Physical Sciences and Mathematics Commons^™

Secondary Structure, A Missing Component Of Sequence- Based Minimotif Definitions, David P. Sargeant, Michael R. Gryk, Mark W. Maciejewsk, Vishal Thapar, Vamsi Kundeti, Sanguthevar Rajasekaran, Pedro Romero, Keith Dunker, Shun-Cheng Li, Tomonori Kaneko, Martin Schiller

Life Sciences Faculty Research

Minimotifs are short contiguous segments of proteins that have a known biological function. The hundreds of thousands of minimotifs discovered thus far are an important part of the theoretical understanding of the specificity of protein-protein interactions, posttranslational modifications, and signal transduction that occur in cells. However, a longstanding problem is that the different abstractions of the sequence definitions do not accurately capture the specificity, despite decades of effort by many labs. We present evidence that structure is an essential component of minimotif specificity, yet is not used in minimotif definitions. Our analysis of several known minimotifs as case studies, analysis …

Achieving High Accuracy Prediction Of Minimotifs, Tian Mi, Sanguthevar Rajasekaran, Jerlin Camilus Merlin, Michael R. Gryk, Martin Schiller

Life Sciences Faculty Research

The low complexity of minimotif patterns results in a high false-positive prediction rate, hampering protein function prediction. A multi-filter algorithm, trained and tested on a linear regression model, support vector machine model, and neural network model, using a large dataset of verified minimotifs, vastly improves minimotif prediction accuracy while generating few false positives. An optimal threshold for the best accuracy reaches an overall accuracy above 90%, while a stringent threshold for the best specificity generates less than 1% false positives or even no false positives and still produces more than 90% true positives for the linear regression and neural network …

Mojave Applied Ecology Notes Fall 2011, E. Cayenne Engel, Scott R. Abella, Kathryn A. Prengaman, Jason Whited, Peter Michel

Mojave Applied Ecology Notes

Paper on impacts of Mojave wildfires through time published, possibilities of catastrophic Mt. Charleston forest fires, vegetation mapping at three national parks, UNLV library’s special collections, and the benefits of scientific publications to managers and stakeholders

Mojave Applied Ecology Notes Summer 2011, Scott R. Abella, Charles W. Denton, David G. Brewer, Rory W. Steinke, Wayne A. Robbie, W. Wallace Covington, E. Cayenne Engel, Ross Guida

Mojave Applied Ecology Notes

Thoughts on fire possibilities on Mount Charleston, estimating historical densities of Ponderosa pine in northern AZ, over-understory changes in the Spring Mountains, seeding effectiveness in Red Rock Canyon, workshop announcements.

Mojave Applied Ecology Notes Spring 2011, Scott R. Abella, Ross Guida, S. D. Smith, Christopher L. Roberts, Haroon Stephen, William J. Smith, Zhongwei Liu, James S. Holland, Aurore Giguet

Mojave Applied Ecology Notes

Red brome distribution in the eastern Mojave Desert, A look at the UNLV xeric gardens and Marjorie Barrick museum, Summary of recent science synthesis efforts

Mojave Applied Ecology Notes Winter 2011, Scott R. Abella, Alice C. Newton, Kenneth Chittick, Pam Sinanian

Mojave Applied Ecology Notes

Lake Mead’s collaborative applied science research program; “annoying the elephant” - ruminations on active management by Alice Newton, Lake Mead NRA vegetation manager; 2012 NWRA Lake Mead symposium sneak peak; assessing forest change using dendrochronology in the Spring Mountains.

