Comparison of the Effects of Recombinant Adenovirus-Mediated

Total Page:16

File Type:pdf, Size:1020Kb

Comparison of the Effects of Recombinant Adenovirus-Mediated Leukemia (2001) 15, 1225–1231 2001 Nature Publishing Group All rights reserved 0887-6924/01 $15.00 www.nature.com/leu Comparison of the effects of recombinant adenovirus-mediated expression of wild- type p53 and p27Kip1 on cell cycle and apoptosis in SUDHL-1 cells derived from anaplastic large cell lymphoma F Turturro1,2, AY Frist1, MD Arnold1, A Pal1, GA Cook1 and P Seth3 1Human Gene Therapy Research Institute, John Stoddard Cancer Center, and 2Division of Hematology-Oncology, VA Central Iowa Health Care System, 3University Research, Des Moines University, Des Moines, IA, USA Recombinant adenoviruses expressing wild-type p53 family including proteins such as p21Waf1 and p57Kip2.11 CKD- Kip1 (AdWTp53) and p27 (Adp27) were used to compare the Is induce cell cycle arrest in G1 by inhibiting the kinase effects on cell cycle and apoptosis in SUDHL-1 cells derived activity ofcomplex cyclin E-CDK2. It has been shown that from human anaplastic large cell lymphoma. Cells infected with Kip1 AdWTp53 and Adp27 showed high level of wild-type p53 and the interaction ofp27 with CDK2-cyclin E complex blocks p27Kip1 expression, respectively. The expression of these pro- phosphorylation ofCDK2 on Thr 160 via a CDK activation teins resulted in G1 arrest after 24 h of infection. Although the kinase.11 Cyclic AMP and other negative regulators ofthe cell cells persisted in G1 arrest in both cell populations after 48 and cycle induce p27Kip1.12 The expression ofp27 Kip1 is downregu- 72 h of infection, the level of apoptosis assessed by TUNEL lated by mitogens.13 Inhibition ofthe p27 Kip1 expression with analysis was higher in cells infected with AdWTp53. Interest- ingly, apoptosis was more pronounced in cells infected with antisense oligonucleotides antagonizes the response to 14 Adp27 after the initial 24 h and reached a steady state at 48 mitogen depletion preventing cell cycle arrest. This indicates and 72 h. A lower MOI of Adp27 resulted in G1 arrest associated that the protein is an essential component ofthe pathway that with a low level of apoptosis in SUDHL-1 cells after 48 h of relates mitogenic signals to the cell cycle.14 Lloyd et al11 have infection. This was correlated with lower expression of p27Kip1. recently defined p27Kip1 a multifunctional protein and have We postulate that the time-lag and the different level of analyzed its putative functions of CDK inhibition, tumor sup- apoptosis occurring in SUDHL-1 cells infected with AdWTp53 and Adp27 are clearly related to the intrinsic biochemical path- pression, induction of apoptosis and cell differentiation. The Kip1 ways solicited. In this context our study provides a model to relevance ofp27 as a prognostic factor and as a tumor investigate these pathways and better understand the biology suppressor protein is underscored by the low incidence of of this particular lymphoma. Our data also support a potential gene mutations in human malignancies.15,16 application of Adp27 for gene therapy of this lymphoma simi- These studies prompted us to investigate whether the larly to AdWTp53 as previously shown. Leukemia (2001) 15, expression ofp27 Kip1 by an adenoviral vector (Adp27) exerted 1225–1231. Keywords: adenovirus; p53; p27Kip1; cyclin-dependent kinase a function similar to exogenously expressed wtp53 in inhibitor; cell cycle; apoptosis SUDHL1cells. Our intent was to evaluate the potential appli- cation ofAdp27 in a cellular model previously used for wtp53, a prototype oftumor suppressor. 