At a glance: Cellular biology for engineers

Engineering contributions have played an important role in the rise and evolution of cellular biology. Engineering technologies have helped biologists to explore the living organisms at cellular and molecular levels, and have created new opportunities to tackle the unsolved biological problems. There is now a growing demand to further expand the role of engineering in cellular biology research. For an engineer to play an effective role in cellular biology, the first essential step is to understand the cells and their components. However, the stumbling block of this step is to comprehend the information given in the cellular biology literature because it best suits the readers with a biological background. This paper aims to overcome this bottleneck by describing the human cell components as micro-plants that form cells as micro-bio-factories. This concept can accelerate the engineers' comprehension of the subject. In this paper, first the structure and function of different cell components are described. In addition, the engineering attempts to mimic various cell components through numerical modelling or physical implementation are highlighted. Next, the interaction of different cell components that facilitate complicated chemical processes, such as energy generation and protein synthesis, are described. These complex interactions are translated into simple flow diagrams, generally used by engineers to represent multi-component processes.

[1]  V. Labhasetwar,et al.  Biodegradable nanoparticles for cytosolic delivery of therapeutics. , 2007, Advanced drug delivery reviews.

[2]  T. Stearns,et al.  Centrosome Duplication A Centriolar Pas de Deux , 2001, Cell.

[3]  S. Stupp,et al.  Supramolecular Materials: Self-Organized Nanostructures , 1997, Science.

[4]  C. Matthai,et al.  Simulation studies of protein translocation in mitochondria , 2004 .

[5]  J. M. T. Thompson,et al.  An introduction to the mechanics of DNA , 2004, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[6]  M. McNiven,et al.  Disruption of Golgi structure and function in mammalian cells expressing a mutant dynamin. , 2000, Journal of cell science.

[7]  Emanuel Petricoin,et al.  Molecular profiling of human cancer , 2000, Nature Reviews Genetics.

[8]  Arkaitz Carracedo,et al.  Cannabinoids induce apoptosis of pancreatic tumor cells via endoplasmic reticulum stress-related genes. , 2006, Cancer research.

[9]  Anders Liljas,et al.  Structural aspects of protein synthesis , 2004, Nature Structural Biology.

[10]  Klaus-Peter Zauner,et al.  Molecular Information Technology , 2005 .

[11]  B. Weigl,et al.  Lab-on-a-chip for drug development. , 2003, Advanced drug delivery reviews.

[12]  L. Guarente,et al.  Link between aging and the nucleolus. , 1997, Genes & development.

[13]  L. Hermo,et al.  The structure of the Golgi apparatus: a sperm’s eye view in principal epithelial cells of the rat epididymis , 1998, Histochemistry and Cell Biology.

[14]  G. Karp.  Cell and molecular biology : concepts and experiments / Gerald Karp , 1996 .

[15]  G. Tigyi,et al.  A glance at the structural and functional diversity of membrane lipids. , 2007, Methods in molecular biology.

[16]  Matsuhiko Nishizawa,et al.  An enzyme-based microfluidic biofuel cell using vitamin K3-mediated glucose oxidation , 2007 .

[17]  William J Croft.  Under the Microscope: A Brief History of Microscopy , 2006 .

[18]  Feng Gao,et al.  An enzymatic glucose/O2 biofuel cell: Preparation, characterization and performance in serum , 2007 .

[19]  A. Claude,et al.  FRACTIONATION OF MAMMALIAN LIVER CELLS BY DIFFERENTIAL CENTRIFUGATION , 1946, The Journal of experimental medicine.

[20]  S. Suresh,et al.  Cell and molecular mechanics of biological materials , 2003, Nature materials.

[21]  Pamela A. Silver,et al.  Nuclear transport and cancer: from mechanism to intervention , 2004, Nature Reviews Cancer.

[22]  Roger Brent,et al.  A partnership between biology and engineering , 2004, Nature Biotechnology.

[23]  K. Kosik.  The neuronal microRNA system , 2006, Nature Reviews Neuroscience.

[24]  W. Gordon Whaley,et al.  The Golgi Apparatus , 1975, Cell Biology Monographs.

