13,024 results for Journal article, ResearchSpace@Auckland

  • Integration of machining and inspection

    Zhao, Y; Xu, Xun (2012)

    Journal article
    The University of Auckland Library

    Fully automated machining would require automatic inspection process planning and real-time inspection result feedback. As inspection process planning is still based on G&M codes containing low-level information or vendor-specific bespoke routines, inspection process planning is mostly isolated from machining process planning. With the development of new data model standards such as STEP and STEP-NC providing high-level product information for the entire manufacturing chain, it is conceivable that both machining and inspection process planning are considered hand-in-hand to generate optimal machining and inspection sequences with real-time measurement result feedback. This paper introduces an integrated process planning system architecture for combined machining and inspection. On-machine inspection (OMI) is chosen to carry out inspection operations in-between machining operations and to provide real-time feedback to process planning. The system is able to automatically insert OMI operations for online measurement. A case study testified the feasibility of the proposed architecture.

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  • An innovative work-loop calorimeter for in vitro measurement of the mechanics and energetics of working cardiac trabeculae

    Taberner, Andrew; Han, June; Loiselle, Denis; Nielsen, Poul (2011)

    Journal article
    The University of Auckland Library

    We describe a unique work-loop calorimeter with which we can measure, simultaneously, the rate of heat production and force-length work output of isolated cardiac trabeculae. The mechanics of the force-length work-loop contraction mimic those of the pressure-volume work-loops experienced by the heart. Within the measurement chamber of a flow-through microcalorimeter, a trabecula is electrically stimulated to respond, under software control, in one of three modes: fixed-end, isometric, or isotonic. In each mode, software controls the position of a linear motor, with feedback from muscle force, to adjust muscle length in the desired temporal sequence. In the case of a work-loop contraction, the software achieves seamless transitions between phases of length control (isometric contraction, isometric relaxation, and restoration of resting muscle length) and force control (isotonic shortening). The area enclosed by the resulting force-length loop represents the work done by the trabecula. The change of enthalpy expended by the muscle is given by the sum of the work term and the associated amount of evolved heat. With these simultaneous measurements, we provide the first estimation of suprabasal, net mechanical efficiency (ratio of work to change of enthalpy) of mammalian cardiac trabeculae. The maximum efficiency is at the vicinity of 12%.

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  • Ribosomal DNA locus evolution in Nemesia: transposition rather than structural rearrangement as the key mechanism?

    Datson, PM; Murray, Brian (2006)

    Journal article
    The University of Auckland Library

    We investigated chromosome evolution in Nemesia using fluorescent in-situ hybridization (FISH) to identify the locations of 5S and 45S (18Y26S) ribosomal genes. Although there was conservation between Nemesia species in chromosome number, size and centromere position, there was large variation in both number and position of ribosomal genes in different Nemesia species (21 different arrangements of 45S and 5S rRNA genes were observed in the 29 Nemesia taxa studied). Nemesia species contained between one and three pairs of 5S arrays and between two and four pairs of 45S arrays. These were either sub-terminally or interstitially located and 45S and 5S arrays were often located on the same chromosome pair. Comparison of the positions of rDNA arrays with meiotic chromosome behaviour in interspecific hybrids of Nemesia suggests that some of the changes in the positions of rDNA have not affected the surrounding chromosome regions, indicating that rDNA has changed position by transposition. Chromosome evolution is frequently thought to occur via structural rearrangements such as inversions and translocations. We suggest that, in Nemesia, transposition of rDNA genes may be equally if not more important in chromosome evolution.

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  • Analysis of individual molecular events of DNA damage response by flow- and image-assisted cytometry.

