-interpret PFGE patterns of a range of probiotic strains. Some probiotic strains from different sources shared highly similar PFGE patterns. CONCLUSIONS: Results document the value of genotypic strain identification methods, combined with phenotypic methods, for determining probiotic strain identity and relatedness. No correlation was found between relatedness determined by carbohydrate fermentation profiles alone compared with PFGE analysis alone. Some commercial strains are probably derived from similar sources. SIGNIFICANCE AND IMPACT OF THE STUDY: This approach is valuable to the probiotic industry to develop commercial strain identification patterns, to provide quality control of strain manufacturing production runs, to track use of protected strains and to determine the relatedness among different research and commercial probiotic strains.

Bacterial Typing Techniques↗
PubMed1995

Assignment of the uteroferrin gene (ACP5) to swine chromosome 2q12-->q21 by fluorescence in situ hybridization.

A cosmid clone containing the uteroferrin gene (ACP5) was selected from a cosmid library of swine genomic fragments by colony hybridization using uteroferrin cDNA as a probe. The genomic fragment thus cloned was examined by Southern blot and sequence analysis which demonstrated that it contained at least a part of the uteroferrin gene. The cosmid clone DNA was labeled with biotin, and used a probe for in situ hybridization to swine chromosomes. Hybridization was visualized by the FITC-labeled streptavidin/biotinylated antistreptavidin system together with R-banding of chromosomes. The hybridization signals revealed that the uteroferrin gene (ACP5) is located on swine chromosome 2q12-->q21.

Acid Phosphatase↗
PubMed2004

Thin is better!: ultrathin cryosection immunocytochemistry.

In immunofluorescence microscopy (IFM), the repression of out of focus fluorescence signal is crucial in order to obtain high-resolution images. One option to acquire high vertical resolution (z-axis resolution) is to produce optical sections with a confocal microscope. The z-axis resolution usually obtained with confocal microscopy of biological samples is about 500 nm. Another option is to produce very thin sections with a cryo-ultramicrotome (physical sections). The ultrathin cryosections we employ are about 100 nm in thickness: thus all of the fluorescence must come from within this 100 nm thickness. The use of ultrathin cryosections permits the acquisition of extremely high-quality images and minimizes the possibility for false localization in IFM (Fig. 1). Ultrathin cryosections can be applied to immunoelectron microscopy (IEM) as well as IFM (Fig. 2). We show new methods of ultrathin cryosection immunocytochemistry(1-3). Human full-term placentas were fixed with 4% paraformaldehyde, solidified with 10% gelatin, infiltrated with 2.3 M sucrose, and then frozen in liquid nitrogen. Ultrathin cryosections were cut with a cryo-ultramicrotome and then transferred to glass cover slips for IFM or to nickel grids for IEM. Cryosections were incubated with mouse anti-p230, a trans-Golgi network marker, and subsequently incubated with Alexa 488-labeled goat anti-mouse IgG or with goat anti-mouse 5-nm colloidal gold particles. For visualization and preservation of ultrastructure of cryosections at the electron microscopic level, the sections on grids were postfixed with ferrocyanide-reduced osmium and then stained with uranyl acetate and lead citrate in polyvinyl alcohol(1). Ultrathin cryosection immunocytochemistry should be an important technique for functional genomics research, especially for the analysis of the in situ expression of target molecules(2,3).

Cryoultramicrotomy↗
PubMed2005

[Genetic analysis of anthocyanin of the anthers and culm pigmentation in common wheat].

Anthocyanin pigmentation of various organs develops during plant ontogeny in response to adverse and damaging abiotic and biotic stressors (environmental factors). Using the monosome method, the genes responsible for anther and culm anthocyanin pigmentation (Pan1 and Pc2, respectively) were localized to 7D chromosome in introgressive lines from crosses between common wheat Triticum aestivum L. and the species Triticum timopheevii Zhuk. Genetic analysis of ten common wheat genotypes using testers carrying genes Pan1, Pn1, and Pn2 showed that these genotypes contained Pan1 and Pn2 genes. Visual examination of plants from 70 and 76 varieties of respectively winter and spring common wheat revealed anthocyanin pigmentation of anthers and culms in 36 varieties. Pan1 and Pn2 genes were presumably introduced into common wheat from Aegilops tauschii (Fig.) Tzvel., a donor of the D genome.

Chromosomes, Plant↗
PubMed1984

High-affinity monoclonal antibodies for the specific recognition and quantification of deoxynucleosides structurally modified by N-nitroso compounds.