2,7 Introduction Apoptosis is involved in growth and differentiation of multi- Materials and methods cellular systems. It has recently been shown that apoptosis follows a persistent G1 arrest during the cell cycle.1 The tumor Cell culture and recombinant adenovirus infection suppressor p53 plays an important role as trans-activator of 7 gene expression ofproteins involved in the regulation ofcell SUDHL-1 cells have been previously described. Cells were cycle arrest.2,3 Mutations that inactivate the p53 tumor sup- cultured in RPMI 1640 (Life Technologies, Gaithersburg, MD, pressor gene are the most common genetic abnormalities in USA) containing 15% heat-inactivated FBS as previously 7 × 5 human malignancies. Genetically engineered p53-deficient described. SUDHL-1 cells (5 10 ) were infected as pre- mice develop spontaneous tumor.4 The tumor suppressor p53 viously described with 100 MOI ofAdNull (adenoviral vector backbone without c-DNA insert), AdWTp53 (expressing regulates the expression ofits target genes by binding to spe- Kip1 7,8,17 cific sequence ofDNA and by interacting with several wtp53) and Adp27 (expressing p27 ). Uninfected cells elements ofthe transcription complex. 1,5 One ofthe target were used as controls (mock). For some experiments 50 MOI proteins that mediates p53-induced cell cycle arrest is the ofAdNull and Adp27 were used. cyclin-dependent kinase inhibitor (CDK-I) p21Waf1.6 We have recently shown that wild-type p53 expressed by the adenovi- ral vector AdWTp53, induced apoptosis in SUDHL-1 cells, Western blot analysis derived from human anaplastic large cell lymphoma (ALCL).7 × 5 Several studies have recently demonstrated that adenoviral SUDHL-1 cells (5 10 ) were infected with recombinant vector-mediated expression ofp27 Kip1 induces cell cycle arrest adenoviruses as described above. Total proteins derived from and apoptosis in cell lines derived from epithelial malig- cells in each group ofinfectionwere separated on gradient nancies.8–10 The CDK-I p27Kip1 is a member ofthe Cip/Kip ready-made polyacrylamide gel (BioRad, Hercules, CA, USA) and transferred to nitrocellulose. Blots were incubated with blocking solution (5% dry milk in PBS/Tween 20) and then probed with primary antibodies anti-p53 (Ab-6, monoclonal; Correspondence: F Turturro, Human Gene Therapy Research Institute, 1415 Woodland Ave, Des Moines, IA, 50309–3203, USA; Fax +1 Oncogene Research Products, Cambridge, MA, USA) and 515–241–8788 anti-p27 (F-8, monoclonal; Santa Cruz Biotechnology, Santa Received 26 February 2001; accepted 23 April 2001 Cruz, CA, USA) for 1 h at room temperature. ␤-Actin antibody Cell cycle and apoptosis induced by exogenous expression of wild-type p53 and p27Kip1 F Turturro et al 1226 (AC-15; Sigma, St Louis, MO, USA) was used as control for some experiments. Blots were subsequently incubated with secondary anti-IgG-HRP conjugated antibody (Sigma). Blots were developed using ECL kit (Amersham Pharmacia, Piscata- way, NJ, USA) and exposed to X-ray film. Cell cycle analysis For DNA content analysis, cells were stained with propidium iodine (PI, Coulter Reagents Kit; Coulter, Miami, FL, USA), as previously described, and analyzed with an Epics cytometer (Coulter) in duplicate after 24, 48 and 72 h of infection.7 His- tograms ofthe percentage ofcells in the G1, G2 