Viral co‐infections in farmed Atlantic salmon,Salmo salar L., displaying myocarditis

Several different viruses have been associated with myocarditis‐related diseases in the Atlantic salmon aquaculture industry. In this study, we investigated the presence of PMCV, SAV, PRV and the recently identified Atlantic salmon calicivirus (ASCV), alone and as co‐infections in farmed Atlantic salmon displaying myocarditis. The analyses were performed at the individual level and comprised qPCR and histopathological examination of 397 salmon from 25 farms along the Norwegian coast. The samples were collected in 2009 and 2010, 5–22 months post‐sea transfer. The study documented multiple causes of myocarditis and revealed co‐infections including individual fish infected with all four viruses. There was an overall correlation between lesions characteristic of CMS and PD and the presence of PMCV and SAV, respectively. Although PRV was ubiquitously present, high viral loads were with a few exceptions, correlated with lesions characteristic of HSMI. ASCV did not seem to have any impact on myocardial infection by PMCV, SAV or PRV. qPCR indicated a negative correlation between PMCV and SAV viral loads. Co‐infections result in mixed and atypical pathological changes which pose a challenge for disease diagnostic work.     

Morphological diversity of Paramoeba perurans trophozoites and their interaction with Atlantic salmon,Salmo salar L., gills

Amoebic gill disease (AGD) caused by the ectoparasite Paramoeba perurans affects several cultured marine fish species worldwide. In this study, the morphology and ultrastructure of P. perurans in vitro and in vivo was investigated using scanning and transmission electron microscopy (SEM and TEM, respectively). Amoebae cultures contained several different morphologies ranging from a distinct rounded cell structure and polymorphic cells with pseudopodia of different lengths and shapes. SEM studies of the gills of AGD‐affected Atlantic salmon, Salmo salar L., revealed the presence of enlarged swellings in affected gill filaments and fusion of adjacent lamellae. Spherical amoebae appeared to embed within the epithelium, and subsequently leave hemispherical indentations with visible fenestrations in the basolateral surface following their departure. These fenestrated structures corresponded to the presence of pseudopodia which could be seen by TEM to penetrate into the epithelium. The membrane–membrane interface contained an amorphous and slightly fibrous matrix. This suggests the existence of cellular glycocalyces and a role for extracellular products in mediating pathological changes in amoebic gill disease.     

Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA

In higher eukaryotes, a multiprotein exon junction complex is deposited on spliced messenger RNAs. The complex is organized around a stable core, which serves as a binding platform for numerous factors that influence messenger RNA function. Here, we present the crystal structure of a tetrameric exon junction core complex containing the DEAD-box adenosine triphosphatase (ATPase) eukaryotic initiation factor 4AIII (eIF4AIII) bound to an ATP analog, MAGOH, Y14, a fragment of MLN51, and a polyuracil mRNA mimic. eIF4AIII interacts with the phosphate-ribose backbone of six consecutive nucleotides and prevents part of the bound RNA from being double stranded. The MAGOH and Y14 subunits lock eIF4AIII in a prehydrolysis state, and activation of the ATPase probably requires only modest conformational changes in eIF4AIII motif I.     

Arginine ammonification assay as a rapid index of gross N mineralization in agricultural soils

Seasonal dynamics of in situ gross nitrogen (N) mineralization rates were measured using the ¹⁵N-NH₄⁺ isotope dilution method in a Danish soil subjected to four different agricultural practices (set aside, barley, winter wheat and clover). Results were compared to arginine ammonification in the soil samples measured as NH₄⁺ production following addition of excess (1 mM) arginine. In the set aside, barley, winter wheat and clover soils the average annual rates of gross N mineralization (0.29, 0.60, 1.34 and 1.75 µg NH₄⁺-N g^-1 day^-1, respectively) and arginine ammonification activity (0.21, 0.55, 0.88, and 1.33 µg NH₄⁺-N g^-1 h^-1, respectively) were well correlated. Furthermore, the seasonal variations of gross N mineralization and arginine ammonification activities were very similar, showing rapid responses to rainfall and generally higher activities in wetted soils. As tested in the laboratory, the arginine ammonification activity correlated well with heterotrophic microbial respiration activity (CO₂ production) in soil samples and further displayed a simple, one-component Michaelis-Menten kinetics with a high affinity for arginine (K_m value of 48 µM LJ µM) as determined from non-linear parameter estimation. This indicated that arginine ammonification activity was primarily due to microorganisms, and the activity was also shown to be at a minimum in sterile soil samples. All evidence thus supported that our standard assay of arginine ammonification activity provides a good index of gross N mineralization rates by the microorganisms in soil under in situ conditions.     

Application of biochar to soil and N2O emissions: potential effects of blending fast‐pyrolysis biochar with anaerobically digested slurry

Soil applications of recalcitrant biochar offer the possibility of mitigating climate change effects through long‐term carbon sequestration and potentially also by reducing emissions of the potent greenhouse gas nitrous oxide (N₂O). This laboratory study examined the effect of combining a fast‐pyrolysis biochar at small (1% by mass) and large (3%) concentrations with anaerobically digested slurry on soil N₂O and carbon dioxide (CO₂) emissions over a period of 55 days. The results showed that fast‐pyrolysis biochar applied on its own increased N₂O emissions from soil. However, when biochar was applied together with slurry, the larger biochar concentration decreased N₂O emissions by 47%, relative to those from the slurry treatment with the smaller biochar concentration. Reduced N₂O emissions coincided with enhanced soil microbial activity and immobilization of nitrogen. A combined application of biochar and anaerobic digested slurry could therefore be beneficial for cropping systems in terms of soil nitrogen retention while concurrently mitigating N₂O fluxes and sequestering carbon in soil.     