The applicability of conventional radiochromatographic procedures to the detection and quantification of specific, carcinogen-induced structural modifications in the DNA of mammalian cells is limited by the necessity of using radioactively labelled agents and by the relatively large amounts of DNA required for analysis of low levels of DNA modification. Recently developed immunoanalytical methods have improved this situation considerably. High-affinity monoclonal antibodies (MAB), in combination with radio- and enzyme-immunoassays, now permit the sensitive detection of alkyldeoxynucleosides in small samples of hydrolysed DNA from tissues and cultured cells exposed previously to non-radioactive (e.g., environmental) alkylating N-nitroso carcinogens. Furthermore, MAB can be used to quantify by direct immunofluorescence (and with the aid of computer-based image analysis of electronically intensified fluorescence signals) specific alkylation products in the DNA of individual cells. With this method, the present detection limit for, e.g. O6-ethyl-2'-deoxyguanosine (O6-EtdGuo) is of the order of 7 X 10(2) O6-EtdGuo molecules per diploid genome. Therefore, cells (e.g. from biopsy material) can now be monitored directly for the presence of specific carcinogen-DNA adducts, or with respect to their capacity to remove enzymatically such modified structures from DNA. In combination with transmission electron microscopy, MAB also permit the direct visualization of specific carcinogen-modified sites in DNA. Thus, O6-EtdGuo can be localized in double-stranded DNA molecules by the binding of a MAB specifically directed against this ethylation product.

Antibodies, Monoclonal↗
PubMed2006

Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns.

MOTIVATION: Large-scale detection and classification of alternative splicing and transcriptional initiation (ASTI) is the first step towards detailed studies of the functional implication and mechanisms of these phenomena. RESULTS: We have developed an algorithm that classifies all observed units of ASTI into an extendable set of distinct types (e.g. cassette type) by converting a collection of alignments between a genomic DNA sequence and cDNA sequences into binary description. This description system can uniquely and compactly encode not only typical patterns but also any rare patterns that are usually collectively assigned to 'others.' More than 150 distinct ASTI types were found when this system was applied to genome-wide detection of ASTI units in human and five other eukaryotes. AVAILABILITY: The data detected by this system are available through ASTRA (http://alterna.cbrc.jp/), a database equipped with a Java-based browser that can interactively reorganize the order of displayed splicing patterns on demand.

Algorithms↗
PubMed1998

Characterization of the mitochondrial genome in childhood multiple sclerosis. II. Multiple sclerosis without optic neuritis and LHON-associated genes.

The occurrence of mitochondrial mutations with primary pathogenic significance for Leber's hereditary optic neuropathy in patients with a multiple sclerosis-like phenotype and the preferential maternal transmission points to an involvement of the mitochondrial genome in conferring increased susceptibility to MS. To evaluate the link between MS and mtDNA variations we investigated a total of thirteen children with MS as well as twenty controls by sequencing eight mitochondrial encoded genes which are known to be the loci for LHON-associated mutations. Numerous synonymous nucleotide substitutions and common polymorphisms were excluded from comparative analyses. No primary LHON mutations were found. Secondary LHON mutations were identified more frequently in control subjects than in the children with MS. The remaining eight discrete missense mutations were chosen for further characterization. Only two of them were found in more than one patient. Our results suggest that nucleotide substitutions within the ND1, ND2, ND4, ND5, ND6, COI, COIII or cytochrome b genes of mtDNA do not contribute to the etiology of typical MS. However, the association of LHON mutations with visual impairment in MS as well as the relationship between phenotypic diversity in certain subgroups of patients with individual mtDNA genotypes merits further investigations.

Adolescent↗
PubMed1995

Identification of vaccine-related polioviruses by hybridization with specific RNA probes.

We developed RNA probes for the identification of poliovirus isolates by blot hybridization. Two sets of vaccine strain-specific probes were prepared. They complemented variable genomic domains within (i) the 5'-untranslated region and (ii) the amino-terminal codons of VP1. An enterovirus group probe (EV/5UT) matching highly conserved 5'-untranslated region sequences was used to estimate the quantities of poliovirus (or enterovirus) RNA in the samples. Poliovirus sequences amplified from Sabin strain virion RNA templates by PCR were inserted into the pUC18 plasmid vector. The antisense PCR primer for each probe set contained sequences encoding a T7 promoter. Hybrids were detected by a sensitive nonisotopic method. RNA probes were labeled by incorporation of digoxigenin-uridylate into the transcripts. The binding of probe to immobilized poliovirus RNAs was visualized by hydrolysis of the chemiluminescent substrate 4-methoxy-4-(3-phosphate-phenyl)-spiro-(1,2-dioxetane-3,2'-adamant ane) catalyzed by alkaline phosphatase conjugated to anti-digoxigenin (Fab) fragments. The specificities of the probes were evaluated with a panel of poliovirus isolates that had previously been characterized by sequence analysis. The RNAs of vaccine-related isolates hybridized with the appropriate probe sets. Wild polioviruses representing a broad spectrum of contemporary genotypes were recognized by the inabilities of their genomes to form stable hybrids with the Sabin strain-specific probes.

