AgMIP Training in Multiple Crop Models and Tools

The Agricultural Model Intercomparison and Improvement Project (AgMIP) has the goal of using multiple crop models to evaluate climate impacts on agricultural production and food security in developed and developing countries. There are several major limitations that must be overcome to achieve this goal, including the need to train AgMIP regional research team (RRT) crop modelers to use models other than the ones they are currently familiar with, plus the need to harmonize and interconvert the disparate input file formats used for the various models. Two activities were followed to address these shortcomings among AgMIP RRTs to enable them to use multiple models to evaluate climate impacts on crop production and food security. We designed and conducted courses in which participants trained on two different sets of crop models, with emphasis on the model of least experience. In a second activity, the AgMIP IT group created templates for inputting data on soils, management, weather, and crops into AgMIP harmonized databases, and developed translation tools for converting the harmonized data into files that are ready for multiple crop model simulations. The strategies for creating and conducting the multi-model course and developing entry and translation tools are reviewed in this chapter

WT1 expression in breast cancer disrupts the epithelial/mesenchymal balance of tumour cells and correlates with the metabolic response to docetaxel

WT1 is a transcription factor which regulates the epithelial-mesenchymal balance during embryonic development and, if mutated, can lead to the formation of Wilms' tumour, the most common paediatric kidney cancer. Its expression has also been reported in several adult tumour types, including breast cancer, and usually correlates with poor outcome. However, published data is inconsistent and the role of WT1 in this malignancy remains unclear. Here we provide a complete study of WT1 expression across different breast cancer subtypes as well as isoform specific expression analysis. Using in vitro cell lines, clinical samples and publicly available gene expression datasets, we demonstrate that WT1 plays a role in regulating the epithelial-mesenchymal balance of breast cancer cells and that WT1-expressing tumours are mainly associated with a mesenchymal phenotype. WT1 gene expression also correlates with CYP3A4 levels and is associated with poorer response to taxane treatment. Our work is the first to demonstrate that the known association between WT1 expression in breast cancer and poor prognosis is potentially due to cancer-related epithelial-to-mesenchymal transition (EMT) and poor chemotherapy response

An AgMIP Framework for Improved Agricultural Representation in Integrated Assessment Models

Integrated assessment models (IAMs) hold great potential to assess how future agricultural systems will be shaped by socioeconomic development, technological innovation, and changing climate conditions. By coupling with climate and crop model emulators, IAMs have the potential to resolve important agricultural feedback loops and identify unintended consequences of socioeconomic development for agricultural systems. Here we propose a framework to develop robust representation of agricultural system responses within IAMs, linking downstream applications with model development and the coordinated evaluation of key climate responses from local to global scales. We survey the strengths and weaknesses of protocol-based assessments linked to the Agricultural Model Intercomparison and Improvement Project (AgMIP), each utilizing multiple sites and models to evaluate crop response to core climate changes including shifts in carbon dioxide concentration, temperature, and water availability, with some studies further exploring how climate responses are affected by nitrogen levels and adaptation in farm systems. Site-based studies with carefully calibrated models encompass the largest number of activities; however they are limited in their ability to capture the full range of global agricultural system diversity. Representative site networks provide more targeted response information than broadly-sampled networks, with limitations stemming from difficulties in covering the diversity of farming systems. Global gridded crop models provide comprehensive coverage, although with large challenges for calibration and quality control of inputs. Diversity in climate responses underscores that crop model emulators must distinguish between regions and farming system while recognizing model uncertainty. Finally, to bridge the gap between bottom-up and top-down approaches we recommend the deployment of a hybrid climate response system employing a representative network of sites to bias-correct comprehensive gridded simulations, opening the door to accelerated development and a broad range of applications

Acute Multiple Organ Failure in Adult Mice Deleted for the Developmental Regulator Wt1

