A method for phenomenological and chemical kinetics study of autocatalytic reactive dissolution by optical microscopy. The case of uranium dioxide dissolution in nitric acid media

Dissolution is a milestone of the head-end of hydrometallurgical processes, as the stabilization rates of the chemical elements determine the process performance and hold-up. This study aims at better understanding the chemical and physico-chemical phenomena of uranium dioxide dissolution reactions in nitric acid media in the Purex process, which separates the reusable materials and the final wastes of the spent nuclear fuels. It has been documented that the attack of sintering-manufactured uranium dioxide solids occurs through preferential attack sites, which leads to the development of cracks in the solids. Optical microscopy observations show that in some cases, the development of these cracks leads to the solid cleavage. It is shown here that the dissolution of the detached fragments is much slower than the process of the complete cleavage of the solid, and occurs with no disturbing phenomena, like gas bubbling. This fact has motivated the measurement of dissolution kinetics using optical microscopy and image processing. By further discriminating between external resistance and chemical reaction, the “true” chemical kinetics of the reaction have been measured, and the highly autocatalytic nature of the reaction confirmed. Based on these results, the constants of the chemical reactions kinetic laws have also been evaluated.

Generating Modeling Data From Repeat-Dose Toxicity Reports

Over the past decades, pharmaceutical companies have conducted a large number of high-quality in vivo repeat-dose toxicity (RDT) studies for regulatory purposes. As part of the eTOX project, a high number of these studies have been compiled and integrated into a database. This valuable resource can be queried directly, but it can be further exploited to build predictive models. As the studies were originally conducted to investigate the properties of individual compounds, the experimental conditions across the studies are highly heterogeneous. Consequently, the original data required normalization/standardization, filtering, categorization and integration to make possible any data analysis (such as building predictive models). Additionally, the primary objectives of the RDT studies were to identify toxicological findings, most of which do not directly translate to in vivo endpoints. This article describes a method to extract datasets containing comparable toxicological properties for a series of compounds amenable for building predictive models. The proposed strategy starts with the normalization of the terms used within the original reports. Then, comparable datasets are extracted from the database by applying filters based on the experimental conditions. Finally, carefully selected profiles of toxicological findings are mapped to endpoints of interest, generating QSAR-like tables. In this work, we describe in detail the strategy and tools used for carrying out these transformations and illustrate its application in a data sample extracted from the eTOX database. The suitability of the resulting tables for developing hazard-predicting models was investigated by building proof-of-concept models for in vivo liver endpoints.

Legacy data sharing to improve drug safety assessment: the eTOX project

The sharing of legacy preclinical safety data among pharmaceutical companies and its integration with other information sources offers unprecedented opportunities to improve the early assessment of drug safety. Here, we discuss the experience of the eTOX project, which was established through the Innovative Medicines Initiative to explore this possibility.

Graphical display of histopathology data from toxicology studies for drug discovery and development: An industry perspective

Histopathology data comprise a critical component of pharmaceutical toxicology studies and are typically presented as finding incidence counts and severity scores per organ, and tabulated on multiple pages which can be challenging for review and aggregation of results. However, the SEND (Standard for Exchange of Nonclinical Data) standard provides a means for collecting and managing histopathology data in a uniform fashion which can allow informatics systems to archive, display and analyze data in novel ways. Various software applications have become available to convert histopathology data into graphical displays for analyses. A subgroup of the FDA-PhUSE Nonclinical Working Group conducted intra-industry surveys regarding the use of graphical displays of histopathology data. Visual cues, use-cases, the value of cross-domain and cross-study visualizations, and limitations were topics for discussion in the context of the surveys. The subgroup came to the following conclusions. Graphical displays appear advantageous as a communication tool to both pathologists and non-pathologists, and provide an efficient means for communicating pathology findings to project teams. Graphics can support hypothesis-generation which could include cross-domain interactive visualizations and/-or aggregating large datasets from multiple studies to observe and/or display patterns and trends. Incorporation of the SEND standard will provide a platform by which visualization tools will be able to aggregate, select and display information from complex and disparate datasets.

