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Modified Kigali Combined Staging Predicts Risk Of Mortality In Hiv-Infected Adults In Lusaka, Zambia, Philip J. Peters, Isaac Zulu, Nzali G. Kancheya, Shabir Lakhi, Elwyn Chomba, Cheswa Vwalika, Dhong-Jin Kim, Ilene Brill, Jareen Meinzen-Derr, Amanda Tichacek, Susan A. Allen

Nebraska Center for Virology: Faculty Publications

We assessed the utility of the modified Kigali combined (MKC) staging system for predicting survival in HIV-infected Zambian adults in a prospective, longitudinal, open cohort. From 1995 to 2004, HIV-discordant couples (one HIV-infected partner and one HIV-negative partner) were recruited from couples’ voluntary counseling and testing centers in Lusaka, Zambia and followed at 3-month intervals. MKC stage, which incorporates clinical stage with erythrocyte sedimentation rate (ESR), hematocrit, and body mass index (BMI), was determined at enrollment. Kaplan–Meier survival and Cox proportional hazard methods were used to calculate median survival and relative hazards. We enrolled 1479 HIV-discordant couples with a combined …

Development Of An Immunofluorescence Assay Using Recombinant Proteins Expressed In Insect Cells To Screen And Confirm Presence Of Human Herpesvirus 8-Specific Antibodies, Veenu Minhas, Lynsey N. Crosby, Kay L. Crabtree, Saul Phiri, Tendai J. M'Soka, Chipepo Kankasa, William J. Harrington, Charles D. Mitchell, Charles Wood

Nebraska Center for Virology: Faculty Publications

Human herpesvirus 8 (HHV-8), or Kaposi’s sarcoma (KS)-associated herpesvirus, has been linked to all forms of KS. The results of most current serological assays for the detection of HHV-8-specific antibodies have low levels of concordance among themselves. To establish a sensitive and specific testing strategy that can be used to screen for HHV-8-specific antibodies, three HHV-8 proteins, ORF65, ORF73, and K8.1A, were expressed by using baculoviral vectors in insect cells and incorporated into a monoclonal antibodyenhanced immunofluorescence assay (mIFA) termed the Sf9 three-antigen mIFA. The results obtained by this mIFA were compared to those obtained by a standard mIFA with …

Small-Molecule Cd4 Mimics Interact With A Highly Conserved Pocket On Hiv-1 Gp120, Navid Madani, Arne Schön, Amy M. Princiotto, Judith M. Lalonde, Joel R. Cpurter, Takahiro Soeta, Danny Ng, Liping Wang, Evan T. Brower, Shi-Hua Xiang, Young Do Kwon, Chih-Chin Huang, Richard Wyatt, Peter D. Kwong, Ernesto Freire, Amos B. Smith Iii, Joseph Sodroski

Nebraska Center for Virology: Faculty Publications

Human immunodeficiency virus (HIV-1) interaction with the primary receptor, CD4, induces conformational changes in the viral envelope glycoproteins that allow binding to the CCR5 second receptor and virus entry into the host cell. The small molecule NBD-556 mimics CD4 by binding the gp120 exterior envelope glycoprotein, moderately inhibiting virus entry into CD4-expressing target cells, and enhancing CCR5 binding and virus entry into CCR5-expressing cells lacking CD4. Studies of NBD-556 analogues and gp120 mutants suggest that: 1) NBD-556 binds within the Phe 43 cavity, a highly conserved, functionally important pocket formed as gp120 assumes the CD4- bound conformation; 2) the NBD-556 …

The Human Immunodeficiency Virus Type 1 Envelope Confers Higher Rates Of Replicative Fitness To Perinatally Transmitted Viruses Than To Nontransmitted Viruses, Xiaohong Kong, John T. West, Hong Zhang, Danielle M. Shea, Tendai J. M’Soka, Charles Wood

Nebraska Center for Virology: Faculty Publications

Selection of a minor viral genotype during perinatal transmission of human Immunodeficiency virus type 1

