From neural stem cells to precursors : Molecular regulation of self-renewal and differentiation

Stem cells are responsible for tissue turnover throughout lifespan. Only highly controlled specific environment, the stem cell niche , can sustain undifferentiated stem cell-pool. The balance between maintenance and differentiation is crucial for individual s health: uncontrolled stem cell self-renewal or proliferation can lead to hyperplasia and mutations that further provoke malignant transformation of the cells. On the other hand, uninhibited differentiation may result in diminished stem cell population, which is unable to maintain tissue turnover. The mechanisms that control the switch from maintenance to differentiation in stem cells are not well known. The same mechanisms that direct the self-renewal and proliferation in normal stem cells are likely to be also involved in maintenance of cancer stem cell . Cancer stem cells exhibit stem cell like properties such as self-renewal- and differentiation capacity and they can also regenerate the tumor tissue. In this thesis, I have investigated the effect of classical oncogenes E6/E7 and c-Myc, tumor suppressors p53 and retinoblastoma (pRb) family, and vascular endothelial growth factor (VEGF) subfamily and glial cell line-derived neurothropic factor (GDNF) family ligands on behavior of embryonic neural stem cells (NSCs) and progenitors. The study includes also the characterization of cytoskeletal tumor suppressor neurofibromatosis 2 (NF2) protein merlin and ezrin-radixin-moesin (ERM) protein ezrin expression in neural progenitors cells and their progeny. This study reveals some potential mechanisms regarding to NSCs maintenance. In summary, the studied molecules are able to shift the balance either towards stem cell maintenance or differentiation; tumor suppressor p53 represses whereas E6/E7 oncogenes and c-Myc increase the proportion of self-renewing and proliferating NSCs or progenitors. The data suggests that active MEK-ERK signaling is critical for self-renewal of normal and oncogene expressing NSCs. In addition, the results indicate that expression of cytoskeletal tumor suppressor merlin and ERM protein ezrin in central nervous system (CNS) tissue and progenitors indicates their role in cell differentiation. Furthermore, the data suggests that VEGF-C a factor involved in lymphatic system development, angiogenesis, neovascularization and metastasis but also in maintenance of some neural populations in brain is a novel thropic factor for progenitors in early sympathetic nervous system (SNS). It seems that VEGF-C dose dependently through ERK-pathway supports the proliferation and survival of early sympathetic progenitor cells, and the effect is comparable to that of GDNF family ligands.

Modeling of heat and mass transfer for solid state fermentation process in tray bioreactor

A mathematical model is developed to simulate oxygen consumption, heat generation and cell growth in solid state fermentation (SSF). The fungal growth on the solid substrate particles results in the increase of the cell film thickness around the particles. The model incorporates this increase in the biofilm size which leads to decrease in the porosity of the substrate bed and diffusivity of oxygen in the bed. The model also takes into account the effect of steric hindrance limitations in SSF. The growth of cells around single particle and resulting expansion of biofilm around the particle is analyzed for simplified zero and first order oxygen consumption kinetics. Under conditions of zero order kinetics, the model predicts upper limit on cell density. The model simulations for packed bed of solid particles in tray bioreactor show distinct limitations on growth due to simultaneous heat and mass transport phenomena accompanying solid state fermentation process. The extent of limitation due to heat and/or mass transport phenomena is analyzed during different stages of fermentation. It is expected that the model will lead to better understanding of the transport processes in SSF, and therefore, will assist in optimal design of bioreactors for SSF.

