Dissertations / Theses on the topic 'Dissertation'
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1
Kastner, Annett. "Inaugural-Dissertation." Doctoral thesis, Universitätsbibliothek Leipzig, 2004. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-37421.
Abstract:
Mit vorliegender Arbeit wurde geprüft, ob an Dislocatio abomasi (DA) erkrankte Rinder vor dem Auftreten klinischer Symptome Veränderungen im Fettstoffwechsel aufweisen und ob Beziehungen zum Endotoxin-Metabolismus bestehen. Dazu wurde ein breites Untersuchungsspektrum zum Fett- und Leberstoffwechsel [b-Hydroxy-Butyrat (BHB), Freie Fettsäuren (FFS), Cholesterol, Tria-cylglycerol (TG), Phospholipide (PL), a-, b-, prä-b-Lipoproteine (LP), Bilirubin, Aspartat-Amino-Transferase (ASAT), Gamma-Glutamyl-Transferase (GGT), Glutamat-Dehydrogenase (GLDH), Lactat-Dehy-drogenase (LDH), Glucose], freies Endotoxin, Endotoxineffektoren [Anti-Lipid A-Antikörper (IgG), C-reaktives Protein (CRP), Leukozytenzahl, Gesamteiweiß, Albumin, Eisen (Fe)] sowie Nat-rium (Na), Kalium (K), Calcium (Ca), Chlorid (Cl), Magnesium (Mg), anorganisches Phosphat, Harnstoff, Creatinin und die Creatinkinase im Blut untersuchtThe displacement of abomasum (DA) frequently occurs in high yielding dairy cows. There is a lack of knowledge of its etiology. This paper examines whether dairy cows with DA show changes in the fat metabolism already in the initial stage, i.e. before clinical symptoms occur. The paper also analyses whether a relationship exists between endotoxin and the fat metabolism. Therefore a large variety of parameters were examined in blood: parameters of the fat and liver metabolism (betahy-droxybutyrat, free fatty acids, cholesterol, TG, phospholipids, alpha-, beta- and pre-beta-lipoproteins, bilirubin, ASAT, GGT, GLDH, LDH, glucose), free endotoxin, anti-lipid-A-antibodies (IgG), C-reactive protein, number of leukocytes, total protein, albumin, Fe as well as Na, K, Ca, Cl, Mg, anorganic phosphate, urine, creatinin and creatinkinase
2
Contreras, Maria Elena. "Paradoja [dissertation]." Diss., Temple University Libraries, 2008. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/926.
Abstract:
Music CompositionD.M.A.
Paradoja: Concerto for Orchestra consists of three contrasting movements: slow, fast, slow (Paradoja = "paradox," Sp.). These movements are framed by a motif that opens and closes each of them, and connects them all. This framing motif is based on an alternation between a rhythmical pattern in the bass drum, and a melody sung by a boy mezzo-soprano, both over a string pedal. The first movement, Lamentos (Sorrows), is dramatic in character; it goes from simple to complex in its orchestration, harmony, texture, dynamics and tempo changes. The second movement, Algarabía (Tangle), reflects a festive affection; it presents a contrast to the first in character, tempo and spirit. The third movement, Sosiego (Serenity) provides a peaceful ending to the piece; it is lighter than the other two movements in texture and orchestration. The general harmonic language of Paradoja: Concerto for Orchestra is non-tonal yet centric, with surface references to functional harmony. However, the pitch content varies from movement to movement. The first movement is highly chromatic and based in the twelve-tone collection. The melodies are created by a combination of small pitch-class sets and sometimes are broken down and distributed among different instruments. Harmony is the result of the juxtaposition and counterpoint of these melodies, which vertically reiterate the same cells or creates new sets. The second movement is based on smaller collections than the first, and it is less chromatic. Contrast is often created by changing the collections or simply transposing them. The third movement is the most homophonic and the least chromatic of all three. It is based on a combination and juxtaposition of diatonic and non-diatonic collections that interact with each other. Paradoja: Concerto for Orchestra is examined in two broad categories. The first is a structural analysis, which includes details of form and pitch selection such as pitch collections, set classes and motives. The second is a stylistic analysis, which includes aspects of style such as rhythm, orchestration. The conclusion refers to the influence of historical models and aspects of the compositional process. Both the structural and stylistic analyses demonstrate how I have tried to merge diverse stylistic music elements to obtain a new personal idiom.
Temple University--Theses
3
deLise, Louis Anthony. "Marimba Rossa [dissertation]." Diss., Temple University Libraries, 2008. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/19912.
Abstract:
Music CompositionPh.D.
ABSTRACT Marimba Rossa is a three-movement concert piece for marimba and symphony orchestra. The 14-minute piece is written in the spirit of the Italian Baroque concertos of Antonio Vivaldi (the "Red Priest" for whom the piece is named), using a harmonic and rhythm language that is heavily influenced by the concert and pop music of the late twentieth-century. Marimba Rossa was composed with the concept of Ars Combinatoria in mind. First espoused by George Rochberg in 1973, Ars Combinatoria is concert music that uses musical gestures drawn from any musical tradition. The accompanying monograph provides a detailed history of the modern concert marimba and an account of the evolution of its concert and popular music repertoire. Specific information about the marimba's origins in Asia, its place in the Bible, the development of the European strohfiedel xylophone, the refinement of the instrument in America, and a discussion of the Guatemalan, Mexican, and Japanese
Temple University--Theses
4
Pantelides, Kate Lisbeth. "Mapping Dissertation Genre Ecology." Scholar Commons, 2013. http://scholarcommons.usf.edu/etd/4557.
Abstract:
Though the pervasive rumor that the “traditional” dissertation persists because of the “I suffered, so they too should suffer” mentality — the professor revenge theory — students are often the ones eager to pin down writing genres so that they can master them. However, hopes to stabilize and thus capture the secret or equation of the dissertation genre are futile, since genres, like language, are alive: rhetorical, evolving, and flexible. Thus, to demonstrate the contemporary context of the dissertation genre, the conflicting perspectives of university stakeholders, the forces working on the genre to enact change, and the process by which genre knowledge develops and transfers in the highest levels of university writing, Mapping Dissertation Genre Ecology explores the discourse, both written and spoken, which constitutes the dissertation as a discursive construct — what I call the dissertation genre ecology.
To better understand how dissertations are shaped institutionally, I ask the following questions: How is the dissertation as a genre constituted by various stakeholder groups at the university? How do these myriad accounts contribute to a larger system, a dissertation genre ecology at the university? And, ultimately, how does the dissertation genre ecology affect genre change? Through the use of rhetorical genre theory, my study develops a broad, interdisciplinary conception of genre, one that is not mired in formalistic worries about fixing genre in place. I use the voices of students and faculty from the humanities and social sciences as well as interdisciplinary documents as data for this project. By examining these discursive artifacts and making institutional tensions explicit, my project has broad implications for WAC/WID literature in transfer and genre studies.
5
Nixon, Julia Anne. "Building decoding fluency : a dissertation." Thesis, University of Canterbury. School of Educational Studies and Human Development, 2005. http://hdl.handle.net/10092/2946.
Abstract:
It has been recognised for many years that competent reading occurs only after a number
of component skills have been mastered. Many studies propose that a lack of phonemic
awareness underpins many of the difficulties children experience in learning to read. A
recent study, however, has suggested that 8 to 9-year old children who are struggling with
reading may be hampered more by poor decoding fluency rather than by inadequate
phonemic awareness. While many component skills of reading have been the focus of
research, there is scant research into interventions designed to build decoding fluency
directly. The present experiment attempted to increase decoding fluency in five, eight and
nine-year old low-progress readers using direct teaching techniques. In addition, the project
aimed to ascertain how long it would take to build decoding fluency and, once increased,
whether the improvement would generalise to faster prose reading. Analysis of the results
showed that it is possible to build decoding fluency directly and that faster decoding
generalises to faster prose reading. These findings have significant implications for both the
diagnosis of reading difficulties in eight and nine-year old children and the teaching of
children who are having difficulty in learning to read.
6
Foley, Virginia P. "Thesis and Dissertation Boot Camp." Digital Commons @ East Tennessee State University, 2018. https://dc.etsu.edu/etsu-works/5982.
7
Redd, Emily, and Virginia P. Foley. "Thesis and Dissertation Boot Camp." Digital Commons @ East Tennessee State University, 2017. https://dc.etsu.edu/etsu-works/5994.
Abstract:
The School of Graduate Studies at East Tennessee State University started the first Thesis and Dissertation Boot Camp program in the fall of 2012 by organizing a team of dedicated faculty and staff to help promote the Boot Camp and to run its sessions. Boot Camp at ETSU has since had great success with participation, positive student feedback, and student success. We have had 268 total registrations and 178 unique participants in Boot Camp from all stages of the writing process and of those who were close to finishing, 94 have graduated, many of whom have credited the Boot Camp program with their success. We advertise 21 to all ETSU graduate students, local and regional institutions, and although they were always welcome, we have recently expanded our advertising to Capstone Project students. Students from all of these groups have participated.
Boot Camp provides dedicated space and time to write free of distractions, with a variety of resources in the same room or just steps away. In this presentation, I will detail how, what, when, and who is involved in setting up and running our boot camps and provide an overview of our optional mini-workshops that are offered during each session. I will also provide an update on how our boot camp has evolved over the past five years and share some data that I am currently working on correlating boot camp attendance with graduation rates. Boot Camp models at other institutions will also be presented for comparison along with tips for setting up a boot camp at your institution.
Another update for this presentation is a personal one. I would like to credit Boot Camp for my own professional growth. Working with boot campers through personal, professional, and academic challenges has tested my ability to be a leader and inspire others to persevere. Boot Camp continues to be a source of pride for me and the School of Graduate Studies at ETSU and I would love the opportunity to share the program again with representatives from other institutions.
8
Quante, Jochen. "Dynamic object process graphs : Dissertation /." Münster : Verl.-Haus Monsenstein und Vannerdat, 2009. http://d-nb.info/994328753/04.
9
Boulton, April Marie. "A summary of dissertation research /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2003. http://uclibs.org/PID/11984.