(HIV-1) has been observed, but there is a lack of information on the correlation of the restrictive transmission

with biological properties of the virus, such as replicative fitness. Recombinant viruses expressing the enhanced

green fluorescent protein or the Discosoma sp. red fluorescent (DsRed2) protein carrying the V1 to V5

regions of env from seven mother-infant pairs (MIPs) infected by subtype C HIV-1 were constructed, and

competition assays were carried out to compare the fitness between the transmitted and nontransmitted

viruses. Flow cytometry was used to …

Varying Efficiency Of Long-Term Replication Of Papillomaviruses In Saccharomyces Cerevisiae, Adam J. Rogers, Malte Loggen, Karen Lee, Peter C. Angeletti

Nebraska Center for Virology: Faculty Publications

Human papillomaviruses (HPVs) replicate in mitotically active basal keratinocytes. Two virally encoded proteins, E1, a helicase, and E2, a transcription factor, are important players in replication and maintenance of HPV episomes. We previously showed that HPV16 could replicate stably in Saccharomyces cerevisiae [Angeletti, P.C., Kim, K., Fernandes, F.J., and Lambert, P.F. (2002)] and we identified cis-elements that mediate replication and maintenance [J. Virol. 76(7), 3350-3358.; Kim, K., Angeletti, P.C., Hassebroek, E.C., and Lambert, P.F. (2005)]. Here, we demonstrate that although multiple HPV genomes replicate stably in yeast, they do so with differing long-term efficiency; HPV6-Ura3 is replicated at the …

Effects Of Shielding Adenoviral Vectors With Polyethylene Glycol On Vector-Specific And Vaccine-Mediated Immune Responses, Eric A. Weaver, Michael A. Barry

Nebraska Center for Virology: Faculty Publications

Many individuals have been previously exposed to human adenovirus serotype 5 (Ad5). This prior immunity has long been known to hinder its use for gene therapy and as a gene-based vaccine. Given these immunogenicity problems, we have tested whether polyethylene glycol (PEG) can blunt immune effects against Ad5 during systemic and mucosal vaccination. Ad5 vectors were covalently modified with 5-, 20-, and 35-kDa linear PEG polymers and evaluated for their ability to produce immune responses against transgene antigen prod- ucts and the vector itself. We show that shielding Ad5 with different-sized PEGs generally reduces transduction and primary antibody responses by …

Missouri River Recovery Program Keeping Recovery On Track: Annual Report

United States Army Corps of Engineers, Omaha District

Each calendar year, the U.S. Army Corps of Engineers produces a report to document the progress of the Missouri River Recovery Program (MRRP). The Annual Report describes the team’s success in meeting the requirements laid out in the U.S. Fish and Wildlife Service’s 2000 Biological Opinion, amended in 2003, on the Operation of the Missouri River Main Stem System, Operation and Maintenance of the Missouri River Bank Stabilization and Navigation Project and Operation of the Kansas River Reservoir System.

This fact sheet will highlight MRRP efforts in 2008, including new projects, program successes and areas for improvement.

Diets Of Lesser Scaup During Spring Migration Throughout The Upper-Midwest Are Consistent With The Spring Condition Hypothesis, Michael J. Anteau, Alan Afton

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

The spring condition hypothesis (SCH) states that the current decline of the North American scaup population (Lesser [Aythya affinis] and Greater Scaup [A. marila] combined) is due to a decline in quality or availability of scaup foods on wintering, spring migration, or breeding areas that has caused a reduction in female body condition and subsequent reproductive success. Our previous research indicated that forage quality in diets of Lesser Scaup (hereafter scaup) at two sites in Northwestern Minnesota was lower in springs 2000-2001 than that reported for springs 1986-1988, consistent with the SCH. Accordingly, we further tested …

Using Plasma-Lipid Metabolites To Index Changes In Lipid Reserves Of Free-Living Lesser Scaup (Aythya Affinis), Michael Anteau, Alan Afton

