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PubMed2005

Genomic regulatory networks and animal development.

The synthesis of gene expression data and cis-regulatory analysis permits the elucidation of genomic regulatory networks. These networks provide a direct visualization of the functional interconnections among the regulatory genes and signaling components leading to cell-specific patterns of gene activity. Complex developmental processes are thereby illuminated in ways not revealed by the conventional analysis of individual genes. In this review, we describe emerging networks in several different model systems, and compare them with the gene regulatory network that controls dorsoventral patterning of the Drosophila embryo.

Animals↗
PubMedDate not supplied

Predicted roles for hypothetical proteins in the low-temperature expressed proteome of the Antarctic archaeon Methanococcoides burtonii.

Using liquid chromatography-mass spectrometry, 528 proteins were identified that are expressed during growth at 4 degrees C in the cold adapted archaeon, Methanococcoides burtonii. Of those, 135 were annotated previously as unique or conserved hypothetical proteins. We have performed a comprehensive, integrated analysis of the latter proteins using threading, InterProScan, predicted subcellular localization and visualization of conserved gene context across multiple prokaryotic genomes. Functional information was obtained for 55 proteins, providing new insight into the physiology of M. burtonii. Many of the proteins were predicted to be involved in DNA/RNA binding or modification and cell signaling, suggesting a complex, uncharacterized regulatory network controlling cellular processes during growth at low-temperature. Novel enzymatic functions were predicted for several proteins, including a putative candidate gene for the posttranslational modification of the key methanogenesis enzyme coenzyme M methyl reductase. A bacterial-like CRISPR locus was identified as a strong candidate for archaeal-bacterial lateral gene transfer. Gene context analysis proved a valuable augmentation to the other predictive methods in several cases, by revealing conserved gene associations and annotations in other microbial genomes. Our results underscore the importance of addressing the "hypothetical protein problem" for a complete understanding of cell physiology.

Adaptation, Physiological↗
PubMed2026

Interactive exploration of biobank-scale ancestral recombination graphs with Lorax.

MOTIVATION: Ancestral Recombination Graphs (ARGs) provide a comprehensive representation of genetic ancestry and underpin analyses of natural selection, disease association, and population history. However, existing visualization tools are limited in scalability and interactivity, making ARGs difficult to explore at biobank scale. RESULTS: We introduce Lorax, a GPU-accelerated, web-native platform for real-time visualization of population-scale ARGs. Lorax integrates genomic position, coalescent time, local genealogy, and metadata, enabling interactive exploration of ancestry and variant inheritance in biobank-scale datasets. AVAILABILITY AND IMPLEMENTATION: Lorax is freely available as a live demo at https://lorax.ucsc.edu/ and as a Python package "lorax-arg" on PyPI. The source code and documentation are available on GitHub at https://github.com/pratikkatte/lorax.

Software↗
PubMed1997

Molecular genetics of open-angle glaucoma, moving from gene localization to predictive testing.

It has long been suspected that genetic factors play a role in open-angle glaucoma. Only recently, however, has the molecular basis of such factors begun to be established, with the primary localization of the GLC1A locus for juvenile-onset and early-onset autosomal dominant open-angle glaucoma on chromosome 1q. These findings are clinically significant in that they allow familial screening of individuals at risk for glaucoma before the onset of irreversible visual impairment. A physical map of the GLC1A genomic region is now available, and the actual GLC1A gene might be identified in the near future. Nevertheless, open-angle glaucoma is a genetically heterogeneous entity, and additional loci have been mapped or proposed. Identification of open-angle glaucoma genes should provide invaluable clues to the disorder's pathophysiology. It could also aid in conceiving novel therapeutic agents and broadening the screening of at-risk subjects.

Chromosome Mapping↗
PubMed1984

Semliki Forest virus penetration from endosomes: a morphological study.

The low pH dependent membrane fusion reaction responsible for the delivery of the Semliki Forest virus genome into the host cell for replication was visualized by electron microscopy. In order to increase the frequency at which fusion images could be detected a reversible inhibitor, ammonium chloride, was used to synchronize endosomal acidification, and 20 degrees C incubation was employed to concentrate virus particles into the endosomal compartment.

Animals↗
PubMed2024

A rapid and simple clonality assay for bovine leukemia virus-infected cells by amplified fragment length polymorphism (AFLP) analysis.

