Systems Biology Commons^™

A Novel Gene Network Inference Algorithm Using Predictive Minimum Description Length Approach, Vijender Chaitankar, Preetam Ghosh, Edward J. Perkins, Ping Gong, Youping Deng, Chaoyang Zhang

Faculty Publications

Background: Reverse engineering of gene regulatory networks using information theory models has received much attention due to its simplicity, low computational cost, and capability of inferring large networks. One of the major problems with information theory models is to determine the threshold which defines the regulatory relationships between genes. The minimum description length (MDL) principle has been implemented to overcome this problem. The description length of the MDL principle is the sum of model length and data encoding length. A user-specified fine tuning parameter is used as control mechanism between model and data encoding, but it is difficult to …

Vegetation Trends On A Waste Rock Repository Cap In The Northern Black Hills, Andrew C. Korth, Gary E. Larson, Lan Xu, Thomas E. Schumacher

The Prairie Naturalist

We assessed successional trends, long-term vegetation sustainability, and soil surface protection during the 2005-2007 growing seasons on the 32-ha Ruby Gulch Waste Rock Repository cap. The cap consisted of 150 cm of rock and soil covering a polyethylene membrane which in turn covered mining waste rock in order to prevent leaching of heavy metals and acidic water into streams. Following construction in 2003, a contractor applied a grass-forb seed mixture to provide soil-surface protection especially for steeply sloped portions of the cap. In 2005, we established 56, 1-m² plots, and 20, 20-m transects to annually measure canopy cover, basal …

Joint Fire Science Program – Lake Mead National Recreation Area Revegetating Burned Arid Lands: Identifying Successful Native Species Using Trait And Competition Analysis: Quarterly Progress Report, Time Period: January 1 — April 30, 2010, Margaret N. Rees

Fire Science

• Article entitled “Competitive Hierarchy of Native Desert Plants with Red Brome (Bromus rubens): Towards Identifying Invasion-Reducing Species" was submitted to the Invasive Plant Science and Management journal
• Maintained nursery plots and added installment of nitrogen treatment.
• Took measurements in nursery (competition) plots and harvested biomass.

29 Years Of Vegetation Community Change Across Environmental Gradients In A Mojave Desert Mountain Range, Christopher L. Roberts, James S. Holland, Scott R. Abella

Graduate Research Symposium (GCUA) (2010 - 2017)

There is a great deal of uncertainty as to how biological communities respond to changes in land use and climate change, a situation particularly relevant in protected areas such as national parks that were designated to conserve specific biological features. Utilizing extant vegetation data sets with repeatable methodology can provide opportunities for insight into previous vegetation change and provide base line data for long-term monitoring projects useful for modeling vegetation community trajectories. We have relocated and resurveyed 106 sites from a vegetation community study initiated in 1979 in the Newberry Mountains, southern Nevada, within Lake Mead National Recreation Area managed …

A Toolkit For Rapid Gene Mapping In The Nematode Caenorhabditis Briggsae, Daniel C. Koboldt, Julia E. Staisch, Bavithra Thillainathan, Karen Haines, Scott Everet Baird, Helen M. Chamberlin, Eric S. Haag, Raymond D. Miller, Bhagwati P. Gupta

Biological Sciences Faculty Publications

Background

The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its genome sequence have prompted researchers to study evolutionary changes in gene function and signaling pathways. These studies rely on the availability of forward genetic tools such as mutants and mapping markers.

Results

We have computationally identified more than 30,000 polymorphisms (SNPs and indels) in C. briggsae strains AF16 and HK104. These include 1,363 SNPs that change restriction enzyme recognition sites (snip-SNPs) and 638 indels that range between 7 …

Evaluating Forensic Dna Evidence, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Establishing Parameters For Objective Interpretation Of Dna Profile Evidence, Dan E. Krane

Biological Sciences Faculty Publications

No abstract provided.

Isoform-Specific Regulation And Localization Of The Coxsackie And Adenovirus Receptor In Human Airway Epithelia, Katherine J.D.A. Excoffon, Nicholas D. Gansemer, Matthew E. Mobily, Philip H. Karp, Kalpaj R. Parekh, Joseph Zabner

Biological Sciences Faculty Publications

Adenovirus is an important respiratory pathogen. Adenovirus fiber from most serotypes co-opts the Coxsackie-Adenovirus Receptor (CAR) to bind and enter cells. However, CAR is a cell adhesion molecule localized on the basolateral membrane of polarized epithelia. Separation from the lumen of the airways by tight junctions renders airway epithelia resistant to inhaled adenovirus infection. Although a role for CAR in viral spread and egress has been established, the mechanism of initial respiratory infection remains controversial. CAR exists in several protein isoforms including two transmembrane isoforms that differ only at the carboxy-terminus (CAR^Ex7 and CAR^Ex8). We found low-level …

Lake Mead National Recreation Area Vegetation Monitoring And Analysis: Final Project Report, Scott R. Abella, Margaret N. Rees

Vegetation Monitoring

Vegetation Monitoring and Analysis at Lake Mead National Recreation Area (NRA) was funded by the Multi-Species Habitat Conservation Plan, Southern Nevada Public Land Management Act, Lower Colorado River Multi-Species Conservation Program, and Lake Mead NRA base-funds. This Cooperative Task Agreement was awarded to the Public Lands Institute (PLI) at the University of Nevada, Las Vegas (UNLV) on September 30, 2006 with the term ending December 31, 2009, as modified. The primary purpose of this Task Agreement was to work within an interagency framework towards the accomplishment of three main vegetation management objectives. These three goals were to: (1) inventory, research …

