Source: Masters Abstracts International, Volume: 47-02, page: 0981. Adviser: Luisa Franzini. Includes bibliographical references.

Thesis (Ph.D)--Biology, Georgia Institute of Technology, 2009. / Committee Chair: Alfred H. Merrill, Jr; Committee Member: John Cairney; Committee Member: M. Cameron Sullards; Committee Member: Marion B. Sewer; Committee Member: Yuhong Fan. Part of the SMARTech Electronic Thesis and Dissertation Collection.

Wireline formation testers are widely used to measure in-situ fluid pressure, to retrieve reservoir fluid samples, and to estimate formation mobility. However, formation-tester measurements are invariably influenced by mud-filtrate invasion due to drilling overbalance pressure, thereby affecting the acquisition of uncontaminated fluid samples and the estimation of in-situ petrophysical properties. Moreover, in cases of stress-sensitive formations, rock mechanical deformation may take place due to the combined effects of in-situ stress, wellbore stress imposed by mud overbalance, and wellbore pressure exerted by the formation tester itself. The latter deformation causes near-borehole perturbations of porosity and permeability that are evidenced by pressure transients measured during build-up and shut-in stages of formation testing, especially when using dual-packer pressure probes. If unaccounted for, such perturbations can also bias the estimation of in-situ fluid and petrophysical properties. Conversely, the detection and quantification of elastic mechanical deformation effects on measured pressure transients can be used to infer the underlying rock elastic and petrophysical properties of the stressed formation. The purpose of this dissertation is twofold: (a) to quantify the relative effects of mud-filtrate invasion and geomechanical deformation on pressure-transient measurements acquired with dual-packer formation testers, with special emphasis on the appraisal of near-borehole porosity and permeability enhancement due to elastic mechanical deformation, and (b) to develop a new method to estimate elastic and petrophysical properties of rock formations from dual-packer pressure transients acquired in mechanically deformable rocks. Numerical simulations of mud-filtrate invasion are performed with an axialsymmetric two-phase (water-oil) method that enforces the specific boundary and source conditions of a wellbore that penetrates horizontal layers. Simulations are performed in a cylindrical system of coordinates using finite differences together with an implicit-pressure, explicit-saturation time-marching approach that also incorporates the dynamic conditions of immiscible mudcake growth due to filtration of solids at the wellbore. Laboratory experiments are conducted to further study pressure transients due to formation testing in the presence of invasion with water-base mud. Experiments include the effects of both mud circulation and mudcake on pressure-transient measurements and are performed on a variety of rock-core samples. Measurements are successfully validated with both the developed simulator and a commercial simulator, thereby lending credence to the assumed model of dynamic solid filtration. The developed mud-filtrate fluid-flow simulator is coupled with a finite-element code that assumes 2D axial-symmetric linear elasticity to quantify geomechanical deformation. Coupling of mechanical deformation with variations of porosity and permeability assumes a staggered-in-time, iteratively coupled volumetric model. We assume a dual-packer formation tester to quantify elastic deformation effects in stress-sensitive formations as a preamble to estimating in-situ elastic and petrophysical properties. It is shown that near-wellbore spatial variations of porosity and permeability due to mechanical deformation can bias the corresponding pressure-transient measurements acquired with the dual-packer formation-tester. The degree of biasing depends on the rigidity of the stressed formation. Finally, we develop a method to estimate in-situ petrophysical and elastic rock properties from pressure-transient measurements acquired with formation-testers in mechanically deformable rocks. Petrophysical and elastic properties will change in both time and space depending on the time evolution of the conditions that influence mechanical deformation. We use a commercial reservoir simulator to calculate pressure transients due to fluid pumpout in the presence of both invasion and mechanical deformation. A pre-stressed initial condition due to mud overbalance is assumed with incremental deformation due to surface force applied by the packers or probes, and active flow imposed by the formation-tester. In so doing, we consider pressure data sets acquired with both flow and observation probes during draw-down and build-up periods. For cases where a-priori information can be sufficiently constrained, our estimation method provides reliable and accurate estimates of petrophysical and elastic properties in the presence of moderate levels of random noise. / text

