University of Córdoba

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

The aim of this review was to survey all fungal pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate which fungal pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 495 votes from the international community, and resulted in the generation of a Top 10 fungal plant pathogen list for Molecular Plant Pathology. The Top 10 list includes, in rank order, (1) Magnaporthe oryzae; (2) Botrytis cinerea; (3) Puccinia spp.; (4) Fusarium graminearum; (5) Fusarium oxysporum; (6) Blumeria graminis; (7) Mycosphaerella graminicola; (8) Colletotrichum spp.; (9) Ustilago maydis; (10) Melampsora lini, with honourable mentions for fungi just missing out on the Top 10, including Phakopsora pachyrhizi and Rhizoctonia solani. This article presents a short resumé of each fungus in the Top 10 list and its importance, with the intent of initiating discussion and debate amongst the plant mycology community, as well as laying down a bench-mark. It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10.

Summary Here, we analysed a wide range of literature data on the leaf dry mass per unit area (LMA). In nature, LMA varies more than 100‐fold among species. Part of this variation ( c . 35%) can be ascribed to differences between functional groups, with evergreen species having the highest LMA, but most of the variation is within groups or biomes. When grown in the same controlled environment, leaf succulents and woody evergreen, perennial or slow‐growing species have inherently high LMA. Within most of the functional groups studied, high‐LMA species show higher leaf tissue densities. However, differences between evergreen and deciduous species result from larger volumes per area (thickness). Response curves constructed from experiments under controlled conditions showed that LMA varied strongly with light, temperature and submergence, moderately with CO 2 concentration and nutrient and water stress, and marginally under most other conditions. Functional groups differed in the plasticity of LMA to these gradients. The physiological regulation is still unclear, but the consequences of variation in LMA and the suite of traits interconnected with it are strong. This trait complex is an important factor determining the fitness of species in their environment and affects various ecosystem processes. Contents Summary 565 I. LMA in perspective 566 II. LMA in the field 567 III. Inherent differences 568 IV. Relation with anatomy and chemical composition 570 V. Environmental effects 572 VI. Differences in space and time 577 VII. Molecular regulation and physiology 579 VIII. Ecological consequences 580 IX. Conclusions and perspectives 582 Acknowledgements 582 References 582 Appendices 587

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Global-scale quantification of relationships between plant traits gives insight into the evolution of the world's vegetation, and is crucial for parameterizing vegetation-climate models. A database was compiled, comprising data for hundreds to thousands of species for the core 'leaf economics' traits leaf lifespan, leaf mass per area, photosynthetic capacity, dark respiration, and leaf nitrogen and phosphorus concentrations, as well as leaf potassium, photosynthetic N-use efficiency (PNUE), and leaf N : P ratio. While mean trait values differed between plant functional types, the range found within groups was often larger than differences among them. Future vegetation-climate models could incorporate this knowledge. The core leaf traits were intercorrelated, both globally and within plant functional types, forming a 'leaf economics spectrum'. While these relationships are very general, they are not universal, as significant heterogeneity exists between relationships fitted to individual sites. Much, but not all, heterogeneity can be explained by variation in sample size alone. PNUE can also be considered as part of this trait spectrum, whereas leaf K and N : P ratios are only loosely related.

This study—based on systematic testing of 30 different wheat crop models against field experiments—shows that many wheat models simulate yields well, but with reduced accuracy at higher temperatures. Extrapolation of the model ensemble response indicates that global wheat production will fall by 6% for each 1 °C increase in temperature. Crop models are essential tools for assessing the threat of climate change to local and global food production1. Present models used to predict wheat grain yield are highly uncertain when simulating how crops respond to temperature2. Here we systematically tested 30 different wheat crop models of the Agricultural Model Intercomparison and Improvement Project against field experiments in which growing season mean temperatures ranged from 15 °C to 32 °C, including experiments with artificial heating. Many models simulated yields well, but were less accurate at higher temperatures. The model ensemble median was consistently more accurate in simulating the crop temperature response than any single model, regardless of the input information used. Extrapolating the model ensemble temperature response indicates that warming is already slowing yield gains at a majority of wheat-growing locations. Global wheat production is estimated to fall by 6% for each °C of further temperature increase and become more variable over space and time.