10
Williams, Anna. "My Gothic dissertation: a podcast." Diss., University of Iowa, 2019. https://ir.uiowa.edu/etd/7046.
Abstract:
In My Gothic Dissertation, I perform an intertextual analysis of Gothic fiction and modern-day graduate education in the humanities. First, looking particularly at the Female Gothic, I argue that the genre contains overlooked educational themes. I read the student-teacher relationships in Ann Radcliffe’s The Mysteries of Udolpho (1794), Mary Shelley’s Frankenstein (1818, 1831), and Charlotte Brontë’s Villette (1853) as critiques of the insidious relationship between knowledge and power. Part literary critic and part literary journalist, I weave through these readings reports of real-life ‘horror stories’ of graduate school, arguing that the power imbalance between Ph.D. advisors and their students can be unexpectedly ‘Gothic’ as well. Drawing on research from the science of learning—developmental psychology, sociology, and pedagogical theory—I advocate for more a student-centered pedagogy in humanities Ph.D. training.
Following in the footsteps of A.D. Carson and Nick Sousanis, I have produced My Gothic Dissertation in a nontraditional format—the podcast. Mixing voice, music, and sound, I dramatize scenes from the novels and incorporate analysis through my narration. The real-life “Grad School Gothic” stories are drawn from personal interviews. Much of the science of learning is drawn from personal interviews with researchers as well, though some material comes from recorded presentations that have been posted to public, online venues such as YouTube. The creative/journalistic style of reporting is heavily influenced by programs such as This American Life, Invisibilia, and Serial, with the dual aims of engaging a broad audience and expanding our modes of scholarly communication beyond the page.
11
Wieland, Nellie Claire. "Scribbledehobble a dissertation on linguistic agency /." Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3259063.
Abstract:
Thesis (Ph. D.)--University of California, San Diego, 2007.Title from first page of PDF file (viewed June 21, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 197-213).
12
Manning, Benjamin J. "ATP-Dependent Heterochromatin Remodeling: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/795.
Abstract:
Eukaryotic DNA is incorporated into the nucleoprotein structure of chromatin. This structure is essential for the proper storage, maintenance, regulation, and function of the genomes’ constituent genes and genomic sequences. Importantly, cells generate discrete types of chromatin that impart distinct properties on genomic loci; euchromatin is an open and active compartment of the genome, and heterochromatin is a restricted and inactive compartment. Heterochromatin serves many purposes in vivo, from heritably silencing key gene loci during embryonic development, to preventing aberrant DNA repeat recombination. Despite this generally repressive role, the DNA contained within heterochromatin must still be repaired and replicated, creating a need for regulated dynamic access into silent heterochromatin. In this work, we discover and characterize activities that the ATP-dependent chromatin remodeling enzyme SWI/SNF uses to disrupt repressive heterochromatin structure.
First, we find two specific physical interactions between the SWI/SNF core subunit Swi2p and the heterochromatin structural protein Sir3p. We find that disrupting these physical interactions results in a SWI/SNF complex that can hydrolyze ATP and slide nucleosomes like normal, but is defective in its ability to evict Sir3p off of heterochromatin. In vivo, we find that this Sir3p eviction activity is required for proper DNA replication, and for establishment of silent chromatin, but not for SWI/SNF’s traditional roles in transcription. These data establish new roles for ATP-dependent chromatin remodeling in regulating heterochromatin.
Second, we discover that SWI/SNF can disrupt heterochromatin structures that contain all three Sir proteins: Sir2p, Sir3p and Sir4p. This new disruption activity requires nucleosomal contacts that are essential for silent chromatin formation in vivo. We find that SWI/SNF evicts all three heterochromatin proteins off of chromatin. Surprisingly, we also find that the presence of Sir2p and Sir4p on chromatin stimulates SWI/SNF to evict histone proteins H2A and H2B from nucleosomes. Apart from discovering a new potential mechanism of heterochromatin dynamics, these data also establish a new paradigm of chromatin remodeling enzyme regulation by nonhistone proteins present on the substrate.
13
Munevar, Steven. "Mechanics of Fibroblast Migration: a Dissertation." eScholarship@UMMS, 2003. https://escholarship.umassmed.edu/gsbs_diss/36.
Abstract:
Cell migration involves complex mechanical interactions between cells or between cells and the underlying substrate. Using a newly developed technique, "traction force microscopy", I have been able to visualize the dynamic characteristics of mechanical forces exerted by migrating fibroblasts such as magnitude, direction, and shear. For NIH 3T3 fibroblasts, I found that the lamellipodium provides nearly all of the force necessary for cell migration. A high shear zone separates the lamellipodium from the remainder of the cell body, suggesting that they are mechanically distinct entities. The timing of the tractions at the leading edge, as well as the spatial distribution, bears no apparent relationship to concurrent local protrusive activities, yet changes in traction force patterns often precede changes in migration direction. In H-ras transformed cells I found isolated regions of weak, transient traction forces in pseudopods all along the cell that appeared to act against one another. The resulting shear pattern suggested that there were multiple disorganized mechanical domains. These results support a frontal towing model for cell migration where the dynamic traction forces at the leading edge served to actively pull the cell body forward. In H-ras transformed cells, the weak poorly coordinated traction forces coupled with weak cell substrate-adhesions were likely responsible for the abnormal motile behavior of these cells. To probe the mechanical interactions beneath various regions of migrating fibroblasts, a cell substrate inhibitor (GRGDTP peptide) was locally applied while imaging stress distribution on the substrate utilizing traction force microscopy. I found that both spontaneous and GRGDTP induced detachment of the trailing edge resulted in extensive cell shortening with no change in overall traction force magnitude or cell migration. Conversely, leading edge disruption resulted in a dramatic global loss of traction forces pnor to any significant cell shortening. These results suggested that fibroblasts transmit their contractile forces to the substrate through two distinct types of adhesions. Leading edge adhesions were unique in their ability to transmit active propulsive forces whereas trailing end adhesions created passive resistance during cell migration and readily redistributed their loads upon detachment. I have also investigated how fibroblasts regulate traction forces based on mechanical input. My results showed that stretching forces applied through the flexible substrate induced increases in both intracellular calcium concentration and traction forces in fibroblasts. Treatment with gadolinium, a well known stretch-activated ion channel inhibitor, was found to inhibit both traction forces and cell migration without inhibiting cellular spread morphology or protrusive activities. Gadolinium treatment also caused a pronounced decrease in vinculin and phosphotyrosine concentrations from focal adhesions. Local application of gadolinium to the trailing region had no detectable effect on overall traction forces or cell migration, whereas local application to the leading edge caused a global inhibition of traction forces and an inhibition of migration. These observations suggest that stretch activated entry of calcium ions in the frontal region serves to regulate the organization of focal adhesions and the output of mechanical forces. Together my experiments elucidate how fibroblasts exert mechanical forces to propel their movements, and how fibroblasts utilize mechanical input to regulate their movements.
14
Loury, Sharon D. "From Dissertation to Program of Research." Digital Commons @ East Tennessee State University, 2010. https://dc.etsu.edu/etsu-works/8200.
15
Donahue, Christine Patricia. "Intracellular Hairpin Ribozyme Catalysis: a Dissertation." eScholarship@UMMS, 1999. https://escholarship.umassmed.edu/gsbs_diss/172.
Abstract:
Ribozymes are catalytic RNA molecules capable of performing functions normally attributed to proteins. The hairpin ribozyme is derived from the (-) strand of the satellite RNA of Tobacco Ringspot Virus, where it functions in processing rolling circle transcription intermediates. The hairpin ribozyme catalyzes the breaking of a phosphodiester bond to form a 2'-3' cyclic phosphate and a 5' OH on the product termini. RNA substrates are recognized through Watson Crick base pairs. In theory, ribozymes are able to cleave any RNA that forms the correct secondary structure. Therefore, ribozymes have been designed to recognize specific targets through base pair interactions with the substrate recognition sequence of the ribozyme. This feature of catalytic RNAs gives them endless potential as antisense reagents.
While tremendous effort has gone into elucidating the kinetic mechanism of ribozymes in vitro, very few studies have addressed ribozyme function in the intracellular environment. Previous studies have had varying success. And while in some cases ribozymes have clearly reduced gene expression, the experiments were not quantitative and did not provide any information regarding the kinetic pathway of catalysis in vivo. Improved understanding of intracellular cleavage reactions requires the development of a system that can directly measure cleavage rates in vivo.
Utilizing a self-cleaving ribozyme cassette inserted into the yeast PGK1 gene we have developed a system to detect ribozyme cleavage products and directly measure the cleavage rates of the hairpin ribozyme in yeast. Furthermore, we have performed controls confirming detected cleavage activity is reflective of intracellular catalysis.
As ribozyme activity requires the formation of a catalytically active structure, cleavage can act as a monitor for the assembly of a functional molecule. We have used this system to address the effect of helix stability on intracellular hairpin ribozyme activity.
The results of these experiments have important implications for the design of antisense ribozymes. Furthermore, catalysis by small RNAs in vivo serves as a model system for more complex RNA catalyzed reactions that are implicated in mRNA processing and translation.
16
Manning, Benjamin J. "ATP-Dependent Heterochromatin Remodeling: A Dissertation." eScholarship@UMMS, 2009. http://escholarship.umassmed.edu/gsbs_diss/795.
Abstract:
Eukaryotic DNA is incorporated into the nucleoprotein structure of chromatin. This structure is essential for the proper storage, maintenance, regulation, and function of the genomes’ constituent genes and genomic sequences. Importantly, cells generate discrete types of chromatin that impart distinct properties on genomic loci; euchromatin is an open and active compartment of the genome, and heterochromatin is a restricted and inactive compartment. Heterochromatin serves many purposes in vivo, from heritably silencing key gene loci during embryonic development, to preventing aberrant DNA repeat recombination. Despite this generally repressive role, the DNA contained within heterochromatin must still be repaired and replicated, creating a need for regulated dynamic access into silent heterochromatin. In this work, we discover and characterize activities that the ATP-dependent chromatin remodeling enzyme SWI/SNF uses to disrupt repressive heterochromatin structure.
