Life Sciences Commons^™

A Temporal Record Of Microplastic Pollution In Mediterranean Seagrass Soils, Martin Dahl, Sanne Bergman, Mats Björk, Elena Diaz-Almela, Maria Granberg, Martin Gullström, Carmen Leiva-Dueñas, Kerstin Magnusson, Candela Marco-Méndez, Nerea Piñeiro-Juncal, Miguel Ángel Mateo

Research outputs 2014 to 2021

© 2021 Elsevier Ltd Plastic pollution is emerging as a potential threat to the marine environment. In the current study, we selected seagrass meadows, known to efficiently trap organic and inorganic particles, to investigate the concentrations and dynamics of microplastics in their soil. We assessed microplastic contamination and accumulation in 210Pb dated soil cores collected in Posidonia oceanica meadows at three locations along the Spanish Mediterranean coast, with two sites located in the Almería region (Agua Amarga and Roquetas) and one at Cabrera Island (Santa Maria). Almería is known for its intense agricultural industry with 30 000 ha of plastic-covered …

Early Tree Performances, Precocity And Fruit Quality Attributes Of Newly Introducedapricot Cultivars Grown Under Western Serbian Conditions, Tomo Milosevic, Nebojsa Milosevic, Ivan Glisic

Turkish Journal of Agriculture and Forestry

In this work, 19 newly introduced and some traditional apricot cultivars were evaluated by 20 phenological and agronomical traits and fruit quality attributes. The results showed a wide variation in phenological data, tree vigour (TCSA), productivity [yield per tree, cumulative yield (CY) and yield efficiency (YE)], and fruit quality attributes such as fruit and stone weight, flesh/stone ratio, fruit dimensions, size, shape index, soluble solids content (SSC), titratable acidity (TA) and ripening index (RI). The average onset of blossoming varied from 16 March to 20 March, whereas harvest was between 1 June and 12 September. The most vigorous trees were …

Investigating Surface Temperature From First Principles: Seedling Survival, Microclimate Buffering, And Implications For Forest Regeneration, Robin Rank

Graduate Student Theses, Dissertations, & Professional Papers

Forests are extremely important ecosystems with large impacts on global water, energy, and biogeochemical cycling, and they provide numerous ecosystems services to human populations. Even though these systems consist of long-lived vegetation, forests are constantly experiencing changes to their extent and composition through the interacting forces of disturbance dynamics and climate change. In semi-arid landscapes like the western United States, patterns of recurring wildfire and subsequent seedling recruitment and forest regeneration are important in establishing the distribution of forests on the landscape. In this context, climate, hydrology, and existing vegetation all act together to limit the current and potential range …

Fxr Agonists Induce Distinct H-12 Structural States, Vikash Kumar

Graduate Student Theses, Dissertations, & Professional Papers

The nuclear receptor ligand-binding domain (LBD) is a highly dynamic entity. The FXR LBD shows multiple low-energy conformational states of the activation function-2 (AF-2) coregulator binding surface upon ligand binding, indicating the complexity of FXR activation. However, it is unknown how ligand binding leads to different conformational states within the AF-2 region centered on helix 12 (H-12) of the LBD. Here we observe the conformation of the coregulator binding surface (H-12 specifically) of FXR upon ligand binding in solution using fluorine-19 (19F) nuclear magnetic resonance (NMR) and simulations of this surface using molecular dynamics. Fluorescence anisotropy of fluorescein-labeled coregulator peptides …

Effects Of Wolf And Grizzly Bear Recovery On Cougars In A Multi-Use System, Jennifer A. Feltner

Graduate Student Theses, Dissertations, & Professional Papers

No abstract provided.

Sula Study Revisited: 20-Year Post-Fire Regeneration In The Southern Bitterroot Valley, Montana., Luke Alan Rymniak

Graduate Student Theses, Dissertations, & Professional Papers

In the summer of 2000, a number of large fires burned in the southern Bitterroot Valley near Sula, Montana. Research was conducted in 2001 and 2003 in the fire-affected areas of the French Basin and Larid Creek areas in order to investigate the effects of environmental variables, fire severity, and post-fire management on vegetation regeneration. In 2020 these areas were remeasured to understand trends over time by evaluating the impact of these same factors 20 years post fire. The results showed that the effects of environmental variables, fire severity, and post-fire management on vegetation regeneration were varied. The most influential …

