Icy: an open bioimage informatics platform for extended reproducible research

Current research in biology uses evermore complex computational and imaging tools. Here we describe Icy, a collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless development of sophisticated imaging workflows. Icy extends the reproducible research principles, by encouraging and facilitating the reusability, modularity, standardization and management of algorithms and protocols. Icy is free, open-source and available at http://icy.bioimageanalysis.org/.     

CML9, a multifunctional Arabidopsis thaliana calmodulin-like protein involved in stress responses and plant growth?

Plants have evolved complex signaling networks to respond to their fluctuating environment and adapt their growth and development. Calcium-dependent signaling pathways play key role in the onset of these adaptive responses. In plant cells, the intracellular calcium transients are triggered by numerous stimuli and it is supposed that the large repertory of calcium sensors present in higher plants could contribute to integrate these signals in physiological responses. Here, we present data on CML9, a calmodulin-like protein that appears to be involved in plant responses to both biotic and abiotic stress. Using a reverse genetic approach based on gain and loss of function mutants, we present here data indicating that this CML might also be involved in root growth control in response to the flagellin, a pathogen-associated molecular pattern (PAMP) also involved in plant immunity.     

Larval Dispersal Modeling of Pearl Oyster Pinctada margaritifera following Realistic Environmental and Biological Forcing in Ahe Atoll Lagoon

Studying the larval dispersal of bottom-dwelling species is necessary to understand their population dynamics and optimize their management. The black-lip pearl oyster (Pinctada margaritifera) is cultured extensively to produce black pearls, especially in French Polynesia''s atoll lagoons. This aquaculture relies on spat collection, a process that can be optimized by understanding which factors influence larval dispersal. Here, we investigate the sensitivity of P. margaritifera larval dispersal kernel to both physical and biological factors in the lagoon of Ahe atoll. Specifically, using a validated 3D larval dispersal model, the variability of lagoon-scale connectivity is investigated against wind forcing, depth and location of larval release, destination location, vertical swimming behavior and pelagic larval duration (PLD) factors. The potential connectivity was spatially weighted according to both the natural and cultivated broodstock densities to provide a realistic view of connectivity. We found that the mean pattern of potential connectivity was driven by the southwest and northeast main barotropic circulation structures, with high retention levels in both. Destination locations, spawning sites and PLD were the main drivers of potential connectivity, explaining respectively 26%, 59% and 5% of the variance. Differences between potential and realistic connectivity showed the significant contribution of the pearl oyster broodstock location to its own dynamics. Realistic connectivity showed larger larval supply in the western destination locations, which are preferentially used by farmers for spat collection. In addition, larval supply in the same sectors was enhanced during summer wind conditions. These results provide new cues to understanding the dynamics of bottom-dwelling populations in atoll lagoons, and show how to take advantage of numerical models for pearl oyster management.     

Trunk's Natural Inclination Influences Stance Limb Kinetics,but Not Body Kinematics,during Gait Initiation in Able Men

The imposing mass of the trunk in relation to the whole body has an important impact on human motion. The objective of this study is to determine the influence of trunk''s natural inclination - forward (FW) or backward (BW) with respect to the vertical - on body kinematics and stance limb kinetics during gait initiation.Twenty-five healthy males were divided based on their natural trunk inclination (FW or BW) during gait initiation. Instantaneous speed was calculated at the center of mass at the first heel strike. The antero-posterior impulse was calculated by integrating the antero-posterior ground reaction force in time. Ankle, knee, hip and thoraco-lumbar (L5) moments were calculated using inverse dynamics and only peaks of the joint moments were analyzed. Among all the investigated parameters, only joint moments present significant differences between the two groups. The knee extensor moment is 1.4 times higher (P<0.001) for the BW group, before the heel contact. At the hip, although the BW group displays a flexor moment 2.4 times higher (P<0.001) before the swing limb''s heel-off, the FW group displays an extensor moment 3.1 times higher (P<0.01) during the swing phase. The three L5 extensor peaks after the toe-off are respectively 1.7 (P<0.001), 1.4 (P<0.001) and 1.7 (P<0.01) times higher for the FW group. The main results support the idea that the patterns described during steady-state gait are already observable during gait initiation. This study also provides reference data to further investigate stance limb kinetics in specific or pathologic populations during gait initiation. It will be of particular interest for elderly people, knowing that this population displays atypical trunk postures and present a high risk of falling during this forward stepping.     