Settlement And Growth Of Quagga Mussels (Dreissenia Rostriformis Bugensis Andrusov, 1897) In Lake Mead, Nevada-Arizona, Usa, Wai Hing Wong, Shawn Gerstenberger, Wen Baldwin, Bryan Moore

Environmental & Occupational Health Faculty Publications

Settlement and growth of quagga mussels Dreissena rostriformis bugensis were monitored in Lake Mead, NV, USA, where the first dreissenid occurrence was confirmed in the western United States. To measure the settlement rate of these invasive mussels, seven acrylonitrile butadiene styrene (ABS) pipes were attached to a line in shallow water (7.7 m below the surface) since November 23, 2007; eight ABS pipes were placed on another line in deep water (13.4 m below the surface) since January 3, 2008. Quagga mussels were sampled from these pipes on March 19, May 21, July 9, October 20, and December 19, 2008. …

Unlv Magazine, Tony Allen, Shane Bevell, Donna Mcaleer, Ched Whitney, Cate Weeks

UNLV Magazine

No abstract provided.

Mojave Applied Ecology Notes Fall 2010, Adria Decorte, Sharon Altman, Alex Suazo

Mojave Applied Ecology Notes

Adria DeCorte defense, Mojave desert inventory and monitoring mapping project, effect of burial depth on Brassica tournefortii seeds

Mojave Applied Ecology Notes Summer 2010, Scott R. Abella, E. Cayenne Engel

Mojave Applied Ecology Notes

Survey of monitoring and management for conservation of rare plants, Roadside restoration techniques in Joshua Tree NP, and an update on renewable energy developments in the Southwestern deserts

Partitioning Of Minimotifs Based On Function With Improved Prediction Accuracy, Sanguthevar Rajasekaran, Tian Mi, Jerlin Camilus Merlin, Aaron Oommen, Patrick R. Gradie, Martin R. Schiller

Life Sciences Faculty Research

Background

Minimotifs are short contiguous peptide sequences in proteins that are known to have a function in at least one other protein. One of the principal limitations in minimotif prediction is that false positives limit the usefulness of this approach. As a step toward resolving this problem we have built, implemented, and tested a new data-driven algorithm that reduces false-positive predictions.

Methodology/Principal Findings

Certain domains and minimotifs are known to be strongly associated with a known cellular process or molecular function. Therefore, we hypothesized that by restricting minimotif predictions to those where the minimotif containing protein and target protein have …

Mojave Applied Ecology Notes Spring 2010, Anna San, Donovan J. Craig, Lindsay P. Chiquoine, Scott R. Abella, E. Cayenne Engel, Christina L. Lund, Jessica E. Spencer, Edward P. Weber Ph.D, Jill E. Craig

Mojave Applied Ecology Notes

Seed removal rates of Sahara mustard by rodents and ants, Mojave Desert Network exotic invasive inventory, gypsum roadside disturbance restoration update, new paper out on post-fire plant establishment, UNLV establishes school of environmental and public affairs

Mojave Applied Ecology Notes Winter 2010, Scott R. Abella, E. Cayenne Engel

Mojave Applied Ecology Notes

Native species interactions with red brome (Bromus rubens), undergraduate and graduate programs at UNLV, what’s growing in the greenhouse?

Mojave Applied Ecology Notes Fall 2009, Tom Monaco, Scott R. Abella, Amber Lee, James E. Deacon

Mojave Applied Ecology Notes

USDA working to manage invasive annual grasses, effects of heat and smoke on red brome soil seed bank, how burial depth and substrate affect germination of Sahara mustard and red brome, environmental effects of the southern Nevada groundwater project

Venn, A Tool For Titrating Sequence Conservation Onto Protein Structures, Jay Vyas, Michael R. Gryk, Martin R. Schiller

Life Sciences Faculty Research

Residue conservation is an important, established method for inferring protein function, modularity and specificity. It is important to recognize that it is the 3D spatial orientation of residues that drives sequence conservation. Considering this, we have built a new computational tool, VENN that allows researchers to interactively and graphically titrate sequence homology onto surface representations of protein structures. Our proposed titration strategies reveal critical details that are not readily identified using other existing tools. Analyses of a bZIP transcription factor and receptor recognition of Fibroblast Growth Factor using VENN revealed key specificity determinants. Weblink: http://sbtools.uchc.edu/venn/.

