Sequence Analysis of the Genome of Piscine Orthoreovirus (PRV) Associated with Heart and Skeletal Muscle Inflammation (HSMI) in Atlantic Salmon (Salmo salar)

Piscine orthoreovirus (PRV) is associated with heart- and skeletal muscle inflammation (HSMI) of farmed Atlantic salmon (Salmo salar). We have performed detailed sequence analysis of the PRV genome with focus on putative encoded proteins, compared with prototype strains from mammalian (MRV T3D)- and avian orthoreoviruses (ARV-138), and aquareovirus (GCRV-873). Amino acid identities were low for most gene segments but detailed sequence analysis showed that many protein motifs or key amino acid residues known to be central to protein function are conserved for most PRV proteins. For M-class proteins this included a proline residue in μ2 which, for MRV, has been shown to play a key role in both the formation and structural organization of virus inclusion bodies, and affect interferon-β signaling and induction of myocarditis. Predicted structural similarities in the inner core-forming proteins λ1 and σ2 suggest a conserved core structure. In contrast, low amino acid identities in the predicted PRV surface proteins μ1, σ1 and σ3 suggested differences regarding cellular interactions between the reovirus genera. However, for σ1, amino acid residues central for MRV binding to sialic acids, and cleavage- and myristoylation sites in μ1 required for endosomal membrane penetration during infection are partially or wholly conserved in the homologous PRV proteins. In PRV σ3 the only conserved element found was a zinc finger motif. We provide evidence that the S1 segment encoding σ3 also encodes a 124 aa (p13) protein, which appears to be localized to intracellular Golgi-like structures. The S2 and L2 gene segments are also potentially polycistronic, predicted to encode a 71 aa- (p8) and a 98 aa (p11) protein, respectively. It is concluded that PRV has more properties in common with orthoreoviruses than with aquareoviruses.     

The relation of emotions to placebo responses

The hypothesis put forth is that expectations of treatment effects reduce negative emotions and thereby reduce symptoms, e.g. pain. Negative emotions increase pain, and it is hypothesized that placebos reduce pain by reducing negative emotions, i.e. feelings of nervousness, fear and anxiety. Placebo analgesia has been shown to be mediated via opioid activity, and relaxation increases opioid activity. The placebo acquires its relaxing effect due to verbal information that pain will be reduced, or due to associations between the placebo and the reduction in pain after effective treatment. Thus, the placebo signals that unpleasantness will be less after administration of the placebo. This involves negative reinforcement which is due to activation of a dopaminergic system that has been found to be activated during placebo analgesia and is involved in positive emotions. The nocebo effect of increased pain is, consistent with this model, because of increased fear and anxiety. The new aspect of the presented model is the hypothesis that expectations reduce negative emotions, and that negative reinforcement that involves the dopaminergic reinforcement system should be a contributor to placebo responses.     

Combined 2D electrophoretic approaches for the study of white lupin mature seed storage proteome

Seed proteome analysis by 2D IEF/SDS-PAGE techniques is challenging for the intrinsic difficulties related to quantitative disparity of the seed proteins, i.e. storage and non-storage proteins, their polymorphic nature, the extensive post-translational modifications and the paucity of deposited primary structures available. Conversely, 2D maps of seed proteomes can be extremely useful for a number of fundamental and applied investigations. In this work, we have used a combination of two experimental approaches to identify the main protein components of an emerging protein-rich legume seed, that is white lupin seed (Lupinus albus, L.). One is the canonical proteomic approach including 2D electrophoretic separation and mass spectrometry of selected trypsin-digested polypeptides; the other approach is a group comparative 2D electrophoretic analysis of cotyledonary protein families. To this second purpose, the three main families of lupin seed proteins, namely alpha-conglutins, the 11S globulin fraction, beta-conglutins, the 7S globulin fraction, and gamma-conglutin, a basic 7S protein, were isolated by conventional biochemical techniques and their 2D reference maps were compared with the total protein map. With the first approach 37 out of 40 spots, making up about 35% of total spot volumes in the 2D map, were found to belong to the main seed protein families. Thanks to cDNA-deduced lupin storage protein sequences, determined on purpose and deposited, most of the identification statistical parameters were very good. Moreover, it was possible to identify several endogenously proteolysed subunits in the map. The second comparative approach, beside confirming these attributions, allowed to allocate 124 polypeptides within the three main lupin protein families. These two approaches proved to be mutually validating and their combined use was effective for the establishment of a seed proteome map even in the case of sequence and protein post-translational processing lack of information. The results obtained also extend our knowledge of the seed storage protein polymorphism of white lupin.     

