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PubMed1995

Demonstration and distribution of HCV RNA sequences by in situ hybridization and HCV-related proteins by immunohistochemistry in the liver tissue of patients with chronic HCV infection.

Nonisotopic in situ cytohybridization of HCV RNA was attempted in liver specimens from 12 chronically hepatitis C virus (HCV) infected patients. Oligonucleotides deduced from 5'-noncoding and core regions of the HCV genome were labeled with digoxigenin and used on paraformaldehyde-fixed frozen liver sections. The hybrids were visualized immunohistochemically with alkaline phosphatase-conjugated anti-digoxigenin and alkaline phosphatase substrate. These findings were correlated with the results of tissue immunohistochemistry for HCV antigens identified with specific mouse monoclonal antibodies developed against c22-3 antigen (Ag), a core-encoded protein, and c100-3 Ag, a NS4-encoded protein, and histologic assessment of each liver. HCV RNA detected in the above assay was predominantly cytoplasmic; it was detected in all 12 patients and in none of the controls. Tissue HCV RNA was associated with the presence of cytoplasmic (c100-3 Ag) and membrane (c22-3 Ag) expression of viral proteins in all 9 patients with histological evidence of chronic progressive liver disease as judged by the presence of piecemeal necrosis, and lobular and portal tract inflammation. Despite the presence of abundant HCV RNA, none of 3 patients without histological evidence of chronic liver disease showed intrahepatocyte expression of viral proteins. These findings support the view that tissue HCV antigens are markers of progressive damage and demonstrate that active liver disease does not occur without such markers. It is proposed that synthesis of viral proteins and membrane accumulation of c22-3 Ag may be involved in the pathogenesis of hepatocyte injury in chronic hepatitis C infection.

Adult↗

PubMed2002

Clusters of transcription-coupled repair in the human genome.

A specialized nucleotide excision repair pathway known as transcription-coupled repair (TCR) counteracts the toxic effects of DNA damage in transcriptionally active genes. The clustering of active genes into gene-rich chromosomal domains predicts that the sites of TCR are unevenly distributed through the genome. To elucidate the genomic organization and chromosomal localization of TCR, we isolated DNA fragments encompassing TCR-mediated repair sites from UV-C irradiated xeroderma pigmentosum group C cells, which can only repair the transcribed strand of active genes. This DNA was used as a molecular probe to visualize TCR in normal metaphase spreads by reverse fluorescence in situ hybridization. Whereas DNA repair sites in normal human cells are evenly distributed through the genome, TCR is highly localized at specific chromosomal domains. Particularly, clusters of TCR sites were identified at early-replicating gene-rich bands and telomeric regions of several chromosomes. High gene-density chromosomes such as chromosome 19 and the GC-rich domains of several chromosomes (T bands) are preferential locations of TCR. Our results demonstrate that the intragenomic localization of TCR resembles the uneven distribution of the human transcriptome, CpG islands, and hyperacetylated histones, enforcing the basic link between DNA repair, transcription, and nuclear organization in a complex genome.

Cells, Cultured↗

PubMed1990

Pili (fimbriae) of Branhamella species.

PURPOSE: Pili (fimbriae) have frequently been found to be involved in the attachment of bacteria to mucosal epithelial cells, an important initial step in the disease process. The purpose of this study was to determine if Branhamella catarrhalis expresses type 4 pili. MATERIALS AND METHODS: Piliated B. catarrhalis phenotypic characteristics of colony morphology, agar corrosion, twitching motility, competence for deoxyribonucleic acid (DNA) transformation, autoagglutination, and pellical formation were observed. DNA was isolated from Branhamella spp. and used in genomic Southern hybridizations with a Moraxella bovis pilin gene as a probe. Electron microscopy of negatively stained bacteria was carried out to visualize pili. RESULTS: B. catarrhalis has several (but not all) of the phenotypic characteristics that are related to the presence of type 4 (MePhe) pili in closely related Moraxella spp., including competence for DNA transformation, autoagglutination, pellicle formation, colony morphology, and pitting of agar. The one phenotype we have not found that is generally characteristic of type 4 piliated bacteria is twitching motility. Genomic Southern hybridization analysis using a cloned M. bovis Q pilin gene as a probe reveals DNA homologous to the Q pilin gene in B. catarrhalis, Branhamella ovis, Branhamella caviae, and Branhamella cuniculi. Examination of B. catarrhalis strain ATCC25240 by electron microscopy reveals two different kinds of pili. One kind appears similar to other type 4 pili, whereas a second class is short pili extending outward from all portions of the bacteria. CONCLUSION: Phenotypic, electron-microscopic, and hybridization data are all consistent with type 4 pili being present on some B. catarrhalis strains.

