Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. strain LH128 in biofilms.

Members of the genus Sphingomonas are important catalysts for removal of polycyclic aromatic hydrocarbons (PAHs) in soil, but their activity can be affected by various stress factors. This study examines the physiological and genome-wide transcription response of the phenanthrene-degrading Sphingomonas sp. strain LH128 in biofilms to solute stress (invoked by 450 mM NaCl solution), either as an acute (4-h) or a chronic (3-day) exposure. The degree of membrane fatty acid saturation was increased as a response to chronic stress. Oxygen consumption in the biofilms and phenanthrene mineralization activities of biofilm cells were, however, not significantly affected after imposing either acute or chronic stress. This finding was in agreement with the transcriptomic data, since genes involved in PAH degradation were not differentially expressed in stressed conditions compared to nonstressed conditions. The transcriptomic data suggest that LH128 adapts to NaCl stress by (i) increasing the expression of genes coping with osmolytic and ionic stress such as biosynthesis of compatible solutes and regulation of ion homeostasis, (ii) increasing the expression of genes involved in general stress response, (iii) changing the expression of general and specific regulatory functions, and (iv) decreasing the expression of protein synthesis such as proteins involved in motility. Differences in gene expression between cells under acute and chronic stress suggest that LH128 goes through changes in genome-wide expression to fully adapt to NaCl stress, without significantly changing phenanthrene degrading activity.

Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.

Nonalcoholic fatty liver disease (NAFLD) clusters in families, but the only known common genetic variants influencing risk are near PNPLA3. We sought to identify additional genetic variants influencing NAFLD using genome-wide association (GWA) analysis of computed tomography (CT) measured hepatic steatosis, a non-invasive measure of NAFLD, in large population based samples. Using variance components methods, we show that CT hepatic steatosis is heritable (∼26%-27%) in family-based Amish, Family Heart, and Framingham Heart Studies (n = 880 to 3,070). By carrying out a fixed-effects meta-analysis of genome-wide association (GWA) results between CT hepatic steatosis and ∼2.4 million imputed or genotyped SNPs in 7,176 individuals from the Old Order Amish, Age, Gene/Environment Susceptibility-Reykjavik study (AGES), Family Heart, and Framingham Heart Studies, we identify variants associated at genome-wide significant levels (p<5×10(-8)) in or near PNPLA3, NCAN, and PPP1R3B. We genotype these and 42 other top CT hepatic steatosis-associated SNPs in 592 subjects with biopsy-proven NAFLD from the NASH Clinical Research Network (NASH CRN). In comparisons with 1,405 healthy controls from the Myocardial Genetics Consortium (MIGen), we observe significant associations with histologic NAFLD at variants in or near NCAN, GCKR, LYPLAL1, and PNPLA3, but not PPP1R3B. Variants at these five loci exhibit distinct patterns of association with serum lipids, as well as glycemic and anthropometric traits. We identify common genetic variants influencing CT-assessed steatosis and risk of NAFLD. Hepatic steatosis associated variants are not uniformly associated with NASH/fibrosis or result in abnormalities in serum lipids or glycemic and anthropometric traits, suggesting genetic heterogeneity in the pathways influencing these traits.

Evolution of proteins after whole-genome duplication

Evolution of proteins after whole-genome duplicationGene and genome duplication are considered major mechanisms in the creation of newfunctions in genomes, or in the refinement of networks by the division of function amongmore genes. In animals, the best demonstrated whole genome duplication occurred at theorigin of Teleost fishes. This makes fishes an ideal model to study the consequences ofgenome duplication, particularly since we have a good sampling of genome sequences,abundant functional information, and a very well studied outgroup: the tetrapodes (includinghuman). More specifically, I studied the consequences of duplication on proteins usingevolutionary models to infer adaptive events. I analysed the influence of positive selection invertebrate genes, by contrasting singleton genes and duplicated genes. The conclusion of theanalyses was threefold: (i) positive selection affects diverse phylogenetic branches anddiverse gene categories during vertebrate evolution; (ii) it concerns only a small proportion ofsites (1%-5%); and (iii) whole genome duplication had no detectable impact on theprevalence of this positive selection.I also studied evolution at the amino acid level with different methods to detect functionalshifts (covarion process and constant-but-different process). As in my previous research, Ifound similar numbers of functional shifts between duplicates and between orthologs.The accepted framework for studies of molecular evolution is that orthologs share the samefunction, whereas the function of paralogs diverges. This framework gives a special place togene duplication in evolution, as the main mechanism for generating novelty. With myprevious results showing that duplication and speciation are not so different, we investigatedthe literature to question the evidence for similar or divergent evolution of gene function afterduplication relative to speciation genes. This led us to propose a more rigorous design offuture studies of gene duplication.Finally, based on my automated protocol, we built a database of positive selection invertebrates' genes, Selectome. This database is freely available on the web and will helpfuture evolutionary as well as biochemical studies.

