Browsing by Author "Bark, David, committee member"

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Open Access
Cardiac computed tomography in dogs: insights into structural imaging and therapeutics
(Colorado State University. Libraries, 2025) Chi, I-Jung Bernard, author; Scansen, Brian, advisor; Orton, E. Christopher, advisor; Visser, Lance, committee member; Bark, David, committee member
Visualization of intracardiac structures with medical imaging has always been a formidable task due to the inherently complex structure of mammalian hearts. Traditional two-dimensional (2D) imaging such as fluoroscopy and 2D echocardiography present challenges in reconstructing the three-dimensional (3D) morphology of cardiac structures and alterations in intracardiac architecture caused by cardiovascular disease. Challenges in accurately visualizing complex cardiac geometry can lead to incomplete or inaccurate assessments during surgical and transcatheter interventions. To overcome this issue, cross-sectional imaging such as cardiac computed tomography (CCT) may be utilized to allow a comprehensive, dynamic, and 3D evaluation of cardiac valves, chambers and major vascular structures. One potential application of 3D imaging is preprocedural prediction of optimal fluoroscopic projections that can be used for intraprocedural guidance of cardiac interventions. For any given cardiac structure, there is an infinite number of 2D projections orthogonal to the straight-on (en face) projection forming a 360-degree circle of perpendicularity. The circle of perpendicularity becomes an arch of perpendicularity when considering projections above the fluoroscopic table only. In Chapter 1, this concept was explored by identifying the en face projections of various cardiac structures on CCT. The arch of perpendicularity (also known as the S curve) can be derived by using a trigonometric formula to solve the spatial relationship between the en face and perpendicular projections. Once the S curves are established, the optimal fluoroscopic projections (OFPs) can then be characterized and used to guide cardiac interventions. Cardiac computed tomography studies from eighteen healthy dogs were used to generate S-curves and OFPs for selected cardiac structures. The projections were defined by the cranial-caudal angulation and left-right rotation angles of the C-arm assuming the dog is in dorsal recumbency. Mean OFP S-curves and 95% confidence curve areas were determined for the aortic, mitral, and pulmonary valve along with interatrial septum. The impact of thoracic conformation on OFPs was found to be non-significant. By analyzing the CCTs from 18 dogs with severe pulmonary stenosis, the S-curves and OFPs of the pulmonary valve were described in Chapter 2. The coordinates of those optimized projections were found to be different from those of healthy dogs. Cardiac computed tomography from dogs with pulmonary stenosis were also used as a reference to examine the accuracy of pulmonary annular diameters measured on transthoracic echocardiography and angiocardiography. It was found that transthoracic echocardiography underestimates pulmonary annular diameter. Angiographic pulmonary annular diameters on standard lateral projection were also shown to be less precise when compared to the measurements made on CCT-derived OFPs. The inodilator pimobendan has been shown to delay the onset of congestive heart failure and decrease cardiac mortality in dogs with degenerative mitral valve disease. The benefit of pimobendan may go beyond its effect on cardiac contractility and vasodilation. In Chapter 3, CCTs from 20 dogs with subclinical degenerative mitral valve disease were used to investigate the effects of pimobendan on mitral annular dynamics. By comparing the mitral annular dynamics before and after the administration of pimobendan, it was shown that pimobendan augmented the systolic contraction of the mitral annulus which likely reduced the regurgitant orifice area and severity of mitral regurgitation. In conclusion, integration of CCT into clinical practice enhances our ability to evaluate and treat structural heart disease. Cardiac computed tomography can also be used as a reference to refine other imaging techniques and investigate the mechanism of action underlying various cardiovascular therapies.