UNLABELLED: Enzootic bovine leukosis (EBL), although eradicated in some European countries, is still the most common neoplastic disease of cattle, caused by the bovine leukemia virus (BLV). During the progression of EBL, BLV-infected cells clonally expand, and some of which result in tumor onset. The clonality of BLV-infected cells is generally evaluated with NGS or Sanger sequencing. Although these methods clearly distinguish EBL from non-EBL cases, the procedures are complex and not practical for routine veterinary diagnosis. In this study, we developed an amplified fragment length polymorphism (AFLP) analysis for BLV clonality assay (BLV-AFLP). This analysis uses restriction enzyme digestion to amplify the chimeric regions of BLV 3' linear transcribed region (LTR) and host genome through conventional polymerase chain reaction (PCR) and visualizes the results by gel-electrophoresis. The method was established using cattle samples representing different stages of the disease: BLV-uninfected, non-EBL, and EBL cattle. Non-EBL cattle showed smeared bands, indicating polyclonal proliferation, while EBL cattle showed distinct bands, indicating clonal expansion. The results of BLV-AFLP correlated well with those of previously reported methods, suggesting its efficacy in detecting clonal proliferation. The validation using blood samples of non-EBL cattle and tumor samples of EBL cattle confirmed that BLV-AFLP could effectively identify clonal proliferation in EBL samples. Moreover, the emergence of dominant clones in the tumor at later stages was successfully detected before EBL onset in some cattle, highlighting its sensitivity and potential for early detection. Overall, BLV-AFLP is suitable for practical use in the field, improving BLV management strategies and minimizing economic losses. IMPORTANCE: Enzootic bovine leukosis (EBL) is routinely diagnosed based on external manifestations at the farm, such as the presence of tumors and/or general lymph node enlargement. However, due to the nonspecific clinical manifestations of EBL, over half of EBL cases are unrecognized at the farm, with most cases being diagnosed during postmortem inspection at the slaughterhouse. Early detection and monitoring of clonal expansion are necessary for managing EBL and reducing economic losses. In this study, we developed BLV-AFLP that represents a significant advancement in the diagnosis of EBL in cattle. This method can rapidly assess the clonal proliferation of BLV-infected cells, crucial for distinguishing between asymptomatic and EBL cattle. Additionally, tracking clonal dynamics offers insights into the disease's progression, potentially providing strategies for avoiding economic losses. Overall, as BLV-AFLP is a simple and rapid test for detecting EBL, it is feasible and efficient for routine veterinary practice.

Leukemia Virus, Bovine↗
PubMed2025

Proteomic comparison of epidemic Australian Bordetella pertussis biofilm cells.

Bordetella pertussis causes whooping cough, a severe respiratory infectious disease. Studies have compared the currently dominant single nucleotide polymorphism (SNP) cluster I (pertussis toxin promoter allele, ptxP3) and previously dominant SNP cluster II (ptxP1) strains as planktonic cells. Since biofilm formation is linked with B. pertussis pathogenesis in vivo, this study compared the biofilm formation capabilities of representative strains of cluster I and cluster II. Confocal laser scanning microscopy found that the cluster I strain had a denser biofilm structure compared to the cluster II strain. Differences in protein abundance of the biofilm cells were then compared using tandem mass tagging and high-resolution multiple reaction monitoring. In total, 1,453 proteins were identified, of which 40 proteins had significant differential abundance between the two strains in biofilm conditions. Of particular interest was a large increase in the abundance of energy metabolism proteins (cytochrome proteins PetABC and BP3650) in the cluster I strain. When the abundance of these proteins was compared between six additional strains from each cluster, it was found that the protein abundance varied between all strains. These findings suggest that there are large levels of individual proteomic diversity between B. pertussis strains in biofilm conditions despite the highly conserved genome of the species. Overall, this study revealed visual differences in biofilm structure between B. pertussis strains and highlighted strain-specific variation in protein abundance that dominates potential cluster-specific changes that may be linked with the dominance of cluster I strains.IMPORTANCEBordetella pertussis causes whooping cough. The currently circulating cluster I strains have taken over previously dominant cluster II strains. It is important to understand the reasons behind this evolution to develop new strategies against the pathogen. Recent studies have shown that B. pertussis can form biofilms during infection. This study compared the biofilm formation capabilities of a cluster I and a cluster II strain and identified visual differences in the biofilms. The protein abundance between these strains grown in biofilms was compared, and proteins identified with varied abundance were measured with additional strains from each cluster. It was found that despite the highly conserved genetics of the species, there was varied protein abundance between the additional strains. This study highlights that strain-specific variation in protein abundance during biofilm conditions may dominate the cluster-specific changes that may be linked to the dominance of cluster I strains.