Fimbriae, Bacterial↗

PubMed2003

Oral and intravenous steroids in giant cell arteritis.

Giant cell arteritis can result in devastating visual loss. Treatment with steroids does result in visual recovery in some patients but the exact percentage is unknown. Intravenous megadose steroids appear to offer some advantage over oral steroids presumably through non-genomic effects, which manifest at doses of 500 mg or more. Side-effects are more likely in the elderly especially those with renal and cardiac co-morbidities. The authors' current recommendation is that intravenous steroids should be given to patients with established visual loss or amaurosis fugax.

Administration, Oral↗

PubMed1981

Electron microscopic studies of bacteriophage phi X174 intact and "eclipsing' particles, and the genome by the staining, and shadowing method.

Bacteriophage phi X174 particles were observed with a new method, a combination of staining and shadowing. Previously we used this technique to obtain clear visualization of the shape of cytoplasmic-polyhedrosis virus, especially the spikes of this particle. The phi X174 particle was observed to be an icosahedral particle of 25 nm in diameter carrying a spike at each vertex. The spike was a pentagonal frustum with a base of 9 nm and a height of 6 nm. When the phage was treated with calcium on the supporting film, the genome extruded from the particle. With the staining and shadowing method, it was clearly observed that the spike was the extruding channel of the genome. The genome extrusion occurred not only a single spike of the particle but also at two or more spikes. This implied that all 12 spikes of the particle had the same abilities to act as the channel of genome extrusion. The released genomes showed various thicknesses and shapes such as bending, looping, or branching, which were thought to reflect to compact form of DNA in a virus particle. The similarly between the spikes of bacteriophage phi X174 and those of cytoplasmic-polyhedrosis virus from silk worm was also discussed.

Bacteriophage phi X 174↗

PubMed2002

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource based on the first complete plant genome.

Arabidopsis thaliana is the first plant for which the complete genome has been sequenced and published. Annotation of complex eukaryotic genomes requires more than the assignment of genetic elements to the sequence. Besides completing the list of genes, we need to discover their cellular roles, their regulation and their interactions in order to understand the workings of the whole plant. The MIPS Arabidopsis thaliana Database (MAtDB; http://mips.gsf.de/proj/thal/db) started out as a repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project and the Arabidopsis Genome Initiative. Our aim is to transform MAtDB into an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities and by creating a comprehensive resource for Arabidopsis as a reference model for other species, including crop plants.

Arabidopsis↗

PubMed1996

Painting rye B chromosomes in wheat: interphase chromatin organization, nuclear disposition and association in plants with two, three or four Bs.

The B chromosomes (Bs) of rye (Secale cereale) have been studied at interphase in terms of their chromatin organization, patterns of nuclear disposition and physical association in plants with two, three, and four Bs. The study was made in the Lindström strain of hexaploid wheat, which carries the rye Bs as an addition line, by in situ hybridization with a B-specific probe and by genomic in situ hybridization (GISH) with rye genomic DNA, enabling whole chromosome painting. Repetitive sequences common to the As and Bs of rye allow for visualization of the rye B at interphase in the wheat background. A B-specific probe enables the orientation of two or more Bs to be determined, and the combination of both probes used together gives information on the disposition of the Bs and on their patterns of physical association within the nucleus. The Bs form linear "strings', and the ends of their long arms, which can be detected by the B-specific probe, are usually located within the hemisphere of the nucleus that has the least condensed chromatin. There is dose-dependent association, and even numbers (2B, 4B) have a greater preference for association than odd ones (3B).

Chromatin↗

PubMed2026

Engineering bubble structures as Cas12a activators for highly sensitive monitoring of WRN helicase function.