[25]  George P Cobb,et al.  microRNAs as oncogenes and tumor suppressors. , 2007, Developmental biology.

[26]  Akihiro Kusumi,et al.  Detection of non-Brownian diffusion in the cell membrane in single molecule tracking. , 2005, Biophysical journal.

[27]  J. Paul Luzio,et al.  Lysosomes: fusion and function , 2007, Nature Reviews Molecular Cell Biology.

[28]  Jamie H. D. Cate,et al.  Structural basis for mRNA and tRNA positioning on the ribosome , 2006, Proceedings of the National Academy of Sciences.

[29]  M. Thiry,et al.  Birth of a nucleolus: the evolution of nucleolar compartments. , 2005, Trends in cell biology.

[30]  Federico Gallo,et al.  Regulating secretory lysosomes. , 2006, Journal of biochemistry.

[31]  E. Davidson,et al.  Modeling transcriptional regulatory networks. , 2002, BioEssays : news and reviews in molecular, cellular and developmental biology.

[32]  Jacques Ohayon,et al.  Transmission of Mechanical Stresses within the Cytoskeleton of Adherent Cells: A Theoretical Analysis Based on a Multi-Component Cell Model , 2004, Acta biotheoretica.

[33]  Herbert Schneckenburger,et al.  Microfluorometry of cell membrane dynamics , 2006, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[34]  E. Ruska,et al.  The development of the electron microscope and of electron microscopy , 1987 .

[35]  Alvis Brazma,et al.  Modelling in molecular biology: describing transcription regulatory networks at different scales , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[36]  Anthony H. Futerman,et al.  The cell biology of lysosomal storage disorders , 2004, Nature Reviews Molecular Cell Biology.

[37]  Richard Bertram,et al.  A simplified model for mitochondrial ATP production. , 2006, Journal of theoretical biology.

[38]  O. Kent,et al.  A small piece in the cancer puzzle: microRNAs as tumor suppressors and oncogenes , 2006, Oncogene.

[39]  I. Braakman,et al.  Protein folding and quality control in the endoplasmic reticulum. , 2004, Current opinion in cell biology.

[40]  Akihiro Kusumi,et al.  Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: high-speed single-molecule tracking of membrane molecules. , 2005, Annual review of biophysics and biomolecular structure.

[41]  P. Morlière,et al.  Endoplasmic reticulum and Golgi apparatus are the preferential sites of Foscan® localisation in cultured tumour cells , 2003, British Journal of Cancer.

[42]  M. Solaiyappan,et al.  Extracellular acidification alters lysosomal trafficking in human breast cancer cells. , 2003, Neoplasia.

[43]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[44]  K. Vinnakota,et al.  Computer Modeling of Mitochondrial Tricarboxylic Acid Cycle, Oxidative Phosphorylation, Metabolite Transport, and Electrophysiology* , 2007, Journal of Biological Chemistry.

[45]  V. Ambros,et al.  An Extensive Class of Small RNAs in Caenorhabditis elegans , 2001, Science.

[46]  R Eils,et al.  3D finite element analysis of uniaxial cell stretching: from image to insight , 2007, Physical biology.

[47]  Keisuke Morishima,et al.  Design principle and prototyping of a direct photosynthetic/metabolic biofuel cell (DPMFC) , 2006 .

[48]  Tim Stearns,et al.  Controlling centrosome number: licenses and blocks. , 2006, Current opinion in cell biology.

[49]  Hai-Tao He,et al.  Dynamics in the plasma membrane: how to combine fluidity and order , 2006, The EMBO journal.

[50]  W. Marshall,et al.  What is the function of centrioles? , 2007, Journal of cellular biochemistry.

[51]  Z. Ezziane.  DNA computing: applications and challenges , 2006 .

[52]  Donald G. Buerk,et al.  Biosensors: Theory and Applications , 1995 .

[53]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.

[54]  K. Guckian,et al.  Mimicking the Structure and Function of DNA: Insights into DNA Stability and Replication. , 2000, Angewandte Chemie.

[55]  Tammer A. Farid,et al.  Electron tunneling chains of mitochondria. , 2006, Biochimica et biophysica acta.