First, we find two specific physical interactions between the SWI/SNF core subunit Swi2p and the heterochromatin structural protein Sir3p. We find that disrupting these physical interactions results in a SWI/SNF complex that can hydrolyze ATP and slide nucleosomes like normal, but is defective in its ability to evict Sir3p off of heterochromatin. In vivo, we find that this Sir3p eviction activity is required for proper DNA replication, and for establishment of silent chromatin, but not for SWI/SNF’s traditional roles in transcription. These data establish new roles for ATP-dependent chromatin remodeling in regulating heterochromatin.
Second, we discover that SWI/SNF can disrupt heterochromatin structures that contain all three Sir proteins: Sir2p, Sir3p and Sir4p. This new disruption activity requires nucleosomal contacts that are essential for silent chromatin formation in vivo. We find that SWI/SNF evicts all three heterochromatin proteins off of chromatin. Surprisingly, we also find that the presence of Sir2p and Sir4p on chromatin stimulates SWI/SNF to evict histone proteins H2A and H2B from nucleosomes. Apart from discovering a new potential mechanism of heterochromatin dynamics, these data also establish a new paradigm of chromatin remodeling enzyme regulation by nonhistone proteins present on the substrate.
17
Leonard, Deborah Marie. "Mechanisms of Endocytic Sorting: A Dissertation." eScholarship@UMMS, 2006. https://escholarship.umassmed.edu/gsbs_diss/245.
Abstract:
Endocytosis is important for the regulation of signal transduction and for the movement of essential cellular components from outside the cell to their appropriate intracellular compartment(s). Two established mechanisms of endocytosis are clathrinmediated (CME) and clathrin-independent endocytosis, and they are responsible for internalization of different ligands. In this study, the newly established technique of total internal reflection fluorescent microscopy (TIRF-M) was used, along with standard biochemical and molecular biological tools, to systematically study the sorting and early trafficking of two established ligands of endocytosis, transferrin (Tf) and epidermal growth factor (EGF).
TIRF-M studies revealed that Tf binds its receptor that is located in large clathrin arrays positioned just below the surface of the cell and that these large clathrin platforms serves as the major site of CME at the plasma membrane. EGF endocytosis is very different and occurs as follows 1) the liganded EGFR recruits Rab5 to the plasma membrane, 2) Rab5 concentrates around vesicles containing liganded EGFR and 3) these vesicles co-localize with EEA1 enriched endosomes. EEA1 was shown to play a pivotal role in EGF endocytosis, establishing a new role for EEA1 in vesicle trafficking in addition to its role in tethering and fusion. Finally, WDFY2, a new FYVE domain protein was shown to decorate a specific subset of vesicles, upstream of the EEA1 vesicle pool that appear to participate in Tf endocytosis. These studies establish new functions and components of endocytosis that enhances our understanding of this complex process.
18
Chen, Xiaochu. "Nuclear Import of Smad: A Dissertation." eScholarship@UMMS, 2011. https://escholarship.umassmed.edu/gsbs_diss/560.
Abstract:
Signal transduction by transforming growth factor β (TGF-β) cytokines is mediated by an evolutionarily conserved mechanism that depends on the Smad proteins to transduce an extracellular stimulus into the nucleus. In the unstimulated state, Smads spontaneously shuttle across the nuclear envelope and distribute throughout the cell. Upon TGF-β or bone morphogenetic protein (BMP) stimulation, the receptor-activated Smads are phosphorylated, assemble into complexes with Smad4, and become mostly localized in the nucleus. Such signal-induced nuclear translocation of activated Smads is essential for TGF-β–dependent gene regulation that is critical for embryonic development and homeostasis. The molecular machinery responsible for this process, especially how the activated Smads are imported as complexes, is not entirely clear. Thus, I became interested in investigating the molecular requirements for nuclear targeting of Smads upon stimulation.
Recently, whole-genome RNAi screening offers a complementary cell-based approach to functionally identify molecules that mediate nuclear accumulation of Smads in response to TGF-β. In the first part of this dissertation, I performed a genome-wide RNAi screen that uncovered the importin moleskin (Msk) required in nuclear import of Dpp-activated MAD. Both genetic and biochemical studies further confirmed this finding. I also investigated Smad interactions with the Msk mammalian orthologues, Importin7 and 8 and validated that Smads are bona fide cargos of Imp7/8.
Besides the importin Msk, the screen also uncovered a subset of nucleoporins as required factors in signal-induced nuclear accumulation of MAD. Thus in the second part of this thesis, I focused on how the NPC mediates this Msk-dependent nuclear import of activated MAD. Most of these nucleoporins, including Sec13, Nup75, Nup93 and Nup205, were thought to be structural nucleoporins without known cargo-specific functions. We, however, demonstrated that this subset of nucleoporins was specifically used in the Msk-dependent nuclear import of activated MAD but not the constitutive import of cargos containing a classic nuclear localization signal (cNLS). I also uncovered novel pathway-specific functions of Sec13 and Nup93.
Regulation of TGF-β signaling can be achieved not only by modulating Smad nuclear translocation but also by modifying Smad phosphorylation status. Previously we identified a kinase, Misshapen (Msn), that caused the linker phosphorylation of MAD, resulting in negative regulation of Dpp signaling (Drosophila BMP). In the third part of this thesis, I investigated the biological relevance of Msn kinase to Dpp signaling in Drosophila wings. Both over-expression and RNAi studies suggest that Msn is a negative regulator of the Dpp/MAD pathway in vivo.
As a whole, my findings delineated two critical requirements for MAD nuclear import: the importin Msk and a unique subset of nucleoporins. For the first time, structural Nups are implicated in the direct involvement of cargo import, providing a unique trans-NPC mechanism.
19
Moore, Nathan F. "Slow-Cycling Cancer Cells: A Dissertation." eScholarship@UMMS, 2012. https://escholarship.umassmed.edu/gsbs_diss/620.
Abstract:
Tumor recurrence after chemotherapy is a major cause of patient morbidity and mortality. Recurrences are thought to be due to small subsets of stem-like cancer cells that are able to survive chemotherapy and drive tumor re-growth. A more complete understanding of stem-like cancer cell regulation is required to develop therapies to better target and eliminate these cells.
Slow-cycling stem cells are integral components of adult epithelial tissues and may give rise to cancer stem cell populations that share similar characteristics. These slow-cycling adult stem cells are inherently resistant to traditional forms of chemotherapy and transference of this characteristic may help to explain therapy resistance in cancer stem cell populations. Using a novel application for the proliferation marker CFSE, we have identified populations of slow-cycling cancer cells with tumor initiating capabilities. As predicted, slow-cycling cancer cells exhibit a multi-fold increase in chemotherapy resistance and retain the ability to re-enter the cell cycle. Furthermore, we observed consistent over-expression of the CDK5 activator, p35, in slow-cycling cancer cells. Manipulation of p35 expression in cancer cells affects cell cycle distribution and survival when these cells are treated with traditional forms of chemotherapy. Additionally, we demonstrate that alterations in p35 expression affect BCL2 levels, suggesting a mechanism for the survival phenotype.
Combined, our data suggest a model whereby slow-cycling stem-like cancer cells utilize the p35/CDK5 complex to slow cell cycling speed and promote resistance to chemotherapy. Future p35 targeting, in combination with traditional forms of chemotherapy, may help eliminate these cells and reduce tumor recurrence rates, increasing long-term patient survival.
20
Bi, Sheng. "Dissertation on competitive and directed search." Thesis, Paris 1, 2015. http://www.theses.fr/2015PA010045/document.
Abstract:
Nous prenons l’approche d’annonce des salaires avec la recherche d’emploi à étudier trois problèmes dans le marché du travail. Le premier problème concerne l’arrêt de travail prématuré des travailleurs. Tel arrêt de travail prématuré crée des risques de chiffre d’affaires pour les entreprises, donc les entreprises veulent proposer des profils de salaire pour minimiser ces risques. Dans ce problème, l’asymétrie de l’information joue un rôle important. Nous adoptons une approche du mécanisme design et considérons les différents timings auxquels l’information privée est réalisée. Dans un papier de suivi, nous proposons une politique d’Age spécifique par laquelle cette inefficacité peut être atténuée, et étudions son implication sur le bien-être et la production globale. Dans le deuxième problème, nous revisitons l’analyse du bien-être de l’impact de la discrimination sur le choix des compétences sous une norme d’embauche multidimensionnelle le long des caractéristiques qui sont soit liées à la productivité soit indépendantes de la productivité. Nous montrons comment l’investissement de compétences stratégique entre le groupe favorise et discrimine se pose. Nous comparons également deux mécanismes de détermination des salaires (salaire annoncé et négocié) pour vérifier la robustesse de résultats. Dans le troisième problème, nous considérons dans quelle mesure l’allocation de chômage et le salaire minimum peuvent corriger les répartitions inefficaces découlant du pouvoir de marche des firmes. Notre contexte concerne les petits marchés ou le ratio travailleurs/firmes ne soit pas grand. L’imperfection de marche vient du fait qu’au marché du travail à petite échelle les firmes paient un niveau de salaire moins que le niveau compétitif. Nous procédons à partir d’un point de vue d’organisation industrielle, et proposons en se concentrant sur la mauvaise répartition d’emploi et de surplus lors de l’analyse de l’efficacité de l’instrument de la politiqueWe take the wage posting approach with search friction to study three issues in labor market. The first issue concerns the premature quitting of workers. Our framework is suitable for contexts such as disability shock, retirement, maternity leaves etc. Such premature quitting creates turnover risks for firms, hence the firms propose wage profiles to minimize or avoid it. In this issue, the asymmetric information plays an important role. We adopt an approach of mechanism design and consider different timings at which the private information is realized. In a follow-up paper, we propose an age-directed policy by which this inefficiency can be alleviated and study its implication on welfare and aggregate output. In the second issue, we revisit welfare analysis of impact of discrimination on skill choice under a multi-dimensional hiring norm along both productivity-related and -unrelated characteristics. We show how strategic skill investment between favored and discriminated group arise. We compare also two wage determination mechanisms (posted and bargained wage). In the third issue, we consider to which extent can the roles of unemployment benefit and minimum wage correct inefficient allocations arising from firms’ market power. Our context concerns small markets where the workers/firms ratio is not large. The market imperfection comes from the fact that in such a small market firms pay less than competitive level of wages. We proceed from an industrial organizational perspective and suggest focusing on both misallocation of labor and surplus when analyzing the effectiveness of the policy instrument
21
Banks, Eric A. "Connexin 45.6 in lens development : a dissertation /." San Antonio : UTHSC, 2007. http://proquest.umi.com/pqdweb?did=1400957401&sid=1&Fmt=2&clientId=70986&RQT=309&VName=PQD.
