Matching Items (148)
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
Alloying in semiconductors has enabled many civilian technologies in optoelectronic, photonic fields and more. While the phenomenon of alloying is well established in traditional bulk semiconductors, owing to vastly available ternary phase diagrams, the ability to alloy in 2D systems are less clear. Recently anisotropic materials such as ReS2 and TiS3 have been extensively studied due to their direct-gap semiconductor and high mobility behaviors. This work is a report on alloys of ReS2 & ReSe2 and TiS3 &TiSe3.
Alloying selenium into ReS2 in the creation of ReS2xSe2-x, tunes the band gap and changes its vibrational spectrum. Depositing this alloy using bottom up approach has resulted in the loss of crystallinity. This loss of crystallinity was evidenced by grain boundaries and point defect shown by TEM images.
Also, in the creation of TiS3xSe3-x, by alloying Se into TiS3, a fixed ratio of 8% selenium deposit into TiS3 host matrix is observed. This is despite the vastly differing precursor amounts and growth temperatures, as evinced by detailed TEM, EDAX, TEM diffraction, and Raman spectroscopy measurements. This unusual behavior contrasts with other well-known layered material systems such as MoSSe, WMoS2 where continuous alloying can be attained. Cluster expansion theory calculations suggest that only limited composition (x) can be achieved. Considering the fact that TiSe3 vdW crystals have not been synthesized in the past, these alloying rejections can be attributed to energetic instability in the ternary phase diagrams estimated by calculations performed. Overall findings highlight potential means and challenges in achieving stable alloying in promising direct gap and high carrier mobility TiS3 materials.
Alloying selenium into ReS2 in the creation of ReS2xSe2-x, tunes the band gap and changes its vibrational spectrum. Depositing this alloy using bottom up approach has resulted in the loss of crystallinity. This loss of crystallinity was evidenced by grain boundaries and point defect shown by TEM images.
Also, in the creation of TiS3xSe3-x, by alloying Se into TiS3, a fixed ratio of 8% selenium deposit into TiS3 host matrix is observed. This is despite the vastly differing precursor amounts and growth temperatures, as evinced by detailed TEM, EDAX, TEM diffraction, and Raman spectroscopy measurements. This unusual behavior contrasts with other well-known layered material systems such as MoSSe, WMoS2 where continuous alloying can be attained. Cluster expansion theory calculations suggest that only limited composition (x) can be achieved. Considering the fact that TiSe3 vdW crystals have not been synthesized in the past, these alloying rejections can be attributed to energetic instability in the ternary phase diagrams estimated by calculations performed. Overall findings highlight potential means and challenges in achieving stable alloying in promising direct gap and high carrier mobility TiS3 materials.
ContributorsAgarwal, Ashutosh (Author) / Tongay, Sefaattin (Thesis advisor) / Green, Matthew (Committee member) / Zhuang, Houlong (Committee member) / Arizona State University (Publisher)
Created2018
Description
Urbanization and woody plant encroachment, with subsequent brush management, are two significant land cover changes that are represented in the southwestern United States. Urban areas continue to grow, and rangelands are undergoing vegetation conversions, either purposely through various rangeland management techniques, or by accident, through inadvertent effects of climate and management. This thesis investigates how areas undergoing land cover conversions in a semiarid region, through urbanization or rangeland management, influences energy, water and carbon fluxes. Specifically, the following scientific questions are addressed: (1) what is the impact of different urban land cover types in Phoenix, AZ on energy and water fluxes?, (2) how does the land cover heterogeneity influence energy, water, and carbon fluxes in a semiarid rangeland undergoing woody plant encroachment?, and (3) what is the impact of brush management on energy, water, and carbon fluxes?
The eddy covariance technique is well established to measure energy, water, and carbon fluxes and is used to quantify and compare flux measurements over different land surfaces. Results reveal that in an urban setting, paved surfaces exhibit the largest sensible and lowest latent heat fluxes in an urban environment, while a mesic landscape exhibits the largest latent heat fluxes, due to heavy irrigation. Irrigation impacts flux sensitivity to precipitation input, where latent heat fluxes increase with precipitation in xeric and parking lot landscapes, but do not impact the mesic system. In a semiarid managed rangeland, past management strategies and disturbance histories impact vegetation distribution, particularly the distribution of mesquite trees. At the site with less mesquite coverage, evapotranspiration (ET) is greater, due to greater grass cover. Both sites are generally net sinks of CO2, which is largely dependent on moisture availability, while the site with greater mesquite coverage has more respiration and generally greater gross ecosystem production (GEP). Initial impacts of brush management reveal ET and GEP decrease, due to the absence of mesquite trees. However the impact appears to be minimal by the end of the productive season. Overall, this dissertation advances the understanding of land cover change impacts on surface energy, water, and carbon fluxes in semiarid ecosystems.