OntoBrowser: a collaborative tool for curation of ontologies by subject matter experts

Summary

The lack of controlled terminology and ontology usage leads to incomplete search results and poor interoperability between databases. One of the major underlying challenges of data integration is curating data to adhere to controlled terminologies and/or ontologies. Finding subject matter experts with the time and skills required to perform data curation is often problematic. In addition, existing tools are not designed for continuous data integration and collaborative curation. This results in time-consuming curation workflows that often become unsustainable. The primary objective of OntoBrowser is to provide an easy-to-use online collaborative solution for subject matter experts to map reported terms to preferred ontology (or code list) terms and facilitate ontology evolution. Additional features include web service access to data, visualization of ontologies in hierarchical/graph format and a peer review/approval workflow with alerting.

Availability and implementation

The source code is freely available under the Apache v2.0 license. Source code and installation instructions are available at http://opensource.nibr.com. This software is designed to run on a Java EE application server and store data in a relational database.

Value of shared preclinical safety studies - The eTOX database

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First analysis of the eTOX database for 1214 drugs or drug candidates.

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Shared data mainly from short term <20 days preclinical studies in rat via oral route.

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Identified the most frequent treatment related findings.

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Evaluated predictivity of clinical chemistry biomarkers.

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Present a first use case of the database during early drug development.

A first analysis of a database of shared preclinical safety data for 1214 small molecule drugs and drug candidates extracted from 3970 reports donated by thirteen pharmaceutical companies for the eTOX project (www.etoxproject.eu) is presented. Species, duration of exposure and administration route data were analysed to assess if large enough subsets of homogenous data are available for building in silico predictive models. Prevalence of treatment related effects for the different types of findings recorded were analysed. The eTOX ontology was used to determine the most common treatment-related clinical chemistry and histopathology findings reported in the database. The data were then mined to evaluate sensitivity of established in vivo biomarkers for liver toxicity risk assessment. The value of the database to inform other drug development projects during early drug development is illustrated by a case study.

Robust and tissue-independent gender-specific transcript biomarkers

CONTEXT

Correct gender assignment in humans at the molecular level is crucial in many scientific disciplines and applied areas.

MATERIALS AND METHODS

Candidate gender markers were identified through supervised statistical analysis of genome wide microarray expression data from human blood samples (N = 123, 58 female, 65 male) as a training set. The potential of the markers to predict undisclosed tissue donor gender was tested on microarray data from 13 healthy and 11 cancerous human tissue collections (internal) and external datasets from samples of varying tissue origin. The abundance of some genes in the marker panel was quantified by RT-PCR as alternative analytical technology.

RESULTS

We identified and qualified predictive, gender-specific transcript markers based on a set of five genes (RPS4Y1, EIF1AY, DDX3Y, KDM5D and XIST).

CONCLUSION

Gene expression marker panels can be used as a robust tissue- and platform-independent predictive approach for gender determination.

Oxidative degradation of bis(2,4,4-trimethylpentyl)dithiophosphinic acid in nitric acid studied by electrospray ionization mass spectrometry

RATIONALE

The selective separation of the minor actinides (Am, Cm) from the lanthanides is a topic of ongoing nuclear fuel cycle research, and dithiophosphinic acids are candidate ligands in these processes. Ligand instability has been noted under radiolytic and harsh acid conditions but explicit degradation pathways for ligands such as bis(2,4,4-trimethylpentyl)-dithiophosphinic acid (CyxH), the major compound in the commercial product Cyanex 301, have been elusive.

METHODS

Organic solutions of CyxH were contacted with aqueous solutions of HNO(3), and their degradation was studied by analyzing samples from these experiments by direct infusion electrospray ionization mass spectrometry. Ions were identified using accurate mass measurement and collision-induced dissociation.

RESULTS

The positive ion spectra contained cationized CyxH cluster ions, and oxidatively coupled species (designated Cyx(2)) cationized by either H or Na. The Cyx(2)-derived ions increased with acid contact time. The negative ion spectra consisted almost entirely of the CyxH conjugate base. The negative ion spectra of the HNO(3)-contacted samples also contained conjugate bases corresponding to the dioxo and perthio derivatives of CyxH.

CONCLUSIONS

CyxH is oxidized by acid contact to form the coupled species Cyx(2), and the dioxo species arise from subsequent oxidation of Cyx(2). Oxidative coupling increases with contact time, and with higher HNO(3) concentrations. The direct infusion measurements provided a simple approach for assessing degradation pathways and kinetics.

MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states

Background

Information obtained by DNA microarray technology gives a rough snapshot of the transcriptome state, i.e., the expression level of all the genes expressed in a cell population at any given time. One of the challenging questions raised by the tremendous amount of microarray data is to identify groups of co-regulated genes and to understand their role in cell functions.

Results

MiCoViTo (Microarray Comparison Visualization Tool) is a set of biologists' tools for exploring, comparing and visualizing changes in the yeast transcriptome by a gene-centric approach. A relational database includes data linked to genome expression and graphical output makes it easy to visualize clusters of co-expressed genes in the context of available biological information. To this aim, upload of personal data is possible and microarray data from fifty publications dedicated to S. cerevisiae are provided on-line. A web interface guides the biologist during the usage of this tool and is freely accessible at .

Conclusions

MiCoViTo offers an easy-to-read picture of local transcriptional changes connected to current biological knowledge. This should help biologists to mine yeast microarray data and better understand the underlying biology. We plan to add functional annotations from other organisms. That would allow inter-species comparison of transcriptomes via orthology tables.

yMGV: a cross-species expression data mining tool

The yeast Microarray Global Viewer (yMGV @ http://transcriptome.ens.fr/ymgv) was created 3 years ago as a database that houses a collection of Saccharomyces cerevisiae and Schizosaccharo myces pombe microarray data sets published in 82 different articles. yMGV couples data mining tools with a user-friendly web interface so that, with a few mouse clicks, one can identify the conditions that affect the expression of a gene or list of genes regulated in a set of experiments. One of the major new features we present here is a set of tools that allows for inter-organism comparisons. This should enable the fission yeast community to take advantage of the large amount of available information on budding yeast transcriptome. New tools and ongoing developments are also presented here.

A general strategy to uncover transcription factor properties identifies a new regulator of drug resistance in yeast

We demonstrate a genomewide approach to determine the physiological role of a putative transcription factor, Ylr266, identified through yeast genome sequencing program. We constructed activated forms of the zinc finger (Zn(2)Cys(6)) protein Ylr266, and we analyzed the corresponding transcriptomes with DNA microarrays to characterize the up-regulated genes. The direct target genes of Ylr266 were further identified by in vivo chromatin immunoprecipitation procedure. The functions of the genes directly controlled by YLR266c are in agreement with the observed drug-resistance phenotype of the cell expressing an activated form of Ylr266. These target genes code for ATP-binding cassette or major facilitator superfamily transporters such as PDR15, YOR1, or AZR1 or for other proteins such as SNG1, YJL216c, or YLL056c which are already known to be involved in the yeast pleiotropic drug resistance (PDR) phenomenon. YLR266c could thus be named PDR8. Overlaps with the other PDR networks argue in favor of a new specific role for PDR8 in connection with the well known PDR regulators PDR1/PDR3 and YRR1. This strategy to identify the regulatory properties of an anonymous transcription factor is likely to be generalized to all the Zn(2)Cys(6) transcription factors from Saccharomyces cerevisiae and related yeasts.

Arrayplot for visualization and normalization of cDNA microarray data

Arrayplot is an application which allows filtering, visualization and normalization of raw cDNA microarray data.

AVAILABILITY

MS-Windows binaries are freely available for non-profit use at http://www.biologie.ens.fr/yeast-publi.html.

SUPPLEMENTARY INFORMATION

Scripts for online creation of Arrayplot files are available at http://transcriptome.ens.fr/lgm_bioinfo/

New insights into the pleiotropic drug resistance network from genome-wide characterization of the YRR1 transcription factor regulation system

