Life Sciences Commons^™

Fitting Time Series Models To Fisheries Data To Ascertain Age, Kathleen S. Kirch, Norou Diawara, Cynthia M. Jones

OES Faculty Publications

The ability of government agencies to assign accurate ages of fish is important to fisheries management. Accurate ageing allows for most reliable age-based models to be used to support sustainability and maximize economic benefit. Assigning age relies on validating putative annual marks by evaluating accretional material laid down in patterns in fish ear bones, typically by marginal increment analysis. These patterns often take the shape of a sawtooth wave with an abrupt drop in accretion yearly to form an annual band and are typically validated qualitatively. Researchers have shown key interest in modeling marginal increments to verify the marks do, …

Flaws In The Methodologies For Organic Carbon Analysis In Seagrass Blue Carbon Soils, Oscar Serrano, Ines Mazarrasa, James W. Fourqurean, Eduard Serrano, Jeffrey Baldock, Jonathan Sanderman

Research outputs 2022 to 2026

The ability to accurately measure organic carbon (OC) in marine sediments or soils is overall taken for granted in scientific communities, yet this seemingly mundane task remains a methodological challenge when the soil matrix contains calcium carbonate (CaCO3), creating inaccuracies in Blue Carbon estimates. Here, we compared five common methods combining acidification, combustion, and wet oxidation pre-treatments for determination of OC in sediments and soils containing CaCO3 based on the analyses of artificial soil mixtures made of different OC and CaCO3 contents, and multiple soils from Australian seagrass cores. The results obtained showed that methods involving acidification pre-treatment entailed −17 …

Analytical Approaches To Improve Accuracy In Solving The Protein Topology Problem, Kamal Al Nasr, Feras Yousef, Ruba Jebril, Christopher Jones

Computer Science Faculty Research

To take advantage of recent advances in genomics and proteomics it is critical that the three-dimensional physical structure of biological macromolecules be determined. Cryo-Electron Microscopy (cryo-EM) is a promising and improving method for obtaining this data, however resolution is often not sufficient to directly determine the atomic scale structure. Despite this, information for secondary structure locations is detectable. De novo modeling is a computational approach to modeling these macromolecular structures based on cryo-EM derived data. During de novo modeling a mapping between detected secondary structures and the underlying amino acid sequence must be identified. DP-TOSS (Dynamic Programming for determining the …

Data Publication With The Structural Biology Data Grid Supports Live Analysis, Peter A. Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C. Tjon, Alejandro Buschiazzo, Ming Lei, Chris Botka, James Withrow, David Neau, Kanagalaghatta Rajashankar, Karen S. Anderson, Richard H. Baxter, Stephen C. Blacklow, Titus J. Boggon, Alexandre M. J. J. Bonvin, Dominika Borek, Tom J. Brett, Amedeo Caflisch, Chung-I Chang, Walter J. Chazin, Kevin D. Corbett, Michael S. Cosgrove, Sean Crosson, Sirano Dhe-Paganon, Enrico Di Cera, Catherine L. Drennan, Michael J. Eck, Brandt F. Eichman, Qing R. Fan, Oleg V. Tsodikov

Pharmaceutical Sciences Faculty Publications

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the …

Evaluation Of The Power And Type 1 Error Of Recently Proposed Family-Based Tests Of Assocations For Rare Variants, Allison Hainline, Carolina Alvarez, Alexander Luedtke, Brian Greco, Andrew Beck, Nathan L. Tintle

Faculty Work Comprehensive List

Until very recently, few methods existed to analyze rare-variant association with binary phenotypes in complex pedigrees. We consider a set of recently proposed methods applied to the simulated and real hypertension phenotype as part of the Genetic Analysis Workshop 18. Minimal power of the methods is observed for genes containing variants with weak effects on the phenotype. Application of the methods to the real hypertension phenotype yielded no genes meeting a strict Bonferroni cutoff of significance. Some prior literature connects 3 of the 5 most associated genes (p <1 × 10−4) to hypertension or related phenotypes. Further methodological development is needed to extend these methods to handle covariates, and to explore more powerful test alternatives.

