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Titin contribution to active muscle
Get PDFThe aim of this dissertation is to compare the traditional ‘muscle as motor’ viewpoint to the alternative viewpoint ‘muscle as composite material’. We make three parts to achieve the aim. We first investigate whether the contribution of activation and length perturbation on muscle force depends on length history. The effect of length history is to alter muscle stiffness. The alteration of muscle stiffness determines the role of activation and length perturbation in determining muscle force. That is, muscle responds to activation and length perturbation depending on length history. Muscle models based on the ‘muscle as motor’ viewpoint fail to predict muscle force accurately under dynamic conditions in part because they cannot account for the history dependence of muscle force. An alternative muscle viewpoint should be able to explain the history dependent muscle force to enlarge our knowledge about how muscle works under dynamic conditions. In the second part, we focus on the ratio of muscle force to stiffness. The ratio of force to stiffness has been believed to be relatively constant during isometric contraction because both isometric force and stiffness are linearly related to the number of formed cross-bridge. However, the ratio depends on shortening velocity as well as is not constant during the isometric force redevelopment period following active shortening. This finding invokes ‘stress-induced inhibition’ where weakly-bound cross bridge generated by active shortening contributes only to stiffness with no contribution to force. The weakly-bound cross bridge is able to explain non-zero y-intercepts of the relationship between force and stiffness, but not the lower slope for the slower velocity. In the ‘stress-induced inhibition’, the slower shortening velocity should distort actin more due to the bigger stress. The more distorted actin induces the bigger number of weakly-bound cross bridge, which should result in the bigger slope of the relationship between force and stiffness. This is not compatible with our results. Another possible explanation of the finding is a change in titin stiffness. According to the winding filament hypothesis, titin equilibrium length is modulated by cross-bridge force. Active shortening at different velocity could generate the different initial conditions for titin strain and equilibrium position, and then titin differently responds to an increase in cross bridge force depending on the initial conditions. The tunable titin stiffness contributes to the variable muscle stiffness.
Finally, this dissertation develops a titin-clutch model based on a composite material viewpoint. The titin-clutch model predicts frequency-dependent muscle force better than the Hill model. The model has three subunits: a contractile, titin, and series elastic element. The pulley connects the titin to the contractile element in series and parallel. The history-dependent pulley position implements the history-dependent contributions of length perturbation and activation to force. When the contractile force increases, pulley rotates counterclockwise direction, then titin element wraps around a pulley. The interaction between them regulates titin stiffness. The dissertation concludes that incorporating a tunable titin spring in muscle models improves the predictions of muscle force under dynamic conditions
The impact of temperature on the epizootic dynamics of Ambystoma tigrinum virus (ATV) epizootics in larval salamanders (Ambystoma mavortium)
Get PDFClimate change could expand pathogen spatial distributions, accelerate transmission cycles, shifts host life cycles, and lead to emergence of disease in naïve host populations, all of which could have complex effects on disease. Quantitative frameworks like disease modeling are needed to improve our ability to predict the effects of climate and disease on host population dynamics. Amphibians are especially vulnerable to these changes, where populations are at risk of declining due to climate change, disease, and potential interaction between threats. Infecting salamander populations across the USA and Arizona, the effects of temperature on Ambystoma tigrinum virus (ATV) and the pathogen’s interaction with its host are not well quantified making risk prediction difficult. We hypothesize seasonal variation in temperature and the resulting fluctuations to the host’s immune system and the virus’ replication rates likely play significant roles in ATV epizootics. Using mechanistic models accounting for temperature and host susceptibility, we evaluate the effects of temperature on ATV disease dynamics at two levels: within and between hosts. To evaluate the effects of dose and temperature within a host, we conducted a viral transmission experiment using larval salamanders. This allowed us to parameterize a full model exploring the effects of temperature on seasonal epizootic dynamics. Our results reveal a clear non-linear effect of temperature on mortality and shedding rates that is likely mediated by temperature-influenced pathogen replication and host immune response, where cumulative mortality and shedding rate peak at 20°C. While an effect of temperature on average transmission rate was not observed, we show variation in host susceptibility increases with temperature. Using model simulations, we see earlier and more rapidly progressing epizootics when temperatures are fixed at 20°C. A fluctuating temperature regime under warmer early season conditions, however, predicts earlier and more rapid epizootics followed by a smaller late-season peak. Our findings demonstrate the utility of combining data and modeling techniques to better understand and forecast the effects of climate and disease on threatened host populations. Future work could link our model to projections of climate change to understand ATV risk in salamander populations in the US Southwest
