The Role of Virulence in In Vivo Superinfection Fitness of the Vertebrate RNA Virus Infectious Hematopoietic Necrosis Virus

We have developed a novel in vivo superinfection fitness assay to examine superinfection dynamics and the role of virulence in superinfection fitness. This assay involves controlled, sequential infections of a natural vertebrate host, Oncorhynchus mykiss (rainbow trout), with variants of a coevolved viral pathogen, infectious hematopoietic necrosis virus (IHNV). Intervals between infections ranged from 12 h to 7 days, and both frequency of superinfection and viral replication levels were examined. Using virus genotype pairs of equal and unequal virulence, we observed that superinfection generally occurred with decreasing frequency as the interval between exposures to each genotype increased. For both the equal-virulence and unequal-virulence genotype pairs, the frequency of superinfection in most cases was the same regardless of which genotype was used in the primary exposure. The ability to replicate in the context of superinfection also did not differ between the genotypes of equal or unequal virulence tested here. For both genotype pairs, the mean viral load of the secondary virus was significantly reduced in superinfection while primary virus replication was unaffected. Our results demonstrate, for the two genotype pairs examined, that superinfection restriction does occur for IHNV and that higher virulence did not correlate with a significant difference in superinfection fitness. To our knowledge, this is the first assay to examine the role of virulence of an RNA virus in determining superinfection fitness dynamics within a natural vertebrate host.     

Fishy Business: The High Seas Boarding and Inspection Regime in the Western and Central Pacific Ocean

The Western and Central Pacific Fisheries Commission (WCPFC) was created in 2004 to more effectively conserve and manage the region's tuna fishery. One of the Commission's principal enforcement tools is the high seas boarding and inspection regime, which authorizes each member state to board and inspect fishing vessels engaged in a regulated fishery to verify compliance with the Commission's conservation and management measures. This article examines the structure of the WCPFC's high seas boarding and inspection regime and analyzes its effectiveness in furthering the Commission's conservations and management mandate.     

Transcriptional Bursting Diversifies the Behaviour of a Toggle Switch: Hybrid Simulation of Stochastic Gene Expression

Hybrid models for gene expression combine stochastic and deterministic representations of the underlying biophysical mechanisms. According to one of the simplest hybrid formalisms, protein molecules are produced in randomly occurring bursts of a randomly distributed size while they are degraded deterministically. Here, we use this particular formalism to study two key regulatory motifs—the autoregulation loop and the toggle switch. The distribution of burst times is determined and used as a basis for the development of exact simulation algorithms for gene expression dynamics. For the autoregulation loop, the simulations are compared to an analytic solution of a master equation. Simulations of the toggle switch reveal a number of qualitatively distinct scenarios with implications for the modelling of cell-fate selection.     

The peptide motif of the single dominantly expressed class I molecule of the chicken MHC can explain the response to a molecular defined vaccine of infectious bursal disease virus (IBDV)

In contrast to typical mammals, the chicken MHC (the BF-BL region of the B locus) has strong genetic associations with resistance and susceptibility to infectious pathogens as well as responses to vaccines. We have shown that the chicken MHC encodes a single dominantly expressed class I molecule whose peptide-binding motifs can determine resistance to viral pathogens, such as Rous sarcoma virus and Marek’s disease virus. In this report, we examine the response to a molecular defined vaccine, fp-IBD1, which consists of a fowlpox virus vector carrying the VP2 gene of infectious bursal disease virus (IBDV) fused with β-galactosidase. We vaccinated parental lines and two backcross families with fp-IBD1, challenged with the virulent IBDV strain F52/70, and measured damage to the bursa. We found that the MHC haplotype B15 from line 15I confers no protection, whereas B2 from line 6₁ and B12 from line C determine protection, although another locus from line 6₁ was also important. Using our peptide motifs, we found that many more peptides from VP2 were predicted to bind to the dominantly expressed class I molecule BF2*1201 than BF2*1501. Moreover, most of the peptides predicted to bind BF2*1201 did in fact bind, while none bound BF2*1501. Using peptide vaccination, we identified one B12 peptide that conferred protection to challenge, as assessed by bursal damage and viremia. Thus, we show the strong genetic association of the chicken MHC to a T cell vaccine can be explained by peptide presentation by the single dominantly expressed class I molecule.     

