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 …

Limnological Assistance For Lake Mead National Recreation Area: Quarterly Report, Period Ending September 30, 2012, Margaret N. Rees

Limnological Studies

Continuation of Project 1

• The research effort titled Growth of adult quagga mussels within Las Vegas Wash/Las Vegas Bay is ongoing.

Continuation of Project 2

• Additional content was contributed to the future NPS-funded U.S. Geological Survey Circular ‘state-of-the-science’ report for Lakes Mead and Mohave. UNLV performed a new co-editing and coordinating task related to this product as the major focus of this quarter’s effort; the master version of this report is on schedule for delivery to the editorial team during the first week of October 2012.

Modification Activities:

Extended Short-term Continued Limnological Assistance

Quagga Mussel Objectives:

• Most juvenile/adult quagga mussel …

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 …

Take Pride In America Phase Iii: Quarterly Progress Report, Period Covering April 25, 2012-July 24, 2012, Margaret N. Rees

Anti-littering Programs

• The GIS database continued to be populated with data.
• Hector’s Helpers added an additional youth group.
• The new website launched and social media efforts began.
• The pilot testing of the litter monitoring program continued.

The University of Nevada Las Vegas Public Lands Institute (PLI) designed the Take Pride in America (TPIA) Phase III work plan based on the strategic plan developed by the Southern Nevada Agency Partnership (SNAP) anti-litter and desert dumping team during Phase II of the program.

Walking Box Ranch Planning And Design Quarterly Progress Report: Period Ending July 10, 2012, Margaret N. Rees

Walking Box Ranch

• BLM informed UNLV that after investigating a concession contract as the appropriate BLM document for the future operating partner, they have concluded that an operating agreement is the preferred document and they are proceeding to complete such an agreement as soon as possible.
• Following a visit to the ranch with BLM, UNLV has completed temporary repairs to ranch house windows, which should mitigate deterioration of the ranch house from water
• UNLV participated in a one-half day meeting with BLM to review Condit’s Extended Content Package #1. As a result of the lack of progress by Condit, UNLV was requested to …

Nevada Interagency Volunteer Program: Helping Hands Across Public Lands – Phase Ii: Quarterly Progress Report, Period Covering January 1, 2012 To March 31, 2012, Margaret N. Rees

Get Outdoors Nevada

• The number of records in the volunteer database increased by 4.96% over the last quarter. The database now contains 7,423 records.
• Results show an average of 1,259 visits per month, and with an average of 3,015 pages viewed per month.
• Get Outdoors Nevada supported 14 volunteer events in a variety of ways. These events utilized 364 volunteers whom contributed approximately 2,414 hours of service.
• Three community outreach events were attended, resulting in 293 direct contacts with 50 names added to the database.
• The automated volunteer orientation training project has been completed and disks have been delivered to the 4 agencies. …

Minimotif Miner 3.0: Database Expansion And Significantly Improved Reduction Of False-Positive Predictions From Consensus Sequences., Tian Mi, Jerlin Camilus Merlin, Sandeep Deverasetty, Michael R. Gryk, Travis J. Bill, Andrew W. Brooks, Logan Lee, Viraj Rathnayake, Christian A. Ross, David P. Sargeant, Christy L. Strong, Paula Watts, Sanguthevar Rajasekaran, Martin Schiller

Life Sciences Faculty Research

Minimotif Miner (MnM available at http://minimotifminer.org or http://mnm.engr.uconn.edu) is an online database for identifying new minimotifs in protein queries. Minimotifs are short contiguous peptide sequences that have a known function in at least one protein. Here we report the third release of the MnM database which has now grown 60-fold to approximately 300,000 minimotifs. Since short minimotifs are by their nature not very complex we also summarize a new set of false-positive filters and linear regression scoring that vastly enhance minimotif prediction accuracy on a test data set. This online database can be used to predict new functions in proteins …