The cost of forest thinning operations in the United States West: a systematic literature review and model development
No full textIncreases in tree regeneration have led to dense forests in the western United States, which has increased hazardous fuels and created favorable environments for landscape-scale wildfires. Mechanical forest thinning treatments have been implemented across the U.S. West to improve forest health and reduce hazardous fuels. However, the main challenge for implementing forest thinning treatments is their economic feasibility because forest thinning treatments require high-cost while they typically focus on harvesting low-value, small-diameter trees. This study was conducted to synthesize the stump-to-truck cost of forest thinning treatments based on research articles published over the last 40 years (1980-2020). I systematically selected and reviewed 21 thinning studies to analyze key variables affecting machine productivity and harvesting costs. I divided the forest operations process into four phases (felling, extraction, processing, and loading) to analyze the machine’s cost and productivity. In the thinning studies, there were various forest machines and tools used for forest thinning operations, and the productivity of each machine was determined by different variables. Here I summarized the common factors driving thinning productivity and costs. For example, tree diameter and machine travel distance commonly affected thinning productivity. The average cost of forest thinning was lowest for a mechanized whole-tree thinning operation at 2,779/ha. Feller-bunchers and skidders showed the highest productivity in felling and extraction machines, respectively. I found that extraction cost in the process of stump-to-truck forest harvesting accounted for the largest proportion of the cost of forest thinning. With the cost data from the selected studies, I developed a spreadsheet-based model for estimating thinning costs associated with various harvesting systems. The model calculates the productivity and cost of the machine used in the stump-to-truck thinning process based on user input information. The results of this literature synthesis and our new thinning cost model and tool can help foresters develop a cost-effective plan for thinning operations, which can drive down the cost of thinning and help meet forest management objectives more efficiently
Investigation of environmental correlates of Ambystoma tigrinum Ranavirus in two Arizona amphibian species
No full textDiseases have been linked to worldwide amphibian declines, with Chytridiomycosis, caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), and viruses in the genus Ranavirus, causing mass mortality events. Despite the clear impact of disease on some amphibian populations, few studies have investigated the relationship between local environmental conditions and the spatial and temporal trends of pathogen infection. Trends and dynamics of disease occurrence and prevalence in host species are not well understood despite seasonality and habitat differences being linked to spatial and temporal disease variability. In this study, we investigated abiotic and biotic environmental conditions that correlate with the occurrence and the prevalence of Ambystoma tigrinum virus (ATV) in western tiger salamanders (Ambystoma mavortium) and Chiricahua leopard frogs (Rana chiricahuensis). We found that for both species, larger site areas resulted in lower prevalence of ATV. Ambystoma mavortium also had higher prevalence in 2019 compared to 2020. Additionally, prevalence tended to increase over each season, with late-season (post-June) prevalence being significantly higher than earlier in the year. Sites with higher amphibian species richness were also found to have higher ATV prevalence. Also, R. chiricahuensis had higher ATV prevalence at sites that also had higher turbidity. Our results generally concur with the few other studies of Bd and Ranavirus, which also show the importance of various environmental conditions related to epizootics. These results show that ATV infection dynamics may be driven by different environmental factors in different host species. Knowledge of wildlife disease trends can be beneficial to management agencies for the conservation of at-risk species, in this case especially for threatened R. chiricahuensis and endangered Sonoran tiger salamanders (Ambystoma tigrinum stebbinsi). Future research should further explore the relationships between disease, various amphibian host species as well as life stages within species, and environmental conditions including abiotic and biotic conditions
Automated Identification of Traffic Detector Malfunctions
Get PDFThis study develops a novel method of detector performance verification by using collected and transcribed drone video data and comparing it to detector event log data. Previous studies have used existing video cameras to provide a higher quality assessment of detector performance through manual verification and transcription. The same level of assessment was required for the detection areas in this work, as they were to be used to develop an algorithm to monitor detector health over time, presuming they were healthy. However, with no cameras onsite, drones were used as part of an analysis process that included drone video collection, data transcription, and comparison to event log detector outputs through two statistical methods. Drone video recordings were higher quality and provided preferable overhead viewing angles than post-mounted intersection cameras otherwise would have. This scope of this study then turns to developing new methods for evaluating detector health using event-based outputs and existing