Cop9 Signalosome Component Csn-5 Promotes Accumulation And Function Of Stem Cell Regulators Fbf-1 And Fbf-2, Emily Osterli

Graduate Student Theses, Dissertations, & Professional Papers

RNA-binding proteins FBF-1 and FBF-2 (FBFs) are required for stem cell maintenance in C. elegans, although the mechanisms by which FBFs protein levels are regulated remain unknown. Using a yeast two-hybrid screen, we identified an interaction between both FBFs and CSN-5, a component of the COP9 (constitutive photomorphogenesis 9) signalosome. This highly conserved COP9 complex can affect protein stability through a range of mechanisms including deneddylation, deubiquitination, and phosphorylation (Wolf et al., 2003). Mapping protein-protein interactions between FBFs and CSN-5 suggested that the MPN (Mpr1/Pad1 N-terminal) metalloprotease domain of CSN-5 interacts with the RNA-binding domain of FBFs at physiologically …

Management And Conservation Of Westslope Cutthroat Trout In An Impacted, Connected River System, Troy Weant Smith

Graduate Student Theses, Dissertations, & Professional Papers

Westslope cutthroat trout Oncorhynchus clarkii lewisi (WCT) is a native species of high conservation value that historically exhibited partially migratory behavior throughout its range. Long-term persistence of WCT is threatened by human habitat modification, fragmentation, introduction of non-native species, and hybridization. As a result of these changes, remnant populations in Montana have shifted toward resident populations in headwater systems and away from migratory populations in larger connected river networks. This is compounded by the historic introduction of rainbow trout O. mykiss (RBT) that hybridize with WCT, especially in larger river habitats. Rock Creek in western Montana, USA was historically managed …

Ensemble Protein Inference Evaluation, Kyle Lee Lucke

Graduate Student Theses, Dissertations, & Professional Papers

The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …

Monitoring The Wetland Landscape: White-Faced Ibis (Plegadis Chihi) Breeding Habitat As A Model Assemblage, Shea P. Coons

Graduate Student Theses, Dissertations, & Professional Papers

Wetlands structure landscape biodiversity by providing critical habitat to numerous fish and wildlife species. However, climate change, growing human populations, and shifting land use practices strain limited water supplies that sustain wetlands in the semi-arid western US. Conserving a wetland network with prominent value to wildlife is paramount to ensure future security of habitat and ecosystem processes. Here, I use white-faced ibis (Plegadis chihi; hereafter ‘ibis’) breeding colonies as a model system to identify and monitor a landscape-scale wetland network across the semi-arid western US. Ibis serve an important role in marking ecologically important wetland networks because they require a …

Collaborative Conservation And Backcountry Weed Control: A Case Study Of The Great Burn Proposed Wilderness, Christopher James Prange

Graduate Student Theses, Dissertations, & Professional Papers

Noxious weeds have become a management priority on public lands in the United States. Managing invasive weed populations in natural areas with complex ecosystems presents issues that need a systems-wide approach over long temporal and spatial scales. This broad-scale problem increasingly demands collaborative efforts. While collaborative conservation has become a tool in natural resource management during the 21^st century, it is less commonly applied in weed control in backcountry wilderness areas. Programs that have been initiated are understudied. Accordingly, this research was conducted through semi-structured interviews to gather perspectives of weed professionals involved in a collaborative backcountry weed program …

A Reintroduction Retrospective: Comparative Fisher (Pekania Pennanti) Survival And Prey Habitat Use In The Cascade Mountains Of Washington State, Tanner S.T. Humphries

Graduate Student Theses, Dissertations, & Professional Papers

Increasing human impacts on biodiversity highlight the global need for ecological restoration. For many wildlife species, reintroduction is necessary to re-establish populations in parts of their historic range where they have been extirpated. Reintroduction efforts are commonly used to help restore ecosystem integrity, but are often expensive, time consuming, and unsuccessful at generating self-sustaining populations. Thus, a more complete understanding of the factors affecting restoration success is important for ensuring successful outcomes and responsible stewardship. Fishers (Pekania pennanti) are one of the most commonly reintroduced carnivores in North America, but the success of such efforts is highly variable, …

Polya: A Tool For Adjudicating Competing Annotations Of Biological Sequences, Kaitlin Carey

