Structural aspects of recently discovered viral deubiquitinating activities

Protein ubiquitination has been identified as a regulatory mechanism in key cellular activities, and deubiquitination is recognized as an important step in processes governed by ubiquitin and ubiquitin-like modifiers. Viruses are known to target ubiquitin and ubiquitin-like modifier pathways using various strategies, including the recruitment of host deubiquitinating enzymes. Deubiquitinating activities have recently been described for proteins from three different virus families (adenovirus, coronavirus and herpesvirus), and predicted for others. This review centers on structural-functional aspects that characterize the confirmed viral deubiquitinating enzymes, and their relationships to established families of cellular deubiquitinating enzymes.     

Serological studies confirm the novel astrovirus HMOAstV-C as a highly prevalent human infectious agent

Molecular identification of a microbe is the first step in determining its prevalence of infection and pathogenic potential. Detection of specific adaptive immune responses can provide insights into whether a microbe is a human infectious agent and its epidemiology. Here we characterized human anti-IgG antibody responses by luciferase immunoprecipitation systems (LIPS) against two protein fragments derived from the capsid protein of the novel HMOAstV-C astrovirus. While antibodies to the N-terminal fragment were not informative, the C-terminal capsid fragment of HMOAstV-C showed a high frequency of immunoreactivity with serum from healthy blood donors. In contrast, a similar C-terminal capsid fragment from the related HMOAstV-A astrovirus failed to show immunoreactivity. Detailed analysis of adult serum from the United Sates using a standardized threshold demonstrated HMOAstV-C seropositivity in approximately 65% of the samples. Evaluation of serum samples from different pediatric age groups revealed that the prevalence of antibodies in 6-12 month, 1-2 year, 2-5 year and 5-10 year olds was 20%, 23%, 32% and 36%, respectively, indicating rising seroprevalence with age. Additionally, 50% (11/22) of the 0-6 month old children showed anti-HMOAstV-C antibody responses, likely reflecting maternal antibodies. Together these results document human humoral responses to HMOAstV-C and validate LIPS as a facile and effective approach for identifying humoral responses to novel infectious agents.     

Activation of progelatinase A by mammalian legumain, a recently discovered cysteine proteinase

The activation of progelatinase A to gelatinase A requires cleavage of an asparaginyl bond to form the N-terminus of the mature enzyme. We have asked whether the activation can be mediated by legumain, the recently discovered lysosomal cysteine proteinase that is specific for hydrolysis of asparaginyl bonds. Addition of purified legumain to the concentrated conditioned medium from HT1080 cell culture that contained both progelatinases A and B caused the conversion of the 72 kDa progelatinase A to the 62 kDa form. The progelatinase B in the medium was unaffected. Incubation of recombinant progelatinase A with legumain resulted in an almost instantaneous activation as judged by the fluorometric assay with a specific gelatinase A substrate, Mca-Pro-Leu-Gly-Leu-Dpa-Ala-Arg-NH2. Legumain also activated progelatinase A when it was in complex with TIMP-2. Zymographic analysis and N-terminal sequencing revealed that legumain cleaved the 72 kDa progelatinase A at the bonds between Asn109-Tyr110 or Asn111-Phe112 to produce the 62 kDa mature enzyme, and that further cleavage at Asn430 also occurred to generate a 36 kDa active form. More 62 kDa gelatinase A was detected in cultures of C13 cells that over-expressed legumain than in those of the control HEK293 cells. We conclude that legumain is clearly capable of processing progelatinase A to the active enzyme in vitro and in cultured cells.     

Estimating abundance, age structure and sex ratio of a recently discovered New Zealand tusked weta

Estimates of abundance, age structure and sex ratio are essential for monitoring the status of populations. We report the first attempt to reliably estimate these parameters in a population of the recently discovered Raukumara tusked weta (Motuweta riparia), which is found almost entirely near streams. On two occasions we searched a 211-m section of creek for 4–5 successive nights and individually marked all weta. We estimated abundance of adults and juveniles using closed-population mark-recapture analysis. The choice of mark-recapture model made a substantial difference to the estimated abundance (116–238) and proportion of juveniles (32–72%). However, no single model was clearly better supported than any other. We therefore used model averaging to account for uncertainty in model choice, giving an estimate of 142 (95% CI 105–231) weta including 56 (95% CI 41–234) adults and 77 (95% CI 46–209) juveniles. This corresponds to a density of 0.11 (95% CI 0.08–0.18) weta per m2, assuming 3 m of habitat on either side of the creek. Recapture probability was much lower for adults (n = 2) than juveniles (n = 10), possibly caused by a difference in handling (adults were held overnight whereas juveniles were not). Slightly more juvenile males (n = 22) were caught than juvenile females (n = 21), but more adult females (n = 51) were caught than adult males (n = 31), suggesting a potentially higher mortality in males. An initial assessment of population size is crucial when considering the conservation status and management strategy of rare animals, such as the highly endangered Middle Island tusked weta. The immediate practical benefit of the methods developed here is therefore clear. In the long-term, these methods also have important implications for the continued monitoring of trends in other threatened invertebrate populations.     