and S phase were expressed as mean ± s.d. Figure 1 Western blot analysis ofwtp53 and p27 Kip1 expression in SUDHL-1 cells after infection with AdWTp53 or Adp27. Cells were infected with 100 MOI of AdNull (adenovirus backbone) AdWTp53 or Adp27. Uninfected cells were used as controls (mock). After 24 h Flow cytometry analysis of apoptosis ofinfectioncell lysates were subjected to Western blot analysis with monoclonal antibody anti-p53 (a) and anti-p27 (b), as described in SUDHL-1 cells were stained for terminal deoxynucleotidyl Materials and methods. transferase (TUNEL) assay after 24, 48 and 72 h of infection with 100 MOI ofAdNull, AdWTp53 and Adp27 as previously described and according to the manufacturer’s instructions (Roche Molecular Biochemicals, Indianapolis, IN, USA).7 Uninfected cells were used as controls. Briefly, TUNEL assay is based on the use ofdeoxynucleotydil transferase(TdT) showed a fainter p53 band (Figure 1a). Unfortunately, the lack ofa control protein as a proofofequal load in this experiment which catalyzes polymerization offluorescein dUTP at strand Kip1 breaks (‘nicks’) offragmentedDNA cleaved during apoptosis. makes the observation that adenovirus-mediated p27 Fluorescein labels incorporated in nucleotide polymers expression downregulates endogenous p53 only speculative. present in cells undergoing apoptosis were analyzed for flu- Further investigation will be necessary. Moreover, SUDHL-1 cells infected with Adp27 showed high level of expression of orescence by using the Epics cytometer. For each group Kip1 (mock, AdNull, and each other viral vectors) one way ANOVA p27 that was absent in the control cells (Figure 1a). These ofthe log ofthe mean intensity ( =⌺log to lin [channel number] data show that recombinant adenovirus-mediated expression × count in the channel/area) ofFITC fluorescence was was highly efficient in these cells. obtained in duplicate.7 DAPI staining cytospin Cell cycle analysis Cells were spun on slides (cytospins) at 1000 r.p.m. for 10 The effects of AdWTp53 and Adp27 on the cell cycle of min and fixed with methanol after 24, 48 and 72 h of infection SUDHL-1 cells were determined by analyzing the DNA con- with AdNull, AdWTp53 and Adp27. Uninfected cells were tent ofthe infectedcells by flow cytometry at varying times used as controls. The nuclei ofthe cells were stained with after infection. Cells kept in separated flasks were analyzed 4Ј,6-diamindino-2-phenylindole (DAPI) for fragmented DNA from 24 h to 72 h after infection. Over this time interval, the content, as previously described.9 Briefly, DAPI was applied fraction of cells in G1 showed a steady increase in SUDHL-1 for 30 min at room temperature on cytospins of infected and cells infected with AdWTp53 and Adp27, whereas no change uninfected cells. After PBS washing, slides were viewed under occurred in the uninfected cells and in the cells infected with the fluorescence microscope. AdNull (Figure 2, upper panel). Except for the cells infected with Adp27 and cells infected with AdWTp53 at 24 h, none ofthe other test populations showed a significant change over Results the time in the fraction of cells in the G2 phase (Figure 2, middle panel). Either G2 arrest or increasing level ofcell Recombinant adenoviral-mediated expression of debris related to apoptosis may cause fluctuation ofthe wtp53 and p27Kip1 in SUDHL-1 cells determined by values, as shown by the broad standard deviation in Figure 2, Western blot analysis middle panel.
