RNAseq analysis of fast skeletal muscle in restriction-fed transgenic coho salmon (Oncorhynchus kisutch) : an experimental model uncoupling the growth hormone and nutritional signals regulating growth

Background Coho salmon (Oncorhynchus kisutch) transgenic for growth hormone (Gh) express Gh in multiple tissues which results in increased appetite and continuous high growth with satiation feeding. Restricting Gh-transgenics to the same lower ration (TR) as wild-type fish (WT) results in similar growth, but with the recruitment of fewer, larger diameter, muscle skeletal fibres to reach a given body size. In order to better understand the genetic mechanisms behind these different patterns of muscle growth and to investigate how the decoupling of Gh and nutritional signals affects gene regulation we used RNA-seq to compare the fast skeletal muscle transcriptome in TR and WT coho salmon. Results Illumina sequencing of individually barcoded libraries from 6 WT and 6 TR coho salmon yielded 704,550,985 paired end reads which were used to construct 323,115 contigs containing 19,093 unique genes of which >10,000 contained >90 % of the coding sequence. Transcripts coding for 31 genes required for myoblast fusion were identified with 22 significantly downregulated in TR relative to WT fish, including 10 (vaspa, cdh15, graf1, crk, crkl, dock1, trio, plekho1a, cdc42a and dock5) associated with signaling through the cell surface protein cadherin. Nineteen out of 44 (43 %) translation initiation factors and 14 of 47 (30 %) protein chaperones were upregulated in TR relative to WT fish. Conclusions TR coho salmon showed increased growth hormone transcripts and gene expression associated with protein synthesis and folding than WT fish even though net rates of protein accretion were similar. The uncoupling of Gh and amino acid signals likely results in additional costs of transcription associated with protein turnover in TR fish. The predicted reduction in the ionic costs of homeostasis in TR fish associated with increased fibre size were shown to involve multiple pathways regulating myotube fusion, particularly cadherin signaling.Publisher PDFPeer reviewe

Improving PARMA Trailing

Taylor introduced a variable binding scheme for logic variables in his PARMA system, that uses cycles of bindings rather than the linear chains of bindings used in the standard WAM representation. Both the HAL and dProlog languages make use of the PARMA representation in their Herbrand constraint solvers. Unfortunately, PARMA's trailing scheme is considerably more expensive in both time and space consumption. The aim of this paper is to present several techniques that lower the cost. First, we introduce a trailing analysis for HAL using the classic PARMA trailing scheme that detects and eliminates unnecessary trailings. The analysis, whose accuracy comes from HAL's determinism and mode declarations, has been integrated in the HAL compiler and is shown to produce space improvements as well as speed improvements. Second, we explain how to modify the classic PARMA trailing scheme to halve its trailing cost. This technique is illustrated and evaluated both in the context of dProlog and HAL. Finally, we explain the modifications needed by the trailing analysis in order to be combined with our modified PARMA trailing scheme. Empirical evidence shows that the combination is more effective than any of the techniques when used in isolation. To appear in Theory and Practice of Logic Programming.Comment: 36 pages, 7 figures, 8 table

Diffusive Transport Enhanced by Thermal Velocity Fluctuations

We study the contribution of advection by thermal velocity fluctuations to the effective diffusion coefficient in a mixture of two indistinguishable fluids. The enhancement of the diffusive transport depends on the system size L and grows as \ln(L/L_0) in quasi two-dimensional systems, while in three dimensions it scales as L_0^{-1}-L^{-1}, where L_0 is a reference length. The predictions of a simple fluctuating hydrodynamics theory are compared to results from particle simulations and a finite-volume solver and excellent agreement is observed. Our results conclusively demonstrate that the nonlinear advective terms need to be retained in the equations of fluctuating hydrodynamics when modeling transport in small-scale finite systems.Comment: To appear in Phys. Rev. Lett., 201