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

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

Continuity of Local Time: An applied perspective

Continuity of local time for Brownian motion ranks among the most notable mathematical results in the theory of stochastic processes. This article addresses its implications from the point of view of applications. In particular an extension of previous results on an explicit role of continuity of (natural) local time is obtained for applications to recent classes of problems in physics, biology and finance involving discontinuities in a dispersion coefficient. The main theorem and its corollary provide physical principles that relate macro scale continuity of deterministic quantities to micro scale continuity of the (stochastic) local time.Comment: To appear in: "The fascination of Probability, Statistics and Their Applications. In honour of Ole E. Barndorff-Nielsen on his 80th birthday

Effects of different photoperiod regimes on the smoltification and seawater adaptation of seawater-farmed rainbow trout (Oncorhynchus mykiss): Insights from Na+, K+-ATPase activity and transcription of osmoregulation and growth regulation genes

Photoperiod is thought to be the main zeitgeber that induces smoltification in salmonids. However, its effects on the smoltification of rainbow trout (Oncorhynchus mykiss) are not fully understood and no published data documents the effects of the photoperiod regime currently used commercially, continuous light (LL). The present study compared the effect of four different photoperiod regimes (i.e. advanced phase photoperiod (APP), delayed phase photoperiod (DPP), LL and simulated natural photoperiod (SNP)) on the smoltification and growth of juvenile rainbow trout during their freshwater phase of winter-spring and the following summer post smolt phase. Smoltification was evaluated by monitoring gill Na+,K+–ATPase (NKA) activity and transcription of NKA α-subunit isoforms 1a and 1b, and Na+,K+,2Cl− cotransporter 1a. Growth was measured as specific growth rate of both length and weight, and through molecular growth proxies such as the levels of circulating insulin-like growth factor 1 (IGF-I) in plasma and transcription of igf-I, igf binding protein 1b (igfbp1b), growth hormone receptor 1 (ghr1) and cathepsin L (ctsl) in the liver. Results indicate that APP induces a longer smolt window and higher levels of plasma IGF-I in both freshwater and seawater (two months post transfer), while DPP led to a shorter smolt window, lower plasma IGF-I levels in freshwater and seawater, an earlier decrease in liver igf-I and ctsl transcription in freshwater (as seen by modelling over time) and lower specific growth rate in freshwater. The transcription analysis of osmoregulatory genes complemented NKA activity and allowed for the detection of a transient response to light and of differences between the osmoregulatory capacity of parr and desmolted fish. Furthermore, an upregulation of the liver transcription of igf-I, ghr1 and ctsl was found in all treatments during the smolt window, which corresponded to the periods with highest growth. Finally, both plasma IGF-I and liver igf-I in seawater were found to be significantly correlated to fish growth in seawater. However, our data did not show that plasma IGF-I prior to seawater transfer could be used as a reliable predictor of growth in seawater. Overall, and especially when compared with other salmonid species, photoperiod seems to be a weaker inducer of smoltification in rainbow trout, according to the parameters that were tested, suggesting that other environmental cues might be more important drivers of this process

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

Effects of temperature and photoperiod on rainbow trout (Oncorhynchus mykiss) smoltification and haematopoiesis

First paragraph: Most freshwater fish would not be able to cope with the osmotic stress intrinsic to seawater, quickly dehydrating and dying, and so are bound to freshwater ecosystems (Quinn et al., 2016). However, anadromous salmonids have developed a strategy to minimize osmotic counter effects, thus allowing them to live in both freshwater, ideal for safe spawning, hatching and early growth stages, and seawater environments, rich in energy resources for fast growth (Hendry et al., 2004; Lima and Dill, 1990)