Cytomegalovirus in the Process of Chronic Allograft Nephropathy

Cytomegalovirus (CMV) is a major cause of morbidity, costs and even mortality in organ transplant recipients. CMV may also enhance the development of chronic allograft nephropathy (CAN), which is the most important cause of graft loss after kidney transplantation. The evidence for the role of CMV in chronic allograft nephropathy is somewhat limited, and controversial results have also been reported. The aim of this study was to investigate the role of CMV in the pathogenesis of CAN. Material for the purpose of this study was available from altogether 70 kidney transplant recipients who received a kidney transplant between the years 1992-2000. CMV infection was diagnosed with pp65 antigenemia test or by viral culture from blood, urine, or both. CMV proteins were demonstrated in the kidney allograft biopsies by immunohistochemisrty and CMV-DNA by in situ hybridization. Cytokines, adhesion molecules, and growth factors were demonstrated from allograft biopsies by immunohistochemistry, and from urinary samples by ELISA-methods. CMV proteins were detectable in the 6-month protocol biopsies from 18/41 recipients with evidence of CMV infection. In the histopathological analysis of the 6-month protocol biopsies, presence of CMV in the allograft together with a previous history of acute rejection episodes was associated with increased arteriosclerotic changes in small arterioles. In urinary samples collected during CMV infection, excretion of TGF-β was significantly increased. In recipients with increased urinary excretion of TGF-β, increased interstitial fibrosis was recorded in the 6- month protocol biopsies. In biopsies taken after an active CMV infection, CMV persisted in the kidney allograft in 17/48 recipients, as CMV DNA or antigens were detected in the biopsies more than 2 months after the last positive finding in blood or urine. This persistence was associated with increased expression of TGF-β, PDGF, and ICAM-1 and with increased vascular changes in the allografts. Graft survival and graft function one and two years after transplantation were reduced in recipients with persistent intragraft CMV. Persistent intragraft CMV infection was also a risk factor for reduced graft survival in Cox regression analysis, and an independent risk factor for poor graft function one and two years after transplantation in logistic regression analysis. In conclusion, these results show that persistent intragraft CMV infection is detrimental to kidney allografts, causing increased expression of growth factors and increased vascular changes, leading to reduced graft function and survival. Effective prevention, diagnosis and treatment of CMV infections may a major factor in improving the long term survival of kidney allograft.

Hematopoietic Stem Cell Development and Transcriptional Regulation

The continuous production of blood cells, a process termed hematopoiesis, is sustained throughout the lifetime of an individual by a relatively small population of cells known as hematopoietic stem cells (HSCs). HSCs are unique cells characterized by their ability to self-renew and give rise to all types of mature blood cells. Given their high proliferative potential, HSCs need to be tightly regulated on the cellular and molecular levels or could otherwise turn malignant. On the other hand, the tight regulatory control of HSC function also translates into difficulties in culturing and expanding HSCs in vitro. In fact, it is currently not possible to maintain or expand HSCs ex vivo without rapid loss of self-renewal. Increased knowledge of the unique features of important HSC niches and of key transcriptional regulatory programs that govern HSC behavior is thus needed. Additional insight in the mechanisms of stem cell formation could enable us to recapitulate the processes of HSC formation and self-renewal/expansion ex vivo with the ultimate goal of creating an unlimited supply of HSCs from e.g. human embryonic stem cells (hESCs) or induced pluripotent stem cells (iPS) to be used in therapy. We thus asked: How are hematopoietic stem cells formed and in what cellular niches does this happen (Papers I, II)? What are the molecular mechanisms that govern hematopoietic stem cell development and differentiation (Papers III, IV)? Importantly, we could show that placenta is a major fetal hematopoietic niche that harbors a large number of HSCs during midgestation (Paper I)(Gekas et al., 2005). In order to address whether the HSCs found in placenta were formed there we utilized the Runx1-LacZ knock-in and Ncx1 knockout mouse models (Paper II). Importantly, we could show that HSCs emerge de novo in the placental vasculature in the absence of circulation (Rhodes et al., 2008). Furthermore, we could identify defined microenvironmental niches within the placenta with distinct roles in hematopoiesis: the large vessels of the chorioallantoic mesenchyme serve as sites of HSC generation whereas the placental labyrinth is a niche supporting HSC expansion (Rhodes et al., 2008). Overall, these studies illustrate the importance of distinct milieus in the emergence and subsequent maturation of HSCs. To ensure proper function of HSCs several regulatory mechanisms are in place. The microenvironment in which HSCs reside provides soluble factors and cell-cell interactions. In the cell-nucleus, these cell-extrinsic cues are interpreted in the context of cell-intrinsic developmental programs which are governed by transcription factors. An essential transcription factor for initiation of hematopoiesis is Scl/Tal1 (stem cell leukemia gene/T-cell acute leukemia gene 1). Loss of Scl results in early embryonic death and total lack of all blood cells, yet deactivation of Scl in the adult does not affect HSC function (Mikkola et al., 2003b. In order to define the temporal window of Scl requirement during fetal hematopoietic development, we deactivated Scl in all hematopoietic lineages shortly after hematopoietic specification in the embryo . Interestingly, maturation, expansion and function of fetal HSCs was unaffected, and, as in the adult, red blood cell and platelet differentiation was impaired (Paper III)(Schlaeger et al., 2005). These findings highlight that, once specified, the hematopoietic fate is stable even in the absence of Scl and is maintained through mechanisms that are distinct from those required for the initial fate choice. As the critical downstream targets of Scl remain unknown, we sought to identify and characterize target genes of Scl (Paper IV). We could identify transcription factor Mef2C (myocyte enhancer factor 2 C) as a novel direct target gene of Scl specifically in the megakaryocyte lineage which largely explains the megakaryocyte defect observed in Scl deficient mice. In addition, we observed an Scl-independent requirement of Mef2C in the B-cell compartment, as loss of Mef2C leads to accelerated B-cell aging (Gekas et al. Submitted). Taken together, these studies identify key extracellular microenvironments and intracellular transcriptional regulators that dictate different stages of HSC development, from emergence to lineage choice to aging.

