Comparative muscle development of scyphozoan jellyfish with simple and complex life cycles

International audienceBackground : Simple life cycles arise from complex life cycles when one or more developmental stages are lost. This raises a fundamental question - how can an intermediate stage, such as a larva, be removed, and development still produce a normal adult? To address this question, we examined the development in several species of pelagiid jellyfish. Most members of Pelagiidae have a complex life cycle with a sessile polyp that gives rise to ephyrae (juvenile medusae); but one species within Pelagiidae, Pelagia noctiluca, spends its whole life in the water column, developing from a larva directly into an ephyra. In many complex life cycles, adult features develop from cell populations that remain quiescent in larvae, and this is known as life cycle compartmentalization and may facilitate the evolution of direct life cycles. A second type of metamorphic processes, known as remodeling, occurs when adult features are formed through modification of already differentiated larval structures. We examined muscle morphology to determine which of these alternatives may be present in Pelagiidae.Results : We first examined the structure and development of polyp and ephyra musculature in Chrysaora quinquecirrha, a close relative of P. noctiluca with a complex life cycle. Using phallotoxin staining and confocal microscopy, we verified that polyps have four to six cord muscles that persist in strobilae and discovered that cord muscles is physically separated from ephyra muscle. When cord muscle is removed from ephyra segments, normal ephyra muscle still develops. This suggests that polyp cord muscle is not necessary for ephyra muscle formation. We also found no evidence of polyp-like muscle in P. noctiluca. In both species, we discovered that ephyra muscle arises de novo in a similar manner, regardless of the life cycle.Conclusions : The separate origins of polyp and ephyra muscle in C. quinquecirrha and the absence of polyp-like muscle in P. noctiluca suggest that polyp muscle is not remodeled to form ephyra muscle in Pelagiidae. Life cycle stages in Scyphozoa may instead be compartmentalized. Because polyp muscle is not directly remodeled, this may have facilitated the loss of the polyp stage in the evolution of P. noctiluca

DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism

Inverted repeat (IR) sequences in DNA can form non-canonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. Firstly, a twist-induced denaturation bubble must diffuse so that its midpoint is near the centre of symmetry of the IR sequence. Secondly, bubble fluctuations must be large enough to allow one of the arms to form a small number of hairpin bonds. Once the first arm is partially formed, the second arm can rapidly grow to a similar size. Because bubbles can twist back on themselves, they need considerably fewer bases to resolve torsional stress than the final cruciform state does. The initially stabilised cruciform therefore continues to grow, which typically proceeds synchronously, reminiscent of the S-type mechanism of cruciform formation. By using umbrella sampling techniques we calculate, for different temperatures and superhelical densities, the free energy as a function of the number of bonds in each cruciform along the correlated but non-synchronous nucleation pathways we observed in direct simulations.Comment: 12 pages main paper + 11 pages supplementary dat

Large Scale Structures a Gradient Lines: the case of the Trkal Flow

A specific asymptotic expansion at large Reynolds numbers (R)for the long wavelength perturbation of a non stationary anisotropic helical solution of the force less Navier-Stokes equations (Trkal solutions) is effectively constructed of the Beltrami type terms through multi scaling analysis. The asymptotic procedure is proved to be valid for one specific value of the scaling parameter,namely for the square root of the Reynolds number (R).As a result large scale structures arise as gradient lines of the energy determined by the initial conditions for two anisotropic Beltrami flows of the same helicity.The same intitial conditions determine the boundaries of the vortex-velocity tubes, containing both streamlines and vortex linesComment: 27 pages, 2 figure

High-resolution genetic analysis reveals extensive gene flow within the jellyfish Pelagia noctiluca (Scyphozoa) in the North Atlantic and Mediterranean Sea