Mineralization of carbon and nitrogen from fresh and anaerobically stored sheep manure in soils of different texture

A sandy loam soil was mixed with three different amounts of quartz sand and incubated with (¹⁵NH₄)₂SO₄ (60 g N g^-1 soil) and fresh or anaerobically stored sheep manure (60 g g^-1 soil). The mineralization-immobilization of N and the mineralization of C were studied during 84 days of incubation at 20°C. After 7 days, the amount of unlabelled inorganic N in the manure-treated soils was 6–10 g N g^-1 soil higher than in soils amended with only (¹⁵NH₄)₂SO₄. However, due to immobilization of labelled inorganic N, the resulting net mineralization of N from manure was insignificant or slightly negative in the three soil-sand mixtures (100% soil+0% quartz sand; 50% soil+50% quartz sand; 25% soil+75% quartz sand). After 84 days, the cumulative CO₂ evolution and the net mineralization of N from the fresh manure were highest in the soil-sand mixutre with the lowest clay content (4% clay); 28% fo the manure C and 18% of the manure N were net mineralized. There was no significant difference between the soil-sand mixtures containing 8% and 16% clay, in which 24% of the manure C and -1% to 4% of the manure N were net mineralized. The higher net mineralization of N in the soil-sand mixture with the lowest clay content was probably caused by a higher remineralization of immobilized N in this soil-sand mixture. Anaerobic storage of the manure reduced the CO₂ evolution rates from the manure C in the three soil-sand mixtures during the initial weeks of decomposition. However, there was no effect of storage on net mineralization of N at the end of the incubation period. Hence, there was no apparent relationship between net mineralization of manure N and C.     

Use of in-growth soil cores in mesh bags for studies of relations between soil compaction and root growth

Using in-growth soil cores in cylindrical mesh bags, the effects of 3 soil compaction treatments on growth of crop roots were studied in a sandy soil. The bags were inserted after crop emergence in holes (70 mm diameter; 60 cm depth) augered in the soil in crop row interspaces. In 1984 (with rapessed), at all sampling dates, root biomass in the inserted cores decreased with increased compaction of the plough layer (0–25 cm) as well as the subsoil (25–60 cm). Root biomass in the subsoil was low. In 1985 (with wheat), the effects of compaction in the subsoil were similar, although root biomass was greater than in 1984. However, in the plough layer there were significant differences in root biomass on only one sampling date. The mesh bag technique should be a useful complement to other field methods in studies of relations between physical soil characteristics or tillage treatments and root growth.     

Error propagation in stock-difference and gain–loss estimates of a forest biomass carbon balance

According to the United Nations International Panel on Climate Change good practice guidance, an annual forest biomass carbon balance (AFCB) can be estimated by either the stock-difference (SD) or the gain–loss (GL) method. An AFCB should be accompanied by an analysis and estimation of uncertainty (EU). EUs are to be practicable and supported by sound statistical methods. Sampling and model errors both contribute to an EU. As sample size increases, the sampling error decreases but not the error due to errors in model parameters. Uncertainty in GL AFCB estimates is dominated by model-parameter errors. This study details the delta technique for obtaining an EU with the SD and the GL method applicable to the carbon in aboveground forest biomass. We employ a Brownian bridge process to annualize the uncertainty in SD AFCBs. A blend of actual and simulated data from three successive inventories are used to demonstrate the application of the delta technique to SD- and GL-derived AFCBs during the years covered by the three inventories (SD) and rescaled national wood volume harvest statistics (GL). Examples are limited to carbon in live trees with a stem diameter of 7 cm or greater. We confirm that a large contribution to the uncertainty in an AFCB comes from models used to estimate biomass. Application of the delta technique to summary statistics can significantly underestimate uncertainty as some sources of uncertainty cannot be quantified from the available information. We discuss limitations and problems with the Monte Carlo technique for quantifying uncertainty in an AFCB.     

In search of a variance estimator for systematic sampling

Seven variance estimators to be used under systematic sampling are evaluated in a simulation study with 270 artificial spatial populations with different levels and structure of autocorrelation. In settings without an auxiliary variable a proposed new spatial resampling estimator RHO is recommended. In setting with an auxiliary variable, an estimator based on post-stratification (PST), and one with a correction for spatial autocorrelation (DOR), generated estimates with less bias than the SRS estimator in the majority of studied settings. Only in populations with either a near zero autocorrelation at the interval of sampling, or a very strong correlation between the target and the auxiliary variable did the otherwise conservative SRS estimator perform as well as the alternatives.     

Critical roles for Rac1 and Rac2 GTPases in B cell development and signaling

The Rac1 guanosine triphosphatase (GTPase) has been implicated in multiple cellular functions, including actin dynamics, proliferation, apoptosis, adhesion, and migration resulting from signaling by multiple receptors, including the B cell antigen receptor (BCR). We used conditional gene targeting to generate mice with specific Rac1 deficiency in the B cell lineage. In the absence of both Rac1 and the highly related Rac2, B cell development was almost completely blocked. Both GTPases were required to transduce BCR signals leading to proliferation, survival and up-regulation of BAFF-R, a receptor for BAFF, a key survival molecule required for B cell development and maintenance.