Aminoterminal amphipathic α-helix AH1 of hepatitis C virus nonstructural protein 4B possesses a dual role in RNA replication and virus production.

Nonstructural protein 4B (NS4B) is a key organizer of hepatitis C virus (HCV) replication complex formation. In concert with other nonstructural proteins, it induces a specific membrane rearrangement, designated as membranous web, which serves as a scaffold for the HCV replicase. The N-terminal part of NS4B comprises a predicted and a structurally resolved amphipathic α-helix, designated as AH1 and AH2, respectively. Here, we report a detailed structure-function analysis of NS4B AH1. Circular dichroism and nuclear magnetic resonance structural analyses revealed that AH1 folds into an amphipathic α-helix extending from NS4B amino acid 4 to 32, with positively charged residues flanking the helix. These residues are conserved among hepaciviruses. Mutagenesis and selection of pseudorevertants revealed an important role of these residues in RNA replication by affecting the biogenesis of double-membrane vesicles making up the membranous web. Moreover, alanine substitution of conserved acidic residues on the hydrophilic side of the helix reduced infectivity without significantly affecting RNA replication, indicating that AH1 is also involved in virus production. Selective membrane permeabilization and immunofluorescence microscopy analyses of a functional replicon harboring an epitope tag between NS4B AH1 and AH2 revealed a dual membrane topology of the N-terminal part of NS4B during HCV RNA replication. Luminal translocation was unaffected by the mutations introduced into AH1, but was abrogated by mutations introduced into AH2. In conclusion, our study reports the three-dimensional structure of AH1 from HCV NS4B, and highlights the importance of positively charged amino acid residues flanking this amphipathic α-helix in membranous web formation and RNA replication. In addition, we demonstrate that AH1 possesses a dual role in RNA replication and virus production, potentially governed by different topologies of the N-terminal part of NS4B.

Combining ability of maize grain yield under different levels of environmental stress

The objectives of this work were to caracterize the tropical maize germplasm and to compare the combining abilities of maize grain yield under different levels of environmental stress. A diallel was performed among tropical maize cultivars with wide adaptability, whose hybrid combinations were evaluated in two sowing dates, in two years. The significance of the environmental effect emphasized the environmental contrasts. Based on grain yield, the environments were classified as favorable (8,331 kg ha-1), low stress (6,637 kg ha-1), high stress (5,495 kg ha-1), and intense stress (2,443 kg ha-1). None of the genetic effects were significant in favorable and intense stress environments, indicating that there was low germplasm variability under these conditions. In low and high stresses, the specific combining ability effects (SCA) were significant, showing that the nonadditive genetic effects were the most important, and that it is possible to select parent pairs with breeding potential. SCA and grain yield showed significant correlations only between the closer environment pairs like favorable/low stress and high/intense stress. The genetic control of grain yield differed under contrasting stress environments for which maize cultivars with wide adaptability are not adequate.

1012-007 Yellow River Headwaters Final Report

The Yellow River Headwaters Watershed (YRHW) drains 26,730 acres of rural land within Winneshiek and Allamakee Counties. While portions of the river have been designated as a High Quality Resource by the State of Iowa, other portions appear on the State's 303(d) List of Impaired Waters due to excessive nutrients, sediment and other water quality issues. The Winneshiek SWCD was fortunate enough to secure WSPF/WPF funds for FY2009 to begin addressing many of the sources of the identified problems, especially along the all-to-critical stream corridor. Initial landowner I producer interest has exceeded expectations and several key BMPs have been installed within the identified critical areas. Yet due to the current budget constraints in the WSPF/WPF programs, we currently have greater landowner I producer interest than we do funds, which is why the District is applying for WIRB funding, to provide supplemental incentives to continue the installation of needed Grade Stabilization Structures, Terraces and Manure Management Systems in identified critical areas. Other funding, currently available to the District, will cover the remaining portions of the project's budget, including staff and our outreach efforts.