Recent advances in supramolecular coordination chemistry allow access to transition-metal complexes of grid-type architecture comprising two-dimensional arrays of metal ions connecting a set of organic ligands in a perpendicular arrangement to generate a multiple wiring network. General design principles for these structures involve the thermodynamically driven synthesis of complex discrete objects from numerous molecular components in a single overall operation. Such supramolecular metal ion arrays combine the properties of their constituent metal ions and ligands, showing unique optical, electrochemical, and magnetic behavior. These features present potential relevance for nanotechnology, particularly in the area of supramolecular devices for information storage and processing. Thus, a dense organization of addressable units is represented by an extended "grid-of-grids" arrangement, formed by interaction of grid-type arrays with solid surfaces.

Educational data mining (EDM) is an emerging interdisciplinary research area that deals with the development of methods to explore data originating in an educational context. EDM uses computational approaches to analyze educational data in order to study educational questions. This paper surveys the most relevant studies carried out in this field to date. First, it introduces EDM and describes the different groups of user, types of educational environments, and the data they provide. It then goes on to list the most typical/common tasks in the educational environment that have been resolved through data-mining techniques, and finally, some of the most promising future lines of research are discussed.

At present and more so in the future, irrigated agriculture will take place under water scarcity. Insufficient water supply for irrigation will be the norm rather than the exception, and irrigation management will shift from emphasizing production per unit area towards maximizing the production per unit of water consumed, the water productivity. To cope with scarce supplies, deficit irrigation, defined as the application of water below full crop-water requirements (evapotranspiration), is an important tool to achieve the goal of reducing irrigation water use. While deficit irrigation is widely practised over millions of hectares for a number of reasons - from inadequate network design to excessive irrigation expansion relative to catchment supplies - it has not received sufficient attention in research. Its use in reducing water consumption for biomass production, and for irrigation of annual and perennial crops is reviewed here. There is potential for improving water productivity in many field crops and there is sufficient information for defining the best deficit irrigation strategy for many situations. One conclusion is that the level of irrigation supply under deficit irrigation should be relatively high in most cases, one that permits achieving 60-100% of full evapotranspiration. Several cases on the successful use of regulated deficit irrigation (RDI) in fruit trees and vines are reviewed, showing that RDI not only increases water productivity, but also farmers' profits. Research linking the physiological basis of these responses to the design of RDI strategies is likely to have a significant impact in increasing its adoption in water-limited areas.

Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.

This article introduces the FAO crop model AquaCrop. It simulates attainable yields of major herbaceous crops as a function of water consumption under rainfed, supplemental, deficit, and full irrigation conditions. The growth engine of AquaCrop is water‐driven , in that transpiration is calculated first and translated into biomass using a conservative, crop‐specific parameter: the biomass water productivity, normalized for atmospheric evaporative demand and air CO 2 concentration. The normalization is to make AquaCrop applicable to diverse locations and seasons. Simulations are performed on thermal time, but can be on calendar time, in daily time‐steps. The model uses canopy ground cover instead of leaf area index (LAI) as the basis to calculate transpiration and to separate out soil evaporation from transpiration. Crop yield is calculated as the product of biomass and harvest index (HI). At the start of yield formation period, HI increases linearly with time after a lag phase, until near physiological maturity. Other than for the yield, there is no biomass partitioning into the various organs. Crop responses to water deficits are simulated with four modifiers that are functions of fractional available soil water modulated by evaporative demand, based on the differential sensitivity to water stress of four key plant processes: canopy expansion, stomatal control of transpiration, canopy senescence, and HI. The HI can be modified negatively or positively, depending on stress level, timing, and canopy duration. AquaCrop uses a relatively small number of parameters (explicit and mostly intuitive) and attempts to balance simplicity, accuracy, and robustness. The model is aimed mainly at practitioner‐type end‐users such as those working for extension services, consulting engineers, governmental agencies, nongovernmental organizations, and various kinds of farmers associations. It is also designed to fit the need of economists and policy specialists who use simple models for planning and scenario analysis.