Graduate Student Theses, Dissertations, & Professional Papers

Annotation of a biological sequence is usually performed by aligning that sequence to a database of known sequence elements. When that database contains elements that are highly similar to each other, the proper annotation may be ambiguous, because several entries in the database produce high-scoring alignments. Typical annotation methods work by assigning a label based on the candidate annotation with the highest alignment score; this can overstate annotation certainty, mislabel boundaries, and fails to identify large scale rearrangements or insertions within the annotated sequence. Here, I present a new software tool, PolyA, that adjudicates between competing alignment-based annotations by computing …

Soda: An Open-Source Library For Visualizing Biological Sequence Annotation, Jack W. Roddy, Travis J. Wheeler

Graduate Student Theses, Dissertations, & Professional Papers

Genome annotation is the process of identifying and labeling known genetic sequences or features within a genome. Across the various subfields within modern molecular biology, there is a common need for the visualization of such annotations. Genomic data is often visualized on web browser platforms, providing users with easy access to visualization tools without the need for installing any software or, in many cases, underlying datasets. While there exists a broad range of web-based visualization tools, there is, to my knowledge, no lightweight, modern library tailored towards the visualization of genomic data. Instead, developers charged with the task of producing …

The Tijeras Pueblo (La 581) Archaeofaunal Project, Emily Lena Jones, Scott Kirk, Caitlin S. Ainsworth, Asia Alsgaard, Jana Valesca Meyer, Cyler Conrad

Anthropology Datasets

These files contain data generated by the Tijeras Pueblo (LA 581) Archaeofaunal Project, a project of the University of New Mexico Department of Anthropology Zooarchaeology Laboratory between 2011 and the present. This project has been supported in part by the National Science Foundation under Grant No. 1732622 and by a grant from the Research Allocations Committee of the University of New Mexico.

These data are the basis of the analyses presented in the following publication:

Jones, Emily Lena, Scott Kirk, Caitlin S. Ainsworth, Asia Alsgaard, Jana Valesca Meyer, and Cyler Conrad. 2021. The Community at the Crossroads: Artiodactyl Exploitation and …

Effects Of Prescribed Fire On Drought Resistance And Recovery In Mixed Conifer Forests Of Lassen Volcanic National Park, California, Zachary J. Wenderott

Cal Poly Humboldt theses and projects

Forests throughout much of the western United States are experiencing increasing climatic variability, often resulting in decreased forest productivity and elevated likelihood of tree mortality. Severe drought, such California’s recent 2012-2015 drought, are projected to increase in intensity, frequency, and severity throughout much of this region in coming years. Forest management has long relied on prescribed fire and mechanical thinning to reduce fuel loads and ameliorate potential fire hazards. These treatments may also have the ability to reduce stand density, alleviate competitive pressures, and allow residual trees access to critical resources during periods of extreme stress. Utilizing a long-term National …

Noninvasive Genetic Sampling With A Bayesian Spatial Capture-Recapture Analysis To Estimate Abundance Of Roosevelt Elk (Cervus Canadensis Roosevelti), Makenzie Henk

Cal Poly Humboldt theses and projects

Determining abundance of Roosevelt elk (Cervus canadensis roosevelti) in central Humboldt County, California has presented a unique challenge to wildlife managers due to the dense forest habitat and the animals’ elusive behavior. As the elk population has increased, so has human-wildlife conflict, and wildlife agencies need efficient and repeatable methods for determining abundance to inform management decisions. Traditional monitoring methods such as helicopter surveys are ineffective due to low sighting probability and strong behavioral responses to the aircraft. They also often lead to biased sex ratios when the distribution of males and females varies across the landscape. Non-invasive …

Grit And Mindset - Unrelated To Performance In A Motor Learning Task, Jacob Smith

Cal Poly Humboldt theses and projects

Objective Research has shown grit and mindset can be improved, but no known research has investigated the effect of learning a new skill on grit and growth mindset. While grit and mindset seem to predict success in education and success, it is also not clear if initial grit or mindset have an effect on motor skill acquisition. The purposes of this research are to investigate if grit and growth mindset are predictors of learning a new skill and if learning a new skill leads to improvement in grit and growth mindset. Methods 14 students enrolled in a motor learning course …

Wingate Muscular Power Test Reference Values For Active Healthy Adults Ages 19-29: Normative Data And Differences Between Sex, Levi Basist

