NADP-Malate Dehydrogenase Gene Evolution in Andropogoneae (Poaceae): Gene Duplication Followed by Sub-functionalization

• Background and Aims Plastid NADP-dependent malate dehydrogenase (MDH) catalyses the conversion of oxaloacetate to malate. In C4 plants, it is involved in photosynthetic carbon assimilation. In Poaceae, one NADP-MDH gene has been identified in rice (C3; Erhartoideae) and maize (C4; Panicoideae), whereas two tandemly repeated genes have been identified in Sorghum (C4; Panicoideae). In the present study, the molecular evolution of the NADP-MDH multigene family was investigated in order to analyse how the C4 isoform has evolved over a broader range of panicoid grasses. • Methods Polymerase chain reaction (PCR)-based cloning was used to isolate cDNAs encoding NADP-MDHs from 15 species of Panicoideae. A gene phylogeny was reconstructed based on cDNA sequences using distance and maximum parsimony methods. Episodic selection along some branches of the phylogenetic tree was tested by analysing non-synonymous and synonymous rate ratios.Transcription of NADP-MDH genes was compared in green leaves of five accessions of Saccharum, Sorghum and Vetiveria using a semi-quantitative PCR approach. • Key Results Phylogenetic analyses of these data support the existence of two NADP-MDH gene lineages (NMDH-I and NMDH-II) in several Andropogoneae (i.e. Saccharum, Sorghum and Vetiveria). Episodic positive selection was shown along the basal branch of the NMDH-II clade. Three amino acid modifications allow the two gene lineages to be distinguished, suggesting a positive selection at these sites. In green leaves, we showed that the transcript accumulation was higher for NMDH-I than for NMDH-II. • Conclusions It is hypothesized that the maintenance of both NADP-MDH genes in some Andropogoneae is due to a partition of the original functions across both copies. NMDH-I probably corresponds to the C4 isoform as previously suggested. Nevertheless, some C4 species (e.g. maize) only have one gene which should be selected for its high expression level in leaves. This study confirms that gene duplicates have been recruited for C4 photosynthesis but are not required in every cas

NADP-malate dehydrogenase gene evolution in Andropogoneae (Poaceae): gene duplication followed by sub-functionalization

• Background and Aims Plastid NADP-dependent malate dehydrogenase (MDH) catalyses the conversion of oxaloacetate to malate. In C(4) plants, it is involved in photosynthetic carbon assimilation. In Poaceae, one NADP-MDH gene has been identified in rice (C(3); Erhartoideae) and maize (C(4); Panicoideae), whereas two tandemly repeated genes have been identified in Sorghum (C(4); Panicoideae). In the present study, the molecular evolution of the NADP-MDH multigene family was investigated in order to analyse how the C(4) isoform has evolved over a broader range of panicoid grasses. • Methods Polymerase chain reaction (PCR)-based cloning was used to isolate cDNAs encoding NADP-MDHs from 15 species of Panicoideae. A gene phylogeny was reconstructed based on cDNA sequences using distance and maximum parsimony methods. Episodic selection along some branches of the phylogenetic tree was tested by analysing non-synonymous and synonymous rate ratios.Transcription of NADP-MDH genes was compared in green leaves of five accessions of Saccharum, Sorghum and Vetiveria using a semi-quantitative PCR approach. • Key Results Phylogenetic analyses of these data support the existence of two NADP-MDH gene lineages (NMDH-I and NMDH-II) in several Andropogoneae (i.e. Saccharum, Sorghum and Vetiveria). Episodic positive selection was shown along the basal branch of the NMDH-II clade. Three amino acid modifications allow the two gene lineages to be distinguished, suggesting a positive selection at these sites. In green leaves, we showed that the transcript accumulation was higher for NMDH-I than for NMDH-II. • Conclusions It is hypothesized that the maintenance of both NADP-MDH genes in some Andropogoneae is due to a partition of the original functions across both copies. NMDH-I probably corresponds to the C(4) isoform as previously suggested. Nevertheless, some C(4) species (e.g. maize) only have one gene which should be selected for its high expression level in leaves. This study confirms that gene duplicates have been recruited for C(4) photosynthesis but are not required in every case

Intervertebral disc characterisation by elastography: a preliminary study.

