Life Sciences Commons^™

Improved Computational Prediction Of Function And Structural Representation Of Self-Cleaving Ribozymes With Enhanced Parameter Selection And Library Design, James D. Beck

Boise State University Theses and Dissertations

Biomolecules could be engineered to solve many societal challenges, including disease diagnosis and treatment, environmental sustainability, and food security. However, our limited understanding of how mutational variants alter molecular structures and functional performance has constrained the potential of important technological advances, such as high-throughput sequencing and gene editing. Ribonuleic Acid (RNA) sequences are thought to play a central role within many of these challenges. Their continual discovery throughout all domains of life is evidence of their significant biological importance (Weinreb et al., 2016). The self-cleaving ribozyme is a class of noncoding Ribonuleic Acid (ncRNA) that has been useful for …

Evaluation Of Energy Release From Wildfires Across The Elevation Gradient, Isabelle Rose Butler

Boise State University Theses and Dissertations

Wildfires are an integral process in vegetative terrestrial land which shape ecosystem functions. A warming climate, however, has increased the size and severity of fires with significant ecosystem and societal implications. Furthermore, warming has changed characteristics of wildfires enabling a median upslope advance of 252 m in high-elevation forest fires from 1984 to 2017, allowing wildfires to burn in areas that were previously too wet to burn frequently. This exposed an additional 81,500 square kilometers (11%) of western US montane forests to fires.

In this thesis, I test the hypothesis that wildfires burn more intensely in high-elevation mesic forests than …

Rapid Production And Purification Of Dye-Loaded Liposomes By Electrodialysis-Driven Depletion, Gamid Abatchev, Andrew Bogard, Zoe Hutchinson, Jason Ward, Daniel Fologea

Physics Faculty Publications and Presentations

Liposomes are spherical-shaped vesicles that enclose an aqueous milieu surrounded by bilayer or multilayer membranes formed by self-assembly of lipid molecules. They are intensively exploited as either model membranes for fundamental studies or as vehicles for delivery of active substances in vivo and in vitro. Irrespective of the method adopted for production of loaded liposomes, obtaining the final purified product is often achieved by employing multiple, time consuming steps. To alleviate this problem, we propose a simplified approach for concomitant production and purification of loaded liposomes by exploiting the Electrodialysis-Driven Depletion of charged molecules from solutions. Our investigations show that …

Sodah: The Soils Data Harmonization Database, An Open-Source Synthesis Of Soil Data From Research Networks, Version 1.0, Marie-Anne De Graaff

Biology Faculty Publications and Presentations

Data collected from research networks present opportunities to test theories and develop models about factors responsible for the long-term persistence and vulnerability of soil organic matter (SOM). Synthesizing datasets collected by different research networks presents opportunities to expand the ecological gradients and scientific breadth of information 55 available for inquiry. Synthesizing these data, are challenging, especially considering the legacy of soils data that has already been collected and an expansion of new network science initiatives. To facilitate this effort, here we present the SOils DAta Harmonization database (SoDaH; https://lter.github.io/som-website, last accessed 15 July 2020), a flexible database designed to harmonize …

Cholesterol And Cholesterol Bilayer Domains Inhibit Binding Of Alpha-Crystallin To The Membranes Made Of The Major Phospholipids Of Eye Lens Fiber Cell Plasma Membranes, Raju Timsina, Geraline Trossi-Torres, Matthew O'Dell, Nawal K. Khadka, Laxman Mainali

Physics Faculty Publications and Presentations

The concentration of α-crystallin decreases in the eye lens cytoplasm, with a corresponding increase in membrane-bound α-crystallin during cataract formation. The eye lens’s fiber cell plasma membrane consists of extremely high cholesterol (Chol) content, forming cholesterol bilayer domains (CBDs) within the membrane. The role of high Chol content in the lens membrane is unclear. Here, we applied the continuous-wave electron paramagnetic resonance spin-labeling method to probe the role of Chol and CBDs on α-crystallin binding to membranes made of four major phospholipids (PLs) of the eye lens, i.e., phosphatidylcholine (PC), sphingomyelin (SM), phosphatidylserine (PS), and phosphatidylethanolamine (PE). Small unilamellar vesicles …

Liposomes Prevent In Vitro Hemolysis Induced By Streptolysin O And Lysenin, Marcelo Ayllon, Gamid Abatchev, Andrew Bogard, Rosey Whiting, Sarah E. Hobdey, Daniel Fologea

