Potential core species and satellite species in the bacterial community within the rabbit caecum

A bacteria library was constructed from the caecum of a rabbit maintained under standard conditions. The complete gene 16S rRNA gene was sequenced. The 228 clones obtained were distributed in 70 operational taxonomic units (OTUs). The large majority of the OTUs were composed of one or two clones and seven OTUs contained half of the sequences. Fourteen sequences had high similarity to the sequence already registered in databases (threshold of 97%). Only one of these sequences has been identified as Variovorax sp. (99% identity). Units were distributed mainly (94%) in the Firmicutes phylum. Three sequences were related to Bacteroidetes. Nine clusters were defined in the phylogenic tree. A great diversity of caecal bacteria of the rabbit was shown. Half of the sequences generated in this library were distributed in the phylogenetic tree near the sequences characterized previously in rabbit caecum (potential core species), and the other half of the sequences were well separated (satellite species)

Distinct spatiotemporal patterns and PARP dependence of XRCC1 recruitment to single-strand break and base excision repair

Single-strand break repair (SSBR) and base excision repair (BER) of modified bases and abasic sites share several players. Among them is XRCC1, an essential scaffold protein with no enzymatic activity, required for the coordination of both pathways. XRCC1 is recruited to SSBR by PARP-1, responsible for the initial recognition of the break. The recruitment of XRCC1 to BER is still poorly understood. Here we show by using both local and global induction of oxidative DNA base damage that XRCC1 participation in BER complexes can be distinguished from that in SSBR by several criteria. We show first that XRCC1 recruitment to BER is independent of PARP. Second, unlike SSBR complexes that are assembled within minutes after global damage induction, XRCC1 is detected later in BER patches, with kinetics consistent with the repair of oxidized bases. Third, while XRCC1-containing foci associated with SSBR are formed both in eu- and heterochromatin domains, BER complexes are assembled in patches that are essentially excluded from heterochromatin and where the oxidized bases are detected

Two-dimensional gel electrophoresis in proteomics: past, present and future

Two-dimensional gel electrophoresis has been instrumental in the birth and developments of proteomics, although it is no longer the exclusive separation tool used in the field of proteomics. In this review, a historical perspective is made, starting from the days where two-dimensional gels were used and the word proteomics did not even exist. The events that have led to the birth of proteomics are also recalled, ending with a description of the now well-known limitations of two-dimensional gels in proteomics. However, the often-underestimated advantages of two-dimensional gels are also underlined, leading to a description of how and when to use two-dimensional gels for the best in a proteomics approach. Taking support of these advantages (robustness, resolution, and ability to separate entire, intact proteins), possible future applications of this technique in proteomics are also mentioned

Multi-scale modeling of the viscoelastic behavior of 3D woven composites

International audienceA method is presented to predict numerically the homogenized viscoelastic behavior of 3D woven composites using only its constituents’ behavior. It is based on elastic homogenizations applied to the Laplace-Carson transform of the time-dependent viscoelastic behavior of the constituents. Two scale changes are necessary: from micro- to meso-scale to obtain the homogenized behavior of the consolidated yarns, and from meso- to macro-scale. The temperature and cure dependent viscoelastic behavior of the matrix is identified from experimental data, using the time-temperature superposition principle with the cure dependent glass transition temperature as reference temperature. The meso-scale representative unit cell of the composite is extracted from X-ray microtomography images. The homogenized viscoelastic behavior is used to calculate the evolution of the apparent moduli of the composite with temperature between -50 °C and 200 °C. The results are in good agreement with experimental data over the temperature range where the matrix behavior was properly identified

Preparation and Deposition of Plant Roots for AFM Nanomechanical Measurements

International audienceIn general, cell growth is a mechanical process that balances internal and externalstresses allowing or limiting expansion. Plant cells are often compared to“hydraulicmachines”due to the similar concept of balanced counterforces between the primarywall stresses and the turgor pressure. Knowledge of the mechanics of plant root cellsis essential to understand how plant wall works and, therefore, how plants grow. Onemethod for qualitative and quantitative analysis of mechanical properties is atomicforce microscopy (AFM) that measures mechanical properties of living cells or tissuesunder conditions close to relevant physiological environments (Arnould et al., 2017,Kozlova et al., 2019, Milani et al., 2011, 2014, Peaucelle et al., 2012, 2011, Torode et al.,2018, Yakubov et al., 2016, Zdunek and Kurenda, 2013, Zhao et al., 2005). In our recentstudy, AFM has been used to investigate properties of root epidermal cells (Balzergueet al., 2017), which are the cells that form the outermost layer of the root. These epi-dermal cells were studied in situ on living seedlings and were therefore still influ-enced by the inherent multicellular properties of the root, which is an improvementover studies conducted on isolated living cells.This chapter explains and illustrates the different steps required to prepare anddeposit the seedling, and in particular the root tip, of the plant on a glass slideready for nanomechanical measurements by AF

Chaine de calcul multi-physique et multi-échelle pour la prévision des contraintes et déformée résiduelles de polymérisation de structures composites

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Chaine de calcul multi-physique et multi-échelle pour la prévision des contraintes et déformée résiduelles de polymérisation de structures composites

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Stiffening of the Plant Root Cell Wall Induced by a Metallic Stress

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