Structure and expression of GSL1 and GSL2 genes encoding gibberellin stimulated-like proteins in diploid and highly heterozygous tetraploid potato reveals their highly conserved and essential status

Background: GSL1 and GSL2, Gibberellin Stimulated-Like proteins (also known as Snakin-1 and Snakin-2), are cysteine-rich peptides from potato (Solanum tuberosum L.) with antimicrobial properties. Similar peptides in other species have been implicated in diverse biological processes and are hypothesised to play a role in several aspects of plant development, plant responses to biotic or abiotic stress through their participation in hormone crosstalk, and redox homeostasis. To help resolve the biological roles of GSL1 and GSL2 peptides we have undertaken an in depth analysis of the structure and expression of these genes in potato. Results: We have characterised the full length genes for both GSL1 (chromosome 4) and GSL2 (chromosome 1) from diploid and tetraploid potato using the reference genome sequence of potato, coupled with further next generation sequencing of four highly heterozygous tetraploid cultivars. The frequency of SNPs in GSL1 and GSL2 were very low with only one SNP every 67 and 53 nucleotides in exon regions of GSL1 and GSL2, respectively. Analysis of comprehensive RNA-seq data substantiated the role of specific promoter motifs in transcriptional control of gene expression. Expression analysis based on the frequency of next generation sequence reads established that GSL2 was expressed at a higher level than GSL1 in 30 out of 32 tissue and treatment libraries. Furthermore, both the GSL1 and GSL2 genes exhibited constitutive expression that was not up regulated in response to biotic or abiotic stresses, hormone treatments or wounding. Potato transformation with antisense knock-down expression cassettes failed to recover viable plants. Conclusions: The potato GSL1 and GSL2 genes are very highly conserved suggesting they contribute to an important biological function. The known antimicrobial activity of the GSL proteins, coupled with the FPKM analysis from RNA-seq data, implies that both genes contribute to the constitutive defence barriers in potatoes. The lethality of antisense knock-down expression of GSL1 and GSL2, coupled with the rare incidence of SNPs in these genes, suggests an essential role for this gene family. These features are consistent with the GSL protein family playing a role in several aspects of plant development in addition to plant defence against biotic stresses. © 2014 Meiyalaghan et al.; licensee BioMed Central Ltd

Whither Capitalism? Financial externalities and crisis

As with global warming, so with financial crises – externalities have a lot to answer for. We look at three of them. First the financial accelerator due to ‘fire sales’ of collateral assets -- a form of pecuniary externality that leads to liquidity being undervalued. Second the ‘risk- shifting’ behaviour of highly-levered financial institutions who keep the upside of risky investment while passing the downside to others thanks to limited liability. Finally, the network externality where the structure of the financial industry helps propagate shocks around the system unless this is checked by some form of circuit breaker, or ‘ring-fence’. The contrast between crisis-induced Great Recession and its aftermath of slow growth in the West and the rapid - and (so far) sustained - growth in the East suggests that successful economic progress may depend on how well these externalities are managed

AgBase: a functional genomics resource for agriculture

BACKGROUND: Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. DESCRIPTION: To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. CONCLUSION: The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms

Novel links between ciliopathies and FGF-related craniofacial syndromes

K Liu1*, JT Tabler1, HL Szabo-Rogers1, A Mesbahi1, C Healy1, W Barrell1, B Wlodarczyk2, Author Affiliations 1 King's College London, UK 2 University of Texas Southwestern, USA 3 University of Texas at Austin, USAOral Presentation : Recent studies suggest that planar cell polarity (PCP) genes coordinate cell polarity, ciliogenesis and signalling during mammalian development. FUZ is a PCP gene implicated in human congenital anomalies, including neural tube defects and orofacial clefting. Our analysis of fuzzy mutant mice reveals ciliogenesis defects in craniofacial tissues as well as a suite of phenotypes reminiscent of FGF-related craniofacial disorders. Mutants have coronal synostosis, shortened facial extensions, low-set ears and a high-arched palate. To our surprise, we found that the facial defects are due to increased neural crest migration into the first branchial arch (BA1), resulting in maxillary hyperplasia. Furthermore, the neural crest cells migrate in a disorganized fashion, deeper than normal and with fewer cell-cell contacts. This ectopic migration correlates with a dramatic increase in FGF signaling, first in the mid-hindbrain boundary, and then in the BA1 epithelia. The increased tissue causes a medial positional shift in the palatal primordia that manifests as a high-arched palate with pseudo-cleft. Genetic loss of fgf8 rescues the maxillary hyperplasia. Taken together, our data suggest a novel interplay between ciliogenesis, FGF signalling and migration of neural crest which may underlie congenital craniofacial dysmorphologies.Molecular [email protected]

