Genetic removal of tri-unsaturated fatty acids suppresses developmental and molecular phenotypes of an Arabidopsis tocopherol-deficient mutant. Whole-body mapping of malondialdehyde pools in a complex eukaryote.

Malondialdehyde (MDA) is a small, ubiquitous, and potentially toxic aldehyde that is produced in vivo by lipid oxidation and that is able to affect gene expression. Tocopherol deficiency in the vitamin E2 mutant vte2-1 of Arabidopsis thaliana leads to massive lipid oxidation and MDA accumulation shortly after germination. MDA accumulation correlates with a strong visual phenotype (growth reduction, cotyledon bleaching) and aberrant GST1 (glutathione S-transferase 1) expression. We suppressed MDA accumulation in the vte2-1 background by genetically removing tri-unsaturated fatty acids. The resulting quadruple mutant, fad3-2 fad7-2 fad8 vte2-1, did not display the visual phenotype or the aberrant GST1 expression observed in vte2-1. Moreover, cotyledon bleaching in vte2-1 was chemically phenocopied by treatment of wild-type plants with MDA. These data suggest that products of tri-unsaturated fatty acid oxidation underlie the vte2-1 seedling phenotype, including cellular toxicity and gene regulation properties. Generation of the quadruple mutant facilitated the development of an in situ fluorescence assay based on the formation of adducts of MDA with 2-thiobarbituric acid at 37 degrees C. Specificity was verified by measuring pentafluorophenylhydrazine derivatives of MDA and by liquid chromatography analysis of MDA-2-thiobarbituric acid adducts. Potentially applicable to other organisms, this method allowed the localization of MDA pools throughout the body of Arabidopsis and revealed an undiscovered pool of the compound unlikely to be derived from trienoic fatty acids in the vicinity of the root tip quiescent center.

Complex regional pain syndrome type I affects brain structure in prefrontal and motor cortex.

The complex regional pain syndrome (CRPS) is a rare but debilitating pain disorder that mostly occurs after injuries to the upper limb. A number of studies indicated altered brain function in CRPS, whereas possible influences on brain structure remain poorly investigated. We acquired structural magnetic resonance imaging data from CRPS type I patients and applied voxel-by-voxel statistics to compare white and gray matter brain segments of CRPS patients with matched controls. Patients and controls were statistically compared in two different ways: First, we applied a 2-sample ttest to compare whole brain white and gray matter structure between patients and controls. Second, we aimed to assess structural alterations specifically of the primary somatosensory (S1) and motor cortex (M1) contralateral to the CRPS affected side. To this end, MRI scans of patients with left-sided CRPS (and matched controls) were horizontally flipped before preprocessing and region-of-interest-based group comparison. The unpaired ttest of the "non-flipped" data revealed that CRPS patients presented increased gray matter density in the dorsomedial prefrontal cortex. The same test applied to the "flipped" data showed further increases in gray matter density, not in the S1, but in the M1 contralateral to the CRPS-affected limb which were inversely related to decreased white matter density of the internal capsule within the ipsilateral brain hemisphere. The gray-white matter interaction between motor cortex and internal capsule suggests compensatory mechanisms within the central motor system possibly due to motor dysfunction. Altered gray matter structure in dorsomedial prefrontal cortex may occur in response to emotional processes such as pain-related suffering or elevated analgesic top-down control.

2009 Annual Report Capitol Planning Commission, January 2010

This 2011 Annual Report further summarizes the work of the Commission during the last year and provides planning recommendations for the future of the Capitol Complex. Please note that Iowa Code Chapter 8A.373 provides that before any physical changes are made to the state capitol complex "it shall be the duty of the officers, commissions, and councils charged by law with the duty of determining such questions to call upon" the Capitol Planning Commission for advice. The Capitol Planning Commission members, as well as DAS Staff, welcome the opportunity to discuss future projects at the request of any legislator.

Synchronization reveals topological scales in complex networks

We study the relationship between topological scales and dynamic time scales in complex networks. The analysis is based on the full dynamics towards synchronization of a system of coupled oscillators. In the synchronization process, modular structures corresponding to well-defined communities of nodes emerge in different time scales, ordered in a hierarchical way. The analysis also provides a useful connection between synchronization dynamics, complex networks topology, and spectral graph analysis.

Self-similarity of complex networks and hidden metric spaces

We demonstrate that the self-similarity of some scale-free networks with respect to a simple degree-thresholding renormalization scheme finds a natural interpretation in the assumption that network nodes exist in hidden metric spaces. Clustering, i.e., cycles of length three, plays a crucial role in this framework as a topological reflection of the triangle inequality in the hidden geometry. We prove that a class of hidden variable models with underlying metric spaces are able to accurately reproduce the self-similarity properties that we measured in the real networks. Our findings indicate that hidden geometries underlying these real networks are a plausible explanation for their observed topologies and, in particular, for their self-similarity with respect to the degree-based renormalization.