    Darzynkiewicz, Z; Traganos, F; Zhao, H; Halicka, HD; Skommer, Joanna; Wlodkowic, Donald (2011)

    Journal article
    The University of Auckland Library

    This chapter describes molecular mechanisms of DNA damage response (DDR) and presents flow- and image-assisted cytometric approaches to assess these mechanisms and measure the extent of DDR in individual cells. DNA damage was induced by cell treatment with oxidizing agents, UV light, DNA topoisomerase I or II inhibitors, cisplatin, tobacco smoke, and by exogenous and endogenous oxidants. Chromatin relaxation (decondensation) is an early event of DDR chromatin that involves modification of high mobility group proteins (HMGs) and histone H1 and was detected by cytometry by analysis of the susceptibility of DNA in situ to denaturation using the metachromatic fluorochrome acridine orange. Translocation of the MRN complex consisting of Meiotic Recombination 11 Homolog A (Mre11), Rad50 homolog, and Nijmegen Breakage Syndrome 1 (NMR1) into DNA damage sites was assessed by laser scanning cytometry as the increase in the intensity of maximal pixel as well as integral value of Mre11 immunofluorescence. Examples of cytometric detection of activation of Ataxia telangiectasia mutated (ATM), and Check 2 (Chk2) protein kinases using phospho-specific Abs targeting Ser1981 and Thr68 of these proteins, respectively are also presented. We also discuss approaches to correlate activation of ATM and Chk2 with phosphorylation of p53 on Ser15 and histone H2AX on Ser139 as well as with cell cycle position and DNA replication. The capability of laser scanning cytometry to quantify individual foci of phosphorylated H2AX and/or ATM that provides more dependable assessment of the presence of DNA double-strand breaks is outlined. The new microfluidic Lab-on-a-Chip platforms for interrogation of individual cells offer a novel approach for DDR cytometric analysis.

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  • Integrated fuzzy signal and ramp-metering at a diamond interchange

    Pham, VC; Alam, F; Potgieter, J; Fang, FC; Xu, WL (2013-06)

    Journal article
    The University of Auckland Library

    We propose a fuzzy logic control for the integrated signal operation of a diamond interchange and its ramp meter, to improve traffic flows on surface streets and motorway. This fuzzy logic diamond interchange (FLDI) comprises of three modules: fuzzy phase timing (FPT) module that controls the green time extension of the current phase, phase logic selection (PLS) module that decides the next phase based on the pre-defined phase sequence or phase logic and, fuzzy ramp-metering (FRM) module that determines the cycle time of the ramp meter based on current traffic volumes and conditions of the surface streets and the motorways. The FLDI is implemented in Advanced Interactive Microscopic Simulator for Urban and Non-Urban Network Version 6 (AIMSUN 6), and compared with the traffic actuated signal control. Simulation results show that the FLDI outperforms the traffic-actuated models with lower system total travel time, average delay, and improvements in downstream average speed and average delay.

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  • Dynamic compensation control of flexible macro-micro manipulator systems

    Yang, TW; Xu, WL; Han, JD (2010)

    Journal article
    The University of Auckland Library

    Macro-micro architecture, which consists of macro and micro manipulators, is used here to eliminate errors at the tip of a flexible manipulator. The macro uses long arms and has such advantages as larger work volume and lower energy consumption but suffers from large deformations and vibrations. The micro is a smaller rigid manipulator and is attached on the end of the macro to isolate the system endpoint from the undesirable flexibility of the macro. Using perturbation theories, a new kinematical method is introduced, first, by redefining the micro's motion as a means of compensating for the errors at the endpoint of the macro. Then, an excellent practical control scheme is proposed to realize the endpoint control with the feedback of joint angles and vibrations. A PD controller is applied to the micro, which augmented the compensation quantities. To damp out vibrations, a nonlinear control law is proposed for the macro, taking the interacting dynamics of the micro to the macro into account. The compensation and control algorithms work very well on a macro-micro setup, and numerous experimental results prove the applicability of the proposed schemes.

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  • Quartz crystal microbalance induced bond rupture sensing for medical diagnostics

    van der Werff, M; Yuan, Y; Hirst, E; Xu, Peter; Chen, H; Bronlund, J (2007)

    Journal article
    The University of Auckland Library

    Disease detection at the point of care could be performed using quartz crystal microbalance (QCM) induced rupture of antibody-antigen bonds. An integrated digital solution for smart sensing is proposed where the QCM is driven and its resonant frequency change is captured as an indication of bond rupture. After reviewing the principle of QCM induced bond rupture, a digital transceiver system is designed and fabricated that integrates transmitter, receiver, amplification, and impedance matching. The system communicates with a PC and its functionalities are implemented in digital signal processor (DSP) software. A benchmark test using biotin and streptavidin bond is conducted and the encouraging results are given

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  • Apoptosis and beyond: cytometry in studies of programmed cell death.