Application Of Family-Based Tests Of Association For Rare Variants To Pathways, Brian Greco, Alexander Luedtke, Allison Hainline, Carolina Alvarez, Andrew Beck, Nathan L. Tintle

Faculty Work Comprehensive List

Pathway analysis approaches for sequence data typically either operate in a single stage (all variants within all genes in the pathway are combined into a single, very large set of variants that can then be analyzed using standard “gene-based” test statistics) or in 2-stages (gene-based p values are computed for all genes in the pathway, and then the gene-based p values are combined into a single pathway p value). To date, little consideration has been given to the performance of gene-based tests (typically designed for a smaller number of single-nucleotide variants [SNVs]) when the number of SNVs in the gene …

Molecular Dynamics Analysis Of Apolipoprotein-D - Lipid Hydroperoxide Interactions: Mechanism For Selective Oxidation Of Met-93, Aaron J. Oakley, Surabhi Bhatia, Heath Ecroyd, Brett Garner

Faculty of Science - Papers (Archive)

Background: Recent studies suggest reduction of radical-propagating fatty acid hydroperoxides to inert hydroxides by interaction with apolipoprotein-D (apoD) Met93 may represent an antioxidant function for apoD. The nature and structural consequences of this selective interaction are unknown.

Methodology/Principal Findings: Herein we used molecular dynamics (MD) analysis to address these issues. Longtimescale simulations of apoD suggest lipid molecules are bound flexibly, with the molecules free to explore multiple conformations in a binding site at the entrance to the classical lipocalin ligand-binding pocket. Models of 5s- 12s- and 15s hydroperoxyeicosatetraenoic acids were created and the lipids found to wrap around Met93 thus …

Police Witness Identification Images: A Geometric Morphometric Analysis, Susan Hayes, Cameron Tullberg

Faculty of Science - Papers (Archive)

Research into witness identification images typically occurs within the laboratory and involves subjective likeness and recognizability judgments. This study analyzed whether actual witness identification images systematically alter the facial shapes of the suspects described. The shape analysis tool, geometric morphometrics, was applied to 46 homologous facial landmarks displayed on 50 witness identification images and their corresponding arrest photographs, using principal component analysis and multivariate regressions. The results indicate that compared with arrest photographs, witness identification images systematically depict suspects with lowered and medially located eyebrows (p=

Direct Detection Of Additives And Degradation Products From Polymers By Liquid Extraction Surface Analysis Employing Chip-Based Nanospray Mass Spectrometry, Martin Paine, Phillip Barker, Shane A. Maclaughlin, Todd W. Mitchell, Stephen J. Blanksby

Faculty of Science - Papers (Archive)

Rationale: Polymer-based surface coatings in outdoor applications experience accelerated degradation due to exposure to solar radiation, oxygen and atmospheric pollutants. These deleterious agents cause undesirable changes to the polymers aesthetic and mechanical properties reducing its lifetime. The use of antioxidants such as hindered amine light stabilisers (HALS) retard these degradative processes, however, mechanisms for HALS action and polymer degradation are poorly understood. Methods: Detection of the hindered amine light stabiliser (HALS) TINUVIN®123 (bis (1-octyloxy-2,2,6,6-tetramethyl-4-piperidyl) sebacate) and the polymer degradation products directly from a polyester-based coil coating was achieved by liquid extraction surface analysis (LESA) coupled to a triple quadrupole QTRAP® …

Analysis Of Macrobenthic Assemblages Of Lake Illawarra, New South Wales, B Li, Robert John Morrison

Faculty of Science - Papers (Archive)

