Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: Extending MapMan ontology for grapevine

<p>Abstract</p> <p>Background</p> <p>Whole genome transcriptomics analysis is a very powerful approach because it gives an overview of the activity of genes in certain cells or tissue types. However, biological interpretation of such results can be rather tedious. MapMan is a software tool that displays large datasets (e.g. gene expression data) onto diagrams of metabolic pathways or other processes and thus enables easier interpretation of results. The grapevine (<it>Vitis vinifera</it>) genome sequence has recently become available bringing a new dimension into associated research. Two microarray platforms were designed based on the TIGR Gene Index database and used in several physiological studies.</p> <p>Results</p> <p>To enable easy and effective visualization of those and further experiments, annotation of <it>Vitis vinifera </it>Gene Index (VvGI version 5) to MapMan ontology was set up. Due to specificities of grape physiology, we have created new pictorial representations focusing on three selected pathways: carotenoid pathway, terpenoid pathway and phenylpropanoid pathway, the products of these pathways being important for wine aroma, flavour and colour, as well as plant defence against pathogens. This new tool was validated on Affymetrix microarrays data obtained during berry ripening and it allowed the discovery of new aspects in process regulation. We here also present results on transcriptional profiling of grape plantlets after exposal to the fungal pathogen <it>Eutypa lata </it>using Operon microarrays including visualization of results with MapMan. The data show that the genes induced in infected plants, encode pathogenesis related proteins and enzymes of the flavonoid metabolism, which are well known as being responsive to fungal infection.</p> <p>Conclusion</p> <p>The extension of MapMan ontology to grapevine together with the newly constructed pictorial representations for carotenoid, terpenoid and phenylpropanoid metabolism provide an alternative approach to the analysis of grapevine gene expression experiments performed with Affymetrix or Operon microarrays. MapMan was first validated on an already published dataset and later used to obtain an overview of transcriptional changes in a susceptible grapevine – <it>Eutypa lata </it>interaction at the time of symptoms development, where we showed that the responsive genes belong to families known to be involved in the plant defence towards fungal infection (PR-proteins, enzymes of the phenylpropanoid pathway).</p

Intentional Technology For Teaching Practice

In today’s era, where educational technology is in a near-constant state of evolution, the imperative is not just to adopt technology, but to do so with a defined purpose and strategy. As educators within military education there is a growing need to discern which technological tools and practices align best with our mission and the goals we set for our students. Teaching is more than just transferring knowledge—it’s about fostering environments conducive to growth, critical thinking, and lifelong learning. This e-book contains collective insights, experiences, and reflections from faculty participating in a Faculty Learning Community (FLC) a yearlong, structured, community of practice, engaged in the thoughtful exploration of educational technology topics during the academic year of 2022-2023 at the Air Force Institute of Technology. Whether by leveraging social annotation tools to engage students in reading, formulating effective methods to produce and utilize educational content, innovating with game-based learning, or seamlessly integrating multiple applications for meaningful classroom experiences, our aim is to provide you with insights and actionable guidance for use within your own classrooms

Pluralism about Knowledge

In this paper I consider the prospects for pluralism about knowledge, that is, the view that there is a plurality of knowledge relations. After a brief overview of some views that entail a sort of pluralism about knowledge, I focus on a particular kind of knowledge pluralism I call standards pluralism. Put roughly, standards pluralism is the view that one never knows anything simpliciter. Rather, one knows by this-or-that epistemic standard. Because there is a plurality of epistemic standards, there is a plurality of knowledge relations. In §1 I argue that one can construct an impressive case for standards pluralism. In §2 I clarify the relationship between standards pluralism, epistemic contextualism and epistemic relativism. In §3 I argue that standards pluralism faces a serious objection. The gist of the objection is that standards pluralism is incompatible with plausible claims about the normative role of knowledge. In §4 I finish by sketching the form that a standards pluralist response to this objection might take

Synthetic retinoid Am80 ameliorates chronic graft-versus-host disease by down-regulating Th1 and Th17.