    Wlodkowic, Donald; Telford, W; Skommer, Joanna; Darzynkiewicz, Z (2011)

    Journal article
    The University of Auckland Library

    A cell undergoing apoptosis demonstrates multitude of characteristic morphological and biochemical features, which vary depending on the inducer of apoptosis, cell type and the "time window" at which the process of apoptosis is observed. Because the gross majority of apoptotic hallmarks can be revealed by flow and image cytometry, the cytometric methods become a technology of choice in diverse studies of cellular demise. Variety of cytometric methods designed to identify apoptotic cells, detect particular events of apoptosis and probe mechanisms associated with this mode of cell death have been developed during the past two decades. In the present review, we outline commonly used methods that are based on the assessment of mitochondrial transmembrane potential, activation of caspases, DNA fragmentation, and plasma membrane alterations. We also present novel developments in the field such as the use of cyanine SYTO and TO-PRO family of probes. Strategies of selecting the optimal multiparameter approaches, as well as potential difficulties in the experimental procedures, are thoroughly summarized.

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  • Rise of the micromachines: microfluidics and the future of cytometry.

    Wlodkowic, Donald; Darzynkiewicz, Z (2011)

    Journal article
    The University of Auckland Library

    The past decade has brought many innovations to the field of flow and image-based cytometry. These advancements can be seen in the current miniaturization trends and simplification of analytical components found in the conventional flow cytometers. On the other hand, the maturation of multispectral imaging cytometry in flow imaging and the slide-based laser scanning cytometers offers great hopes for improved data quality and throughput while proving new vistas for the multiparameter, real-time analysis of cells and tissues. Importantly, however, cytometry remains a viable and very dynamic field of modern engineering. Technological milestones and innovations made over the last couple of years are bringing the next generation of cytometers out of centralized core facilities while making it much more affordable and user friendly. In this context, the development of microfluidic, lab-on-a-chip (LOC) technologies is one of the most innovative and cost-effective approaches toward the advancement of cytometry. LOC devices promise new functionalities that can overcome current limitations while at the same time promise greatly reduced costs, increased sensitivity, and ultra high throughputs. We can expect that the current pace in the development of novel microfabricated cytometric systems will open up groundbreaking vistas for the field of cytometry, lead to the renaissance of cytometric techniques and most importantly greatly support the wider availability of these enabling bioanalytical technologies.

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  • Biological implications of polymeric microdevices for live cell assays.

    Wlodkowic, Donald; Faley, S; Skommer, Joanna; McGuinness, D; Cooper, JM (2009-12-01)

    Journal article
    The University of Auckland Library

    Lab-on-a-chip technologies have the potential to deliver significant technological advances in modern biomedicine, through the ability to provide appropriate low-cost microenvironments for screening cells. However, to date, few studies have investigated the suitability of poly(dimethylsiloxane) (PDMS) for live cell culture. Here, we describe an inexpensive method for production of reusable, optical-grade PDMS microculture chips which provide a static and self-contained microwell system analogous to conventional polystyrene multiwell plates. We use these structures to probe the effects of PDMS upon live cell culture bioassays, using time-lapse fluorescence imaging to explore the toxicity of the substrate. We use three model systems to explore the efficacy of the microstructured devices: (i) live cell culture, (ii) adenoviral gene delivery to mammalian cells, and (iii) gravity enforced formation of multicellular tumor spheroids (MCTS). Results show that PDMS is nontoxic to cells, as their viability and growth characteristic in PDMS-based platforms is comparable to that of their polystyrene counterparts.

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  • Impaired DNA damage response--an Achilles' heel sensitizing cancer to chemotherapy and radiotherapy.