A Proposed Syntax For Minimotif Semantics, Version 1., Jay Vyas, Ronald J. Nowling, Mark W. Maciejewski, Sanguthevar Rajasekaran, Michael R. Gryk, Martin R. Schiller

Life Sciences Faculty Research

BACKGROUND:

One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of …

Mojave Applied Ecology Notes Summer 2009, Kevin E. Oliver, Dianne N. Bangle, E. Cayenne Engel, Lindsay P. Chiquoine, Scott R. Abella

Mojave Applied Ecology Notes

BLM and wildfire protection in the Mojave, studies of the sticky ringstem flowering phenology in Lake Mead NRA, restoration work within gypsum soils, post-fire response synthesis for Mojave and Sonoran deserts

Mojave Applied Ecology Notes Spring 2009, Russell Scofield, Michele Slaton Ph.D, Alexis Suazo, Donovan J. Craig

Mojave Applied Ecology Notes

California desert managers group, vegetation monitoring in Death Valley, undergraduate research symposium at UNLV, response of Sahara mustard to water and disturbance, JFS update

Mojave Applied Ecology Notes Winter 2009, Scott R. Abella, Lindsay P. Chiquoine, Alice C. Newton

Mojave Applied Ecology Notes

Chronology of forest structure and use in the Spring Mountains, Soil-Tech’s restoration work balancing construction with nature, species performance and treatment effectiveness for revegetation projects, and strategic research areas for Mojave conservation and management

Minimotif Miner 2nd Release: A Database And Web System For Motif Search, Sanguthevar Rajasekaran, Sudha Balla, Patrick R. Gradie, Michael R. Gryk, Krishna Kadaveru, Vamsi Kundeti, Mark W. Maciejewski, Tian Mi, Nicholas Rubino, Jay Vyas, Martin R. Schiller

Life Sciences Faculty Research

Minimotif Miner (MnM) consists of a minimotif database and a web-based application that enables prediction of motif-based functions in user-supplied protein queries. We have revised MnM by expanding the database more than 10-fold to approximately 5000 motifs and standardized the motif function definitions. The web-application user interface has been redeveloped with new features including improved navigation, screencast-driven help, support for alias names and expanded SNP analysis. A sample analysis of prion shows how MnM 2 can be used.

Mojave Applied Ecology Notes Fall 2008, Alice Miller, Joshua Hoines, Scott R. Abella

Mojave Applied Ecology Notes

Effects of wildfires in Joshua Tree National Park, Blackbrush masting volunteer seed collection effort, new book chapter on Mojave revegetation, Natural Areas Association presentations.

Mojave Applied Ecology Notes Summer 2008, Doug Merkler, Scott R. Abella, Dianne N. Bangle, Donovan J. Craig, Jessica E. Spencer, Alex Suazo

Mojave Applied Ecology Notes

Soil climate project, rare plant monitoring, JFS update, granivory and Sahara mustard

Mojave Applied Ecology Notes Spring 2008, Lesley Defalco, E. Cayenne Engel, Scott R. Abella, Jessica E. Spencer, Jill E. Craig

Mojave Applied Ecology Notes

Post-fire restoration, fire chronosequence study, Joint Fire Science update, Weed Sentry program and DNWR surveys

Mojave Applied Ecology Notes Winter 2008, Scott R. Abella, E. Cayenne Engel, Jill E. Craig

Mojave Applied Ecology Notes

Mojave Desert collaborative projects, fire history in Spring Mountains, Northshore Road rehabilitation, wildfires and invasive plants in American deserts conference, weed sentry surveys

Land Cover Types Of The Las Vegas Wash, Nevada, Seth A. Shanahan, Dave Silverman, Art Ehrenberg

Publications (WR)

Vegetation type, extent, continuity, and structure are some of the most important factors that determine wildlife diversity and distribution. Other contributing factors that shape wildlife communities include disturbance, competition, climate, and water availability. Because vegetation communities in the southwestern U.S. gradate sharply along zones of soil moisture, wildlife are often restricted to specific vegetation types. Along the Las Vegas Wash (Wash), Nevada, more than 250 wildlife species have been documented to occur in distinct wetland, riparian, and upland vegetation types. Recent studies have investigated the diversity and distribution of amphibians, birds, fishes, mammals, and reptiles (Shanahan 2005, 2005a, Van Dooremolen …