The Werner syndrome helicase (WRN) is a critical synthetic lethal target in microsatellite instability cancers, essential for resolving complex genomic structures like replication bubbles and R-loops. However, strategies to simultaneously discriminate WRN activity on DNA versus DNA-RNA substrates in living cells are lacking. Here, we developed a structure-specific CRISPR/Cas12a biosensing strategy to visualize WRN functional activity by engineering bubble-structure probes. These probes were rationally designed to structurally mimic DNA replication bubbles and R-loop associated DNA-RNA hybrids. Upon specific unwinding by WRN, the probes release a sequestered activator strand that triggers Cas12a trans-cleavage, effectively converting the unwinding event into an amplified fluorescent signal. This assay achieves low picomolar sensitivity (LODs: 5.6-6.0 pM) and exceptional selectivity against homologous RecQ helicases. Uniquely, this strategy enables the parallel quantification of WRN activity on both substrate types, providing insights into distinct WRN-mediated pathways for resolving genomic stress. We further demonstrated the strategy's utility by visualizing endogenous WRN dynamics in living cells and profiling the efficacy of small-molecule inhibitors. This work offers a powerful molecular toolkit for dissecting WRN biology and facilitating high-throughput drug screening in targeted cancer therapy.

Werner Syndrome Helicase↗

PubMed1993

Distribution of DNA in human Sertoli cell nucleoli.

For better understanding of nucleolar architecture, different techniques have been used to localize DNA within the dense fibrillar component (DF) or within the fibrillar centers (FC) by electron microscopy (EM). Since it still remains controversial which components contain DNA, we investigated the distribution of DNA in human Sertoli cells using various approaches. In situ hybridization (ISH) with human total genomic DNA as probe and the use of anti-DNA antibody were followed by immunogold detection. This allowed statistical evaluation of the signal density over individual components. The Feulgen-like osmium-ammine (OA) technique for the selective visualization of DNA was also applied. The anti-DNA antibodies detected DNA in mitochondria, in chromatin, and in the DF of the nucleolus. ISH using human total genomic DNA showed similar labeling patterns. The OA technique revealed DNA filaments in the FC and focal agglomerates of decondensed DNA within the DF. We conclude that (a) EM staining techniques that utilize colloidal gold appear to be less sensitive for DNA detection than the OA method, (b) the DF consists of different domains with different molecular composition, and (c) decondensed DNA is not necessarily confined to one particular nucleolar component.

Cell Nucleolus↗

PubMed2006

Visualizing networks.

An interrelated set of genes or proteins can be represented effectively as a network that describes physical interactions, regulatory relationships, or metabolic pathways. Visualizing a network can be a helpful method to extract biological meaning and to generate testable hypotheses about large-scale biological data. This chapter describes some potential rationales for visualizing networks of microarray and other data types, which can be integrated and filtered to show potentially significant relationships. It also presents a practical introduction to Osprey and Cytoscape, two software platforms that are powerful tools for visualizing, integrating, and manipulating networks.

Animals↗

PubMed2000

Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551.

The genome sequences of two virulent strains of Mycobacterium tuberculosis (H37Rv and CDC 1551) are now available. CDC 1551 is a recent clinical isolate and H37Rv is a commonly used lab strain which has been subject to in vitro passage. The two strains have been shown to display differing phenotypes both in vivo and in vitro. The proteome of the two strains grown in liquid culture were examined over time to determine whether there are any major differences between them at the protein level and the differences were compared to the genome data. Total cell lysates of the two strains were analysed by two-dimensional electrophoresis. Approximately 1750 protein spots were visualized by silver staining and the protein profiles of the two strains were found to be highly similar. Out of a total of 17 protein spot differences, seven were unique to CDC 1551 and three to H37Rv. Two further spots showed increased intensity in H37Rv, one spot showed differing vertical mobility between the strains and four showed differing spot intensities with time. Twelve of the spot differences were identified using mass spectrometry; however, no obvious association with phenotype could be deduced. When genome differences were analysed and related to the proteome differences, a mobility shift identified in the MoxR protein could be explained by a point mutation at the gene level. This proteome analysis reveals that, despite having been maintained under vastly different conditions, namely in vitro passage and in vivo transmission, these two strains have remained highly similar.

Bacterial Proteins↗

PubMed2026

Deep learning-based multimodal pathogenomics integration for precision cancer prognosis.

