Farmer knowledge identifies a competitive bean ideotype for maize–bean intercrop systems in Rwanda

Background: Plant genotypes are rarely developed for mixed cropping systems despite the potential of these systems to provide multiple ecosystem services. One of the most ubiquitously grown mixed cropping systems is a common bean (Phaseolus vulgaris L.) and maize (Zea mays L.) intercrop, but there is little consensus among researchers, and few known studies document farmer knowledge, about superior bean genotypes specifically for this intercrop system. Participatory plant breeding (PPB) is a well-accepted method of selecting varieties with farmers and could be a useful tool for identifying genotypes for intercrops. We used sole crop and intercrop PPB on-farm trials (n = 13) and interviews (n = 59) to document farmer knowledge about climbing bean genotypes and adaptation for intercrops in Rwanda, where smallholder farmers have traditionally grown beans and maize for generations. Results: Qualitative analysis demonstrated that farmers considered distinct attributes for different cropping systems. In intercrops, farmer evaluation prioritized five factors: universal traits and trait-based competitive ability, intrinsic competitive ability, environmental adaptation, and management. Farmers consider intrinsic competitive ability crucial, whereas most other studies have neglected this attribute in intercrop breeding strategies. Furthermore, farmers identified specific attributes that constitute an intercrop bean ideotype: adaptation, restricted height, columnar plant structure, even distribution of pods, fewer leaves, and earlier maturity. Farmers also had specific techniques for testing cropping system and environment interactions. Conclusions: PPB on-farm trial evaluations and interviews with farmers allowed us to combine traditional agroecological knowledge with plant breeding research to generate new knowledge that contributes to our understanding of intercrop breeding and bean traits for intercrops. Farmers demonstrated sophisticated understanding of methods to identify genotype adaptation, competitive ability, and specific traits that together create a bean ideotype for maize–bean cropping systems. Empowering farmers through on-farm testing of diverse genotypes, and even populations, could be a practical solution to expensive genotype by environment trials and improve the identification of highly adaptive and productive genotypes for diverse and resilient cropping systems

Perennial grain crops in the West Soudanian Savanna of Mali: perspectives from agroecology and gendered spaces

Perennial grain crops may play an important role in environmentally sound and socially just food systems for Africa. We study the future possibility of integrating perennial grains into Malian farming systems from the perspective of agroecology, and more specifically using a gendered space approach. We interviewed 72 farmers across the sorghum-growing region of Mali. We found that perennial grains offer a vision for transforming human relations with nature that mirrors the resource sharing of customary land tenure, including patterns of extensive and intensive land use in time and space. Women interviewees identified a broad set of potential advantages and challenges to perennial grain production. Advantages include reduced labour, saving seed, and improving food security. Women farmers were concerned about livestock, water access, and resource limitations. We argue that perennial grains may increase access to land and natural resources for women farmers. Perennial grains may improve soil quality, reduce labour early in the rainy season, and provision more resources from fallow lands. Pastoralists stand to benefit from improved pastures in the dry season. We conclude that investments are needed to develop viable crop types in consideration of the complexity of West African farming systems and the local needs of women farmers and pastoralists

A critical review of the impacts of cover crops on nitrogen leaching, net greenhouse gas balance and crop productivity

This work contributes to the UK-China Virtual Joint Centre N-Circle (grant number BB/N013484/1), SuperG (funded under EU Horizon 2020 programme) and ADVENT (grant number NE/M019691/1). DRC was supported by the UK-China Virtual joint Centre for Agricultural Nitrogen (CINAg, BB/N013468/1) and the UK-Brazil Virtual Joint Centre to deliver enhanced N-use efficiency via an integrated soil-plant systems approach (NUCLEUS), which are jointly supported by Newton fund via UK BBSRC and NERC. Jaak Truu received financing from Estonian Research Council (grant PRG548).Peer reviewedPublisher PD

