The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.

The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.

Sampling Daphnia's expressed genes: preservation, expansion and invention of crustacean genes with reference to insect genomes

Background

Functional and comparative studies of insect genomes have shed light on the complement of genes, which in part, account for shared morphologies, developmental programs and life-histories. Contrasting the gene inventories of insects to those of the nematodes provides insight into the genomic changes responsible for their diversification. However, nematodes have weak relationships to insects, as each belongs to separate animal phyla. A better outgroup to distinguish lineage specific novelties would include other members of Arthropoda. For example, crustaceans are close allies to the insects (together forming Pancrustacea) and their fascinating aquatic lifestyle provides an important comparison for understanding the genetic basis of adaptations to life on land versus life in water.

Results

This study reports on the first characterization of cDNA libraries and sequences for the model crustacean Daphnia pulex. We analyzed 1,546 ESTs of which 1,414 represent approximately 787 nuclear genes, by measuring their sequence similarities with insect and nematode proteomes. The provisional annotation of genes is supported by expression data from microarray studies described in companion papers. Loci expected to be shared between crustaceans and insects because of their mutual biological features are identified, including genes for reproduction, regulation and cellular processes. We identify genes that are likely derived within Pancrustacea or lost within the nematodes. Moreover, lineage specific gene family expansions are identified, which suggest certain biological demands associated with their ecological setting. In particular, up to seven distinct ferritin loci are found in Daphnia compared to three in most insects. Finally, a substantial fraction of the sampled gene transcripts shares no sequence similarity with those from other arthropods. Genes functioning during development and reproduction are comparatively well conserved between crustaceans and insects. By contrast, genes that were responsive to environmental conditions (metal stress) and not sex-biased included the greatest proportion of genes with no matches to insect proteomes.

Conclusion

This study along with associated microarray experiments are the initial steps in a coordinated effort by the Daphnia Genomics Consortium to build the necessary genomic platform needed to discover genes that account for the phenotypic diversity within the genus and to gain new insights into crustacean biology. This effort will soon include the first crustacean genome sequence.

Daphnia magna ecotoxicogenomics provides mechanistic insights into metal toxicity

Toxicogenomics has provided innovative approaches to chemical screening, risk assessment, and predictive toxicology. If applied to ecotoxicology, genomics tools could greatly enhance the ability to understand the modes of toxicity in environmentally relevant organisms. Daphnia magna, a small aquatic crustacean, is considered a "keystone" species in ecological food webs and is an indicator species for toxicant exposure. Our objective was to demonstrate the potential utility of gene expression profiling in ecotoxicology by identifying novel biomarkers and uncovering potential modes of action in D. magna. Using a custom D. magna cDNA microarray, we identified distinct expression profiles in response to sublethal copper, cadmium, and zinc exposures and discovered specific biomarkers of exposure including two probable metallothioneins, and a ferritin mRNA with a functional IRE. The gene expression patterns support known mechanisms of metal toxicity and reveal novel modes of action including zinc inhibition of chitinase activity. By integrating gene expression profiling into an environmentally important organism, this study provides experimental support for the utility of ecotoxicogenomics.

The reproductive effects of beta interferon therapy in pregnancy: a longitudinal cohort

OBJECTIVE

To determine whether interferon therapy during human pregnancy increases reproductive risks in women.

METHODS

This longitudinal, controlled cohort study consisted of three groups of women: an exposed group, a disease matched unexposed group, and a healthy comparative group. Subjects were selected from women contacting the Motherisk Program regarding maternal beta interferon exposure, mostly for multiple sclerosis during pregnancy, from 1997 to 2004. After delivery all of the women were re-contacted for a follow-up interview regarding maternal health, pregnancy outcome, and neonatal health.

RESULTS

The study group (n = 16 women, 23 pregnancies) were exposed to interferon beta-1a (Avonex, Rebif) and interferon-1b (Betaseron). There was a decrease in mean birth weight in the exposed group (3,189 +/- 416 g) as compared to healthy controls (3,783 +/- 412 g, p = 0.002). Women exposed to beta interferon had a higher rate of miscarriages and stillbirths (39.1%) vs healthy controls (5%) (p = 0.03), even after correction for potential confounders. There were two major malformations (abnormality in the X chromosome, Down's syndrome) among exposed fetuses.