1 - A survey of the macrobenthos community was carried out in Lake Illawarra, NSW, Australia, during April and May 2011. 2 - The aim of this study was to understand the current status of the characteristic macrobenthic fauna community, and the temporal changes over the past 30 years, as well as the impacts of anthropogenic activities on the benthic ecosystem. 3- Fifteen stations were selected as representative of three main areas of the lake (the entrance channel, the central basin and the sublittoral fringe), which might be impacted by different kinds of human activities. 4 - A total of …

A Petrological, Mineralogical And Geochemical Analysis Of Listwaenite Alteration At Spring Creek Bingara In The Great Serpentinite Belt, New England, Nsw, E Holcroft, Solomon Buckman, I Neuss

Faculty of Science - Papers (Archive)

No abstract provided.

Autonomous Greenhouse Gas Measurement System For Analysis Of Gas Migration On Landfill Sites, Stephen Beirne, Breda M. Kierman, Cormac Fay, Colum Foley, Brian Corcoran, Alan F. Smeaton, Dermot Diamond

Faculty of Science - Papers (Archive)

This paper describes the design, development and validation of an autonomous gas sensing platform prototype for monitoring of the greenhouse gases, methane (CH₄) and carbon dioxide (CO₂). The deployment undertaken for validation of the developed prototype monitored landfill gas migration to perimeter borehole wells on a landfill site. Target gas concentrations were captured via infrared gas sensors tuned for each target gas and data reported to an offsite data collection point at 12 hour intervals. This bespoke platform and the accompanying data recording and interface software provide a flexible alternative to the presently employed labor intensive, …

Development And Application Of A System For The Analysis Of Atmospheric, Water And Sediment Nitrogen And Carbon, Ann Stavert, Stephen R. Wilson, Dianne F. Jolley

Faculty of Science - Papers (Archive)

Eutrophication and climate change, key environmental concerns, are both linked to the carbon and nitrogen cycles hence the improved understanding of these cycles is essential. Currently, there is no system that simultaneously measures the fluxes of the three key gas phase products of nitrogen and carbon cycling (CO2, CH4 and N2O) in submerged ecosystems with hourly time resolution. A “Lake-in-a-box” (mesocosm) was developed in the laboratory which allowed the monitoring of key components of the carbon and nitrogen cycles within the air, water and sediments. The approach is automated, simple and time efficient and novel in its ability to examine …

Nmr Analysis Of The Dynamic Exchange Of The Ns2b Cofactor Between Open And Closed Conformations Of The West Nile Virus Ns2b-Ns3 Protease, X Su, Kiyoshi Ozawa, R Qi, S G. Vasudevan, S P. Lim, G Otting

Faculty of Science - Papers (Archive)

Background: The two-component NS2B-NS3 proteases of West Nile and dengue viruses are essential for viral replication and established targets for drug development. In all crystal structures of the proteases to date, the NS2B cofactor is located far from the substrate binding site (open conformation) in the absence of inhibitor and lining the substrate binding site (closed conformation) in the presence of an inhibitor. Methods: In this work, nuclear magnetic resonance (NMR) spectroscopy of isotope and spin-labeled samples of the West Nile virus protease was used to investigate the occurrence of equilibria between open and closed conformations in solution. Findings: In …

High Resolution Analysis Of Uranium And Thorium Concentration As Well As U-Series Isotope Distributions In A Neanderthal Tooth From Payre (Ardeche, France) Using Laser Ablation Icp-Ms, R. Grun, Maxime Aubert, Renaud C. Joannes-Boyau, M-H Moncel

Faculty of Science - Papers (Archive)

We have mapped U (238U) and Th (232Th) elemental concentrations as well as U-series isotope distributions in a Neanderthal tooth from the Middle Palaeolithic site of Payre using laser ablation ICP-MS. The U-concentrations in an enamel section varied between 1 and 1500 ppb. The U-concentration maps show that U-migration through the external enamel surface is minute, the bulk of the uranium having migrated internally via the dentine into the enamel. The uranium migration and uptake is critically dependent on the mineralogical structure of the enamel. Increased U-concentrations are observed along lineaments, some of which are associated with cracks, and others …

