Banana and plantain (Musa) genomics: Missing opportunity?

Poster presented at 2009 Annual Research Meeting of the Generation Challenge Programme. Bamako (Mali), 20-23 Sep 200

Genomic analysis of NAC transcription factors in banana (Musa acuminata) and definition of NAC orthologous groups for monocots and dicots

Identifying the molecular mechanisms underlying tolerance to abiotic stresses is important in crop breeding. A comprehensive understanding of the gene families associated with drought tolerance is therefore highly relevant. NAC transcription factors form a large plant-specific gene family involved in the regulation of tissue development and responses to biotic and abiotic stresses. The main goal of this study was to set up a framework of orthologous groups determined by an expert sequence comparison of NAC genes from both monocots and dicots. In order to clarify the orthologous relationships among NAC genes of different species, we performed an in-depth comparative study of four divergent taxa, in dicots and monocots, whose genomes have already been completely sequenced: Arabidopsis thaliana, Vitis vinifera, Musa acuminata and Oryza sativa. Due to independent evolution, NAC copy number is highly variable in these plant genomes. Based on an expert NAC sequence comparison, we propose forty orthologous groups of NAC sequences that were probably derived from an ancestor gene present in the most recent common ancestor of dicots and monocots. These orthologous groups provide a curated resource for large-scale protein sequence annotation of NAC transcription factors. The established orthology relationships also provide a useful reference for NAC function studies in newly sequenced genomes such as M. acuminata and other plant species

Analysis of the evolution of quality of life of patients with spinal cord injury throughout the clinical trial with spinal epidural electrical stimulation (EES) in combination with Robot-assisted neurorehabilitation (STIMO)

Main Idea: Analysis of the evolution of quality of life (QoL) of patients with spinal cord injury (SCI) throughout the clinical trial STImulation of Movement Overground (STIMO) with spinal epidural electrical stimulation (EES) in combination with Robot-assisted neurorehabilitation. ClinicalTrials.gov Identifier: NCT02936453. Introduction: As already cited in the STIMO protocol, SCI patients usually have a diminished QoL. This new therapy, by EES in combination with a robot-assisted neurorehabilitation, being tested for the very first time in humans will enhance the ability to stand and walk which has an impact on these patients’ day to day living as the increased independence in activities of daily living is a key point in the QoL index. The study only takes into consideration objective test values obtained in the walking laboratory, and excludes the global, subjective changes in day to day living. An evaluation pertaining specifically to patients with spinal cord injury, more precise and detailed than at STIMO study initiation, therefore seems to be a significant addition. Objective: To put in place a more detailed and effective system for the evaluation of QoL of STIMO trial patients. To enable a more in-depth analysis that goes further than the SF-36 questionnaire that is used in the original protocol. Method: A subjective, specific and internationally recognized questionnaire, the WHOQOL-Bref was added to the study at the following timepoints: pre-rehabilitation, intermediate, post-rehabilitation, 3-months extension, 6-month extension. Analysis of functional independence with the SCIM III at pre-rehab, intermediate, post-rehab and both extensions. Analysis of the evolution of HRQoL with the SF-36 at pre-implantations, pre-rehabilitation, post-rehabilitation and 6-months extension. Expected results: Concurring with the expected results of the STIMO trial, we hope to obtain an improvement in the patients’ QoL. We hypothesize that there will be a correlation between the objective values obtained in the walking lab of functional independence evaluated with the SCIM III questionnaire and of health-related QoL obtained through the SF-36 questionnaire, and the subjective values in the patients’ everyday environment evaluated with the WHOQOL-Bref survey. Added value: This analysis will add a more thorough and detailed dimension to the evaluation of the QoL, including more parameters than just the ability to move and walk during the experiment. It will take into consideration the psychological, social, environmental point of view of the patient. In the end, these values that influence the patients’ day to day living are significant for the end results of the trial

Strain versus stress in a model granular material: a Devil's staircase

The series of equilibrium states reached by disordered packings of rigid, frictionless discs in two dimensions, under gradually varying stress, are studied by numerical simulations. Statistical properties of trajectories in configuration space are found to be independent of specific assumptions ruling granular dynamics, and determined by geometry only. A monotonic increase in some macroscopic loading parameter causes a discrete sequence of rearrangements. For a biaxial compression, we show that, due to the statistical importance of such events of large magnitudes, the dependence of the resulting strain on stress direction is a Levy flight in the thermodynamic limit.Comment: REVTeX, 4 pages, 5 included PostScript figures. New version altered throughout text, very close to published pape