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

Understanding daily lipid-reserve changes in migrating wild birds is important for habitat assessment and species conservation. Plasma-lipid metabolites have been used to estimate rates of lipid accumulation or catabolism in small-bodied wild birds(<75 g), but this has not been validated for larger-bodied wild birds such as waterfowl. We developed an index for detecting whether individual birds accumulate or catabolize lipid reserves by regressing plasma-lipid metabolite levels(triglyceride and β-hydroxybutyrate) and known one-day mass changes(daily mass change) of 22 free-living Lesser Scaup (Aythya affinis; a larger-bodied species with typical mass range 600–1,000 g). Triglyceride and β-hydroxybutyrate predicted 75% of the variation in daily mass change (F = 28.85, df = 2 and 19, P < 0.001). Triglyceride was positively correlated (P = 0.029) with mass change, and β-hydroxybutyrate was negatively cor¬related (P < 0.001) with mass change (daily mass change = –54.49+ 11.82 [triglyceride] – 28.65 [β-hydroxybutyrate log]). Our results in¬dicate that triglyceride and β-hydroxybutyrate can estimate one-day changes in mass of free-living wild Lesser Scaup, which provides an index to daily changes in lipid reserves and should be useful for assessing quality of migration habitat.

A Two-Part Measure Of Degree Of Invasion For Cross-Community Comparisons, Qinfeng Guo, Amy Symstad

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

Invasibility is a critical feature of ecological communities, especially for management decisions. To date, invasibility has been measured in numerous ways. Although most researchers have used the richness (or number) of exotic species as a direct or indirect measure of community invasibility, others have used alternative measures such as the survival, density, or biomass of either a single or all exotic species. These different measures, even when obtained from the same communities, have produced inconsistent results and have made comparisons among communities difficult. Here, we propose a measure of the degree of invasion (DI) of a community as a surrogate …

Comparing Local Vs. Global Visible And Near-Infrared (Visnir) Diffuse Reflectance Spectroscopy (Drs) Calibrations For The Prediction Of Soil Clay, Organic C And Inorganic C, Joel B. Sankey, David J. Brown, Melisa L. Bernard, Rick L. Lawrence

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

Local, field-scale, VisNIR-DRS soil calibrations generally yield the most accurate predictions but require a substantial number of local calibration samples at every application site. Global to regional calibrations are more economically efficient, but don't provide sufficient accuracy for many applications. In this study, we quantified the value of augmenting a large global spectral library with relatively few local calibration samples for VisNIR-DRS predictions of soil clay content (clay), organic carbon content (SOC), and inorganic carbon content (IC). VisNIR models were constructed with boosted regression trees employing global, local+global, and local spectral data, using local samples from two low-relief, sedimentary bedrock …

Missouri River Recovery Program: Emergent Sandbar Habitat Program

United States Army Corps of Engineers, Omaha District

States, cities and individuals benefit greatly from a healthy and thriving Missouri River. Maintaining a healthy river, including protecting species that live along the river, is a top priority for the U.S. Army Corps of Engineers and the U.S. Congress.

The survival of the endangered least tern and threatened piping plover is crucial to maintaining a thriving ecosystem on the Missouri River. While both shorebirds nest elsewhere as well, the sandbars of the Missouri River and reservoir shorelines are important to their overall survival. In 2002, the U.S. Fish and Wildlife Service designated areas along much of the Missouri River …

Missouri River Recovery Program: Using The Best Available Science: Monitoring Program

United States Army Corps of Engineers, Omaha District

There is a growing body of information surrounding the manner in which a healthy
river system, such as the Missouri River, functions naturally. As we work towards mitigation, recovery and ultimately restoration, an extensive science program has been implemented so that our actions can be assessed and adjusted as we move towards meeting Missouri River Recovery Program (MRRP) goals.

Missouri River Recovery Program: Finding The Right Balance: Sediment Management

United States Army Corps of Engineers, Omaha District

The goal of the Missouri River Recovery Program (MRRP) is to create a sustainable ecosystem for the river’s native species while protecting and maintaining the Corps’ congressionally-authorized project purposes. Many of the river’s uses – such as habitat, agriculture, municipal water use, flood protection, navigation and hydropower – can be threatened by imbalanced sediment distribution in sections of the Missouri River and its tributaries.

Missouri River Recovery Program: The Perils Of The Pallid Sturgeon

United States Army Corps of Engineers, Omaha District

The pallid sturgeon is native to the Yellowstone River, Missouri River, middle and lower Mississippi River, and the lower segments of their major tributaries. It is a bottom-dwelling fish that lives in large, turbid, freeflowing rivers. The pallid sturgeon has poor vision and relies on its highly sensitive barbels to locate food. Individuals can live up to 70 years, and females do not reproduce until they are 15 to 20 years old.