    Darzynkiewicz, Z; Traganos, F; Wlodkowic, Donald (2009-12-25)

    Journal article
    The University of Auckland Library

    Despite the progress in targeting particular molecular abnormalities specific to different cancers (targeted therapy), chemo- and radiotherapies are still the most effective of all anticancer modalities. Induction of DNA damage and inhibition of cell proliferation are the objects of most chemotherapeutic agents and radiation. Their effectiveness was initially thought to be due to the high rate of proliferation of cancer cells. However, normal cell proliferation rate in some tissues often exceeds that of curable tumors. Most tumors have impaired DNA damage response (DDR) and the evidence is forthcoming that this confers sensitivity to chemo- or radiotherapy. DDR is a complex set of events which elicits a plethora of molecular interactions engaging signaling pathways designed to: (a) halt cell cycle progression and division to prevent transfer of DNA damage to progeny cells; (b) increase the accessibility of the damaged sites to the DNA repair machinery; (c) engage DNA repair mechanisms and (d) activate the apoptotic pathway when DNA cannot be successfully repaired. A defective DDR makes cancer cells unable to effectively stop cell cycle progression, engage in DNA repair and/or trigger the apoptotic program when treated with DNA damaging drugs. With continued exposure to the drug, such cells accumulate DNA damage which leads to their reproductive death that may have features of cell senescence. Cancers with nonfunctional BRCA1 and BRCA2 are particularly sensitive to combined treatment with DNA damaging drugs and inhibitors of poly(ADP-ribose) polymerase. Antitumor strategies are being designed to treat cancers having particular defects in their DDR, concurrent with protecting normal cells.

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  • Interaction of a non-self-adjoint one-dimensional continuum and moving multi-degree-of-freedom oscillator

    Omenzetter, Piotr (2012)

    Journal article
    The University of Auckland Library

    A method for computing the dynamic responses due to the interaction of two non-self-adjoint systems: a linear, one-dimensional (1D) continuum and a linear, multi-degree-of-freedom (MDOF) oscillator travelling over the continuum, is presented. The solution method is applicable to a broad class of 1D continua, whose dynamics may be governed by various linear operators and subjected to different boundary conditions. The problem is reduced to the integration of a system of linear differential equations with time dependent coefficients. These coefficients are found to depend on eigenvalues as well as eigenfunctions and eigenvectors of the continuum and the oscillator. Two examples are included, representing bridge and railway track vibrations, to demonstrate the application of the method and discuss its convergence.

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  • Microfluidic single cell arrays to interrogate signalling dynamics of individual, patient-derived hematopoietic stem cells.

    Faley, SL; Copland, M; Wlodkowic, Donald; Kolch, W; Seale, KT; Wikswo, JP; Cooper, JM (2009-09-21)

    Journal article
    The University of Auckland Library

    Stem cells hold great promise as a means of treating otherwise incurable, degenerative diseases due to their ability both to self-renew and differentiate. However, stem cell damage can also play a role in the disease with the formation of solid tumors and leukaemias such as chronic myeloid leukaemia (CML), a hematopoietic stem cell (HSC) disorder. Despite recent medical advances, CML remains incurable by drug therapy. Understanding the mechanisms which govern chemoresistance of individual stem cell leukaemias may therefore require analysis at the single cell level. This task is not trivial using current technologies given that isolating HSCs is difficult, expensive, and inefficient due to low cell yield from patients. In addition, hematopoietic cells are largely non-adherent and thus difficult to study over time using conventional cell culture techniques. Hence, there is a need for new microfluidic platforms that allow the functional interrogation of hundreds of non-adherent single cells in parallel. We demonstrate the ability to perform assays, normally performed on the macroscopic scale, within the microfluidic platform using minimal reagents and low numbers of primary cells. We investigated normal and CML stem cell responses to the tyrosine kinase inhibitor, dasatinib, a drug approved for the treatment of CML. Dynamic, on-chip three-color cell viability assays revealed that differences in the responses of normal and CML stem/progenitor cells to dasatinib were observed even in the early phases of exposure, during which time normal cells exhibit a significantly elevated cell death rate, as compared to both controls and CML cells. Further studies show that dasatinib does, however, markedly reduce CML stem/progenitor cell migration in situ.

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  • Damage classification and estimation in experimental structures using time series analysis and pattern recognition

    De Lautour, OR; Omenzetter, Piotr (2010)

    Journal article
    The University of Auckland Library

    Developed for studying long sequences of regularly sampled data, time series analysis methods are being increasingly investigated for the use of Structural Health Monitoring (SHM). In this research, Autoregressive (AR) models were used to fit the acceleration time histories obtained from two experimental structures: a 3-storey bookshelf structure and the ASCE Phase II Experimental SHM Benchmark Structure, in undamaged and limited number of damaged states. The coefficients of the AR models were considered to be damage-sensitive features and used as input into an Artificial Neural Network (ANN). The ANN was trained to classify damage cases or estimate remaining structural stiffness. The results showed that the combination of AR models and ANNs are efficient tools for damage classification and estimation, and perform well using small number of damage-sensitive features and limited sensors.