There is much interest in the mechanisms that regulate adult tissue homeostasis and their relationship to processes governing foetal development. Mice deleted for the Wilms' tumour gene, Wt1, lack kidneys, gonads, and spleen and die at mid-gestation due to defective coronary vasculature. Wt1 is vital for maintaining the mesenchymal–epithelial balance in these tissues and is required for the epithelial-to-mesenchyme transition (EMT) that generates coronary vascular progenitors. Although Wt1 is only expressed in rare cell populations in adults including glomerular podocytes, 1% of bone marrow cells, and mesothelium, we hypothesised that this might be important for homeostasis of adult tissues; hence, we deleted the gene ubiquitously in young and adult mice. Within just a few days, the mice suffered glomerulosclerosis, atrophy of the exocrine pancreas and spleen, severe reduction in bone and fat, and failure of erythropoiesis. FACS and culture experiments showed that Wt1 has an intrinsic role in both haematopoietic and mesenchymal stem cell lineages and suggest that defects within these contribute to the phenotypes we observe. We propose that glomerulosclerosis arises in part through down regulation of nephrin, a known Wt1 target gene. Protein profiling in mutant serum showed that there was no systemic inflammatory or nutritional response in the mutant mice. However, there was a dramatic reduction in circulating IGF-1 levels, which is likely to contribute to the bone and fat phenotypes. The reduction of IGF-1 did not result from a decrease in circulating GH, and there is no apparent pathology of the pituitary and adrenal glands. These findings 1) suggest that Wt1 is a major regulator of the homeostasis of some adult tissues, through both local and systemic actions; 2) highlight the differences between foetal and adult tissue regulation; 3) point to the importance of adult mesenchyme in tissue turnover

Linear domain interactome and biological function of anterior gradient 2

The Anterior Gradient 2 (AGR2) protein has been implicated in a variety of biological systems linked to cancer and metastasis, tamoxifen-induced drug resistance, pro-inflammatory diseases like IBD and asthma, and limb regeneration. The molecular mechanisms by which AGR2 mediates these various phenotypes in disease progression in both cancer and IBD are poorly understood, as is the biological function(s) of AGR2 under non-disease conditions. Here, we use a combination of biochemical techniques, organ culture, cell biology and mouse genetics to investigate the biological significance of AGR2 both in cell lines and in vivo. We present data based on phage-peptide inter-actomics screens suggesting a role for AGR2 in mediating the maturation and trafficking of a class of membrane and secretory proteins, and investigate a putative interaction between AGR2 and one member of this class of proteins. We also describe the construction of a universal vector for use in making a variety of transgenic animals, and then present data showing its use as a promoter reporter, and attempt to investigate the temporal and spatial expression of AGR2 in the developing and adult mouse. Further, we present data describing the localisation pattern of AGR2 in the developing murine kidney using a combination of organ culture and antibody staining, and suggest a role for AGR2 in the developing kidney based on this data that is in agreement with a chaperone function for membrane and secretory proteins. Together, these data suggest that AGR2 has an intrinsic consensus docking site for a subset of its client proteins, that AGR2 plays a role in protein maturation in ciliated cell types, and provides a novel biological model to dissect the role of AGR2 in ER-trafficking

Primers and pDONR vectors used in the generation of pENTR vectors.

<p>Primers and pDONR vectors used in the generation of pENTR vectors.</p

The <i>Six2</i>^+/GCiP allele based on the pMULTIrec system.

<p><b>A.</b> Retrival of the <i>Six2</i>-GCIP targeting vector. <b>B.</b> Targeting of the <i>Six2</i> locus. <b>C.</b> Confirmation of correct targeting of the <i>Six2</i> locus (restriction enzyme and probe indicated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062054#pone-0062054-g004" target="_blank">figure 4B</a>). <b>D.. </b><i>Six2</i>^+/GCiP<i>Rosa26</i>^tdRFP kidney in culture showing GFP and RFP signals. <b>E.. </b><i>Six2</i>^+/GCiP<i>Rosa26</i>^tdRFP kidney in culture showing GFP and RFP signals and Cdh1 antibody staining. CM: cap mesenchyme; UB: ureteric bud; N: nephron.</p

The <i>Six2</i>-GCiP BAC construct made using pMULTIrec.

<p><b>A.</b> The four-fragment and dual selection cassette from pMULTIrec was cloned in a <i>Six2</i> containing BAC replacing the start codon. <b>B.</b> GFP imaging of a E13.5 embryo carrying the <i>Six2</i>-GCiP BAC. <b>C.</b> GFP imaging of whole mount E13.5 kidneys. <b>D.</b> E13.5 <i>Six2</i>-GCiP BAC kidneys cultured for four days showing GFP expression in the cap mesenchyme and Cdh1 expression in the ureteric bud.</p

Efficiency of the Gateway reactions used.

<p>Efficiency of the Gateway reactions used.</p

The <i>Nanog</i>-KiP BAC made from a modified pMULTIrec vector.

<p><b>A.</b> Generation of the <i>Nanog</i>-KiP BAC. <b>B, C.</b> mKate2 (B) and brightfield signals of iPS clones derived from <i>Nanog</i>-KiP BAC MEFs. <b>D, E.</b> mKate2 (B) and brightfield signals of iPS clones derived from wild type MEFs.</p