Quasistatic granular material rheology from particle simulations

We report on the quasistatic behaviour of model granular materials, as probed by DEM simulations of isotropic compression and triaxial compression tests, focussing on the macroscopic behaviour dependence on control parameters expressed in dimensionless forms that combine contact laws with test conditions, and on the influence of the initial state. A discussion of the microscopic origins of strain, which in some situations of small strains and stable contact networks are due to contact deflections, and in other cases results from the continuous breaking and repairing of networks under varying loads provides a useful classification of rheological regimes. Some guidelines for parameter choices in numerical simulations, and for some homogenization approaches, are inferre

Dynamic glass transition: bridging the gap between mode-coupling theory and the replica approach

We clarify the relation between the ergodicity breaking transition predicted by mode-coupling theory and the so-called dynamic transition predicted by the static replica approach. Following Franz and Parisi [Phys. Rev. Lett. 79, 2486 (1997)], we consider a system of particles in a metastable state characterized by non-trivial correlations with a quenched configuration. We show that the assumption that in a metastable state particle currents vanish leads to an expression for the replica off-diagonal direct correlation function in terms of a replica off-diagonal static four-point correlation function. A factorization approximation for this function results in an approximate closure for the replica off-diagonal direct correlation function. The replica off-diagonal Ornstein-Zernicke equation combined with this closure coincides with the equation for the non-ergodicity parameter derived using the mode-coupling theory.Comment: revised version; to be published in EP

A study of local government HIV/AIDS projects in South Africa

The primary goal of this study was to survey local government HIV/AIDS projects in South Africa.A total of 240 questionnaires were sent to local municipalities nationally between May and July 2002.A total of 44 municipalities returned their questionnaires, covering 53 projects. Most projects focused on prevention and awareness and the majority had awareness/prevention/information as part of their objectives as well as their activities. Home/community-based care was also prominent. It seems that in the future the focus of programme development will shift in this direction. Major constraints were a lack of funds, transport and trained personnel. Future emphasis must thus be put on these components. In addition government needs to put more resources into local government HIV/AIDS programmes since this tier will be the nodal point for national combatting of the HIV/AIDS epidemic. SAHARA-J (2004) 1(2): 99-106 Keywords: local government, HIV/AIDS, home/community-based care, Department of Social Development. RÉSUMÉ Le but principal de cette étude fut de sonder des projets du VIH/SIDA dans le gouvernement local en Afrique du Sud. Deux cents quarante questionnaires ont été envoyés aux municipalités locales du pays à partir du mois de mai jusqu'au mois de juillet 2002. Au total, 44 municipalités ont renvoyé leurs questionnaires. Ce derniers couvrent 53 projets. La plupart de projets se sont concentrés sur la prévention et la prise de conscience alors que la majorité de projets incluent la prise de conscience, la prévention et l'information parmi leurs objectif et leurs activités. Les soins à domicile ou dans la communauté étaient également saillants. Il semble que dans l'avenir le développement de programme se focalisera vers cette direction. Les contraintes majeures furent le manque de fonds, du transport et du personnel qualifié. De ce fait, dans l'avenir l'accent doit être mis sur ces facteurs. De plus, le gouvernement doit procurer davantage des ressources pour les programmes du VIH/SIDA au gouvernement local vu que cette étape sera le centre d'intérêt vis-à-vis le combat national contre l'épidémie du VIH/SIDA. SAHARA-J (2004) 1(2): 99-106 Mots clés: le gouvernement local, le VIH/SIDA, les soins à domicile ou dans la communauté, le Département de Développement Social

Scattering by a toroidal coil

In this paper we consider the Schr\"odinger operator in ${\mathbb R}^3$ with a long-range magnetic potential associated to a magnetic field supported inside a torus ${\mathbb{T}}$. Using the scheme of smooth perturbations we construct stationary modified wave operators and the corresponding scattering matrix $S(\lambda)$. We prove that the essential spectrum of $S(\lambda)$ is an interval of the unit circle depending only on the magnetic flux $\phi$ across the section of $\mathbb{T}$. Additionally we show that, in contrast to the Aharonov-Bohm potential in ${\mathbb{R}}^2$, the total scattering cross-section is always finite. We also conjecture that the case treated here is a typical example in dimension 3.Comment: LaTeX2e 17 pages, 1 figur