Chronic GVHD (cGVHD) is a main cause of late death and morbidity after allogeneic hematopoietic cell transplantation, but its pathogenesis remains unclear. We investigated the roles of Th subsets in cGVHD with the use of a well-defined mouse model of cGVHD. In this model, development of cGVHD was associated with up-regulated Th1, Th2, and Th17 responses. Th1 and Th2 responses were up-regulated early after BM transplantation, followed by a subsequent up-regulation of Th17 cells. Significantly greater numbers of Th17 cells were infiltrated in the lung and liver from allogeneic recipients than those from syngeneic recipients. We then evaluated the roles of Th1 and Th17 in cGVHD with the use of IFN-γ-deficient and IL-17-deficient mice as donors. Infusion of IFN-γ(-/-) or IL-17(-/-) T cells attenuated cGVHD in the skin and salivary glands. Am80, a potent synthetic retinoid, regulated both Th1 and Th17 responses as well as TGF-β expression in the skin, resulting in an attenuation of cutaneous cGVHD. These results suggest that Th1 and Th17 contribute to the development of cGVHD and that targeting Th1 and Th17 may therefore represent a promising therapeutic strategy for preventing and treating cGVHD

Magmatic and tectonic extension at mid-ocean ridges : 2. Origin of axial morphology

Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 9 (2008): Q09O12, doi:10.1029/2008GC001970.We investigate the origin of mid-ocean ridge morphology with numerical models that successfully predict axial topographic highs, axial valleys, and the transition between the two. The models are time-dependent, simulating alternating tectonic and magmatic periods where far-field extension is accommodated by faulting and by magmatism, respectively. During tectonic phases, models predict faults to grow on either side of the ridge axis and axial height to decrease. During magmatic phases, models simulate magmatic extension by allowing the axial lithosphere to open freely in response to extension. Results show that fault size and spacing decreases with increasing time fraction spent in the magmatic phase F M . Magmatic phases also simulate the growth of topography in response to local buoyancy forces. The fundamental variable that controls the transition between axial highs and valleys is the “rise-sink ratio,” (F M /F T )(τ T /τ M ), where F M /F T is the ratio of the time spent in the magmatic and tectonic periods and τ T /τ M is the ratio of the characteristic rates for growing topography during magmatic phases (1/τ M ) and for reducing topography during tectonic phases (1/τ T ). Models predict the tallest axial highs when (F M /F T )(τ T /τ M ) ≫ 1, faulted topography without a high or valley when (F M /F T )(τ T /τ M ) ∼ 1, and the deepest median valleys when (F M /F T )(τ M /τ T ) < 1. New scaling laws explain a global negative correlation between axial topography and lithosphere thickness as measured by the depths of axial magma lenses and microearthquakes. Exceptions to this trend reveal the importance of other behaviors such as a predicted inverse relation between axial topography and spreading rate as evident along the Lau Spreading Center. Still other factors related to the frequency and spatial pervasiveness of magmatic intrusions and eruptions, as evident at the Mid-Atlantic and Juan de Fuca ridges, influence the rise-sink-ratio (F M /F T )(τ T /τ M ) and thus axial morphology.Funding for this research was provided by NSF grants OCE-0327018 (MDB), OCE-0548672 (MDB), OCE-0327051 (GI), and OCE-0351234 (GI)

Sulfide geochronology along the Endeavour Segment of the Juan de Fuca Ridge

Forty-nine hydrothermal sulfide-sulfate rock samples from the Endeavour Segment of the Juan de Fuca Ridge, northeastern Pacific Ocean, were dated by measuring the decay of 226Ra (half-life of 1600 years) in hydrothermal barite to provide a history of hydrothermal venting at the site over the past 6000 years. This dating method is effective for samples ranging in age from ∼200 to 20,000 years old and effectively bridges an age gap between shorter- and longer-lived U-series dating techniques for hydrothermal deposits. Results show that hydrothermal venting at the active High Rise, Sasquatch, and Main Endeavour fields began at least 850, 1450, and 2300 years ago, respectively. Barite ages of other inactive deposits on the axial valley floor are between ∼1200 and ∼2200 years old, indicating past widespread hydrothermal venting outside of the currently active vent fields. Samples from the half-graben on the eastern slope of the axial valley range in age from ∼1700 to ∼2925 years, and a single sample from outside the axial valley, near the westernmost valley fault scarp is ∼5850 ± 205 years old. The spatial relationship between hydrothermal venting and normal faulting suggests a temporal relationship, with progressive younging of sulfide deposits from the edges of the axial valley toward the center of the rift. These relationships are consistent with the inward migration of normal faulting toward the center of the valley over time and a minimum age of onset of hydrothermal activity in this region of 5850 years

