Development and Validation of an Analytical Modeling Tool for Solar Borehole Heat Exchangers

Current numerical modeling solutions used for subsurface heat flow, such as the Berkeley TOUGH codes, are often difficult to use and time-consuming compared to analytical modeling methods. However, current analytical modeling methods for subsurface heat flow and groundwater cannot accurately model the subsurface in 3 dimensions, a feature paramount to the planning and installation of thermal borehole heat exchangers used in environmental remediation. This research developed a novel 3-dimensional analytical modeling tool for solar-powered borehole heat exchangers. The analytical modeling tool can plan thermal remediation systems while being more straightforward to operate than current numerical modeling software. By creating a publicly available tool to enable the efficient installation of solar borehole heat exchangers, this research aims to further the reach of remediation systems by optimizing their implementation, ultimately reducing groundwater contamination which harms our limited freshwater reserves and the environment. The 3-dimensional analytical modeling tool features a novel analytically based mathematical solution for heat flow with in-depth features similar to more complicated numerical models. The program can model heat conduction from multiple borehole heat exchangers in 3 dimensions with variable heat flow rates while accounting for surface boundary conditions and groundwater flow. The model can plot temperature readings and map thermal contours at any location. These novel features were then validated by testing the analytical model against the proven numerical TOUGH EOS1 and EOS3 numerical modeling codes. In addition, the model was tested against two field sites where the model developed here proved accurate when applied to real-world data

Neonatal Infection with Species C Adenoviruses Confirmed in Viable Cord Blood Lymphocytes

Credible but conflicting reports address the frequency of prenatal infection by species C adenovirus. This question is important because these viruses persist in lymphoid cells and suppress double-stranded DNA-break repair. Consequently, prenatal adenovirus infections may generate the aberrant clones of lymphocytes that precede development of childhood acute lymphoblastic leukemia (ALL). The present study was designed to overcome technical limitations of prior work by processing cord blood lymphocytes within a day of collection, and by analyzing sufficient numbers of lymphocytes to detect adenovirus-containing cells at the lower limits determined by our previous studies of tonsil lymphocytes. By this approach, adenoviral DNA was identified in 19 of 517 (3.7%) samples, providing definitive evidence for the occurrence of prenatal infection with species C adenoviruses in a significant fraction of neonates predominantly of African American and Hispanic ancestry. Cord blood samples were also tested for the presence of the ETV6-RUNX1 translocation, the most common genetic abnormality in childhood ALL. Using a nested PCR assay, the ETV6-RUNX1 transcript was detected in four of 196 adenovirus-negative samples and one of 14 adenovirus-positive cord blood samples. These findings indicate that this method will be suitable for determining concordance between adenovirus infection and the leukemia-associated translocations in newborns

The role of cytostructure in the control of protein synthesis and the prompt heat shock response

Bibliography: v.2, leaves 286-318.Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1987.Vita.by David Arnold Ornelles.Ph.D

Compartmentalisation and localisation of the translation initiation factor (eIF) 4F complex in normally growing fibroblasts

Previous observations of association of mRNAs and ribosomes with subcellular structures highlight the importance of localised translation. However, little is known regarding associations between eukaryotic translation initiation factors and cellular structures within the cytoplasm of normally growing cells. We have used detergent-based cellular fractionation coupled with immunofluorescence microscopy to investigate the subcellular localisation in NIH3T3 fibroblasts of the initiation factors involved in recruitment of mRNA for translation, focussing on eIF4E, the mRNA cap-binding protein, the scaffold protein eIF4GI and poly(A) binding protein (PABP). We find that these proteins exist mainly in a soluble cytosolic pool, with only a subfraction tightly associated with cellular structures. However, this "associated" fraction was enriched in active "eIF4F" complexes (eIF4E.eIF4G.eIF4A.PABP). Immunofluorescence analysis reveals both a diffuse and a perinuclear distribution of eIF4G, with the perinuclear staining pattern similar to that of the endoplasmic reticulum. eIF4E also shows both a diffuse staining pattern and a tighter perinuclear stain, partly coincident with vimentin intermediate filaments. All three proteins localise to the lamellipodia of migrating cells in close proximity to ribosomes, microtubules, microfilaments and focal adhesions, with eIF4G and eIF4E at the periphery showing a similar staining pattern to the focal adhesion protein vinculin

