Matching Items (177)
Description
One of the fundamental questions in molecular biology is how genes and the control of their expression give rise to so many diverse phenotypes in nature. The mRNA molecule plays a key role in this process as it directs the spatial and temporal expression of genetic information contained in the DNA molecule to precisely instruct biological processes in living organisms. The region located between the STOP codon and the poly(A)-tail of the mature mRNA, known as the 3′Untranslated Region (3′UTR), is a key modulator of these activities. It contains numerous sequence elements that are targeted by trans-acting factors that dose gene expression, including the repressive small non-coding RNAs, called microRNAs.
Recent transcriptome data from yeast, worm, plants, and humans has shown that alternative polyadenylation (APA), a mechanism that enables expression of multiple 3′UTR isoforms for the same gene, is widespread in eukaryotic organisms. It is still poorly understood why metazoans require multiple 3′UTRs for the same gene, but accumulating evidence suggests that APA is largely regulated at a tissue-specific level. APA may direct combinatorial variation between cis-elements and microRNAs, perhaps to regulate gene expression in a tissue-specific manner. Apart from a few single gene anecdotes, this idea has not been systematically explored.
This dissertation research employs a systems biology approach to study the somatic tissue dynamics of APA and its impact on microRNA targeting networks in the small nematode C. elegans. In the first aim, tools were developed and applied to isolate and sequence mRNA from worm intestine and muscle tissues, which revealed pervasive tissue-specific APA correlated with microRNA regulation. The second aim provides genetic evidence that two worm genes use APA to escape repression by microRNAs in the body muscle. Finally, in aim three, mRNA from five additional somatic worm tissues was sequenced and their 3′ends mapped, allowing for an integrative study of APA and microRNA targeting dynamics in worms. Together, this work provides evidence that APA is a pervasive mechanism operating in somatic tissues of C. elegans with the potential to significantly rearrange their microRNA regulatory networks and precisely dose their gene expression.
Recent transcriptome data from yeast, worm, plants, and humans has shown that alternative polyadenylation (APA), a mechanism that enables expression of multiple 3′UTR isoforms for the same gene, is widespread in eukaryotic organisms. It is still poorly understood why metazoans require multiple 3′UTRs for the same gene, but accumulating evidence suggests that APA is largely regulated at a tissue-specific level. APA may direct combinatorial variation between cis-elements and microRNAs, perhaps to regulate gene expression in a tissue-specific manner. Apart from a few single gene anecdotes, this idea has not been systematically explored.
This dissertation research employs a systems biology approach to study the somatic tissue dynamics of APA and its impact on microRNA targeting networks in the small nematode C. elegans. In the first aim, tools were developed and applied to isolate and sequence mRNA from worm intestine and muscle tissues, which revealed pervasive tissue-specific APA correlated with microRNA regulation. The second aim provides genetic evidence that two worm genes use APA to escape repression by microRNAs in the body muscle. Finally, in aim three, mRNA from five additional somatic worm tissues was sequenced and their 3′ends mapped, allowing for an integrative study of APA and microRNA targeting dynamics in worms. Together, this work provides evidence that APA is a pervasive mechanism operating in somatic tissues of C. elegans with the potential to significantly rearrange their microRNA regulatory networks and precisely dose their gene expression.
ContributorsBlazie, Stephen M (Author) / Mangone, Marco (Thesis advisor) / LaBaer, Josh (Committee member) / Lake, Doug (Committee member) / Newfeld, Stuart (Committee member) / Arizona State University (Publisher)
Created2016
Description
This dissertation will investigate two of the most promising high-capacity anode
materials for lithium-based batteries: silicon (Si) and metal lithium (Li). It will focus on
studying the mechanical behaviors of the two materials during charge and discharge and
understanding how these mechanical behaviors may affect their electrochemical
performance.