09006-003 Bear Creek Watershed Final Report

Bear Creek is an impaired warm water fishery designated as class B(LR) by the Iowa DNR and is on 303 impaired waters list for fish kills and ammonia. Bear Creek is located in eastern Delaware County. This project is designed to improve the water quality of Bear Creek by educating the landowners, operators and watershed community about the importance of this water resource. The goal of the Bear Creek Watershed Project is to improve the water quality of Bear Creek by reducing the amounts of ammoniated manure discharge, fecal coliform bacteria, sediment, nitrogen, and phosphorous. The Bear Creek Watershed Project has been a watershed project since July 2004, first as a Demo project FY 2004-2005 and then full time WSPF/319 project FY06-09. Fish kills have not occurred in 2008-2009. Sediment delivery has decreased in the Bear Creek Watershed by 5,328 tons per year. The objectives of this watershed project will be to improve Livestock Waste Storage, to improve Livestock Waste Usage, to decrease Sediment Losses, and to improve Education & Area Outreach. This project will install 2 manure storage structures (EQIP/project funded), 19 ac of CRP waterways, 12 ac of project waterways, 17 ac of CRP filter strips along stream, 12 water and sediment control basins, 18,000 ft of terraces, 350 ac of new notill planting, and 3,700 ft of streambank protection.

09029-015 Otter Creek Watershed Final Report

The City of West Union has been selected by Iowa Department of Economic Development as a Green Pilot Community. A major project within this designation is the reconstruction of the downtown business district public infrastructure in a sustainable, innovative, and replicable way. A key component of this project is replacement of the impermeable street and sidewalk surfacing with a porous paver system. This system, along with bio-retention cells in intersection bumpouts and sidewalk planters, will infiltrate, then cleanse and cool the storm water prior to a very slow discharge rate to Otter Creek. The project area will see a 95% reduction in peak discharge rate for a 100 year storm and a 20% reduction in runoff volume. West Union is located within the Otter Creek watershed, a designated cold water trout stream just below the city. Fayette County Soil and Water Conservation District and IDNR consider improvement of the water quality of Otter Creek to be very important. This reconstruction of downtown West Union in a sustainable manner will be the start of an overall Otter Creek watershed improvement project.

Iowa's Mississippi River Trail Plan, 2003

The Mississippi River Trail (MRT) is a world-class bicycle trail that will follow the Mississippi River all the way from its headwaters in Minnesota to the Gulf of Mexico. The trail is partially completed; much of it is still in the planning and development stages. When complete, the MRT will Link over 2,000 miles of recreational trails through 10 states, including 280 miles in Iowa. Designated as a National Millennium Trail, the MRT will preserve natural environments along the river, stimulate economic growth in river communities, and provide bicyclists access to a variety of landscapes, history, and culture. The Iowa Department of Transportation commissioned the Center for Transportation Research and Education at Iowa State University to develop a plan for a safe, economically beneficial, and scenic MRT route through Iowa. This report presents the MRT plan for Iowa. It is organized in the following chapters: Executive Summary; (1) Introduction - vision statement and objectives; (2) Iowa MRT Minimum Design Standards; (3) Iowa MRT Route Analysis; (4) Recommended Improvement Plan; (5) MRT Implementation; and (6) Estimated Benefits and Impacts of the Iowa MRT. Additional information is provided in the following appendices: (A) GIS Analysis for the MRT; (B) Iowa MRT Maps; (C) Public Input; (D) Public Comments; and (E) References.

05046-017 Dry Run Creek Watershed Final Report

Dry Run Creek Watershed was designated an impaired waterbody by DNR in 2002, following an assessment of the biota in the stream by DNR Biologist, Tom Wilton. Subsequent studies by IOWATER Snapshot effort in 2003, found e-coli bacteria concentrations and high nitrate readings in excess of the State of Iowa limits for recreational streams. The Dry Run Creek Watershed Improvement Project is comprised of five major components. Three components will feature demonstrations of structural best management practices (BMPs) to protect water quality in Dry Run Creek. The fourth is an educational workshop to "kick-off" the initiative and background the stakeholders of the watershed in new stormwater management strategies for water quality protection. The fifth is a monitoring program that will provide data on the effectiveness of the practices to be demonstrated. Measurable outcomes from these projects include monitoring to document the effectiveness of infiltration­ based BMPs to reduce pollutant loading in urban stormwater runoff and reducing the volume of stormwater discharged directly into Dry Run Creek via storm sewer flows. Understanding of and social acceptance of new stormwater strategies and practices will also be monitored by surveys of watershed stakeholders and compared to findings of a survey done before the start of the project.