Murine norovirus increases atherosclerotic lesion size and macrophages in Ldlr(-/-) mice

Murine norovirus (MNV) is prevalent in rodent facilities in the United States. Because MNV has a tropism for macrophages and dendritic cells, we hypothesized that it may alter phenotypes of murine models of inflammatory diseases, such as obesity and atherosclerosis. We examined whether MNV infection influences phenotypes associated with diet-induced obesity and atherosclerosis by using Ldlr(-/-) mice. Male Ldlr(-/-) mice were maintained on either a diabetogenic or high-fat diet for 16 wk, inoculated with either MNV or vehicle, and monitored for changes in body weight, blood glucose, glucose tolerance, and insulin sensitivity. Influence of MNV on atherosclerosis was analyzed by determining aortic sinus lesion area. Under both dietary regimens, MNV-infected and control mice gained similar amounts of weight and developed similar degrees of insulin resistance. However, MNV infection was associated with significant increases in aortic sinus lesion area and macrophage content in Ldlr(-/-) mice fed a high-fat diet but not those fed a diabetogenic diet. In conclusion, MNV infection exacerbates atherosclerosis in Ldlr(-/-) mice fed a high-fat diet but does not influence obesity- and diabetes-related phenotypes. Increased lesion size was associated with increased macrophages, suggesting that MNV may influence macrophage activation or accumulation in the lesion area.     

The origin of Hydrilla verticillata recently discovered at a South African dam

Hydrilla was discovered during February 2006 at the Pongolapoort dam on the Pongola river, KwaZulu-Natal, South Africa. Four South African plants along with 30 others from around the world were analyzed using the trnL intron and trnL-F intergenic spacer of the chloroplast. The sequence data yielded major clusters of worldwide hydrilla almost identical to earlier RAPD studies with superior definition of the relationships between clusters. The sequences of the South African specimens were identical with Malaysian and Indonesian samples. Interviews with aquatic plant dealers indicate Malaysia is a major source of aquatic species for the trade in South Africa.     

Population characteristics,habitat and diet of a recently discovered stingray Dasyatis marianae: implications for conservation

This study examined population density, habitat and diet of Dasyatis marianae, a recently discovered species, in the reef complex of Maracajaú in Rio Grande do Norte state, Brazil. The highest concentration of D. marianae occurred in seagrass beds. Habitat use differed significantly between sex and age classes, with females and juveniles using areas other than reefs. Females utilized primarily seagrass beds and juveniles occurred mainly along the sandy bottom near the beach, highlighting the importance of protecting these areas. Dasyatis marianae diet was characterized primarily by crustaceans (91·9% index of relative importance, I_RI), including shrimp, crabs and lobsters. The availability of prey in different habitat types influences occupation by D. marianae, but the prey selectivity of D. marianae, among other factors, may affect this relationship. Intense shrimp and lobster fishing in the region probably has an effect on preferred prey resources of this ray. Information on feeding habits of this species contributes to a better understanding of trophic dynamics and food webs, which is critical if ecosystem principles are to be integrated into fisheries management.     

Epibiotic bacteria associated with the recently discovered Yeti crab, Kiwa hirsuta

The Yeti crab, Kiwa hirsuta Macpherson et al., is the single known species in a recently discovered crab family Kiwaidae (Decapoda: Galatheoidea) from deep-sea hydrothermal vents. Its chelipeds, walking legs and the ventral surface of its cephalothorax are covered with dense setae that, in turn, are covered with clusters of filamentous bacteria, making the crab appear extraordinarily 'hairy'. Electron microscopy revealed dense bacterial clusters attached to the chitinous outer layer of the setae. Molecular phylogenetic analyses revealed the setae-associated bacteria to be dominated by epsilon-Proteobacteria ( approximately 56% of the recovered ribotypes), gamma-Proteobacteria ( approximately 25%) and Bacteroidetes ( approximately 10%). Fluorescence in situ microscopy confirmed the attachment of filamentous epsilon-Proteobacteria on setae, but no specialized morphological structures appeared to exist for bacterial attachment. Key enzymes involved in the reductive tricarboxylic acid cycle (ATP-dependent citrate lyase) and sulfite oxidation or dissimilatory sulfate reduction (bidirectional APS reductase) were detected. Consequently, the potential for carbon fixation and cycling of reduced and oxidized sulfur appear to exist in the dense microflora that grows on the crab's setae.     

