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Protein-Protein Docking Using Region-Based 3d Zernike Descriptors., Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Background

Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur.

Results

We present a novel protein docking algorithm based …

Application Of 3d Zernike Descriptors To Shape-Based Ligand Similarity Searching, Vishwesh Venkatraman, Padmasini Ramji Chakravarthy, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Background

The identification of promising drug leads from a large database of compounds is an important step in the preliminary stages of drug design. Although shape is known to play a key role in the molecular recognition process, its application to virtual screening poses significant hurdles both in terms of the encoding scheme and speed.

Results

In this study, we have examined the efficacy of the alignment independent three-dimensional Zernike descriptor (3DZD) for fast shape based similarity searching. Performance of this approach was compared with several other methods including the statistical moments based ultrafast shape recognition scheme (USR) and SIMCOMP, …

Meiosis Drives Extraordinary Genome Plasticity In The Haploid Fungal Plant Pathogen Mycosphaerella Graminicola, Alexander H.J. Wittenberg, Theo A. J. Van Der Lee, Sarrah Ben M'Barek, Sarah B. Ware, Stephen B. Goodwin, Andrzej Kilian, Richard G.F. Visser, Gert H.J. Kema, Henk J. Schouten

Department of Botany and Plant Pathology Faculty Publications

Meiosis in the haploid plant-pathogenic fungus Mycosphaerella graminicola results in eight ascospores due to a mitotic division following the two meiotic divisions. The transient diploid phase allows for recombination among homologous chromosomes. However, some chromosomes of M. graminicola lack homologs and do not pair during meiosis. Because these chromosomes are not present universally in the genome of the organism they can be considered to be dispensable. To analyze the meiotic transmission of unequal chromosome numbers, two segregating populations were generated by crossing genetically unrelated parent isolates originating from Algeria and The Netherlands that had pathogenicity towards durum or bread wheat, …

Examining The Nature Of Technology Graduate Education, Nathan Hartman, Marvin Sarapin, Gary Bertoline, Susan Sarapin

Computer Graphics Technology Faculty Publications

According to the Association of Technology, Management, and Applied Engineering (ATMAE), graduate-level studies in technology are designed to prepare technologists to focus on the applied challenges of society, industry, and government through integration- and implementation- oriented activities (2009). Although the association’s affiliated institutions and membership have been interested in research and graduate education for many years, increased discussion is needed concerning both the goals and delivery of graduate programs leading to master’s and doctoral degrees related to the field for the 21st century. Many of the academic participants in this organization, as well as others, work at universities that include …

Lifting The Museum's Burden From The Backs Of The University: Should The Art Collection Be Treated As Part Of The Endowment Symposium: Tax-Exempt Organizations And The State: New Conditions On Exempt Status, Linda Sugin

Faculty Scholarship

A few universities in economic straits have recently attempted to sell artwork to address their financial woes, causing much consternation in the museum community. This Article relates the stories of some institutions' attempts to deaccession artworks, and explains why universities may suddenly perceive their art collections as important assets to monetize. It contends that the universities and their critics have fundamentally divergent conceptions of the role of the art collection in the university, which explains why they cannot agree on the legal responsibilities of universities vis-a-vis their art. The critics have a strong cultural-property conception that privileges art, while these …

Global Warming, Convective Threshold And False Thermostats, I. N. Williams, R. T. Pierrehumbert, M. Huber

Department of Earth, Atmospheric, and Planetary Sciences Faculty Publications

No abstract provided.

Numerical Simulation Of Gas-Phonon Coupling In Thermal Transpiration Flows, Xiaohui Guo, Dhruv Singh, Jayathi Murthy, Alina A. Alexeenko

School of Aeronautics and Astronautics Faculty Publications

Thermal transpiration is a rarefied gas flow driven by a wall temperature gradient and is a promising mechanism for gas pumping without moving parts, known as the Knudsen pump. Obtaining temperature measurements along capillary walls in a Knudsen pump is difficult due to extremely small length scales. Meanwhile, simplified analytical models are not applicable under the practical operating conditions of a thermal transpiration device, where the gas flow is in the transitional rarefied regime. Here, we present a coupled gas-phonon heat transfer and flow model to study a closed thermal transpiration system. Discretized Boltzmann equations are solved for molecular transport …