Recommended publications
  • Neurogenic Decisions Require a Cell Cycle Independent Function of The
    RESEARCH ARTICLE Neurogenic decisions require a cell cycle independent function of the CDC25B phosphatase Fre´ de´ ric Bonnet1†, Angie Molina1†, Me´ lanie Roussat1, Manon Azais2, Sophie Bel-Vialar1, Jacques Gautrais2, Fabienne Pituello1*, Eric Agius1* 1Centre de Biologie du De´veloppement, Centre de Biologie Inte´grative, Universite´ de Toulouse, CNRS, UPS, Toulouse, France; 2Centre de Recherches sur la Cognition Animale, Centre de Biologie Inte´grative., Universite´ de Toulouse, CNRS, UPS, Toulouse, France Abstract A fundamental issue in developmental biology and in organ homeostasis is understanding the molecular mechanisms governing the balance between stem cell maintenance and differentiation into a specific lineage. Accumulating data suggest that cell cycle dynamics play a major role in the regulation of this balance. Here we show that the G2/M cell cycle regulator CDC25B phosphatase is required in mammals to finely tune neuronal production in the neural tube. We show that in chick neural progenitors, CDC25B activity favors fast nuclei departure from the apical surface in early G1, stimulates neurogenic divisions and promotes neuronal differentiation. We design a mathematical model showing that within a limited period of time, cell cycle length modifications cannot account for changes in the ratio of the mode of division. Using a CDC25B point mutation that cannot interact with CDK, we show that part of CDC25B activity is independent *For correspondence: of its action on the cell cycle. [email protected] (FP); [email protected] (EA) †These authors contributed equally to this work Introduction In multicellular organisms, managing the development, homeostasis and regeneration of tissues Competing interests: The requires the tight control of self-renewal and differentiation of stem/progenitor cells.
    [Show full text]
  • On Cellular Automaton Approaches to Modeling Biological Cells
    ON CELLULAR AUTOMATON APPROACHES TO MODELING BIOLOGICAL CELLS MARK S. ALBER∗, MARIA A. KISKOWSKIy , JAMES A. GLAZIERz , AND YI JIANGx Abstract. We discuss two different types of Cellular Automata (CA): lattice-gas- based cellular automata (LGCA) and the cellular Potts model (CPM), and describe their applications in biological modeling. LGCA were originally developed for modeling ideal gases and fluids. We describe several extensions of the classical LGCA model to self-driven biological cells. In partic- ular, we review recent models for rippling in myxobacteria, cell aggregation, swarming, and limb bud formation. These LGCA-based models show the versatility of CA in modeling and their utility in addressing basic biological questions. The CPM is a more sophisticated CA, which describes individual cells as extended objects of variable shape. We review various extensions to the original Potts model and describe their application to morphogenesis; the development of a complex spatial struc- ture by a collection of cells. We focus on three phenomena: cell sorting in aggregates of embryonic chicken cells, morphological development of the slime mold Dictyostelium discoideum and avascular tumor growth. These models include intercellular and extra- cellular interactions, as well as cell growth and death. 1. Introduction. Cellular automata (CA) consist of discrete agents or particles, which occupy some or all sites of a regular lattice. These par- ticles have one or more internal state variables (which may be discrete or continuous) and a set of rules describing the evolution of their state and position (in older models, particles usually occupied all lattice sites, one particle per node, and did not move).
    [Show full text]
  • Proteomic and Bioinformatic Investigation of Altered Pathways in Neuroglobin-Deficient Breast Cancer Cells
    molecules Article Proteomic and Bioinformatic Investigation of Altered Pathways in Neuroglobin-Deficient Breast Cancer Cells Michele Costanzo 1,2 , Marco Fiocchetti 3 , Paolo Ascenzi 3, Maria Marino 3 , Marianna Caterino 1,2,* and Margherita Ruoppolo 1,2,* 1 Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; [email protected] 2 CEINGE—Biotecnologie Avanzate S.C.Ar.L., 80145 Naples, Italy 3 Department of Science, University Roma Tre, 00146 Rome, Italy; marco.fi[email protected] (M.F.); [email protected] (P.A.); [email protected] (M.M.) * Correspondence: [email protected] (M.C.); [email protected] (M.R.) Abstract: Neuroglobin (NGB) is a myoglobin-like monomeric globin that is involved in several processes, displaying a pivotal redox-dependent protective role in neuronal and extra-neuronal cells. NGB remarkably exerts its function upon upregulation by NGB inducers, such as 17β-estradiol (E2) and H2O2. However, the molecular bases of NGB’s functions remain undefined, mainly in non- neuronal cancer cells. Human MCF-7 breast cancer cells with a knocked-out (KO) NGB gene obtained using CRISPR/Cas9 technology were analyzed using shotgun label-free quantitative proteomics in comparison with control cells. The differential proteomics experiments were also performed after treatment with E2, H2O2, and E2 + H2O2. All the runs acquired using liquid chromatography–tandem mass spectrometry were elaborated within the same MaxQuant analysis, leading to the quantification Citation: Costanzo, M.; Fiocchetti, of 1872 proteins in the global proteomic dataset. Then, a differentially regulated protein dataset was M.; Ascenzi, P.; Marino, M.; Caterino, M.; Ruoppolo, M.