Open Access
Characterization of the unique biomechanical behavior of right ventricle using experimental and constitutive modeling approaches
(Colorado State University. Libraries, 2022) Liu, Wenqiang, author; Wang, Zhijie, advisor; Puttlitz, Christian, committee member; Bark, David, committee member; Chicco, Adam, committee member
Ventricle dysfunction leads to high morbidity and mortality in heart failure patients. It is known that right and left ventricles (RV&LV) are distinct in their embryologic origins, anatomies and functions, as well as the pathophysiology of ventricular failure. However, how exactly the RV is distinct from the LV in their biomechanical properties remains incompletely understood. Furthermore, the prevalence of RV failure is significantly increased in the later stages of diseases such as pulmonary hypertension (PH) and heart failure with preserved ejection fraction, and the clinical management and treatment of RV failure are persistently challenging. This calls for a further understanding of the mechanisms of RV failure including the biomechanical mechanism. In addition, ventricular tissues are viscoelastic, which means both energy storage (originated from elasticity) and energy loss (originated from viscosity) are present during the deformation. However, the investigation of ventricular tissue viscoelasticity is much less than that of the elasticity, and it is largely unknown how the RV viscoelastic behavior changes during RV failure progression and impacts on the physiological function of the chamber. To fill these knowledge gaps, the overall goal of my study was to investigate the unique biomechanical properties of the RV in its physiological and pathological functions using experimental and constitutive modeling approaches. The Specific Aims are: 1) Develop the experimental protocols and characterize ventricular tissue passive static and dynamic mechanical properties in both large and small animals; 2) Adapted and performed constitutive modeling of ventricular tissue static and dynamic mechanical behaviors; 3) Quantify the changes in RV biomechanics during the maladaptive remodeling induced by pulmonary hypertension. At the completion of my study, I established the ex vivo testing protocols and provided fundamental data regarding static and dynamic mechanical differences between the healthy left and right chambers to delineate the unique biomechanical properties of the RV. I also adapted the constitutive models to capture static and dynamic mechanical behaviors of the RV. Finally, I quantified the biomechanical changes of the RV during the RV failure development and offered new insights in the contributions of the RV tissue biomechanics to the organ function. The findings were obtained from both large and small animals' species, which are translational to human diseases and a strong addition to the current literature of RV failure. More importantly, the investigation on the viscoelastic (dynamic) mechanical properties of the RV and the changes of viscoelasticity in RV failure progression is highly novel. The constitutive modeling of the RV biaxial viscoelastic behavior is pioneering and unique in the computational study of the RV. In summary, this study will deepen the understanding of the biomechanical mechanisms of RV failure and assist with the development of new computational tools for diagnosis and treatment strategies.
Open Access
Design and evaluation of an instrumented microfluidic organotypic device and sensor module for organ-on-a-chip applications
(Colorado State University. Libraries, 2020) Richardson, Alec Evan, author; Henry, Charles, advisor; Tobet, Stuart, advisor; Bark, David, committee member; Abdo, Zaid, committee member
Organ and tissue-on-a-chip technologies are powerful tools for drug discovery and disease modeling, yet many of these systems rely heavily on in vitro cell culture to create reductionist models of tissues and organs. Therefore, Organ-on-chip devices recapitulate some tissue functions and are useful for high-throughput screening but fail to capture the richness of cellular interactions of tissues in vivo because they lack the cellular diversity and complex architecture of native tissue. This thesis describes the design and testing of 1) a microfluidic organotypic device (MOD) for culture of murine intestinal tissue and 2) a microfluidic sensor module to be implemented inline with the MOD for real-time sensing of analytes and metabolites. The MOD houses full-thickness murine intestinal tissue, including muscular, neural, immune, and epithelial components. We used the MOD system to maintain murine intestinal explants for 72 h ex vivo. Explants cultured in the MOD formed a barrier between independent fluidic channels perfused with media, which is critical to recapitulating intestinal barrier function in vivo. We also established differential oxygen concentrations in the fluidic channels and showed that more bacteria were present on the tissue's mucosal surface when exposed to near-anoxic media. The sensor module is a reversibly sealed microfluidic device with magnetic connections that can withstand high backpressures. Further, electrodes housed in commercial finger-tight fittings were integrated into the sensor module in a plug-and-play format. Future work will include developing electrochemical/optical sensors for various biological compounds relevant to intestinal physiology. Ultimately, the MOD and sensor module will be implemented in long-term microbiome studies to elucidate the relationship among microbial, epithelial, neuro and immune components of the gut wall in health and disease.