The Stability Of Psychopathy Across Adolescence, Donald Lynam, Richard Charnigo, Terrie E. Moffitt, Adrian Raine, Rolf Loeber, Madga Stouthamer-Loeber

Department of Psychological Sciences Faculty Publications

The current diagnostic system suggests that personality disorder categories be applied to children and adolescents in rare circumstances because of expected changes in personality pathology across development. The present study examined the stability in personality pathology, specifically psychopathy, across childhood and adolescence. Using a short form of the CPS and mixed models incorporating fixed and random effects, we examined the reliability, individual stability, mean-level stability, and predictive utility of juvenile psychopathy as a function of age (i.e., from 7 to 17 years old) in over 1,500 boys from the three cohorts of the Pittsburgh Youth Study. If adolescent development contributes …

Direct And Indirect Effects Of Climate Change On A Prairie Plant Community, Peter B. Adler, James Leiker, Jonathan M. Levine

Wildland Resources Faculty Publications

Background

Climate change directly affects species by altering their physical environment and indirectly affects species by altering interspecific interactions such as predation and competition. Recent studies have shown that the indirect effects of climate change may amplify or counteract the direct effects. However, little is known about the the relative strength of direct and indirect effects or their potential to impact population persistence.

Methodology/Principal Findings

We studied the effects of altered precipitation and interspecific interactions on the low-density tiller growth rates and biomass production of three perennial grass species in a Kansas, USA mixed prairie. We transplanted plugs of each …

The Fourth Level Of Social Structure In A Multi-Level Society: Ecological & Social Functions Of Clans In Hamadryas Baboons, Amy Schreier, Larissa Swedell

Publications and Research

Hamadryas baboons are known for their complex, multi-level social structure consisting of troops, bands, and one-male units (OMUs) [Kummer, 1968]. Abegglen [1984] observed a 4^th level of social structure comprising several OMUs that rested near one another on sleeping cliffs, traveled most closely together during daily foraging, and sometimes traveled as subgroups independently from the rest of the band. Abegglen called these associations “clans” and suggested that they consisted of related males. Here we confirm the existence of clans in a second wild hamadryas population, a band of about 200 baboons at the Filoha site in lowland Ethiopia. During …

Male Aggression Towards Females In Hamadryas Baboons: Conditioning, Coercion And Control, Larissa Swedell, Amy Schreier

Publications and Research

No abstract provided.

Dystopian Surface, Utopian Dream: Wittman Ah Sing Foresees Postethnic Humanity, Seo-Young J. Chu

Publications and Research

"Dystopian Surface, Utopian Dream" examines the postethnic and the posthuman in fiction by Maxine Hong Kingston, Octavia Butler, and Isaac Asimov.

Biology And Impacts Of Pacific Island Invasive Species. 5. Eleutherodactylus Coqui, The Coqui Frog (Anura: Leptodactylidae), Karen H. Beard, William C. Pitt, Emily A. Price

United States Department of Agriculture Wildlife Services: Staff Publications

The nocturnal, terrestrial frog Eleutherodactylus coqui, known as the Coqui, is endemic to Puerto Rico and was accidentally introduced to Hawai‘i via nursery plants in the late 1980s. Over the past two decades E. coqui has spread to the four main Hawaiian Islands, and a major campaign was launched to eliminate and control it. One of the primary reasons this frog has received attention is its loud mating call (85–90 dB at 0.5 m). Many homeowners do not want the frogs on their property, and their presence has influenced housing prices. In addition, E. coqui has indirectly impacted the …

An Overview Of Historical Beaver Management In Arizona, Christopher Carrillo, David Bergman, Jimmy D. Taylor Ii, Dale L. Nolte, Patrick Viehoever, Mike Disney

