Biology Commons^™

Missing Gene Identification Using Functional Coherence Scores, Meghana Chitale, Ishita K. Khan, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Reconstructing metabolic and signaling pathways is an effective way of interpreting a genome sequence. A challenge in a pathway reconstruction is that often genes in a pathway cannot be easily found, reflecting current imperfect information of the target organism. In this work, we developed a new method for finding missing genes, which integrates multiple features, including gene expression, phylogenetic profile, and function association scores. Particularly, for considering function association between candidate genes and neighboring proteins to the target missing gene in the network, we used Co-occurrence Association Score (CAS) and PubMed Association Score (PAS), which are designed for capturing functional …

Flexc: Protein Flexibility Prediction Using Context-Based Statistics, Predicted Structural Features, And Sequence Information, Ashraf Yaseen, Mais Nijim, Brandon Williams, Lei Qian, Min Li, Jianxin Wang, Yaohang Li

Computer Science Faculty Publications

The fluctuation of atoms around their average positions in protein structures provides important information regarding protein dynamics. This flexibility of protein structures is associated with various biological processes. Predicting flexibility of residues from protein sequences is significant for analyzing the dynamic properties of proteins which will be helpful in predicting their functions.

Geospatial Approaches To Support Pelagic Conservation Planning And Adaptive Management, L. M. Wedding, Sara M. Maxwell, D. Hyrenbach, D. C. Dunn, J. J. Roberts, D. Briscoe, E. Hines, P. N. Halpin

Biological Sciences Faculty Publications

Place-based management in the open ocean faces unique challenges in delineating boundaries around temporally and spatially dynamic systems that span broad geographic scales and multiple management jurisdictions, especially in the 'high seas'. Geospatial technologies are critical for the successful design of pelagic conservation areas, because they provide information on the spatially and temporally dynamic oceanographic features responsible for driving species distribution and abundance in the open ocean, the movements of protected species, and the spatial patterns of distribution of potential threats. Nevertheless, there are major challenges to implementing these geospatial approaches in the open ocean. This Theme Section seeks to …

Impacts Of Recreational Aviation On Wildlife: The Physiological Stress Response In White-Tailed Deer (Odocoileus Virginianus) And Associated User Perceptions, Devin W. Landry

Graduate Student Theses, Dissertations, & Professional Papers

Recreational aviation on public lands may negatively impact wildlife. However, land-use decisions need to balance user need with wildlife impact. We know very little about 1) how back country airstrip use affects local wildlife, or 2) attitudes and perceptions of recreational pilots toward possible management actions. For my Master’s research, I investigated how aircraft activity influenced physiological measures of stress in white-tailed deer, while also modeling how psychometrics such as wildlife attitudes and place attachment predict the willingness of recreational pilots engage in impact-mitigating behaviors. I measured physiological stress through non-invasive sampling of stress hormones in fecal samples (fecal glucocorticoid …

Juvenile Survival And Adult Return As A Function Of Freshwater Rearing Life History For Coho Salmon In The Klamath River Basin, Molly Gorman

Cal Poly Humboldt theses and projects

The Scott and Shasta rivers, Klamath River tributaries, experience spatial disparity in habitat quality in spring and summer as a result of historical and current land-use. Juvenile Coho Salmon (Oncorhynchus kisutch) born in the upper tributary reaches often rear in natal streams before migrating to sea. However, those born in the lower reaches often encounter unsuitable habitat and emigrate during their first spring to seek non-natal rearing habitats. It is assumed that these early outmigrants are population losses. This study evaluated first-summer survival, and contribution to the adult population, of non-natal rearing juveniles in the Klamath River Basin. …

Revised Distributional Estimates For The Recently Discovered Olinguito (Bassaricyon Neblina), Using Museum And Science Records, Beth E. Gerstner

Dissertations and Theses

In the context of global change, a necessary first step for the conservation of species is gaining a good understanding of their distributional limits. This is especially important for biodiversity hotspots with high endemism such as the Northern Andes. The olinguito (Procyonidae: Bassaricyon neblina) is a recently described, medium-sized carnivoran found in Northern Andean cloud forests. A preliminary distributional model was published along with the original description, and I here provide revised distributional estimates using updated locality records and more current ENM methods. I build ecological niche models in Maxent using occurrence data (georeferenced museum records and citizen science-derived photo-vouchers) …