Historical records indicate that the pallid sturgeon was never a common species, but it has experienced significant declines in distribution and abundance over the last 75 years. During …

Missouri River Recovery Program: Spring Rise And The Missouri River

United States Army Corps of Engineers, Omaha District

Spring rise is a term used to describe the natural fluctuations in a river’s water level. Flooding is a natural part of a river’s relationship with its surrounding floodplain, and a river’s native wildlife and plant life become specially adapted to a river’s annual rise and fall. The frequency, duration, magnitude and timing of a river’s floods determine the types of species that associate with the river, over time creating an interdependent food web and ecosystem. In addition to controlling river biodiversity, spring rises affect the physical environment by adding nutrients to the surroundings, creating habitats for certain species, and …

U.S. Army Corps Of Engineers Omaha District Quarterly Drought Report, February 2008

United States Army Corps of Engineers, Omaha District

Current Conditions

Reservoir Predictions

Drought Outlook

Missouri River Region Mountain Snowpack Report

Ft. Peck, Montana

Reservoir Elevation Overview

Water Intake Overview

Access Overview

Noxious Weeds Overview

Cultural Resources Overview

Garrison, North Dakota

Reservoir Elevation Overview

Water Intake Overview

Access Overview

Boat Ramp Information

Noxious Weeds Overview

Cultural Resources Overview

Other Areas of Interest/Concern

Oahe, South Dakota

Reservoir Elevation Overview

Water Intake Overview

Access Overview

Noxious Weeds Overview

Cultural Resources Overview

Mainstem Reservoir Storage Comparison Water Years 2004, 2005, 2006, 2007, 2008

Ft. Peck, MT

Garrison, ND

Oahe, SD

Effects, Uptake, And Fate Of 2,4,6-Trinitrotoluene Aged In Soil In Plants And Worms, Elly Ph Best, Henry E. Tatem, Kaaren N. Geter, Melissa L. Wells, Brian K. Lane

United States Army Corps of Engineers, Omaha District

The present study was aimed at providing data to be used at predicting exposure-based effects of 2,4,6-trinitrotoluene (TNT) aged in soil on endpoint organisms representing two trophic levels. These data can be used to define criteria or reference values for environmental management and conducting specific risk assessment. Long-term exposure tests were conducted to evaluate sublethal toxicity and uptake of aged soil-based explosives, with TNT as the main contaminant. In these tests, plants were exposed for 55 d, and biomass and explosives residues were determined. Worms were exposed for 28 and 42 d, and biomass, number, and tissue residues were determined. …

Impact Of West Nile Virus And Other Mortality Factors On American White Pelicans At Breeding Colonies In The Northern Plains Of North America, Marsha A. Sovada, Pamela J. Pietz, Kathryn A. Converse, D. Tommy King, Erik K. Hofmeister, Paulette Scherr, Hon S. Ip

United States Geological Survey, Northern Prairie Wildlife Research Center: Publications

American white pelicans (Pelecanus erythrorhynchos) are colonial-nesting birds and their breeding sites are concentrated in a few small areas, making this species especially vulnerable to factors that can influence productivity, such as disease, disturbance, predation, weather events and loss of nesting habitat. Nearly half of the American white pelican population breeds at four colonies in the northern plains: Chase Lake National Wildlife Refuge (NWR) in North Dakota, Bitter Lake (Waubay NWR) in South Dakota, Medicine Lake NWR in Montana, and Marsh Lake in Minnesota. Thus, sustained productivity at these colonies is crucial to the health of the entire …

Plant-Feeding Hemiptera And Orthoptera Communities In Native And Restored Mesic Tallgrass Prairies, Kristine T. Nemec, Thomas B. Bragg