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  • Prediction of seismic-induced structural damage using artificial neural networks

    de Lautour, OR; Omenzetter, Piotr (2009)

    Journal article
    The University of Auckland Library

    Contemporary methods for estimating the extent of seismic-induced damage to structures include the use of nonlinear finite element method (FEM) and seismic vulnerability curves. FEM is applicable when a small number of predetermined structures is to be assessed, but becomes inefficient for larger stocks. Seismic vulnerability curves enable damage estimation for classes of similar structures characterised by a small number of parameters, and typically use only one parameter to describe ground motion. Hence, they are unable to extend damage prognosis to wider classes of structures, e.g. buildings with a different number of storeys and/or bays, or capture the full complexity of the relationship between damage and seismic excitation parameters. Motivated by these shortcomings, this study presents a general method for predicting seismic-induced damage using Artificial Neural Networks (ANNs). The approach was to describe both the structure and ground motion using a large number of structural and ground motion properties. The class of structures analysed were 2D reinforced concrete (RC) frames that varied in topology, stiffness, strength and damping, and were subjected to a suite of ground motions. Dynamic structural responses were simulated using nonlinear FEM analysis and damage indices describing the extent of damage calculated. Using the results of the numerical simulations, a mapping between the structural and ground motion properties and the damage indices was than established using an ANN. The performance of the ANN was assessed using several examples and the ANN was found to be capable of successfully predicting damage.

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  • Application of time series analysis for bridge monitoring

    Omenzetter, Piotr; Brownjohn, JMW (2006)

    Journal article
    The University of Auckland Library

    Despite recent considerable advances in structural health monitoring (SHM) of civil infrastructure, converting large amounts of data from SHM systems into usable information and knowledge remains a great challenge. This paper addresses the problem through the analysis of time histories of static strain data recorded by an SHM system installed in a major bridge structure and operating continuously for a long time. The reported study formulates a vector seasonal autoregressive integrated moving average (ARIMA) model for the recorded strain signals. The coefficients of the ARIMA model are allowed to vary with time and are identified using an adaptive Kalman filter. The proposed method has been used for analysis of the signals recorded during the construction and service life of the bridge. By observing various changes in the ARIMA model coefficients, unusual events as well as structural change or damage sustained by the structure can be revealed.

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  • Flow cytometry-based apoptosis detection.

    Wlodkowic, Donald; Skommer, Joanna; Darzynkiewicz, Z (2009)

    Journal article
    The University of Auckland Library

    An apoptosing cell demonstrates multitude of characteristic morphological and biochemical features, which vary depending on the stimuli and the cell type. The gross majority of classical apoptotic hallmarks can be rapidly examined by flow and image cytometry. Cytometry thus became a technology of choice in diverse studies of cellular demise. A large variety of cytometric methods designed to identify apoptotic cells and probe mechanisms associated with this mode of cell demise have been developed during the past two decades. In the present chapter, we outline a handful of commonly used methods that are based on the assessment of: mitochondrial transmembrane potential, activation of caspases, plasma membrane alterations and DNA fragmentation.

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  • ER-Golgi network--a future target for anti-cancer therapy.

    Wlodkowic, Donald; Skommer, Joanna; McGuinness, D; Hillier, C; Darzynkiewicz, Z (2009-11)