Red List Of Marine Bony Fishes Of The Eastern Central Atlantic, Beth Polidoro, Gina Ralph, Kyle Strongin, Michael Harvey, Kent Carpenter, Titus Ayo Adeofe, Rachel Arnold, Paul Bannerman, Jean Noel Bibang Bi Nguema, Jack Buchanan, Khairdine Mohamed Abdallahi Camara, Youssouf Hawa Camara, Kadiatou Cissoko, Bruce B. Collette, Mia T. Comeros-Raynal, Godefroy De Bruyne, Madeleine Diouf, Roger Djiman, Mathieu Ducrocq, Ofer Gon, Antony S. Harold, Heather Harwell, Craig Hilton-Taylor, Andrew Hines, P. Alexander Hulley, Tomio Iwamoto, Steen Knudsen, Jean De Dieu Lewembe, Christi Linardich, Ken Lindeman, Ebou Mass Mbye, Jean Egard Mikolo, Vanda Monteiro, Jean Bernard Mougoussi, Thomas Munroe, Jean Hervé Mve Beh, Francis K.E. Nunoo, Caroline Pollock, Stuart Poss, Richmond Quartey, Barry Russell, Alphonse Sagna, Catherine Sayer, Aboubacar Sidibe, William Smith-Vaniz, Emilie Stump, Mor Sylla, Luis Tito De Morais, Jean-Christophe Vié, Akanbi Williams

Biological Sciences Faculty Publications

The Red List of marine bony fishes of the Eastern Central Atlantic (ECA) is a review of the conservation status of all native marine bony fishes in ECA according to the global Categories and Criteria of the IUCN Red List of Threatened Species. It identifies those species that are threatened with extinction at the global level and occur within the ECA region. This comprehensive assessment, which is the first of its kind in the ECA, aims to provide improved knowledge of species presence and extinction risk status for the purposes of guiding conservation actions and improved policies for these species …

Selective Mutation Accumulation: A Computational Model Of The Paternal Age Effect, Eoin C. Whelan, Alexander C. Nwala, Christopher Osgood, Stephan Olariu

Biological Sciences Faculty Publications

Motivation: As the mean age of parenthood grows, the effect of parental age on genetic disease and child health becomes ever more important. A number of autosomal dominant disorders show a dramatic paternal age effect due to selfish mutations: substitutions that grant spermatogonial stem cells (SSCs) a selective advantage in the testes of the father, but have a deleterious effect in offspring. In this paper we present a computational technique to model the SSC niche in order to examine the phenomenon and draw conclusions across different genes and disorders.

Results: We used a Markov chain to model the probabilities of …

Are We Missing Important Areas In Pelagic Marine Conservation? Redefining Conservation Hotspots In The Ocean, Dana K. Briscoe, Sara M. Maxwell, Raphael Kudela, Larry B. Crowder

Biological Sciences Faculty Publications

The protection of biodiversity is one of the most important goals in terrestrial and marine conservation. Marine conservation approaches have traditionally followed the example of terrestrial initiatives. However, patterns, processes, habitats, and threats differ greatly between the 2 systems - and even within the marine environment. As a result, there is still a lack of congruence as to how to best identify and prioritize conservation approaches moving from the static terrestrial and nearshore realm into a more fluid, 3-dimensional pelagic realm. To address this problem, we investigate how the conservation science literature has been used to inform and guide management …

Nickel And Copper Mixture Toxicity To Daphnia In Soft Water, Prachi Deshpande

Theses and Dissertations (Comprehensive)

Industrially important metals, such as Cu and Ni, sometimes are present at elevated concentrations in lakes, including those in the Sudbury, ON region. Although they are essential metals, their divalent-cation state (Cu²⁺ and Ni²⁺) can be toxic at high concentrations in the water. The free-ion toxicity of each of these metals has been studied in isolation, but rarely as a mixture. The economic importance of Cu²⁺ and Ni²⁺ makes them essential to study in the context of mixture toxicity. The objectives were to: (1) determine Cu and Ni mixture toxicity to Daphnia through acute LC50 …

Do Toxicity Modifying Factors Influence Acute Or Chronic Toxicity Of Thulium To Hyalella Azteca?, Alexandria H. Loveridge

Theses and Dissertations (Comprehensive)

The industrial demand for rare earth elements (REEs) is growing and as a result, environmental exposure is a concern. Very little is understood about the toxicity of REEs in aquatic environments. The objective of this research is to evaluate the acute and chronic toxicity of Tm and to also understand the toxicity modifying influence of dissolved organic matter (DOM) and cationic competition (Ca2+, Mg2+ and Na+). Furthermore, the aim of this study was to determine linkages between Tm bioaccumulation, growth and survival during chronic exposures. Standard methods (Environment Canada) were followed for both 96h acute and 14d chronic tests, in …

Rcd+: Fast Loop Modeling Server, José R. López-Blanco, Alejandro J. Canosa-Valis, Yaohang Li, Pablo Chacón

