pISTil: a pipeline for yeast two-hybrid Interaction Sequence Tags identification and analysis

High-throughput screening of protein-protein interactions opens new systems biology perspectives for the comprehensive understanding of cell physiology in normal and pathological conditions. In this context, yeast two-hybrid system appears as a promising approach to efficiently reconstruct protein interaction networks at the proteome-wide scale. This protein interaction screening method generates a large amount of raw sequence data, i.e. the ISTs (Interaction Sequence Tags), which urgently need appropriate tools for their systematic and standardised analysis.Journal Articleinfo:eu-repo/semantics/publishe

Eikonal phase retrieval: Unleashing the fourth generation sources potential for enhanced propagation based tomography on biological samples

The evolution of synchrotrons towards higher brilliance beams has increased the possible sample-to-detector propagation distances for which the source confusion circle does not lead to geometrical blurring. This makes it possible to push near-field propagation driven phase contrast enhancement to the limit, revealing low contrast features which would otherwise remain hidden under an excessive noise-to-signal ratio. Until today this possibility was hindered, in most objects of scientific interest, by the simultaneous presence of strong phase gradient regions and low contrast features. The strong gradients, when enhanced with the now possible long propagation distances, induce such strong phase effects that the linearisation assumptions of current state-of-the-art single-distance phase retrieval filters are broken, and the resulting image quality is jeopardized. Our work provides an innovative algorithm which efficiently performs the phase retrieval task over the entire near-field range, producing images of exceptional quality for mixed objects

Mosaic Convergence of Rodent Dentitions

BACKGROUND:Understanding mechanisms responsible for changes in tooth morphology in the course of evolution is an area of investigation common to both paleontology and developmental biology. Detailed analyses of molar tooth crown shape have shown frequent homoplasia in mammalian evolution, which requires accurate investigation of the evolutionary pathways provided by the fossil record. The necessity of preservation of an effective occlusion has been hypothesized to functionally constrain crown morphological changes and to also facilitate convergent evolution. The Muroidea superfamily constitutes a relevant model for the study of molar crown diversification because it encompasses one third of the extant mammalian biodiversity. METHODOLOGY/PRINCIPAL FINDINGS:Combined microwear and 3D-topographic analyses performed on fossil and extant muroid molars allow for a first quantification of the relationships between changes in crown morphology and functionality of occlusion. Based on an abundant fossil record and on a well resolved phylogeny, our results show that the most derived functional condition associates longitudinal chewing and non interlocking of cusps. This condition has been reached at least 7 times within muroids via two main types of evolutionary pathways each respecting functional continuity. In the first type, the flattening of tooth crown which induces the removal of cusp interlocking occurs before the rotation of the chewing movement. In the second type however, flattening is subsequent to rotation of the chewing movement which can be associated with certain changes in cusp morphology. CONCLUSION/SIGNIFICANCE:The reverse orders of the changes involved in these different pathways reveal a mosaic evolution of mammalian dentition in which direction of chewing and crown shape seem to be partly decoupled. Either can change in respect to strong functional constraints affecting occlusion which thereby limit the number of the possible pathways. Because convergent pathways imply distinct ontogenetic trajectories, new Evo/Devo comparative studies on cusp morphogenesis are necessary

Topographic maps applied to comparative molar morphology: the case of murine and cricetine dental plans (Rodentia, Muroidea)

International audienceWe developed a new method to generate topographic maps of tooth crowns from X-ray synchrotron microtomographic data. Maps are drawn after cervix-plane orientation of tooth image stacks, without the need for a geographic information system. Classical topographic maps with contour lines are complemented by slope maps and angularity maps. Cartography allows precise comparisons of cusps morphologies, and quantification of the directions of cusp axis elongation and slope. Application of this method to muroid rodents with cricetine and murine dental patterns reveals clear-cut differences in cusps morphology that are indicative of the direction of the chewing movement, in agreement with wear facet analyses. Rodents with a murine dental pattern were derived from ancestors with a cricetine pattern, and their origin is associated with important changes in cusp morphology and organization. In order to understand such evolutionary change, our investigation is applied to a sample of extant and fossil muroid rodents that are characterized by either a murine dental plan or a cricetine one, or a dental pattern intermediate between those of cricetines and murines

Turonian-Coniacian silicified plants from the flints of Claix (Charente, western France)

National audienceIn western France, most of Cretaceous plant megaremains are preserved as impressions (external casts) in clay or compressions with or without cuticle in lignite. Remains are commonly highly flattened and only the gross morphology can be provided. When the cuticle is preserved, it shows casts of the most peripheral epidermal cells, allowing the description of microstructural details such as morphology and size of ordinary cells and stomatal apparatuses. However, compressions with cuticles never preserved histology. Silica-rich nodules have been recently collected in surface alterite and Palaeolithic or Neolithic habitats of Claix (Charente, western France). Some of the flints contain diverse plant megaremains. Specimens were examined under light microscopy (LM) and scanning electron microscopy (SEM). In order to detect fossil inclusions inside flints we made preliminary imaging testsusing high resolution and high energy X-ray synchrotron microtomography (PPC-SRμCT). The plant assemblage is late Turonianearlymost Coniacian in age and consists of abundant leafy axes of conifers (Brachyphyllum Brongn., Frenelopsis (Schenk) emend. J. Watson, and Geinitzia Endl.) and rare leaves of angiosperms and pinnae of ferns. Such plant diversity is for the first time observed is post-Cenomanian flints from this part of Europe. Bycontrast with most of lignitic plant beds of western France, the plants from the flints of Claix are exquisitely preserved in three dimensions, showing details of cuticle and inner tissues. It consists of silicified petrification/permineralization, the origin of the silicification being questionable

Will fault localization work for these failures? An automated approach to predict effectiveness of fault localization tools

Background: Firm attachments binding muscles to skeleton are crucial mechanical components of the vertebrate body. These attachments (entheses) are complex three-dimensional structures, containing distinctive arrangements of cells and fibre systems embedded in the bone, which can be modified during ontogeny. Until recently it has only been possible to obtain 2D surface and thin section images of entheses, leaving their 3D histology largely unstudied except by extrapolation from 2D data. Entheses are frequently preserved in fossil bones, but sectioning is inappropriate for rare or unique fossil material. Methodology/Principal Findings: Here we present the first non-destructive 3D investigation, by propagation phase contrast synchrotron microtomography (PPC-SR mu CT), of enthesis histology in extant and fossil vertebrates. We are able to identify entheses in the humerus of the salamander Desmognathus from the organization of bone-cell lacunae and extrinsic fibres. Statistical analysis of the lacunae differentiates types of attachments, and the orientation of the fibres, reflect the approximate alignment of the muscle. Similar histological structures, including ontogenetically related pattern changes, are perfectly preserved in two 380 million year old fossil vertebrates, the placoderm Compagopiscis croucheri and the sarcopterygian fish Eusthenopteron foordi. Conclusions/Significance: We are able to determine the position of entheses in fossil vertebrates, the approximate orientation of the attached muscles, and aspects of their ontogenetic histories, from PPC-SRmCT data. Sub-micron microtomography thus provides a powerful tool for studying the structure, development, evolution and palaeobiology of muscle attachments