traffic flow theory. Event-based detector data outputs were used to develop empirical Volume vs. Density curves, per Greenshield’s Fundamental Model. Using integration, these empirical lines were compared with a conceptual Volume vs. Density curve for each detector, generated using average headway data and the posted speed limit. Additionally, detector performance and site information were used to model a predicted Volume versus Density relationship for each detector based upon collected data, which was then compared with the Conceptual line in the same manner as the empirical lines. The outcomes of both of these comparisons were then used to create a database to be used for assessing detector health within the structure of an algorithm. The algorithm is then presented and discussed, followed by directions for future research, lessons learned, and limitations of this work
An evauation of ammonia as a tool for eradication of aquatic invasive species
No full textAquatic invasive species (AIS) can cause significant harm to ecosystems, biodiversity, and the economy. Methods for controlling AIS are currently limited to mechanical removal which can be labor intensive and minimally effective, or a very limited number of chemical piscicides each with their own risks. In many situations, the use of chemicals for removal of invasive aquatic species is the only solution with a high probability for complete eradication. Ammonia-based piscicides may have the potential to effectively euthanize fish with fewer risks than other currently available piscicides. Toxicity of ammonia to gill breathing organisms and its natural denitrification through the nitrogen cycle make it an excellent candidate for controlling AIS. To explain the intended use pattern of ammonia-based piscicides in better detail this document summarizes completed field trials and additional experiments testing the persistence of artificially elevated ammonia. Laboratory toxicity trials exposing green sunfish, fathead minnow and black bullhead catfish to four low level ammonia concentrations suggest that lethal concentrations of ammonia are 5ppm when using a pH increaser. Adding a pH increaser increases the toxicity of ammonia reducing the amount of ammonia needed to effectively eradicate AIS and achieving an effective kill within four hours. Increasing pH did not change the amount of time necessary for ammonia to detoxify in field or laboratory trials. Results from field trials indicate that detoxification of ammonia requires an average of two to three weeks in a lentic system.
Although regulations related to the development of aquatic use pesticides are clearly defined by the Environmental Protection Agency, policy created at the state level in Arizona further restricts research activity related to piscicides on public lands. However, obtaining these data may be easier in other states that do not have laws specifically related to the use of piscicides. Incorporating in-situ bioassays prior to experimental trials will help inform where and when a treatment is likely to be effective
The health effects of transboundary pollution and environmental cooperation
Get PDFTransboundary pollution problems cause deadly diseases, which unlike other factors, is a shared concern for states. However, there is a gap in the International Relations literature on whether health influences states to collectively cooperate to regulate transboundary pollution problems. This is important because environmental agreements that regulate transboundary pollution problems contribute in reducing diseases and therefore, protect human health. In this research, I therefore determine whether disease health effects increase the timeliness at which states adopt environmental agreements using 6 agreement case studies and 350 state case studies. The findings for the agreement case studies demonstrate that states adopt environmental agreements, which regulate transboundary air, marine, and land pollution problems that cause greater overall disease health effects, within a shorter time. Despite data limitations, roughly half of the state case studies also provide further support that states adopt environmental agreements within a shorter time when they individually experience greater disease health effects. Therefore, I suggest that future research should consider further investigating and defining health as a motivating factor that encourages states to collectively address environmental problems in a timely manner. Also, worth considering, is defining health as one of the key factors that shapes state self-interest in international environmental politics. Likewise, environmental governance ought to take health seriously by enforcing states take a more active than precautionary approach to health when collectively formulating environmental agreements that regulate transboundary pollution problems. This is especially important because environmental agreements can help protect human health from the disease effects of serious future transboundary problems such as climate change
Exploring the relationship between Helicobacter pylori and Native Americans living in northern Arizona
Get PDFIncidence and mortality rate of gastric cancer among Native Americans issignificantly higher than for Non-Hispanic White people. Many factors can contribute to
this discrepancy such as diet, lifestyle, adequate sanitary living conditions and genetic
factors. One known cause of stomach cancer is infection with the bacterium Helicobacter
pylori. Some bacterial genetic factors give an advantage to the bacterium, the presence
of the cagA gene and the genotype of the vacA gene (“s” and “m” regions). In this study,
we collected and screened 210 biopsies from Native Americans patients living in Northern
Arizona. DNA was isolated from these specimens and tested for the presence of H. pylori.