Computer Science Faculty Publications

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop …

Assessing Shoreline Change And Vegetation Cover Adjacent To Back-Barrier Shoreline Stabilization Structures In Georgia Estuaries, Katherine R. Wakefield

College of Graduate Studies: Theses & Dissertations

Anthropogenic stabilization of erosional shorelines by hard-armoring structures is used for protection of property, especially if buildings, historical monuments, cultural resources, or other infrastructure are present. The post-installation effects of shoreline stabilization structures on adjacent shorelines in the back-barrier marshes of coastal Georgia are a concern, and interest in living shorelines as erosion control devices has increased because of their use of natural materials and vegetation. AMBUR shoreline analysis software was used to calculate pre-and post-installation shoreline change rates of shorelines adjacent to riprap and bulkhead structures. There was no significant difference between the post-installation shoreline change rates of the …

Spanish River Carbonatite: Its Benefits And Potential Use As A Soil Supplement In Agriculture, James J

Theses and Dissertations (Comprehensive)

A critical problem facing agriculture today is being able to consistently and sustainably provide plants with adequate nutrients for growth. With this problem being exacerbated by the ever-increasing human population, new perspectives and techniques are required to ensure global food security. In order to fully realize potential solutions, however, plant growth and nutrition cannot be exclusively focused upon. The soil-microorganism-plant system is comprised of many interconnected and interdependent processes that together support plant growth: it is upon these processes that the focus must be placed. In this work, the agromineral Spanish River Carbonatite (SRC) is characterized using the framework of …

The Vascular Flora Of Wayne County, Mississippi, Daniel M. Mcnair

Master's Theses

The vascular flora of Wayne County, Mississippi, was surveyed from 2013–2015, and the species of native and naturalized plants are listed. In total, 1,135 species were identified from field collections, previously collected herbarium specimens, and field observations. These belong to 556 genera and 165 families. Four of these species represent first recorded occurrences in the state of Mississippi: Blyxa aubertii Rich., Gomphrena serrata Pav. ex Moq., Isoetes valida (Engelm.) Clute, and Polypogon interruptus Kunth. GPS coordinates are given for important collection sites representing the diversity of plant communities in the county. All voucher specimens from the survey are deposited in …

Dynamics Of An Sir Model With Nonlinear Incidence And Treatment Rate, Balram Dubey, Preeti Dubey, Uma S. Dubey

Applications and Applied Mathematics: An International Journal (AAM)

In this paper, global dynamics of an SIR model are investigated in which the incidence rate is being considered as Beddington-DeAngelis type and the treatment rate as Holling type II (saturated). Analytical study of the model shows that the model has two equilibrium points (diseasefree equilibrium (DFE) and endemic equilibrium (EE)). The disease-free equilibrium (DFE) is locally asymptotically stable when reproduction number is less than one. Some conditions on the model parameters are obtained to show the existence as well as nonexistence of limit cycle. Some sufficient conditions for global stability of the endemic equilibrium using Lyapunov function are obtained. …

Decomposition And Nitrogen Dynamics Of Turtle Grass (Thalassia Testudinum) In A Subtropical Estuarine System, Monica Delgado

Theses and Dissertations

Seagrass beds are pivotal in the functioning of coastal ecosystems in terms of productivity, organic matter turnover and nutrient cycling. Aiming to document decay and nitrogen (N) dynamics of turtle grass (Thalassia testudinum) in a subtropical estuarine system, decomposition patterns of leaves and rhizomes were characterized and compared. Nitrogen usage during decomposition of tissues, and of live tissues and epiphytes growing on live leaves, was also quantified and compared. Stable isotope ratios allowed tracing N within the seagrass bed, following N incorporation into seagrass tissues from the surrounding media (water, sediment). Leaves had a higher N content and decomposed at …

Production And Harvest Of Microalgae In Wastewater Raceways With Resource Recycling, Alexander Colin Roberts

Master's Theses

Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research.

A pilot facility was operated with nine CO₂-supplemented raceway ponds, each with a 33-m² surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously fed …

Assessing The Importance Of Nurse Plant Associations To The Growth Of Pre-~Reproductive Yucca Brevifolia, Eric James Chameroy

UNLV Theses, Dissertations, Professional Papers, and Capstones

Facilitation and competition among plant species, in addition to abiotic factors, play an important role in determining plant community structure in arid and semi-arid environments. I conducted a study in Dry Lake Valley, Lincoln County, Nevada, USA to investigate the importance of nurse plant associations to pre-reproductive Yucca brevifolia (Joshua tree). Dry Lake Valley lies within a transition desert between the Mojave and Great Basin Deserts with ecotonal plant communities consisting of species representative of both deserts. A vegetation survey described the communities in which this study was conducted as a Y. brevifolia woodland dominated by an understory of Ephedra …