Physics Faculty Publications and Presentations

The need for alternatives to antibiotics in the fight against infectious diseases has inspired scientists to focus on antivirulence factors instead of the microorganisms themselves. In this respect, prior work indicates that tiny, enclosed bilayer lipid membranes (liposomes) have the potential to compete with cellular targets for toxin binding, hence preventing their biological attack and aiding with their clearance. The effectiveness of liposomes as decoy targets depends on their availability in the host and how rapidly they are cleared from the circulation. Although liposome PEGylation may improve their circulation time, little is known about how such a modification influences their …

New Applications For The Kinetic Exclusion Assay (Kinexa), Mark Harrison Smith

Boise State University Theses and Dissertations

This dissertation examines the fundamental principles and applicability of the kinetic exclusion assay (KinExA), developed and marketed by Sapidyne Instruments of Boise, Idaho, since 1995. Chapter One reviews and consolidates the manufacturer’s guidance and many early papers that delineate the practical and theoretical aspects of the technology. In brief, KinExA is a two stage analytical system. In stage one, a number of solutions are prepared, whereby one of the partners is kept constant (the constant binding partner, or CBP), while the other (the titrant) is varied, usually in serial dilution. As the titrant is increased, the free CBP decreases, and …

Abundance, Distribution, And Growth Characteristics Of Three Keystone Vachellia Trees In Gebel Elba National Park, South-Eastern Egypt, Ahmed M. Abbas, Mohammed Al-Kahtani, Stephen J. Novak, Wagdi Saber Soliman

Biology Faculty Publications and Presentations

This study was conducted to evaluate the abundance and distribution pattern of three keystone Vachellia taxa in wadi Khoda and wadi Rahaba, Gebel Elba National Park, a protected area in south-eastern Egypt. These taxa included Vachellia tortilis subsp. tortilis, Vachellia tortilis subsp. raddiana, and Vachellia ehrenbergiana. In wadi Khoda, only two of these taxa were detected (V. tortilis subsp. raddiana and V. tortilis subsp. tortilis), while all three taxa were encountered in wadi Rahaba. The density of trees in wadi Khoda was 34.3 plant ha⁻¹ compared to 26.3 plant ha⁻¹ in …

A Record Of Vapour Pressure Deficit Preserved In Wood And Soil Across Biomes, Adrian Broz, Gregory J. Retallack, Toby M. Maxwell, Lucas C.R. Silva

Biology Faculty Publications and Presentations

The drying power of air, or vapour pressure deficit (VPD), is an important measurement of potential plant stress and productivity. Estimates of VPD values of the past are integral for understanding the link between rising modern atmospheric carbon dioxide (pCO₂) and global water balance. A geological record of VPD is needed for paleoclimate studies of past greenhouse spikes which attempt to constrain future climate, but at present there are few quantitative atmospheric moisture proxies that can be applied to fossil material. Here we show that VPD leaves a permanent record in the slope (S) of least-squares …

Socio-Hydrology: An Interplay Of Design And Self-Organization In A Multilevel World, Vicken Hillis

Human-Environment Systems Research Center Faculty Publications and Presentations

The emerging field of socio-hydrology is a special case of social-ecological systems research that focuses on coupled human-water systems, exploring how the hydrologic cycle and human cultural traits coevolve and how such coevolutions lead to phenomena of relevance to water security and sustainability. As such, most problems tackled by socio-hydrology involve some aspects of engineering design, such as large-scale water infrastructure, and self-organization in a broad context, such as cultural change at the population level and the hydrologic shift at the river basin or aquifer level. However, within the field of socio-hydrology, it has been difficult to find general theories …

Observed Defects Of Swiss Cheese Based On The Microbiome Contribution To The Production Of Organic Acids, Vannessa D. Campfield

Boise State University Theses and Dissertations

The United States Department of Agriculture downgrades on the order of 17% of all Swiss cheese produced in the United States due to defects. Many of these defects are related to improper eye formation, number, distribution, or size; leading to an industry loss of over $69 million per annum. The microbiome in Swiss-type cheeses plays a significant role in eye development due to production of organic acids and gaseous emissions contingent on bacterial abundance and phenotype. The relationship between bacteria and the organic acids they produce leading to Swiss cheese defects can be correlated using Next-generation sequencing and high-performance liquid …

Analytic Solutions For Diffusion On Path Graphs And Its Application To The Modeling Of The Evolution Of Electrically Indiscernible Conformational States Of Lysenin, K. Summer Ware