If positive, a PCR was conducted to determine the status of cagA and vacA genes.
Sequencing allowed us to determine the genotypes of these two genes and
epidemiological data from patients was used to determine associations between clinical
findings and H. pylori cagA and vacA genotypes. Our research found a positive
association between the cagA genotype and esophageal findings. Severe cases of gastric
disease were linked with presence of the vacA “m1” allele. The vacA s1m1genotype was
the most common and was associated with cagA presence. The cagA ABC EPIYA motif
was the most common genotype, and isolates expressing cagA ABC EPIYA motifs and
vacA s1m1 alleles are known to be virulent. These results show that more virulent H. pylori strains are associated with more severe outcomes among Native Americans living
in Northern Arizona
Multi-proxy evidence for climatic and environmental change during the late glacial and Holocene at Kelly Lake, Kenai Peninsula, Alaska
No full textPast climate reconstructions using multiple proxies from lake sediments are crucial to developing our understanding of environmental and landscape response to climate change. Previous research on hydroclimatic change, particularly changes in the Aleutian Low (AL) pressure system in the North Pacific region, and the effects on aquatic and terrestrial ecosystems in south-central Alaska during the last deglacial and Holocene is extensive, but our understanding of the changing influence of groundwater on lake ecosystems is lacking. Although they are rare, freshwater calcium carbonate (marl) deposits in lakes on the Kenai Peninsula, Alaska, provide the opportunity to reconstruct past changes in hydroclimate and groundwater influence on the lake. A 6.2-m-long sediment core from Kelly Lake (KLY18-4; 4 m depth; 60.514°N, 150.374°W) was dated using 14C and analyzed for multiple proxy types in both the inorganic and organic matter including: isotopes of carbon and oxygen in marl calcite (δ13Cmarl and δ18Omarl), and isotopes of carbon (ẟ13COM) and abundances of C and N in organic matter. Bulk sediment analyses include organic matter (OM) and calcium carbonate (CaCO3) contents, along with visual stratigraphy and sediment flux. The results show that Kelly Lake was deglaciated prior to 14.6 ka (14,600 cal yr BP). By 14.0 ka, marl deposition dominated the core site, with CaCO3 precipitation driven by groundwater solute input and mediated by shallow-water charophytes. The Younger Dryas climate reversal is not well expressed in the proxy data from Kelly Lake. However, marl deposition decreased as organic and clastic matter increased between around 12.2 and 11.5 ka. This shift, together with an increase in both δ13Cmarl and δ18Omarl values and a decrease in CaCO3 content during this interval indicate an increase in the influence of meteoric water on the Kelly Lake hydrologic budget under wet conditions, possibly driven by a strengthened AL. A shift to lower δ13Cmarl and δ18Omarl values at around 11.5 ka is attributed to an increase in the proportion of groundwater relative to meteoric water in the lake, driven by drier conditions. Fluctuations in δ13COM values parallel those in δ13Cmarl prior to ~11.0 ka, indicating that lacustrine primary producers, likely charophytes, were utilizing the same carbon species as was consumed during CaCO3 precipitation. After ~11.0 ka, these datasets diverge and δ13COM values remain very low (~ –38.0‰) for the remainder of the early Holocene, indicating methanogenesis and methanotrophy under relatively warm conditions, an increase in soil-derived dissolved inorganic carbon from the increasingly vegetated catchment area, or a combination of both. Geological methane could be an additional influence. Beginning around 9 ka, δ13COM values increase, indicating that algal photosynthesis shifted toward using CO2 as the availability of dissolved atmospheric CO2 increased. The proportion of meteoric to groundwater input continued to increase, the surrounding coniferous forest became established, and by 8 ka, CaCO3 deposition ceased. Two millennial-scale increases in sediment flux during the middle and late Holocene reflect increases in runoff driven by strengthening of the AL. This study has broader implications for understanding groundwater influence on lake ecosystems in the face of climate change. Additionally, this study provides new insights into marl lake systems and the environmental conditions under which marl was deposited during the late glacial and early Holocene
