Genomic signatures predict migration and spawning failure in wild Canadian salmon

Long-term population viability of Fraser River sockeye salmon (Oncorhynchus nerka) is threatened by unusually high levels of mortality as they swim to their spawning areas before they spawn. Functional genomic studies on biopsied gill tissue from tagged wild adults that were tracked through ocean and river environments revealed physiological profiles predictive of successful migration and spawning. We identified a common genomic profile that was correlated with survival in each study. In ocean-tagged fish, a mortality-related genomic signature was associated with a 13.5-fold greater chance of dying en route. In river-tagged fish, the same genomic signature was associated with a 50% increase in mortality before reaching the spawning grounds in one of three stocks tested. At the spawning grounds, the same signature was associated with 3.7-fold greater odds of dying without spawning. Functional analysis raises the possibility that the mortality-related signature reflects a viral infection.     

Nitrogen leaching and soil organic carbon sequestration of a Barley crop with improved N use efficiency – A regional case study

The potential of modified spring barley crops with improved nitrogen (N) use efficiency to reduce nitrogen (N) leaching and to increase soil organic carbon (SOC) storage was assessed at the regional scale. This was done using simulation model applications designed for reporting according to the Helcom (Helsinki Commission) and Kyoto protocols. Using model simulations based on modified crops N dynamics and SOC were assessed for three agro-ecological regions (latitudes ranging 55°20′–60°40′ N) in Sweden over a 20-year period. The modified N use properties of spring barley were implemented in the SOILNDB model (simulating soil C, N, water and heat, and plant N dynamics) by changing the parameters for root N uptake efficiency and plant N demand within a range given by previous model applications to different crops. A doubling of the daily N uptake efficiency and increased N demand (by ca 30%) reduced N leaching by 24%–31%, increased plant N content by 9%–12%, depending on region. The effects of the modified crop on SOC was simulated with the ICBM model, resulting in an increased SOC content (0–25 cm depth) by 57–79 kg?C?ha^?1?y^?1. The results suggest that a modified crop might reduce N leaching from spring barley area, in a range similar to the targets of relevant environmental protection directives, a result which held more in the northern than southern regions. The simulated SOC increase on a hectare basis was highest for the central region and least for the most northern region. For the total agricultural area the share of spring barley area was small and more crops would need to be modified to reach the emission reduction targets.     

Mineralogy and Weathering of Smelter-Derived Spherical Particles in Soils: Implications for the Mobility of Ni and Cu in the Surficial Environment

Spherical particles have been sampled from soils and silica-rich rock coatings close to major smelter centers at Coppercliff, Coniston, and Falconbridge in the Sudbury area, Canada. Detailed analyses employing optical microscopy, scanning electron microscopy, transmission electron microscopy, micro-Raman spectroscopy, and M?ssbauer spectroscopy have been conducted to elucidate their nature, origin and potential alteration. The spherical particles are on the nano- to millimeter-size range and are composed principally of magnetite, hematite, Fe-silicates (olivine, pyroxenes), heazlewoodite, bornite, pyrrhotite, spinels (including trevorite and cuprospinel), delafossite, and cuprite or tenorite. The spinels present have variable Cu and Ni contents, whereas delafossite and cuprite are Ni free. Texturally, the spherical particles are composed of a Fe-oxide?CFe-silicate matrix with sulfide inclusions. The matrix displays growth features of a Fe-rich phase that commonly form during rapid cooling and transformation processes within smelter and converter facilities. Examination of weathered spherical particles indicates that some sulfide inclusions have dissolved prior to the alteration of the Fe-silicates and oxides and that the weathering of Fe-silicates occurs simultaneously with the transformation of magnetite into hematite. A higher proportion of Cu vs. Ni in the clay and organic fraction noted in the Sudbury soils is explained by (1) the formation of stronger adsorption complexes between Cu and the corresponding surface species and (2) the preferential release of Cu vs. Ni by smelter-derived particles. The latter mechanism is based on the observations that (a) cuprospinels have higher dissolution rates than Ni spinels, (b) a larger proportion of Cu occurs in the nanometer-size (and thus more soluble) fraction of the emitted particles, and (c) Ni spinels of relatively low solubility form in the alteration zone of heazlewoodite inclusions.     

