Physical Sciences and Mathematics Commons^™

Quantification Of Organic Carbon Sequestered By Biogenic Iron Sulfide Minerals In Long-Term Anoxic Laboratory Incubations, Nader Nabeh, Cheyenne Brokaw, Aude Picard

Life Sciences Faculty Research

Organic carbon sequestration in sedimentary environments controls oxygen and carbon dioxide concentrations in the atmosphere. While minerals play an important role in the preservation of organic carbon, there is a lack of understanding about the formation and stability of organo-mineral interactions in anoxic environments, especially those involving authigenic iron sulfide minerals. In this study, we quantified organic carbon and nitrogen sequestered in biogenic iron sulfide minerals co-precipitated with sulfate-reducing bacteria (SRB) in freshwater and marine conditions in long-term laboratory experiments. The amounts of C and N associated with biogenic iron sulfide minerals increased with increasing cell biomass concentrations available in …

Localization Of Native Mms13 To The Magnetosome Chain Of Magnetospirillum Magneticum Amb-1 Using Immunogold Electron Microscopy, Immunofluorescence Microscopy And Biochemical Analysis, Zachery Oestreicher, Carmen Valverde-Tercedor, Eric Mumper, Lumarie Pérez-Guzmán, Nadia N. Casillas-Ituarte, Concepcion Jimenez-Lopez, Dennis A. Bazylinski, Steven K. Lower, Brian H. Lower

Life Sciences Faculty Research

Magnetotactic bacteria (MTB) biomineralize intracellular magnetite (Fe3O4 ) crystals surrounded by a magnetosome membrane (MM). The MM contains membrane-specific proteins that control Fe3O4 mineralization in MTB. Previous studies have demonstrated that Mms13 is a critical protein within the MM. Mms13 can be isolated from the MM fraction of Magnetospirillum magneticum AMB-1 and a Mms13 homolog, MamC, has been shown to control the size and shape of magnetite nanocrystals synthesized in-vitro. The objective of this study was to use several independent methods to definitively determine the localization of native Mms13 in M. magneticum AMB-1. Using Mms13-immunogold labeling and transmission electron microscopy …

Resilience And Alternative Stable States After Desert Wildfires, Scott R. Abella, Dominic M. Gentilcore, Lindsay P. Chiquoine

Life Sciences Faculty Research

Improving models of community change is a fundamental goal in ecology and has renewed importance during global change and increasing human disturbance of the biosphere. Using the Mojave Desert (southwestern United States) as a model system, invaded by nonnative plants and subject to wildfire disturbances, we examined models of resilience, alternative stable states, and convergent-divergent trajectories for 36 yr of plant community change after 31 wildfires in communities dominated by the native shrubs Larrea tridentata or Coleogyne ramosissima. Perennial species richness on average was fully resilient within 23 yr after disturbance in both community types. Perennial cover was fully resilient …

Assessing The Potential For Greater Solar Development In West Texas, Usa, Dale D. Devitt, M. H. Young, J. P. Pierre

Life Sciences Faculty Research

As population and economies continue to grow on a global scale, so too does the demand for energy. To improve reliability and independence of energy supplies, the U.S. and many other countries are seeking internally-sourced renewable energy; solar is one such renewable-energy source that meets these criteria. However, all energy sources exert some environmental impacts. In the case of solar, direct impacts stem mostly from alteration of land needed to host infrastructure. Understanding the environmental upside and downside potential of solar energy systems allows a more comprehensive, side-by-side comparison with different energy sources. In this article, we focus on the …

Insight On Thermal Stability Of Magnetite Magnetosomes: Implications For The Fossil Record And Biotechnology, Jefferson Cypriano, Mounib Bahri, Kassioge Dembele, Walid Baaziz, Pedro Leao, Dennis A. Bazylinski, Fernanda Abreu, Ovidiu Ersen, Marcos Farina, Jacques Werckmann

Life Sciences Faculty Research

Magnetosomes are intracellular magnetic nanocrystals composed of magnetite (Fe3O4) or greigite (Fe3S4), enveloped by a lipid bilayer membrane, produced by magnetotactic bacteria. Because of the stability of these structures in certain environments after cell death and lysis, magnetosome magnetite crystals contribute to the magnetization of sediments as well as providing a fossil record of ancient microbial ecosystems. The persistence or changes of the chemical and magnetic features of magnetosomes under certain conditions in different environments are important factors in biotechnology and paleomagnetism. Here we evaluated the thermal stability of magnetosomes in a temperature range between 150 and 500 °C subjected …

Effects Of Rate Of Drying, Life History Phase, And Ecotype On The Ability Of The Moss Bryum Argenteum To Survive Desiccation Events And The Influence On Conservation And Selection Of Material For Restoration, Joshua Lee Greenwood, Lloyd R. Stark, Lindsay P. Chiquoine