Federal Highway Administration Finding of No Significant Impact for the Council Bluffs Interstate System Improvements Project, August 23, 2012

FHWA and the Iowa Department of Transportation are proposing geometric and capacity improvements to the Interstate 29 and Interstate 80 mainline in Segment 3 and the I-80/I-29 East System interchange, the South Expressway interchange, the U.S. Highway 275 interchange, and the Madison Avenue interchange to to safely and efficiently of transportation in the City of Council Bluffs, the Iowa DOT is also proposing to eliminate several railroad alignments and to develop new, consolidated tracks in Segment 3.

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.

Record of Decision Council Bluffs Interstate System (I-29, I-80 and I-480) Improvements Project TIER 1 Environmental Impact Statement Council Bluffs, Iowa to Omaha, Nebraska FHWA-IA- EIS-04-01F Project Number: IM-029-3(62)54—13-78 Submitted Pursuant to 42 USC 4332(2)(c) and 49 USC 303, October 2008

The Federal Highway Administration (FHWA) approves the selection of the Reconstruction of All or Part of the Interstate (Construction Alternative) as the Preferred Alternative to provide improvements to the interstate system in the Omaha/Council Bluffs metropolitan area, extending across the Missouri River on Interstate 80 to east of the Interstate 480 interchange in Omaha, Nebraska. The study considered long-term, broad-based transportation improvements along Interstate I-29 (I-29), I-80, and I-480, including approximately 18 mainline miles of interstate and 14 interchanges (3 system, 11 service), that would add capacity and correct functional issues along the mainline and interchanges and upgrade the I-80 Missouri River Crossing. FHWA also approves the decisions to provide full access between West Broadway and I-29, design the I-80/I-29 overlap section as a dual-divided freeway, and locating the new I-80 Missouri River Bridge north of the existing bridge. Improvements to the interstate system, once implemented, would bring the segments of I-80 and I-29 (see Figure 1) up to current engineering standards and accommodate future traffic needs. This Record of Decision (ROD) concludes Tier 1 of the Council Bluffs Interstate System (CBIS) Improvements Project. Tier 1 included an examination 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 consisted of a sufficient level of engineering and environmental detail to assist decision makers in selecting a preferred transportation strategy. During Tier 1 a Draft EIS (FHWA-IA- EIS-04-01D) was developed which was approved by FHWA, Iowa DOT, and Nebraska Department of Roads (NDOR) in November 2004 with comments accepted through March 15, 2005. The Draft EIS summarized the alternatives that were considered to address the transportation needs around Council Bluffs; identified reconstruction of all or part of the interstate, the “Construction Alternative,” as the Preferred Alternative; identified three system-level decisions that needed to be made at the Tier 1 level; and invited comment on the issues. The Final EIS (FHWA-IA- EIS-04-01F) further documented the Construction Alternative as the Preferred Alternative and identified the recommended decisions for the three system level decisions that needed to be made in Tier 1. This ROD defines the Selected Alternative determined in the Tier 1 studies.

Council Bluffs Interstate System Improvement Project Tier 2, Segment 3 Pottawatomie County, Iowa Environmental Assessment, March 2011

This Tier 2 Environmental Assessment (EA) presents the results of studies and analyses conducted to determine the potential impacts of proposed improvements in Segment 3 of the Council Bluffs Interstate System (CBIS) in the Council Bluffs metropolitan area. This document is tiered to the Tier 1 Draft and Final Environmental Impact Statements (EIS) that evaluated impacts of the overall CBIS Improvements Project, which includes five segments of independent utility1 This EA on Segment 3 of the Project is divided into the following sections: and encompasses 18 mainline miles of Interstate and 14 interchanges along Interstate 80 (I-80), Interstate 29 (I-29), and Interstate 480 (I-480). More information about the tiering process is found below under Project Background. • Section 1 provides background information on the Project and discusses the relationship between the earlier Tier 1 EIS and this Tier 2 EA. It also discusses the proposed action and the area studied, the purpose of the Project, and the need for the Project based on transportation problems that currently exist or are expected in the future. • Section 2, Alternatives, identifies the range of alternatives considered for Segment 3 to address the transportation problems identified in Section 1. It also identifies the alternatives retained for further study in this EA and the preferred Segment 3 alternative. • Section 3, Affected Environment and Environmental Consequences, describes the general environment for each resource affected by the proposed improvements. It also describes the potential environmental impacts of the Segment 3 Project and methods to avoid, minimize, and mitigate impacts. • Section 4, Disposition, lists the agencies and organizations that will receive copies of this EA and the locations at which this EA will be available for public review. • Section 5, Comments and Coordination, summarizes the agency coordination and public involvement efforts in conjunction with the Segment 3 Project. • Section 6, Conclusion and Recommendation, summarizes resource impacts. • Section 7, References, lists the sources cited in this EA. For Segment 3, the Federal Highway Administration (FHWA) and Iowa Department of Transportation (Iowa DOT) determined that an EA is the appropriate level of Tier 2 study to comply with the National Environmental Policy Act (NEPA) requirements. The primary purpose of an EA is to clearly establish the significance of a project’s environmental impacts. That analysis is included in this document.

Design, data management, and population baseline characteristics of the PERFORM magnetic resonance imaging project.