Remote sensing assessment of semi-arid forest structure changes and ecohydrological responses to thinning-based restoration practices
Get PDFThe expansive ponderosa pine forests across the southwestern U.S. have grown significantly denser over the last century, altering the historical ecological functioning, health, and resilience of the entire ecosystem. Coupled with the ongoing threats posed from climate change, namely hotter and drier regional weather conditions, these forests are increasingly vulnerable to drought-related stress and mortality. To help combat these and other deleterious effects, landscape-scale (400+ ha) forest restoration thinning has been used to promote vegetation health and help stabilize regional ecohydrological systems. Assessing restoration-based forest structure changes and the effects of altered forest structure on surface water resources are key to improving management practices. Remote sensing methodologies and datasets offer accurate, cost-effective, and timely ways to quantify aspects of both forest structure and ecohydrological conditions across multiple spatial scales. In this dissertation, I use high-resolution remote sensing to develop and test novel methodologies for quantifying forest structure, snow cover, and soil moisture conditions in response to a restoration thinning treatment. First, I used unmanned aerial vehicle (UAV) image‐derived Structure‐from‐Motion (SfM) models and high‐resolution multispectral orthoimagery to quantify vertical and horizontal forest structure at both the fine‐ (<4 ha) and mid‐scales (4–400 ha) and assess specific objectives of a restoration thinning project. I found that estimates of fine-scale forest structure were most accurate in low‐density conditions, with significantly degraded accuracies in high‐density conditions. Mid‐scale estimates of forest structure behaved similarly across the density gradient. Overall, I found that a majority of the prescription objectives were met in the post‐thinning conditions, demonstrating the effectiveness of UAV image data in quantifying forest structure changes from thinning treatments. Next, I use UAV multispectral imagery and SfM models to quantify snow cover dynamics and examine the effects of forest structure shading on persistent snow cover. I first develop a method with 90.2% accuracy to identify persistent snow cover using repeat UAV imagery (n = 11 dates) across the 76-ha forest. Using the SfM-derived trees (98% accuracy, n = 1,280 trees) and forest structure variables, I show that forest canopy shading was a significant driver of persistent snow cover patches (R² = 0.70). Overall, my results indicate that UAV image-derived forest structure metrics can be used to accurately predict snow patch size and persistence, providing insight into the importance of forest canopy shading in the amount and distribution of persistent seasonal snow cover. Finally, I use dense soil water potential time-series data across the same thinned forest site to assess soil moisture availability and persistence in response to seasonal drought and forest structure conditions. Using terrestrial lidar data, I assess how fine-scale forest structure components drive differences in the timing, magnitude, and amount of soil drying across soil depths during the seasonal drought period. Results show significant differences in soil moisture response between two abnormally dry years, across all soil depths (25, 50, and 100 cm), and from specific forest structure metrics. Taken together, these studies provide a detailed methodological assessment of the efficacy of high-resolution remote sensing datasets in quantifying forest structure changes from thinning-based restoration and impacts of forest structure on specific ecohydrological components, and importantly how forest management can be used to optimize the availability of water resources in the semi-arid ponderosa pine forests