Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon

BACKGROUND: Salmonid fishes are among the most widely studied model fish species but reports on systematic evaluation of reference genes in qRT-PCR studies is lacking. RESULTS: The stability of six potential reference genes was examined in eight tissues of Atlantic salmon (Salmo salar), to determine the most suitable genes to be used in quantitative real-time RT-PCR analyses. The relative transcription levels of genes encoding 18S rRNA, S20 ribosomal protein, β-actin, glyceraldehyde-3P-dehydrogenase (GAPDH), and two paralog genes encoding elongation factor 1A (EF1A(A )and EF1A(B)) were quantified in gills, liver, head kidney, spleen, thymus, brain, muscle, and posterior intestine in six untreated adult fish, in addition to a group of individuals that went through smoltification. Based on calculations performed with the geNorm VBA applet, which determines the most stable genes from a set of tested genes in a given cDNA sample, the ranking of the examined genes in adult Atlantic salmon was EF1A(B)>EF1A(A)>β-actin>18S rRNA>S20>GAPDH. When the same calculations were done on a total of 24 individuals from four stages in the smoltification process (presmolt, smolt, smoltified seawater and desmoltified freshwater), the gene ranking was EF1A(B)>EF1A(A)>S20>β-actin>18S rRNA>GAPDH. CONCLUSION: Overall, this work suggests that the EF1A(A )and EF1A(B )genes can be useful as reference genes in qRT-PCR examination of gene expression in the Atlantic salmon

Reference installation for the German grid initiative D-Grid

The D-Grid reference installation is a test platform for the German grid initiative. The main task is to create the grid prototype for software and hardware components needed in the D-Grid community. For each grid-related task field different alternative middleware is included. With respect to changing demands from the community, new versions of the reference installation are released every six months

Plant root associated chitinases: structures and functions

Chitinases degrade chitin, a linear homopolymer of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc) residues found in the cell walls of fungi and the exoskeletons of arthropods. They are secreted by the roots into the rhizosphere, a complex and dynamic environment where intense nutrient exchange occurs between plants and microbes. Here we modeled, expressed, purified, and characterized Zea mays and Oryza sativa root chitinases, and the chitinase of a symbiotic bacterium, Chitinophaga oryzae 1303 for their activities with chitin, di-, tri-, and tetra-saccharides and Aspergillus niger, with the goal of determining their role(s) in the rhizosphere and better understanding the molecular mechanisms underlying plant-microbe interactions. We show that Zea mays basic endochitinase (ZmChi19A) and Oryza sativa chitinase (OsChi19A) are from the GH19 chitinase family. The Chitinophaga oryzae 1303 chitinase (CspCh18A) belongs to the GH18 family. The three enzymes have similar apparent KM values of (20-40 µM) for the substrate 4-MU-GlcNAc3. They vary in their pH and temperature optima with OsChi19A activity optimal between pH 5–7 and 30–40°C while ZmChi19A and CspCh18A activities were optimal at pH 7-9 and 50–60°C. Modeling and site-directed mutation of ZmChi19A identified the catalytic cleft and the active residues E147 and E169 strategically positioned at ~8.6Å from each other in the folded protein. Cleavage of 4-MU-GlcNAc3 was unaffected by the absence of the CBD but diminished in the absence of the flexible C-terminal domain. However, unlike for the soluble substrate, the CBD and the newly identified flexible C-terminal domain were vital for inhibiting Aspergillus niger growth. The results are consistent with the involvement of the plant chitinases in defense against pathogens like fungi that have chitin exoskeletons. In summary, we have characterized the functional features and structural domains necessary for the activity of two plant root chitinases that are believed to be involved in plant defense and a bacterial chitinase that, along with the plant chitinases, may participate in nutrient recycling in the rhizosphere

Gyroscopic motion of superfluid trapped atomic condensates

The gyroscopic motion of a trapped Bose gas containing a vortex is studied. We model the system as a classical top, as a superposition of coherent hydrodynamic states, by solution of the Bogoliubov equations, and by integration of the time-dependent Gross-Pitaevskii equation. The frequency spectrum of Bogoliubov excitations, including quantum frequency shifts, is calculated and the quantal precession frequency is found to be consistent with experimental results, though a small discrepancy exists. The superfluid precession is found to be well described by the classical and hydrodynamic models. However the frequency shifts and helical oscillations associated with vortex bending and twisting require a quantal treatment. In gyroscopic precession, the vortex excitation modes $m=\pm 1$ are the dominant features giving a vortex kink or bend, while the $m=+2$ is found to be the dominant Kelvin wave associated with vortex twisting.Comment: 18 pages, 7 figures, 1 tabl

How do individuals cope with stress? Behavioural, physiological and neuronal differences between proactive and reactive coping styles in fish

Contains fulltext : 169006.pdf (publisher's version ) (Open Access

GMSE: an R package for generalised management strategy evaluation

1. Management strategy evaluation (MSE) is a powerful tool for simulating all key aspects of natural resource management under conditions of uncertainty. 2. We present the R package GMSE, which applies genetic algorithms to provide a generalised tool for simulating adaptive decision‐making management scenarios between stakeholders with competing objectives under complex social‐ecological interactions and uncertainty. 3. GMSE models can be agent‐based and spatially explicit, incorporating a high degree of realism through mechanistic modelling of links and feedbacks among stakeholders and with the ecosystem; additionally, user‐defined sub‐models can also be incorporated as functions into the broader GMSE framework. 4. We show how GMSE simulates a social‐ecological system using the example of an adaptively managed waterfowl population on an agricultural landscape; simulated waterfowl exploit agricultural land, causing conflict between conservation interests and the interest of food producers maximising their crop yield. 5. The R package GMSE is open source under GNU Public License; source code and documents are freely available on GitHub

Can screening and brief intervention lead to population-level reductions in alcohol-related harm?