Quantitative information from magnetic resonance imaging (MRI) may substantiate clinical findings and provide additional insight into the mechanism of clinical interventions in therapeutic stroke trials. The PERFORM study is exploring the efficacy of terutroban versus aspirin for secondary prevention in patients with a history of ischemic stroke. We report on the design of an exploratory longitudinal MRI follow-up study that was performed in a subgroup of the PERFORM trial. An international multi-centre longitudinal follow-up MRI study was designed for different MR systems employing safety and efficacy readouts: new T2 lesions, new DWI lesions, whole brain volume change, hippocampal volume change, changes in tissue microstructure as depicted by mean diffusivity and fractional anisotropy, vessel patency on MR angiography, and the presence of and development of new microbleeds. A total of 1,056 patients (men and women ≥ 55 years) were included. The data analysis included 3D reformation, image registration of different contrasts, tissue segmentation, and automated lesion detection. This large international multi-centre study demonstrates how new MRI readouts can be used to provide key information on the evolution of cerebral tissue lesions and within the macrovasculature after atherothrombotic stroke in a large sample of patients.

Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl.

Taphrina deformans is a fungus responsible for peach leaf curl, an important plant disease. It is phylogenetically assigned to the Taphrinomycotina subphylum, which includes the fission yeast and the mammalian pathogens of the genus Pneumocystis. We describe here the genome of T. deformans in the light of its dual plant-saprophytic/plant-parasitic lifestyle. The 13.3-Mb genome contains few identifiable repeated elements (ca. 1.5%) and a relatively high GC content (49.5%). A total of 5,735 protein-coding genes were identified, among which 83% share similarities with other fungi. Adaptation to the plant host seems reflected in the genome, since the genome carries genes involved in plant cell wall degradation (e.g., cellulases and cutinases), secondary metabolism, the hallmark glyoxylate cycle, detoxification, and sterol biosynthesis, as well as genes involved in the biosynthesis of plant hormones. Genes involved in lipid metabolism may play a role in its virulence. Several locus candidates for putative MAT cassettes and sex-related genes akin to those of Schizosaccharomyces pombe were identified. A mating-type-switching mechanism similar to that found in ascomycetous yeasts could be in effect. Taken together, the findings are consistent with the alternate saprophytic and parasitic-pathogenic lifestyles of T. deformans. IMPORTANCE: Peach leaf curl is an important plant disease which causes significant losses of fruit production. We report here the genome sequence of the causative agent of the disease, the fungus Taphrina deformans. The genome carries characteristic genes that are important for the plant infection process. These include (i) proteases that allow degradation of the plant tissues; (ii) secondary metabolites which are products favoring interaction of the fungus with the environment, including the host; (iii) hormones that are responsible for the symptom of severely distorted leaves on the host; and (iv) drug detoxification enzymes that confer resistance to fungicides. The availability of the genome allows the design of new drug targets as well as the elaboration of specific management strategies to fight the disease.

Report of agreed upon procedure of the Medicaid demonstration project, entitled IowaCare, for the year ended June 30, 2011

Report of agreed upon procedure of the Medicaid demonstration project, entitled IowaCare, for the year ended June 30, 2011

Council Bluffs Interstate System Improvements Project Pottawattamie County, IA and Douglas County, Nebraska, July 19, 2005

The Iowa Department of Transportation (Iowa DOT), Nebraska Department of Roads (NDOR), and the Federal Highway Administration (FHWA) are proposing improvements to the interstate system in the Omaha/Council Bluffs metropolitan area, extending across the Missouri River on Interstate 80 (I-80) to east of the Interstate 480 (I-480) interchange in Omaha, Nebraska (see Figure 1-1). The study considers long-term, broad-base transportation improvements along Interstate I-29 (I-29), I-80, 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.

Council Bluffs Interstate System Improvements Project Pottawattamie County, IA and Douglas County, Nebraska, July 19, 2005

The Iowa Department of Transportation (Iowa DOT), Nebraska Department of Roads (NDOR), and the Federal Highway Administration (FHWA) are proposing improvements to the interstate system in the Omaha/Council Bluffs metropolitan area, extending across the Missouri River on Interstate 80 (I-80) to east of the Interstate 480 (I-480) interchange in Omaha, Nebraska (see Figure 1-1). The study considers long-term, broad-base transportation improvements along Interstate I-29 (I-29), I-80, 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.

Chicago to Iowa City Passenger Rail Project Financial Plan, September 2009

The Chicago to Iowa City Intercity Passenger Rail Program (Program) is a joint undertaking of the Iowa Department of Transportation (Iowa DOT) and the Illinois Department of Transportation (Illinois DOT). The purpose of the Program is to reestablish passenger rail services from Chicago to Iowa City, independently and in concert with the MWRRI (Midwest Regional Rail Initiative). The Chicago to Iowa City Corridor is one part of the vision established by the MWRRI to expand existing and develop new regional passenger rail service to meet existing and future travel demands in the Midwest. This project will expand and create a rail transportation alternative to supplant private automobile, bus, and air travel between Chicago and Iowa City, and intermediate points, and to create new transportation opportunity and capability for people who cannot meet their transportation needs with private automobile, bus and air modes.

Genome sequence of the pea aphid Acyrthosiphon pisum

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.