    [Show full text]
  • Increased Processing of SINE B2 Ncrnas Unveils a Novel Type Of
    RESEARCH ARTICLE Increased processing of SINE B2 ncRNAs unveils a novel type of transcriptome deregulation in amyloid beta neuropathology Yubo Cheng1,2,3,4†, Luke Saville1,2,3,4†, Babita Gollen1,2,3,4†, Christopher Isaac1,2,3,4†, Abel Belay1,2,3,4, Jogender Mehla3, Kush Patel1,2,3, Nehal Thakor1,2,3, Majid H Mohajerani3, Athanasios Zovoilis1,2,3,4* 1Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Canada; 2Southern Alberta Genome Sciences Centre, University of Lethbridge, Lethbridge, Canada; 3Canadian Centre for Behavioral Neuroscience, University of Lethbridge, Lethbridge, Canada; 4Alberta RNA Research and Training Institute, University of Lethbridge, Lethbridge, Canada Abstract The functional importance of many non-coding RNAs (ncRNAs) generated by repetitive elements and their connection with pathologic processes remains elusive. B2 RNAs, a class of ncRNAs of the B2 family of SINE repeats, mediate through their processing the transcriptional activation of various genes in response to stress. Here, we show that this response is dysfunctional during amyloid beta toxicity and pathology in the mouse hippocampus due to increased levels of B2 RNA processing, leading to constitutively elevated B2 RNA target gene expression and high Trp53 levels. Evidence indicates that Hsf1, a master regulator of stress response, mediates B2 RNA *For correspondence: processing in hippocampal cells and is activated during amyloid toxicity, accelerating the [email protected] processing of SINE RNAs and gene hyper-activation. Our study reveals that in mouse, SINE RNAs † constitute a novel pathway deregulated in amyloid beta pathology, with potential implications for These authors contributed equally to this work similar cases in the human brain, such as Alzheimer’s disease (AD).
    [Show full text]
  • Genetic Algorithms and Their Application to In-Silico Evolution of Genetic Regulatory Networks
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Hertfordshire Research Archive Genetic Algorithms and their Application to in-silico Evolution of Genetic Regulatory Networks Johannes F. Knabe‡†, Katja Wegner†, Chrystopher L. Nehaniv‡†, and Maria J. Schilstra†* †Biological and Neural Computation Laboratory, and ‡Adaptive Systems Research Group, STRI, University of Hertfordshire, Hatfield, AL10 9AB United Kingdom *To whom correspondence should be addressed ([email protected]) i. Abstract A genetic algorithm (GA) is a procedure that mimics processes occurring in Darwinian evolution to solve computational problems. A GA introduces variation through “mutation” and “recombination” in a “population” of possible solutions to a problem, encoded as strings of characters in “genomes”, and allows this population to evolve, using selection procedures that favor the gradual enrichment of the gene pool with the genomes of the “fitter” individuals. GA’s are particularly suitable for optimization problems in which an effective system design or set of parameter values is sought. In nature, genetic regulatory networks (GRN’s) form the basic control layer in the regulation of gene expression levels. GRN’s are composed of regulatory interactions between genes and their gene products, and are, inter alia, at the basis of the development of single fertilized cells into fully grown organisms. This paper describes how GA’s may be applied to find functional regulatory schemes and parameter values for models that capture the fundamental GRN characteristics. The central ideas behind evolutionary computation and GRN modeling, and the considerations in GA design and use are discussed, and illustrated with an extended example.