Trend Analysis Of Greenhouse Gases Over Europe Measured By A Network Of Ground-Based Remote Ftir Instruments, T Gardiner, A Forbes, M De Maziere, C Vigouroux, E Mahieu, P Demoulin, Voltaire A. Velazco, J Notholt, T Blumenstock, F Hase, I Kramer, R Sussmann, W Stremme, J Mellqvist, A Strandberg, K Ellingsen, M Gauss

Faculty of Science - Papers (Archive)

This paper describes the statistical analysis of annual trends in long term datasets of greenhouse gas measurements taken over ten or more years. The analysis technique employs a bootstrap resampling method to determine both the long-term and intra-annual variability of the datasets, together with the uncertainties on the trend values.

Wearable Technology For The Real-Time Analysis Of Sweat During Exercise, D Morris, B Schazmann, Y Wu, C Fay, Stephen T. Beirne, C Slater, King-Tong Lau, Gordon G. Wallace, Dermot Diamond

Faculty of Science - Papers (Archive)

-Textile based sensors which can be used to measure the chemical composition of bodily fluids represents a major advancement in the area of wearable technology. BIOTEX is an EU funded project aiming to develop such sensors with a particular interest in monitoring perspiration. A textile based fluid handling system has been developed for sample collection and transport. Sodium, conductivity and pH sensors have also been developed. This paper details the integration and testing of these sensors. Results show that the developed system can collect and analyze sweat in real time during exercise and transmit this data wirelessly to a remote …

Experiences With Tracking The Effects Of Changing Requirements On Morphbank: A Web-Based Bioinformatics Application, Subhajit Datta, Robert Van Engelen, David Gaitros, Neelima Jammigumpula

Research Collection School Of Computing and Information Systems

In this paper, we present a case study of applying the metrics Mutation Index, Component Set, Dependency Index on Morphbank- a web based bioinformatics application - to track the effects of changing requirements on a software system and suggest design modifications to mitigate such impact. Morphbank is "an open web repository of biological images documenting specimen-based research in comparative anatomy, morphological phylogenetics, taxonomy and related fields focused on increasing our knowledge about biodiversity". This paper discusses the context of the case study, analyzes the results, highlights observations and learning, and mentions directions of future work.

Co Measurements From The Ace-Fts Satellite Instrument: Data Analysis And Validation Using Ground-Based, Airborne And Spaceborne Observations, C Clerbaux, M George, S Turquety, K A. Walker, Nicholas B. Jones, David W. Griffith, C P Rinsland, E Mahieu, M De Maziere, A. Kagawa, J Hannigan, M Coffey, F Hase, M Hopfner, P Duchatelet, I Kramer, A Strandberg, K Strong, Y Kasai, B Barret, P Ricaud, D Murtagh, E Dupuy, V Catoire, C Robert, C Senten, N J. Livesey, M Luo, M Lopez-Puertas, Ph Medelec, A Pazmino, H Pumphrey, T Borsdorff, P F. Coheur, J P. Cammas, James Drummond, R De Zafra, M Deeter, L Emmons, F Eddounia, J C. Gille, E Le Flochmoen, C Boone, B Funke, M Schneider, G P. Stiller, P Bernath, D P. Edwards

Faculty of Science - Papers (Archive)

The Atmospheric Chemistry Experiment (ACE) mission was launched in August 2003 to sound the atmosphere by solar occultation. Carbon monoxide (CO), a good tracer of pollution plumes and atmospheric dynamics, is one of the key species provided by the primary instrument, the ACE-Fourier Transform Spectrometer (ACE-FTS). This instrument performs measurements in both the CO 1-0 and 2-0 ro-vibrational bands, from which vertically resolved CO concentration profiles are retrieved, from the mid-troposphere to the thermosphere. This paper presents an updated description of the ACE-FTS version 2.2 CO data product, along with a comprehensive validation of these profiles using available observations (February …