Yrr1p is a recently described Zn(2)Cys(6) transcription factor involved in the pleiotropic drug resistance (PDR) phenomenon. It is controlled in a Pdr1p-dependent manner and is autoregulated. We describe here a new genome-wide approach to characterization of the set of genes directly regulated by Yrr1p. We found that the time-course production of an artificial chimera protein containing the DNA-binding domain of Yrr1p activated the 15 genes that are also up-regulated by a gain-of-function mutant of Yrr1p. Gel mobility shift assays showed that the promoters of the genes AZR1, FLR1, SNG1, YLL056C, YLR346C, and YPL088W interacted with Yrr1p. The putative consensus Yrr1p binding site deduced from these experiments, (T/A)CCG(C/T)(G/T)(G/T)(A/T)(A/T), is strikingly similar to the PDR element binding site sequence recognized by Pdr1p and Pdr3p. The minor differences between these sequences are consistent with Yrr1p and Pdr1p and Pdr3p having different sets of target genes. According to these data, some target genes are directly regulated by Pdr1p and Pdr3p or by Yrr1p, whereas some genes are indirectly regulated by the activation of Yrr1p. Some genes, such as YOR1, SNQ2, and FLR1, are clearly directly controlled by both classes of transcription factor, suggesting an important role for the corresponding membrane proteins.

Genome-wide analysis of mRNAs targeted to yeast mitochondria

It is agreed that nuclear-encoded mitochondrial proteins are post-translationally targeted to mitochondria, even if, in some cases, a co-translational phase can assist the import of precursor proteins. We used yeast DNA microarrays to analyse the mRNA populations associated with free and mitochondrion-bound polysomes. As expected, many mRNAs, known to encode mitochondrial proteins, are localized to free cytoplasmic polysomes, but many are localized to mitochondrion-bound polysomes. Furthermore, the 3'-UTR of six randomly chosen mitochondrion-bound mRNAs contains sufficient information to target, in vivo, non-translatable RNA to the vicinity of mitochondria. Interestingly, genes producing mRNAs that are targeted to mitochondria are mainly of ancient bacterial origin, whereas those producing mRNAs that are translated in the cytoplasm are mainly of eukaryotic origin. These observations, which support the recent hypotheses concerning the dual origin of the mitochondrial proteome, provide new insights into the biogenesis of mitochondria.

yMGV: helping biologists with yeast microarray data mining

yMGV (yeast Microarray Global Viewer) was designed to provide biologists with meaningful information from genome-wide yeast expression data. The database includes most of the available expression data published on yeast microarrays over the last 4 years. It provides customizable tools for the rapid visualization of expression profiles associated with a set of genes from all published experiments. It also allows users to compare the results from different publications so that they can identify genes with common expression profiles. We used yMGV to perform global analyses to find a gene expression profile specific for given biological conditions and to locate functional gene clusters on chromosomes. Other organisms will be added to this database. yMGV is accessible on the web at http://transcriptome.ens.fr/ymgv.

Transcriptional induction of repair genes during slowing of replication in irradiated Saccharomyces cerevisiae

We investigated the inhibition of cell-cycle progression and replication and the induction of the transcriptional response in diploid budding yeast populations exposed to two different doses of gamma-rays resulting in 15 and 85% survival respectively. We studied the kinetics of the cellular response to ionizing treatment during the period required for all of the surviving cells to achieve at least one cell division. The length of these periods increased with the dose. Irradiated populations arrested as large-budded cells containing partially replicated chromosomes. The extent of the S-phase was proportional to the amount of damage and lasted 3 or 7h depending on the irradiation dose. In parallel to the division study, we carried out a kinetic analysis of the expression of 126 selected genes by use of dedicated microarrays. About 26 genes were induced by irradiation and displayed various pattern of expression. Interestingly, 10 repair genes (RAD51, RAD54, CDC8, MSH2, RFA2, RFA3, UBC5, SRS2, SPO12 and TOP1), involved in recombination and DNA synthesis, display similar regulation of expression in the two irradiated populations. Their pattern of expression were confirmed by Northern analysis. At the two doses, the expression of this group of genes closely followed the extended replication period, and their expression resumed when replication restarted. These results suggest that the damage-induced response and DNA synthesis are closely regulated during repair. The analysis of the promoter regions indicates a high occurrence of the three MCB, HAP and UASH regulatory boxes in the promoters of this group of genes. The association of the three boxes could confer an irradiation-replication specific regulation.

yMGV: a database for visualization and data mining of published genome-wide yeast expression data

The yeast Microarray Global Viewer (yMGV) is an on-line database providing a synthetic view of the transcriptional expression profiles of Saccharomyces cerevisiae genes in most of the published expression datasets. yMGV displays a one-screen graphical representation of gene expression variations for each published genome-wide experiment, allowing quick retrieval of experimental conditions affecting expression of this gene. yMGV also provides tools to isolate groups of genes sharing similar transcription profiles in a defined subset of experiments. Additionally, yMGV furnishes a set of statistical tools for critical assessment of published data. We therefore believe that yMGV is an efficient tool that affords a quick and comprehensive overview of microarray data and generates new gene classifications. As of 20 March 2001 the yMGV database contains 6 000 000 measurements, representing genome-wide expression comparisons of 932 experiments from 39 microarray publications. The yMGV interface is available at http://transcriptome.ens.fr/ymgv/.