Robot Guided ‘Pen Skill’ Training in Children with Motor Difficulties

Motor deficits are linked to a range of negative physical, social and academic consequences. Haptic robotic interventions, based on the principles of sensorimotor learning, have been shown previously to help children with motor problems learn new movements. We therefore examined whether the training benefits of a robotic system would generalise to a standardised test of ‘pen-skills’, assessed using objective kinematic measures [via the Clinical Kinematic Assessment Tool, CKAT]. A counterbalanced, cross-over design was used in a group of 51 children (37 male, aged 5-11 years) with manual control difficulties. Improved performance on a novel task using the robotic device could be attributed to the intervention but there was no evidence of generalisation to any of the CKAT tasks. The robotic system appears to have the potential to support motor learning, with the technology affording numerous advantages. However, the training regime may need to target particular manual skills (e.g. letter formation) in order to obtain clinically significant improvements in specific skills such as handwriting

CellCognition : time-resolved phenotype annotation in high-throughput live cell imaging

Author Posting. © The Authors, 2010. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Methods 7 (2010): 747-754, doi:10.1038/nmeth.1486.Fluorescence time-lapse imaging has become a powerful tool to investigate complex dynamic processes such as cell division or intracellular trafficking. Automated microscopes generate time-resolved imaging data at high throughput, yet tools for quantification of large-scale movie data are largely missing. Here, we present CellCognition, a computational framework to annotate complex cellular dynamics. We developed a machine learning method that combines state-of-the-art classification with hidden Markov modeling for annotation of the progression through morphologically distinct biological states. The incorporation of time information into the annotation scheme was essential to suppress classification noise at state transitions, and confusion between different functional states with similar morphology. We demonstrate generic applicability in a set of different assays and perturbation conditions, including a candidate-based RNAi screen for mitotic exit regulators in human cells. CellCognition is published as open source software, enabling live imaging-based screening with assays that directly score cellular dynamics.Work in the Gerlich laboratory is supported by Swiss National Science Foundation (SNF) research grant 3100A0-114120, SNF ProDoc grant PDFMP3_124904, a European Young Investigator (EURYI) award of the European Science Foundation, an EMBO YIP fellowship, and a MBL Summer Research Fellowship to D.W.G., an ETH TH grant, a grant by the UBS foundation, a Roche Ph.D. fellowship to M.H.A.S, and a Mueller fellowship of the Molecular Life Sciences Ph.D. program Zurich to M.H. M.H. and M.H.A.S are fellows of the Zurich Ph.D. Program in Molecular Life Sciences. B.F. was supported by European Commission’s seventh framework program project Cancer Pathways. Work in the Ellenberg laboratory is supported by a European Commission grant within the Mitocheck consortium (LSHG-CT-2004-503464). Work in the Peter laboratory is supported by the ETHZ, Oncosuisse, SystemsX.ch (LiverX) and the SNF

Near-field Electrical Detection of Optical Plasmons and Single Plasmon Sources

Photonic circuits can be much faster than their electronic counterparts, but they are difficult to miniaturize below the optical wavelength scale. Nanoscale photonic circuits based on surface plasmon polaritons (SPs) are a promising solution to this problem because they can localize light below the diffraction limit. However, there is a general tradeoff between the localization of an SP and the efficiency with which it can be detected with conventional far-field optics. Here we describe a new all-electrical SP detection technique based on the near-field coupling between guided plasmons and a nanowire field-effect transistor. We use the technique to electrically detect the plasmon emission from an individual colloidal quantum dot coupled to an SP waveguide. Our detectors are both nanoscale and highly efficient (0.1 electrons/plasmon), and a plasmonic gating effect can be used to amplify the signal even higher (up to 50 electrons/plasmon). These results enable new on-chip optical sensing applications and are a key step towards "dark" optoplasmonic nanocircuits in which SPs can be generated, manipulated, and detected without involving far-field radiation.Comment: manuscript followed by supplementary informatio

CD47 plays a critical role in T-cell recruitment by regulation of LFA-1 and VLA-4 integrin adhesive functions