Carbon acquisition by diatoms

Diatoms are responsible for up to 40% of primary productivity in the ocean, and complete genome sequences are available for two species. However, there are very significant gaps in our understanding of how diatoms take up and assimilate inorganic C. Diatom plastids originate from secondary endosymbiosis with a red alga and their Form ID Rubisco (ribulose-1,5-bisphosphate carboxylase-oxygenase) from horizontal gene transfer, which means that embryophyte paradigms can only give general guidance as to their C acquisition mechanisms. Although diatom Rubiscos have relatively high CO₂ affinity and CO₂/O₂ selectivity, the low diffusion coefficient for CO₂ in water has the potential to restrict the rate of photosynthesis. Diatoms growing in their natural aquatic habitats operate inorganic C concentrating mechanisms (CCMs), which provide a steady-state CO₂ concentration around Rubisco higher than that in the medium. How these CCMs work is still a matter of debate. However, it is known that both CO₂ and HCO₃⁻ are taken up, and an obvious but as yet unproven possibility is that active transport of these species across the plasmalemma and/or the four-membrane plastid envelope is the basis of the CCM. In one marine diatom there is evidence of C₄-like biochemistry which could act as, or be part of, a CCM. Alternative mechanisms which have not been eliminated include the production of CO₂ from HCO₃⁻ at low pH maintained by a H⁺ pump, in a compartment close to that containing Rubisco.     

A genome-wide linkage scan identifies multiple chromosomal regions influencing serum lipid levels in the population on the Samoan islands

Abnormal lipid levels are important risk factors for cardiovascular diseases. We conducted genome-wide variance component linkage analyses to search for loci influencing total cholesterol (TC), LDL, HDL and triglyceride in families residing in American Samoa and Samoa as well as in a combined sample from the two polities. We adjusted the traits for a number of environmental covariates, such as smoking, alcohol consumption, physical activity, and material lifestyle. We found suggestive univariate linkage with log of the odds (LOD) scores > 3 for LDL on 6p21-p12 (LOD 3.13) in Samoa and on 12q21-q23 (LOD 3.07) in American Samoa. Furthermore, in American Samoa on 12q21, we detected genome-wide linkage (LOD(eq) 3.38) to the bivariate trait TC-LDL. Telomeric of this region, on 12q24, we found suggestive bivariate linkage to TC-HDL (LOD(eq) 3.22) in the combined study sample. In addition, we detected suggestive univariate linkage (LOD 1.9-2.93) on chromosomes 4p-q, 6p, 7q, 9q, 11q, 12q 13q, 15q, 16p, 18q, 19p, 19q and Xq23 and suggestive bivariate linkage (LOD(eq) 2.05-2.62) on chromosomes 6p, 7q, 12p, 12q, and 19p-q. In conclusion, chromosome 6p and 12q may host promising susceptibility loci influencing lipid levels; however, the low degree of overlap between the three study samples strongly encourages further studies of the lipid-related traits.     

Transthoracic echocardiography for imaging of the different coronary artery segments: a feasibility study

Background

Cardiac resynchronisation therapy (CRT) improves mortality and morbidity in heart failure patients with wide QRS. Observational studies suggest that patients having more left ventricular dyssynchrony pre-implantation obtain greater benefit on ventricular function and symptoms with CRT.

Aim

To provide an analysis of the prevalence and type of dyssynchrony in patients included in the CARE-HF trial.

Methods

100 patients 67 (58 to 71) years were examined with echocardiography including tissue doppler imaging before receiving a CRT-pacemaker. Atrio-ventricular dyssynchrony (LVFT/RR) was defined as left ventricular filling time <40% of the RR-interval. Inter-ventricular mechanical delay (IVMD) was measured as the difference in onset of Doppler-flow in the pulmonary and aortic outflow tracts >40 ms. Intra-ventricular (regional) dyssynchrony in a 16-segment model was expressed either as a delayed longitudinal contraction (DLC) during the postsystolic phase or by tissue synchronisation imaging (TSI) with a predefined time-difference in systolic maximal velocities >85 ms.