[56]  Zhiping Hu,et al.  The Study of Golgi Apparatus in Alzheimer’s Disease , 2007, Neurochemical Research.

[57]  Samuel I Stupp,et al.  Peptide-amphiphile nanofibers: A versatile scaffold for the preparation of self-assembling materials , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Christopher J. Fielding,et al.  Lipid rafts and caveolae : from membrane biophysics to cell biology , 2006 .

[59]  Peter Friedland,et al.  Discovering the Secrets of DNA , 1985, Computer.

[60]  Nadav Skjøndal-Bara,et al.  Dynamic Model of the Process of Protein Synthesis in Eukaryotic Cells , 2007 .

[61]  Thomas Cremer,et al.  Higher order chromatin architecture in the cell nucleus: on the way from structure to function , 2004, Biology of the cell.

[62]  Caroline Ash.  Hooke's microscope , 1998 .

[63]  R. Dahm.  Discovering DNA: Friedrich Miescher and the early years of nucleic acid research , 2007, Human Genetics.

[64]  Tom Misteli,et al.  The Cell Nucleus and Aging: Tantalizing Clues and Hopeful Promises , 2005, PLoS biology.

[65]  Joachim Frank,et al.  Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps. , 2006, Annual review of biophysics and biomolecular structure.

[66]  S. Singer,et al.  The Fluid Mosaic Model of the Structure of Cell Membranes , 1972, Science.

[67]  Frédéric Barrière,et al.  A laccase-glucose oxidase biofuel cell prototype operating in a physiological buffer , 2006 .

[68]  T. Henzinger,et al.  Executable cell biology , 2007, Nature Biotechnology.

[69]  G. Palade,et al.  The Golgi apparatus (complex)-(1954-1981)-from artifact to center stage , 1981, The Journal of cell biology.

[70]  Gregory A Weiss,et al.  The origins of chemical biology , 2006, Nature chemical biology.

[71]  D. Maysinger,et al.  Nanoparticles and cells: good companions and doomed partnerships. , 2007, Organic & biomolecular chemistry.

[72]  Michael Edidin,et al.  Lipids on the frontier: a century of cell-membrane bilayers , 2003, Nature Reviews Molecular Cell Biology.

[73]  H. Lodish.  Molecular Cell Biology , 1986 .

[74]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[75]  Oleg Varlamov,et al.  Dynamic transport of SNARE proteins in the Golgi apparatus. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[76]  F. Boisvert,et al.  The multifunctional nucleolus , 2007, Nature Reviews Molecular Cell Biology.

[77]  P. McNamara,et al.  Trends in RNA research , 2006 .

[78]  Dannel McCollum,et al.  Centrosomes in cellular regulation. , 2005, Annual review of cell and developmental biology.

[79]  P. Mazzarello.  A unifying concept: the history of cell theory , 1999, Nature Cell Biology.

[80]  Tushar K. Bera,et al.  Cell membrane as a model for the design of semifluorinated ion-selective nanostructured supramolecular systems , 2002 .

[81]  Allan J. Tobin,et al.  Asking About Cells , 1996 .

[82]  D. Germain,et al.  Targeting the Cytoplasmic and Nuclear Functions of Signal Transducers and Activators of Transcription 3 for Cancer Therapy , 2007, Clinical Cancer Research.

[83]  Guido Kroemer,et al.  Lysosomes and autophagy in cell death control , 2005, Nature Reviews Cancer.

[84]  M. Stewart.  Molecular mechanism of the nuclear protein import cycle , 2007, Nature Reviews Molecular Cell Biology.

[85]  Evgeny Nudler,et al.  RNA polymerase: the vehicle of transcription. , 2008, Trends in microbiology.

[86]  D. Crothers,et al.  Nucleic Acids: Structures, Properties, and Functions , 2000 .

[87]  I. Scheffler,et al.  A century of mitochondrial research: achievements and perspectives. , 2001, Mitochondrion.

[88]  M. Olivier.  A haplotype map of the human genome , 2003, Nature.

[89]  Robert W. Taylor,et al.  Mitochondrial DNA mutations in human disease , 2005, Nature Reviews Genetics.