A broad overview on magnetically recoverable nanocatalysts is presented and the use of magnetic nanomaterials as catalysts is discussed. Magnetic materials are used as organocatalysts and their applications range to challenging reactions, such as hydroformylation and olefin metathesis. Magnetic nanomaterials are also being used in environmental applications, such as for photo- and biocatalysis and for the adsorption and removal of pollutants from air and water. These materials show great promise as enantioselective catalysts, which are used extensively for the synthesis of medicines, drugs, and other bioactive molecules. By functionalizing these materials using chiral ligands, a series of chiral nanocatalysts can be designed, offering great potential to reuse these otherwise expensive catalyst systems. Characterization of magnetic catalysts is often a challenging task, and NMR characterization of these catalysts is difficult because the magnetic nature of the materials interferes with the magnetic field of the spectrometer.

Two critical limitations for using current satellite sensors in real-time crop management are the lack of imagery with optimum spatial and spectral resolutions and an unfavorable revisit time for most crop stress-detection applications. Alternatives based on manned airborne platforms are lacking due to their high operational costs. A fundamental requirement for providing <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">useful</i> remote sensing products in agriculture is the capacity to combine high spatial resolution and quick turnaround times. Remote sensing sensors placed on unmanned aerial vehicles (UAVs) could fill this gap, providing low-cost approaches to meet the critical requirements of spatial, spectral, and temporal resolutions. This paper demonstrates the ability to generate quantitative remote sensing products by means of a helicopter-based UAV equipped with inexpensive thermal and narrowband multispectral imaging sensors. During summer of 2007, the platform was flown over agricultural fields, obtaining thermal imagery in the 7.5-13-mum region (40-cm resolution) and narrowband multispectral imagery in the 400-800-nm spectral region (20-cm resolution). Surface reflectance and temperature imagery were obtained, after atmospheric corrections with MODTRAN. Biophysical parameters were estimated using vegetation indices, namely, normalized difference vegetation index, transformed chlorophyll absorption in reflectance index/optimized soil-adjusted vegetation index, and photochemical reflectance index (PRI), coupled with SAILH and FLIGHT models. As a result, the image products of leaf area index, chlorophyll content ( <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">C</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ab</sub> ), and water stress detection from PRI index and canopy temperature were produced and successfully validated. This paper demonstrates that results obtained with a low-cost UAV system for agricultural applications yielded comparable estimations, if not better, than those obtained by traditional manned airborne sensors.

Chickpea (Cicer arietinum) is the second most widely grown legume crop after soybean, accounting for a substantial proportion of human dietary nitrogen intake and playing a crucial role in food security in developing countries. We report the ∼738-Mb draft whole genome shotgun sequence of CDC Frontier, a kabuli chickpea variety, which contains an estimated 28,269 genes. Resequencing and analysis of 90 cultivated and wild genotypes from ten countries identifies targets of both breeding-associated genetic sweeps and breeding-associated balancing selection. Candidate genes for disease resistance and agronomic traits are highlighted, including traits that distinguish the two main market classes of cultivated chickpea--desi and kabuli. These data comprise a resource for chickpea improvement through molecular breeding and provide insights into both genome diversity and domestication.

We constructed highly oriented and ordered macropores within metal-organic framework (MOF) single crystals, opening up the area of three-dimensional-ordered macro-microporous materials (that is, materials containing both macro- and micropores) in single-crystalline form. Our methodology relies on the strong shaping effects of a polystyrene nanosphere monolith template and a double-solvent-induced heterogeneous nucleation approach. This process synergistically enabled the in situ growth of MOFs within ordered voids, rendering a single crystal with oriented and ordered macro-microporous structure. The improved mass diffusion properties of such hierarchical frameworks, together with their robust single-crystalline nature, endow them with superior catalytic activity and recyclability for bulky-molecule reactions, as compared with conventional, polycrystalline hollow, and disordered macroporous ZIF-8.