Stochastic Models For Plant Microtubule Self-Organization And Structure, Ezgi Can Eren, Ram Dixit, Natarajan Gautam

Biology Faculty Research

One of the key enablers of shape and growth in plant cells is the cortical microtubule (CMT) system, which is a polymer array that forms an appropriately-structured scaffolding in each cell. Plant biologists have shown that stochastic dynamics and simple rules of interactions between CMTs can lead to a coaligned CMT array structure. However, the mechanisms and conditions that cause CMT arrays to become organized are not well understood. It is prohibitively time-consuming to use actual plants to study the effect of various genetic mutations and environmental conditions on CMT self-organization. In fact, even computer simulations with multiple replications are …

Linkages Among Fluorescent Dissolved Organic Matter, Dissolved Amino Acids And Lignin-Derived Phenols In River-Influenced Ocean Margins, Youhei Yamashita, Cédric G. Fichot, Yuan Shen, Rudolf Jaffé, Ronald Benner

Faculty Publications

Excitation emission matrix (EEM) fluorescence spectroscopy coupled with parallel factor analysis (PARAFAC) is commonly used to investigate the dynamics of dissolved organic matter (DOM). However, a lack of direct comparisons with known biomolecules makes it difficult to substantiate the molecular composition of specific fluorescent components. Here, coincident surface-water measurements of EEMs, dissolved lignin, and total dissolved amino acids (TDAA) acquired in the northern Gulf of Mexico were used to investigate the relationships between specific fluorescent components and DOM biomolecules. Two terrestrial humic-like components identified by EEM-PARAFAC using samples obtained from river to offshore waters were strongly linearly correlated with dissolved …

Genus-Wide Assessment Of Bactrurus (Amphipoda: Crangonyctidae) Informs Conservation And Management Of Groundwater Habitats, Matthew L. Niemiller, Steven J. Taylor

National Cave and Karst Management Symposia

No abstract provided.

Karst Wreckage: Subterranean Fauna As Collateral Damage, Julian J. Lewis, Salisa L. Lewis

National Cave and Karst Management Symposia

No abstract provided.

Managing The Spread Of Pseudogymnoascus Destructans And Conserving Bats Threatened By White-Nose Syndrome In North America, Jeremy Coleman, Jonathan D. Reichard, Richard Geboy, Christopher Servheen, Christina Kocer, Mike Armstrong

National Cave and Karst Management Symposia

No abstract provided.

Strip Adaptive Cluster Sampling With Application To Cave Crickets, Kurt Lewis Helf

National Cave and Karst Management Symposia

No abstract provided.

Monitoring In-Cave Resources With Reduced Impact And Increased Quantitative Capacity: Developing Photogrammetry Methodologies For In Cave Environments, Robyn L. Henderek, John R. Wood, Benjamin W. Tobin

National Cave and Karst Management Symposia

No abstract provided.

The Extirpation Of A Population Of The Endangered Illinois Cave Amphipod (Gammarus Acherondytes) By An Exotic Species: The Wednesday Cave Debacle, Julian J. Lewis, Salisa L. Lewis

National Cave and Karst Management Symposia

No abstract provided.

White-Nose Syndrome Response At Mammoth Cave National Park, Rickard S. Toomey

National Cave and Karst Management Symposia

No abstract provided.

Two Distinct Modes Of Metal Ion Binding In The Nuclease Active Site Of A Viral Dna-Packaging Terminase: Insight Into The Two-Metal-Ion Catalytic Mechanism, Haiyan Zhao, Zihan Lin, Anna Y. Lynn, Brittany Varnado, John A. Beutler, Ryan P. Murelli, Stuart F.J. Le Grice, Liang Tang

Publications and Research

Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 A° . Such proximity of the two metal ions may play an essential role in catalysis by …

Taxonomy Of The Bitentaculate Cirratulidae (Polychaeta), Stacy A. Tewari

Graduate Masters Theses

The bitentaculate cirratulid polychaetes are an important faunal element of both near shore and deep-sea benthic faunal communities. The true diversity of the family is currently unknown due to a large number of undescribed species and erroneously applied “cospmopolitan” names being applied to local species. Cirratulids have been misidentified even in the local waters near the University of Massachusetts Boston. The current study presents six new species from North America. Caulleriella venefica, Chaetozone anasimus, Chaetozone diodonta, and Chaetozone hystricosus are described from Boston Harbor and Massachusetts Bay where only two species had previously been reported. Aphelochaeta bullata …