Boise State University Theses and Dissertations

Memory is traditionally thought of as a biological function of the brain. In recent years, however, researchers have found that some stimuli-responsive molecules exhibit memory-like behavior manifested as history-dependent hysteresis in response to external excitations. One example is lysenin, a pore-forming toxin found naturally in the coelomic fluid of the common earthworm Eisenia fetida. When reconstituted into a bilayer lipid membrane, this unassuming toxin undergoes conformational changes in response to applied voltages. However, lysenin is able to "remember" past history by adjusting its conformational state based not only on the amplitude of the stimulus but also on its previous …

Kinetic Exclusion Assay Of Biomolecules By Aptamer Capture, Mark H. Smith, Daniel Fologea

Physics Faculty Publications and Presentations

DNA aptamers are short nucleotide oligomers selected to bind a target ligand with affinity and specificity rivaling that of antibodies. These remarkable features recommend aptamers as candidates for analytical and therapeutic applications that traditionally use antibodies as biorecognition elements. Numerous traditional and emerging analytical techniques have been proposed and successfully implemented to utilize aptamers for sensing purposes. In this work, we exploited the analytical capabilities offered by the kinetic exclusion assay technology to measure the affinity of fluorescent aptamers for their thrombin target and quantify the concentration of analyte in solution. Standard binding curves constructed by using equilibrated mixtures of …

Integrating National Ecological Observatory Network (Neon) Airborne Remote Sensing And In-Situ Data For Optimal Tree Species Classification, Victoria M. Scholl, Megan E. Cattau, Maxwell B. Joseph, Jennifer K. Balch

Human-Environment Systems Research Center Faculty Publications and Presentations

Accurately mapping tree species composition and diversity is a critical step towards spatially explicit and species-specific ecological understanding. The National Ecological Observatory Network (NEON) is a valuable source of open ecological data across the United States. Freely available NEON data include in-situ measurements of individual trees, including stem locations, species, and crown diameter, along with the NEON Airborne Observation Platform (AOP) airborne remote sensing imagery, including hyperspectral, multispectral, and light detection and ranging (LiDAR) data products. An important aspect of predicting species using remote sensing data is creating high-quality training sets for optimal classification purposes. Ultimately, manually creating training data …

Temporary Membrane Permeabilization Via The Pore-Forming Toxin Lysenin, Nisha Shrestha, Christopher A. Thomas, Devon Richtsmeier, Andrew Bogard, Rebecca Hermann, Malyk Walker, Gamid Abatchev, Raquel J. Brown, Daniel Fologea

Physics Faculty Publications and Presentations

Pore-forming toxins are alluring tools for delivering biologically-active, impermeable cargoes to intracellular environments by introducing large conductance pathways into cell membranes. However, the lack of regulation often leads to the dissipation of electrical and chemical gradients, which might significantly affect the viability of cells under scrutiny. To mitigate these problems, we explored the use of lysenin channels to reversibly control the barrier function of natural and artificial lipid membrane systems by controlling the lysenin’s transport properties. We employed artificial membranes and electrophysiology measurements in order to identify the influence of labels and media on the lysenin channel’s conductance. Two cell …

Operational Large-Area Land-Cover Mapping: An Ethiopia Case Study, Trevor Caughlin

Biology Faculty Publications and Presentations

Knowledge of land cover and land use nationally is a prerequisite of many studies on drivers of land change, impacts on climate, carbon storage and other ecosystem services, and allows for sufficient planning and management. Despite this, many regions globally do not have accurate and consistent coverage at the national scale. This is certainly true for Ethiopia. Large-area land-cover characterization (LALCC), at a national scale is thus an essential first step in many studies of land-cover change, and yet is itself problematic. Such LALCC based on remote-sensing image classification is associated with a spectrum of technical challenges such as data …

Incorporating Wildlife Connectivity Into Forest Plan Revision Under The United States Forest Service's 2012 Planning Rule, Matthew A. Williamson, Tyler G. Creech, Gunnar Carnwath, Beverly Dixon, Virginia Kelly

Human-Environment Systems Research Center Faculty Publications and Presentations

The United States Forest Service promulgated new planning regulations under the National Forest Management Act in 2012 (i.e., the Planning Rule). These new regulations include the first requirements in U.S. public land management history for National Forests to evaluate, protect, and/or restore ecological connectivity as they revise their land management plans. Data and resource limitations make single-species, functional connectivity analyses for the myriad species that occur within the 78 million ha the Forest Service manages implausible. We describe an approach that relies on freely available data and generic species, virtual species whose profile consists of ecological requirements designed to reflect …

A Systematic Review Of Participatory Scenario Planning To Envision Mountain Social-Ecological Systems Futures, Kelly A. Hopping