United States Department of Agriculture Wildlife Services: Staff Publications

In the mid-1820s, Anglo-American fur trappers, known as "mountain men," entered Arizona and began trapping beaver (Castor canadensis). In Arizona there have been a number of famous mountain men such as Sylvester and James Pattie, Ewing Young, Jededia Smith, and Bill Williams who trapped along the waterways in northern and southern Arizona. Although the heyday of mountain men lasted only a few decades due to a population decline of beaver, management of these animals continues to this day. The purpose of managing beavers shifted from monetary gain to controlling wildlife damage. During the late 1900s, beaver were still …

Ctenosaura Similis (Black Spiny-Tailed Iguana), ,I>Gopherus Polyphemus (Gopher Tortoise) Concurrent Burrow Use, Richard M. Engeman, Bernice Constantin, Missy Christie, Parker Hall

United States Department of Agriculture Wildlife Services: Staff Publications

Ctenosaura similis is exotic to Florida (Meshaka et al. 2004. The Exotic Amphibians and Reptiles of Florida, Krieger Publ. Co., Malabar, Florida. 155 pp.), whereas Gopherus polyphemus is listed as a species of special concern by the state of Florida (Florida Wildlife Code Chap. 39 F.A.C.), and as a threatened species by the Florida Committee on Rare and Endangered Plants and Animals (FCREPA) (Moler 1992. Rare and Endangered Biota of Florida: Volume III, Reptiles and Amphibians. University Press of Florida, Gainesville, Florida. 291 pp.).

Relating Ten Years Of Northern Raccoon Road-Kill Data To Their Attraction To Sea Turtle Nests, Richard M. Engeman, Alice Bard, Henry T. Smith, N. Paige Groninger

United States Department of Agriculture Wildlife Services: Staff Publications

One of the primary threats to sea turtle reproduction in Florida is nest predation by Northern Raccoons (Procyon lotor). We examined 10 years of nest deposition data from a high-density sea turtle nesting beach at Sebastian Inlet State Park, Florida, USA, along with data on raccoon road-kills from the adjacent road, and data on park attendance (as an index of local traffic) to make inferences about raccoon activity patterns relative to turtle nesting. Northern Raccoon road-kills diminished during turtle nesting, even though local traffic was higher. Virginia Opossums (Didelphis virginiana), the only other mammal consistently found …

Surveillance For Highly Pathogenic Avian Influenza In Wild Birds In The Usa, Thomas J. Deliberto, Seth R. Swafford, Dale L. Nolte, Kerri Pedersen, Mark W. Lutman, Brandon S.. Schmit, John A. Baroch, Dennis J. Kohler, Alan B. Franklin

United States Department of Agriculture Wildlife Services: Staff Publications

As part of the USA’s National Strategy for Pandemic Influenza, an Interagency Strategic Plan for the Early Detection of Highly Pathogenic H5N1 Avian Influenza in Wild Migratory Birds was developed and implemented. From 1 April 2006 through 31 March 2009, 261 946 samples from wild birds and 101 457 wild bird fecal samples were collected in the USA; no highly pathogenic avian influenza was detected. The United States Department of Agriculture, and state and tribal cooperators accounted for 213 115 (81%) of the wild bird samples collected; 31, 27, 21 and 21% of the samples were collected from the Atlantic, …

Captive Coyotes Compared To Their Counterparts In The Wild: Does Environmental Enrichment Help?, John A. Shivik, Gernrna L. Palmer, Eric M. Gese, Britta Osthaus

United States Department of Agriculture Wildlife Services: Staff Publications

This article attempts to determine the effects of environment (captive or wild) and a simple form of environmental enrichment on the behavior and physiology of a nonhuman animal. Specifically, analyses first compared behavioral budgets and stereotypic behavior of captive coyotes (Canis latrans) in kennels and pens to their counterparts in the wild. Second, experiments examined the effect of a simple form of environmental enrichment for captive coyotes (food-filled bones) on behavioral budgets, stereotypes, and corticosteroid levels. Overall, behavioral budgets of captive coyotes in both kennels and pens were similar to those observed in the wild, but coyotes in …

West Nile Virus Detection In Nonvascular Feathers From Avian Carcasses, Nicole M. Nemeth, Ginger R. Young, Kristen L. Burkhalter, Aaron C. Brault, William K. Reisen, Nicholas Komar