BiomecAM chai

Evaluation of a patient-specific finite-element model to simulate conservative treatment in adolescent idiopathic scoliosis

PublishedJournal ArticleAuthor's accepted manuscript.Study design: Retrospective validation study. Objectives: To propose a method to evaluate, from a clinical standpoint, the ability of a finite-element model (FEM) of the trunk to simulate orthotic correction of spinal deformity and to apply it to validate a previously described FEM. Summary of background data: Several FEMs of the scoliotic spine have been described in the literature. These models can prove useful in understanding the mechanisms of scoliosis progression and in optimizing its treatment, but their validation has often been lacking or incomplete. Methods: Three-dimensional (3D) geometries of 10 patients before and during conservative treatment were reconstructed from biplanar radiographs. The effect of bracing was simulated by modeling displacements induced by the brace pads. Simulated clinical indices (Cobb angle, T1-T12 and T4-T12 kyphosis, L1-L5 lordosis, apical vertebral rotation, torsion, rib hump) and vertebral orientations and positions were compared to those measured in the patients' 3D geometries. Results: Errors in clinical indices were of the same order of magnitude as the uncertainties due to 3D reconstruction; for instance, Cobb angle was simulated with a root mean square error of 5.7°, and rib hump error was 5.6°. Vertebral orientation was simulated with a root mean square error of 4.8° and vertebral position with an error of 2.5 mm. Conclusions: The methodology proposed here allowed in-depth evaluation of subject-specific simulations, confirming that FEMs of the trunk have the potential to accurately simulate brace action. These promising results provide a basis for ongoing 3D model development, toward the design of more efficient orthoses.ParisTech BiomecAM chair programProteorParisTechYves Cotrel Foundation

Non-invasive biomechanical characterization of intervertebral discs by shear wave ultrasound elastography: a feasibility study.

PublishedJournal ArticleThe final publication is available at Springer via http://dx.doi.org/10.1007/s00330-014-3382-8OBJECTIVES: Although magnetic resonance is widely spread to assess qualitatively disc morphology, a simple method to determine reliably intervertebral disc status is still lacking. Shear wave elastography is a novel technique that allows quantitative evaluation of soft-tissues' mechanical properties. The aim of this study was to assess preliminary the feasibility and reliability of mechanical characterization of cervical intervertebral discs by elastography and to provide first reference values for asymptomatic subjects. METHODS: Elastographic measurements were performed to determine shear wave speed (SWS) in C6-C7 or C7-T1 disc of 47 subjects; repeatability and inter-operator reproducibility were assessed. RESULTS: Global average shear wave speed (SWS) was 3.0 ± 0.4 m/s; measurement repeatability and inter-user reproducibility were 7 and 10%, respectively. SWS was correlated with both subject's age (p = 1.3 × 10(-5)) and body mass index (p = 0.008). CONCLUSIONS: Shear wave elastography in intervertebral discs proved reliable and allowed stratification of subjects according to age and BMI. Applications could be relevant, for instance, in early detection of disc degeneration or in follow-up after trauma; these results open the way to larger cohort studies to define the place of this technique in routine intervertebral disc assessment. KEY POINTS: A simple method to obtain objectively intervertebral disc status is still lacking. Shear wave elastography was applied in vivo to assess intervertebral discs. Elastography showed promising results in biomechanical disc evaluation. Elastography could be relevant in clinical routine for intervertebral disc assessment.ParisTech BiomecAM chair programParisTechYves Cotrel FoundationsSociété GénéraleProteorCove

Experience With Radical Resection in The Management of Proximal Bile Duct Cancer

Multiple surgical and nonsurgical approaches have been advocated for the treatment of proximal bile duct cancer. However, survival appears longest when a resection can be performed. Fifteen patients treated at a university center were managed with an aggressive surgical approach. Resection of the tumor was performed in 13 of 15 patients (87%). Of the patients undergoing resection, major hepatic resection was performed in 8 (62%), while excision of vessels with reconstruction was performed in 5 (38%). Eleven of the 13 resected patients (85%) were discharged from the hospital. Clinical symptoms of recurrent disease occurred between 3 and 36 months after surgery in 7 patients, 6 of whom have died. Three other patients are alive at 5, 21, and 36 months without clinical evidence of recurrence. There was no correlation between the completeness of resection and the duration of disease-free survival

In vivo cervical intervertebral disc characterisation by elastography.