Augmenting process elicitation with visual priming: An empirical exploration of user behaviour and modelling outcomes

Business process models have become an effective way of examining business practices to identify areas for improvement. While common information gathering approaches are generally efficacious, they can be quite time consuming and have the risk of developing inaccuracies when information is forgotten or incorrectly interpreted by analysts. In this study, the potential of a role-playing approach to process elicitation and specification has been examined. This method allows stakeholders to enter a virtual world and role-play actions similarly to how they would in reality. As actions are completed, a model is automatically developed, removing the need for stakeholders to learn and understand a modelling grammar. An empirical investigation comparing both the modelling outputs and participant behaviour of this virtual world role-play elicitor with an S-BPM process modelling tool found that while the modelling approaches of the two groups varied greatly, the virtual world elicitor may not only improve both the number of individual process task steps remembered and the correctness of task ordering, but also provide a reduction in the time required for stakeholders to model a process view.

Water balance modelling in a tropical watershed under deciduous forest (Mule Hole, India): Regolith matric storage buffers the groundwater recharge process

Accurate estimations of water balance are needed in semi-arid and sub-humid tropical regions, where water resources are scarce compared to water demand. Evapotranspiration plays a major role in this context, and the difficulty to quantify it precisely leads to major uncertainties in the groundwater recharge assessment, especially in forested catchments. In this paper, we propose to assess the importance of deep unsaturated regolith and water uptake by deep tree roots on the groundwater recharge process by using a lumped conceptual model (COMFORT). The model is calibrated using a 5 year hydrological monitoring of an experimental watershed under dry deciduous forest in South India (Mule Hole watershed). The model was able to simulate the stream discharge as well as the contrasted behaviour of groundwater table along the hillslope. Water balance simulated for a 32 year climatic time series displayed a large year-to-year variability, with alternance of dry and wet phases with a time period of approximately 14 years. On an average, input by the rainfall was 1090 mm year(-1) and the evapotranspiration was about 900 mm year(-1) out of which 100 mm year(-1) was uptake from the deep saprolite horizons. The stream flow was 100 mm year(-1) while the groundwater underflow was 80 mm year(-1). The simulation results suggest that (i) deciduous trees can uptake a significant amount of water from the deep regolith, (ii) this uptake, combined with the spatial variability of regolith depth, can account for the variable lag time between drainage events and groundwater rise observed for the different piezometers and (iii) water table response to recharge is buffered due to the long vertical travel time through the deep vadose zone, which constitutes a major water reservoir. This study stresses the importance of long term observations for the understanding of hydrological processes in tropical forested ecosystems. (C) 2009 Elsevier B.V. All rights reserved.