Human-Environment Systems Research Center Faculty Publications and Presentations

Mountain social-ecological systems (MtSES) provide crucial ecosystem services to over half of humanity. However, populations living in these highly varied regions are now confronted by global change. It is critical that they are able to anticipate change to strategically manage resources and avoid potential conflict. Yet, planning for sustainable, equitable transitions for the future is a daunting task, considering the range of uncertainties and the unique character of MtSES. Participatory scenario planning (PSP) can help MtSES communities by critically reflecting on a wider array of innovative pathways for adaptive transformation. Although the design of effective approaches has been widely discussed, …

Comprehensive Investigation Of Bioactive Steroidal Alkaloids In Veratrum Californicum, Matthew West Turner

Boise State University Theses and Dissertations

Veratrum californicum, commonly referred to as corn lily or Californian false hellebore, grows in high mountain meadows and produces bioactive steroidal alkaloids, including cyclopamine. Cyclopamine is a potent inhibitor of the Hedgehog (Hh) signaling pathway. Our lab has optimized methods to extract cyclopamine and related steroidal alkaloids from V. californicum, and implemented in-house Hh signaling bioactivity evaluation of these steroidal alkaloids using a Shh-Light II cell assay. A survey of extraction methods and solvents resulted in the identification of conditions most favorable for alkaloid extraction yield and antagonist activity in the Shh-Light II cell assay. The highest amount …

Informing Field Management Decisions To Enhance Alfalfa Seed Production Using Remote Sensing, Thomas V. Van Der Weide

Boise State University Theses and Dissertations

The development rate of alfalfa seed crop depends on both environmental conditions and management decisions. Crop management decisions, such as determining when to release pollinators to optimize pollination, can be informed by the identification of plant development stages from remote sensing data. I first identify what electromagnetic wavelengths are sensitive to alfalfa plant development stages using hyperspectral data. A Random Forest regression is used to determine the best Vegetation Index (VI) to monitor how much of the plant is covered in flower. The results indicate that Blue, Green, and Near-Infrared are the important electromagnetic wavelengths for the VI. Imagery collected …

Reduced-Impact Logging For Climate Change Mitigation (Ril-C) Can Halve Selective Logging Emissions From Tropical Forests, Anand Roopsind

Biology Faculty Publications and Presentations

Selective logging causes at least half of the emissions from tropical forest degradation. Reduced-impact logging for climate (RIL-C) is proposed as a way to maintain timber production while minimizing forest damage. Here we synthesize data from 61 coordinated field-based surveys of logging impacts in seven countries across the tropics. We estimate that tropical selective logging emitted 834 Tg CO₂ in 2015, 6% of total tropical greenhouse gas emissions. Felling, hauling, and skidding caused 59%, 31%, and 10% of these emissions, respectively. We suggest that RIL-C incentive programs consider a feasible target carbon impact factor of 2.3 Mg emitted per …

Examining Interactions Between And Among Predictors Of Net Ecosystem Exchange: A Machine Learning Approach In A Semi-Arid Landscape, Qingtao Zhou, Aaron Fellows, Gerald N. Flerchinger, Alejandro N. Flores

Geosciences Faculty Publications and Presentations

Net ecosystem exchange (NEE) is an essential climate indicator of the direction and magnitude of carbon dioxide (CO₂) transfer between land surfaces and the atmosphere. Improved estimates of NEE can serve to better constrain spatiotemporal characteristics of terrestrial carbon fluxes, improve verification of land models, and advance monitoring of Earth’s terrestrial ecosystems. Spatiotemporal NEE information developed by combining ground-based flux tower observations and spatiotemporal remote sensing datasets are of potential value in benchmarking land models. We apply a machine learning approach (Random Forest (RF)) to develop spatiotemporally varying NEE estimates using observations from a flux tower and several …

Sustainability Partnerships And Viticulture Management In California, Vicken Hillis, Mark Lubell, Matthew Hoffman

Human-Environment Systems Research Center Faculty Publications and Presentations

Agricultural regions in the United States are experimenting with sustainability partnerships that, among other goals, seek to improve growers' ability to manage their vineyards sustainably. In this paper, we analyze the association between winegrape grower participation in sustainability partnership activities and practice adoption in three winegrowing regions of California. Using data gathered from a survey of 822 winegrape growers, we find a positive association between participation and adoption of sustainable practices, which holds most strongly for practices in which the perceived private benefits outweigh the costs, and for growers with relatively dense social networks. We highlight the mechanisms by which …

Helping Farmers And Reducing Car Crashes: The Surprising Benefits Of Predators, Christopher O'Bryan, Eve Mcdonald-Madden, James Watson, Neil Carter

Human-Environment Systems Research Center Faculty Publications and Presentations

Humans may be Earth’s apex predator, but the fleeting shadow of a vulture or the glimpse of a big cat can cause instinctive fear and disdain. But new evidence suggests that predators and scavengers are much more beneficial to humans than commonly believed, and that their loss may have greater consequences than we have imagined.