1010-005 Bloody Run Creek Watershed Final Report

The City of Marquette lies in the 65,000 acre Mississippi River watershed, and is surrounded by steep bluffs. Though scenic, controlling water runoff during storm events presents significant challenges. Flash-flooding from the local watershed has plagued the city for decades. The people of Marquette have committed to preserve the water quality of key natural resources in the area including the Bloody Run Creek and associated wetlands by undertaking projects to control the spread of debris and sediment caused by excess runoff during area storm events. Following a July 2007 storm (over 8” of rain in 24 hours) which caused unprecedented flood damage, the City retained an engineering firm to study the area and provide recommendations to eliminate or greatly reduce uncontrolled runoff into the Bloody Run Creek wetland, infrastructure damage and personal property loss. Marquette has received Iowa Great Places designation, and has demonstrated its commitment to wetland preservation with the construction of Phase I of this water quality project. The Bench Area Storm Water Management Plan prepared by the City in 2008 made a number of recommendations to mitigate flash flooding by improving storm water conveyance paths, detention, and infrastructure within the Bench area. Due to steep slopes and rocky geography, infiltration based systems, though desirable, would not be an option over surface based systems. Runoff from the 240 acre watershed comes primarily from large, steep drainage areas to the south and west, flowing to the Bench area down three hillside routes; designated as South East, South Central and South West. Completion of Phase I, which included an increased storage capacity of the upper pond, addressed the South East and South Central areas. The increased upper pond capacity will now allow Phase II to proceed. Phase II will address runoff from the South West drainage area; which engineers have estimated to produce as much water volume as the South Central and South East areas combined. Total costs for Phase I are $1.45 million, of which Marquette has invested $775,000, and IJOBS funding contributed $677,000. Phase II costs are estimated at $617,000. WIRB funding support of $200,000 would expedite project completion, lessen the long term debt impact to the community and aid in the preservation of the Bloody Run Creek and adjoining wetlands more quickly than Marquette could accomplish on its own.

Fish Habitat Indicators for the Assessment of Wadeable, Warmwater Streams

Physical habitat characteristics such as stream width, depth, instream cover, and substrate composition are important environmental factors that shape Iowa’s stream fish species assemblages. The Iowa Department of Natural Resources (IDNR) stream biological assessment program collects physical habitat data to help interpret fish assemblage sampling results in order to assess stream health condition and the attainment status of designated aquatic life uses. The quantitative habitat indicators and interpretative guidelines developed in this study are designed for specific applications within the stream bioassessment program. These tools might also be useful to natural resource managers for purposes such as stream habitat improvement prioritization, goal-setting, and performance assessment.

Development of herbicide-tolerant irrigated rice cultivars

The objective of this work was to develop new irrigated rice lines tolerant to imidazolinone herbicides. The backcross breeding procedure was used to transfer the imidazolinone tolerance allele from mutant 93AS3510 to the recurrent parents 'BRS 7 Taim' and 'BRS Pelota'. Individual herbicide-tolerant plants were selected in each generation, for three backcrossings (RC1 to RC3), followed by three selfing generations (RC3F1 to RC3F3). The best four RC3F3 lines for agronomic traits were genotyped with 44 microsatellite markers. The observed conversion index of the new imidazolinone-tolerant lines varied from 91.86 to 97.67%. Pairwise genetic distance analysis between these lines and 22 accessions from the Embrapa's Rice Germplasm Bank clustered the new lines with their respective recurrent parents, but not with 'IRGA 417', which was originally used as recurrent parent to derive IRGA 422 CL, the only imidazolinone-tolerant irrigated rice cultivar recommended for cultivation in Brazil. Therefore, these lines represent new options of genetically diverse imidazolinone-tolerant rice accessions. Lines CNA10756 ('BRS Sinuelo CL') and CNA10757 will be released for cultivation in the Clearfield irrigated rice production system in Rio Grande do Sul, Brazil.

Prospective assessment of trocar-specific morbidity in laparoscopy.