Highly biocompatible and water-dispersible, amine functionalized magnetite nanoparticles, prepared by a low temperature, air-assisted polyol process: a new platform for bio-separation and diagnostics

A low temperature polyol process, based on glycolaldehyde mediated partial reduction of FeCl3 center dot 6H(2)O at 120 degrees C in the presence of sodium acetate as an alkali source and 2,2'-(ethylenedioxy)-bis-(ethylamine) as an electrostatic stabilizer has been used for the gram-scale preparation of biocompatible, water-dispersible, amine functionalized magnetite nanoparticles (MNPs) with an average diameter of 6 +/- 0.75 nm. With a reasonably high magnetization (37.8 e.m.u.) and amine groups on the outer surface of the nanoparticles, we demonstrated the magnetic separation and concentration implications of these ultrasmall particles in immunoassay. MRI studies indicated that these nanoparticles had the desired relaxivity for T-2 contrast enhancement in vivo. In vitro biocompatibility, cell uptake and MR imaging studies established that these nanoparticles were safe in clinical dosages and by virtue of their ultrasmall sizes and positively charged surfaces could be easily internalized by cancer cells. All these positive attributes make these functional nanoparticles a promising platform for further in vitro and in vivo evaluations.

Process variables in biomimetic synthesis of silver nanoparticles by aqueous extract of Azadirachta indica (Neem) leaves

Owing to widespread applications, synthesis and characterization of silver nanoparticles is recently attracting considerable attention. Increasing environmental concerns over chemical synthesis routes have resulted in attempts to develop biomimetic approaches. One of them is synthesis using plant parts, which eliminates the elaborate process of maintaining the microbial culture and often found to be kinetically favourable than other bioprocesses. The present study deals with investigating the effect of process variables like reductant concentrations, reaction pH, mixing ratio of the reactants and interaction time on the morphology and size of silver nanoparticles synthesized using aqueous extract of Azadirachta indica (Neem) leaves. The formation of crystalline silver nanoparticles was confirmed using X-ray diffraction analysis. By means of UV spectroscopy, Scanning and Transmission Electron Microscopy techniques, it was observed that the morphology and size of the nanoparticles were strongly dependent on the process parameters. Within 4 h interaction period, nanoparticles below 20-nm-size with nearly spherical shape were produced. On increasing interaction time (ageing) to 66 days, both aggregation and shape anisotropy (ellipsoidal, polyhedral and capsular) of the particles increased. In alkaline pH range, the stability of cluster distribution increased with a declined tendency for aggregation of the particles. It can be inferred from the study that fine tuning the bioprocess parameters will enhance possibilities of desired nano-product tailor made for particular applications.

Reactive Pulsed Laser Deposition of titanium nitride thin film: Optimization of process parameters using Secondary Ion Mass Spectrometry

Reactive Pulsed Laser Deposition is a single step process wherein the ablated elemental metal reacts with a low pressure ambient gas to form a compound. We report here a Secondary Ion Mass Spectrometry based analytical methodology to conduct minimum number of experiments to arrive at optimal process parameters to obtain high quality TiN thin film. Quality of these films was confirmed by electron microscopic analysis. This methodology can be extended for optimization of other process parameters and materials. (C) 2009 Elsevier B.V. All rights reserved.

'Wet N2O oxidation' process and interface state density characterization of nanoscale nitrided SiO2 for flash memory application

In this paper we first present the 'wet N2O' furnace oxidation process to grow nitrided tunnel oxides in the thickness range 6 to 8 nm on silicon at a temperature of 800 degrees C. Electrical characteristics of MOS capacitors and MOSFETs fabricated using this oxide as gate oxide have been evaluated and the superior features of this oxide are ascertained The frequency response of the interface states, before and after subjecting the MOSFET gate oxide to constant current stress, is studied using a simple analytical model developed in this work.