22
Freier, Andreas [Verfasser]. "Integrative Modellierung metabolischer Netzwerke : Dissertation / Andreas Freier." Aachen : Shaker, 2005. http://d-nb.info/1186587652/34.
23
Yang, Chao-Shun. "Molecular Landscape of Induced Reprogramming: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/698.
Abstract:
Recent breakthroughs in creating induced pluripotent stem cells (iPS cells) provide alternative means to obtain embryonic stem (ES) cell-like cells without destroying embryos by introducing four reprogramming factors (Oct3/4, Sox2, and Klf4/c-Myc or Nanog/Lin28) into somatic cells. However, the molecular basis of reprogramming is largely unknown. To address this question, we employed microRNAs, small molecules, and conducted genome-wide RNAi screen, to investigate the regulatory mechanisms of reprogramming.
First we showed that depleting miR-21 and miR-29a enhances reprogramming in mouse embryonic fibroblasts (MEFs). We also showed that p53 and ERK1/2 pathways are regulated by miR-21 and miR-29a and function in reprogramming.
Second, we showed that computational chemical biology combined with genomic analysis can be used to identify small molecules regulating reprogramming. We discovered that the NSAID Nabumetone and the anti-cancer drug OHTM could replace Sox2 during reprogramming. Nabumetone could also replace c-Myc or Sox2 without compromising self-renewal and pluripotency of derived iPS cells.
To identify the cell-fate determinants during reprogramming, we integrated a genome-wide RNAi screen with transcriptome analysis to dissect the molecular requirements in reprogramming. We found that extensive interactions of embryonic stem cell core circuitry regulators are established in mature iPS cells, including Utf1, Nr6a1, Tdgf1, Gsc, Fgf10, T, Chrd, Dppa3, Fgf17, Eomes, Foxa2. Remarkably, genes with non-differential change play the most critical roles in the transitions of reprogramming. Functional validation showed that some genes act as essential or barrier roles to reprogramming. We also identified several genes required for maintaining ES cell properties. Altogether, our results demonstrate the significance of miRNA function in regulating multiple signaling networks involved in reprogramming. And our work further advanced the reprogramming field by identifying several new key modulators.
24
Nayar, Ribhu. "IRF4 Does the Balancing Act: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/746.
Abstract:
CD8+ T cell differentiation is a complex process that requires integration of signals from the TCR, co-stimulatory molecules and cytokines. Ligation of the peptide-MHC complex with the cognate TCR initiates a downstream signaling cascade of which the IL-2 inducible T-cell kinase (ITK) is a key component. Loss of ITK results in a measured reduction in T cell activation. Consequently, Itk deficient mice have defects in thymic selection, CD8+ T cell expansion and differentiation in response to virus infections, and generate a unique population of innate-like CD8+ T cells. The mechanisms that translate TCR and ITK-derived signals into distinct gene transcription programs that regulate CD8+ T cell differentiation are not defined. Our microarray screen identified IRF4 as a potential transcription factor mediating the differentiation of innate-like T cells, and antiviral CD8+ T cell in response to acute and chronic LCMV infections.
Innate-like CD8+ T cells are characterized by their high expression of CD44, CD122, CXCR3, and the transcription factor Eomesodermin (Eomes). One component of this altered development is a non-CD8+ T cell-intrinsic role for IL-4. We show that IRF4 expression is induced upon TCR signaling and is dependent on ITK activity. In contrast to WT cells, activation of IRF4-deficient CD8+ T cells leads to rapid and robust expression of Eomes, which is further enhanced by IL-4 stimulation. These data indicate that ITK signaling promotes IRF4 up-regulation following CD8+ T cell activation and that this signaling xii pathway normally suppresses Eomes expression, thereby regulating the differentiation pathway of CD8+ T cells.
ITK deficient mice also have reduced expansion of CD8+ T cells in response to acute LCMV infections. We show that IRF4 is transiently upregulated to differing levels in murine CD8+ T cells, based on the strength of TCR signaling. In turn, IRF4 controls the magnitude of the CD8+ T cell response to acute virus infection in a dose-dependent manner. Furthermore, the expression of key transcription factors such as T cell factor 1 and Eomesodermin are highly sensitive to graded levels of IRF4. In contrast, T-bet expression is less dependent on IRF4 levels and is influenced by the nature of the infection. These data indicate that IRF4 is a key component that translates the strength of TCR signaling into a graded response of virus-specific CD8+ T cells.
The data from these studies indicated a pivotal role of IRF4 in regulating the expression of T-bet and Eomes. During persistent LCMV infections, CD8+ T cells differentiate into T-bethi and Eomeshi subsets, both of which are required for efficient viral control. We show that TCR signal strength regulates the relative expression of T-bet and Eomes in antigen-specific CD8+ T cells by modulating levels of IRF4. Reduced IRF4 expression results in skewing of this ratio in favor of Eomes, leading to lower proportions and numbers of T-bet+ Eomes- precursors and poor control of LCMV Clone 13 infection. Altering this ratio in favor of T-bet xiii restores the differentiation of T-bet+ Eomes- precursors and the protective balance of T-bet to Eomes required for efficient viral control. These data highlight a critical role for IRF4 in regulating protective anti-viral CD8+ T cell responses by ensuring a balanced ratio of T-bet to Eomes, leading to the ultimate control of this chronic viral infection.
25
Bennett, Gwendolyn M. "Chromatin Regulators and DNA Repair: A Dissertation." eScholarship@UMMS, 2014. https://escholarship.umassmed.edu/gsbs_diss/742.
Abstract:
DNA double-strand break (DSB) repair is essential for maintenance of genome stability. However, the compaction of the eukaryotic genome into chromatin creates an inherent barrier to any DNA-mediated event, such as during DNA repair. This demands that there be mechanisms to modify the chromatin structure and thus access DNA. Recent work has implicated a host of chromatin regulators in the DNA damage response and several functional roles have been defined. Yet the mechanisms that control their recruitment to DNA lesions, and their relationship with concurrent histone modifications, remain unclear. We find that efficient DSB recruitment of many yeast chromatin regulators is cell-cycle dependent. Furthering this, we find recruitment of the INO80, SWR-C, NuA4, SWI/SNF, and RSC enzymes is inhibited by the non-homologous end joining machinery, and that their recruitment is controlled by early steps of homologous recombination. Strikingly, we find no significant role for H2A.X phosphorylation (γH2AX) in the recruitment of chromatin regulators, but rather that their recruitment coincides with reduced levels of γH2AX. We go on to determine the chromatin remodeling enzyme Fun30 functions in histone dynamics surround a DSB, but does not significantly affect γH2AX dynamics. Additionally, we describe a conserved functional interaction among the chromatin remodeling enzyme, SWI/SNF, the NuA4 and Gcn5 histone acetyltransferases, and phosphorylation of histone H2A.X. Specifically, we find that the NuA4 and Gcn5 enzymes are both required for the robust recruitment of SWI/SNF to a DSB, which in turn promotes the phosphorylation of H2A.X.
26
Dobson, Jason R. "Nuclear Organization in Breast Cancer: A Dissertation." eScholarship@UMMS, 2013. https://escholarship.umassmed.edu/gsbs_diss/650.
Abstract:
The nuclear matrix (NM) is a fibrogranular network of ribonucleoproteins upon which transcriptional complexes and regulatory genomic sequences are organized. A hallmark of cancer is the disorganization of nuclear architecture; however, the extent to which the NM is involved in malignancy is not well studied.
The RUNX1 and RUNX2 proteins form complexes within the NM to promote hematopoiesis and osteoblastogenesis, respectively at the transcriptional level. RUNX1 and RUNX2 are both expressed in breast cancer cells (BrCCs); however, their genome-wide BrCC functions are unknown. RUNX1 and RUNX2 activate many tumor suppressor pathways in blood and bone lineages, respectively, including attenuation of protein synthesis and cell growth via suppression of ribosomal RNA (rRNA) transcription, which appears contrary to Runx-expression in highly proliferative BrCCs. To define roles for RUNX1 and RUNX2 in BrCC phenotype, we examined the involvement of RUNX1 and RUNX2 in rRNA transcription and generated a genome-wide model for RUNX1 and RUNX2-binding and transcriptional regulation. To validate gene expression patterns identified in our screen, we developed a Real-Time qPCR primer design program, which allows rapid, high-throughput design of primer pairs (FoxPrimer). In BrCCs, RUNX1 and RUNX2 regulate genes that promote invasiveness and do not affect rRNA transcription, protein synthesis, or cell growth. We have characterized in vitro functions of Runx proteins in BrCCs; however, the relationships between Runx expression and diagnostic/prognostic markers of breast cancer (BrCa) in patients are not well studied. Immunohistochemical detection of RUNX1 and RUNX2 in BrCa tissue microarrays reveals RUNX1 expression is associated with early, smaller tumors that are ER+ (estrogen receptor), HER2+, p53-, and correlated with androgen receptor (AR) expression; RUNX2 expression is associated with late-stage, larger tumors that are HER2+. These results show that the functions and expression patterns of NM-associated RUNX1 and RUNX2 are context-sensitive, which suggests potential disease-specific roles.