Role of the cytoskeleton in laminin induced mammary gene expression

The differentiation of rat mammary epithelial cells is characterized both by morphologic changes and by the expression of a group of milk protein genes. We have previously shown that by culturing these cells on the basement membrane glycoprotein laminin, the synthesis of the milk proteins, transferrin, Α-casein, and Α-lactalbumin is induced. In order to determine if this effect is mediated through the cytoskeleton, we have treated these cells with cytochalasin D and colchicine. Treatment with cytochalasin D or colchicine for 24 h inhibits the accumulation of Α-casein, transferrin, and Α-lactalbumin without significant effect on general protein synthesis. Pulse chase studies show that cytochalasin D does not alter the intracellular turnover of Α-casein or transferrin. Additionally, treatment with cytochalasin D causes an early (within 1 h) increase in secretion of Α-casein and transferrin suggesting that the actin cytoskeleton provides a meshwork for secretory vesicles. The disruption of this network enhances the secretion of preformed proteins. However, long term (24 h) treatment with cytochalasin D inhibits synthesis of these milk proteins. Northern blot analysis indicates that treatment with cytochalasin D or colchicine inhibits the laminin induced increase in Α-casein, Α-lactalbumin, and transferrin mRNAs. These studies indicate that the major effect of the cytoskeleton on laminin induced milk protein gene expression occurs at the level of accumulation of mRNAs for these proteins. We conclude that the expression of laminin induced milk protein gene expression in primary rat mammary cultures depends on the integrity of the actin and microtubule cytoskeleton.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/49876/1/1041350103_ftp.pd

Adenoviral Producer Cells

Adenovirus (Ad) vectors, in particular those of the serotype 5, are highly attractive for a wide range of gene therapy, vaccine and virotherapy applications (as discussed in further detail in this issue). Wild type Ad5 virus can replicate in numerous tissue types but to use Ad vectors for therapeutic purposes the viral genome requires modification. In particular, if the viral genome is modified in such a way that the viral life cycle is interfered with, a specific producer cell line is required to provide trans-complementation to overcome the modification and allow viral production. This can occur in two ways; use of a producer cell line that contains specific adenoviral sequences incorporated into the cell genome to trans-complement, or use of a producer cell line that naturally complements for the modified Ad vector genome. This review concentrates on producer cell lines that complement non-replicating adenoviral vectors, starting with the historical HEK293 cell line developed in 1977 for first generation Ad vectors. In addition the problem of replication-competent adenovirus (RCA) contamination in viral preparations from HEK293 cells is addressed leading to the development of alternate cell lines. Furthermore novel cell lines for more complex Ad vectors and alternate serotype Ad vectors are discussed

Adenovirus DNA in Guthrie cards from children who develop acute lymphoblastic leukaemia (ALL)

Aims: The aim of this thesis was to increase understanding of how molecular processes influence the development and risk assessment of childhood leukemia. Studies I and II investigates whether a specific virus infection in utero could be involved in a “first hit” in leukemogenesis. Studies III and IV examine whether alterations in protein expression from cell cycle regulating genes may predict a relapse in children with myeloid malignancies undergoing hematopoietic stem cell transplantation (HSCT). Background: Genetic alterations, analyzed at time of diagnosis in children who develop leukemia, have been traced back to neonatal dried blood spots (DBS). This suggests that the majority of chromosome translocations occur in utero during fetal hematopoiesis, generating a “first hit”. A “second hit” is then required to generate a leukemic clone. Today, experiments in vitro, animal models, and clinical observations have revealed that several viruses are oncogenic and capable of initiating a genetic alteration. Smith M postulated the theory that an in utero infection might be the “first hit”, causing genetic aberrations that could later lead to the development of the leukemic clone, which is supported by the early age of onset and space-time clustering data, based on time, place of birth, and diagnosis. Leukemia develops as a result of hematopoietic or lymphoid tissue with uncontrolled cell division. Normally cell division is controlled by the cell cycle, the network of which is complex with numerous regulating proteins both up and down stream, but also containing several feedback loops. The important regulators of this process are tumor suppressor genes, essential for normal cell proliferation and differentiation as well as for controlling DNA integrity. Errors in these genes or their protein expression affect the ability of the cell to check for DNA damage, thus tumors may occur. Proteins from these genes could serve as prognostic markers and predict relapse. Methods: In studies I and II we investigated neonatal DBS by PCR for the presence of adenovirus DNA (243 samples) and the three newly discovered polyomaviruses (50 samples) from children who later developed leukemia but also from controls (486 and 100 samples respectively). In studies III and IV we explored the expression of one (p53) respectively four (p53, p21, p16 and PTEN) cell cycle regulating proteins in bone marrow at diagnosis as well as pre and post HSCT in myeloid malignancies in children. We retrospectively collected clinical data and bone marrow samples from 33 children diagnosed with chronic myeloid malignancies (MDS, JMML and CML), 34 children diagnosed with AML as well as 55 controls. The samples were prepared by tissue micro array (TMA) as well as immunohistochemistry and examined for protein expression in a light microscope. Results: In study I we detected adenovirus DNA in only two patients who later developed leukemia, but in none of the controls. In study II all the samples were negative for KIPyV, WUPyV and MCPyV DNA in both patients and controls. In study III we found an overexpression of p53 protein at diagnosis that significantly predicted relapse after HSCT in children with rare chronic myeloid malignancies. In study IV a significantly higher p53 expression was found in the relapse compared to the non-relapse group at six months post HSCT in children with AML, suggesting that p53 may be used as prognostic markers for predicting a relapse. In addition, the calculated cut off level for p53 at diagnosis (study III) and at six months (study IV) post HSCT was approximately 20%, which indicates that a p53 expression over 20% may predict relapse in children with myeloid malignancies. Conclusion: Although we did not find an association between adenoviruses or the three newly discovered polyomaviruses and the development of childhood leukemia, a virus could still be involved in this process; the virus may have escaped detection, other new viruses could be involved or a virus could precipitate the “second hit”. We suggest that evaluation of p53 protein expression may be used as a supplement to regular prognostic markers both pre and post HSCT. To further evaluate this, a prospective multicenter study has been started