BACKGROUND: The purpose of the present study was to challenge the hypothetical advantage of single port laparoscopy (SPL) over conventional laparoscopy by measuring prospectively the morbidity specifically related to conventional trocar sites (TS). METHODS: From November 2010 to December 2011, 300 patients undergoing various laparoscopic procedures were enrolled. Patient, surgery, and trocar characteristics were recorded. We evaluated at three time points (in-hospital and at 1 and 6 months postoperatively) specifically for each TS, pain (Visual Analog Scale), morbidity (infection, hematoma, hernia), and cosmesis (Patient Scar Assessment Score; PSAS). Patients designated their "worst TS," and a composite endpoint "bad TS" was defined to include any adverse outcome at a TS. RESULTS: We analyzed 1,074 TS. Follow-up was >90 %. Pain scores of >3/10 at 1 and 6 months postoperatively, were reported by 3 and 1 % of patients at the 5 mm TS and by 9 and 1 % at the larger TS, respectively (5 mm TS vs larger TS; p = 0.001). Pain was significantly lower for TS located in the lower abdomen than for the upper abdomen or the umbilicus (p = 0.001). The overall complication rate was <1 % and significantly lower for the 5 mm TS (hematoma p = 0.046; infection p = 0.0001). No hernia was found. The overall PSAS score was low and significantly lower for the 5 mm TS (p = 0.0001). Significant predictors of "bad TS" were larger TS (p = 0.001), umbilical position (p = 0.0001), emergency surgery (p = 0.0001), accidental trocar exit (p = 0.022), fascia closure (p = 0.006), and specimen extraction site (p = 0.0001). CONCLUSIONS: Specific trocar morbidity is low and almost negligible for 5 mm trocars. The umbilicus appears to be an unfavorable TS.

Phytogeographical origin of Madeiran common beans based on phaseolin patterns

The objective of this work was to determine the geographic origin of the Madeiran common bean (Phaseolus vulgaris) gene pool. Phaseolin patterns of 50 accessions representing the diversity of common bean collected in Madeira, Portugal, and conserved in the ISOPlexis Germplasm Bank, were analysed using the Experion automated electrophoresis system, based on lab-on-a-chip technology. Five common bean standard varieties with typical phaseolin patterns were used to determine the phytogeographical origin of the Madeiran common bean accessions. Ninety two percent of the accessions exhibited a phaseolin pattern consistent with the one of common bean types belonging to the Andean gene pool, while the origin of the remaining 8% of the accessions was indistinguishable. The application of a similarity coefficient of 85%, based on Pearson correlations, increases the number of accessions with uncertain pattern. The analytical approach used permitted the determination of the origin of the common bean gene pool, which is Andean in 98% of the cases, and clustering of the observed variability among the Madeiran common beans.

The complementary strand of the human T-cell leukemia virus type 1 RNA genome encodes a bZIP transcription factor that down-regulates viral transcription.

The RNA genome of the human T-cell leukemia virus type 1 (HTLV-1) codes for proteins involved in infectivity, replication, and transformation. We report in this study the characterization of a novel viral protein encoded by the complementary strand of the HTLV-1 RNA genome. This protein, designated HBZ (for HTLV-1 bZIP factor), contains a N-terminal transcriptional activation domain and a leucine zipper motif in its C terminus. We show here that HBZ is able to interact with the bZIP transcription factor CREB-2 (also called ATF-4), known to activate the HTLV-1 transcription by recruiting the viral trans-activator Tax on the Tax-responsive elements (TxREs). However, we demonstrate that the HBZ/CREB-2 heterodimers are no more able to bind to the TxRE and cyclic AMP response element sites. Taking these findings together, the functional inactivation of CREB-2 by HBZ is suggested to contribute to regulation of the HTLV-1 transcription. Moreover, the characterization of a minus-strand gene protein encoded by HTLV-1 has never been reported until now.

Iowa Energy Office Program Initiatives, April 2015

The Iowa Economic Development Authority (IEDA) Energy Office sets energy policy direction for Iowa and receives designated funding from the State Energy Program Formula from the Department of Energy to carry out designated energy activities. These activities include promoting energy efficiency, biofuels and renewable energy.

Genetic parameters and variability in physic nut accessions during early developmental stages

The objective of this work was to estimate the genetic parameters and variability among accessions (half-sib families) of physic nut (Jatropha curcas) during the early stages of development. For this study, 110 accessions in the first year of development of the physic nut germplasm bank, maintained at Embrapa Cerrados, DF, Brazil, were evaluated in situ. The experiment was established in a randomized complete block design, with two replicates and five plants per plot arranged in rows at 4x2 m spacing. Grain yield, total number of branches per plant, plant height, stem diameter, canopy projection on the row, canopy projection between rows, canopy volume, number of days until first flowering and height of the first inflorescence were evaluated. Estimates of vegetative genetic parameters showed the existence of genetic variability in the physic nut germplasm bank. Physic nut accessions of the germplasm bank were grouped into five similarity groups based on character divergence. Although preliminary, the obtained results are promising for showing potential for Jatropha improvement with selective efficiency.