Las Vegas Wash Water Quality Monitoring Program: 1996 Report Of Findings, Richard A. Roline, James J. Sartoris, U.S. Bureau Of Reclamation, U.S. Geological Survey

Publications (WR)

Las Vegas Wash, a natural wash east of the city of Las Vegas, Nevada, carries stormwater, groundwater drainage, and sewage effluent from three sewage treatment plants to Lake Mead. The Wash provides nearly the only surface water outlet for the entire 2,193 mi² of Las Vegas Valley. A drainage area of 1,586 mi² contributes directly to the Wash through surface flow which is channeled to Las Vegas Bay of Lake Mead, while drainage of the remaining 607 mi² is presumably subsurface and may drain toward Las Vegas Wash.

In the 1930's and 1940's, sewage treatment plants were …

Study Of Existing Information Concerning Water Quality Within Lake Mead, Vicki Scharnhorst, Southern Nevada Water Authority

Publications (WR)

The purpose of Task 010A15M of the Southern Nevada Water Authority (SNWA) Treatment and Transmission Facility (TTF) contract is to conduct a study of existing information concerning water quality within Lake Mead and identify additional water quality studies that are needed to supplement existing data.

The objective of this task is not to discuss treatability of the raw water source; this is addressed by Task 010A18M, "Define Water Treatment Requirements." In addition, a narrative on the effect of pending Safe Drinking Water Act amendments and a determination of treated water quality goals is included in Task 010A16M, "Review Safe Drinking …

Identification Of Tire Leachate Toxicants And A Risk Assessment Of Water Quality Effects Using Tire Reefs In Canals, S. M. Nelson, G. Mueller, D. C. Hemphill, U.S. Bureau Of Reclamation

Publications (WR)

Cover is an important component of aquatic habitat and fisheries management. Fisheries biologists often try to improve habitats through the addition of natural and artificial material to improve cover diversity and complexity. Habitat-improvement programs range from submerging used Christmas trees to more complex programs using sophisticated artificial habitat modules. Used automobile tires have been employed in the large scale construction of reefs and fish attractors in marine environments and to a lesser extent in freshwater and have been recognized as a durable, inexpensive and long-lasting material which benefits fishery communities.

Recent studies by the U.S. Bureau of Reclamation have quantified …

Southern Nevada Effluent Wetlands: A Proposed Cooperative Venture Between The Bureau Of Reclamation & City Of Las Vegas, Bureau Of Reclamation

Publications (WR)

Throughout North America there is a growing interest in constructed wetlands, both as relatively inexpensive, low-maintenance systems for removing nutrients from wastewater, and as a means of using municipal wastewater to enhance wildlife habitat and create public use opportunities. Because wetlands appear to have good potential as a component in the overall management of scarce water resources, the Bureau of Reclamation (Reclamation) has undertaken several cooperative research and demonstration projects to evaluate their effectiveness in a variety of local environments.

While a number of projects have demonstrated that wetlands can be beneficially employed to improve water quality, few such projects …

Littoral And Limnetic Zooplankton Communities In Lake Mead, Nevada-Arizona, Usa, Patrick J. Sollberger, Larry J. Paulson

Publications (WR)

Zooplankton were collected from adjacent littoral and limnetic sites in Lake Mead, Nevada-Arizona, USA. Limnetic species dominated both littoral and limnetic zooplankton communities; littoral species rarely exceeded 2% of monthly total zooplankton densities. Low species richness of littoral taxa and high similarity in species composition between littoral and limnetic habitats appeared to result from uniform horizontal physical and chemical environments, due to horizontal mixing, and from the absence aquatic macrophytes.

Significant differences in spatial distribution occurred in phytoplankton biomass, total zooplankton density, and fish "abundances; highest concentrations of these factors occurred nearest an inflow high in nutrients and progressively declined …