Open Access
Force spectroscopy and dynamics in biological systems
(Colorado State University. Libraries, 2019) Schroder, Bryce William, author; Krapf, Diego, advisor; Bark, David, committee member; Popat, Ketul, committee member; DeLuca, Jennifer, committee member
Communication is key to any process involving the transmission of information or some sort of signal. For communication to occur, a signal must be created that can be detected. Cells communicate through cues transmitted in the forms of chemical and mechanical signals. The most fundamental means for transmitting chemical cues is through the process of diffusion. A single particle undergoing diffusion is considered to undergo Brownian motion, which can be modelled as a random walk. The random walk behavior is characteristic of both the particles properties and the fields in which it is occurring. An unbiased walk will be completely random without outside influence. A biased walk will be random within the confines of a potential influencing its direction. Both are Stochastic processes characterized through probabilistic models with known solutions. The work herein presents the development of single molecule experiments and the associated particle tracking tools targeting particles undergoing biased random walks within a trapping potential on or near a cellular membrane. In the first set of experiments, the trapping potential, an optical tweezers setup, has been developed and employed in measuring cellular membrane biophysical properties as well as blebbing forces. The optical trap was also used to directly measure flow driven forces in live embryonic zebrafish, the first known measurements of this kind. In the second set of experiments, synthetic lipid bilayers provided a trapping potential in a single dimension for protein binding experiments leading to exchanges between free, 3-dimensional diffusion and bound, or biased, 2-dimensional diffusion. In all cases, stochastic models have been used in conjunction with image-based particle tracking tools to better characterize the biophysical properties and forces associated with the cellular membrane and its means of signal transduction. These measurements are key to understanding both the chemical and mechanical signaling means by which the cellular membrane transduces an external signal into an internal response.
Open Access
Sustainability tradeoffs within photoautotrophic cultivation systems: integrating physical and lifecycle modeling for design and optimization
(Colorado State University. Libraries, 2018) Quiroz-Arita, Carlos Enrique, author; Bradley, Thomas H., advisor; Bark, David, committee member; Blaylock, Myra, committee member; Marchese, Anthony, committee member; Sharvelle, Sybil, committee member; Willson, Bryan, committee member
Photoautotroph-based biofuels are considered one of the most promising renewable resources to meet the global energy requirements for transportation systems. Long-term research and development has resulted in demonstrations of microalgae areal oil productivities that are higher than crop-based biofuels, about 10 times that of palm oil and about 130 times that of soybean. Cyanobacteria is reported to have ~4 times the areal productivity of microalgae on an equivalent energy basis. Downstream of this cultivation process, the cyanobacteria biomass and bioproducts can be supplied to biorefineries producing feed, biomaterials, biosynthetic chemicals, and biofuels. As such, cyanobacteria, and microalgae-based systems can be a significant contributor to more sustainable energy and production systems. This research presents novel means to be able to analyze, integrate, assess, and design sustainable photoautotrophic biofuel and bioproduct systems, as defined using lifecycle assessment methods (LCA). As part of a broad collaboration between industry, academia, and the national laboratories, I have developed models and experiments to quantify tradeoffs among the scalability, sustainability, and technical feasibility of cyanobacteria biorefineries and microalgae cultivation systems. A central hypothesis to this research is that the lifecycle energy costs and benefits, the cultivation productivity, and the scalability of any given organism or technology is governed by the fluid mechanics of the photobioreactor systems. The fluid characteristics of both open raceway ponds and flat photobioreactors, are characterized through industrial-scale experiment and modeling. Turbulent mixing is studied by applying Acoustic Doppler Velocimetry (ADV), Particle Image Velocimetry (PIV), and computational fluid dynamics (CFD) characterization tools. The implications of these fluid conditions on photoautotrophic organisms are studied through cultivation and modeling of the cyanobacteria, Synechocystis sp. PCC6803. Growth-stage models of this cyanobacteria include functions dependent on incident radiation, temperature, nutrient availability, dark and photo-respiration. By developing an integrated approach to laboratory experimentation and industrial-scale growth experiments, we have validated models to quantify the scalability and sustainability of these novel biosystems. These capabilities are utilized to perform long-term and industrially-relevant assessments of the costs and benefits of these promising technologies, and will serve to inform the biological engineering research and development of new organisms.