[90]  Barbara Baird,et al.  Visualization of plasma membrane compartmentalization with patterned lipid bilayers. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[91]  M. Esteller.  Cancer epigenomics: DNA methylomes and histone-modification maps , 2007, Nature Reviews Genetics.

[92]  Marty C. Brandon,et al.  Mitochondrial mutations in cancer , 2006, Oncogene.

[93]  John L Cleveland,et al.  Targeting lysosomal degradation induces p53-dependent cell death and prevents cancer in mouse models of lymphomagenesis. , 2008, The Journal of clinical investigation.

[94]  Elizabeth W. Jones,et al.  Genetics: Analysis of Genes and Genomes , 2001 .

[95]  Reiko Nagai,et al.  Structural basis of cytoplasmic streaming in Characean internodal cells. A hydrodynamic analysis , 1988, Protoplasma.

[96]  Samuel I Stupp,et al.  Presentation of RGDS epitopes on self-assembled nanofibers of branched peptide amphiphiles. , 2006, Biomacromolecules.

[97]  John F. Marko,et al.  Introduction to Single-DNA Micromechanics , 2005 .

[98]  L. Zhang,et al.  Nanoparticles in Medicine: Therapeutic Applications and Developments , 2008, Clinical pharmacology and therapeutics.

[99]  C Zhu,et al.  Cell mechanics: mechanical response, cell adhesion, and molecular deformation. , 2000, Annual review of biomedical engineering.

[100]  B. Palsson,et al.  The evolution of molecular biology into systems biology , 2004, Nature Biotechnology.

[101]  Chi Li,et al.  Bax and Bak can localize to the endoplasmic reticulum to initiate apoptosis , 2003, The Journal of cell biology.

[102]  Jonathan S Weissman,et al.  Decay of Endoplasmic Reticulum-Localized mRNAs During the Unfolded Protein Response , 2006, Science.

[103]  A. Rowat,et al.  Characterization of the elastic properties of the nuclear envelope , 2005, Journal of The Royal Society Interface.

[104]  Albertha J. M. Walhout,et al.  Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. , 2006, Genome research.

[105]  M. Paul,et al.  Cancer — the mitochondrial connection , 2007, Biologia.

[106]  S. Joseph,et al.  After the ribosome structure: how does translocation work? , 2003, RNA.

[107]  Qiang Du,et al.  Modeling the spontaneous curvature effects in static cell membrane deformations by a phase field formulation , 2005 .

[108]  Ole H. Petersen,et al.  The Endoplasmic Reticulum as an Integrator of Multiple Dendritic Events , 2008, The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry.

[109]  James A. Shapiro,et al.  Genome Informatics: The Role of DNA in Cellular Computations , 2006 .

[110]  Jeff Hardin,et al.  The World of the Cell , 1986 .

[111]  Mark Stoneking,et al.  Mitochondrial DNA and human evolution. , 2005, Annual review of genomics and human genetics.

[112]  C G Orton,et al.  Medical physics: some recollections in diagnostic X-ray imaging and therapeutic radiology. , 2000, Radiology.

[113]  Eldon J. Gardner.  Principles of Genetics , 1961 .

[114]  W Alt,et al.  Cytoplasm dynamics and cell motion: two-phase flow models. , 1999, Mathematical biosciences.

[115]  David Tollervey,et al.  The function and synthesis of ribosomes , 2001, Nature Reviews Molecular Cell Biology.

[116]  Renaud Mahieux,et al.  Centrosome and retroviruses: The dangerous liaisons , 2007, Retrovirology.

[117]  D. Ron,et al.  Endoplasmic reticulum stress signaling in disease. , 2006, Physiological reviews.

[118]  Aarne Halme,et al.  Direct methanol biocatalytic fuel cell--considerations of restraints on electron transfer. , 2006, Biosensors & bioelectronics.

[119]  F. Barr,et al.  The Golgi apparatus: going round in circles? , 2002, Trends in cell biology.