Transcriptomes, transcription activators and microarrays

Gene-specific transcription activators are among the main factors which specifically shape the transcriptome profiles. It is tempting to take advantage of their properties to decipher the genome expression circuitry. The advent of microarray technology has offered fantastic opportunities to quickly analyze the expression profiles dictated by specific transcription factors. This review will first focus on the strategies which have been devised to control the activity of transcription factors and in the second part on the microarray experiments which addressed the role of these transcription factors in the genome-wide expression profile. This last part will mainly consider the case of the yeast Saccharomyces cerevisiae genome. All the collected data are available through the on-line database yTAFNET (http://transcriptome.ens.fr/ytafnet/). yTAFNET is designed to help the characterization of connections between the different yeast regulatory networks.

An artificial transcription activator mimics the genome-wide properties of the yeast Pdr1 transcription factor

We analysed the genome-wide regulatory properties of an artificial transcription activator in which the DNA-binding domain of the yeast transcription factor, Pdr1, was fused to the activation domain of Gal4 (Pdr1*GAD). This Pdr1*GAD chimera was put under the control of the inducible GAL1 promoter. DNA microarray analyses showed that all the target genes upregulated by the well-studied native gain-of-function Pdr1-3 mutant were similarly activated by the chimerical factor Pdr1*GAD upon galactose induction. Additionally, this kinetic approach led us not only to confirm previously published targets, but also to define a hierarchy among members of the Pdr1 regulon. Our observations prove, for the first time at the complete genome level, that the DNA-binding domain of Pdr1 is sufficient to guide its specificity. We propose that this approach could be useful for the study of new transcription factors identified in silico from sequenced organisms. Complete data are available at www.biologie.ens.fr/yeast-publi.html.

Genome microarray analysis of transcriptional activation in multidrug resistance yeast mutants

The cDNA from activated mutants of the homologous transcription factors Pdr1p and Pdr3p was used to screen DNA microarrays of the Saccharomyces cerevisiae complete genome. Twenty-six overexpressed targets of the PDR1-3 and/or PDR3-7 mutants were identified. Twenty-one are new targets, the majority of which are of unknown function. In addition to well known ABC transporters, these targets appear to be involved in transport or in membrane lipids and cell wall biosyntheses. Several of the targets seem to contribute to the cell defence against a variety of stresses. Pdr1p and Pdr3p do not act similarly on all targets. Unexpectedly, the expression of 23 other genes appeared to be repressed in the PDR1-3 and/or PDR3-7 mutants. In contrast to the majority of the activated genes, none of the repressed genes contains pleiotropic drug resistance binding sites in their promoter.

Human growth hormone stimulates proteinase activities of rabbit bone cells via IGF-I

Human growth hormone (hGH) and human insulin-like growth factor-I (hIGF-I) are known to have a marked influence on osteoclastic formation and bone resorption in an unfractionated rabbit bone cell model. This study investigated the effects of both of these factors on the induction of cysteine-proteinases and matrix metalloproteinase-2 (MMP-2) and MMP-9. After 4 days of rabbit bone cell culture, hGH and hIGF-I significantly modulated cathepsin, MMP-9 (latent form) and MMP-2 (active form) activities. Similar studies were performed in the presence of parathyroid hormone (hPTH). hPTH increased MMP-2 and MMP-9 activities whereas it had no effect on the production of cathepsins by bone cells. When neutralizing anti-hIGF-1 antiserum was added to the culture, the stimulatory effects of hGH were totally abolished, indicating that hGH-modulated cathepsin and metalloproteinase activities were partly mediated by local hIGF-I secretion. Cysteine-proteinase activities released by purified osteoclasts were very low and were not modulated by hGH and h-IGF-I. However, hIGF-I but not hGH increased MMP-2 and MMP-9 activities released by purified osteoclasts. It may be concluded that hGH markedly stimulates the expression of proteinases in total rabbit bone cells via local hIGF-I production by stromal cells. Cysteine-proteinase activities are mainly produced by non-osteoclastic cells, while MMP-2 and MMP-9 modulated by hIGF-I are mainly expressed by osteoclastic cells.