Masses for Galactic Beat Cepheids

Accurate mass determinations for Cepheids may be used to determine the degree of excess mixing in the interiors of their main-sequence progenitors : the larger the excess mixing, the larger the luminosity of the Cepheid of a given mass, or the smaller the mass of a Cepheid with given luminosity. Dynamical masses determined recently for a few Cepheid binaries indicate excess mixing somewhat stronger than that corresponding to the convective overshoot models by Schaller et al. Beat Cepheids can be used similarly to test main-sequence mixing in stellar interiors. The period ratios for beat Cepheids depend on luminosity, heavy element abundance, and mass. By comparing pulsational models and the obser- T eff, vationally derived luminosity, metallicities, and period ratios it is possible to obtain masses for these T eff, stars, the so-called beat masses. With the old opacities masses much smaller than the evolutionary masses were obtained. With the new OPAL opacities a beat mass close to the dynamical mass was obtained for the binary beat Cepheid Y Carinae, showing that it is now possible to obtain reliable beat masses. In this paper, we determine beat masses for seven Galactic beat Cepheids for which photometric and spectroscopic data are available. We Ðnd an average mass around 4.2 ^ 0.3 for these stars, M_ though the actual error limits for each star may be larger mainly because of uncertainties in E(B[V ) and the heavy element abundances. (As derived spectroscopically, beat Cepheids are in general metalpoor, with The relation between the derived beat masses and the luminosities [0.4[[Fe/H][ 0.0). again indicates excess mixing that is somewhat larger than that corresponding to the models by Schaller et al

Surface rupture of the Hundalee fault during the 2016 Mw 7.8 Kaikōura earthquake

The Hundalee fault is one of at least 20 faults that ruptured during the 2016 M w Mw 7.8 Kaikōura earthquake in the northeast of the South Island of New Zealand. Here, we document a 12‐km onshore section of the Hundalee fault that exhibited surface rupture from this event. To the northeast of our observations, the fault crosses the coast, and independent seabed surveys show that the 2016 rupture continued at least 2 km offshore. No surface rupture was observed across the southwestern section of the Hundalee fault, which crosses hilly vegetated terrain and poorly consolidated valley‐floor sediment. However, previous Interferometric Synthetic Aperture Radar (InSAR) analyses suggest that a 9‐km‐long section of the fault did rupture. Hence, the minimum length of the 2016 rupture along the Hundalee fault is 23 km. Field measurements indicate oblique dextral‐reverse slip along northeast‐trending Hundalee fault sections and reverse‐sinistral slip along north to north‐northeast‐trending sections. This is consistent with the regional principal horizontal shortening direction. Maximum vertical and horizontal offset measurements are 2.5±0.5 2.5±0.5 and 3.7±0.5  m 3.7±0.5  m , respectively. The discontinuous and irregular surface ruptures we observed are characteristic of a structurally immature fault, yet previous geological mapping indicates that the Hundalee fault is a regionally significant fault with >1‐km >1‐km late Cenozoic throw. Furthermore, a 60‐m‐wide sequence of fault rocks exposed by the rupture indicates that slip has localized into <10‐cm‐thick <10‐cm‐thick gouge zones, as anticipated for a mature fault. Therefore, a discrepancy exists between geological evidence of the Hundalee fault being a structurally mature fault and the characteristics of the 2016 rupture. We speculate that this signifies that the 2016 rupture was imposed on the Hundalee fault by movement across an inefficient multifault network rather than independent rupture of the Hundalee fault itself