[120]  Yehuda G Assaraf,et al.  Cytoplasmic Confinement of Breast Cancer Resistance Protein (BCRP/ABCG2) as a Novel Mechanism of Adaptation to Short-Term Folate Deprivation , 2005, Molecular Pharmacology.

[121]  R. Pillai.  MicroRNA function: multiple mechanisms for a tiny RNA? , 2005, RNA.

[122]  John M. Walker,et al.  Molecular Biology and Biotechnology , 1988 .

[123]  Andreas Deutsch,et al.  Dynamics of cell and tissue motion , 1997 .

[124]  Shelley D Minteer,et al.  Microchip-based ethanol/oxygen biofuel cell. , 2005, Lab on a chip.

[125]  M. Yoneyama,et al.  Cytoplasmic double-stranded DNA sensor , 2007, Nature Immunology.

[126]  U. Kubitscheck,et al.  Single nuclear pores visualized by confocal microscopy and image processing. , 1996, Biophysical journal.

[127]  N. Wang,et al.  Prestress mediates force propagation into the nucleus. , 2005, Biochemical and biophysical research communications.

[128]  M. C. Dal Canto,et al.  The Golgi apparatus and the pathogenesis of Alzheimer's disease. , 1996 .

[129]  C. Nicchitta,et al.  Stable ribosome binding to the endoplasmic reticulum enables compartment-specific regulation of mRNA translation. , 2005, Molecular biology of the cell.

[130]  Ed Hurt,et al.  Exporting RNA from the nucleus to the cytoplasm , 2007, Nature Reviews Molecular Cell Biology.

[131]  A. Linstedt,et al.  Capacity of the golgi apparatus for biogenesis from the endoplasmic reticulum. , 2003, Molecular biology of the cell.

[132]  M. Jäättelä,et al.  Lysosomes as targets for cancer therapy. , 2005, Cancer research.

[133]  A. Taddei,et al.  Active genes at the nuclear pore complex. , 2007, Current opinion in cell biology.

[134]  Murad Banaji,et al.  A generic model of electron transport in mitochondria. , 2006, Journal of theoretical biology.

[135]  E. Gulbins,et al.  Role of Mitochondria in Apoptosis , 2003, Experimental physiology.

[136]  Brian Storrie,et al.  Capacity of the Golgi apparatus for cargo transport prior to complete assembly. , 2006, Molecular biology of the cell.

[137]  D. Ron,et al.  Translational control in the endoplasmic reticulum stress response. , 2002, The Journal of clinical investigation.

[138]  T. Heimburg,et al.  Thermal Biophysics of Membranes , 2007 .

[139]  M. Qumsiyeh,et al.  Structure and function of the nucleus: anatomy and physiology of chromatin , 1999, Cellular and Molecular Life Sciences CMLS.

[140]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[141]  Andrea Ballabio,et al.  A block of autophagy in lysosomal storage disorders. , 2008, Human molecular genetics.

[142]  Peter J. Ortoleva,et al.  Simulating cellular dynamics through a coupled transcription, translation, metabolic model , 2003, Comput. Biol. Chem..

[143]  T. Kirchhausen,et al.  An emergency response team for membrane repair , 2005, Nature Reviews Molecular Cell Biology.

[144]  Howard J Worman,et al.  The nuclear envelope and human disease. , 2004, Physiology.

[145]  Pall Thordarson,et al.  Photoinduced reduction of catalytically and biologically active Ru(II)bisterpyridine-cytochrome c bioconjugates. , 2007, Chemical communications.

[146]  Alexander M. Gorlov,et al.  Helical Turbines for the Gulf Stream : Conceptual Approach to Design of a Large Scale Floating Power Farm , 1998 .

[147]  G. Kroemer,et al.  Mitochondria in cancer , 2006, Oncogene.

[148]  Ash A. Alizadeh,et al.  Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling , 2000, Nature.

[149]  Bruce R. Korf,et al.  Human Genetics and Genomics , 2006 .

[150]  M Bettencourt-Dias,et al.  Revisiting the Role of the Mother Centriole in Centriole Biogenesis , 2007, Science.

[151]  Bertrand Jordan,et al.  DNA Microarrays: Gene Expression Applications , 2001, Principles and Practice.