The intent of this study was to determine what students perceive as caring behaviors in teachers, whether those views match teachers’ perceptions, whether these vary depending on students’ academic track, and whether teachers are observed to exhibit the behaviors identified by their students as indicative of caring. Eighty-two majority Hispanic high school students and eight teachers completed a four-section survey about caring behavior. These teachers and students were also observed four times in the classroom. The survey contained Likert scale and open-ended questions about teachers’ caring behaviors. It also probed how the students’ own teachers interacted with them daily in the classroom and their personal open-ended opinion about how teachers show that they care or do not care about them. Two groups were studied, specifically Advanced Placement (AP) and Regular students, to find out whether academic placement caused students’ to categorize caring behaviors of teachers differently. Results of the study indicated a significant difference in AP and Regular students’ attitudes about how teachers treat them. Teachers’ perceptions were also compared to students’ perception and differences were found. Differences included how often teachers interact in one-on-one conversations about certain issues with students, such as the need to complete homework assignments. Within these conversations some issues were reported to occur more frequently by teachers than students. On other issues, like disrupting class, there was agreement, but only for specific teachers and subjects. In addition, STEM and non-STEM classes were investigated and it was discovered that these students responded differently about the frequency with which their teachers had conversations with them about specific issues. Differences included disrupting class, not completing assignments, interests and things that are important to students, and plans for college and work. Observations made by this researcher further support the idea that there is similarity in how students define caring behaviors, but what behaviors they experience, like assisting in homework or listening to personal needs, is different. Although trends observed in this study are suggestive, more research is required to support the idea that academic placement and subject make a difference in students’ experiences of caring behaviors in teachers. / text

published_or_final_version / Anatomy / Master / Master of Philosophy

The principal isoform of Src homology (SH) 2-domain containing 5' inositol phosphatase protein 1 (SHIP) is a 145kDa protein primarily expressed by cells of the hematopoietic compartment. The enzymatic activity of SHIP is responsible for hydrolyzing the 5' phosphate of phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P3), and thereby preventing the recruitment of pleckstrin homology domain containing effector proteins. Furthermore, SHIP contains protein-protein interaction domains, such as an SH2 domain, two NPXY and several proline-rich motifs. All of these different domains endow SHIP with the capacity to impact signaling pathways important for proliferation, survival, differentiation and activation. Therefore, we hypothesized that SHIP-deficiency could result in the loss of hematopoietic cell homeostasis and functionTo this verify this hypothesis, we first studied the effect of SHIP ablation on hematopoietic stem cell (HSC) proliferation, survival, function and hom ing. Most interestingly we observed that SHIP impacts HSC homeostasis and their ability to home appropriately to the bone marrow. Then, since SHIP was shown to be activated after engagement of the c-mpl receptor by its ligand, thrombopoietin, we studied the impact of SHIP deletion on the function of megakaryocytes, the major target cell of that cytokine. We found that SHIP is also important for homeostasis of the megakaryocyte compartment. Thirdly, we studied the role of SHIP in natural killer (NK) cells biology. We observed that F4 generation SHIP-/- mice have increased NK cells in their spleen and that these cells exhibit a disrupted receptor repertoire. We verified the hypothesis that SHIP helps shape the receptor repertoire of NK cells, mainly through regulation of cell survival and proliferation. Also included, is a study on the role of a SHIP isoform lacking the SH2-domain, called stem cell-SHIP (s-SHIP) in the biology of embryonic stem (ES) cells. To date, this isoform i s expressed by stem/progenitor cells and not by normal differentiated cells. Due to its specific expression pattern, s-SHIP has the potential to have an important role in stem cell biology.