Meta-Analysis of Quantification Methods Shows that Archaea and Bacteria Have Similar Abundances in the Subseafloor

There is no universally accepted method to quantify bacteria and archaea in seawater and marine sediments, and different methods have produced conflicting results with the same samples. To identify best practices, we compiled data from 65 studies, plus our own measurements, in which bacteria and archaea were quantified with fluorescent in situ hybridization (FISH), catalyzed reporter deposition FISH (CARD-FISH), polyribonucleotide FISH, or quantitative PCR (qPCR). To estimate efficiency, we defined “yield” to be the sum of bacteria and archaea counted by these techniques divided by the total number of cells. In seawater, the yield was high (median, 71%) and was similar for FISH, CARD-FISH, and polyribonucleotide FISH. In sediments, only measurements by CARD-FISH in which archaeal cells were permeabilized with proteinase K showed high yields (median, 84%). Therefore, the majority of cells in both environments appear to be alive, since they contain intact ribosomes. In sediments, the sum of bacterial and archaeal 16S rRNA gene qPCR counts was not closely related to cell counts, even after accounting for variations in copy numbers per genome. However, qPCR measurements were precise relative to other qPCR measurements made on the same samples. qPCR is therefore a reliable relative quantification method. Inconsistent results for the relative abundance of bacteria versus archaea in deep subsurface sediments were resolved by the removal of CARD-FISH measurements in which lysozyme was used to permeabilize archaeal cells and qPCR measurements which used ARCH516 as an archaeal primer or TaqMan probe. Data from best-practice methods showed that archaea and bacteria decreased as the depth in seawater and marine sediments increased, although archaea decreased more slowly.     

Interannual variation in seasonal drivers of soil respiration in a semi-arid Rocky Mountain meadow

Semi-arid ecosystems with annual moisture inputs dominated by snowmelt cover much of the western United States, and a better understanding of their seasonal drivers of soil respiration is needed to predict consequences of climatic change on soil CO₂ efflux. We assessed the relative importance of temperature, moisture, and plant phenology on soil respiration during seasonal shifts between cold, wet winters and hot, dry summers in a Rocky Mountain meadow over 3.5 separate growing seasons. We found a consistent, unique pattern of seasonal hysteresis in the annual relationship between soil respiration and temperature, likely representative for this ecosystem type, and driven by (1) continued increase in soil T after summer senescence of vegetation, and (2) reduced soil respiration during cold, wet periods at the beginning versus end of the growing season. The timing of meadow senescence varied between years with amount of cold season precipitation, but on average occurred 45 days before soil temperature peaked in late-summer. Autumn soil respiration was greatest when substantial autumn precipitation events occurred early. Surface CO₂ efflux was temporarily decoupled from respiratory production during winter 2006/2007, due to effects of winter surface snow and ice on mediating the diffusion of CO₂ from deep soil horizons to the atmosphere. Upon melt of a capping surface ice layer, release of soil-stored CO₂ was determined to be 65 g C, or ~10 % of the total growing season soil respiration for that year. The shift between soil respiration sources arising from moisture-limited spring plant growth and autumn decomposition indicates that annual mineralization of soil carbon will be less dependent on projected changes in temperature than on future variations in amount and timing of precipitation for this site and similar semi-arid ecosystems.     