12 pages, 5 figures, 3 tables, supporting Information http://onlinelibrary.wiley.com/doi/10.1111/bij.12654/suppinfoDespite the importance of gelatinous zooplankton as components of marine ecosystems, both ecologically and socio-economically, relatively little information is known about population persistence or connectivity in jellyfish. In the present study, we employed a combination of nuclear microsatellite markers and sequence data from the mitochondrial cytochrome oxidase I (COI) gene to determine levels and patterns of population genetic structuring in the holoplanktonic jellyfish Pelagia noctiluca across the northeast Atlantic Ocean and Mediterranean Sea. Our results indicate a high degree of connectivity in P. noctiluca, with little evidence of geographical structuring of genetic variation. A small but significant differentiation of Atlantic Ocean and Mediterranean stocks was detected based on the microsatellite data, but no evidence of differentiation was observed with the mtDNA, probably due to the higher power of the microsatellites to detect low levels of genetic structuring. Two clearly distinct groups of genotypes were observed within the mtDNA COI, which probably diverged in the early Pleistocene, but with no evidence of geographical structuring. Palaeodistribution modelling of P. noctiluca at the Last Glacial Maximum (LGM; c. 21 Kya) indicated large areas of suitable habitat south of the species’ current-day distribution, with little reduction in area. The congruent evidence for minimal genetic differentiation from the nuclear microsatellites and the mtDNA, coupled with the results of the palaeodistribution modelling, supports the idea of long-term population stability and connectivity, thus providing key insights into the population dynamics and demography of this important speciesFergal Glynn’s PhD was funded by the Department of Agriculture and Rural Development, Northern Ireland (DARDNI). Martin Lilley was funded by l’Agence Nationale de la Recherche projects ‘Ecogely’ ANR-10-PDOC-005-01 and ‘NanoDeconGels’ ANR-12-EMMA-0008Peer Reviewe

The effect of organelle discovery upon sub-cellular protein localisation.

Prediction of protein sub-cellular localisation by employing quantitative mass spectrometry experiments is an expanding field. Several methods have led to the assignment of proteins to specific subcellular localisations by partial separation of organelles across a fractionation scheme coupled with computational analysis. Methods developed to analyse organelle data have largely employed supervised machine learning algorithms to map unannotated abundance profiles to known protein–organelle associations. Such approaches are likely to make association errors if organelle-related groupings present in experimental output are not included in data used to create a protein–organelle classifier. Currently, there is no automated way to detect organelle-specific clusters within such datasets. In order to address the above issues we adapted a phenotype discovery algorithm, originally created to filter image-based output for RNAi screens, to identify putative subcellular groupings in organelle proteomics experiments. We were able to mine datasets to a deeper level and extract interesting phenotype clusters for more comprehensive evaluation in an unbiased fashion upon application of this approach. Organelle-related protein clusters were identified beyond those sufficiently annotated for use as training data. Furthermore, we propose avenues for the incorporation of observations made into general practice for the classification of protein–organelle membership from quantitative MS experiments. Biological significance Protein sub-cellular localisation plays an important role in molecular interactions, signalling and transport mechanisms. The prediction of protein localisation by quantitative mass-spectrometry (MS) proteomics is a growing field and an important endeavour in improving protein annotation. Several such approaches use gradient-based separation of cellular organelle content to measure relative protein abundance across distinct gradient fractions. The distribution profiles are commonly mapped in silico to known protein–organelle associations via supervised machine learning algorithms, to create classifiers that associate unannotated proteins to specific organelles. These strategies are prone to error, however, if organelle-related groupings present in experimental output are not represented, for example owing to the lack of existing annotation, when creating the protein–organelle mapping. Here, the application of a phenotype discovery approach to LOPIT gradient-based MS data identifies candidate organelle phenotypes for further evaluation in an unbiased fashion. Software implementation and usage guidelines are provided for application to wider protein–organelle association experiments. In the wider context, semi-supervised organelle discovery is discussed as a paradigm with which to generate new protein annotations from MS-based organelle proteomics experiments. This article is part of a Special Issue entitled: New Horizons and Applications for Proteomics [EuPA 2012]

