Coffee Somatic Embryogenesis: How Did Research, Experience Gained and Innovations Promote the Commercial Propagation of Elite Clones From the Two Cultivated Species?

Since the 1990s, somatic embryogenesis (SE) has enabled the propagation of selected varieties, Arabica F1 hybrid and Robusta clones, originating from the two cultivated coffee species, Coffea arabica and Coffea canephora, respectively. This paper shows how mostly empirical research has led to successful industrial transfers launched in the 2000s in Latin America, Africa, and Asia. Coffee SE can be considered as a model for other woody perennial crops for the following reasons: (i) a high biological efficiency has been demonstrated for propagated varieties at all developmental stages, and (ii) somaclonal variation is understood and mastered thanks to intensive research combining molecular markers and field observations. Coffee SE is also a useful model given the strong economic constraints that are specific to this species. In brief, SE faced four difficulties: (i) the high cost of SE derived plants compared to the cost of seedlings of conventional varieties, (ii) the logistic problems involved in reaching small-scale coffee growers, (iii) the need for certification, and (iv) the lack of solvency among small-scale producers. Nursery activities were professionalized by introducing varietal certification, quality control with regard to horticultural problems and somaclonal variation, and sanitary control for Xylella fastidiosa. In addition, different technology transfers were made to ensure worldwide dissemination of improved F1 Arabica hybrids and Robusta clones. Innovations have been decisive for successful scaling-up and reduction of production costs, such as the development of temporary immersion bioreactors for the mass production of pre-germinated embryos, their direct sowing on horticultural soil, and the propagation of rejuvenated SE plants by rooted mini-cuttings. Today, SE is a powerful tool that is widely used in coffee for biotechnological applications including propagation and genetic transformation. Basic research has recently started taking advantage of optimized SE protocols. Based on -omics methodologies, research aims to decipher the molecular events involved in the key developmental switches of coffee SE. In parallel, a high-throughput screening of active molecules on SE appears to be a promising tool to speed-up the optimization of SE protocols

Sustainability of bio-jetfuel in Malaysia

Aviation represents a small but growing share of global CO2 emissions (2-3%), and Southeast Asia is where this industry grows the fastest. The industry targets 50% reduction in net CO2 emission by 2050, and will need at least 2 million tonnes of biofuel by 2020. In Southeast Asia, competition between natural spaces (such as tropical forests) and biofuel development should be avoided. A complex interaction of political, sociological and natural factors influence the logistics, the infrastructures and the potential sustainability of biofuel. The contrasted growing conditions, and the geographically scattered nature of the potential resources for aviation industry, add to the complexity. Building visions and actions necessitates a range of assessments and researches, to insure sustainability of appropriate scenarios and pathways. In Malaysia, a consortium established a Center of Excellence on Biomass Valorisation for aviation, in order to study the biomass feedstocks and pathways which are necessary to meet the industry target, and to ensure sustainability

Kayrebt: An Activity Diagram Extraction and Visualization Toolset Designed for the Linux Codebase

International audienceWe present Extractor and Viewer, two tools from the Kayrebt toolset. The former is a plugin for the Gnu Compiler Collection (GCC) which builds pseudo-UML2 activity diagrams from C source code. It is specifically designed to handle the Linux kernel, a large and complex codebase. Use cases for this tool are numerous. The diagrams extracted from the C source code can be used to get a better insight of the control or data flow inside a program, or to evaluate the complexity of a function at a glance. Kayrebt::Viewer is a GUI designed for visualizing and navigating between the diagrams to explore source code

A single-step method for RNA isolation from tropical crops in the field

International audienceThe RNAzol RT reagent was used to provide pure RNA from human cells. We develop a protocol using RNAzol RT reagent to extract pure RNA from plants tissues and demonstrate that this RNA extraction method works not only at room temperature but also at elevated temperatures and provides the simplest and most effective single-step method to extract pure and undegraded RNA directly from tropical plants in the field. RNA extraction directly in a complex field environment opens up the way for studying gene-environment interactions at transcriptome level to decipher the complex regulatory network involved in multiple-stress responses

Verifying the Reliability of Operating System-Level Information Flow Control Systems in Linux

International audienceInformation Flow Control at Operating System (OS) level features interesting properties and have been an active topic of research for years. However, no implementation can work reliably if there does not exist a way to correctly and precisely track all information flows occurring in the system. The existing implementations for Linux are based on the Linux Security Modules (LSM) framework which implements hooks at speciic points in code where any security mechanism may interpose a security decision in the execution. However, previous works on the verification of LSM only addressed access control and no work has raised the question of the reliability of information flow control systems built on LSM. In this work, we present a compiler-assisted and reproducible static analysis on the Linux kernel to verify that the LSM hooks are correctly placed with respect to operations generating information flows so that LSM-based information flow monitors can properly track all information flows. Our results highlight flaws in LSM that we propose to solve, thus improving the suitability of this framework for the implementation of information flow monitors