Two functionally disparate genomic sequence types bind to the NM: matrix associated regions (MARs) are functionally associated with transcriptional repression and scaffold associated regions (SARs) are functionally associated with actively expressed genes. It is unknown whether malignant nuclear disorganization affects the functions of MARs/SARs in BrCC. We have refined a method to isolate nuclear matrix associated DNA (NM-DNA) from a structurally preserved NM and applied this protocol to normal mammary epithelial cells and BrCCs. To define transcriptional functions for NM-DNA, we developed a computational algorithm (PeaksToGenes), which statistically tests the associations of experimentally-defined NM-DNA regions and ChIP-seq-defined positional enrichment of several histone marks with transcriptome-wide gene expression data. In normal mammary epithelial cells, NM-DNA is enriched in both MARs and SARs, and the positional enrichment patterns of MARs and SARs are strongly associated with gene expression patterns, suggesting functional roles. In contrast, the BrCCs are significantly enriched in the silencing mark H3K27me3, and the NM-DNA is enriched in MARs and depleted of SARs. The MARs/SARs in the BrCCs are only weakly associated with gene expression patterns, suggesting that loss of normal DNA-matrix associations accompanies the disease state. Our results show that structural preservation of the in situ NM allows isolation of both MARs and SARs, and further demonstrate that in a disorganized, cancerous nucleus, normal transcriptional functions of NM-DNA are disrupted.
Our studies on nuclear organization in BrCC, show that the disorganized phenotype of the cancer cell nucleus is accompanied by deregulated transcriptional functions of two constituents of the NM. These results reinforce the role of the NM as an important structure-function component of gene expression regulation.
27
Dobson, Jason R. "Nuclear Organization in Breast Cancer: A Dissertation." eScholarship@UMMS, 2004. http://escholarship.umassmed.edu/gsbs_diss/650.
Abstract:
The nuclear matrix (NM) is a fibrogranular network of ribonucleoproteins upon which transcriptional complexes and regulatory genomic sequences are organized. A hallmark of cancer is the disorganization of nuclear architecture; however, the extent to which the NM is involved in malignancy is not well studied.
The RUNX1 and RUNX2 proteins form complexes within the NM to promote hematopoiesis and osteoblastogenesis, respectively at the transcriptional level. RUNX1 and RUNX2 are both expressed in breast cancer cells (BrCCs); however, their genome-wide BrCC functions are unknown. RUNX1 and RUNX2 activate many tumor suppressor pathways in blood and bone lineages, respectively, including attenuation of protein synthesis and cell growth via suppression of ribosomal RNA (rRNA) transcription, which appears contrary to Runx-expression in highly proliferative BrCCs. To define roles for RUNX1 and RUNX2 in BrCC phenotype, we examined the involvement of RUNX1 and RUNX2 in rRNA transcription and generated a genome-wide model for RUNX1 and RUNX2-binding and transcriptional regulation. To validate gene expression patterns identified in our screen, we developed a Real-Time qPCR primer design program, which allows rapid, high-throughput design of primer pairs (FoxPrimer). In BrCCs, RUNX1 and RUNX2 regulate genes that promote invasiveness and do not affect rRNA transcription, protein synthesis, or cell growth. We have characterized in vitro functions of Runx proteins in BrCCs; however, the relationships between Runx expression and diagnostic/prognostic markers of breast cancer (BrCa) in patients are not well studied. Immunohistochemical detection of RUNX1 and RUNX2 in BrCa tissue microarrays reveals RUNX1 expression is associated with early, smaller tumors that are ER+ (estrogen receptor), HER2+, p53-, and correlated with androgen receptor (AR) expression; RUNX2 expression is associated with late-stage, larger tumors that are HER2+. These results show that the functions and expression patterns of NM-associated RUNX1 and RUNX2 are context-sensitive, which suggests potential disease-specific roles.
Two functionally disparate genomic sequence types bind to the NM: matrix associated regions (MARs) are functionally associated with transcriptional repression and scaffold associated regions (SARs) are functionally associated with actively expressed genes. It is unknown whether malignant nuclear disorganization affects the functions of MARs/SARs in BrCC. We have refined a method to isolate nuclear matrix associated DNA (NM-DNA) from a structurally preserved NM and applied this protocol to normal mammary epithelial cells and BrCCs. To define transcriptional functions for NM-DNA, we developed a computational algorithm (PeaksToGenes), which statistically tests the associations of experimentally-defined NM-DNA regions and ChIP-seq-defined positional enrichment of several histone marks with transcriptome-wide gene expression data. In normal mammary epithelial cells, NM-DNA is enriched in both MARs and SARs, and the positional enrichment patterns of MARs and SARs are strongly associated with gene expression patterns, suggesting functional roles. In contrast, the BrCCs are significantly enriched in the silencing mark H3K27me3, and the NM-DNA is enriched in MARs and depleted of SARs. The MARs/SARs in the BrCCs are only weakly associated with gene expression patterns, suggesting that loss of normal DNA-matrix associations accompanies the disease state. Our results show that structural preservation of the in situ NM allows isolation of both MARs and SARs, and further demonstrate that in a disorganized, cancerous nucleus, normal transcriptional functions of NM-DNA are disrupted.
Our studies on nuclear organization in BrCC, show that the disorganized phenotype of the cancer cell nucleus is accompanied by deregulated transcriptional functions of two constituents of the NM. These results reinforce the role of the NM as an important structure-function component of gene expression regulation.
28
Bennett, Gwendolyn M. "Chromatin Regulators and DNA Repair: A Dissertation." eScholarship@UMMS, 2012. http://escholarship.umassmed.edu/gsbs_diss/742.
Abstract:
DNA double-strand break (DSB) repair is essential for maintenance of genome stability. However, the compaction of the eukaryotic genome into chromatin creates an inherent barrier to any DNA-mediated event, such as during DNA repair. This demands that there be mechanisms to modify the chromatin structure and thus access DNA. Recent work has implicated a host of chromatin regulators in the DNA damage response and several functional roles have been defined. Yet the mechanisms that control their recruitment to DNA lesions, and their relationship with concurrent histone modifications, remain unclear. We find that efficient DSB recruitment of many yeast chromatin regulators is cell-cycle dependent. Furthering this, we find recruitment of the INO80, SWR-C, NuA4, SWI/SNF, and RSC enzymes is inhibited by the non-homologous end joining machinery, and that their recruitment is controlled by early steps of homologous recombination. Strikingly, we find no significant role for H2A.X phosphorylation (γH2AX) in the recruitment of chromatin regulators, but rather that their recruitment coincides with reduced levels of γH2AX. We go on to determine the chromatin remodeling enzyme Fun30 functions in histone dynamics surround a DSB, but does not significantly affect γH2AX dynamics. Additionally, we describe a conserved functional interaction among the chromatin remodeling enzyme, SWI/SNF, the NuA4 and Gcn5 histone acetyltransferases, and phosphorylation of histone H2A.X. Specifically, we find that the NuA4 and Gcn5 enzymes are both required for the robust recruitment of SWI/SNF to a DSB, which in turn promotes the phosphorylation of H2A.X.
29
Nayar, Ribhu. "IRF4 Does the Balancing Act: A Dissertation." eScholarship@UMMS, 2001. http://escholarship.umassmed.edu/gsbs_diss/746.
Abstract:
CD8+ T cell differentiation is a complex process that requires integration of signals from the TCR, co-stimulatory molecules and cytokines. Ligation of the peptide-MHC complex with the cognate TCR initiates a downstream signaling cascade of which the IL-2 inducible T-cell kinase (ITK) is a key component. Loss of ITK results in a measured reduction in T cell activation. Consequently, Itk deficient mice have defects in thymic selection, CD8+ T cell expansion and differentiation in response to virus infections, and generate a unique population of innate-like CD8+ T cells. The mechanisms that translate TCR and ITK-derived signals into distinct gene transcription programs that regulate CD8+ T cell differentiation are not defined. Our microarray screen identified IRF4 as a potential transcription factor mediating the differentiation of innate-like T cells, and antiviral CD8+ T cell in response to acute and chronic LCMV infections.
Innate-like CD8+ T cells are characterized by their high expression of CD44, CD122, CXCR3, and the transcription factor Eomesodermin (Eomes). One component of this altered development is a non-CD8+ T cell-intrinsic role for IL-4. We show that IRF4 expression is induced upon TCR signaling and is dependent on ITK activity. In contrast to WT cells, activation of IRF4-deficient CD8+ T cells leads to rapid and robust expression of Eomes, which is further enhanced by IL-4 stimulation. These data indicate that ITK signaling promotes IRF4 up-regulation following CD8+ T cell activation and that this signaling xii pathway normally suppresses Eomes expression, thereby regulating the differentiation pathway of CD8+ T cells.
ITK deficient mice also have reduced expansion of CD8+ T cells in response to acute LCMV infections. We show that IRF4 is transiently upregulated to differing levels in murine CD8+ T cells, based on the strength of TCR signaling. In turn, IRF4 controls the magnitude of the CD8+ T cell response to acute virus infection in a dose-dependent manner. Furthermore, the expression of key transcription factors such as T cell factor 1 and Eomesodermin are highly sensitive to graded levels of IRF4. In contrast, T-bet expression is less dependent on IRF4 levels and is influenced by the nature of the infection. These data indicate that IRF4 is a key component that translates the strength of TCR signaling into a graded response of virus-specific CD8+ T cells.
The data from these studies indicated a pivotal role of IRF4 in regulating the expression of T-bet and Eomes. During persistent LCMV infections, CD8+ T cells differentiate into T-bethi and Eomeshi subsets, both of which are required for efficient viral control. We show that TCR signal strength regulates the relative expression of T-bet and Eomes in antigen-specific CD8+ T cells by modulating levels of IRF4. Reduced IRF4 expression results in skewing of this ratio in favor of Eomes, leading to lower proportions and numbers of T-bet+ Eomes- precursors and poor control of LCMV Clone 13 infection. Altering this ratio in favor of T-bet xiii restores the differentiation of T-bet+ Eomes- precursors and the protective balance of T-bet to Eomes required for efficient viral control. These data highlight a critical role for IRF4 in regulating protective anti-viral CD8+ T cell responses by ensuring a balanced ratio of T-bet to Eomes, leading to the ultimate control of this chronic viral infection.
30
Yang, Chao-Shun. "Molecular Landscape of Induced Reprogramming: A Dissertation." eScholarship@UMMS, 2002. http://escholarship.umassmed.edu/gsbs_diss/698.
