Making open data work for plant scientists

Despite the clear demand for open data sharing, its implementation within plant science is still limited. This is, at least in part, because open data-sharing raises several unanswered questions and challenges to current research practices. In this commentary, some of the challenges encountered by plant researchers at the bench when generating, interpreting, and attempting to disseminate their data have been highlighted. The difficulties involved in sharing sequencing, transcriptomics, proteomics, and metabolomics data are reviewed. The benefits and drawbacks of three data-sharing venues currently available to plant scientists are identified and assessed: (i) journal publication; (ii) university repositories; and (iii) community and project-specific databases. It is concluded that community and project-specific databases are the most useful to researchers interested in effective data sharing, since these databases are explicitly created to meet the researchers’ needs, support extensive curation, and embody a heightened awareness of what it takes to make data reuseable by others. Such bottom-up and community-driven approaches need to be valued by the research community, supported by publishers, and provided with long-term sustainable support by funding bodies and government. At the same time, these databases need to be linked to generic databases where possible, in order to be discoverable to the majority of researchers and thus promote effective and efficient data sharing. As we look forward to a future that embraces open access to data and publications, it is essential that data policies, data curation, data integration, data infrastructure, and data funding are linked together so as to foster data access and research productivity

Opportunities in plant synthetic biology

Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology

Combination of Pretreatment with White Rot Fungi and Modification of Primary and Secondary Cell Walls Improves Saccharification

Plant cell walls have protective and structural functions conferring resistance to degradation. The lignin and hemicellulose network surrounding the cellulose microfibrils is insoluble unless subjected to harsh treatments. As lignin, pectin and xylan are effective barriers to cellulose extraction and hydrolysis, reducing their presence in cell walls improves saccharification. Microorganisms that can depolymerise lignin are of extreme interest to the biofuel industry. White rot fungi can be effective in pretreatment of lignocellulosic biomass prior to saccharification. Here, we show the cumulative effects of pretreating biomass with two white rot fungi, Phanerochaete chrysosporium and Trametes cingulata, on tobacco lines with reduced lignin or xylan, caused by suppression of the CINNAMOYL-CoA REDUCTASE, CINNAMATE-4-HYDROXYLASE, TOBACCO PEROXIDASE 60 or UDP-GLUCURONATE DECARBOXYLASE and on Arabidopsis thaliana with reduced de-esterified homogalacturonan content, obtained by overexpressing a pectin methyl esterase inhibitor or constitutively expressing the Aspergillus nigerPOLYGALACTURONASE II gene. Tests were extended to fresh material from an Arabidopsis mutant for a cell wall peroxidase. We demonstrate that fungal pretreatment is a reliable method of improving cellulose accessibility in biofuel feedstocks, fresh material and cell wall residues from different plants. These results contribute to the understanding of the consequences of primary and secondary cell wall perturbations on lignocellulosic biomass accessibility to white rot fungi and on saccharification yield. A comparison of the effects of P. chrysosporium and T. cingulata on tobacco saccharification also highlights the limitation of current knowledge in this research field and the necessity to systematically test culture conditions to avoid generalisations. © 2014 The Author(s)