United States Department of Agriculture Wildlife Services: Staff Publications

West Nile virus (WNV) is a public health threat and has caused the death of thousands of North American birds. As such, surveillance for WNV has been ongoing, utilizing numerous biological specimens and testing methods. Nonvascular (i.e., fully grown) feathers would provide a simple method of collection from either dead or live birds of all ages and molt cycles, with presumably less biosafety risk compared with other specimen types, including feather pulp. The current study evaluates WNV detection in nonvascular feathers removed from naturally infected avian carcasses of several species groups. Feathers of corvid passeriforms had the highest sensitivity of …

Parasite Species Associated With Wild Plateau Pika (Ochotona Curzoniae) In Southeastern Qinghai Province, China, Chengmin Wang, Hongxuan He, Ming Li, Fumin Lei, J. Jeffrey Root, Yanyun Wu, Jianhua Qin

United States Department of Agriculture Wildlife Services: Staff Publications

A survey was conducted to determine the prevalence and seasonal abundance of egg, larval, and adult stages of helminths; oocyts of protozoans; and ectoparasites of plateau pikas (Ochotona curzoniae) in seven areas of southeastern Qinghai Province, China, during August 2006 and May 2007. Fecal samples collected from 430 plateau pikas were examined by the modified McMaster technique, which revealed that 83% of the samples contained eggs from two or more helminth species. Mean fecal egg counts were generally moderate and showed the same trend irrespective of the age or sex of the pikas. The prevalence and counts of …

Synthesis Of Best Practices In Transportation Security, Volume Ii: Emergency Response, Rodrigo Vargas, Jon D. Fricker

JTRP Technical Reports

Part I of the research focused on developing a methodology to identify and evaluate the most critical and vulnerable INDOT assets. This method aims at obtaining an index that reflects the vulnerability and criticality of an asset on the basis of multiple performance criteria. This methodology was tested on the seven INDOT districts. Because not all the factors that influence the vulnerability do have same weight, the analytical hierarchical process is used to obtain the weights for the criteria. Countermeasures are suggested as a part of the research to reduce the vulnerability of a given asset based on its relevant …

G-Trace: Rapid Gal4-Based Cell Lineage Analysis In Drosophila, Cory J. Evans, John M. Olson, Kathy T. Ngo, Eunha Kim, Noemi E. Lee, Edward Kuoy, Alexander N. Patananan, Daniel Sitz, Phuong Thao Tran, Minh Tu Do, Kevin Yackle, Albert Cespedes, Volker Hartenstein, Gerald B. Call, Utpal Banerjee, Miriam Beyder, Kush V. Bhatt, Chinmay Bhoot, Aaron W. Bradshaw, Tierney G. Brannigan, Boyu Cao, Yancey Y. Cashell, Timothy Chai, Alex W. Chan, Carissa Chan, Inho Chang, Jonathan Chang, Michael T. Chang, Patrick W. Chang, Stephen Chang, Neel Chari

Biology Faculty Works

We combined Gal4-UAS and the FLP recombinase–FRT and fluorescent reporters to generate cell clones that provide spatial, temporal and genetic information about the origins of individual cells in Drosophila melanogaster. We named this combination the Gal4 technique for real-time and clonal expression (G-TRACE). The approach should allow for screening and the identification of real-time and lineage-traced expression patterns on a genomic scale.

Biofuels, Bioenergy, And Bioproducts From Sustainable Agricultural And Forest Crops, Michael D. Casler, Rob B. Mitchell, Jim Richardson, Ronald S. Zalesny Jr.

