Life Sciences Commons^™

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

Distribution And Site Selection Of Le Conte's And Crissal Thrashers In The Mojave Desert: A Multi-Model Approach, Dawn Marie Fletcher

UNLV Theses, Dissertations, Professional Papers, and Capstones

Information on the distribution and habitat requirements of a species are critical components to the development of meaningful conservation plans. Such knowledge, however, is particularly difficult to obtain for species that are elusive and occur at low densities, such as the Le Conte's ( Toxostoma lecontei ) and Crissal (Toxostoma crissale ) thrashers. In association with a regional conservation plan, I evaluated the distribution and habitat selection of these thrashers within Clark County, Nevada in the eastern Mojave Desert. I used a call-broadcast approach to sample 432 stratified random locations, detecting Le Conte's thrashers at 45 locations and Crissal …

Arid Climate Decomposition And Decay: A Taphonomic Study Using Swine, James William Munkres

UNLV Theses, Dissertations, Professional Papers, and Capstones

The present project analyzes the taphonomic processes and variables involved in the decomposition and desiccation of animal remains in an arid/hyper-arid environment. The study and the derived data will assist in determining postmortem intervals for remains in modern contexts, inform judgments made regarding mortuary habits and techniques in archaeological contexts, and will improve our knowledge regarding taphonomic processes. Manner of deposition, the depositional surface/medium and arid-climate specific variables (temperature, water, insect activity, weathering, pH levels, and soil characteristics) were examined in this study. Reported observations are limited to the first ten months following death from early December through early October …

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.

An Algorithm For Identifying Novel Targets Of Transcription Factor Families: Application To Hypoxia-Inducible Factor 1 Targets, Yue Jiang, Bojan Cukic, Donald A. Adjeroh, Heath D. Skinner, Jie Lin, Qingxi J. Shen, Bing-Hua Jiang

Electrical & Computer Engineering Faculty Research

Efficient and effective analysis of the growing genomic databases requires the development of adequate computational tools. We introduce a fast method based on the suffix tree data structure for predicting novel targets of hypoxia-inducible factor 1 (HIF-1) from huge genome databases. The suffix tree data structure has two powerful applications here: one is to extract unknown patterns from multiple strings/sequences in linear time; the other is to search multiple strings/sequences using multiple patterns in linear time. Using 15 known HIF-1 target gene sequences as a training set, we extracted 105 common patterns that all occur in the 15 training genes …