A distinction is made between the clinical and public health justifications for screening and brief intervention (SBI) against hazardous and harmful alcohol consumption. Early claims for a public health benefit of SBI derived from research on general medical practitioners' (GPs') advice on smoking cessation, but these claims have not been realized, mainly because GPs have not incorporated SBI into their routine practice. A recent modeling exercise estimated that, if all GPs in England screened every patient at their next consultation, 96% of the general population would be screened over 10 years, with 70-79% of excessive drinkers receiving brief interventions (BI); assuming a 10% success rate, this would probably amount to a population-level effect of SBI. Thus, a public health benefit for SBI presupposes widespread screening; but recent government policy in England favors targeted versus universal screening, and in Scotland screening is based on new registrations and clinical presentation. A recent proposal for a national screening program was rejected by the UK National Health Service's National Screening Committee because 1) there was no good evidence that SBI led to reductions in mortality or morbidity, and 2) a safe, simple, precise, and validated screening test was not available. Even in countries like Sweden and Finland, where expensive national programs to disseminate SBI have been implemented, only a minority of the population has been asked about drinking during health-care visits, and a minority of excessive drinkers has been advised to cut down. Although there has been research on the relationship between treatment for alcohol problems and population-level effects, there has been no such research for SBI, nor have there been experimental investigations of its relationship with population-level measures of alcohol-related harm. These are strongly recommended. In this article, conditions that would allow a population-level effect of SBI to occur are reviewed, including their political acceptability. It is tentatively concluded that widespread dissemination of SBI, without the implementation of alcohol control measures, might have indirect influences on levels of consumption and harm but would be unlikely on its own to result in public health benefits. However, if and when alcohol control measures were introduced, SBI would still have an important role in the battle against alcohol-related harm

Perioperative Research into Memory (PRiMe): Cognitive impairment following a severe burn injury and critical care admission, part 1

Introduction An investigation into long-term cognitive impairment and Quality of Life (QoL) after severe burns. Methods A proof of principle, cohort design, prospective, observational clinical study. Patients with severe burns (>15% TBSA) admitted to Burns ICU for invasive ventilation were recruited for psychocognitive assessment with a convenience sample of age and sex-matched controls. Participants completed psychological and QoL questionnaires, the Cogstate® electronic battery, Hopkins Verbal Learning, Verbal Fluency and Trail making tasks. Results 15 patients (11M, 4F; 41 ± 14 years; TBSA 38.4% ± 18.5) and comparators (11M, 4F; 40 ± 13 years) were recruited. Burns patients reported worse QoL (Neuro-QoL Short Form v2, patient 30.1 ± 8.2, control 38.7 ± 3.2, p = 0.0004) and cognitive function (patient composite z-score 0.01, IQR −0.11 to 0.33, control 0.13, IQR 0.47–0.73, p = 0.02). Compared to estimated premorbid FSIQ, patients dropped an equivalent of 8 IQ points (p = 0.002). Cognitive function negatively correlated with burn severity (rBaux score, p = 0.04). QoL strongly correlated with depressive symptoms (Rho = −0.67, p = 0.009) but not cognitive function. Conclusions Severe burns injuries are associated with a significant, global, cognitive deficit. Patients also report worse QoL, depression and post-traumatic stress. Perceived QoL from cognitive impairment was more closely associated with depression than cognitive impairment

High-field Phase Diagram and Spin Structure of Volborthite Cu3V2O7(OH)2/2H2O

We report results of 51V NMR experiments on a high-quality powder sample of volborthite Cu3V2O7(OH)2/2H2O, a spin-1/2 Heisenberg antiferromagnet on a distorted kagome lattice. Following the previous experiments in magnetic fields $B$ below 12 T, the NMR measurements have been extended to higher fields up to 31 T. In addition to the two already known ordered phases (phases I and II), we found a new high-field phase (phase III) above 25 T, at which a second magnetization step has been observed. The transition from the paramagnetic phase to the antiferromagnetic phase III occurs at 26 K, which is much higher than the transition temperatures from the paramagnetic to the lower field phases I (B < 4.5 T) and II (4.5 < B < 25 T). At low temperatures, two types of the V sites are observed with different relaxation rates and line shapes in phase III as well as in phase II. Our results indicate that both phases II and III exhibit a heterogeneous spin state consisting of two spatially alternating Cu spin systems, one of which exhibits anomalous spin fluctuations contrasting with the other showing a conventional static order. The magnetization of the latter system exhibits a sudden increase upon entering into phase III, resulting in the second magnetization step at 26 T.We discuss the possible spin structure in phase III.Comment: 9 pages, 12 figure

Putative spin-nematic phase in BaCdVO(PO4_{4})2_{2}

We report neutron scattering and AC magnetic susceptibility measurements of the 2D spin-1/2 frustrated magnet BaCdVO(PO$_{4}$)$_{2}$. At temperatures well below $T_{\sf N}\approx 1K$, we show that only 34 % of the spin moment orders in an up-up-down-down strip structure. Dominant magnetic diffuse scattering and comparison to published $\mu$sr measurements indicates that the remaining 66 % is fluctuating. This demonstrates the presence of strong frustration, associated with competing ferromagnetic and antiferromagnetic interactions, and points to a subtle ordering mechanism driven by magnon interactions. On applying magnetic field, we find that at $T=0.1$ K the magnetic order vanishes at 3.8 T, whereas magnetic saturation is reached only above 4.5 T. We argue that the putative high-field phase is a realization of the long-sought bond-spin-nematic state