Bordetella pertussis↗
PubMed1983

Higher-order structure of chromatin from resting cells. I. Electron microscopy of chromatin from calf thymus.

Extremely large domains of the genome of resting cells (calf thymus) have been visualized in the electron microscope by combining mild extraction procedures with a non-artifactual method of mounting the sample (the phospholipid monolayer technique). The observed chromatin strands, free from distortion, reach contour lengths up to 60 micrometers. After lysis of the nuclei, four classes of fibres may be identified on the basis of their diameters (30, 24, 18 and 11 nm, respectively). The morphology of giant chromatin strands is strikingly regular; long trains of equally sized, arc-shaped segments are observed, their length being, in many cases, multiples of a fixed value. The inflection points delimiting contiguous segments are often associated with laminar fragments of the nuclear envelope or, less frequently, linked to fibrillar elements. It appears that higher-order structures of chromatin in resting cells conform, to a large extent, to a so called 'drapery-like' mode, according to which a continuous strand runs between contiguous anchorage sites placed on the nuclear envelope. Because of the presence of regularly spaced inflection points, this organization is much more ordered than expected. Spontaneous unwinding of the fibres at low ionic strength, limited nuclease digestion, and relaxation in the presence of ethidium bromide, have been used as probes of the conformation. All these experiments rule out its identification with a single-strand helix. The final ordered state is attained by folding the basic 11 nm strand and by winding up this configuration on itself. This leads to a coiled-coil or 'rope-like' model. The 11 nm strand is 'punctuated' by sharp kinks. Roughly, it may be assimilated to a chain of semirigid, freely joined elements. As a consequence, local flexibility is greatly enhanced, so allowing the assembly mode described.

Animals↗
PubMed2000

[Molecular genetics of pigmentary retinopathies: identification of mutations in CHM, RDS, RHO, RPE65, USH2A and XLRS1 genes].

PURPOSE: To evaluate the occurrence and inheritance of various types of pigmentary retinopathy in patients followed at the outpatient clinic in the university hospital, Montpellier, France. To characterize genes and mutations causing these conditions. METHODS: Ophthalmic examination and various visual tests were performed. Mutations were sought from genomic DNA by PCR amplification of exons associated with single-strand conformation analysis and/or direct sequencing. RESULTS: Among 315 patients over an 8-year period, cases of retinitis pigmentosa (63.2%), Usher's syndrome (10.2%), Stargardt's disease (5.4%), choroideremia (3.2%), Leber's congenital amaurosis (3.2%), congenital stationary night blindness (2.9%), cone dystrophy (2.5%), dominant optic atrophy (1.9%), X-linked juvenile retinoschisis (1.6%), Best's disease (1.6%), and others (4.3%) were diagnosed. In retinitis pigmentosa, inheritance could be determined in 54.2% of the cases including dominant autosomic (26.6%), recessive autosomic (22.6%), and X-linked cases (5%) while it could not be confirmed in 45.7% of the cases (simplex cases in the majority). For the 6 examined genes, mutations were found in 22 out of 182 propositus (12.1%). Analysis of phenotype-genotype correlations indicates that in retinitis pigmentosa, RDS is more frequently associated with macular involvement and retinal flecks, RHO with regional disease, and RPE65 with the great severity of the disease with some cases of Leber's congenital amaurosis. CONCLUSIONS: Identification of genes may help in diagnosis and in genetic counseling, especially in simplex cases with retinitis pigmentosa. In this latter condition, molecular diagnosis will be necessary to rationalize future treatments.

Adaptor Proteins, Signal Transducing↗
PubMed1984

Analysis of meiotic development in Coprinus cinereus.

The basidiomycete Coprinus cinereus offers many advantages for molecular analyses of meiosis. Fruiting body development is highly synchronous, and chromosome behaviour can be visualized using the light microscope. Furthermore, the small genome size (3.7 X 10(7) bp/haploid nucleus) facilitates molecular cloning procedures, and genetic characterization is reasonably advanced. To analyse controls of the meiotic process, we have isolated genomic sequences which are differentially expressed during Coprinus development by comparative cDNA hybridization to cloned genomic segments. We have concluded that fruiting body morphogenesis is associated with extensive changes in steady-state RNA levels in this fungus.

Agaricales↗
PubMed2006

Natural language processing and visualization in the molecular imaging domain.