Adenovirus DNA is detected at increased frequency in Guthrie cards from children who develop acute lymphoblastic leukaemia

Epidemiological evidence suggests that childhood acute lymphoblastic leukaemia (ALL) may be initiated by an in infection in utero. Adenovirus DNA was detected in 13 of 49 neonatal blood spots from ALL patients but only in 3 of 47 controls (P=0.012) suggesting a correlation between prenatal adenovirus infection and the development of AL

Interactions Between Laminin Receptor and the Cytoskeleton During Translation and Cell Motility

Human laminin receptor acts as both a component of the 40S ribosomal subunit to mediate cellular translation and as a cell surface receptor that interacts with components of the extracellular matrix. Due to its role as the cell surface receptor for several viruses and its overexpression in several types of cancer, laminin receptor is a pathologically significant protein. Previous studies have determined that ribosomes are associated with components of the cytoskeleton, however the specific ribosomal component(s) responsible has not been determined. Our studies show that laminin receptor binds directly to tubulin. Through the use of siRNA and cytoskeletal inhibitors we demonstrate that laminin receptor acts as a tethering protein, holding the ribosome to tubulin, which is integral to cellular translation. Our studies also show that laminin receptor is capable of binding directly to actin. Through the use of siRNA and cytoskeletal inhibitors we have shown that this laminin receptor-actin interaction is critical for cell migration. These data indicate that interactions between laminin receptor and the cytoskeleton are vital in mediating two processes that are intimately linked to cancer, cellular translation and migration

Regulation of rat mammary gene expression by extracellular matrix components

In the mammary gland the induction and maintenance of differentiation are dependent on both lactogenic hormones and the extracellular matrix (ECM). Since mammary epithelial cells differentiate on a basement membrane in vivo we have examined the effects of basement membrane components on the expression of milk protein genes in primary rat mammary cultures. We examined the effects of a basement membrane gel derived from the Englebreth-Holm-Swarm tumor as well as its major component, laminin, on the expression of a group of milk protein genes. We demonstrate that the basement membrane gel induces [alpha]-casein and [alpha]-lactalbumin ([alpha]-LA) accumulation up to 160- and 70-fold, respectively, of that on tissue culture plastic. Laminin, a major component of the basement membrane, also caused significant induction of these same proteins. In order to determine whether these ECM effects occurred at a translational or post-translational level, pulse-chase experiments were performed. These experiments demonstrated that a laminin substratum selectively effects milk protein turnover and secretion. In order to demonstrate whether ECM effects occurred at the level of steady state accumulation of mRNA we performed dot blot and Northern analyses using cloned cDNA probes for [alpha]-, [beta]-, and [gamma]-caseins and [alpha]-LA. These studies demonstrated that ECM components induced [alpha]- and [beta]-caseins up to 10-fold and [alpha]-LA up to 3-fold, with no significant effect on [gamma]-casein. These results demonstrate that milk protein genes are not coordinately regulated by ECM components. Furthermore, since the amount of induction of milk proteins exceeds the amount of induction of mRNAs for these proteins, we conclude that in our system a major effect of ECM components is at the translational and/or post-translational levels. Based on these findings we propose a model in which basement membrane components effect mammary gene expression at multiple levels.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26485/1/0000021.pd