Life Sciences Faculty Research

Desiccation stress is frequently experienced by the moss Bryum argenteum and can influence survival, propagation and niche selection. We attempted to disentangle the interacting factors of life history phase (five categories) and rate of desiccation (time allotted for induction of desiccation tolerance) for 13 ecotypes of B. argenteum. Using chlorophyll fluorescence as a stress index, we determined how these parameters influenced desiccation tolerance. Rate of drying and life phase significantly affected desiccation tolerance. The reaction norms of desiccation tolerance displayed by the 13 ecotypes showed a substantial degree of variation in phenotypic plasticity. We observed differences in survival and fluorescence …

Reproduction And Dispersal Of Biological Soil Crust Organisms, Steven D. Warren, Larry L. St. Clair, Lloyd R. Stark, Louise A. Lewis, Nuttapon Pombubpa, Tania Kurbessoian, Jason E. Stajich, Zachary T. Aanderud

Life Sciences Faculty Research

Biological soil crusts (BSCs) consist of a diverse and highly integrated community of organisms that effectively colonize and collectively stabilize soil surfaces. BSCs vary in terms of soil chemistry and texture as well as the environmental parameters that combine to support unique combinations of organisms—including cyanobacteria dominated, lichen-dominated, and bryophyte-dominated crusts. The list of organismal groups that make up BSC communities in various and unique combinations include—free living, lichenized, and mycorrhizal fungi, chemoheterotrophic bacteria, cyanobacteria, diazotrophic bacteria and archaea, eukaryotic algae, and bryophytes. The various BSC organismal groups demonstrate several common characteristics including—desiccation and extreme temperature tolerance, production of various …

Linking Gait Dynamics To Mechanical Cost Of Legged Locomotion, David V. Lee, Sarah L. Harris

Life Sciences Faculty Research

For millenia, legged locomotion has been of central importance to humans for hunting, agriculture, transportation, sport, and warfare. Today, the same principal considerations of locomotor performance and economy apply to legged systems designed to serve, assist, or be worn by humans in urban and natural environments. Energy comes at a premium not only for animals, wherein suitably fast and economical gaits are selected through organic evolution, but also for legged robots that must carry sufficient energy in their batteries. Although a robot's energy is spent at many levels, from control systems to actuators, we suggest that the mechanical cost of …

Assessing Near Surface Hydrologic Processes And Plant Response Over A 1600 M Mountain Valley Gradient In The Great Basin, Nv, U.S.A., Dale Devitt, Brian Bird, Brad Lyles, Lynn Fenstermaker, Richard Jasoni, Scotty Strachan, Jay Arnone Iii, Franco Biondi, Scott Mensing, Laurel Saito

Life Sciences Faculty Research

This study investigated near surface hydrologic processes and plant response over a 1600 m mountain-valley gradient located in the Great Basin of North America (Nevada, U.S.A.) as part of a long-term climate assessment study. The goal was to assess shifts in precipitation, soil water status and associated drainage with elevation and how this influenced evapotranspiration and plant cover/health estimated by a satellite-derived Normalized Difference Vegetation Index (NDVI), all to better understand how water is partitioned in a mountain valley system. Data were acquired during a three-year period from meteorological stations located in five plant communities ranging in elevation from 1756 …

How Much Water Can We Save By Achieving Renewable Portfolio Standards In The Southwest United States?, Yuzhen Feng, Sachiko Sueki, Dale Devitt, Kumud Acharya

Life Sciences Faculty Research

Electricity in the Southwestern United States is primarily generated with water intensive steam turbines. If energy demand continues to rise this will lead to a further rise in water demand. A comprehensive understanding of water consumption and withdrawal for utility scale generation of electricity is necessary before any improvements in the water efficiency of such systems in arid environments can be made. This study estimated and compared the water usage associated with thermoelectric generation (i.e., natural gas, coal), and solar energy, in the five driest Colorado River Basin states: Utah, New Mexico, Nevada, Arizona, and California. This study also examined …

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 …

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 …

Scireader Enables Reading Of Medical Content With Instantaneous Definitions, Patrick R. Gradie, Megan Litster, Rinu Thomas, Jay Vyas, Martin Schiller

Life Sciences Faculty Research

Background

A major problem patients encounter when reading about health related issues is document interpretation, which limits reading comprehension and therefore negatively impacts health care. Currently, searching for medical definitions from an external source is time consuming, distracting, and negatively impacts reading comprehension and memory of the material.

Methods

SciReader was built as a Java application with a Flex-based front-end client. The dictionary used bySciReader was built by consolidating data from several sources and generating new definitions with a standardized syntax. The application was evaluated by measuring the percentage of words defined in different documents. A survey was used …

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 …

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 …

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.