CONCLUSIONS

Beta interferon therapy in the first trimester of pregnancy appears to be associated with an increased risk for fetal loss and low birth weight.

Reappraisal of histologic features of the acute cutaneous graft-versus-host reaction based on an allogeneic rodent model

We employed a rat model of complete major histocompatibility complex-mismatched allogeneic bone marrow transplantation to better characterize the histologic expression of the acute cutaneous graft-versus-host reaction (GVHR), compared with changes due to the preparative regimen. Cyclosporin A abolished the development of this GVHR. Low levels of dyskeratotic cells were present in all groups (allogeneic and syngeneic transplants with and without cyclosporin A) and, alone, were insufficient to diagnose a cutaneous GVHR. A consistent histologic feature of the GVHR was significant lymphoid infiltration of the dermis. The pattern of cytotoxic folliculitis involved follicular epithelium above the entry of sebaceous glands. Immunostain for major histocompatibility complex class II, IA, and IE antigens revealed that dendritic cells within the follicle were limited to this upper region and that lower follicular epithelium did not upregulate expression with evolution of the GVHR. Based on this model, we conclude 1) that the diagnostic scheme for the acute cutaneous GVHR should include lymphoid infiltration of the dermis, 2) that the preparative regimen (including total body irradiation) induces persistent low levels of dyskeratotic cells (two to three cells/linear mm of epidermis), and 3) that the pattern of follicular involvement may relate to the distribution of dendritic cells and to an inability of lower follicular epithelium to upregulate major histocompatibility complex class II antigens.

Histologic comparison of autologous graft-vs-host reaction and cutaneous eruption of lymphocyte recovery

BACKGROUND AND DESIGN

The cutaneous eruptions due to allogeneic graft-vs-host disease, autologous graft-vs-host disease, and lymphocyte recovery occur in the setting of peripheral leukocyte reconstitution after marrow aplasia. Since the eruptions of lymphocyte recovery (ELR) and autologous graft-vs-host disease develop in the presence of histocompatibility, we question whether reliable histologic differentiation is possible. To this end, we performed a retrospective, blind analysis of 38 skin biopsy specimens obtained from patients who received autologous marrow transplants or intensive chemotherapy alone for various malignant neoplasms.

RESULTS

In 31% of the cases, we were unable to distinguish between an ELR and a grade 2 graft-vs-host reaction. In 40% of the ELR specimens, a significant number of dyskeratotic keratinocytes were present, leading to the false interpretation of a grade 2 graft-vs-host reaction. Satellite cell necrosis was observed in both groups. The patterns of dyskeratotic keratinocytes were similar; one ELR specimen displayed prominent follicular involvement. Most ELR specimens were consistent with grade 1 graft-vs-host reaction changes.

CONCLUSIONS

These findings indicate that the presence of dyskeratotic keratinocytes is not specific for a graft-vs-host reaction and that cutaneous eruptions after autologous marrow transplantation are best considered an ELR.

Multiple methicillin-resistant Staphylococcus aureus strains as a cause for a single outbreak of severe disease in hospitalized neonates

Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of nosocomial infection. Outbreaks of infection caused by these pathogens are generally considered to be traceable to introduction of single strains into a hospital population. A large outbreak of bacteremic disease that recently occurred in our neonatal intensive care unit (11 episodes in 10 patients) involved 9 low birth weight infants and was associated with serious infection (4 episodes of meningitis). To determine the role of a single point source in this outbreak, isolates were characterized based on phenotypic and genotypic analyses. Phenotypic analysis included assessing hemolytic activity, phage typing, antimicrobial susceptibility testing and methicillin resistance population analysis. Genotypic analysis included assessment of plasmid profiles, dot-blot hybridization, restriction enzyme fragment pattern analysis and hybridization analysis of chromosomal DNA using a panel of staphylococcal gene probes. This analysis established that at least two distinct strains of MRSA were responsible for disease during this outbreak. This experience demonstrates the potential for MRSA to cause severe disease in the neonatal intensive care unit and indicates that the epidemiology of MRSA outbreaks is more complex than the spread of a single strain of bacteria.