    [Show full text]
  • Self-Reproduction Based on Turing Machines
    MEASURES OF ORGANIZATION IN A MODEL OF CELLULAR SELF-REPRODUCTION BASED ON TURING MACHINES WALTER R. STAHL OREGON REGIONAL PRIMATE RESEARCH CENTER BEAVERTON, OREGON 1. Introductory summary The late John von Neumann first realized that self-reproduction, as observed in biological systems, was a legitimate problem of mathematics, specifically of automata and algorithm theory. He founded the study of self-reproduction in systems of "natural automata." This report deals with the self-organizing prop- erties of a new type of cellular self-reproduction model. The action of enzymes is simulated by Turing machines acting as molecular automata or computers, with their highly standardized coding corresponding to genes of the cell. Com- puter experiments have been done to test the stability and logical homeostatic properties of a 36 gene cell model. It is shown that the system will continue to organize itself and reproduce in spite of a variety of environmental deficiencies and disturbances, and also to repair itself after certain kinds of injury. The most pertinent organizational criteria for the described model are amounts of "energy" and "time cycles" needed to reach maturity and reproduce. Comparisons are drawn between these organizational measures and thermodynamic informa- tional parameters such as Gibbsean chemical potential and entropy. The total amount of genetic and cellular information can be quantified in the cell model and this helps clarify some confusing aspects of genetic information measures. The model is highly idealized. It bears somewhat the same relationship to real cells as computer circuits do to the brain, but shows that automata theory can be applied to molecular biology in a meaningful way.
    [Show full text]
  • Metabolic Network Modeling with Model Organisms
    Available online at www.sciencedirect.com ScienceDirect Metabolic network modeling with model organisms L Safak Yilmaz and Albertha JM Walhout Flux balance analysis (FBA) with genome-scale metabolic reconstruct a genome-scale metabolic network model network models (GSMNM) allows systems level predictions of (GSMNM), which is then used to calculate the flux metabolism in a variety of organisms. Different types of distribution over the entire network in any defined con- predictions with different accuracy levels can be made dition for the organism (see below). For model organisms, depending on the applied experimental constraints ranging high-quality genomic annotations allow the reconstruc- from measurement of exchange fluxes to the integration of tion of comprehensive GSMNMs that can be parame- gene expression data. Metabolic network modeling with model terized and validated with publically available experi- organisms has pioneered method development in this field. In mental datasets. In addition, since many properties of addition, model organism GSMNMs are useful for basic metabolic networks are conserved across taxa, model understanding of metabolism, and in the case of animal organism GSMNMs can be used to study human disease models, for the study of metabolic human diseases. Here, we with animal models, while plant models can instruct discuss GSMNMs of most highly used model organisms with agriculture. the emphasis on recent reconstructions. Here, we first summarize the basics of genome-scale meta- Address bolic network modeling, and then explore GSMNMs Program in Systems Biology, Program in Molecular Medicine, University and their applications in common model organisms [3] of Massachusetts Medical School, Worcester, MA, United States (Figure 1).