In the first part, amorphous Si anode will be studied. Despite many existing studies
on silicon (Si) anodes for lithium ion batteries (LIBs), many essential questions still exist
on compound formation, composition, and properties. Here it is shown that some
previously accepted findings do not truthfully reflect the actual lithiation mechanisms in
realistic battery configurations. Furthermore the correlation between structure and
mechanical properties in these materials has not been properly established. Here, a rigorous
and thorough study is performed to comprehensively understand the electrochemical
reaction mechanisms of amorphous-Si (a-Si) in a realistic LIB configuration. In-depth
microstructural characterization was performed and correlations were established between
Li-Si composition, volumetric expansion, and modulus/hardness. It is found that the
lithiation process of a-Si in a real battery setup is a single-phase reaction rather than the
accepted two-phase reaction obtained from in-situ TEM experiments. The findings in this
dissertation establish a reference to quantitatively explain many key metrics for lithiated a
Si as anodes in real LIBs, and can be used to rationally design a-Si based high-performance
LIBs guided by high-fidelity modeling and simulations.
In the second part, Li metal anode will be investigated. Problems related to dendrite
growth on lithium metal anodes such as capacity loss and short circuit present major
barriers to the next-generation high-energy-density batteries. The development of
successful mitigation strategies is impeded by the incomplete understanding of the Li
dendrite growth mechanisms. Here the enabling role of plating residual stress in dendrite
initiation through novel experiments of Li electrodeposition on soft substrates is confirmed,
and the observations is explained with a stress-driven dendrite growth model. Dendrite
growth is mitigated on such soft substrates through surface-wrinkling-induced stress
relaxation in deposited Li film. It is demonstrated that this new dendrite mitigation
mechanism can be utilized synergistically with other existing approaches in the form of
three-dimensional (3D) soft scaffolds for Li plating, which achieves superior coulombic
efficiency over conventional hard copper current collectors under large current density.
materials for lithium-based batteries: silicon (Si) and metal lithium (Li). It will focus on
studying the mechanical behaviors of the two materials during charge and discharge and
understanding how these mechanical behaviors may affect their electrochemical
performance.
In the first part, amorphous Si anode will be studied. Despite many existing studies
on silicon (Si) anodes for lithium ion batteries (LIBs), many essential questions still exist
on compound formation, composition, and properties. Here it is shown that some
previously accepted findings do not truthfully reflect the actual lithiation mechanisms in
realistic battery configurations. Furthermore the correlation between structure and
mechanical properties in these materials has not been properly established. Here, a rigorous
and thorough study is performed to comprehensively understand the electrochemical
reaction mechanisms of amorphous-Si (a-Si) in a realistic LIB configuration. In-depth
microstructural characterization was performed and correlations were established between
Li-Si composition, volumetric expansion, and modulus/hardness. It is found that the
lithiation process of a-Si in a real battery setup is a single-phase reaction rather than the
accepted two-phase reaction obtained from in-situ TEM experiments. The findings in this
dissertation establish a reference to quantitatively explain many key metrics for lithiated a
Si as anodes in real LIBs, and can be used to rationally design a-Si based high-performance
LIBs guided by high-fidelity modeling and simulations.
In the second part, Li metal anode will be investigated. Problems related to dendrite
growth on lithium metal anodes such as capacity loss and short circuit present major
barriers to the next-generation high-energy-density batteries. The development of
successful mitigation strategies is impeded by the incomplete understanding of the Li
dendrite growth mechanisms. Here the enabling role of plating residual stress in dendrite
initiation through novel experiments of Li electrodeposition on soft substrates is confirmed,
and the observations is explained with a stress-driven dendrite growth model. Dendrite
growth is mitigated on such soft substrates through surface-wrinkling-induced stress
relaxation in deposited Li film. It is demonstrated that this new dendrite mitigation
mechanism can be utilized synergistically with other existing approaches in the form of
three-dimensional (3D) soft scaffolds for Li plating, which achieves superior coulombic
efficiency over conventional hard copper current collectors under large current density.