United States Army Corps of Engineers, Omaha District

Aboveground Hemiptera and Orthoptera communities were compared among three native and three restored mesic tallgrass prairies along the Platte River in central Nebraska to assess both the relative success of restored sites and the relationship between insect and plant communities. Hemiptera and Orthoptera were sampled using sweep nets in early June, mid-July, and mid-August 2000. Plant species composition was assessed in early June and mid-August. A total of 89 Auchenorrhyncha (71 Cicadellidae, 15 Fulgoroidea, and 3 Membracidae) and 23 orthopterans (15 Acrididae and 8 Tettigoniidae) were collected. Eighty-five plant species were observed in combined study sites. Shannon diversity was significantly …

Towards Universal Cover Decoding, Nathan Axvig, Deanna Dreher, Katherine Morrison, Eric T. Psota, Lance C. Pérez, Judy L. Walker

Department of Mathematics: Faculty Publications

Low complexity decoding of low-density paritycheck (LDPC) codes may be obtained from the application of iterative message-passing decoding algorithms to the bipartite Tanner graph of the code. Arguably, the two most important decoding algorithms for LDPC codes are the sum-product decoder and the min-sum (MS) decoder. On a bipartite graph without cycles (a tree), the sum-product decoder minimizes the probability of bit error, while the min-sum decoder minimizes the probability of word error [9]. While the behavior of sum-product and min-sum is easily understood when operating on trees, their behavior becomes much more difficult to characterize when the Tanner graph …

Ldpc Codes From Voltage Graphs, Christine A. Kelley, Judy L. Walker

Department of Mathematics: Faculty Publications

Several well-known structure-based constructions of LDPC codes, for example codes based on permutation and circulant matrices and in particular, quasi-cyclic LDPC codes, can be interpreted via algebraic voltage assignments. We explain this connection and show how this idea from topological graph theory can be used to give simple proofs of many known properties of these codes. In addition, the notion of abelianinevitable cycle is introduced and the subgraphs giving rise to these cycles are classified. We also indicate how, by using more sophisticated voltage assignments, new classes of good LDPC codes may be obtained.

Average Min-Sum Decoding Of Ldpc Codes, Nathan Axvig, Deanna Dreher, Katherine Morrison, Eric T. Psota, Lance C. Pérez, Judy L. Walker

Department of Mathematics: Faculty Publications

Simulations have shown that the outputs of minsum (MS) decoding generally behave in one of two ways: the output either eventually stabilizes at a codeword or eventually cycles through a finite set of vectors that may include both codewords and non-codewords. This inconsistency in MS across iterations has significantly contributed to the difficulty in studying the performance of this decoder. To overcome this problem, a new decoder, average min-sum (AMS), is proposed; this decoder outputs the average of the min-sum output vectors over a finite set of iterations. Simulations comparing MS, AMS, linear programming (LP) decoding, and maximum likelihood (ML) …

Numerical Simulation Of A Novel Blast Wave Mitigation Device, Zhenbi Su, Wen Peng, Zhaoyan Zhang, George Gogos, Reed Skaggs, Bryan Cheeseman

Department of Mechanical and Materials Engineering: Faculty Publications

This paper proposes a novel blast wave mitigation device, consisting of a piston–cylinder assembly. A shock wave is induced inside the device when it is subject to a blast wave. The shock wave propagates inside the device and is reflected repeatedly. The physical processes within the blast wave mitigation device are simulated numerically. Numerical predictions are in excellent agreement with analytical solutions for special cases of the investigated problem that are available in the literature. The peak pressure on the base of the device caused by the blast wave is studied using a number of design parameters. The numerical simulation …

A Dgge-Cloning Method To Characterize Arbuscular Mycorrhizal Community Structure In Soil, Zhanbei Liang, Rhae A. Drijber, Donald J. Lee, Ismail M. Dwiekat, Steven D. Harris, David A. Wedin

Department of Plant Pathology: Faculty Publications

Although arbuscular mycorrhizal fungi (AMF) are crucial for ecosystem functioning, characterizing AMF community structure in soil is challenging. In this study, nested polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) were combined with cloning of fungal 18S ribosomal gene fragments for the rapid comparison of AMF community structure in soil. Reference AMF isolates, representing four major genera of AMF, were used to develop the method. Sequential amplification of 18S rDNA fragments by nested PCR using primer pairs AM1-NS31 and Glo1-NS31GC followed by DGGE analysis yielded a high-resolution band profile. In parallel, 18S rDNA fragment clone libraries were constructed …