    [Show full text]
  • Multicellular Models Bridging Intracellular Signaling and Gene Transcription to Population Dynamics
    processes Article Multicellular Models Bridging Intracellular Signaling and Gene Transcription to Population Dynamics Mohammad Aminul Islam 1,† , Satyaki Roy 2,†, Sajal K. Das 2 and Dipak Barua 1,* 1 Department of Chemical and Biochemial Engineering, Missouri University of Science and Technology, Rolla, MO 65409, USA; [email protected] 2 Department of Computer Science, Missouri University of Science and Technology, Rolla, MO 65409, USA; [email protected] (S.R.); [email protected] (S.K.D.) * Correspondence: [email protected]; Tel.: +1-573-341-7560 † These authors contributed equally to this work. Received: 26 July 2018; Accepted: 31 October 2018; Published: 4 Novemeber 2018 Abstract: Cell signaling and gene transcription occur at faster time scales compared to cellular death, division, and evolution. Bridging these multiscale events in a model is computationally challenging. We introduce a framework for the systematic development of multiscale cell population models. Using message passing interface (MPI) parallelism, the framework creates a population model from a single-cell biochemical network model. It launches parallel simulations on a single-cell model and treats each stand-alone parallel process as a cell object. MPI mediates cell-to-cell and cell-to-environment communications in a server-client fashion. In the framework, model-specific higher level rules link the intracellular molecular events to cellular functions, such as death, division, or phenotype change. Cell death is implemented by terminating a parallel process, while cell division is carried out by creating a new process (daughter cell) from an existing one (mother cell). We first demonstrate these capabilities by creating two simple example models. In one model, we consider a relatively simple scenario where cells can evolve independently.
    [Show full text]
  • Multisite Mechanisms for Ultrasensitivity in Signal Transduction
    Noname manuscript No. (will be inserted by the editor) Multisite Mechanisms for Ultrasensitivity in Signal Transduction Germ´an A. Enciso the date of receipt and acceptance should be inserted later Abstract One of the key aspects in the study of cellular communication is understanding how cells receive a continuous input and transform it into a discrete, all-or-none output. Such so-called ultrasensitive dose responses can also be used in a variety of other contexts, from the efficient transport of oxygen in the blood to the regulation of the cell cycle and gene expression. This chapter provides a self contained mathematical review of the most important molecular models of ultrasensitivity in the literature, with an emphasis on mechanisms involving multisite modifications. The models described include two deeply influential systems based on allosteric behavior, the MWC and the KNF models. Also included is a description of more recent work by the author and colleagues of novel mechanisms using alternative hypotheses to create ultrasensitive behavior. Keywords Systems Biology · Ultrasensitivity · Allostery · Cooperativity · Signal Transduction 1 Introduction: Ultrasensitive Dose Responses Chemical reaction networks (CRN) lie at the heart of many biochemical pro- cesses inside the cell. They have been extensively modeled to understand the behavior of specific systems, and they have also been systematically studied at the theoretical level [5,14,21]. Although often implicitly assumed to con- verge globally towards a unique equilibrium in chemical engineering and other applications, CRNs can have exceedingly complex dynamical behavior. More- over, many biological systems have arguably evolved towards precisely such relatively rare complex examples, driven by a need to exhibit behaviors such as oscillations (e.g.
    [Show full text]
  • Integrated Approach for Identifying the Molecular, Cellular, and Host Responses to Chemical Insults
    Integrated Approach for Identifying the Molecular, Cellular, and Host Responses to Chemical Insults Audrey E. Fischer, Emily P. English, Julia B. Patrone, Kathlyn Santos, Jody B. G. Proescher, Rachel S. Quizon, Kelly A. Van Houten, Robert S. Pilato, Eric J. Van Gieson, and Lucy M. Carruth e performed a pilot study to characterize the molecular, cellular, and whole-organism response to nonlethal chemical agent exposure in the central nervous system. Multiple methodologies were applied to measure in vitro enzyme inhibition, neuronal cell pathway signaling, and in vivo zebrafish neural development in response to challenge with two different classes of chemical compounds. While all compounds tested exhibited expected enzyme inhibitory activity against acetylcholinesterase (AChE), a well-characterized target of chemical agents, distinct differences between chemical exposures were detected in cellular toxicity and pathway target responses and were tested in a zebrafish model. Some of these differences have not been detected using conventional chemical toxicity screening methods. Taken together, the data demonstrate the potential value of an integrated, multimethodological approach for improved target and pathway identification for subsequent diagnostic and therapeutic biomarker development. INTRODUCTION To build capability and leverage new and growing cell models to complete living organisms. Regardless of biology and chemistry expertise at APL, a collabora- the model selected, challenges exist in sample collection, tive, cross-departmental effort was established through a dose determination, and biases inherent in each assay/ series of related independent research and development technology. Therefore, multiple experimental methodol- (IR&D) projects. The focus of this effort was on mitiga- ogies brought to bear on a particular biological question tion of chemical and biological threat agents.