Abstract:
Recent breakthroughs in creating induced pluripotent stem cells (iPS cells) provide alternative means to obtain embryonic stem (ES) cell-like cells without destroying embryos by introducing four reprogramming factors (Oct3/4, Sox2, and Klf4/c-Myc or Nanog/Lin28) into somatic cells. However, the molecular basis of reprogramming is largely unknown. To address this question, we employed microRNAs, small molecules, and conducted genome-wide RNAi screen, to investigate the regulatory mechanisms of reprogramming.
First we showed that depleting miR-21 and miR-29a enhances reprogramming in mouse embryonic fibroblasts (MEFs). We also showed that p53 and ERK1/2 pathways are regulated by miR-21 and miR-29a and function in reprogramming.
Second, we showed that computational chemical biology combined with genomic analysis can be used to identify small molecules regulating reprogramming. We discovered that the NSAID Nabumetone and the anti-cancer drug OHTM could replace Sox2 during reprogramming. Nabumetone could also replace c-Myc or Sox2 without compromising self-renewal and pluripotency of derived iPS cells.
To identify the cell-fate determinants during reprogramming, we integrated a genome-wide RNAi screen with transcriptome analysis to dissect the molecular requirements in reprogramming. We found that extensive interactions of embryonic stem cell core circuitry regulators are established in mature iPS cells, including Utf1, Nr6a1, Tdgf1, Gsc, Fgf10, T, Chrd, Dppa3, Fgf17, Eomes, Foxa2. Remarkably, genes with non-differential change play the most critical roles in the transitions of reprogramming. Functional validation showed that some genes act as essential or barrier roles to reprogramming. We also identified several genes required for maintaining ES cell properties. Altogether, our results demonstrate the significance of miRNA function in regulating multiple signaling networks involved in reprogramming. And our work further advanced the reprogramming field by identifying several new key modulators.
31
Sambt, Jože Malačič Janez. "National transfer accounts for Slovenia : doctoral dissertation /." Ljubljana : [J. Sambt], 2009. http://www.cek.ef.uni-lj.si/doktor/sambt283.pdf.
32
Murray, John Courtney Hughson D. Thomas. "Matthias Scheeben on faith : the doctoral dissertation /." Lewiston : Queenston : N. Y. ; Canada : E. Mellen press, 1987. http://catalogue.bnf.fr/ark:/12148/cb34948997x.
33
Kundu, Sharmistha. "Chromatin Remodeling and Transcriptional Memory: A Dissertation." eScholarship@UMMS, 2008. https://escholarship.umassmed.edu/gsbs_diss/408.
Abstract:
Transcriptional regulation of gene expression is critical for all unicellular and multicellular organisms. The ability to selectively induce or repress expression of only a few genes from the entire genome gives cells the ability to respond to changing environmental conditions, grow and proliferate. Multicellular organisms begin life as a single totipotent cell, which undergoes many cell divisions during embryonic and later postnatal development. During this process, the dividing cells of the embryo progressively lose their pluripotency and adopt restricted cell fates. Cell fate restriction leads different cell types to gain unique transcriptional profiles. This transcriptional profile or gene expression pattern not only defines the cell types and restricts the ways in which they can respond to signals, it also has to be faithfully re-established in the progeny of these fate-restricted cells when they divide.
Different mechanisms have evolved in multicellular organisms to propagate transcriptional memory of cell identity. Most of mechanisms involve modifications of chromatin such as epigenetic modification of DNA or alterations of associated histones. In contrast to multicellular organisms which have considerable cellular diversity and a long lifespan for which cell fates and transcriptional memory needs to be maintained, single celled budding yeast, Sachharomyces cerevisiae have a life cycle of about 90 minutes in normal nutrient rich conditions. However, even budding yeast have tremendous potential to respond to changing environmental conditions like nutrient availability by inducing expression of various genes. We observed that members of the GAL gene cluster, which encodes genes induced in response to and for metabolizing the sugar galactose, showed heritable transcriptional memory of previous activation. This dissertation thesis describes the studies I have done for my graduate research to define this phenomenon of transcriptional memory at the yeast GALgenes and to determine the mechanism by which it can be formed and inherited.
Chapter I gives an introduction to different mechanisms of establishing transcriptional memory in unicellular and multicellular organisms. Chromatin based mechanisms have been well studied in multicellular organisms but not observed in budding yeast. We compare chromatin based or nuclear inheritance with cytoplasmic inheritance that can be observed in yeast. Chapter II describes work done to define the phenomenon of transcriptional memory at GAL1 gene. We define this as a faster rate of induction of the GAL1 gene, compared to a naïve gene, after a brief period of repression. We show that this cellular memory persists through mitosis and can be passed on to the next generation. We also show that chromatin remodeling enzymes appear to be required for rapid reinduction, raising the question if yeast may also possess chromatin associated, nuclear mechanisms for cellular memory. Chapter III describes experiments that show that cellular memory observed at GAL1 is cytoplasmic in nature and also compares our work with similar examples observed recently by other groups. Finally, Chapter IV offers a perspective of the significance of such cellular memory mechanisms in budding yeast and outlines some potential further experiments to better understand the control of GAL1 induction kinetics.
34
Mehrotra, Swarna. "IAP Regulation of Tumor Metastasis: A Dissertation." eScholarship@UMMS, 2009. https://escholarship.umassmed.edu/gsbs_diss/437.
Abstract:
The dissemination of tumor cells to distant organs i.e. metastasis is an exceedingly complex process leading to 90% of all cancer deaths. Despite being so clinically important, little is known about this process that requires tumor cells to leave the primary tumor site, intravasate and transport through the blood stream, extravasate and colonize at secondary sites leading to distant metastases. Survivin, a member of the IAP (Inhibitor of Apoptosis) family with known functions in apoptosis and mitosis, is highly expressed in aggressive tumors and is associated with poor prognosis and adverse clinical outcome. But the mechanistic role of survivin in metastatic dissemination has not been investigated. In this study, we demonstrate an important and novel role of survivin in activating a broad gene expression program in tumor cells. Of particular importance is the upregulation of a distinct class of cell adhesion molecules, particularly fibronectin. This IAP mediated gene regulation requires synergistic intermolecular cooperation between survivin and its related cofactor molecule, XIAP that results in activation of NF-κB dependent fibronectin gene expression. The binding of fibronectin with its cognate cell surface receptors initiates outside–in signaling leading to the autocrine and paracrine activation of cell motility kinases, FAK and Src, in turn leading to enhanced tumor invasion and metastasis. The importance of survivin and XIAP in the process of metastasis has also been demonstrated in vivousing intrasplenic injections in mouse models.
Overall this study is the first to place survivin upstream of transcriptional activation of gene expression particularly fibronectin. In addition, it also demonstrates the importance of survivin-XIAP complex in mediating NF-κB activation which in turn switches on the expression of various target genes involved in tumor metastasis. Hence this study dissects the upstream and downstream requirements of survivin- XIAP complex mediated tumor dissemination and metastasis.
Significance of this Study
The hallmark of end-stage cancer is metastasis, an incurable condition almost invariably associated with death from disease. Despite a better understanding of the metastatic process, and the identification of key gene expression requirements of this pathway, the development of anti-metastatic therapies has lagged behind, with no viable options being currently offered in the clinical setting. Our findings that Inhibitor of Apoptosis (IAP) proteins functions as metastasis-promoting genes independently of cell survival, but through activation of cell motility could have important ramifications for the broader application of IAP antagonists currently in early clinical trials, as novel anti-metastatic therapies.
35
Cullion, Kathleen J. "Mechanisms of NOTCH1 Mediated Leukemogenesis: A Dissertation." eScholarship@UMMS, 2009. https://escholarship.umassmed.edu/gsbs_diss/537.
Abstract:
Gain of function NOTCH1 mutations are common in both patients with T-ALL and in mouse models of the disease. Inhibiting the Notch pathway in T-ALL cell lines results in growth arrest and/or apoptosis in vitro, suggesting a requirement for Notch signaling in T-ALL. Therefore, we sought to examine the role of Notch1 signaling in both premalignancy and in the maintenance of leukemic growth. Using a murine model of T-ALL, in which expression of the Tal1 and Lmo2 oncogenes arrests thymocyte development, our preleukemic studies reveal that Notch1 mutations are early events that contribute to the clonal expansion of DN3 and DN4 progenitors. We also demonstrate that progenitors are maintained within the tumor and are enriched in leukemia-initiating cell (L-IC) activity, suggesting Notch1 may contribute to L-IC self-renewal. By studying the effects of Notch signaling in murine T-ALL cell lines, we also demonstrate that Notch1 promotes the proliferation and survival of leukemic blasts through regulation of Lef1 and the Akt/mTOR pathways.
Given that T-ALL cell lines are dependent on Notch signaling in vitro, we investigated the effects of Notch inhibition in vivo. We provide evidence that Notch1 can be successfully targeted in vivo and that Notch inhibition, with γ-secretase inhibitors (GSIs), significantly extends the survival of leukemic mice. We also demonstrate that administration of GSIs in combination with rapamycin inhibits human T-ALL growth and extends survival in a mouse xenograft model. Given that NOTCH1 may be required to maintain both L-IC and bulk leukemic growth, targeting NOTCH1 may prove to be an efficacious targeted therapy for T-ALL patients with aberrant NOTCH1 activation.
36
Broderick, Jennifer A. "Cooperativity in Mammalian RNA Silencing: A Dissertation." eScholarship@UMMS, 2011. https://escholarship.umassmed.edu/gsbs_diss/548.
Abstract:
Argonaute proteins are the core component of an RNA silencing complex. The human genome encodes four Argonaute paralogs –Ago1, Ago2, Ago3 and Ago4– proteins that are guided to target mRNAs by microRNAs. More than 500 miRNAs are conserved between mammals, and each microRNA can repress hundreds of genes, regulating almost every cellular process. We still do not fully understand the molecular mechanisms by which miRNAs regulate gene expression. Although we understand many aspects of microRNA biogenesis and formation of the RNA-induced silencing complex, much less is known about the subsequent steps leading to target mRNA regulation.