Numerical studies on channel formation and growth during solidification: Effect of process parameters

In the present work, solidification of a hyper-eutectic ammonium chloride solution in a bottom-cooled cavity (i.e. with stable thermal gradient) is numerically studied. A Rayleigh number based criterion is developed, which determines the conditions favorable for freckles formation. This criterion, when expressed in terms of physical properties and process parameters, yields the condition for plume formation as a function of concentration, liquid fraction, permeability, growth rate of a mushy layer and thermophysical properties. Subsequently, numerical simulations are performed for cases with initial and boundary conditions favoring freckle formation. The effects of parameters, such as cooling rate and initial concentration, on the formation and growth of freckles are investigated. It was found that a high cooling rate produced larger and more defined channels which are retained for a longer durations. Similarly, a lower initial concentration of solute resulted in fewer but more pronounced channels. The number and size of channels are also found to be related to the mushy zone thickness. The trends predicted with regard to the variation of number of channels with time under different process conditions are in accordance with the experimental observations reported in the literature.

Process makes perfect: High-performance design creates healthy environments for high-performance learning

Considering the staggering benefits of high-performance schools, it seems an obvious choice to “go green.” High-performance schools offer an exceptionally cost-effective means to enhance student learning, using on average 33 percent less energy than conventionally designed schools, and provide substantial health gains, including reduced respiratory problems and absenteeism. According to the 2006 study, Greening America's Schools, Costs and Benefits, co-sponsored by the American Institute of Architects (AIA) and Capital E, a green building consulting firm, high-performance lighting is a key element of healthy learning environments, contributing to improved test scores, reduced off-task behavior, and higher achievement among students. Few argue this point more convincingly than architect Heinz Rudolf, of Portland-Oregon-based Boora Architects, who has designed sustainable schools for more than 80 school districts in Oregon, Washington, Colorado, and Wyoming, and has pioneered the high-performance school movement. Boora's recently completed project, the Baker Prairie Middle School in Canby, Oregon is one of the most sustainable K-12 facilities in the state, and illustrates Rudolf's progressive and research-intensive approach to school design.

Automated Discovery of Structured Process Models: Discover Structured vs. Discover and Structure

This paper addresses the problem of discovering business process models from event logs. Existing approaches to this problem strike various tradeoffs between accuracy and understandability of the discovered models. With respect to the second criterion, empirical studies have shown that block-structured process models are generally more understandable and less error-prone than unstructured ones. Accordingly, several automated process discovery methods generate block-structured models by construction. These approaches however intertwine the concern of producing accurate models with that of ensuring their structuredness, sometimes sacrificing the former to ensure the latter. In this paper we propose an alternative approach that separates these two concerns. Instead of directly discovering a structured process model, we first apply a well-known heuristic technique that discovers more accurate but sometimes unstructured (and even unsound) process models, and then transform the resulting model into a structured one. An experimental evaluation shows that our “discover and structure” approach outperforms traditional “discover structured” approaches with respect to a range of accuracy and complexity measures.

Fracture process zone size and true fracture energy of concrete using acoustic emission

Acoustic emission (AE) energy, instead of amplitude, associated with each of the event is used to estimate the fracture process zone (FPZ) size. A steep increase in the cumulative AE energy of the events with respect to time is correlated with the formation of FPZ. Based on the AE energy released during these events and the locations of the events, FPZ size is obtained. The size-independent fracture energy is computed using the expressions given in the boundary effect model by least squares method since over-determined system of equations are obtained when data from several specimens are used. Instead of least squares method a different method is suggested in which the transition ligament length, measured from the plot of histograms of AE events plotted over the un-cracked ligament, is used directly to obtain size-independent fracture energy. The fracture energy thus calculated seems to be size-independent.

Process-dependent magnetic properties of Co-doped ZnO in bulk and thin film form

Structural, optical and magnetic studies of Co-doped ZnO have been carried out for bulk as well as thin films. The magnetic studies revealed the superparamagnetic nature for low-temperature synthesized samples, indicating the presence of cobalt metallic clusters, and this is supported by the optical studies. For the high-temperature sintered samples one obtains paramagnetism. The optical studies reveal the presence of Co2+ ions in the tetrahedral sites indicating proper doping. Interestingly, the films deposited by laser ablation from the paramagnetic target showed room temperature ferromagnetism. It appears that the magnetic nature of this system is process dependent.