Soil bacteria and fungi play key roles in the functioning of terrestrial ecosystems, yet our understanding of their responses to climate change lags significantly behind that of other organisms. This gap in our understanding is particularly true for drylands, which occupy ∼41% of Earth´s surface, because no global, systematic assessments of the joint diversity of soil bacteria and fungi have been conducted in these environments to date. Here we present results from a study conducted across 80 dryland sites from all continents, except Antarctica, to assess how changes in aridity affect the composition, abundance, and diversity of soil bacteria and fungi. The diversity and abundance of soil bacteria and fungi was reduced as aridity increased. These results were largely driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. Aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and fungal communities were dominated by Ascomycota. Our results fill a critical gap in our understanding of soil microbial communities in terrestrial ecosystems. They suggest that changes in aridity, such as those predicted by climate-change models, may reduce microbial abundance and diversity, a response that will likely impact the provision of key ecosystem services by global drylands.

This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.

Increasing demand for fuels and chemicals, driven by factors including over-population, the threat of global warming and the scarcity of fossil resources, strains our resource system and necessitates the development of sustainable and innovative strategies for the chemical industry. Our society is currently experiencing constraints imposed by our resource system, which drives industry to increase its overall efficiency by improving existing processes or finding new uses for waste. Food supply chain waste emerged as a resource with a significant potential to be employed as a raw material for the production of fuels and chemicals given the abundant volumes globally generated, its contained diversity of functionalised chemical components and the opportunity to be utilised for higher value applications. The present manuscript is aimed to provide a general overview of the current and most innovative uses of food supply chain waste, providing a range of worldwide case-studies from around the globe. These studies will focus on examples illustrating the use of citrus peel, waste cooking oil and cashew shell nut liquid in countries such as China, the UK, Tanzania, Spain, Greece or Morocco. This work emphasises 2nd generation food waste valorisation and re-use strategies for the production of higher value and marketable products rather than conventional food waste processing (incineration for energy recovery, feed or composting) while highlighting issues linked to the use of food waste as a sustainable raw material. The influence of food regulations on food supply chain waste valorisation will also be addressed as well as our society's behavior towards food supply chain waste. “There was no ways of dealing with it that have not been known for thousands of years. These ways are essentially four: dumping it, burning it, converting it into something that can be used again, and minimizing the volume of material goods – future garbage – that is produced in the first place.” William Rathje on waste (1945–2012) – Director of the Tucson Garbage project.

Agricultural soil erosion is thought to perturb the global carbon cycle, but estimates of its effect range from a source of 1 petagram per year(-1) to a sink of the same magnitude. By using caesium-137 and carbon inventory measurements from a large-scale survey, we found consistent evidence for an erosion-induced sink of atmospheric carbon equivalent to approximately 26% of the carbon transported by erosion. Based on this relationship, we estimated a global carbon sink of 0.12 (range 0.06 to 0.27) petagrams of carbon per year(-1) resulting from erosion in the world's agricultural landscapes. Our analysis directly challenges the view that agricultural erosion represents an important source or sink for atmospheric CO2.

Both in practice and policy a new model of rural development is emerging. This paper reflects the discussions in the impact research programme and suggests that at the level of associated theory also a fundamental shift is taking place. The modernization paradigm that once dominated policy, practice and theory is being replaced by a new rural development paradigm. Rural development is analyzed as a multi‐level, multi‐actor and multi‐facetted process rooted in historical traditions that represents at all levels a fundamental rupture with the modernization project. The range of new quality products, services and forms of cost reduction that together comprise rural development are understood as a response by farm families to both the eroding economic base of their enterprises and to the new needs and expectations European society has of the rural areas. Rural development therefore is largely an autonomous, self‐driven process and in its further unfolding agriculture will continue to play a key role, although it is a role that may well change. This article provides an introduction to the nine papers of this ‘special issue’ and the many reconfiguration processes embodied in rural development that they address.in rural development