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

This issue of BioEnergy Research highlights the Short Rotation Crops International Conference held in Bloomington, Minnesota in August 2008. This is the first special issue of BioEnergy Research, with several additional special issues planned in the next year, focused on the three U.S. Department of Energy Bioenergy Research Centers (Great Lakes Bioenergy Research Center, BioEnergy Science Center, and Joint BioEnergy Institute), and emerging technologies for biodiesel production. The purpose of these special issues is to highlight emerging research efforts in the areas of biomass, biofuels, and bioenergy. The Short Rotation Crops International Conference represented a unique opportunity for communication …

A Weighing Lysimeter For Crop Water Use Determination In The Jordan Valley, Jordan, Steven R. Evett, Naem T. Mazahrih, Mohammed A. Jitan, Mahmoud H. Sawalha, Paul D. Colaizzi, James E. Ayars

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Efficiency of water use in irrigated agriculture can be improved by providing irrigation scheduling information to farmers. Since 2003, the Middle Eastern Regional Irrigation Management Information Systems (MERIMIS) project has focused on improving irrigation scheduling in Jordan, Palestine, and Israel with cooperators from the region and the U.S. Their efforts have established a network of 15 weather stations to support an irrigation scheduling service using the paradigm that crop water use is equal to a reference evapotranspiration (ETr) value (calculated from weather data) multiplied by a crop coefficient. Because crop coefficients developed in one region often do not transfer exactly …

Expanding The Crime Of Genocide To Include Ethnic Cleansing: A Return To Established Principles In Light Of Contemporary Interpretations, Micol Sirkin

Seattle University Law Review

It may be surprising to discover that ethnic cleansing is legally distinct from genocide considering that the media use these terms interchangeably. Currently, no formal legal definition of ethnic cleansing exists. This Comment specifies how ethnic cleansing fits into the definition of genocide’s distinctly destructive purpose and effect. I argue that because ethnic cleansing and genocide result in similar harms and derive from similar agendas, international courts ought to find perpetrators guilty of the crime of genocide when genocidal acts are committed with the intent to create an ethnically homogenous territory. A policy of ethnic cleansing is a genocidal policy. …

Finally, Your Love Poem, Elizabeth Stephenson Bohlke

Electronic Theses and Dissertations

No abstract provided.

Assessment Of The Tissue Distribution Of A Novel Binding Site For Angiotensins Ii And Iii In The Mouse, Felicia Rabey

Electronic Theses and Dissertations

No abstract provided.

Integrating Genomics And Phylogenetics In Understanding The History Of Trichinella Species, Dante Zarlenga, B. Rosenthal, E. Hoberg, M. Mitreva

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

In 2004, funding was received by Washington University’s Genome Sequencing Center through NHGRI, to completely sequence several nematode genomes as part of a holistic effort to advance our understanding of the human genome and evolution within the Metazoa. Trichinella spiralis was among this group of worms because of its strategic location at the base of the phylum Nematoda, and the belief that extant species represented an ancient divergent event that occurred as early as the Paleozoic. At the same time, a concerted effort was put forth to solidify the phylogeny of extant species of Trichinella based upon molecular analyses of …

A New Genus Of Flea Beetles (Coleoptera: Chrysomelidae) From The South Of Brazil, Adelita M. Linzmeier, Alexander S. Konstantinov

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Deciplatus, a new genus of Monoplatina with two new species (D. jundiaiensis and D. nigritus), from the south of Brazil is described and illustrated.Deciplatus is compared to Ulrica Scherer and Laselva Furth. Use of the name Monoplatina is clarified.

New Genera And Species Of Leaf Beetles (Coleoptera: Chrysomelidae) From China And South Korea, I.K. Lopatin, Alexander S. Konstantinov

United States Department of Agriculture-Agricultural Research Service / University of Nebraska-Lincoln: Faculty Publications

Two new genera from China (Taumaceroides Lopatin and Yunnaniata Lopatin) and 11 new species (Smaragdina quadrimaculata Lopatin, S. oblongum Lopatin, Hyphaenia volkovitshi Lopatin, Arthrotus daliensis Lopatin, Taumaceroides sinicus Lopatin, Yunnaniata konstantinovi Lopatin, Calomicrus yunnanus Lopatin, C. minutissimus Lopatin, Hermaeophaga belkadavi Konstantinov, H. dali Konstantinov from China, and H. korotyaevi Konstantinov from South Korea) are described and illustrated. A key to Hermaeophaga species of Eurasia is presented. Since Hermaeophaga dali was collected feeding on Paederia foetida L. (Rubiaceae), which is an invasive noxious weed in the United States, this species has potential as a biological control agent of this weed.