Dynamics of fluctuations in an optical analog of the Laval nozzle

Using the analogy between the description of coherent light propagation in a medium with Kerr nonlinearity by means of nonlinear Schr\"odinger equation and that of a dissipationless liquid we propose an optical analogue of the Laval nozzle. The optical Laval nozzle will allow one to form a transonic flow in which one can observe and study a very unusual dynamics of classical and quantum fluctuations including analogue of the Hawking radiation of real black holes. Theoretical analysis of this dynamics is supported by numerical calculations and estimates for a possible experimental setup are presented.Comment: 7 pages, 4 figure

Keck Planet Imager and Characterizer (KPIC): status update

Here we report on the status of the The Keck Planet Imager and Characterizer (KPIC), which is an on-going series of upgrades to the W.M. Keck II adaptive optics system and instrument suite focused on exoplanet imaging and spectroscopic characterization. The KPIC infrared pyramid wavefront sensor and fiber injection unit to high-resolution infrared spectrograph NIRSPEC have been assembled, integrated and are under-going tests at the University of Hawaii before installation at the Summit in the Fall of 2018

Photosynthetic acclimation of Nannochloropsis oculata investigated by multi-wavelength chlorophyll fluorescence analysis

Multi-wavelength chlorophyll fluorescence analysis was utilised to examine the photosynthetic efficiency of the biofuel-producing alga Nannochloropsis oculata, grown under two light regimes; low (LL) and high (HL) irradiance levels. Wavelength dependency was evident in the functional absorption cross-section of Photosystem II (σII(λ)), absolute electron transfer rates (ETR(II)), and non-photochemical quenching (NPQ) of chlorophyll fluorescence in both HL and LL cells. While σII(λ) was not significantly different between the two growth conditions, HL cells upregulated ETR(II) 1.6-1.8-fold compared to LL cells, most significantly in the wavelength range of 440-540nm. This indicates preferential utilisation of blue-green light, a highly relevant spectral region for visible light in algal pond conditions. Under these conditions, the HL cells accumulated saturated fatty acids, whereas polyunsaturated fatty acids were more abundant in LL cells. This knowledge is of importance for the use of N. oculata for fatty acid production in the biofuel industry. © 2014 Elsevier Ltd

The star-formation history of the universe - an infrared perspective

A simple and versatile parameterized approach to the star formation history allows a quantitative investigation of the constraints from far infrared and submillimetre counts and background intensity measurements. The models include four spectral components: infrared cirrus (emission from interstellar dust), an M82-like starburst, an Arp220-like starburst and an AGN dust torus. The 60 $\mu$m luminosity function is determined for each chosen rate of evolution using the PSCz redshift data for 15000 galaxies. The proportions of each spectral type as a function of 60 $\mu$m luminosity are chosen for consistency with IRAS and SCUBA colour-luminosity relations, and with the fraction of AGN as a function of luminosity found in 12 $\mu$m samples. The luminosity function for each component at any wavelength can then be calculated from the assumed spectral energy distributions. With assumptions about the optical seds corresponding to each component and, for the AGN component, the optical and near infrared counts can be accurately modelled. A good fit to the observed counts at 0.44, 2.2, 15, 60, 90, 175 and 850 $\mu$m can be found with pure luminosity evolution in all 3 cosmological models investigated: $\Omega_o$ = 1, $\Omega_o$ = 0.3 ($\Lambda$ = 0), and $\Omega_o$ = 0.3, $\Lambda$ = 0.7. All 3 models also give an acceptable fit to the integrated background spectrum. Selected predictions of the models, for example redshift distributions for each component at selected wavelengths and fluxes, are shown. The total mass-density of stars generated is consistent with that observed, in all 3 cosmological models.Comment: 20 pages, 25 figures. Accepted for publication in ApJ. Full details of models can be found at http://astro.ic.ac.uk/~mrr/countmodel