ContributorsWang, Xu (Author) / Jiang, Hanqing (Thesis advisor) / Yu, Hongbin (Thesis advisor) / Chan, Candace (Committee member) / Wang, Liping (Committee member) / Qiong, Nian (Committee member) / Arizona State University (Publisher)
Created2018
Description
Advancements in thermal interface materials (TIMs) allows for the creation of new and more powerful electronics as they increase the heat transfer from the component to the heat sink. Current industrial options provide decent heat transfer, but the creation of TIMs with higher thermal conductivities is needed. In addition, if these TIMs are elastic in nature, their effectiveness can greatly increase as they can deal with changing interfaces without degradation of their properties. The research performed delves into this idea, creating elastic TIMs using liquid metal (LM), in this case galinstan, along with other matrix particles embedded in Polydimethylsiloxane (PDMS) to create an easy to use, relatively inexpensive, thermally conductive, but electrically insulative, pad with increased thermal conductivity from industrial solutions.
The pads were created using varying amounts of LM and matrix materials ranging from copper microspheres to diamond powder mixed into PDMS using a high-speed mixer. The material was then cast into molds and cured to create the pads. Once the pads were created, the difficulty came in quantifying their thermal properties. A stepped bar apparatus (SBA) following ASTM D5470 was created to measure the thermal resistance of the pads but it was determined that thermal conductivity was a more usable metric of the pads’ performance. This meant that the pad’s in-situ thickness was needed during testing, prompting the installation of a linear encoder to measure the thickness. The design and analysis of the necessary modification and proposed future design is further detailed in the following paper.
The pads were created using varying amounts of LM and matrix materials ranging from copper microspheres to diamond powder mixed into PDMS using a high-speed mixer. The material was then cast into molds and cured to create the pads. Once the pads were created, the difficulty came in quantifying their thermal properties. A stepped bar apparatus (SBA) following ASTM D5470 was created to measure the thermal resistance of the pads but it was determined that thermal conductivity was a more usable metric of the pads’ performance. This meant that the pad’s in-situ thickness was needed during testing, prompting the installation of a linear encoder to measure the thickness. The design and analysis of the necessary modification and proposed future design is further detailed in the following paper.
ContributorsKemme, Nicholas (Author) / Rykaczewski, Konrad (Thesis advisor) / Wang, Robert (Thesis advisor) / Wang, Liping (Committee member) / Arizona State University (Publisher)
Created2017
Description
In a 2004 paper, John Nagy raised the possibility of the existence of a hypertumor \emph{i.e.}, a focus of aggressively reproducing parenchyma cells that invade part or all of a tumor. His model used a system of nonlinear ordinary differential equations to find a suitable set of conditions for which these hypertumors exist. Here that model is expanded by transforming it into a system of nonlinear partial differential equations with diffusion, advection, and a free boundary condition to represent a radially symmetric tumor growth. Two strains of parenchymal cells are incorporated; one forming almost the entirety of the tumor while the much more aggressive strain
appears in a smaller region inside of the tumor. Simulations show that if the aggressive strain focuses its efforts on proliferating and does not contribute to angiogenesis signaling when in a hypoxic state, a hypertumor will form. More importantly, this resultant aggressive tumor is paradoxically prone to extinction and hypothesize is the cause of necrosis in many vascularized tumors.
appears in a smaller region inside of the tumor. Simulations show that if the aggressive strain focuses its efforts on proliferating and does not contribute to angiogenesis signaling when in a hypoxic state, a hypertumor will form. More importantly, this resultant aggressive tumor is paradoxically prone to extinction and hypothesize is the cause of necrosis in many vascularized tumors.