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes

Background

Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions.

Results

We present a computational method, ADseq, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADseq provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADseq to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes.

Conclusions

We demonstrate the method’s ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression.

     

Assessing the sensitivity of bivalve populations to global warming using an individual‐based modelling approach

Climate change exposes benthic species populations in coastal ecosystems to a combination of different stressors (e.g., warming, acidification and eutrophication), threatening the sustainability of the ecological functions they provide. Thermal stress appears to be one of the strongest drivers impacting marine ecosystems, acting across a wide range of scales, from individual metabolic performances to geographic distribution of populations. Accounting for and integrating the response of species functional traits to thermal stress is therefore a necessary step in predicting how populations will respond to the warming expected in coming decades. Here, we developed an individual‐based population model using a mechanistic formulation of metabolic processes within the framework of the dynamic energy budget theory. Through a large number of simulations, we assessed the sensitivity of population growth potential to thermal stress and food conditions based on a climate projection scenario (Representative Concentration Pathway; RCP8.5: no reduction of greenhouse gas emissions). We focused on three bivalve species with contrasting thermal tolerance ranges and distinct distribution ranges along 5,000 km of coastline in the NE Atlantic: the Pacific oyster (Magallana gigas), and two mussel species: Mytilus edulis and Mytilus galloprovincialis. Our results suggest substantial and contrasting changes within species depending on local temperature and food concentration. Reproductive phenology appeared to be a core process driving the responses of the populations, and these patterns were closely related to species thermal tolerances. The nonlinear relationship we found between individual life‐history traits and response at the population level emphasizes the need to consider the interactions resulting from upscaling across different levels of biological organisation. These results underline the importance of a process‐based understanding of benthic population response to seawater warming, which will be necessary for forward planning of resource management and strategies for conservation and adaptation to environmental changes.     

In Vivo Random Mutagenesis of Bacillus subtilis by Use of TnYLB-1, a mariner-Based Transposon

This report describes the construction and characterization of a mariner-based transposon system designed to be used in Bacillus subtilis, but potentially applicable to other gram-positive bacteria. Two pUC19-derived plasmids were created that contain the mariner-Himar1 transposase gene, modified for expression in B. subtilis, under the control of either σ^A- or σ^B-dependent promoters. Both plasmids also contain a transposable element (TnYLB-1) consisting of a Kan^r cassette bracketed by the Himar1-recognized inverse terminal repeats, as well as the temperature-sensitive replicon and Erm^r gene of pE194ts. TnYLB-1 transposes into the B. subtilis chromosome with high frequency (10⁻²) from either plasmid. Southern hybridization analyses of 15 transposants and sequence analyses of the insertion sites of 10 of these are consistent with random transposition, requiring only a “TA” dinucleotide as the essential target in the recipient DNA. Two hundred transposants screened for sporulation proficiency and auxotrophy yielded five Spo⁻ clones, three with insertions in known sporulation genes (kinA, spoVT, and yqfD) and two in genes (ybaN and yubB) with unknown functions. Two auxotrophic mutants were identified among the 200 transposants, one with an insertion in lysA and another in a gene (yjzB) whose function is unknown.     

Étude biostratigraphique et paléoenvironnementale des diatomées pyritisées de l'intervalle Paléocène supérieur-Éocène inférieur du sondage de Saint-Josse (France)

