A genomic view of the NOD-like receptor family in teleost fish: identification of a novel NLR subfamily in zebrafish

<p>Abstract</p> <p>Background</p> <p>A large multigene family of NOD-like receptor (NLR) molecules have been described in mammals and implicated in immunity and apoptosis. Little information, however, exists concerning this gene family in non-mammalian taxa. This current study, therefore, provides an in-depth investigation of this gene family in lower vertebrates including extensive phylogenetic comparison of zebrafish NLRs with orthologs in tetrapods, and analysis of their tissue-specific expression.</p> <p>Results</p> <p>Three distinct NLR subfamilies were identified by mining genome databases of various non-mammalian vertebrates; the first subfamily (NLR-A) resembles mammalian NODs, the second (NLR-B) resembles mammalian NALPs, while the third (NLR-C) appears to be unique to teleost fish. In zebrafish, NLR-A and NLR-B subfamilies contain five and six genes respectively. The third subfamily is large, containing several hundred NLR-C genes, many of which are predicted to encode a C-terminal B30.2 domain. This subfamily most likely evolved from a NOD3-like molecule. Gene predictions for zebrafish NLRs were verified using sequence derived from ESTs or direct sequencing of cDNA. Reverse-transcriptase (RT)-PCR analysis confirmed expression of representative genes from each subfamily in selected tissues.</p> <p>Conclusion</p> <p>Our findings confirm the presence of multiple NLR gene orthologs, which form a large multigene family in teleostei. Although the functional significance of the three major NLR subfamilies is unclear, we speculate that conservation and abundance of NLR molecules in all teleostei genomes, reflects an essential role in cellular control, apoptosis or immunity throughout bony fish.</p

An absorbing boundary formulation for the stratified, linearized, ideal MHD equations based on an unsplit, convolutional perfectly matched layer

Perfectly matched layers are a very efficient and accurate way to absorb waves in media. We present a stable convolutional unsplit perfectly matched formulation designed for the linearized stratified Euler equations. However, the technique as applied to the Magneto-hydrodynamic (MHD) equations requires the use of a sponge, which, despite placing the perfectly matched status in question, is still highly efficient at absorbing outgoing waves. We study solutions of the equations in the backdrop of models of linearized wave propagation in the Sun. We test the numerical stability of the schemes by integrating the equations over a large number of wave periods.Comment: 8 pages, 7 figures, accepted, A &

Detecting genetic regions associated with height in the native ponies of the British Isles by using high density SNP genotyping

Height is an important characteristic in the equine industry, although little is known about its genetic control in native British breeds of ponies. This study aimed to map QTL data with the withers height in four pony breeds native to the British Isles, including two different sections within Welsh Cobs. In this study, a genome-wide analysis approach using the Illumina Equine SNP50 Infinium BeadChip was applied to 105 ponies and cobs. Analysis identified 222 highly significant height-associated SNPs (P < 10-5), among which three SNPs on ECA9 have also been previously reported elsewhere. The highest number of significant SNPs associated to height in the native British horses were located on ECA1, ECA8 and ECA16

Banking from Leeds, not London: regional strategy and structure at the Yorkshire Bank, 1859–1952

Industrial philanthropist Edward Akroyd created the Yorkshire Penny Savings Bank in 1859. Despite competition from the Post Office Savings Bank after 1861 and a serious reserve problem in 1911, it sustained his overall strategy to become a successful regional bank. Using archival and contemporary sources to build on recent scholarship illustrating how savings banks were integrated into local economies and the complementary roles of philanthropy and paternalism, we analyse an English regional bank's strategy, including an assessment of strategic innovation, ownership changes and management structure. This will demonstrate that the founder's vision continued, even though the 1911 crisis radically altered both strategy and structure

Phospho-regulation of ATOH1 Is Required for Plasticity of Secretory Progenitors and Tissue Regeneration

The intestinal epithelium is largely maintained by&nbsp;self-renewing stem cells but with apparently committed progenitors also contributing, particularly following tissue damage. However, the mechanism of, and requirement for, progenitor plasticity in mediating pathological response remain unknown. Here we show that phosphorylation of the transcription factor Atoh1 is required for both the contribution of secretory progenitors to the stem cell pool and for a robust regenerative response. As confirmed by lineage tracing, Atoh1+ cells (Atoh1(WT)CreERT2 mice) give rise to multilineage intestinal clones both in the steady state and&nbsp;after tissue damage. In a phosphomutant Atoh1(9S/T-A)CreERT2 line, preventing phosphorylation of ATOH1 protein acts to promote secretory differentiation and inhibit the contribution of progenitors to self-renewal. Following chemical colitis, Atoh1+ cells of Atoh1(9S/T-A)CreERT2 mice have reduced clonogenicity that affects overall regeneration. Progenitor plasticity maintains robust self-renewal in the intestinal epithelium, and the balance between stem and progenitor fate is directly coordinated by ATOH1 multisite phosphorylation

The Flux-Anomaly-Forced Model Intercomparison Project (FAFMIP) contribution to CMIP6: investigation of sea-level and ocean climate change in response to CO₂ forcing

The Flux-Anomaly-Forced Model Intercomparison Project (FAFMIP) aims to investigate the spread in simulations of sea-level and ocean climate change in response to CO2 forcing by atmosphere–ocean general circulation models (AOGCMs). It is particularly motivated by the uncertainties in projections of ocean heat uptake, global-mean sea-level rise due to thermal expansion and the geographical patterns of sea-level change due to ocean density and circulation change. FAFMIP has three tier-1 experiments, in which prescribed surface flux perturbations of momentum, heat and freshwater respectively are applied to the ocean in separate AOGCM simulations. All other conditions are as in the pre-industrial control. The prescribed fields are typical of pattern and magnitude of changes in these fluxes projected by AOGCMs for doubled CO2 concentration. Five groups have tested the experimental design with existing AOGCMs. Their results show diversity in the pattern and magnitude of changes, with some common qualitative features. Heat and water flux perturbation cause the dipole in sea-level change in the North Atlantic, while momentum and heat flux perturbation cause the gradient across the Antarctic Circumpolar Current. The Atlantic meridional overturning circulation (AMOC) declines in response to the heat flux perturbation, and there is a strong positive feedback on this effect due to the consequent cooling of sea-surface temperature in the North Atlantic, which enhances the local heat input to the ocean. The momentum and water flux perturbations do not substantially affect the AMOC. Heat is taken up largely as a passive tracer in the Southern Ocean, which is the region of greatest heat input, while the weakening of the AMOC causes redistribution of heat towards lower latitudes. Future analysis of these and other phenomena with the wider range of CMIP6 FAFMIP AOGCMs will benefit from new diagnostics of temperature and salinity tendencies, which will enable investigation of the model spread in behaviour in terms of physical processes as formulated in the models