The eddy covariance technique is well established to measure energy, water, and carbon fluxes and is used to quantify and compare flux measurements over different land surfaces. Results reveal that in an urban setting, paved surfaces exhibit the largest sensible and lowest latent heat fluxes in an urban environment, while a mesic landscape exhibits the largest latent heat fluxes, due to heavy irrigation. Irrigation impacts flux sensitivity to precipitation input, where latent heat fluxes increase with precipitation in xeric and parking lot landscapes, but do not impact the mesic system. In a semiarid managed rangeland, past management strategies and disturbance histories impact vegetation distribution, particularly the distribution of mesquite trees. At the site with less mesquite coverage, evapotranspiration (ET) is greater, due to greater grass cover. Both sites are generally net sinks of CO2, which is largely dependent on moisture availability, while the site with greater mesquite coverage has more respiration and generally greater gross ecosystem production (GEP). Initial impacts of brush management reveal ET and GEP decrease, due to the absence of mesquite trees. However the impact appears to be minimal by the end of the productive season. Overall, this dissertation advances the understanding of land cover change impacts on surface energy, water, and carbon fluxes in semiarid ecosystems.
ContributorsTempleton, Nicole Pierini (Author) / Vivoni, Enrique R (Thesis advisor) / Archer, Steven R (Committee member) / Mascaro, Giuseppe (Committee member) / Scott, Russell L. (Committee member) / Wang, Zhi-Hua (Committee member) / Arizona State University (Publisher)
Created2017
Description
Cancer therapy selects for cancer cells resistant to treatment, a process that is fundamentally evolutionary. To what extent, however, is the evolutionary perspective employed in research on therapeutic resistance and relapse? We analyzed 6,228 papers on therapeutic resistance and/or relapse in cancers and found that the use of evolution terms in abstracts has remained at about 1% since the 1980s. However, detailed coding of 22 recent papers revealed a higher proportion of papers using evolutionary methods or evolutionary theory, although this number is still less than 10%. Despite the fact that relapse and therapeutic resistance is essentially an evolutionary process, it appears that this framework has not permeated research. This represents an unrealized opportunity for advances in research on therapeutic resistance.
ContributorsAktipis, C. Athena (Author) / Kwan, Sau (Author) / Johnson, Kathryn (Author) / Neuberg, Steven (Author) / Maley, Carlo C. (Author) / College of Liberal Arts and Sciences (Contributor)
Created2011-11-17
Description
This study examines the spatial and temporal patterns of the surface urban heat island (SUHI) intensity in the Phoenix metropolitan area and the relationship with land use land cover (LULC) change between 2000 and 2014. The objective is to identify specific regions in Phoenix that have been increasingly heated and cooled to further understand how LULC change influences the SUHI intensity. The data employed include MODerate-resolution Imaging Spectroradiometer (MODIS) land surface temperature (LST) 8-day composite June imagery, and classified LULC maps generated using 2000 and 2014 Landsat imagery. Results show that the regions that experienced the most significant LST changes during the study period are primarily on the outskirts of the Phoenix metropolitan area for both daytime and nighttime. The conversion to urban, residential, and impervious surfaces from all other LULC types has been identified as the primary cause of the UHI effect in Phoenix. Vegetation cover has been shown to significantly lower LST for both daytime and nighttime due to its strong cooling effect by producing more latent heat flux and less sensible heat flux. We suggest that urban planners, decision-makers, and city managers formulate new policies and regulations that encourage residential, commercial, and industrial developers to include more vegetation when planning new construction.