Skeletal muscle has a remarkable capacity for regeneration, mediated by muscle stem cells that can self-renew or differentiate to form the mature myofibers of the tissue. Several human diseases are characterized by a loss of function and strength in skeletal muscle, with impairments in the ability to regenerate and consequent decreases in quality of life and increases in mortality. The work in this dissertation has focused on developing methods for combating muscle disease. This goal has been approached through attempts at cell replacement therapy - by generating muscle cells that can be engrafted in vivo. I also investigated the influence on regeneration of the skeletal muscle microenvironment (skeletal muscle-resident fibroblasts), and systemic environment (inflammation in myogenic and non-myogenic tissues), both of which were found to affect skeletal muscle stem cell behavior and the efficiency of myogenic regeneration. Ultimately, these studies identified novel factors that impair or improve skeletal muscle differentiation, and that offer the potential to modulate the process of muscle regeneration. In the process of investigating if induced pluripotent stem cells from skeletal muscle retain an epigenetic memory conducive to myogenic differentiation, I discovered that precursor cells in skeletal muscle reprogram to a pluripotent state more efficiently. However, these induced pluripotent stem cells, like embryonic stem cells, retain strong barriers to skeletal muscle differentiation. Together, these findings offer insights into the process of muscle regeneration, and suggest new potential pathways towards treatment of muscle disease.

Medulloblastoma, the most common pediatric malignant brain tumor, is comprised of a heterogeneous group of tumors with distinct molecular subtypes and clinical outcomes. In particular, tumors with a cancer stem cell (CSC) population have been observed to be more resistant to conventional therapies, necessitating the elucidation of pathways important in this population. Work in our lab has shown that neurosphere culture-enriched cells from Ptch1LacZ/+;Trp53-/- mouse medulloblastomas exhibit properties of self-renewal, expression of neural stem cell (NSC) markers and potent tumor-initiation. The pathway dependencies and mechanisms of self-renewal in these medulloblastoma neurospheres (MBNS) have not yet been characterized.

Somatic cells can be reprogrammed into induced pluripotent stem (iPS) cells by over expression of the transcription factors OCT4, SOX2, KLF4 and c-MYC. Using serial live cell immunofluorescence imaging of human fibroblasts undergoing reprogramming, we traced the emergence of nascent iPS cell colonies among heterogeneous cell populations and defined the kinetics of marker expression. We identified distinct colony types that morphologically resemble embryonic stem (ES) cells yet differ in molecular phenotype and differentiation potential. By analyzing expression of pluripotency markers, methylation at the OCT4 and NANOG promoters, and differentiation into teratomas, we determined that only one colony type represented bona fide iPS cells, whereas the others represented reprogramming intermediates. Proviral silencing and expression of TRA-1-60, DNMT3B, and REX1 distinguished the fully reprogrammed state, whereas Alkaline Phosphatase, SSEA-4, GDF3, hTERT and NANOG proved insufficient as markers. Reprogramming in chemically defined medium favored formation of bona fide iPS cell colonies relative to partially reprogrammed colonies. These data highlight the need for rigorous characterization and standardization of putative iPS cells.

Stem cell biologists creating cells and tissues for therapies, disease modeling, and drug screening have observed that differentiating pluripotent stem cells (PSCs) tend to produce cells at an embryonic stage of development but have difficulty maturing into adult definitive cells. A better understanding of developmental maturation will provide insights into embryogenesis and permit more accurate disease modeling. In the hematopoietic system, primitive and definitive cells are distinguished by functional transplantation assays, well characterized cell surface antigens, and gene expression signatures. We examined the transition in vivo in transplanted murine hematopoietic stem cells (HSCs) and in vitro in human PSC (hPSC) derived red blood cells (RBCs). We found that the hematopoietic microenvironment of the recipient significantly affects the outcome of HSC transplantation. The earliest embryonic HSCs perform better in neonatal recipients, whereas more mature adult-like HSCs perform better in adult recipients. The preference may be related to different active hematopoietic niches in neonates and adults, as we observed adult HSCs homing to different tissues in neonatal and adult recipients. Additionally, we found that proliferation may enhance the neonatal engraftment potential of adult-like HSCs. Our data highlight the importance of the host environment on transplantation outcomes, and point to the neonatal transplant model as a tool to functionally examine the earliest HSCs and primitive derivatives of PSCs.