Results

LVFT/RR was present in 34% and IVMD in 60% of patients while intra-ventricular dyssynchrony was present in 85% (DLC) and 86% (TSI) with a high agreement between the measures (Kappascore 0.86–1.00), indicating the methods being interchangeable. Patients with cardiomyopathy (53%) were more likely to have LVFT/RR <40% (45% vs. 21% (p= 0.02)) and more segments affected by intra-ventricular dyssynchrony 4(3, 5) vs. 3(1, 4), p = 0.002, compared to patients with ischemic heart disease.

Conclusion

The prevalence of intra-ventricular dyssynchrony is high in patients with heart failure, wide QRS and depressed systolic function. Most important, TSI appears to be a fast and reliable method to identify patients with intra-ventricular dyssynchrony likely to benefit from CRT.     

Trigonal bipyramidal iron(III) and manganese(III) oxo, sulfido, and selenido complexes. An electronic-structural overview

Using density functional theory calculations, we have carried out a broad survey of trigonal bipyramidal iron(III) and manganese(III) oxo, sulfido, selenido, and hydroxo complexes, with tripodal tetradentate "triureidoamine" supporting ligands. The calculations reproduce the experimentally observed high-spin states of these compounds; a multifunctional analysis suggests that the high-spin nature of these species follows largely from their trigonal bipyramidal geometry. In conjunction with earlier calculations, the present study provides a broad overview of spin density profiles in iron-oxo species in general. Iron-oxo d(pi)-p(pi) interactions invariably result in a substantial spin density on the oxygen, which in turn may be significantly tuned by hydrogen bonding interactions. The oxygen spin densities are smaller in analogous manganese-oxo species, indicating that manganese is less adept at pi-bonding than iron, which parallels earlier findings on porphyrin systems. The Fe(III)-S/Se spin density profiles provide one of the first confirmations in a transition metal context of Schleyer's prediction that the heavier p-block elements are as effective as their second-row congeners in terms of their pi-donating ability.     

Lack of competition between barnacle geese Branta leucopsis and pink-footed geese Anser brachyrhynchus during the pre-breeding period in Svalbard

The feeding ecology of barnacle geese and pink-footed geese was studied in Sassendalen, Svalbard during the pre-nesting period (late May) to assess the potential for inter-specific competition. Barnacle geese fed almost exclusively (97%) by grazing above-ground plant material, mostly (79%) along snow edges in moss-mat habitats. Pink-footed geese fed mostly (93%) by excavating below-ground parts of plants, mostly (56%) away from snow and were more evenly distributed between habitat types. Barnacle goose faeces contained mostly (62%) moss, that of pink-footed geese mostly (48%) below-ground plant storage organs (especially Bistorta viviparum L.). Principal components analysis of dropping contents showed no overlap in species diet in allopatry or sympatry. There was little overlap in diet and feeding ecology of the two species at this pre-nesting feeding site. Hence, unless increased goose feeding densities affect future vegetation density and composition, under present circumstances, increasing numbers of either species is unlikely to affect foraging conditions for the other at this important stage in the annual cycle. However, such changes could have local density-dependent intra-specific effects.     

Estimation of population firing rates and current source densities from laminar electrode recordings

This model study investigates the validity of methods used to interpret linear (laminar) multielectrode recordings. In computer experiments extracellular potentials from a synaptically activated population of about 1,000 pyramidal neurons are calculated using biologically realistic compartmental neuron models combined with electrostatic forward modeling. The somas of the pyramidal neurons are located in a 0.4 mm high and wide columnar cylinder, mimicking a stimulus-evoked layer-5 population in a neocortical column. Current-source density (CSD) analysis of the low-frequency part (<500 Hz) of the calculated potentials (local field potentials, LFP) based on the ‘inverse’ CSD method is, in contrast to the ‘standard’ CSD method, seen to give excellent estimates of the true underlying CSD. The high-frequency part (>750 Hz) of the potentials (multi-unit activity, MUA) is found to scale approximately as the population firing rate to the power 3/4 and to give excellent estimates of the underlying population firing rate for trial-averaged data. The MUA signal is found to decay much more sharply outside the columnar populations than the LFP.