Distilling the role of ecosystem services in the Sustainable Development Goals

Achieving well-being for all, while protecting the environment, is one of the most pressing global challenges of our time, and a central idea in the UN Sustainable Development Goals (SDGs). We believe that integrating ecosystem services, the benefits nature provides to people, into strategies for meeting the SDGs can help achieve this. Many development goals are likely underpinned by the delivery of one or more ecosystem services. Understanding how these services could support multiple development targets will be essential for planning synergistic and cost-effective interventions. Here we present the results of an expert survey on the contributions of 16 ecosystem services to achieving SDG targets linked to environment and human well-being, and review the capacity of modelling tools to evaluate SDG-relevant ecosystem services interactions. Survey respondents judged that individual ecosystem services could make important contributions to achieving 41 targets across 12 SDGs. The provision of food and water, habitat & biodiversity maintenance, and carbon storage & sequestration were perceived to each make contributions to >14 SDG targets, suggesting cross-target interactions are likely, and may present opportunities for synergistic outcomes across multiple SDGs. Existing modelling tools are well-aligned to support SDG-relevant ecosystem service planning. Together, this work identifies entry points and tools to further analyze the role of ecosystem services to support the SDGs

Field experiments underestimate aboveground biomass response to drought

Researchers use both experiments and observations to study the impacts of climate change on ecosystems, but results from these contrasting approaches have not been systematically compared for droughts. Using a meta-analysis and accounting for potential confounding factors, we demonstrate that aboveground biomass responded only about half as much to experimentally imposed drought events as to natural droughts. Our findings indicate that experimental results may underestimate climate change impacts and highlight the need to integrate results across approaches

Effects of variable magma supply on mid-ocean ridge eruptions : constraints from mapped lava flow fields along the Galápagos Spreading Center

Author Posting. © American Geophysical Union, 2012. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 13 (2012): Q08014, doi:10.1029/2012GC004163.Mapping and sampling of 18 eruptive units in two study areas along the Galápagos Spreading Center (GSC) provide insight into how magma supply affects mid-ocean ridge (MOR) volcanic eruptions. The two study areas have similar spreading rates (53 versus 55 mm/yr), but differ by 30% in the time-averaged rate of magma supply (0.3 × 106 versus 0.4 × 106 m3/yr/km). Detailed geologic maps of each study area incorporate observations of flow contacts and sediment thickness, in addition to sample petrology, geomagnetic paleointensity, and inferences from high-resolution bathymetry data. At the lower-magma-supply study area, eruptions typically produce irregularly shaped clusters of pillow mounds with total eruptive volumes ranging from 0.09 to 1.3 km3. At the higher-magma-supply study area, lava morphologies characteristic of higher effusion rates are more common, eruptions typically occur along elongated fissures, and eruptive volumes are an order of magnitude smaller (0.002–0.13 km3). At this site, glass MgO contents (2.7–8.4 wt. %) and corresponding liquidus temperatures are lower on average, and more variable, than those at the lower-magma-supply study area (6.2–9.1 wt. % MgO). The differences in eruptive volume, lava temperature, morphology, and inferred eruption rates observed between the two areas along the GSC are similar to those that have previously been related to variable spreading rates on the global MOR system. Importantly, the documentation of multiple sequences of eruptions at each study area, representing hundreds to thousands of years, provides constraints on the variability in eruptive style at a given magma supply and spreading rate.This work was supported by the National Science Foundation grants OCE08–49813, OCE08–50052, and OCE08– 49711.2013-02-2