Base Sequence↗
PubMed1992

Detection and characterization of "chimeric" yeast artificial chromosome clones by fluorescent in situ suppression hybridization.

"Chimeric" yeast artificial chromosomes (YACs) are clones containing two or more noncontiguous segments of DNA and represent the most common artifact found in total genomic YAC libraries currently used for large-scale genome mapping. These YACs create spurious mapping information that complicates the construction of YAC contigs and leads to erroneous maps during chromosome walks. The presence of these artifactual clones necessitates laborious and time-consuming characterization of each isolated YAC clone, either by comparison of the physical map of the YAC with the corresponding source genomic DNA, or by demonstrating discrepant chromosomal origins for the two ends of the YAC by hybridization or polymerase chain reaction (PCR). Here, we describe a rapid and sensitive method for the assessment of YAC colinearity by fluorescence in situ suppression hybridization (FISSH) by utilizing fluorescein-12-dUTP for labeling YAC clones. We have analyzed 51 YACs and found that 43% (22 out of 51) are chimeric and significantly larger (302 kb) than colinear ones (228 kb). One of the 51 YAC clones (2%) examined contains portions of three chromosomes and 2 (4%) seem to map to a chromosome different than that of the identifying STS. FISSH analysis offers a straightforward visualization of the entire YAC insert on the chromosomes and can be used to examine many YACs simultaneously in few days.

Artifacts↗
PubMed2002

Genome-wide dynamic transcriptional profiling of the light-to-dark transition in Synechocystis sp. strain PCC 6803.

We report the results of whole-genome transcriptional profiling of the light-to-dark transition with the model photosynthetic prokaryote Synechocystis sp. strain PCC 6803 (Synechocystis). Experiments were conducted by growing Synechocystis cultures to mid-exponential phase and then exposing them to two cycles of light/dark conditions, during which RNA samples were obtained. These samples were probed with a full-genome DNA microarray (3,169 genes, 20 samples) as well as a partial-genome microarray (88 genes, 29 samples). We concluded that (i) 30-min sampling intervals accurately captured transcriptional dynamics throughout the light/dark transition, (ii) 25% of the Synechocystis genes (783 genes) responded positively to the presence of light, and (iii) the response dynamics varied greatly for individual genes, with a delay of up to 120 to 150 min for some genes. Four classes of genes were identified on the basis of their dynamic gene expression profiles: class I (108 genes, 30-min response time), class II (279 genes, 60 to 90 min), class III (258 genes, 120 to 150 min), and class IV (138 genes, 180 min). The dynamics of several transcripts from genes involved in photosynthesis and primary energy generation are discussed. Finally, we applied Fisher discriminant analysis to better visualize the progression of the overall transcriptional program throughout the light/dark transition and to determine those genes most indicative of the lighting conditions during growth.

Cyanobacteria↗
PubMed2000

Two-dimensional map of the proteome of Haemophilus influenzae.

We have constructed a two-dimensional database of the proteome of Haemophilus influenzae, a bacterium of medical interest of which the complete genome, comprising about 1742 open reading frames, has been sequenced. The soluble protein fraction of the microorganism was analyzed by two-dimensional electrophoresis, using immobilized pH gradient strips of various pH regions, gels with different acrylamide concentrations and buffers with different trailing ions. In order to visualize low-copy-number gene products, we employed a series of protein extraction and sample application approaches and several chromatographic steps, including heparin chromatography, chromatofocusing and hydrophobic interaction chromatography. We have also analyzed the cell envelope-bound protein fraction using either immobilized pH gradient strips or a two-detergent system with a cationic detergent in the first and an anionic detergent in the second-dimensional separation. Different proteins (502) were identified by matrix-assisted laser desorption/ionization mass spectrometry and amino acid composition analysis. This is at present one of the largest two-dimensional proteome databases.

Databases, Factual↗