Stand density and fertilization effects on aboveground allocation patterns and stem form of Pinus sylvestris in young stands

The increasing demand for forest biomass for energy generation could be partially met by growing denser stands and use of fertilizer. Before this is done at large scale, more knowledge of the effects of stand density and fertilization on aboveground allocation patterns and stem form is needed. Therefore, effects of pre-commercial thinning (PCT) to 3000 stems ha^?1, an unthinned dense control (C), and PCT combined with two levels of fertilization (100 kg ha^?1 of nitrogen applied either during the establishment of the field experiment (F1) or annually (F2)) were examined in 23- to 26-year-old Scots pine (Pinus sylvestris L.) stands six years after the establishment of the field experiment. In total, 114 sample trees were harvested using destructive biomass sampling. The growth allocation and stem form of trees with diameter at breast height (DBH; 1.3 m height) >5.0 cm were not affected by either the PCT or fertilization. Small trees (DBH < 5 cm) in denser, unthinned control plots had more slender stems (lower DBH/height ratios) and allocated less growth to branches and foliage than trees in PCT plots. Fertilization had little effect on the stem form and growth allocation of the smallest trees. Therefore, effects of stem density and fertilization on stem form and growth allocation to foliage were only found for small suppressed trees, and the treatments had very little influence on dominant and codominant trees.     

In vivo transmission studies of ��Candidatus Mycoplasma turicensis�� in the domestic cat

The natural transmission routes of the three feline haemotropic mycoplasmas – Mycoplasma haemofelis, ‘Candidatus Mycoplasma haemominutum’, and ‘Candidatus Mycoplasma turicensis’ (CMt) – are largely unknown. Since CMt has been detected in the saliva of infected cats using PCR, we hypothesised that direct transmission via social or aggressive contact may occur. The aim of this study was to evaluate this transmission route. CMt-positive saliva and blood samples were obtained from three prednisolone-treated specific pathogen-free (SPF) cats that were infected intraperitoneally with CMt. Five SPF cats were inoculated with CMt-positive saliva or blood subcutaneously to mimic cat bites, and five cats were inoculated orally with blood or oronasally with saliva to mimic social contact. Blood samples were monitored for CMt infection using quantitative real-time PCR and for seroconversion using a novel western blot assay. Neither oronasal nor subcutaneous inoculation with CMt-positive saliva led to CMt infection in the recipient cats, as determined by PCR, independent of prior prednisolone treatment. However, when blood containing the same CMt dose was given subcutaneously, 4 of the 5 cats became PCR-positive, while none of the 5 cats inoculated orally with up to 500 μL of CMt-positive blood became PCR-positive. Subsequently, the latter cats were successfully subcutaneously infected with blood. All 13 CMt-exposed cats seroconverted. In conclusion, CMt transmission by social contact seems less likely than transmission by aggressive interaction. The latter transmission may occur if the recipient cat is exposed to blood from an infected cat.     

Influence of different litter quality on the abundance of genes involved in nitrification and denitrification after freezing and thawing of an arable soil

Due to disruption of soil aggregates and cell lysis and the subsequent release of organic C and N, increased microbial N transformation processes can be observed after freeze–thaw cycles. In a microcosm study, we investigated the influence of plant residues with different C/N ratios (lucerne-clover-grass-mix and wheat straw) on N transformations and the abundance pattern of the corresponding functional genes in an arable soil after freezing and thawing. Unfrozen soil samples, continuously incubated at 10°C, served as control. Concentration of soil NH₄⁺, NO₃⁻, and water-extractable organic C (WEOC) as well as genes involved in nitrification and denitrification, quantified by real-time PCR, were determined before freezing and 1, 3, and 7 days after thawing. The amounts of inorganic N and WEOC as well as the investigated gene abundance pattern did hardly differ between control samples and samples subjected to freezing and thawing that have been amended with straw. In contrast, clear alterations of the measured parameters and abundances were observed after freezing and thawing in samples being amended with the lucerne-clover-grass-mix compared to the control samples.     