PublishedJournal ArticleThis is an Accepted Manuscript of an article published by Taylor & Francis in Computer Methods in Biomechanics and Biomedical Engineering on 30/07/2014, available online: http://www.tandfonline.com/10.1080/10255842.2014.931515Not availableParisTech BiomecAM chair programProteorSociété GénéraleCoveaParisTechYves Cotrel Foundation

Intervertebral disc characterization by shear wave elastography: An in vitro preliminary study.

Published onlineJOURNAL ARTICLEAuthor's accepted (post-print) manuscriptThe final version of record is available at http://dx.doi.org/10.1177/0954411914540279Patient-specific numerical simulation of the spine is a useful tool both in clinic and research. While geometrical personalization of the spine is no more an issue, thanks to recent technological advances, non-invasive personalization of soft tissue's mechanical properties remains a challenge. Ultrasound elastography is a relatively recent measurement technique allowing the evaluation of soft tissue's elastic modulus through the measurement of shear wave speed. The aim of this study was to determine the feasibility of elastographic measurements in intervertebral disc. An in vitro approach was chosen to test the hypothesis that shear wave speed can be used to evaluate intervertebral disc mechanical properties and to assess measurement repeatability. In total, 11 oxtail intervertebral discs were tested in compression to determine their stiffness and apparent elastic modulus at rest and at 400 N. Elastographic measurements were performed in these two conditions and compared to these mechanical parameters. The protocol was repeated six times to determine elastographic measurement repeatability. Average shear wave speed over all samples was 5.3 ± 1.0 m/s, with a repeatability of 7% at rest and 4.6% at 400 N; stiffness and apparent elastic modulus were 266.3 ± 70.5 N/mm and 5.4 ± 1.1 MPa at rest, respectively, while at 400 N they were 781.0 ± 153.8 N/mm and 13.2 ± 2.4 MPa, respectively. Correlations were found between elastographic measurements and intervertebral disc mechanical properties; these preliminary results are promising for further in vivo application.ParisTech BiomecAM chair programProteorParisTechYves Cotrel Foundation

Filmic geographies: audio-visual, embodied-material

Although conventionally described as a ‘visual’ method, film-making is also increasingly used within research on embodiment. However, much remains to be said about the ability of filmic methods to enhance researchers’ capacity to think and research through the body. Drawing on my experience of making four research films, in this paper, I attempt to advance this agenda in three steps. First, I introduce anthropological work on the filming body to shed light on the technologically-mediated encounters that enfold around a camera and discuss how they might inform geographical thinking. Second, I describe the corporeally-mediated object ecologies that take shape within the filming setting and highlight how a camera might make objects ‘speak’. Finally, I discuss the affective dimension of screening research films to research participants and the contribution of such intense events to the articulation of collective matters of concerns. Through these three themes, I make the case for understanding knowledge production as located not merely in encounters with filmed audio-visual content, but also in the embodied-material encounters of bodies and objects around the filming and screening apparatus. I finally discuss the implications of these reflections for conceptualising the ‘body’ within embodied methods in social and cultural geography

Amélioration de la connaissance des causes d'incendie de forêt et mise en place d'une base de données géoréférencées

Dans le cadre du programme Forest Focus, le Cemagref d'Aix-en-Provence a réalisé un guide technique intitulé « Amélioration de la connaissance des causes de départ de feu de forêt » et l'agence MTDA a développé le prototype d'un module de saisie et de cartographie interactive des incendies de forêt. Cet article présente la méthode d'investigation de recherche des causes de départ de feu adaptée au contexte méditerranéen français ; un encadré concerne spécifiquement le module de saisie et de cartographie interactive permettant d'alimenter une base de données géoréférencées