Deep ultraviolet resonance Raman spectroscopy of membrane proteins

Title from PDF of title page (University of Missouri--Columbia, viewed on February 27, 2013).The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file.Dissertation advisor: Dr. Jason CooleyIncludes bibliographical references.Vita.Ph. D. University of Missouri--Columbia 2012."December 2012"Despite the various protein structure determination methods in use, a need still exists for adequate resolution of membrane protein structure while remaining rapid and inexpensive. Deep-UV resonance Raman (DUVRR) spectroscopy addresses this need and also offers a high sensitivity to the protein backbone such that membrane proteins require no further modification from their native state in the lipid bilayer. DUVRR spectroscopy is a mature technique for secondary structure determination of aqueous proteins but had not been seriously explored as a means of structure determination for membrane proteins. Early progress in characterizing the secondary structure of the lipid-solvated cytochrome bc1 complex led to exploring other membrane proteins mostly based on the α-helix motif. DUVRR is not limited to proper membrane proteins, but also interrogates lipophilic protein-like structures such as the depsipeptide valinomycin. We find DUVRR spectroscopy characterizes membrane protein structure as well as aqueous protein structure. Additionally, it can describe the degree to which the protein backbone is embedded into the membrane. This largely is explained by the absence of hydrogen bonding from water to the amide backbone and its effect on the carbonyl stretching mode in DUVRR spectra. These findings are promising and indicate a need for further investigation of the variety of secondary structures formed in the lipid bilayer.Includes bibliographical reference

Instance-based Learning in Multi-cue Diagnosis

Decision heuristics are often described as fast and frugal, taking little time and few computations to make a gooddecision (Gigerenzer & Todd, 1999). Fast & Frugal Trees (F&FTs) are a type of decision heuristic that are a special case ofdecision trees in which there is a possible exit out of the decision process at every node in the tree (Luan, Schooler, & Gigerenzer,2011). We present predictions from a computational process model of learning in a multi-cue diagnosis task with and withoutinformation acquisition costs and across different penalty values for errors. The model uses Instance-Based Learning Theory(IBLT) to acquire new knowledge and makes precise performance predictions across a range of dependent variables. We willcompare the a priori model predictions to F&FT-constrained machine learning results on the same stimuli and also to empiricalresults collected from human participants making decisions in the same environment

Climate change, crops and commodity traders : subnational trade analysis highlights differentiated risk exposure

The global food system is increasingly interconnected and under pressure to support growing demand. At the same time, crop production is facing new and uncertain impacts from climate change. To date, understanding how downstream supply chain actors, such as commodity traders, are exposed to climate change risks has been difficult due to a lack of high-resolution climate and trade data. However, the recent availability of supply chain data linking subnational production to downstream actors, and gridded projections of crop yield under climate change, allows us to assess individual commodity trader exposure to long-term climate change risk. We apply such an analysis to soy production in Brazil, the world’s largest soy exporter. Whilst uncertainty across crop models’ yield projections means it remains difficult to accurately predict how production across the region will be affected by climate change, we demonstrate that the risk exposure of trading actors differs substantially due to the heterogeneity in their sourcing. Our study offers a first attempt to analyze subnational climate risk to individual trading actors operating across an entire production landscape, leading to more precise risk exposure analysis. With sufficient subnational data, this method can be applied to any crop and country combination, and in the context of wider food security issues, it will be pertinent to apply these methods across other production systems and downstream actors in the food system. Introductio

A spatially explicit approach to assessing commodity-driven fertilizer use and its impact on biodiversity

Global demand for food, including rising consumption of meat and dairy products, is increasing pressure on the environment and natural resources, often in locations distant from points of consumption. To identify and quantify consumer driven impacts and the components of the supply chain where sustainability interventions will be most effective, spatially explicit consumption-linked indicators that encompass environmental risks are required. Large amounts of phosphorus fertilizers are used in Brazilian soybean cultivation, which potentially cause eutrophication and impact freshwater species. We use a sub-national trade model to develop a spatially explicit approach for assessing commodity-driven phosphorus fertilizer use and its potential impact on biodiversity linked to four key consumers. The use of phosphorus for embedded consumption per capita of Brazilian soybean in China, the EU, the UK, and Sweden are estimated at municipal level and combined with metrics that influence losses of phosphorus to create a normalised relative risk index. The relative risk index is presented in geospatial visualisations to explore geographical patterns of risk to freshwater biodiversity and make the link between consumer and producer countries less obscure. The results indicate high phosphorus-linked species risk in municipalities within Mato Grosso, Rio Grande do Sul, Paraná, and Goiás. Sweden and the UK generate the highest relative risk and the geographical patterns of risk differ between the investigated consuming countries, showing that smaller countries can have relatively large impacts at a spatially explicit scale. In the Amazon biome, risk of nutrient losses and biodiversity are relatively high, creating concerns as soybean production is expanding into the area. The results and methodological approach can contribute to understanding of accountability, agency, and increased transparency for the governance of global supply chains, necessary for enabling transformations towards sustainable food systems