Molecular imaging is at the crossroads of genomic sciences and medical imaging. Information within the molecular imaging literature could be used to link to genomic and imaging information resources and to organize and index images in a way that is potentially useful to researchers. A number of natural language processing (NLP) systems are available to automatically extract information from genomic literature. One existing NLP system, known as BioMedLEE, automatically extracts biological information consisting of biomolecular substances and phenotypic data. This paper focuses on the adaptation, evaluation, and application of BioMedLEE to the molecular imaging domain. In order to adapt BioMedLEE for this domain, we extend an existing molecular imaging terminology and incorporate it into BioMedLEE. BioMedLEE's performance is assessed with a formal evaluation study. The system's performance, measured as recall and precision, is 0.74 (95% CI: [.70-.76]) and 0.70 (95% CI [.63-.76]), respectively. We adapt a JAVA viewer known as PGviewer for the simultaneous visualization of images with NLP extracted information.

Animals↗
PubMed1996

Visualization of viral candidate cDNAs in infectious brain fractions from Creutzfeldt-Jakob disease by representational difference analysis.

Creutzfeldt-Jakob Disease (CJD), a neurodegenerative and dementing disease of later life, is caused by a viruslike entity that is incompletely characterized. As in scrapie, all more purified infectious brain preparations contain nucleic acids. However, it has not been possible to visualize unique bands that may derive from a viral genome. We here used a subtractive strategy known as representational difference analysis (RDA) to uncover such sequences. To reduce the complexity of starting target nucleic acids, sucrose gradients were first used to select nuclease resistant particles with a defined 120S size. In CJD this single 120S gradient peak is highly enriched for infectivity, and contains reduced amounts of PrP (Proc. Natl. Acad. Sci. 92, 5124-8, 1995). Parallel 120S fractions from uninfected brain were made to generate subtractor sequences. 120S particles were lysed in GdnSCN, and ng amounts of released RNA were purified for random-primed cDNA synthesis. To capture representative fragments of 100-500 bp, cDNAs were cleaved with Mbo I for adaptor ligation and amplification. In the first experiment with moderate RDA selection, it was possible to visualize clones from CJD cDNA that did not hybridize to control cDNA. In the second experiment, more exhaustive subtractions yielded a discrete set of CJD derived gel bands. Competitive hybridization showed a subset of these bands were not present in either the control 120S cDNA or in the hamster genome. This represents the first demonstration of apparently CJD-specific nucleic acid bands in more purified infectious preparations. Although exhaustive cloning, sequencing and correlative titration studies need to be done, it is encouraging that most of the viral candidates selected thus far have no significant homology with any previously described sequence in the database.

Animals↗
PubMed2026

Engineered Ratiometric Near-Infrared Probes Enable Dual-Organelle Visualization of G-Quadruplex in Living Cells.

G-quadruplexes (G4s) participate in nuclear genome regulation and mitochondrial metabolism, but tools for monitoring both compartments in the same living cell remain limited. Here, we report PEG-INR-Me, a ratiometric near-infrared (NIR) probe designed for simultaneous visualization of nuclear and mitochondrial G4-associated signals. G4 binding enhances the long-wavelength emission, whereas the short-wavelength channel serves as an operational normalization channel under matched acquisition conditions. Accordingly, cellular Channel640/Channel560 values are interpreted as relative readouts within a defined compartment and experiment, rather than as absolute comparisons of G4 abundance between organelles. PEG-INR-Me revealed parallel cell-cycle-associated changes in nuclear and mitochondrial signals, higher signals in cancer cells than in noncancerous cells, and concurrent decreases during cisplatin treatment followed by partial recovery after caspase inhibition. These observations establish temporal concordance between mitochondria and nucleus. Following direct local administration, the probe also distinguished 4T1 tumors from a contralateral subcutaneous control site. PEG-INR-Me therefore provides a dual-compartment imaging platform for investigating nuclear and mitochondrial G4-associated dynamics, and their mechanistic relationship deserves to be further investigated.

G‐Quadruplexes↗
PubMed1999

Imaging of single DNA molecule: applications to high-resolution genomic studies.