CD47 plays an important but incompletely understood role in the innate and adaptive immune responses. CD47, also called integrin-associated protein, has been demonstrated to associate in cis with β1 and β3 integrins. Here we test the hypothesis that CD47 regulates adhesive functions of T-cell α4β1 (VLA-4) and αLβ2 (LFA-1) in in vivo and in vitro models of inflammation. Intravital microscopy studies reveal that CD47(−/−) Th1 cells exhibit reduced interactions with wild-type (WT) inflamed cremaster muscle microvessels. Similarly, murine CD47(−/−) Th1 cells, as compared with WT, showed defects in adhesion and transmigration across tumor necrosis factor-α (TNF-α)–activated murine endothelium and in adhesion to immobilized intercellular adhesion molecule 1 (ICAM-1) and vascular cell adhesion protein 1 (VCAM-1) under flow conditions. Human Jurkat T-cells lacking CD47 also showed reduced adhesion to TNF-α–activated endothelium and ICAM-1 and VCAM-1. In cis interactions between Jurkat T-cell β2 integrins and CD47 were detected by fluorescence lifetime imaging microscopy. Unexpectedly, Jurkat CD47 null cells exhibited a striking defect in β1 and β2 integrin activation in response to Mn(2+) or Mg(2+)/ethylene glycol tetraacetic acid treatment. Our results demonstrate that CD47 associates with β2 integrins and is necessary to induce high-affinity conformations of LFA-1 and VLA-4 that recognize their endothelial cell ligands and support leukocyte adhesion and transendothelial migration

Development of Cysteine-Free Fluorescent Proteins for the Oxidative Environment

Molecular imaging employing fluorescent proteins has been widely used to highlight specific reactions or processes in various fields of the life sciences. Despite extensive improvements of the fluorescent tag, this technology is still limited in the study of molecular events in the extracellular milieu. This is partly due to the presence of cysteine in the fluorescent proteins. These proteins almost cotranslationally form disulfide bonded oligomers when expressed in the endoplasmic reticulum (ER). Although single molecule photobleaching analysis showed that these oligomers were not fluorescent, the fluorescent monomer form often showed aberrant behavior in folding and motion, particularly when fused to cysteine-containing cargo. Therefore we investigated whether it was possible to eliminate the cysteine without losing the brightness. By site-saturated mutagenesis, we found that the cysteine residues in fluorescent proteins could be replaced with specific alternatives while still retaining their brightness. cf(cysteine-free)SGFP2 showed significantly reduced restriction of free diffusion in the ER and marked improvement of maturation when fused to the prion protein. We further applied this approach to TagRFP family proteins and found a set of mutations that obtains the same level of brightness as the cysteine-containing proteins. The approach used in this study to generate new cysteine-free fluorescent tags should expand the application of molecular imaging to the extracellular milieu and facilitate its usage in medicine and biotechnology

Functional KV10.1 Channels Localize to the Inner Nuclear Membrane

Ectopically expressed human KV10.1 channels are relevant players in tumor biology. However, their function as ion channels at the plasma membrane does not totally explain their crucial role in tumors. Both in native and heterologous systems, it has been observed that a majority of KV10.1 channels remain at intracellular locations. In this study we investigated the localization and possible roles of perinuclear KV10.1. We show that KV10.1 is expressed at the inner nuclear membrane in both human and rat models; it co-purifies with established inner nuclear membrane markers, shows resistance to detergent extraction and restricted mobility, all of them typical features of proteins at the inner nuclear membrane. KV10.1 channels at the inner nuclear membrane are not all transported directly from the ER but rather have been exposed to the extracellular milieu. Patch clamp experiments on nuclei devoid of external nuclear membrane reveal the existence of channel activity compatible with KV10.1. We hypothesize that KV10.1 channels at the nuclear envelope might participate in the homeostasis of nuclear K+, or indirectly interact with heterochromatin, both factors known to affect gene expression