Powering Ocean Giants: The Energetics of Shark and Ray Megafauna

Shark and ray megafauna have crucial roles as top predators in many marine ecosystems, but are currently among the most threatened vertebrates and, based on historical extinctions, may be highly susceptible to future environmental perturbations. However, our understanding of their energetics lags behind that of other taxa. Such knowledge is required to answer important ecological questions and predict their responses to ocean warming, which may be limited by expanding ocean deoxygenation and declining prey availability. To develop bioenergetics models for shark and ray megafauna, incremental improvements in respirometry systems are useful but unlikely to accommodate the largest species. Advances in biologging tools and modelling could help answer the most pressing ecological questions about these iconic species

Using supply chain data to monitor zero deforestation commitments: an assessment of progress in the Brazilian soy sector

Zero deforestation commitments (ZDCs) are voluntary initiatives where companies or countries pledge to eliminate deforestation from their supply chains. These commitments offer much promise for sustainable commodity production, but are undermined by a lack of transparency about their coverage and impacts. Here, using state-of-the-art supply chain data, we introduce an approach to evaluate the impact of ZDCs, linking traders and international markets to commodity-associated deforestation in the sub-national jurisdictions from which they source. We focus on the Brazilian soy sector, where we find that ZDC coverage is increasing, but under-represents the Cerrado biome where most soy-associated deforestation currently takes place. Though soy-associated deforestation declined in the Amazon after the introduction of the Soy Moratorium, we observe no change in the exposure of companies or countries adopting ZDCs to soy-associated deforestation in the Cerrado. We further assess the formulation and implementation of these ZDCs and identify several systematic weaknesses that must be addressed to increase the likelihood that they achieve meaningful reductions in deforestation in future. As the 2020 deadline for several of these commitments approaches, our approach can provide independent monitoring of progress toward the goal of ending commodity-associated deforestation

Convocation

Program listing performers and works performe

Microbiome alteration Via Fecal Microbiota Transplantation Is Effective For Refractory Immune Checkpoint inhibitor-induced Colitis

Immune checkpoint inhibitors (ICIs) target advanced malignancies with high efficacy but also predispose patients to immune-related adverse events like immune-mediated colitis (IMC). Given the association between gut bacteria with response to ICI therapy and subsequent IMC, fecal microbiota transplantation (FMT) represents a feasible way to manipulate microbial composition in patients, with a potential benefit for IMC. Here, we present a large case series of 12 patients with refractory IMC who underwent FMT from healthy donors as salvage therapy. All 12 patients had grade 3 or 4 ICI-related diarrhea or colitis that failed to respond to standard first-line (corticosteroids) and second-line immunosuppression (infliximab or vedolizumab). Ten patients (83%) achieved symptom improvement after FMT, and three patients (25%) required repeat FMT, two of whom had no subsequent response. At the end of the study, 92% achieved IMC clinical remission. 1

Temperate infection in a virus–host system previously known for virulent dynamics

The blooming cosmopolitan coccolithophore Emiliania huxleyi and its viruses (EhVs) are a model for density-dependent virulent dynamics. EhVs commonly exhibit rapid viral reproduction and drive host death in high-density laboratory cultures and mesocosms that simulate blooms. Here we show that this system exhibits physiology-dependent temperate dynamics at environmentally relevant E. huxleyi host densities rather than virulent dynamics, with viruses switching from a long-term non-lethal temperate phase in healthy hosts to a lethal lytic stage as host cells become physiologically stressed. Using this system as a model for temperate infection dynamics, we present a template to diagnose temperate infection in other virus–host systems by integrating experimental, theoretical, and environmental approaches. Finding temperate dynamics in such an established virulent host–virus model system indicates that temperateness may be more pervasive than previously considered, and that the role of viruses in bloom formation and decline may be governed by host physiology rather than by host–virus densities

Simplicity in Visual Representation: A Semiotic Approach

Simplicity, as an ideal in the design of visual representations, has not received systematic attention. High-level guidelines are too general, and low-level guidelines too ad hoc, too numerous, and too often incompatible, to serve in a particular design situation. This paper reviews notions of visual simplicity in the literature within the analytical framework provided by Charles Morris' communication model, specifically, his trichotomy of communication levels—the syntactic, the semantic, and the pragmatic. Simplicity is ultimate ly shown to entail the adjudication of incompatibilities both within, and between, levels.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/68281/2/10.1177_105065198700100103.pd