Antibodies to varicella-zoster virus modulate antigen distribution but fail to induce viral persistence in vitro

Varicella-zoster virus (VZV) persists in human sensory ganglia. One of the hypotheses to explain the induction or the maintenance of VZV latency is that it could be promoted by the immune response itself. It is known that in the case of viruses which bud off the infected cell membrane, virus-specific antibodies can induce antigenic modulation, i.e., spatial redistribution of viral antigens and modulation of their synthesis. To determine whether antigenic modulation occurs during VZV infection in vitro and could possibly be involved in viral persistence, we have grown infected cells in the presence of anti-VZV antibodies either transiently or permanently. The distribution of immune complexes and viral proteins was then analyzed. In transient immunomodulation experiments, the distribution of one or more viral antigens was modified not only in the cytoplasmic membranes but also in the cytoplasm and nucleoplasm of infected cells. When infected cells were kept permanently in the presence of antibodies, the same pattern of redistribution of immune complexes was observed and the localization of internal viral glycoproteins was significantly modified. However, antibodies did not prevent the lytic effect of infection; they altered neither the infectious virus yield nor the Western immunoblot pattern of viral proteins, suggesting that immunomodulation is not the primary effector of viral persistence.

An in vivo model of varicella-zoster virus latent infection of dorsal root ganglia

We describe here the first in vivo model of varicella-zoster virus (VZV) latent infection in the adult rat peripheral nervous system. Infected Mewo cells were injected subcutaneously along the spine of healthy adult rats. No clinical sign of infection was observed even 9 months after inoculation. Humoral immune response to VZV was detected in all infected animals throughout the study (9 months). The presence of viral material in dissociated and cultured dorsal root ganglia (DRG) from inoculated animals was studied by immunoperoxidase and in situ hybridization. When DRGs from infected animals were plated in culture from 1 month and up to 9 months after inoculation, viral nucleic acids and proteins were detected in neurons. Furthermore, trypsinization and subcultivation of infected neurons in culture is needed to reactivate infectious virus at least in some of the neurons. This model provides a useful tool for studying 1) the molecular mechanisms leading to an in vivo latency, 2) the role of the immune system, in particular cellular immunity, on the establishment, maintenance, and reactivation of latency, 3) the neurotropism of mutant viruses, and 4) the effects of antiviral agents.

Acute and persistent varicella-zoster virus infection of human and murine neuroblastoma cell lines

Human and murine neuroblastoma cell lines were infected in vitro with varicella-zoster virus (VZV). Infected human neuroblastoma cells (IMR-32) supported the synthesis of abundant viral antigens as detected by indirect immunoperoxidase labeling using human serum rich in anti-VZV antibodies and did not survive the infection. In situ hybridization (ISH) with VZV-cloned probes revealed a strong hybridization signal in these infected cells. During cultivation, the virus was released in the culture medium, and viral polypeptides were revealed by Western blotting of infected cells, using either a monoclonal anti-gpI antibody or a rabbit antiserum. All these findings indicate that IMR-32 cells support a productive and lytic infection by VZV, whether infected by cell-free virus or by cocultivation with infected cells. Murine neuroblastoma cells (neuro-2A) survived VZV infection and did not produce any infectious virus. No VZV-specific proteins were detected in infected cells either by immunolabeling or by Western blotting. However, viral nucleic acids could be detected by ISH, indicating that mouse neuroblastoma cells displayed a nonproductive, nonlytic infection. Infected neuro-2A cells have been examined by ISH using probes corresponding to immediate early (IE) genes 4, 62, and 63 and late (L) gene 31 encoding gpII. A strong hybridization signal was detected when infected cells were probed with a fragment containing the IE genes 62 and 63. Lower levels of hybridization were detected with the other probes, corresponding to IE or L genes. These systems allow comparative molecular analysis of persistent and acute infection of nerve cells by VZV.