Mammalian microRNAs rarely have complete complementarity to their target mRNAs so, instead of endonucleolytic cleavage by Ago2, microRNAs destabilize or repress translation of target mRNAs. Here I explored the functional limits of Argonaute proteins bound to their targets directly and indirectly through microRNAs in mammalian cells. I revealed the different abilities for Argonaute proteins bound at multiple sites in a target to generate cooperativity in silencing based on the extent of pairing between the microRNA and target mRNA. Further, I harnessed the endogenous microRNA silencing mechanism to repress an mRNA that is not a direct target of the microRNA by tethering the RNA-induced silencing complex to the 3´ UTR of an mRNA. This strategy allows tissue-specific gene silencing due to the limited endogenous expression profile of the recruited microRNA. Efforts made herein further our mechanistic knowledge of microRNA-induced gene silencing in mammalian cells and advance microRNA-based strategies toward treating human disease.
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Shearstone, Jeffrey R. "Global DNA Demethylation During Erythropoiesis: A Dissertation." eScholarship@UMMS, 2011. https://escholarship.umassmed.edu/gsbs_diss/549.
Abstract:
In the mammalian genome, 5‟-CpG-3‟ dinucleotides are frequently methylated, correlating with transcriptional silencing. Genome-wide waves of demethylation are thought to occur only twice during development, in primordial germ cells and in the pre-implantation embryo. They are followed by de novo methylation, setting up a pattern that is inherited throughout development. No global methylation changes are thought to occur during further somatic development, although methylation does alter at gene-specific loci, contributing to tissue-specific patterns of gene expression. Here we studied DNA methylation in differentiating mouse erythroblasts in vivo using several approaches including genomic-scale, reduced representation bisulfite sequencing (RRBS). Surprisingly, demethylation at the erythroid-specific β-globin locus was coincident with a wave of global DNA demethylation at most genomic elements, including repetitive elements and genes silenced in erythropoiesis. Over 30% of total methylation is irreversibly lost during erythroid differentiation. Demethylation occurred through a passive mechanism, requiring the rapid DNA replication triggered with the onset of erythroid terminal differentiation. Global loss of DNA methylation was not associated with a global increase in transcription, as determined by GeneChip analysis. We propose that global demethylation is a consequence of cellular mechanisms required for the rapid demethylation and induction of β-globin and other erythroid genes. Our findings demonstrate that, contrary to previously held dogma, DNA demethylation can occur globally during somatic cell differentiation, providing a new experimental model for the study of global demethylation in development and disease.
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Rogers, Jeffrey Scott. "Characterization of JNK Binding Proteins: A Dissertation." eScholarship@UMMS, 2005. https://escholarship.umassmed.edu/gsbs_diss/222.
Abstract:
The JNK signal transduction pathway mediates a broad, complex biological process in response to inflammatory cytokines and environmental stress. These responses include cell survival and apoptosis, proliferation, tumorigenesis and the immune response. The divergent cellular responses caused by the JNK signal transduction pathway are often regulated by spatial and cell type contexts, as well as the interaction with other cellular processes. The discovery of additional components of the JNK signal transduction pathway are critical to elucidate the stress response mechanisms in cells.
This thesis first discusses the cloning and characterization of two novel members of the JNK signal transduction pathway. JIP1 and JMP1 were initially identified from a murine embryo library through a yeast Two-Hybrid screen to identify novel JNK interacting proteins. Full length cDNAs of both genes were cloned and analyzed. JIP1 represents the first member of the JIP group of JNK scaffold proteins which were characterized. The JNK binding domain (JBD) of JIP1 matches the D-domain consensus of other JNK binding proteins, and it demonstrates JNK binding both in vitro and in vivo. This JNK binding was demonstrated to inhibit JNK signal transduction and over-expression of JIP1 inhibits the JNK mediated pre-B cell transformation by bcr-abl. Over-expressed JIP1 also sequesters JNK in the cytoplasm, which may be a mechanism of the inhibition of JNK signaling. A new, high-resolution digital imaging microscopy technique using deconvolution demonstrated the absence of JNK1 in the nucleus of co-transfected JIP1 and JNK1 cells.
The other protein discussed in this thesis is JMP1, a novel JNK binding, microtubule co-localized protein. There is a JBD in the JMP1 carboxyl end and a consensus D-domain within this region. The JMP1 JBD demonstrates an increased association with phospho-JNK from UV irradiated cells compared to un-irradiated cells in vivo. JMP1 also has 12 WD-repeat motifs in its amino terminal end which are required for microtubule co-localization. JMP1 demonstrates a cell cycle specific localization at the mitotic spindle poles. This co-localization is dependent on intact microtubules and the amino-terminal WD-repeats are required for this localization. JMP1 mRNA is highly expressed in testis tissues. Immunocytochemistry on murine testis sections using an affinity purified anti-JMP1 antibody demonstrates JMP1 protein in the lumenal compartment of the seminiferous tubules. JMP1 protein is expressed in primary and secondary spermatocytes, cells which are actively undergoing meiosis.
The results obtained from the localization of JMP1 in meiotic spermatocytes led to an investigation of the roles of JNK signal transduction in the testis. The testis is an active region of cellular proliferation, apoptosis and differentiation, which make it an appealing model for studying JNK signal transduction. However, the roles JNK signaling have in the testis are poorly understood. I investigated the reproduction capability of Jnk3-/- male mice and discovered older Jnk3-/- males had a reduced capacity to impregnate females compared to younger animals and age-matched wild type controls. The testis morphology and sperm motility of these animals were similar to wild-type animals, and there was no alteration of apoptosis in the testis. The final section of this thesis involves the study of this breeding defect and investigating for cellular defects that might account for this age-related Jnk3-/- phenotype.
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Lewis, Sylvester. "Dissertation: Sociodemographics and Pancreatic Cancer Survival Rate." ScholarWorks, 2018. https://scholarworks.waldenu.edu/dissertations/5745.
Abstract:
Pancreatic carcinoma or pancreatic cancer (PaCa) is an insidious disease with a prognosis of 6- to 12-month survival time for a late stage diagnosis. This problem has become crucial given that no study to date had been able to establish a definitive association between independent factors (other than a few diseases) and the survival rate of pancreatic cancer. The purpose of this quantitative, cross-sectional study was to determine whether an association exists between the independent, sociodemographic variables (marital status, age, education, income, and employment) and the outcome variable of survival rate. The social cognitive theory was the framework that provided the blueprint throughout the development of this study and helped guide the analysis of the secondary data, which was procured from the surveillance, epidemiology, and end results program. The sample of 56,166 participants was collected from 2009 to 2013 and Cox proportional hazard was used to analyze the data and arrive at the answers to the research hypotheses. A Cox proportional hazard model was used to analyze whether an association existed between each of the independent variables and the outcome variable. The analysis showed significant association between age, education, income, and employment and survival rate. It was not the same for marital status. These findings could stimulate social change by allowing stakeholders and other policy makers to become aware of the role that sociodemographic factors can play in health care. In addition, a need exists for effective research to be undertaken in the prevention and intervention of this disease. This could then lead to private and public health innovations and procedures to benefit patients with PaCa.
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Restrepo, Juan Gabriel. "Dissertation prospectus : dynamics on networks of coupled oscillators." College Park, Md. : University of Maryland, 2005. http://hdl.handle.net/1903/2425.
Abstract:
Thesis (Ph. D.) -- University of Maryland, College Park, 2005.Thesis research directed by: Applied Mathematics and Scientific Computation Program. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Bi, Sheng [Verfasser]. "Dissertation on Competitive and Directed Search / Sheng BI." Bielefeld : Universitätsbibliothek Bielefeld, 2016. http://d-nb.info/1081487941/34.
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Bouayad, Lina. "Analytics and Healthcare Costs (A Three Essay Dissertation)." Scholar Commons, 2015. http://scholarcommons.usf.edu/etd/5876.
Abstract:
Both literature and practice have looked at different strategies to diminish healthcare associated costs. As an extension to this stream of research, the present three paper dissertation addresses the issue of reducing elevated healthcare costs using analytics. The first paper looks at extending the benefits of auditing algorithms from mere detection of fraudulent providers to maximizing the deterrence from inappropriate behavior. Using the structure of the physicians' network, a new auditing algorithm is developed. Evaluation of the algorithm is performed using an agent-based simulation and an analytical model. A case study is also included to illustrate the application of the algorithm in the warranty domain. The second paper relies on experimental data to build a personalized medical recommender system geared towards re-enforcing price-sensitive prescription behavior. The study analyzes the impact of time pressure, and procedure cost and prescription prevalence/popularity on the physicians' use of the system's recommendations. The third paper investigates the relationship between patients' compliance and healthcare costs. The study includes a survey of the literature along with a longitudinal analysis of patients' data to determine factors leading to patients' non-compliance, and ways to alleviate it.
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Sans, Oda. "Reconstruction probability of distributed secret sharing schemes Dissertation." Münster Verl.-Haus Monsenstein und Vannerdat, 2006. http://deposit.d-nb.de/cgi-bin/dokserv?id=3055126&prov=M&dok_var=1&dok_ext=htm.
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Diogenes, Anibal. "Prolactin modulation of trigeminal sensory neurons : a dissertation /." San Antonio : UTHSC, 2006. http://proquest.umi.com/pqdweb?did=1246523531&sid=1&Fmt=2&clientId=70986&RQT=309&VName=PQD.
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Li, Yu. "Quality Control of Plasma Membrane Proteins: A Dissertation." eScholarship@UMMS, 1999. http://escholarship.umassmed.edu/gsbs_diss/240.