BACKGROUND: Recent studies have revealed valuable prognostic insights in haematoxylin and eosin (H&E)-stained histological sections and transcriptomic profiles, suggesting potential applications in machine learning. However, existing methods lack sufficient intra- and inter-modal interactions, and face challenges in clinical validation due to incomplete multimodal data. METHODS: We proposed PathoGems (PathoGenomics-based integrative survival prediction), a weakly-supervised, interpretable multimodal learning framework that integrates histology and genomic profiles for precise cancer prognosis prediction. To evaluate the robustness of PathoGems, we initially curated a dataset of 1965 cases across four cohorts from The Cancer Genome Atlas (TCGA), including breast, colorectal, glioblastoma, and esophageal cancers. For external validation, PathoGems was further evaluated on four independent cohorts, consisting of 76 breast cancer and 41 esophageal squamous cell carcinoma cases from Zhejiang Cancer Hospital, as well as 102 colorectal cancer and 58 glioblastoma cases from the Clinical Proteomic Tumor Analysis Consortium (CPTAC). RESULTS: PathoGems effectively stratified patients into favorable and unfavorable risk groups, revealing significant differences in histological patterns, genomic features, and overall survival (log-rank test, p < 0.05). Moreover, the model’s predictions are further supported by visualization and transcriptomic analysis, enhancing interpretability and reliability. CONCLUSIONS: By fusing histological and clinicogenomic multimodal models, PathoGems will provide a solid foundation for developing an innovative tool that aids clinicians in making informed decisions and selection personalized treatment strategies for cancer patients.

Humans↗

PubMed2005

A new nucleotide-composition based fingerprint of SARS-CoV with visualization analysis.

It has been observed by conducting an extensive analysis of the two-dimensional cellular automata images of known SARS-CoV genome sequences that the V-shaped cross-lines only exist in some special locations, and hence can be used as a fingerprint to identify the SARS sequences. Such a discovery can be used to rapidly and reliably diagnose SARS coronavirus for both basic research in laboratories and practical application in clinics.

Algorithms↗

PubMed2005

Visualizing chromosomes as transcriptome correlation maps: evidence of chromosomal domains containing co-expressed genes--a study of 130 invasive ductal breast carcinomas.

Completion of the working draft of the human genome has made it possible to analyze the expression of genes according to their position on the chromosomes. Here, we used a transcriptome data analysis approach involving for each gene the calculation of the correlation between its expression profile and those of its neighbors. We used the U133 Affymetrix transcriptome data set for a series of 130 invasive ductal breast carcinomas to construct chromosomal maps of gene expression correlation (transcriptome correlation map). This highlighted nonrandom clusters of genes along the genome with correlated expression in tumors. Some of the gene clusters identified by this method probably arose because of genetic alterations, as most of the chromosomes with the highest percentage of correlated genes (1q, 8p, 8q, 16p, 16q, 17q, and 20q) were also the most frequent sites of genomic alterations in breast cancer. Our analysis showed that several known breast tumor amplicons (at 8p11-p12, 11q13, and 17q12) are located within clusters of genes with correlated expression. Using hierarchical clustering on samples and a Treeview representation of whole chromosome arms, we observed a higher-order organization of correlated genes, sometimes involving very large chromosomal domains that could extend to a whole chromosome arm. Transcription correlation maps are a new way of visualizing transcriptome data. They will help to identify new genes involved in tumor progression and new mechanisms of gene regulation in tumors.

Breast Neoplasms↗

PubMed1997

Genome size, secondary simplification, and the evolution of the brain in salamanders.

Compared to other vertebrates, even including lampreys and hagfishes in some respects, salamanders exhibit a relatively simple organization of brain and sense organs which is illustrated here using the visual system as an example. The greatest simplicity is found in the bolitoglossine salamanders, yet all bolitoglossines possess highly projectile tongues and rely on vision for survival; furthermore, some species are agile and acrobatic. The unusual features of the visual system of salamanders include small numbers of large neurons, a low degree of morphological differentiation among neurons, a small proportion of myelinated axons in the optic nerve, and an optic tectum consisting essentially of a periventricular cellular layer and a superficial fiber layer. Similar features are found throughout the central nervous system of salamanders and in the lateral line, auditory and olfactory systems as well. Phylogenetic analysis shows that the most parsimonious interpretation of these data is that the simple organization of the brain and sense organs of salamanders was derived secondarily from a more complex ancestral state. We hypothesize that increased genome size has led to simplification of the nervous system in salamanders. Increased genome size appears to have had profound effects on neural development in salamanders, leading to paedomorphosis, the retention of juvenile or even embryonic characteristics into adulthood. In particular, large genome size is associated with large cell size and reduced rates of cell proliferation, migration and differentiation. Secondary simplification has constrained the function of the salamanders' visual system, primarily by increasing cell size and decreasing cell numbers. However, it also has provided an opportunity for the evolution of compensating mechanisms, which have helped to restore or even enhance visual function. Most apparent among the compensatory mechanisms of bolitoglossine salamanders is the presence of well developed ipsilateral retinotectal projections, which apparently enhance depth perception. It is difficult to explain the unusual history of the nervous system in salamanders solely in terms of natural selection and adaptation. Increasing genome size through selfish replication appears to have played a major role in the evolution of salamander brains by imposing functional constraints as well as creating opportunities for overcoming them.