Single molecule analysis of DNA has revealed new insights into its structural and physical properties. The application of new methods for manipulating and visualizing DNA has resulted in important advances in high-resolution physical mapping of the genome and quantitative cytogenetic studies of genomic abnormalities (Lichter 1997). Studies of single molecules of DNA have employed a variety of approaches including electron microscopy, atomic force microscopy, scanning-tunneling microscopy and fluorescence microscopy. A number of new technologies have recently been developed to exploit fluorescence microscopy's full potential for genomic analysis and the fine mapping of subtle genetic alterations. In the case of the latter application, particular emphasis has been placed on developing new methods for stretching DNA for high-resolution fluorescence in-situ hybridization studies. We have recently described a process called molecular combing according to which single DNA molecules bound by their extremities to a solid surface are uniformly stretched and aligned by a receding air/water interface (Bensimon et al. 1994). In the following, we will review recent developments concerning molecular combing and discuss its current and potential applications for the high-resolution mapping of the human genome, the detection and quantification of subtle genomic imbalances and the positional cloning of disease-related genes.

Chromosome Aberrations↗
PubMed2004

CRAVE: a database, middleware and visualization system for phenotype ontologies.

MOTIVATION: A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. RESULTS: CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

Algorithms↗
PubMed2003

Gene Expression Dynamics Inspector (GEDI): for integrative analysis of expression profiles.

UNLABELLED: Genome-wide expression profiles contain global patterns that evade visual detection in current gene clustering analysis. Here, a Gene Expression Dynamics Inspector (GEDI) is described that uses self-organizing maps to translate high-dimensional expression profiles of time courses or sample classes into animated, coherent and robust mosaics images. GEDI facilitates identification of interesting patterns of molecular activity simultaneously across gene, time and sample space without prior assumption of any structure in the data, and then permits the user to retrieve genes of interest. Important changes in genome-wide activities may be quickly identified based on 'Gestalt' recognition and hence, GEDI may be especially useful for non-specialist end users, such as physicians. AVAILABILITY: GEDI v1.0 is written in Matlab, and binary Matlab.dll files which require Matlab to run can be downloaded for free by academic institutions at http://www.chip.org/~ge/gedihome.html SUPPLEMENTARY INFORMATION: http://www.chip.org/~ge/gedihome.html

Algorithms↗
PubMed2005

Genome annotation of Anopheles gambiae using mass spectrometry-derived data.

BACKGROUND: A large number of animal and plant genomes have been completely sequenced over the last decade and are now publicly available. Although genomes can be rapidly sequenced, identifying protein-coding genes still remains a problematic task. Availability of protein sequence data allows direct confirmation of protein-coding genes. Mass spectrometry has recently emerged as a powerful tool for proteomic studies. Protein identification using mass spectrometry is usually carried out by searching against databases of known proteins or transcripts. This approach generally does not allow identification of proteins that have not yet been predicted or whose transcripts have not been identified. RESULTS: We searched 3,967 mass spectra from 16 LC-MS/MS runs of Anopheles gambiae salivary gland homogenates against the Anopheles gambiae genome database. This allowed us to validate 23 known transcripts and 50 novel transcripts. In addition, a novel gene was identified on the basis of peptides that matched a genomic region where no gene was known and no transcript had been predicted. The amino termini of proteins encoded by two predicted transcripts were confirmed based on N-terminally acetylated peptides sequenced by tandem mass spectrometry. Finally, six sequence polymorphisms could be annotated based on experimentally obtained peptide sequences. CONCLUSION: The peptide sequences from this study were mapped onto the genomic sequence using the distributed annotation system available at Ensembl and can be visualized in the context of all other existing annotations. The strategy described in this paper can be used to correct and confirm genome annotations and permit discovery of novel proteins in a high-throughput manner by mass spectrometry.

Animals↗
PubMed2004

Aligning multiple genomic sequences with the threaded blockset aligner.

We define a "threaded blockset," which is a novel generalization of the classic notion of a multiple alignment. A new computer program called TBA (for "threaded blockset aligner") builds a threaded blockset under the assumption that all matching segments occur in the same order and orientation in the given sequences; inversions and duplications are not addressed. TBA is designed to be appropriate for aligning many, but by no means all, megabase-sized regions of multiple mammalian genomes. The output of TBA can be projected onto any genome chosen as a reference, thus guaranteeing that different projections present consistent predictions of which genomic positions are orthologous. This capability is illustrated using a new visualization tool to view TBA-generated alignments of vertebrate Hox clusters from both the mammalian and fish perspectives. Experimental evaluation of alignment quality, using a program that simulates evolutionary change in genomic sequences, indicates that TBA is more accurate than earlier programs. To perform the dynamic-programming alignment step, TBA runs a stand-alone program called MULTIZ, which can be used to align highly rearranged or incompletely sequenced genomes. We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser.

Animals↗