Winter annual alternative crops for enhanced sustainability in Iowa cropping systems

Cropping systems that consist of corn (Zea mays L.)-corn or alternate year corn-soybean [Glycine max (L.) Merr.] rotations can degrade environmental resources due to increased susceptibility to topsoil erosion and nitrate (NO3) leaching. Winter annual crops such as winter canola (Brassica napus L.) and winter wheat (Triticum aestivum L.) can provide a positive environmental and economic impact when included in crop rotations. However, winter canola has not been shown to overwinter consistently in Iowa, and agronomic and economic considerations need to be addressed when relay intercropping soybeans with winter wheat production. The work presented in this thesis is an effort to assess the suitability of these two alternative crops in the conventional Iowa crop rotation of corn and soybean. Based on observations from in-field experiments, it is determined that interseeding winter canola into standing soybeans in early September will provide greater environmental services including, nitrogen accumulation and canopy cover, when compared to later seeding dates. However, successful overwintering of winter canola may still be limited by Iowa winter conditions and the cold tolerance of winter canola varieties. Early September seeded winter canola has the ability to accrue sufficient heat units for proper fall plant development before the onset of winter to potentially survive winter and produce yield. Therefore, we recommend that winter canola should be used with caution in Iowa cropping systems until winter canola variety cold tolerance is suitable to Iowa winter conditions, or is seeded in early September and receives adequate rainfall for proper germination and establishment. Furthermore, a decision case study created for this thesis provides students in Higher Learning, the opportunity to determine the management decisions, economics, and challenges involved with relay intercropping winter wheat and soybean. Economic analyses determine that when proper precautions and agronomic considerations are taken, relay intercropping can lower input costs and increase profit

Dual adjacency matrix : exploring link groups in dense networks

Node grouping is a common way of adding structure and information to networks that aids their interpretation. However, certain networks benefit from the grouping of links instead of nodes. Link communities, for example, are a form of link groups that describe high-quality overlapping node communities. There is a conceptual gap between node groups and link groups that poses an interesting visualization challenge. We introduce the Dual Adjacency Matrix to bridge this gap. This matrix combines node and link group techniques via a generalization that also enables it to be coordinated with a node-link-contour diagram. These methods have been implemented in a prototype that we evaluated with an information scientist and neuroscientist via interviews and prototype walk-throughs. We demonstrate this prototype with the analysis of a trade network and an fMRI correlation network

Targeting T cells to treat atherosclerosis: Odyssey from bench to bedside

More than 150 years from the initial description of inflammation in atherosclerotic plaques, randomized clinical trials to test anti-inflammatory therapies in atherosclerosis have recently been initiated. Lymphocytes and macrophages are main participants in the inflammatory response in atherosclerosis. T lymphocytes operate mainly by exerting strong influences on the function of many cells in the immune system and beyond, and co-ordinating their interactions. Importantly, T lymphocytes are not a homogenous population, but include several subsets with specialized functions that can either promote or suppress inflammation. The interactions between these T-lymphocyte subsets have critical consequences on the course and outcome of inflammation. The complexity of the inflammatory response in atherosclerosis poses significant challenges on translating experimental findings into clinical therapies and makes the journey from bench to bedside an arduous one. Here, we summarize recent advances on the role of CD4 + T cells in the inflammatory process in atherosclerosis and discuss potential therapies to modulate these lymphocytes that may provide future breakthroughs in the treatment of atherosclerosis

eXamine: a Cytoscape app for exploring annotated modules in networks

Background. Biological networks have growing importance for the interpretation of high-throughput "omics" data. Statistical and combinatorial methods allow to obtain mechanistic insights through the extraction of smaller subnetwork modules. Further enrichment analyses provide set-based annotations of these modules. Results. We present eXamine, a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. Our approach extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours. Conclusions. We implemented eXamine as a freely available Cytoscape app. Using eXamine we study a module that is activated by the virally-encoded G-protein coupled receptor US28 and formulate a novel hypothesis about its functioning

Functional consequences of sphingomyelinase-induced changes in erythrocyte membrane structure.

Inflammation enhances the secretion of sphingomyelinases (SMases). SMases catalyze the hydrolysis of sphingomyelin into phosphocholine and ceramide. In erythrocytes, ceramide formation leads to exposure of the removal signal phosphatidylserine (PS), creating a potential link between SMase activity and anemia of inflammation. Therefore, we studied the effects of SMase on various pathophysiologically relevant parameters of erythrocyte homeostasis. Time-lapse confocal microscopy revealed a SMase-induced transition from the discoid to a spherical shape, followed by PS exposure, and finally loss of cytoplasmic content. Also, SMase treatment resulted in ceramide-associated alterations in membrane-cytoskeleton interactions and membrane organization, including microdomain formation. Furthermore, we observed increases in membrane fragility, vesiculation and invagination, and large protein clusters. These changes were associated with enhanced erythrocyte retention in a spleen-mimicking model. Erythrocyte storage under blood bank conditions and during physiological aging increased the sensitivity to SMase. A low SMase activity already induced morphological and structural changes, demonstrating the potential of SMase to disturb erythrocyte homeostasis. Our analyses provide a comprehensive picture in which ceramide-induced changes in membrane microdomain organization disrupt the membrane-cytoskeleton interaction and membrane integrity, leading to vesiculation, reduced deformability, and finally loss of erythrocyte content. Understanding these processes is highly relevant for understanding anemia during chronic inflammation, especially in critically ill patients receiving blood transfusions

Crucial Role of the CB3-Region of Collagen IV in PARF-Induced Acute Rheumatic Fever

Acute rheumatic fever (ARF) and rheumatic heart disease are serious autoimmune sequelae to infections with Streptococcus pyogenes. Streptococcal M-proteins have been implicated in ARF pathogenesis. Their interaction with collagen type IV (CIV) is a triggering step that induces generation of collagen-specific auto-antibodies. Electron microscopy of the protein complex between M-protein type 3 (M3-protein) and CIV identified two prominent binding sites of which one is situated in the CB3-region of CIV. In a radioactive binding assay, M3-protein expressing S. pyogenes and S. gordonii bound the CB3-fragment. Detailed analysis of the interactions by surface plasmon resonance measurements and site directed mutagenesis revealed high affinity interactions with dissociation constants in the nanomolar range that depend on the recently described collagen binding motif of streptococcal M-proteins. Because of its role in the induction of disease-related collagen autoimmunity the motif is referred to as “peptide associated with rheumatic fever” (PARF). Both, sera of mice immunized with M3-protein as well as sera from patients with ARF contained anti-CB3 auto-antibodies, indicating their contribution to ARF pathogenesis. The identification of the CB3-region as a binding partner for PARF directs the further approaches to understand the unusual autoimmune pathogenesis of PARF-dependent ARF and forms a molecular basis for a diagnostic test that detects rheumatogenic streptococci