Consequences Of More Extreme Precipitation Regimes For Terrestrial Ecosystems, S. D. Smith, C. Beier, Aimee T. Classen, Melinda D. Smith, Jana L. Heisler, S. W. Leavitt, Alan K. Knapp, D. Briske, Y. Luo, M. Reichstein, J. E. Bell, Philip A. Fay, R. Sherry, Benjamin Smith

Life Sciences Faculty Research

Amplification of the hydrological cycle as a consequence of global warming is forecast to lead to more extreme intra-annual precipitation regimes characterized by larger rainfall events and longer intervals between events. We present a conceptual framework, based on past investigations and ecological theory, for predicting the consequences of this underappreciated aspect of climate change. We consider a broad range of terrestrial ecosystems that vary in their overall water balance. More extreme rainfall regimes are expected to increase the duration and severity of soil water stress in mesic ecosystems as intervals between rainfall events increase. In contrast, xeric ecosystems may exhibit …

Monitoring Temporal Change In Riparian Vegetation Of Great Basin National Park, E. A. Beever, D. A. Pyke, J. C. Chambers, F. Landau, S. D. Smith, K. Murray

Life Sciences Faculty Research

Disturbance in riparian areas of semiarid ecosystems involves complex interactions of pulsed hydrologic flows, herbivory, fire, climatic effects, and anthropogenic influences. We resampled riparian vegetation within ten 10-m × 100-m plots that were initially sampled in 1992 in 4 watersheds of the Snake Range, east central Nevada. Our finding of significantly lower coverage of grasses, forbs, and shrubs within plots in 2001 compared with 1992 was not consistent with the management decision to remove livestock grazing from the watersheds in 1999. Change over time in cover of life-forms or bare ground was not predicted by scat counts within plots in …

Structure Of Woody Riparian Vegetation In Great Basin National Park, S. D. Smith, K. J. Murray, F. H. Landau, A. M. Sala

Life Sciences Faculty Research

The community composition and population structure of the woody riparian vegetation in Great Basin National Park are described. Community analyses were accomplished by sampling 229 plots along an elevational gradient of 8 major stream systems in the Park. TWINSPAN analysis identified 4 primary species groups that were characterized by Populus tremuloides (aspen), Abies concolor (white fir), Rosa woodsii (Woods rose), and Populus angustifolia (narrowleaf cottonwood) as dominants, respectively. Detrended Correspondence Analysis (DECORANA) showed that the most important environmental factors associated with the distribution of species were elevation and slope, with flood-related physiographic factors having a secondary effect. Analysis of size-class …

Fire In A Riparian Shrub Community: Postburn Water Relations In The Tamarix-Salix Association Along The Lower Colorado River, S. D. Smith, D. E. Busch

Life Sciences Faculty Research

Higher water potentials in recovering burned salt-cedar (Tamarix ramosissima) relative to unburned plants and the opposite situation in willow (Salix gooddingii) provide evidence that postfire water stress is reduced in the former but not the latter. Similarly, diurnal patterns of stomatal conductance in these taxa are consistent with the existence of more vigor in burned salt-cedar than willow. Plots of water potential and transpiration demonstrate that hydraulic efficiencies may contribute to differences in fire recovery.

Riparian Plant Water Relations Along The North Fork Of The Kings River, California, J. L. Nachlinger, S. D. Smith, R. J. Risser

Life Sciences Faculty Research

Plant water relations of five obligate ripar-ian species were studied along California's North Fork Kings River. Diurnal stomatal conductance, transpi-ration, and xylem pressure potentials were measured throughout the 1986 growing season and in mid-season in 1987. Patterns were similar for all species although absolute values varied considerably. Maximum stomatal conductance occurred early in the day and season during favorable environmental conditions and decreased as air temperature and the vapor pressure difference between the leaf and air increased. Maximum transpiration rates occurred in mid-morning and mid-summer resulting in estimated daily water losses per unit sunlit leaf area of 163-328 mol H2O …

Water Relations Of Obligate Riparian Plants As A Function Of Streamflow Diversion On The Bishop Creek Watershed, S. D. Smith, J. L. Nachlinger, A. B. Wellington, C. A. Fox

Life Sciences Faculty Research

We investigated the water relations of obli-gate riparian plants on paired diverted and undiverted reaches on Bishop Creek, Eastern Sierra Nevada. Ri-parian plants on diverted reaches had reduced stomatal conductance and water potential compared to plants on undiverted reaches in a dry year, but not in a high runoff year. Juvenile plants on diverted reaches had reduced stomatal conductance and lower midday water potentials relative to surrounding mature trees, a trend that was not observed on undiverted reaches. Plants on diverted reaches possessed significantly smaller, thicker leaves and a reduced total leaf area relative to trees on streamside reaches. Reduced …

An Isotopic Analysis Of The Hydrology And Riparian Vegetation Water Sources On Bishop Creek, M. L. Space, J. W. Hess, S. D. Smith

Life Sciences Faculty Research

Five power generation plants along an eleven kilometer stretch divert Bishop Creek water for hydro-electric power. Stream diversion may be adversely affecting the riparian vegetation. Stable isotopic analysis is employed to determine surface water/ground-water interactions along the creek. surface water originates primarily from three headwater lakes. Discharge into Bishop Creek below the headwaters is primarily derived from ground water. The average δD and δ18O values are significantly different for surface water and ground water that an isotopic analysis can delineate between these two components of flow. Therefore isotopic shifts along the creek can determine gaining reaches. In addition, by knowing …