    Journal article
    The University of Auckland Library

    Tumor cell demise is an important event in the elimination of abnormal malignant cells and provides an important mechanism of natural tumor suppression. Abnormalities incapacitating these finely tuned processes provide a strong advantage for cancer clones to succeed in evading both the physiological control systems and therapeutic intervention. Expanding our knowledge of the molecular "crosstalks" that regulate tumor cell demise is crucial in guiding the successful design of future anti-cancer therapeutics. Although currently available data indicate that elimination of malignant cells often depends on classical apoptotic pathways (mitochondrial and/or death-receptor pathways), the evidence is mounting that alternative apoptotic and non-apoptotic pathways may effectively contribute to tumor cell death. The assumption that every organelle is capable of sensing, amplificating and executing cell death is also a relatively novel and unexplored concept. As recently shown, the secretory pathway can be actively involved in sensing stress stimuli and possibly even initiating and propagating cell death signaling. Experimental evidence indicates that ER and Golgi apparatus can activate both pro-survival (recovery) mechanisms as well as cell suicide programs if the stress-signaling threshold is exceeded. It is thus conceivable that the fragile balance of protein trafficking between various subcellular compartments provides an exceptional therapeutic opportunity. Interestingly, a growing number of reports recognize novel therapeutic targets, including proteins in control of endoplasmic reticulum (ER) and Golgi homeostasis. Further studies are, however, needed to elucidate precise signaling pathways emanating from ER-Golgi compartment. Development of more potent and selective small-molecule drugs that activate ER-Golgi mediated cell demise is also needed. As the interest in the role of ER-Golgi network during cancer cell death has been gaining momentum, we attempt here to critically appraise current status of development of investigational anti-cancer agents that target ER and/or Golgi.

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  • Chip-based dynamic real-time quantification of drug-induced cytotoxicity in human tumor cells.

    Wlodkowic, Donald; Skommer, Joanna; McGuinness, D; Faley, S; Kolch, W; Darzynkiewicz, Z; Cooper, JM (2009-08-15)

    Journal article
    The University of Auckland Library

    Cell cytotoxicity tests are among the most common bioassays using flow cytometry and fluorescence imaging analysis. The permeability of plasma membranes to charged fluorescent probes serves, in these assays, as a marker distinguishing live from dead cells. Since it is generally assumed that probes, such as propidium iodide (PI) or 7-amino-actinomycin D (7-AAD), are themselves cytotoxic, they are currently generally used only as the end-point markers of assays for live versus dead cells. In the current study, we provide novel insights into potential applications of these classical plasma membrane integrity markers in the dynamic tracking of drug-induced cytotoxicity. We show that treatment of a number of different human tumor cell lines in cultures for up to 72 h with the PI, 7-AAD, SYTOX Green (SY-G), SYTOX Red (SY-R), TO-PRO, and YO-PRO had no effect on cell viability assessed by the integrity of plasma membrane, cell cycle progression, and rate of proliferation. We subsequently explore the potential of dynamic labeling with these markers in real-time analysis, by comparing results from both conventional cytometry and microfluidic chips. Considering the simplicity of the staining protocols and their low cost combined with the potential for real-time data collection, we show how that real-time fluorescent imaging and Lab-on-a-Chip platforms have the potential to be used for automated drug screening routines.

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  • Brefeldin A triggers apoptosis associated with mitochondrial breach and enhances HA14-1- and anti-Fas-mediated cell killing in follicular lymphoma cells.

    Wlodkowic, Donald; Skommer, Joanna; Pelkonen, J (2007-12)

    Journal article
    The University of Auckland Library

    Follicular lymphoma (FL) remains a fatal disease of increasing worldwide incidence. Since patients with FL eventually develop resistance to conventional anticancer agents, and due to BCL-2 overexpression present with profoundly compromised execution of mitochondrial pathway of apoptosis, targeting alternative pathways of cell demise may appear therapeutically beneficial. Herein we report for the first time the effects of an ER-Golgi transport inhibitor, Brefeldin A (BFA), alone and in combination with a small molecule Bcl-2 inhibitor HA14-1 or agonistic anti-Fas mAb, in the recently established human FL cell lines. All cell lines tested were sensitive to BFA-induced cytotoxicity and apoptosis. Moreover BFA-induced cell death was associated with profound ER stress, mitochondrial breach and subsequent caspase cascade activation, including caspase 2 activation. Interestingly, BFA-induced ER stress did not result in appearance of autophagic morphology in FL cells. Of importance, small molecule Bcl-2 antagonist, HA14-1 and agonistic anti-Fas mAb significantly enhanced BFA-mediated cytotoxicity and apoptosis, revealing novel and previously unexplored means to enhance ER stress-mediated cell killing in follicular lymphoma cells.

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