Cal Poly Humboldt theses and projects

The Wingate Muscular Power Test (WMPT) has existed for several decades and to this day is considered the gold standard for evaluating an individual’s muscular power. However, the utility of this test is predicated on having accurate and relevant normative data with which to compare individual results. At present, the existing literature on this subject is either several decades old and/or inclusive of only specific subject groups (i.e. men only or sport-specific athletes). This study presents WMPT normative values for active healthy adults ages 19-29, separated by sex. The sample consisted of 330 active healthy volunteers (186 men and 144 …

Comparison Of Low-Cost Commercial Unpiloted Digital Aerial Photogrammetry To Airborne Laser Scanning Across Multiple Forest Types In California, James Edward Lamping

Cal Poly Humboldt theses and projects

Science-based forest management requires quantitative information about forest attributes traditionally collected via sampled field plots in a forest inventory program. Remote sensing tools, such as active three-dimensional (3D) Light Detection and Ranging (lidar), are increasingly utilized to supplement and even replace field-based forest inventories. However, lidar remains cost prohibitive for smaller areas and repeat measurement, often limiting its use to single acquisitions of large contiguous areas. Recent advancements in unpiloted aerial systems (UAS), digital aerial photogrammetry (DAP) and high precision global positioning systems (HPGPS) have the potential to provide low-cost time and place flexible 3D data to support forest inventory …

The Politics Of Biomass Energy In California: How External Benefits Are Used To Support An Economically Marginal Sector, Dana L. Dysthe

Cal Poly Humboldt theses and projects

Since the 1990s, there has been a decline in biomass energy generation in California. In order to promote state governmental policies aiming to increase biomass energy generation in California, the sector has been linked to a series of external benefits that biomass energy purportedly brings. Through document analysis, semi-structured interviews, and participant observation, five distinct external benefits were identified that have been used to promote the biomass energy sector. These external benefits are: renewable energy generation, air quality improvements, promotion of forest restoration and fuel removal projects, disposal of wood waste from agricultural and forestry sectors, and rural economic development. …

Comparison Of Standard And Environmental Dna Methods For Estimating Chinook Salmon Smolt Abundance In The Klamath River, California, Doyle Joseph Coyne

Cal Poly Humboldt theses and projects

Evaluating abundance of juvenile salmonids is critical to conservation and management. Current abundance estimation involves use of rotary screw traps and mark-recapture studies. Use of environmental DNA (eDNA) in water samples offers a noninvasive and less expensive approach that may potentially improve or eventually replace traditional monitoring. Here I evaluate the utility of eDNA to predict weekly abundance estimates of outmigrating Chinook salmon (Oncorhynchus tshawytscha) smolts in the Klamath River, California. A total of 15 water samples were collected per week over the 17-week smolt outmigration in both 2019 and 2020. Chinook salmon eDNA concentration in each water …

The Homology Of Sarcopterygian Gills, Kyle Orr

Cal Poly Humboldt theses and projects

Vertebrate gills may be either external (protruding from the body surface) or internal (enclosed in a chamber). Among living amphibians, external gills are found in salamander larvae and neotenes, early frog larvae, and caecilian embryos; internal gills are found only in later-stage frog larvae. Evidence for internal gills has also been found in stem tetrapods, and amphibian-like external gills have been found in some fossil temnospondyls and anthracosaurs. Gill homology among these groups and life stages has long been questioned. To address this, scanning electron microscopy, vascular casting, and paraffin sectioning were utilized to study the morphology of gills and …

Seed Bank Composition Within Two Sagebrush Communities: A Comparison Of Drought, Microsite, And Aboveground Community Effects, Allison Marie Nunes

Cal Poly Humboldt theses and projects

Soil seed banks are critical biodiversity repositories for many dryland plant communities. Understanding how environmental factors alter seed bank composition can provide valuable information on ecological processes within a community and be useful for creating land management strategies. Using the seedling emergence method, I characterized the seed bank of two adjacent dryland plant communities that vary in dominant sagebrush species, structure, and function. Specifically, within an Artemisia arbuscula dominated community and Artemisia cana dominated community, I assessed the influence of three environmental factors on each seed bank: experimentally imposed drought, shrub microsites (compared to interspaces), and aboveground vegetation. Within the …

Recreation, Vegetation Management, And Disease Impact Sympatric Carnivore Activity In California's East Bay Parks, Leigh J. Douglas