Animals↗

PubMed1988

Normal human genomic restriction-fragment patterns and polymorphisms revealed by hybridization with the entire dystrophin cDNA.

Since the complete cDNA for the gene that causes X-linked recessive Duchenne/Becker muscular dystrophy (DMD/BMD) when mutated or deleted has recently been cloned and made generally available, DNA-based diagnostic studies of affected males and their families have entered into a new era. This communication sets forth the standard patterns of restriction fragments that are detected when normal human DNA cleaved with either HindIII or BglII is hybridized with seven contiguous segments comprising the entire 14-kb cDNA. Collectively, the more than 60 restriction fragments allow visualization of approximately 350 (HindIII) to 400 (BglII) kbp. This corresponds to the exon-containing one-fifth of the total genomic length of this gene, including the 3' untranslated region. Twelve two-allele restriction-site polymorphisms that span the entire length of the gene were detected with the cDNA probes and allele frequencies determined. A diagnostic approach is proposed that starts with deletion screening of DNA from male probands, includes carrier detection based on relative fragment intensities, and extends to RFLP detection using the same autoradiographs prepared for deletion screening. Our results on deletion analysis of 32 DMD/BMD families are presented in an accompanying paper.

DNA↗

PubMed2025

HSDSnake: a user-friendly SnakeMake pipeline for analysis of duplicate genes in eukaryotic genomes.

SUMMARY: Gene duplication is a well-known driver of molecular evolution-it acts as a source of genetic novelty, thereby providing the raw substrate for organismal adaption. However, detecting different types of gene duplicates and comparing them in sequence datasets can be difficult. Existing tools can identify and classify gene duplicates that have arisen by various processes, but have limitations; for example, some do not have a user-friendly workflow and can include many intermediate steps requiring manual adjustments of parameters and/or are not maintained for the benefit of research community members. Here, we have developed HSDSnake, a user-friendly SnakeMake pipeline that can detect and classify gene duplications into five categories: dispersed, proximal, tandem, transposed, and whole genome. It also curates and evaluates the highly similar gene duplicates (HSDs) in each gene duplication category with reliance on both sequence similarity and conserved domains. Lastly, the detected gene duplicates can be visualized within a KEGG functional pathway framework and the substitution rates (Ka, Ks, and their Ka/Ks ratio) can be analyzed for all the duplicate gene pairs. We demonstrate HSDSnake's capabilities by analyzing two reference genomes directly downloaded from NCBI and provide detailed instructions for each step. AVAILABILITY AND IMPLEMENTATION: The HSDSnake pipeline uses SnakeMake and Conda to run and install dependencies. The distribution version is available online at GitHub: https://github.com/zx0223winner/HSDSnake and the archived version at Zenodo is https://doi.org/10.5281/zenodo.15521945.

Software↗

PubMed1994

Altered electrophoretic behavior of DNA due to short-time UV-B irradiation.

UV-B irradiation is often inevitable for visualization of DNA fragments after ethidium bromide staining. Three different simple-repeat-containing, double-stranded genomic DNA fragments were analyzed for UV-B (312 nm) damage using different gel electrophoretic systems. The effects of UV-B light were obvious after 5 min (31.5 kJ/m2) of irradiation in native polyacrylamide gel electrophoresis (PAGE). Standard single-strand conformation analyses revealed no alterations while a modification did. Sodium dodecyl sulfate (SDS)-PAGE was found to be highly sensitive with regard to the detection of damages and their time/dosage dependency. In addition, SDS-PAGE analysis pointed to different events occurring during UV-B irradiation. Alterations in DNA conformation were detected in every single strand analyzed after 1 min (6.3 kJ/m2) of UV-B exposure. Gel retardation analyses revealed significant changes of protein binding to target DNAs after 2 min of irradiation--possibly stemming from structural modifications and/or originating from binding sites for proteins involved in DNA repair.

Base Sequence↗