Towards a Formal Semantics for System Calls in terms of Information Flow

ISBN: 978-1-61208-399-5ISSN: 2308-4243International audienceWe propose a new semantics for system calls, which focuses on the information flows they generate in a UNIX OS. We built a prototypal model of an OS and system calls using the concurrent transaction logic along with its interpreter. We have yet a few results and applications that show the usefulness of our semantics to model an OS from a kernel point of view. Once completed, we expect our semantics to enable us to extensively test security software implemented inside the kernel, among other use cases

Information Flow Tracking for Linux Handling Concurrent System Calls and Shared Memory

International audienceInformation flow control can be used at the Operating System level to enforce restrictions on the diffusion of security-sensitive data. In Linux, information flow trackers are often implemented as Linux Security Modules. They can fail to monitor some indirect flows when flows occur concurrently and affect the same containers of information. Furthermore, they are not able to monitor the flows due to file mappings in memory and shared memory between processes. We first present two attacks to evade state-of-the-art LSM-based trackers. We then describe an approach, formally proved with Coq to perform information flow tracking able to cope with concurrency and in-memory flows. We demonstrate its implementability and usefulness in Rfblare, a race condition-free version of the flow tracking done by KBlare

Suivi de flux d'information correct sous Linux

National audienceÀ l’échelle des systèmes d’exploitation, le contrôle de flux d’information porte sur la façon dont les données circulent entre des objets tels que les pro- cessus, les fichiers, les sockets réseau, etc. afin de prévenir les fuites et mo- difications illégales d’information. La maîtrise des flux d’information peut servir de multiples objectifs si l’on peut garantir la qualité des implémenta- tions des moniteurs de flux d’information. Nous avons étudié Laminar [3], KBlare [6] et Weir [2], des moniteurs de flux d’information dont l’implé- mentation repose sur l’interface des Linux Security Modules (LSM). Même si LSM a été conçu à l’origine pour le contrôle d’accès [5], ces implémenta- tions laissent à penser que cette interface offre, d’un point de vue pratique, un bon support pour l’implémentation d’un moniteur de flux d’information. Nous examinons donc ici la question suivante : Est-il possible d’implémenter de manière fiable le contrôle de flux d’information sous Linux en se basant sur LSM? Nous décrivons ici deux axes de réflexion, l’un ayant conduit à vérifier une condition nécessaire, l’autre à proposer une condition suffisante pour répondre à cette question. Nous décrivons aussi Rfblare, la principale contribution pratique issue de ces travaux. Rfblare est une nouvelle version du suivi de flux d’information de KBlare résistante aux conditions de concur- rence entre appels système

Are Genetic and Epigenetic Instabilities of Plant Embryogenic Cells a Fatality? The Experience of Coffee Somatic Embryogenesis

International audienceIn plants, undifferentiated or totally differentiated cells can be easily in vitro cultured to generate undifferentiated embryogenic cells that can regenerate complete plants. This is the most spectacular expression of totipotency. Embryogenic cells represent a key material in plant biotechnologies as they are used in many processes aimingat asexual reproduction by somatic embryogenesis (SE), genetic transformation, protoplast regeneration and cryopreservation. Nevertheless, tissue culture systems that involve the acquisition of competence for totipotency and extensive cell division remain risky with respect to genome and epigenome instabilities. Particularly, the use ofembryogenic cell suspensions has frequently been associated with an increased likelihood of genetic instability and somaclonal variation (SV) in the regenerated plants. SV is a major concern in all in vitro vegetative plant propagation systems because it leads to the loss of genetic fidelity. Since 20 years, embryogenic cell suspension based SE techniques have been applied to coffee for the large-scale dissemination of exceptional Arabica hybrids. Here, we present our production and research experience showing that SE is efficient and reliable for true-to-type propagation. Over 99% of coffee trees regenerated fully conform to the mother plant, both morphologically - they grow, flower and produce normally. Hence strong genetic and epigenetic changes in proliferating embryogenic cells are not a fatality. The results also demonstrated the importance of embryogenic culture age on SV and hence the non-random natureof this phenomenon. The genetic and epigenetic alterations are particularly limited during SE. The main change in most of phenotypic variants was aneuploidy showing that mitotic aberrations play a major role in SV in coffee. These results provide a proof of concept for the use of embryogenic cell suspensions with other plant species: a revolution in the world of plant micropropagation on an industrial scale