Purification of clinical-grade disulfide stabilized antibody fragment variable—Pseudomonas exotoxin conjugate (dsFv-PE38) expressed in Escherichia coli

Immunotoxins are rationally designed cancer targeting and killing agents. Disulfide stabilized antibody Fv portion—toxin conjugates (dsFv-toxin) are third generation immunotoxins containing only the antibody fragment variable portions and a toxin fused to the V_H or V_L. Pseudomonas exotoxin fragment (PE-38) is a commonly used toxin in immunotoxin clinical trials. dsFv-toxin purification was previously published, but the recovery was not satisfactory. This report describes the development of a cGMP production process of the dsFv-toxin that incorporated a novel purification method. The method has been successfully applied to the clinical manufacturing of two dsFv-PE38 immunotoxins, MR1-1 targeting EGFRvIII and HA22 targeting CD22. The two subunits, V_L and V_H PE-38 were expressed separately in Escherichia coli using recombinant technology. Following cell lysis, inclusion bodies were isolated from the biomass harvested from fermentation in animal source component-free media. The dsFv-toxin was formed after denaturation and refolding, and subsequently purified to homogeneity through ammonium sulfate precipitation, hydrophobic interaction and ion-exchange chromatography steps. It was shown, in a direct comparison experiment using MR1-1 as model protein, that the recovery from the new purification method was improved three times over that from previously published method. The improved recovery was also demonstrated during the clinical production of two dsFv-PE38 immunotoxins—MR1-1 and HA22.     

Roles of sulfate adsorption and base cation supply in controlling the chemical response of streams of western Virginia to reduced acid deposition

Micro-organisms are vital for the functioning of all food webs and are the major drivers of the global biogeochemical cycles. The microbial community compositions and physicochemical conditions of the different water masses in the North Sea, a biologically productive sea on the northwestern European continental shelf, were studied during two summer cruises, in order to provide detailed baseline data for this region and examine its microbial biogeography. For each cruise the stations were clustered according to their physicochemical characteristics and their microbial community composition. The largest cluster, which covered most of the central and northern North Sea, consisted of stations that were characterized by a thermally stratified water column and had low chlorophyll a autofluorescence and generally low microbial abundances. The second main cluster contained stations that were dominated by picoeukaryotes and showed the influence of influxes of North Atlantic water via the English Channel and south of the Shetland Islands. The third main cluster was formed by stations that were dominated by cyanobacteria and nanoeukaryotes in the reduced salinity Norwegian Coastal and Skagerrak waters, while the fourth cluster represented the German Bight, a region with strong riverine input, high nutrient concentrations, and consequently high heterotrophic bacterial and viral abundances. Despite the complex and dynamic hydrographic nature of the North Sea, the consistent distinctions in microbiology between these different hydrographic regions during both cruises illustrate the strong links between the microbial community and its environment, as well as the possibility to use microorganisms for long-term monitoring of environmental change.     

High diving metabolism results in a short aerobic dive limit for Steller sea lions (Eumetopias jubatus)

The diving capacity of marine mammals is typically defined by the aerobic dive limit (ADL) which, in lieu of direct measurements, can be calculated (cADL) from total body oxygen stores (TBO) and diving metabolic rate (DMR). To estimate cADL, we measured blood oxygen stores, and combined this with diving oxygen consumption rates (VO₂) recorded from 4 trained Steller sea lions diving in the open ocean to depths of 10 or 40 m. We also examined the effect of diving exercise on O₂ stores by comparing blood O₂ stores of our diving animals to non-diving individuals at an aquarium. Mass-specific blood volume of the non-diving individuals was higher in the winter than in summer, but there was no overall difference in blood O₂ stores between the diving and non-diving groups. Estimated TBO (35.9 ml O₂ kg^?1) was slightly lower than previously reported for Steller sea lions and other Otariids. Calculated ADL was 3.0 min (based on an average DMR of 2.24 L O₂ min^?1) and was significantly shorter than the average 4.4 min dives our study animals performed when making single long dives—but was similar to the times recorded during diving bouts (a series of 4 dives followed by a recovery period on the surface), as well as the dive times of wild animals. Our study is the first to estimate cADL based on direct measures of VO₂ and blood oxygen stores for an Otariid and indicates they have a much shorter ADL than previously thought.