Abstract:
The temperature-sensitive α-factor receptor (Ste2-3p) and arginine permease (Can1tsp) were found to provide the model substrates for quality control of plasma membrane proteins in Saccharomyces cerevisiae. When the ste2-3 mutant cells were grown at 34°C, Ste2-3p failed to accumulate at the plasma membrane and was delivered to the vacuole for degradation without traversing the plasma membrane. Upon reaching the vacuole, cytoplasmic domains of both Ste2p and Ste2-3p appeared within the vacuolar lumen. Four stp mutants were identified to suppress temperature-sensitive defects in both Ste2-3p and Can1tsp. The stp22 and STP26 mutations also caused missorting of vacuolar protein carboxypeptidase Y, and a subset of vacuolar protein sorting mutants (vps) suppressed ste2-3 mutation. In the stp22 mutant, both Ste2p and Ste2-3p accumulated in the prevacuolar compartment (PVC) and on the plasma membrane. Three independent mutations that bypassed the phenotype of stp22Δ mutant were identified and mapped to the SNF8 locus, and they were found to affect a single amino acid residue (G209D). The mutant protein, Snf8bpp, but not Snf8p, was able to compensate for the lack of functional Stp22p and to restore PVC-to-vacuole trafficking. The order of function for some VPS genes involved in PVC-to-vacuole traffic (class E) was determined by using this special snf8bp allele. In addition, a PtdIns 4-kinase encoded by the PIK1 gene was found to be involved in Ste2-3p trafficking, possibly affecting the PVC function.
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Rhodes, Alison M. "Yoga for Traumatic Stress: A Three Paper Dissertation." Thesis, Boston College, 2014. http://hdl.handle.net/2345/bc-ir:104088.
Abstract:
Thesis advisor: Paul KlineThis three paper dissertation considers whether yoga--a popular mind-body practice combining physical postures and movement, mindfulness, and breath exercises--may be a useful component of treatment for adult trauma survivors. The first paper involves a systematic review and meta-analyses of the current evidence base for yoga in the treatment of anxiety, depression, and PTSD among trauma survivors. The second and third papers are grounded in a single, mixed-methods multi-wave data source aimed at examining yoga's contribution to recovery for adult women who have complex trauma histories (i.e., sustained and/or multiple traumatic experiences such as recurring physical or sexual abuse). The second paper is a quantitative study employing hierarchical linear and logistic regression to examine associations between yoga practice and reductions in traumatic symptomology over time. The third paper is a hermeneutic phenomenological study exploring how women with complex trauma histories experience practicing yoga and its potential role in their coping and healing processes over time. Taken together, these three papers offer insights into the complex healing needs of adult survivors suffering from the effects of traumatization, and the promising role of yoga within their recovery processes
Thesis (PhD) — Boston College, 2014
Submitted to: Boston College. Graduate School of Social Work
Discipline: Social Work
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Hietpas, Ryan T. "Experimental Illumination of Comprehensive Fitness Landscapes: A Dissertation." eScholarship@UMMS, 2013. https://escholarship.umassmed.edu/gsbs_diss/667.
Abstract:
Evolution is the single cohesive logical framework in which all biological processes may exist simultaneously. Incremental changes in phenotype over imperceptibly large timescales have given rise to the enormous diversity of life we witness on earth both presently and through the natural record. The basic unit of evolution is mutation, and by perturbing biological processes, mutations may alter the fitness of an individual. However, the fitness effect of a mutation is difficult to infer from historical record, and complex to obtain experimentally in an efficient and accurate manner.
We have recently developed a high throughput method to iteratively mutagenize regions of essential genes in yeast and subsequently analyze individual mutant fitness termed Exceedingly Methodical and Parallel Investigation of Randomized Individual Codons (EMPIRIC). Utilizing this technique as exemplified in Chapters II and III, it is possible to determine the fitness effects of all possible point mutations in parallel through growth competition followed by a high throughput sequencing readout. We have employed this technique to determine the distribution of fitness effects in a nine amino acid region of the Hsp90 gene of S. cerevisiae under elevated temperature, and found the bimodal distribution of fitness effects to be remarkably consistent with near-neutral theory. Comparing the measured fitness effects of mutants to the natural record, phylogenetic alignments appear to be a poor predictor of experimental fitness.
In Chapter IV, to further interrogate the properties of this region, library competition under conditions of elevated temperature and salinity were performed to study the potential of protein adaptation. Strikingly, whereas both optimal and elevated temperatures produced no statistically significant beneficial mutations, under conditions of elevated salinity, adaptive mutations appear with fitness advantages up to 8% greater than wild type. Of particular interest, mutations conferring fitness benefits under conditions of elevated salinity almost always experience a fitness defect in other experimental conditions, indicating these mutations are environmentally specialized. Applying the experimental fitness measurements to long standing theoretical predictions of adaptation, our results are remarkably consistent with Fisher’s Geometric Model of protein evolution.
Epistasis between mutations can have profound effects on evolutionary trajectories. Although the importance of epistasis has been realized since the early 1900s, the interdependence of mutations is difficult to study in vivo due to the stochastic and constant nature of background mutations. In Chapter V, utilizing the EMPIRIC methodology allows us to study the distribution of fitness effects in the context of mutant genetic backgrounds with minimal influence from unintended background mutations. By analyzing intragenic epistatic interactions, we uncovered a complex interplay between solvent shielded structural residues and solvent exposed hydrophobic surface in the amino acid 582-590 region of Hsp90. Additionally, negative epistasis appears to be negatively correlated with mutational promiscuity while additive interactions are positively correlated, indicating potential avenues for proteins to navigate fitness ‘valleys’.
In summary, the work presented in this dissertation is focused on applying experimental context to the theory-rich field of evolutionary biology. The development and implementation of a novel methodology for the rapid and accurate assessment of organismal fitness has allowed us to address some of the most basic processes of evolution including adaptation and protein expression level. Through the work presented here and by investigators across the world, the application of experimental data to evolutionary theory has the potential to improve drug design and human health in general, as well as allow for predictive medicine in the coming era of personalized medicine.
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Shea, Jeremy M. "Paternal Effects on Metabolism in Mammals: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/759.
Abstract:
The following work demonstrates that paternal diet controls medically important metabolic phenotypes in offspring. We observe transmission of dietary information to the zygote via sperm, and this information evades reprogramming that typically occurs after fertilization. Cytosine methylation is implicated as a major contributor to meiotic epigenetic inheritance in several transgenerational phenomena. Our extensive characterization of the sperm methylome reveals that diet does not significantly affect methylation patterns. However, we find that extensive epivariability in the sperm epigenome makes important contributions to offspring variation. Importantly, coordinate cytosine methylation and copy number changes over the ribosomal DNA locus contributes to variation in offspring metabolism. Thus, rDNA variability acts independently of postadolescent paternal diet to influence offspring metabolism. Therefore, at least two mechanisms exist for epigenetically controlling offspring metabolism: stochastic epivariation and diet acting by an unknown mechanism to further modulate metabolism. This work argues that an offspring's phenotype can no longer be viewed solely as the result of genetic interactions with the developmental environment - the additional influences of paternal environment and inherited epigenetic variability must also be considered. These findings reveal novel contributions to metabolism that could revolutionize how we think about the risk factors for human health and disease.
49
Dolgin, Natasha H. "Frailty and Outcomes in Liver Transplantation: A Dissertation." eScholarship@UMMS, 2016. https://escholarship.umassmed.edu/gsbs_diss/817.
Abstract:
In recent years, the transplant community has explored and adopted tools for quantifying clinical insight into illness severity and frailty. This dissertation work explores the interplay between objective and subjective assessments of physical health status and the implications for liver transplant candidate and recipient outcomes. The first aim characterizes national epidemiologic trends and the impact of Centers for Medicare and Medicaid quality improvement policies on likelihood of waitlist removal based on the patient being too frail to benefit from liver transplant (“too sick to transplant”). This aim includes more than a decade (2002–2012) of comprehensive national transplant waitlist data (Scientific Registry of Transplant Recipients (SRTR)). The second aim will assess and define objective parameters of liver transplant patient frailty by measuring decline in lean core muscle mass (“sarcopenia”) using abdominal CT scans collected retrospectively at a single U.S. transplant center between 2006 and 2015. The relationship between these objective sarcopenia measures and subjective functional status assessed using the Karnofsky Functional Performance (KPS) scale are described and quantified. The third aim quantifies the extent to which poor functional status (KPS) pre-transplant is associated with worse post-transplant survival and includes national data on liver transplantations conducted between 2005 and 2014 (SRTR). The results of this dissertation will help providers in the assessment of frailty and subsequent risk of adverse outcomes and has implications for strategic clinical management in anticipation of surgery. This research will also to serve to inform national policy on the design of transplant center performance measures.
50
Akie, Thomas E. "Regulation of Metabolism by Hepatic OXPHOS: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/857.
Abstract:
Non-alcoholic fatty liver disease (NAFLD) is an increasingly prevalent issue in the modern world, predisposing patients to serious pathology such as cirrhosis and hepatocellular carcinoma. Mitochondrial dysfunction, and in particular, diminished hepatic oxidative phosphorylation (OXPHOS) capacity, have been observed in NAFLD livers, which may participate in NAFLD pathogenesis.
To examine the role of OXPHOS in NAFLD, we generated a model of enhanced hepatic OXPHOS using mice with liver-specific transgenic expression of LRPPRC, a protein which activates mitochondrial transcription and augments OXPHOS capacity. When challenged with high-fat feeding, mice with enhanced hepatic OXPHOS were protected from the development of liver steatosis and inflammation, critical components in the pathogenesis of NAFLD. This protection corresponded to increased liver and whole-body insulin sensitivity. Moreover, mice with enhanced hepatic OXPHOS have increased availability of oxidized NAD+, which promotes complete fatty acid oxidation in hepatocytes.
Interestingly, mice with enhanced hepatic OXPHOS were also protected from obesogenic effects of long-term high-fat feeding. Consistent with this, enhanced hepatic OXPHOS increased energy expenditure and adipose tissue oxidative gene expression, suggesting a communication between the liver and adipose tissue to promote thermogenesis. Examination of pro-thermogenic molecules revealed altered bile acid composition in livers and serum of LRPPRC transgenic mice. These mice had increased expression of bile acid synthetic enzymes, genes which are induced by NAD+ dependent deacetylase SIRT1 activation of the transcriptional co-regulator PGC-1a. These findings suggest that enhanced hepatic OXPHOS transcriptionally regulates bile acid synthesis and dictates whole-body energy expenditure, culminating in protection from obesity.