Modifications on the heterocyclic base of acyclovir: syntheses and antiviral properties

A group of compounds was prepared in which variations of the ring portion of the acyclovir (ACV) structure were made. These modifications included monocyclic (isocytosine, triazole, imidazole), bicyclic (8-azapurine, pyrrolo[2,3-d]pyrimidine, pyrazolo[3,4-d]pyrimidine) and tricyclic (linear benzoguanine) congeners. The derivatives were evaluated against herpes simplex virus type 1 (HSV-1) by the plaque-inhibition and plaque-reduction methods with only the 8-azapurine analogue 28 showing some activity. In a test measuring the ability of these compounds to inhibit the HSV-1 thymidine kinase, 28 and the tricyclic derivative 38 exhibited competition with ACV for binding to the enzyme. The inability of the group to exert significant antiherpetic action is attributed to their lack of phosphorylation to the requisite triphosphate stage.

A novel method for detecting the antiviral activity of flavans in their vapour phase

This report describes a new method for detecting and measuring the antiviral activity of volatile compounds. This method, the vapour phase test, is a modification of the conventional plaque reduction test, in that the compounds instead of being incorporated in the overlay medium were deposited on the inner surface of the Petri dish lid. During the incubation period, the compounds (if volatile) permeated the overlay medium before exerting their antiviral effect. Compounds which have or may come to clinical trial against rhinovirus infections were compared by normal plaque reduction assays and by means of this new technique. Flavans were shown able to exert their antiviral activity in the vapour phase and thus display an advantage over non-volatile compounds. The report also briefly shows how the technique was used to evaluate the structure-activity relationships in a series of analogous compounds.

Acyclovir treatment of experimental herpetic keratitis in the rabbit eye

In the rabbit eye model of experimental herpetic keratitis a satisfactory cure was obtained with ointments containing 1 percent, 2 percent, and 3 percent acyclovir, and also with idoxuridine. Trifluorothymidine and vidarabine were less effective in the particular conditions of the experiment. A cure was also obtained with acyclovir sodium salt injected intravenously, thus demonstrating that a local infection of the eye can be treated systematically.

4',6-Dichloroflavan (BW683C), a new anti-rhinovirus compound

Derivatives of flavan have been synthesized as chemical intermediates, but the only reported biological action is the ability of certain alkyl and alkoxy derivatives to lower blood cholesterol concentrations¹. It was therefore surprising to discover that flavan itself (Table 1) is a highly effective inhibitor of the replication of certain serotypes of rhinovirus, and that a simple derivative, BW683C (4′,6-dichloroflavan), is the most potent antiviral compound yet reported. The present work examines the antiviral activity of flavan derivatives with a view to selecting the compound most suitable for trial in volunteers infected with a common cold virus.

Successful treatment of experimental B virus (Herpesvirus simiae) infection with acyclovir

The efficacy of the new nucleoside analogue acyclovir against B virus (Herpesvirus simiae) was investigated in rabbits and Vero cells infected with 2-136 and 0.3-1.0 TCD50 of the virus respectively. In the Vero cells 1 mg of acyclovir/1 reduced the yield of virus by 90%, which was slightly less than the effect on herpes simplex virus. Results in the rabbits varied with the interval between doses, duration of treatment, and delay before starting treatment. Acyclovir controlled an otherwise lethal infection when given not less than eight-hourly for 14 days. Withdrawing treatment after 9-10 days resulted in late-onset fatal disease in some rabbits. Treatment begun within 24 hours after infection gave complete protection, and rabbits first treated up to five days after infection showed a significant reduction in mortality (p less than 0.001). The plasma half life of acyclovir is twice as long in man as in rabbits and progression of the disease is much slower. Hence acyclovir may be useful for post-exposure prophylaxis against B virus infection in man and possibly also for treatment of the disease.