Cal Poly Humboldt theses and projects

East Bay Regional Park District designated over 1000 ha of protected wildland-urban interface habitat in the hills of California’s East Bay Area for invasive tree removal to reduce fire risk and restore native habitat over a 10-year period starting in 2016. From June to November 2019, 36 camera traps were deployed using a stratified two-pronged detection approach of surveying recreation and wildlife trails to assess the impact of vegetation management on the spatiotemporal distribution of sympatric carnivore species while accounting for potential impacts of human activity and proximity to development. The sampling effort resulted in 5,191 cumulative trap nights, 2,739 …

Evaluating Immaturity Risk In Young Stands Of The Serotinous Knobcone Pine (Pinus Attenuata), Katherine Marlin

Cal Poly Humboldt theses and projects

As wildfire becomes increasingly frequent, many plant populations risk local extirpation if fire recurs too soon, a problem dubbed “immaturity risk”. We studied the regeneration of a serotinous conifer species, knobcone pine (Pinus attenuata), as a function of the time between high-severity fires (6-79 years). We evaluated age, cone production, and regeneration at two burned sites in northern California, the Ranch Fire (2018) in Mendocino National Forest, and the Carr Fire (2018) in Whiskeytown National Recreation Area. We found an average of 30.5 filled seeds in closed, brown cones (42% viability of filled seeds). The bulk of the …

Do Beaver Dam Analogues Act As Passage Barriers To Juvenile Coho Salmon And Juvenile Steelhead Trout?, Christopher G. O'Keefe

Cal Poly Humboldt theses and projects

In the Pacific Northwest, the human-caused reduction of quality and quantity of freshwater rearing habitat is a limiting factor for Pacific Salmon populations. Beaver dam analogues (BDAs) increase suitable rearing habitat for juvenile salmonids and promote the restoration of critical stream processes. Installing BDAs is an increasingly popular alternative to more intensive restoration techniques, due to the relatively low cost and effort required to install BDA structures. However, widespread installation of BDAs has been slowed by regulatory agencies’ concerns that BDAs may impede fish passage. Few studies have empirically assessed the extent to which BDAs impede fish passage, and no …

Social Comparison Tendencies And The Reward Value Of Same-Sex Beauty Among Heterosexual Women, Melissa M. Martin Ms.

Cal Poly Humboldt theses and projects

Previous studies have suggested that heterosexual women, but not heterosexual men, find same sex beauty rewarding. This finding has been attributed to a “greater bisexual interest among heterosexual women”, but no other explanations have been offered or tested. The current study aimed to explore social comparison tendencies as a potential alternate explanation to this previously observed finding. Twenty-three heterosexual women completed a series of questionnaires designed to assess their social comparison tendencies (the social comparison orientation scale, the physical appearance comparison scale, and the intrasexual competition scale). They also completed a “pay-per-view” keypress task to measure the reward value of …

Building Habitat Suitability Models To Examine Distribution Shifts For The Black-Headed Grosbeak, Hairy Woodpecker, And Yellow-Rumped Warbler Due To Drought, Fire, And Bark Beetle Infestation In The Pacific Northwest, Holli Nicole Pruhsmeier

Cal Poly Humboldt theses and projects

Spatial models that describe species distributions are valuable in determining how environmental impacts, such as drought, fire, and bark beetle infestations, have shifted these distributions and guide management decisions. In this thesis, I begin by comparing the utility of two datasets by building habitat suitability models for Black-headed Grosbeak, Hairy Woodpecker, and Yellow-rumped Warbler. By combining the datasets, I created response curves that explain habitat associations I expected from each species. I expanded upon the methods section to compare pre- and post-drought data from the 2011 California multi-year drought and evaluate how the three avian species have shifted their habitat …

Evaluating The Effects Of Atlantic Menhaden Management And Environmental Change On The Northwest Atlantic Ocean Ecosystem, Maxwell T. Grezlik

Cal Poly Humboldt theses and projects

Atlantic Menhaden (Brevoortia tyrannus) is an abundant forage fish species whose management has recently shifted from using single species reference points to ecological reference points. This type of management allows for the ecological role (e.g., supporting predators) of the species to be considered when making management decisions, and is part of a growing global movement towards ecosystem-based fisheries management. One model that aided in this transition from single species to ecological reference points was the Northwest Atlantic Continental Shelf (NWACS13) model created using Ecopath with Ecosim (Buchheister et al. 2017). Here, I updated and expanded the NWACS13 model …