Clustering in complex networks. I. General formalism

We develop a full theoretical approach to clustering in complex networks. A key concept is introduced, the edge multiplicity, that measures the number of triangles passing through an edge. This quantity extends the clustering coefficient in that it involves the properties of two¿and not just one¿vertices. The formalism is completed with the definition of a three-vertex correlation function, which is the fundamental quantity describing the properties of clustered networks. The formalism suggests different metrics that are able to thoroughly characterize transitive relations. A rigorous analysis of several real networks, which makes use of this formalism and the metrics, is also provided. It is also found that clustered networks can be classified into two main groups: the weak and the strong transitivity classes. In the first class, edge multiplicity is small, with triangles being disjoint. In the second class, edge multiplicity is high and so triangles share many edges. As we shall see in the following paper, the class a network belongs to has strong implications in its percolation properties.

Simple model for nonexponential relaxation in complex fluids

The nonexponential relaxation occurring in complex dynamics manifested in a wide variety of systems is analyzed through a simple model of diffusion in phase space. It is found that the inability of the system to find its equilibrium state in any time scale becomes apparent in an effective temperature field, which leads to a hierarchy of relaxation times responsible for the slow relaxation phenomena.

Clustering in complex networks. II. Percolation properties

The percolation properties of clustered networks are analyzed in detail. In the case of weak clustering, we present an analytical approach that allows us to find the critical threshold and the size of the giant component. Numerical simulations confirm the accuracy of our results. In more general terms, we show that weak clustering hinders the onset of the giant component whereas strong clustering favors its appearance. This is a direct consequence of the differences in the k-core structure of the networks, which are found to be totally different depending on the level of clustering. An empirical analysis of a real social network confirms our predictions.

Council Bluffs Interstate System Improvements Project Pottawatomie County, Iowa and Douglas County, Nebraska Project Number: IM-029-3(62)54-13-78, November 2004

The Iowa Department of Transportation (Iowa DOT), Nebraska Department of Roads (NDOR), and the Federal Highway Administration (FHWA) are proposing to improve the interstate system around Council Bluffs with improvements extending across the Missouri River on I-80 to east of the I-480 interchange in Omaha, Nebraska, see Figure 1-1. The study considers long-term, broad-based transportation improvements along I-80, I-29, and I-480, including approximately 18 mainline miles of interstate and 14 interchanges (3 system1, 11 service), that would add capacity and correct functional issues along the mainline and interchanges and upgrade the I-80 Missouri River Crossing. These improvements, once implemented, would bring the segments of I-80 and I-29 up to current engineering standards and modernize the roadway to accommodate future traffic needs. In 2001, Iowa DOT and FHWA initiated the Council Bluffs Interstate System (CBIS) Improvements Project. The agencies concluded that the environmental study process would be conducted in two stages; that is, a tiered approach would be applied. The project is being conducted pursuant to the National Environmental Policy Act (NEPA) regulations issued by the Council on Environmental Quality (CEQ), 40 Code of Federal Regulations (CFR) Part 1502.20, and FHWA 23 CFR Part 771.111, that permit tiering for large, complex NEPA studies. Tier 1 is an examination of the overall interstate system improvement needs, including a clear explanation of the area’s transportation needs, a study of alternatives to satisfy them, and broad consideration of potential environmental and social impacts. The Tier 1 evaluation is at a sufficient level of engineering and environmental detail to assist decision makers in selecting a preferred transportation strategy. Tier 1 includes preparation of a draft and final Environmental Impact Statement (EIS) that would disclose the potential environmental and social effects (evaluated at a planning level that considers a variety of conceptual designs) of the proposed improvements. The final EIS will conclude with a Record of Decision (ROD) that states the preferred plan for improvements to be implemented. Essentially, the Tier 1 document will establish the planning framework for the needed improvements. Because the scope of the overall system improvements is large, the interstate improvements would be implemented as a series of individual projects that fit into the overall planning framework. The Tier 1 Area of Potential Impact, which is discussed in detail in Section 4 is an alternative that considers a combination of the most reasonable concepts that have been developed, buffered by approximately 100 or more feet to ensure that any Tier 2 design modifications would remain inside the outer boundary.

Protein-protein interactions between adenovirus DNA polymerase and nuclear factor I mediate formation of the DNA replication preinitiation complex.

The in vitro adenovirus (Ad) DNA replication system provides an assay to study the interaction of viral and host replication proteins with the DNA template in the formation of the preinitiation complex. This initiation system requires in addition to the origin DNA sequences 1) Ad DNA polymerase (Pol), 2) Ad preterminal protein (pTP), the covalent acceptor for protein-primed DNA replication, and 3) nuclear factor I (NFI), a host cell protein identical to the CCAAT box-binding transcription factor. The interactions of these proteins were studied by coimmunoprecipitation and Ad origin DNA binding assays. The Ad Pol can bind to origin sequences only in the presence of another protein which can be either pTP or NFI. While NFI alone can bind to its origin recognition sequence, pTP does not specifically recognize DNA unless Ad Pol is present. Thus, protein-protein interactions are necessary for the targetting of either Ad Pol or pTP to the preinitiation complex. DNA footprinting demonstrated that the Ad DNA site recognized by the pTP.Pol complex was within the first 18 bases at the end of the template which constitutes the minimal origin of replication. Mutagenesis studies have defined the Ad Pol interaction site on NFI between amino acids 68-150, which overlaps the DNA binding and replication activation domain of this factor. A putative zinc finger on the Ad Pol has been mutated to a product that fails to bind the Ad origin sequences but still interacts with pTP. These results indicate that both protein-protein and protein-DNA interactions mediate specific recognition of the replication origin by Ad DNA polymerase.