Open Access
The cardiac jelly extracellular matrix contributes to valve development and overall cardiac function
(Colorado State University. Libraries, 2022) Ostwald, Paige, author; Garrity, Deborah, advisor; Bark, David, committee member; Bedinger, Patricia, committee member; Nishimura, Erin, committee member; Peers, Graham, committee member
Nearly 2.6 million infants are born every year with a congenital cardiac anomaly across the entire globe. Congenital heart defects (CHDs) within the valve occur in over 50% of cases. 56% of heart defects have an unknown etiology, illuminating the need for continuous research on heart development and potential causes. Before the valve is a mature structure with established leaflets, the heart forms two endocardial cushions that press together to occlude blood flow between chambers. The cushions are composed of an extracellular matrix called the cardiac jelly (CJ). Previous studies have found evidence of the vital role the cardiac jelly plays within the developing valve for structure, genetic signaling and cell organization. Here, we present a specific role the cardiac jelly plays in valve function and overall cardiac output. To alter the cardiac jelly, we used a morpholino approach in a zebrafish model to increase, decrease and structurally compromise the cardiac jelly. By doing so, we found decreased valve cell differentiation with decreased CJ and increased valve cell differentiation with increased CJ. Using high-speed video technology, we also found decreased valve opening regardless of cardiac jelly alteration, resulting in reduced overall cardiac function. Our results suggest that the function of the endocardial cushions relies on an appropriate presence of CJ. We next investigated just how the cardiac jelly may be altered during development. To do so, we exposed zebrafish embryos to hyperglycemic conditions during the initial and critical heart development period. We found that when embryos absorb over 1.5-fold more D-glucose due to high-glucose conditions, they exhibit significant alterations to CJ width. Altered CJ due to hyperglycemic conditions affected valve differentiation, valve opening, and cardiac function, particularly when embryos have absorbed over a 2-fold increase of glucose. Together, these results show the structural role of the cardiac jelly to support endocardial cushion opening which will supply enough oxygenated blood to the embryo.
Open Access
The role of FLNC in the contractility of the heart and valve development in zebrafish
(Colorado State University. Libraries, 2020) Alshahrani, Areej Ali, author; Garrity, Deborah, advisor; Mueller, Rachel, committee member; Bark, David, committee member
Dilated Cardiomyopathy (DCM) is the most common type of cardiomyopathy disease that causes heart muscle defects. DCM is characterized by a dilated left ventricular chamber and systolic dysfunction that results in congestive heart failure. Although the cause of DCM is not fully understood, evidence supports the hypothesis that costameric proteins contribute to muscle dysfunction linked to cardiomyopathy. In fact, the mutation of FLNC has been linked to many muscle disease including myofibrila myopathies (MFM) and different types of cardiomyopathy. However, the mechanisms underlying the variability between MFM and cardiac disease is a field of interest. Patients with DCM shown to carry truncating variants whereas patients with hypertrophic cardiomyopathy (HCM) carried missense variants. Additionally, patients with other types of cardiomyopathy carried missense or in-frame indel variants (Ader, Groote et al.). This seems to suggest that different mechanisms may be at play regarding the role of FLNC in cardiac developments and they remain unclear. It would be interesting to examine if a similar correlation holds in animal model like zebrafish. Therefore, our group has developed the zebrafish model for study of the FLNC contribution to cardiac phenotypes. Here, we used several FLNC mutant lines to investigate how FLNC directly or indirectly affects development of the atrioventricular (AV) valve. To date, little data indicate whether or not increased RFF is pathologic. This project will test the overarching hypothesis that flnc depletion causes changes in RFF, which lead to aberrant valve development, which in turn affects overall heart function. We find that the cardiac morphological phenotype of most single FLNC alleles showed normal heart parameters such as heart rate, stroke volume, cardiac output and reverse flow fraction. However, flcnbexon14-/- allele exhibited a decreased in stroke volume and cardiac output whereas RFF is intact. Furthermore, using an immunocytochemistry to examine a correlation that may exist between the strength of the cardiac phenotype and the presence of valve defects indicate that valve defects presented in flncb truncation mutants, and suggest that defects in flncbexon35-/- embryos are more severe. In support of this finding, our qPCR study displayed that expression levels of klf2a and klf2b in flncaexon1-/- ; flncbexon14-/- double mutant hearts were significantly decreased. In addition, Prior studies have proposed that massive formation of intracellular protein aggregates imposes toxic impacts that contribute to the skeletal muscle degeneration observed in myofibrillar myopathy (Fichna, Maruszak et al. 2018). We demonstrated that the truncated protein either exerts a direct toxic effect, and/or sequesters wildtype FLNC leading to insufficiency phenotypes.