    [Show full text]
  • Evolution and Analysis of Genetic Networks for Stable Cellular Growth and Regeneration
    Honda Research Institute Europe GmbH https://www.honda-ri.de/ Evolution and Analysis of Genetic Networks for Stable Cellular Growth and Regeneration Lisa Schramm, Yaochu Jin, Bernhard Sendhoff 2012 Preprint: This is an accepted article published in Artificial Life. The final authenticated version is available online at: https://doi.org/[DOI not available] Powered by TCPDF (www.tcpdf.org) Evolution and Analysis of Genetic Lisa Schramm** Networks for Stable Cellular Technische Universität Darmstadt Growth and Regeneration Yaochu Jin† University of Surrey ‡ Bernhard Sendhoff*, Honda Research Institute Europe Abstract A computational model is presented that simulates stable growth of cellular structures that are in some cases capable of regeneration. In the model, cellular growth is governed by a Keywords gene regulatory network. By evolving the parameters and structure Cellular growth, development, of the genetic network using a modified evolution strategy, a regeneration, stability, gene regulatory network, motifs, evolutionary strategy dynamically stable state can be achieved in the developmental process, where cell proliferation and cell apoptosis reach an A version of this paper with color figures is equilibrium. The results of evolution with different setups in available online at http://dx.doi.org/10.1162/ fitness evaluation during the development are compared with artl_a_00075. Subscription required. respect to their regeneration capability as well as their gene regulatory network structure. Network motifs responsible for stable growth and regeneration that emerged from the evolution are also analyzed. We expect that our findings can help to gain a better understanding of the process of growth and regeneration inspired by biological systems, in order to solve complex engineering problems, such as the design of self-healing materials.
    [Show full text]
  • Cell-Substrate Mechanics Guide Collective Cell Migration Through Intercellular Adhesion: a Dynamic finite Element Cellular Model
    Noname manuscript No. (will be inserted by the editor) Cell-substrate mechanics guide collective cell migration through intercellular adhesion: A dynamic finite element cellular model Jieling Zhao∗ · Farid Manuchehrfar · Jie Liang Received: date / Accepted: date Abstract During the process of tissue formation and through intercellular adhesions. Our study illustrates regeneration, cells migrate collectively while remain- that our finite element cellular model can be employed ing connected through intercellular adhesions. However, to study broad problems of complex tissue in dynamic the roles of cell-substrate and cell-cell mechanical inter- changes at subcellular level. actions in regulating collective cell migration are still Keywords Collective cell migration · Finite element unclear. In this study, we employ a newly developed model · Cell-substrate mechanics · Intercellular finite element cellular model to study collective cell adhesion · DyCelFEM migration by exploring the effects of mechanical feed- back between cell and substrate and mechanical sig- nal transmission between adjacent cells. Our viscoelas- 1 Introduction tic model of cells consists many triangular elements and is of high-resolution. Cadherin adhesion between Cells are the fundamental units of living body. They cells are modeled explicitly as linear springs at sub- undergo programmed motilities and rearrangements to cellular level. In addition, we incorporate a mechano- form biological tissues (Alberts, 2008). During the pro- chemical feedback loop between cell-substrate mechan- cess of tissue formation and regeneration such as em- ics and Rac-mediated cell protrusion. Our model can bryonic development, organ morphogenesis, and wound reproduce a number of experimentally observed pat- healing, cells migrate collectively as adherent groups (Friedl terns of collective cell migration during wound heal- and Gilmour, 2009; Rørth, 2007).
    [Show full text]