An evaluation of surface meteorology and fluxes over the Iceland and Greenland Seas in ERA5 reanalysis: the impact of sea ice distribution

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Renfrew, I. A., Barrell, C., Elvidge, A. D., Brooke, J. K., Duscha, C., King, J. C., Kristiansen, J., Cope, T. L., Moore, G. W. K., Pickart, R. S., Reuder, J., Sandu, I., Sergeev, D., Terpstra, A., Vage, K., & Weiss, A. An evaluation of surface meteorology and fluxes over the Iceland and Greenland Seas in ERA5 reanalysis: the impact of sea ice distribution. Quarterly Journal of the Royal Meteorological Society, (2020): 1-22, doi:10.1002/qj.3941.The Iceland and Greenland Seas are a crucial region for the climate system, being the headwaters of the lower limb of the Atlantic Meridional Overturning Circulation. Investigating the atmosphere–ocean–ice processes in this region often necessitates the use of meteorological reanalyses—a representation of the atmospheric state based on the assimilation of observations into a numerical weather prediction system. Knowing the quality of reanalysis products is vital for their proper use. Here we evaluate the surface‐layer meteorology and surface turbulent fluxes in winter and spring for the latest reanalysis from the European Centre for Medium‐Range Weather Forecasts, i.e., ERA5. In situ observations from a meteorological buoy, a research vessel, and a research aircraft during the Iceland–Greenland Seas Project provide unparalleled coverage of this climatically important region. The observations are independent of ERA5. They allow a comprehensive evaluation of the surface meteorology and fluxes of these subpolar seas and, for the first time, a specific focus on the marginal ice zone. Over the ice‐free ocean, ERA5 generally compares well to the observations of surface‐layer meteorology and turbulent fluxes. However, over the marginal ice zone, the correspondence is noticeably less accurate: for example, the root‐mean‐square errors are significantly higher for surface temperature, wind speed, and surface sensible heat flux. The primary reason for the difference in reanalysis quality is an overly smooth sea‐ice distribution in the surface boundary conditions used in ERA5. Particularly over the marginal ice zone, unrepresented variability and uncertainties in how to parameterize surface exchange compromise the quality of the reanalyses. A parallel evaluation of higher‐resolution forecast fields from the Met Office's Unified Model corroborates these findings.This study was part of the Iceland Greenland Seas Project. Funding was from the NERC AFIS grant (NE/N009754/1), the ALERTNESS (Advanced models and weather prediction in the Arctic: enhanced capacity from observations and polar process representations) project (Research Council of Norway project number 280573), the Trond Mohn Foundation (BFS2016REK01), and the National Science Foundation grant OCE‐1558742. The Leosphere WindCube v2 and the Wavescan buoy are part of the OBLO (Offshore Boundary Layer Observatory) infrastructure funded by the Research Council of Norway (project number 227777)

Bad faith in All’s Well That Ends Well

All’s Well That Ends Well is a complicated and disturbing play that has a comic ending, but which seems anything but a comedy with a forced marriage based on bed-trickery between the reluctant Bertram and the feisty and witty Helena. Unsurprisingly, audiences have tended to side with Helena and the play has been classified as a “problem comedy” ever since William Lawrence identified this particular group of Shakespeare plays nearly a century ago. I want to argue in this essay that the play might better be classified as an “equivocation” play alongside Macbeth, Othello, and Troilus and Cressida and that the anxieties about fidelity, honesty and truthfulness in marriage need to be read in terms of the fear of religious tolerance/intolerance which dominated religious politics in the early years of James’s reign before the passing of the Oath of Allegiance (1606). The play is notable for its interest in chop logic, which the clown in particular displays throughout the play, a counterpoint to the arguments of Bertram and Helena who want very different things, but who are bound together as future husband and wife. Although the language of treason and treachery is used throughout, the play is less interested in answering the question of how far one can trust a stranger within than the issue of how far one can accommodate the needs of others. This article is published as part of a collection to commemorate the 400th anniversary of William Shakespeare’s death