Treatment of experimental herpes simplex keratitis with acycloguanosine

Acycloguanosine, a recently developed compound with high inhibitory activity against viruses belonging to the herpes group, has been evaluated in experimental herpes simplex keratitis in rabbits in comparison with trifluorothymidine and preparations of idoxuridine and vidarabine at present in clinical use. All compunds were used in the form of ophthalmic ointments which were applied 5 times a day at intervals of 2 hours. Treatment began on the third day of infection and was continued for 4 days. Complete cure was obtained with acycloguanosine and idoxurdine; trifluorothymidine and vidarabine were considerably less effective. Acycloguanosine was equally effective when given intravenously in the form of its sodium salt, and could be detected in the tear fluid in inhibitory concentrations when given by mouth. The compound was relatively free from toxicity.

9-(2-hydroxyethoxymethyl) guanine activity against viruses of the herpes group

Of a series of nucleoside analogues synthesised, 9-(2-hydroxyethoxymethyl) guanine was found to have marked antiviral activity in animal models of herpes virus infections, associated with very low toxicity.

The relative potencies of anti-influenza compounds

The relative potencies of some standard anti-influenza compounds have been examined in vitro by plaque reduction in calf kidney cells, and in vivo by reduction in virus titers of the lungs of infected mice. Strains belonging to the four subtypes H0N1, H1N1, H2N2, and H3N2 were employed to compare the activity of amantadine hydrochloride and ribavirin. In vitro for all strains except A/NWS/OO(H0N1) amantadine hydrochloride was 3-4 times more active than ribavirin. In vivo with sensitive strains amantadine hydrochloride produced a plateau effect at higher dose levels, but at lower dose levels was marginally more active than ribavirin. The sensitivity of A/Hong Kong/1/68 (H3N2) to amantadine hydrochloride, rimantadine hydrochloride, cyclooctylamine, and ribavirin was also investigated. In vitro rimantadine hydrochloride was similar in activity to amantadine hydrochloride and ribavirin, but cyclooctylamine was considerably less active. In vivo cyclooctylamine was active only at 150 mg/kg/day, whereas rimantadine hydrochloride produced a plateau effect over a range of concentrations from 9,12-150 mg/kg/day.

Relative potencies of anti-herpes compounds

Assessment of the relative potencies of compounds that inhibit the multiplication of herpesvirus is rendered difficult by the fact that they have been investigated by different workers who were not using comparable test systems. The relative and absolute potencies of idoxuridine, cytarabine, vidarabine, trifluorothymidine, and ara-DAP have therefore been evaluated by plaque inhibition, plaque reduction, and yield reduction tests, the most satisfactory dose-response lines being obtained by plaque reduction. The results obtained for five strains of type 1 and five of type 2 herpesvirus indicated that cytarabine was the most active compound, followed by idoxuridine and trifluorothymidine; vidarabine and ara-DAP were found to be the least active compounds. From comparisons of ED50 values derived from the dose-response lines it was found that the greater sensitivity of type 1 strains reported in the literature could only be confirmed with idoxuridine, since considerable overlaps in type sensitivity were observed with the other compounds.

Chemoprophylaxis of smallpox and treatment of vaccinia gangrenosa with 1-methylisatin 3-thiosemicarbazone

Erythromycin synthesis was markedly impaired in submerged cultures under high carbon dioxide tensions. Growth of Streptomyces erythreus, however, was unaltered by increased carbon dioxide.

Adenovirus multiplication: inhibition by methisazone

Methisazone (5 to 40 microM) inhibited the multiplication of types 3, 7, 9, 11, 14, 16, 17, 21, and 28 adenovirus; SV15 (a simian adenovirus) was also inhibited. A study of adenovirus 11 under single-cycle conditions showed that multiplication of the virus, was completely inhibited by 30 microM methisazone when addition of the compound was delayed until 13 hours after infection. A survey showed that the structure-activity relations of the action of methisazone against adenoviruses and pox viruses are similar.