Nutrigenomics Applied To An Animal Model Of Inflammatory Bowel Diseases: Transcriptomic Analysis Of The Effects Of Eicosapentaenoic Acid-And Arachidonic Acid-Enriched Diets, Nicole Roy, Matthew Barnett, Bianca Knoch, Yvonne Dommels, Warren Mcnabb

Faculty of Science - Papers (Archive)

In vivo models of Inflammatory Bowel Diseases (IBD) elucidate important mechanisms of chronic inflammation. Complex intestinal responses to food components create a unique “fingerprint” discriminating health from disease. Five-week-old IL10−/− and C57BL/6J (C57; control) mice were inoculated orally with complex intestinal microflora (CIF) and/or pure cultures of Enterococcus faecalis and E. faecalis (EF) aiming for more consistent inflammation of the intestinal mucosa. Inoculation treatments were compared to non-inoculated IL10−/− and C57 mice, either kept in specific pathogen free (SPF) or conventional conditions (2×5 factorial design). At 12 weeks of age, mice were sacrificed for intestinal histological (HIS) and transcriptomic analysis …

Mechanochemical Coupling In The Myosin Motor Domain. Ii. Analysis Of Critical Residues, Haibo Yu, Liang Ma, Yang Yang, Qiang Cui

Faculty of Science - Papers (Archive)

An important challenge in the analysis of mechanochemical coupling in molecular motors is to identify residues that dictate the tight coupling between the chemical site and distant structural rearrangements. In this work, a systematic attempt is made to tackle this issue for the conventional myosin. By judiciously combining a range of computational techniques with different approximations and strength, which include targeted molecular dynamics, normal mode analysis, and statistical coupling analysis, we are able to identify a set of important residues and propose their relevant function during the recovery stroke of myosin. These analyses also allowed us to make connections with …

Comparative Analysis Of Virulence Genes, Genetic Diversity, And Phylogeny Of Commensal And Enterotoxigenic Escherichia Coli Isolates From Weaned Pigs, Xi-Yang Wu, Toni A. Chapman, Darren J. Trott, Karl A Bettelheim, Thuy N. Do, Steve Driesen, Mark J. Walker, James Chin

Faculty of Science - Papers (Archive)

If the acquisition of virulence genes (VGs) for pathogenicity were not solely acquired through horizontal gene transfers of pathogenicity islands, transposons, and phages, then clonal clusters of enterotoxigenic Escherichia coli (ETEC) would contain few or even none of the VGs found in strains responsible for extraintestinal infections. To evaluate this possibility, 47 postweaning diarrhea (PWD) ETEC strains from different geographical origins and 158 commensal E. coli isolates from the gastrointestinal tracts of eight group-housed healthy pigs were screened for 36 extraintestinal and 18 enteric VGs using multiplex PCR assays. Of 36 extraintestinal VGs, only 8 were detected (fimH, …

Slides: Community Ownership And Management Of Productive Forestland: Building Natural And Social Capital, Keith Bisson, Rodger Krussman

Community-Owned Forests: Possibilities, Experiences, and Lessons Learned (June 16-19)

Presenters: Keith Bisson, Quebec-Labrador Foundation, and Rodger Krussman, The Trust for Public Land

20 slides

Doing Discourse Analysis, Gordon R. Waitt

Faculty of Science - Papers (Archive)

My hope in writing this chapter is to generate enthusiasm for geographical research employing discourse analysis. My intention is to provide some advice on doing discourse analysis to facilitale the design of research. I first outline why some geographers have been inspired by this approach. I suggest how Foucauldian discourse analysis is a break from other critical methods applied to textual analysis, including content analysis, semiology, and iconography. The theoretical underpinnings of the method provided by Michel Foucault, a French poststructuralist philosopher, is a key source of difference. I therefore condense Michel Foucault's contribution to discourse analysis by sketching out …