Biotic Responses To Climate Change In The Great Basin And Mojave Desert: Vegetation, David Charlet, Patrick Leary

2010 Annual Nevada NSF EPSCoR Climate Change Conference

84 PowerPoint slides Convener: Franco Biondi, UNR & Michael Young, DRI Session 4: Ecological Change and Water Resources Abstract: -The Problem -To detect changes in vegetation as it responds to changes in climate, we must first know where the vegetation is now -GAP (Geographic Approach to Protection of Biodiversity) map --National project to map land cover throughout the US. --Nevada map (Edwards et al. 1996) -Southwest ReGAP map --Land cover map for southwestern US (Prior-Magee et al. 2007) to correct problems identified in GAP map

Large Scale Reverse Genetics In Arabidopsis: Case Studies From The Chloroplast 2010 Project, Imad Ajjawi, Yan Lu, Linda Savage, Shannon Bell, Robert Last

Yan Lu

No abstract provided.

Desempenho Do Bicho-Da-Seda (Lepidoptera: Bombycidae) Sob O Efeito Da Adição De Minerais Nas Folhas De Amoreira Antes E Depois Do Trato Alimentar, Rodrigo Souza Santos Rss

Rodrigo Souza Santos RSS

No abstract provided.

Improvement Of The Stoichiometric Network Analysis For Determination Of Instability Conditions Of Complex Nonlinear Reaction Systems, Zeljko D. Cupic

Zeljko D Cupic

No abstract provided.

Sustainability Through Profitability: The Triple Bottom Line, Connie I. Reimers-Hild

Kimmel Education and Research Center - Presentations and White Papers

Today’s highly competitive, globalized world requires organizations and businesses to think differently about how they are going to stay in business. Businesses can no longer afford to focus on profits as their sole purpose for existence. Organizations must instead think about the “Triple Bottom Line” and its implications for their ability to grow their brand, customer loyalty and profits.

From Energy Gradient And Natural Selection To Biodiversity And Stability Of Ecosystems, Bo Deng

Faculty Publications, Department of Mathematics

The purpose of this paper is to incorporate well-established ecological principles into a foodweb model consisting of four trophic levels --- abiotic resources, plants, herbivores, and carnivores. The underlining principles include Kimura's neutral theory of genetic evolution, Liebig's Law of the Minimum for plant growth, Holling's functionals for herbivore foraging and carnivore predation, the One-Life Rule for all organisms, and Lotka-Volterra's model for intraand interspecific competitions. Numerical simulations of the model led to the following statistical findings: (a) particular foodwebs can give contradicting observations on biodiversity and productivity, in particular, all known functional forms -- - positive, negative, sigmoidal, and …

An Inventory And Condition Survey Of The Western Australian Part Of The Nullarbor Region, P A. Waddell, A K. Gardner, P Hennig

Technical Bulletins

The inventory and condition survey of the Western Australian part of the Nullarbor region, undertaken by the Department of Agriculture and Food, Western Australia (DAFWA) between 2005 and 2007, describes and maps the natural resources of the region. This survey report provides a baseline record of the existence and condition of the area's natural resources, to assist with the planning and implementation of land management practices. The report identified and described the condition of soils, landforms, vegetation, habitat, ecosystems, and declared plants and animals. It also assessed the impact of pastoralism and made land management recommendations. The Nullarbor region has …

The Coal River Basin: A 2009 Water Budget Study, R. Dale Biller

Theses, Dissertations and Capstones

The Coal River Watershed covers an area of some 890 square miles in southern West Virginia of which 863 square miles was investigated in this study. Both online and field data were collected over period from January 13, 2009 to January 13, 2010. The basin was studied as a closed system having an input, which was precipitation, and outputs, rainfall interception, evapotranspiration, and stream discharge that was separated into base flow and overland flow.

The effective rainfall of the watershed was calculated using the Thiessen polygon method to be 42 inches for the year, 48% of that water discharged by …

Cellular And Molecular Dissection Of Pluripotent Adult Somatic Stem Cells In Planarians, Norito Shibata, Labib Rouhana, Kiyokazu Agata

Biological Sciences Faculty Publications

Freshwater planarians, Plathelminthes, have been an intriguing model animal of regeneration studies for more than 100 years. Their robust regenerative ability is one of asexual reproductive capacity, in which complete animals develop from tiny body fragments within a week. Pluripotent adult somatic stem cells, called neoblasts, assure this regenerative ability. Neoblasts give rise to not only all types of somatic cells, but also germline cells. During the last decade, several experimental techniques for the analysis of planarian neoblasts at the molecular level, such as in situ hybridization, RNAi and fluorescence activated cell sorting, have been established. Moreover, information about genes …

Robust Dynamic Balance Of Ap-1 Transcription Factors In A Neuronal Gene Regulatory Network., Gregory M Miller, Babatunde A Ogunnaike, James S Schwaber, Rajanikanth Vadigepalli

Department of Pathology, Anatomy, and Cell Biology Faculty Papers

BACKGROUND: The octapeptide Angiotensin II is a key hormone that acts via its receptor AT1R in the brainstem to modulate the blood pressure control circuits and thus plays a central role in the cardiac and respiratory homeostasis. This modulation occurs via activation of a complex network of signaling proteins and transcription factors, leading to changes in levels of key genes and proteins. AT1R initiated activity in the nucleus tractus solitarius (NTS), which regulates blood pressure, has been the subject of extensive molecular analysis. But the adaptive network interactions in the NTS response to AT1R, plausibly related to the development of …