Climate Change, Cattle, And The Challenge Of Sustainability In A Telecoupled System In Africa, Tara S. Easter, Alexander K. Killion, Neil H. Carter

Ecology, Evolution, and Behavior

Information, energy, and materials are flowing over greater distances than in the past, changing the structure and feedbacks within and across coupled human and natural systems worldwide. The telecoupling framework was recently developed to understand the feedbacks and multidirectional flows characterizing social and environmental interactions between distant systems. We extend the application of the telecoupling framework to illustrate how flows in beef affect and are affected by social-ecological processes occurring between distant systems in Africa, and how those dynamics will likely change over the next few decades because of climate-induced shifts in a major bovine disease, trypanosomosis. The disease is …

Hexarray: A Novel Self-Reconfigurable Hardware System, Fady Hussein

Boise State University Theses and Dissertations

Evolvable hardware (EHW) is a powerful autonomous system for adapting and finding solutions within a changing environment. EHW consists of two main components: a reconfigurable hardware core and an evolutionary algorithm. The majority of prior research focuses on improving either the reconfigurable hardware or the evolutionary algorithm in place, but not both. Thus, current implementations suffer from being application oriented and having slow reconfiguration times, low efficiencies, and less routing flexibility. In this work, a novel evolvable hardware platform is proposed that combines a novel reconfigurable hardware core and a novel evolutionary algorithm.

The proposed reconfigurable hardware core is a …

A Meta-Analysis Of Soil Biodiversity Impacts On The Carbon Cycle, M.-A. De Graaff, J. Adkins, P. Kardol, H. L. Throop

Biology Faculty Publications and Presentations

Loss of biodiversity impacts ecosystem functions, such as carbon (C) cycling. Soils are the largest terrestrial C reservoir, containing more C globally than the biotic and atmospheric pools together. As such, soil C cycling, and the processes controlling it, has the potential to affect atmospheric CO₂ concentrations and subsequent climate change. Despite the growing evidence of links between plant diversity and soil C cycling, there is a dearth of information on whether similar relationships exist between soil biodiversity and C cycling. This knowledge gap occurs even though there has been increased recognition that soil communities display high levels of …

Dendrochronological Reconstruction Of Fire, Bogus Basin Area Boise National Forest, Amy L. Cutter

Student Research Initiative

Since people have settled along the Boise Front, there have been very few documented fire disturbances. This is likely an outcome of fire suppression policies. There is evidence, visible as scars on living trees, that the old growth ponderosa pines located on the East Side Trail in the Boise National Forest have withstood multiple fires. Samples were collected by using a chainsaw to remove small, partial cross-sections from several trees. The Boise Front master chronology was used to accurately cross-date the fire-scarred samples using COFECHA. Analysis of the samples revealed ten fire events ranging from 1709 to 1889. The fire …

Idaho Bird Observatory: Research, Education, Conservation - 24/7, Elise Faike

Jay D. Carlisle

The Idaho Bird Observatory’s Lucky Peak bird monitoring station atop the foothills overlooking Boise is unique. During fall migration, it’s the only place in western North America that hosts some form of songbird or raptor research all day and all night—for downright fun 24/7!

Reproducibility Of Soil Moisture Ensembles When Representing Soil Parameter Uncertainty Using A Latin Hypercube–Based Approach With Correlation Control, Alejandro N. Flores, Dara Entekhabi, Rafael L. Bras

Alejandro N. Flores

Representation of model input uncertainty is critical in ensemble-based data assimilation. Monte Carlo sampling of model inputs produces uncertainty in the hydrologic state through the model dynamics. Small Monte Carlo ensemble sizes are desirable because of model complexity and dimensionality but potentially lead to sampling errors and correspondingly poor representation of probabilistic structure of the hydrologic state. We compare two techniques to sample soil hydraulic and thermal properties (SHTPs): (1) Latin Hypercube (LH) based sampling with correlation control and (2) random sampling from SHTP marginal distributions. A hydrology model is used to project SHTP uncertainty onto the soil moisture state …