This paper presents the results of a biostratigraphic analysis of pyritized diatom assemblages in the Saint-Josse core (CC82) located in the northern part of the Paris basin (coordinates: X =555?000, Y =307?324 and Z =56.9 m). During the Paleocene-Eocene this locality was situated in a small bight of the North Sea Basin. The results are obtained from sediments of the Thanet and Mont-Bernon group equivalents belonging to the Paleocene-Eocene interval. Thirteen samples were studied and eleven contain pyritized diatoms. By epigenesis, the siliceous frustule of the diatom is changed into a pyritized skeleton with all the ornamentation very well preserved such as the velum, the areolae, the labiate processes, etc. Dispersive X-Ray analyses show this complete replacement of silica by pyrite. Another form of pyritization is crystallization of pyrite (in cubes, pyritohedrons, octahedrons, framboids) in internal cavities of the diatoms to produce internal moulds, also called steinkerns, which preserve the external morphology of the diatoms and some details such as the girdle. Despite pyritization, diatoms can often be recognized at the species level; brackish and marine species were observed but no fresh water specimens were encountered. Pyrite is easily altered into iron oxides. In outcrops, pyritized diatoms can be obscured or destroyed by oxidation. We have chosen borehole samples for this study to avoid the affects of weathering. Deposits from the Sorrus Unit (of the Thanet Group) have low abundances of pyritized diatoms (3 to 25 specimens per sample). This unit contains allochtonous diatom assemblages comprising Actinoptychussenarius, Coscinodiscus morsianus var. morsianus, and Coscinodiscus morsianus var. moelleri. Sample 34.31-34.45 from this unit is particularly interesting. It contains three specimens of Paralia siberica var. laevis, which is typical of an estuarine or littoral paleoenvironment, and corresponds to the more continental deposit of the Sorrus Unit. Seven samples, taken in the Argile de Saint-Aubin Unit (from the Mont-Bernon Group), contain more than 200 pyritized diatoms and between 9 to 16 different species per sample. A brackish assemblage (Actinoptychus senarius, Coscinodiscus commutatus and Stellarima microtrias) and a marine assemblage (C. morsianus var. morsianus, Coscinodiscus var. moelleri, Fenestrella antiqua, Odontellaheibergii, Rhizosolenia sp. 1 and Trinacria regina) are observed. The brackish assemblage expands in the upper part of the Saint-Aubin Unit indicating more widespread brackish paleoenvironmental conditions. Pyritized diatoms are important fossil markers in the Paris basin mainly when siliceous fossils (silicoflagellates or radiolarians) and others microfossils (foraminifers and dinoflagellates) are very poor or absent. Two diatom assemblages have been identified in the Saint-Josse borehole. The first assemblage D1, comprising C. morsianus var. moelleri (high occurrence), C. morsianus (a few) and T. regina (rare), is recorded in the Sorrus, La Calotterie, Bois Gorguette, Le Goulet and lower Saint-Aubin Units. The second assemblage D2, characterized by great abundance of F. antiqua and decreasing numbers of C. morsianus species, is found in the upper part of the Saint-Aubin Unit. These diatom assemblages can be correlated with other biozonations established in the North Sea basin and based on nannoplankton and diatoms (King, 1983), diatoms (Mitlehner, 1996) and calcareous nannoplankton (Martini, 1971). F. antiqua and C. morsianus var. moelleri are the more important diatom species encountered. F. antiqua (previously named Coscinodiscus sp. 1, King, 1983) is the fossil marker used by King to define his NSP4 biozone. The base of NSP4 corresponds to the lowest occurrence of F. antiqua and the top is marked by the highest occurrence of this species. The Sorrus, La Calotterie, Bois Gorguette, Le Goulet and Saint-Aubin (“Sparnacian” stage) Units, the last one comprising F. antiqua (increasing to acme), correspond to the NSP4 zone of King (1983). The Mont-Hulin and Château de la Bruyère Units correspond probably to the NSP5 zone of King (1983). F. antiqua and C. morsianus var. moelleri were also used by Mitlehner (1996) to differentiate the NSP4a zone (low abundance of F. antiqua and abundance of C. morsianus var. moelleri) from the NSP4b zone (great abundance and acme of F. antiqua). The abundance of C. morsianus var. moelleri is recorded in the lower part of Saint-Aubin Unit and the abundance of F. antiqua (high peak at 46% in the sample 17.87) is found in the upper part of Saint-Aubin Unit. Therefore, Sorrus, La Calotterie, Bois Gorguette, Le Goulet and the lower part of Saint-Aubin Units are correlated with the NSP4a zone and the upper part of Saint-Aubin Unit with the NSP4b zone. By correlating the calcareous nannoplankton biozonation (NP) of Martini (1971) with the biozonation of King (1983), adapted by Mitlehner (1996), the boundary between the NP9 and NP10 zones could be located in the 18.75-17.87 interval and the NP10-NP11 boundary at the top of Saint-Aubin Unit. Lithostratigraphic correlations between the units of the Saint-Josse borehole (Paris basin) and the formations of the North Sea basin can be established. The great abundance of C. morsianus var. moelleri and the great abundance (including acme) of F. antiqua are respectively recorded in the Sele and Balder Formations. Therefore, the interval Sorrus/lower Saint-Aubin Units is correlated with the Sele Formation and upper part of Saint-Aubin Unit with the Balder Formation.