Mechanisms of toxicity of 3-alkylpyridinium polymers from marine sponge Reniera sarai

Polymeric 3-alkylpyridinium salts (poly-APS) present in the marine sponge Reniera sarai show a broad spectrum of biological activities. They are lytic to erythrocytes and various other mammalian cells, enabling the transfection of the latter with alien DNA. Furthermore, they show inhibitory effects to marine bacteria and can inhibit fouling of micro- and macroorganisms to submerged surfaces. Finally, poly-APS act as potent cholinesterase inhibitors. The kinetics of acetylcholinesterase inhibition by poly-APS in vitro is complex and comprises several successive phases ending in irreversible inhibition of the enzyme. The latter is accounted for by aggregation and precipitation of the enzyme-inhibitor complexes. Poly-APS are lethal to rats in concentrations above 2.7 mg/kg. Monitoring of the basic vital functions and histopathological analysis showed that the effects directly ascribable to acetylcholinesterase inhibition are only observed after application of lower concentrations of poly-APS. At higher concentrations, such effects were masked by other, more pronounced and faster developing lethal effects of the toxin, such as haemolysis and platelet aggregation.     

Effect of Different Fertilizer Treatments on Quantity of Soil Microbes and Structure of Ammonium Oxidizing Bacterial Community in a Calcareous Purple Paddy Soil

The quantity of soil microbes and the structure of ammonium oxidizing bacterial （AOB） community were analyzed using the dilution plate counting and most probable number method （MPN）, and denaturing gradient gel electrophoresis （DGGE）, respectively. Fertilizer application tended to increase the number of soil microbes and alter the AOB community compared to the control with no fertilizer application （CK）. Among the eight fertilizer treatments, soil samples from the treatments of mineral fertilizers （e.g., N, P, K） in combination with farmyard manure （M） had greater number.s of soil microbes and more complex structure of AOB community than those receiving mineral fertilizers alone. The principal component analyses （PCA） for ammonium oxidizing bacterial community structure showed that the eight fertilizer treatments could be divided into two PCA groups （PCA1 and PCA2）. For the soil sampled after rice harvest, PCA1 included NP, NM, NPM and NPKM fertilizer treatments, while PCA2 was consisted of CK, N, M and NPK fertilizer treatments. For soil samples collected after wheat harvest, PCA1 was consisted of M, NM, NPM and NPKM fertilizer treatments, while PCA2 was composed of CK, N, NP and NPK fertilizer treatments. For a given rotation, the richness of AOB community in PCA1 was greater than that in PCA2. In addition, AOB community structure was more complex in the soil after rice harvest than that after wheat harvest. The results indicated that different fertilizer treatments resulted in substantial changes of soil microbe number and AOB community. Furthermore, mineral fertilizers （N, NP, NPK） combined with farmyard manure were effective for increasing the quantity of soil microbes, enriching AOB community, and improving the soil biofertility.     

The acute stress response in fed and food deprived Atlantic cod, Gadus morhua L.

The aim of the present study was to evaluate the effect of stress and nutritional state (fed vs food deprived) on the generalized stress response and intestinal integrity in Atlantic cod (Gadus morhua L.). Cod in feeding or food deprived states were subjected to 15 min of acute stress (exhaustive exercise). Blood was collected at 9 intervals from before stress (t = 0), to t = 48 h post stress and analysed for blood haematocrit and haemoglobin, and plasma cortisol, lactate, glucose, osmolality, chloride, as well as the tissue damage indicators glutamate oxaloacetate transaminase, glutamate pyruvate transaminase and thiobarbituric acid reactive substances. Intestinal segments were prepared for histology with the same intervals, while assessment of intestinal integrity and microbiology was performed at t = 0, 4 and 48 h post stress.Subjecting cod to exhaustive stress initiated a standard stress response including increased blood Hct and plasma cortisol, glucose, chloride, osmolality and lactate. Food deprived fish did in general have reduced stress resistance compared to fed fish. For many parameters, cod returned slowly to basal levels. Cellular indicators of tissue damage and oxidative stress increased in a biphasic manner following stress. Stress did not affect gut histology but did transiently increase gut permeability. Furthermore, stress had no effect on the adherent bacterial population level in midgut, but did cause a small decrease in hindgut (non-significant) and hindgut chamber (p < 0.05). Isolates belonging to Carnobacterium were predominant but not affected by stress.In conclusion, food deprived cod are less resistant to stress than fed cod. The magnitude of the response is less than in salmonids, but the effects are persistent (including tissue damage indicators and oxidative stress) and may have negative long term consequences. The gut is relatively resistant to stress, there is however a transient increase in the intestinal permeability and alterations in microbiota that may indicate lower protection against invading pathogens.