ContributorsAlvarez, Roberto L (Author) / Milner, Fabio A (Thesis advisor) / Nagy, John D. (Committee member) / Kuang, Yang (Committee member) / Thieme, Horst (Committee member) / Mahalov, Alex (Committee member) / Smith, Hal (Committee member) / Arizona State University (Publisher)
Created2014
Description
Predicting the timing of a castrate resistant prostate cancer is critical to lowering medical costs and improving the quality of life of advanced prostate cancer patients. We formulate, compare and analyze two mathematical models that aim to forecast future levels of prostate-specific antigen (PSA). We accomplish these tasks by employing clinical data of locally advanced prostate cancer patients undergoing androgen deprivation therapy (ADT). While these models are simplifications of a previously published model, they fit data with similar accuracy and improve forecasting results. Both models describe the progression of androgen resistance. Although Model 1 is simpler than the more realistic Model 2, it can fit clinical data to a greater precision. However, we found that Model 2 can forecast future PSA levels more accurately. These findings suggest that including more realistic mechanisms of androgen dynamics in a two population model may help androgen resistance timing prediction.
ContributorsBaez, Javier (Author) / Kuang, Yang (Author) / College of Liberal Arts and Sciences (Contributor)
Created2016-11-16
Description
Background:
Data assimilation refers to methods for updating the state vector (initial condition) of a complex spatiotemporal model (such as a numerical weather model) by combining new observations with one or more prior forecasts. We consider the potential feasibility of this approach for making short-term (60-day) forecasts of the growth and spread of a malignant brain cancer (glioblastoma multiforme) in individual patient cases, where the observations are synthetic magnetic resonance images of a hypothetical tumor.
Results:
We apply a modern state estimation algorithm (the Local Ensemble Transform Kalman Filter), previously developed for numerical weather prediction, to two different mathematical models of glioblastoma, taking into account likely errors in model parameters and measurement uncertainties in magnetic resonance imaging. The filter can accurately shadow the growth of a representative synthetic tumor for 360 days (six 60-day forecast/update cycles) in the presence of a moderate degree of systematic model error and measurement noise.
Conclusions:
The mathematical methodology described here may prove useful for other modeling efforts in biology and oncology. An accurate forecast system for glioblastoma may prove useful in clinical settings for treatment planning and patient counseling.
ContributorsKostelich, Eric (Author) / Kuang, Yang (Author) / McDaniel, Joshua (Author) / Moore, Nina Z. (Author) / Martirosyan, Nikolay L. (Author) / Preul, Mark C. (Author) / College of Liberal Arts and Sciences (Contributor)
Created2011-12-21
Description
Glioblastoma multiforme (GBMs) is the most prevalent brain tumor type and causes approximately 40% of all non-metastic primary tumors in adult patients [1]. GBMs are malignant, grade-4 brain tumors, the most aggressive classication as established by the World Health Organization and are marked by their low survival rate; the median survival time is only twelve months from initial diagnosis: Patients who live more than three years are considered long-term survivors [2]. GBMs are highly invasive and their diffusive growth pattern makes it impossible to remove the tumors by surgery alone [3]. The purpose of this paper is to use individual patient data to parameterize a model of GBMs that allows for data on tumor growth and development to be captured on a clinically relevant time scale. Such an endeavor is the rst step to a clinically applicable predictions of GBMs. Previous research has yielded models that adequately represent the development of GBMs, but they have not attempted to follow specic patient cases through the entire tumor process. Using the model utilized by Kostelich et al. [4], I will attempt to redress this deciency. In doing so, I will improve upon a family of models that can be used to approximate the time of development and/or structure evolution in GBMs. The eventual goal is to incorporate Magnetic Resonance Imaging (MRI) data into a parameterized model of GBMs in such a way that it can be used clinically to predict tumor growth and behavior. Furthermore, I hope to come to a denitive conclusion as to the accuracy of the Koteslich et al. model throughout the development of GBMs tumors.
ContributorsManning, Miles (Author) / Kostelich, Eric (Thesis director) / Kuang, Yang (Committee member) / Preul, Mark (Committee member) / Barrett, The Honors College (Contributor) / College of Liberal Arts and Sciences (Contributor)
Created2012-12