Virulence Diversity Of The Common Bean Rust Pathogen Within And Among Individual Bean Fields And Development Of Sampling Strategies, C. Jochua, M. I. V. Amane, J. R. Steadman, X. Xue, K. M. Eskidge

Department of Plant Pathology: Faculty Publications

There is a dearth of information on pathogen variation within an individual field. In this study, virulence diversity of Uromyces appendiculatus, cause of bean rust, within individual fields was investigated. From six bean fields in the United States, Honduras, Dominican Republic, and South Africa, 380 U. appendiculatus isolates were differentiated into 65 virulence phenotypes on bean lines containing Andean- and Middle American-derived rust resistance genes. Race variation among bean rust isolates from different geographic regions was found, and virulence phenotypes found in fields from tropical and subtropical regions were more virulent and diverse than those found in fields from …

Branching Of Fungal Hyphae: Regulation, Mechanisms And Comparison With Other Branching Systems, Steven D. Harris

Department of Plant Pathology: Faculty Publications

The ability of rapidly growing hyphae to generate new polarity axes that result in the formation of a branch represents one of the most important yet least understood aspects of fungal cell biology. Branching is central to the development of mycelial colonies and also appears to play a key role in fungal interactions with other organisms. This review presents a description of the two major patterns of hyphal branching, apical and lateral, and highlights the roles of internal and external factors in the induction of branch formation. In addition, potential mechanisms underlying branch site selection are outlined, and the possible …

First Report Of Annual Bluegrass Weevil, Listronotus Maculicollis, Damage In Ohio, John L. Koenig, David J. Shetlar, Joseph W. Rimelspach, Michael J. Boehm

Department of Plant Pathology: Faculty Publications

Annual bluegrass weevil [Listronotus maculicollis (Kirby) (1)] larvae, pupae, and adults were recovered and identified in a sample received by the C. Wayne Ellett Plant and Pest Diagnostic Clinic (CWEPPDC) at Ohio State University on 19 June 2007. Damage to the approaches and collars of four golf course putting greens was detected by the superintendent of Stonewater Golf Club, Highland Heights, OH (a suburb of Cleveland) during the week of 11 June 2007. The superintendent suspected damage from the larvae of the black turfgrass ataenius, Ataenius spretulus (1). Insecticide applications applied to suppress black turfgrass ataenius did not provide …

Rapid Development Of Fungicide Resistance By Sclerotinia Homoeocarpa On Turfgrass, Young-Ki Jo, Seog Won Chang, Michael J. Boehm, Geunhwa Jung

Department of Plant Pathology: Faculty Publications

Dollar spot, caused by Sclerotinia homoeocarpa, is the most prevalent and economically important turfgrass disease in North America. Increasing levels of fungicide resistance, coupled with tightening environmental scrutiny of existing fungicides, has left fewer options for managing dollar spot. More knowledge about S. homoeocarpa populations is needed to improve dollar spot management strategies, especially with respect to minimizing the development of fungicide resistance. Population diversity of S. homoeocarpa was examined using inter-simple sequence repeat markers and vegetative compatibility assays. Two subgroups were found in S. homoeocarpa field populations on both fairway and putting green turfgrass at a research field …

Inoculation Strategies To Assess Biological Interactions Between Fusarium And Alternaria Species Infecting Sorghum, Deanna L. Funnell-Harris, Jeffrey F. Pedersen

Department of Plant Pathology: Faculty Publications

New cultivars of sorghum are being developed for increased food use, as livestock feed, and for the bioenergy industry by manipulation of secondary metabolic pathways through breeding. Previous work has suggested that such modifications may have an impact on cultivar response to fungal pathogens. We investigated four inoculation strategies that may be used in studies involving pathogens of sorghum. Plants of elite sorghum genotypes ‘Wheatland’ and RTx430, commonly used in breeding programs, were inoculated with isolates of Alternaria alternata, Fusarium equiseti, Fusarium proliferatum, Fusarium solani, Fusarium thapsinum, and Fusarium verticillioides recovered from field-grown sorghum. Wound inoculation of the peduncles …