ContributorsWang, Chuyuan (Author) / Myint, Soe (Author) / Wang, Zhi-Hua (Author) / Song, Jiyun (Author) / College of Liberal Arts and Sciences (Contributor)
Created2016-02-26
Description
Hyperspectral imaging is a novel technology which allows for the collection of reflectance spectra of a sample in-situ and at a distance. A rapidly developing technology, hyperspectral imaging has been of particular interest in the field of art characterization, authentication, and conservation as it avoids the pitfalls of traditional characterization techniques and allows for the rapid and wide collection of data never before possible. It is hypothesized that by combining the power of hyperspectral imaging with machine learning, a new framework for the in-situ and automated characterization and authentication of artworks can be developed. This project, using the CMYK set of inks, began the preliminary development of such a framework. It was found that hyperspectral imaging and machine learning as a combination show significant potential as an avenue for art authentication, though further progress and research is needed to match the reliability of status quo techniques.
ContributorsChowdhury, Tanzil Aziz (Author) / Newman, Nathan (Thesis director) / Tongay, Sefaattin (Committee member) / School of Politics and Global Studies (Contributor) / Materials Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Studies on urban heat island (UHI) have been more than a century after the phenomenon was first discovered in the early 1800s. UHI emerges as the source of many urban environmental problems and exacerbates the living environment in cities. Under the challenges of increasing urbanization and future climate changes, there is a pressing need for sustainable adaptation/mitigation strategies for UHI effects, one popular option being the use of reflective materials. While it is introduced as one effective method to reduce temperature and energy consumption in cities, its impacts on multi-dimensional environmental sustainability and large-scale non-local effect are inadequately explored. This paper provides a synthetic overview of potential environmental impacts of reflective materials at a variety of scales, ranging from energy load on a single building to regional hydroclimate. The review shows that mitigation potential of reflective materials depends on a portfolio of factors, including building characteristics, urban environment, meteorological and geographical conditions, to name a few. Precaution needs to be exercised by city planners and policy makers for large-scale deployment of reflective materials before their environmental impacts, especially on regional hydroclimates, are better understood. In general, it is recommended that optimal strategy for UHI needs to be determined on a city-by-city basis, rather than adopting a “one-solution-fits-all” strategy.
ContributorsYang, Jiachuan (Contributor) / Wang, Zhi-Hua (Correspondent) / Kaloush, Kamil (Contributor)
Created2015-06-11
Description
Transition metal dichalcogenides (TMDs) are a family of layered crystals with the chemical formula MX2 (M = W, Nb, Mo, Ta and X = S, Se, Te). These TMDs exhibit many fascinating optical and electronic properties making them strong candidates for high-end electronics, optoelectronic application, and spintronics. The layered structure of TMDs allows the crystal to be mechanically exfoliated to a monolayer limit, where bulk-scale properties no longer apply and quantum effects arise, including an indirect-to-direct bandgap transition. Controllably tuning the electronic properties of TMDs like WSe2 is therefore a highly attractive prospect achieved by substitutionally doping the metal atoms to enable n- and p-type doping at various concentrations, which can ultimately lead to more effective electronic devices due to increased charge carriers, faster transmission times and possibly new electronic and optical properties to be probed. WSe2 is expected to exhibit the largest spin splitting size and spin-orbit coupling, which leads to exciting potential applications in spintronics over its similar TMD counterparts, which can be controlled through electrical doping. Unfortunately, the well-established doping technique of ion implantation is unable to preserve the crystal quality leading to a major roadblock for the electronics applications of tungsten diselenide. Synthesizing WSe2 via chemical vapor transport (CVT) and flux method have been previously established, but controllable p-type (niobium) doping WSe2 in low concentrations ranges (<1 at %) by CVT methods requires further experimentation and study. This work studies the chemical vapor transport synthesis of doped-TMD W1-xNbxSe2 through characterization techniques of X-ray Diffraction, Scanning Electron Microscopy, Energy Dispersive X-ray Spectroscopy, and X-ray Photoelectron Spectroscopy techniques. In this work, it is observed that excess selenium transport does not enhance the controllability of niobium doping in WSe2, and that tellurium tetrachloride (TeCl4) transport has several barriers in successfully incorporating niobium into WSe2.
ContributorsRuddick, Hayley (Author) / Tongay, Sefaattin (Thesis director) / Jiao, Yang (Committee member) / Barrett, The Honors College (Contributor) / Materials Science and Engineering Program (Contributor)
Created2024-05