Confirmation Of The Structure Of Oxystemokerrin By Single Crystal X-Ray Structural Analysis And A Proposed Biosynthesis, Pitchaya Mungkornasawakul, Hayden Matthews, Alison T. Ung, Stephen G. Pyne, Araya Jatisatienr, Wilford Lie, Brian W. Skelton, Allan H. White

Faculty of Science - Papers (Archive)

The crystal structure of the pentacyclic Stemona alkaloid oxystemokerrin (2), isolated from the roots of Stemona kerrii, is reported, confirming the structure proposed for this compound in a contemporaneous spectroscopic study. This compound is a diastereomer of stemocurtisinol (3), whose structure we have recently reported from S. curtisii, also confirmed by a single-crystal X-ray study. These alkaloids have opposite configurations at C-4 and C-19. A possible biosynthetic pathway for the biosynthesis of 2 and 3 is proposed.

Quasi-Static Analysis Of Defected Ground Structure, Nemai C. Karmakar, Sushim Mukul Roy, Isaac Balbin, Gerhard F. Swiegers

Faculty of Science - Papers (Archive)

A quasi-static equivalent circuit model of a dumbbell shaped defected ground structure (DGS) is developed. The equivalent circuit model is derived from the equivalent inductance and capacitance developed due to the perturbed returned current path on the ground and the narrow gap, respectively. The theory is validated against the commercial full-wave solver CST Microwave Studio. Finally, the calculated results are compared with the measured results. Good agreement between the theory, the commercially available numerical analyses and the experimental results validates the developed theoretical model.

Analysis Of The Mechanism By Which Calcium Negatively Regulates The Tyrosine Phosphorylation Cascade Associated With Sperm Capacitation, Mark Baker, Louise Hethrington, Heath W. Ecroyd, Shaun D. Roman, Robert J. Aitken

Faculty of Science - Papers (Archive)

The capacitation of mammalian spermatozoa involves the activation of a cAMP-mediated signal transduction pathway that drives tyrosine phosphorylation via mechanisms that are unique to this cell type. Controversy surrounds the impact of extracellular calcium on this process, with positive and negative effects being recorded in independent publications. We clearly demonstrate that the presence of calcium in the external medium decreases tyrosine phosphorylation in both human and mouse spermatozoa. Under these conditions, a rise in intracellular pH was recorded, however, this event was not responsible for the observed changes in phosphotyrosine expression. Rather, the impact of calcium on tyrosine phosphorylation in …

Can Managers Adapt To New Relationships And Roles Under Nfma?, Elizabeth Estill

The National Forest Management Act in a Changing Society, 1976-1996: How Well Has It Worked in the Past 20 Years?: Will It Work in the 21st Century? (September 16-18)

5 pages.

A Trophic Gradient Analysis Of Lake Powell: The 1994 Utah State University Aquatic Ecology Laboratory Analyses, Wayne A. Wurtsbaugh, Megan Barker, Ron Brunson, David Fogle, Scott Hawxhurst, Chad Mellison, Lis Phillips, Felipe Queiroz, Daniel Zamecnik

Watershed Sciences Faculty Publications

From 9-11 April, 1994, the Aquatic Ecology Laboratory Class (FW462) of Utah State University sampled the upper reaches of Lake Powell to assess if a trophic gradient existed. We °ampled physical and chemical parameters (temperature, oxygen, conductivity, and total phosphorus), phytoplankton chlorophyll a, littoral and pelagic zooplankton biomass and composition, littoral and profundal benthic invertebrates, and fish abundance measured in the littoral zone (gill nets) and the pelagic zone (hydroacoustics). Data was collected along the upper 50 miles of the reservoir between Bullfrog and the Hite marina near the Colorado River inflow.

Our field trip was done just prior to …

Taking A Cat Map: Genome Analysis By Supercomputer, Jose V. Lopez

Marine & Environmental Sciences Faculty Articles

No abstract provided.