Health status of a recently discovered population of feral swine in Kansas.

Twenty feral hogs (Sus scrofa) from a newly discovered population on Fort Riley Army Base (Kansas, USA) were shot and examined from November 1993 through February 1994 to assess the health of the population. The hogs were generally healthy, although serologic evidence indicated that some individuals had been exposed to parvovirus, enterovirus, and swine influenza. We found no indications of brucellosis, pseudorabies, or porcine respiratory and reproductive syndrome. Lung worms (Metastrongylus spp.), round worms (Ascaris suum), and whipworms (Trichuris suis) were found in nine, four and two of the hogs, respectively. Seven hogs had infestations of lice (Haematopinus suis). Fence-line contacts were documented between four wild boars and domestic sows, and in three cases wild boars entered pens containing domestic sows. We recommend that hogs be examined periodically from this and other wild populations to monitor health status since new animals may enter populations through deliberate translocation, escape from shooting preserves or domestic swine producers, or dispersal from other feral populations.     

Ferroplasma and relatives, recently discovered cell wall-lacking archaea making a living in extremely acid, heavy metal-rich environments

For several decades, the bacterium Acidithiobacillus (previously Thiobacillus) has been considered to be the principal acidophilic sulfur- and iron-oxidizing microbe inhabiting acidic environments rich in ores of iron and other heavy metals, responsible for the metal solubilization and leaching from such ores, and has become the paradigm of such microbes. However, during the last few years, new studies of a number of acidic environments, particularly mining waste waters, acidic pools, etc., in diverse geographical locations have revealed the presence of new cell wall-lacking archaea related to the recently described, acidophilic, ferrous-iron oxidizing Ferroplasma acidiphilum. These mesophilic and moderately thermophilic microbes, representing the family Ferroplasmaceae, were numerically significant members of the microbial consortia of the habitats studied, are able to mobilize metals from sulfide ores, e.g. pyrite, arsenopyrite and copper-containing sulfides, and are more acid-resistant than iron and sulfur oxidizing bacteria exhibiting similar eco-physiological properties. Ferroplasma cell membranes contain novel caldarchaetidylglycerol tetraether lipids, which have extremely low proton permeabilities, as a result of the bulky isoprenoid core, and which are probably a major contributor to the extreme acid tolerance of these cell wall-less microbes. Surprisingly, several intracellular enzymes, including an ATP-dependent DNA ligase have pH optima close to that of the external environment rather than of the cytoplasm. Ferroplasma spp. are probably the major players in the biogeochemical cycling of sulfur and sulfide metals in highly acidic environments, and may have considerable potential for biotechnological applications such as biomining and biocatalysis under extreme conditions.     

Reproductive biology, species status and taxonomic relationships of four recently discovered galaxiid fishes in a New Zealand river

The reproductive biology of four recently discovered, largely allopatric non-migratory Galaxias species in the Taieri River, New Zealand, was compared with the closely related Galaxias vulgaris . Timing of spawning was similar (late winter/spring) but spawning habitat, spawning behaviour and nest structure differed among the Taieri species and G. vulgaris . Patterns of fecundity also differed among the Taieri species but, with G. vulgaris , they form a distinct group of galaxiids with maxima of 800–1500 eggs having diameters of 2·3–2·8 μn. The different spawning behaviours of the Taieri galaxiids, in particular the differences in spawning orientation, provide evidence for prezygotic isolating mechanisms and support their status as separate species. In cladistics terms, the results indicate that Galaxias anomalus, G. eldoni and G. vulgaris are sister taxa, while G. depressiceps and Galaxias sp. form a second cluster.     

Genome sequence of a highly prevalent porcine partetravirus in Mainland China

Partetravirus is a novel defined genus of animal parvoviruses. Here, we first report the genome sequence of porcine partetravirus strain JSNJ62, which is highly prevalent in mainland China. It will help in understanding the epidemiology and molecular characteristics of the porcine partetravirus.