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Potential Roles for Diatomists in Nanotechnology

Potential Roles for Diatomists in Nanotechnology. Richard Gordon, Armchair Diatomist (i.e., Theoretical Biologist) University of Manitoba 17th North American Diatom Symposium, October 23, 2003. Workshop on Diatom Nanotechnology.

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Potential Roles for Diatomists in Nanotechnology

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  1. Potential Roles for Diatomistsin Nanotechnology Richard Gordon, Armchair Diatomist (i.e., Theoretical Biologist) University of Manitoba 17th North American Diatom Symposium, October 23, 2003

  2. Workshop on Diatom Nanotechnology • Supported by:National Institute of Biomedical Imaging and Bioengineering (NIBIB) at the U.S. National Institutes of Health

  3. PI Name: Kenneth H. Sandhage • PI Email: sandhage.1@osu.edu • PI Title: Co-Chair, with Richard Gordon (Canada) and Frithjof A.S. Sterrenburg (Netherlands) • Project Title: Diatom Nanotechnology Workshop • Abstract: We are organizing the world’s first workshop devoted to nanotechnology grown or fabricated with the aid of microrganisms known as diatoms. Diatoms are single-celled algae that make exterior shells consisting of amorphous silica nanoparticles that are self-assembled into ornate, three-dimensional structures. About 200,000 diatom species are available, each of which possesses a unique shape with fine (meso-to-nanoscale) features. The objective of this Workshop is to explore the utilization of diatoms, or diatom-derived structures, in nanotechnology. The Workshop will be part of the 17th North American Diatom Society meeting (http://serc.fiu.edu/periphyton/NADS/Homepage.html, organized by Evelyn Gaiser, Southeast Environmental Res. Ctr., Florida International University, gaisere@fiu.edu), October 21-26, 2003, at a field station on the Florida Keys. It will provide a unique opportunity for nanotechnologists and diatomists to interact and jumpstart this highly-interdisciplinary emerging field of research and development. Papers, in the form of reviews and tutorials, will be published in a special issue of the Journal of Nanoscience and Nanotechnology. Every group known to us, working on diatom nanotechnology, will be represented.

  4. A First (Ignored?) Paper • Gordon, R. & B.D. Aguda (1988). Diatom morphogenesis: natural fractal fabrication of a complex microstructure. In: Harris, G. & C. Walker, eds., Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Part 1/4: Cardiology and Imaging, 4-7 Nov.1988, New Orleans, LA, USA , New York: Institute of Electrical and Electronics Engineers, 10 , p. 273-274.

  5. Abstract • Diatom shells are intricate structures made by single algal cells with a spacing between parts of about 0.1 µm. They appear to be formed by instabilities in diffusion-limited precipitation of amorphous, colloidal silica. The patterns are apparently modified by surface diffusion during their formation. They present a possible means of microfabrication of intricate structures.

  6. Coming up • A special issue of Journal of Nanoscience and Nanotechnology on diatom nanotechnology is in the works. Guest editors: me, Ken Sandhage and Frithjof Sterrenburg • Ken wants to organize a whole conference on the subject for next year:Ken.Sandhage@mse.gatech.edu • Lots of papers and posters here on diatom nanotech, so I have as much to learn as the rest of you, and won’t attempt a review in the midst of the avalanche.

  7. Actually, diatom nanotech is 140 years old, started by Max Schultze (1825-1874) in 1863. Last cited 1876.

  8. Max Schultze’s diatom papersMax Johann Sigismund Schultze, 1825–74 German anatomist and histologist .Professor extraordinarius of anatomy, Halle University, 1854–9; professor of anatomy and director of the Anatomisches Institut, Bonn University, from 1859. Founder of the Archiv für mikroskopische Anatomie und Entwicklungsmechanik, 1865, and editor, 1865–74.http://darwin.lib.cam.ac.uk/perl/nav?pclass=name&pkey=Schultze%2C%20M.%20J.%20S. • Schultze, M.J.S. (1863a). The structure of diatom shells, compared with certain siliceous pellicles artificially prepared from fluoride of silicium/Die Structur der Diatomeenschale, verglichen mit gewissen aus Fluorkiesel kuenstlich darstellbaren Kieselhauten. Naturhistorischer Verein der Rheinlande und Westfalens Verhandlungen 20, 1-42. • Schultze, M.J.S. (1863b). On the structure of the valve in the Diatomacea, as compared with certain siliceous pellicles produced artificially by the decomposition in moist air of fluo-silicic acid gas (fluoride of silicium). Quart. J. Microscop. Sci.new series 3, 120-134. • Schultze, M.J.S. (1865). Die Bewegung der Diatomeen/The movement of diatoms. Archiv für Mikroskopische Anatomie1, 376-402.

  9. Where do the bumps and patterns come from? • It took 100 years before an explanation was forthcoming: • Mullins, W.W. & R.F. Sekerka (1963). Morphological stability of a particle growing by diffusion or heat flow. J. Appl. Physics34(2), 323-329.

  10. We now call it DLA =Diffusion Limited Aggregation • 1. For diatoms, need a spatially distributed source of silica particles, probably 50 nm or so spheres. • 2. These diffuse inside the silicalemma, a flat membrane bag inside the cell. This permits high silica concentration and prevents convection. • 3. Need a “sink”, a structure onto which the silica particles precipitate (“aggregate”). • 4. New particles must stick to already precipitated particles. • 5. Sintering smooths the precipitated structure.

  11. The DLA concept, nothing more than computer simulation of Mullins & Sekerka (1963), might actually have been introduced first for diatoms: “I agree, of course, that Mullins & Sekerka had the core idea. I met Bill Mullins at a meeting. I don't think he ever paid any attention to DLA.” Leonard M. Sander, Oct. 20, 2003. • Gordon, R., R.W. Drum & A. Thurlbeck (1980). The chemical basis for diatom morphogenesis: instabilities in diffusion-limited amorphous precipitation generate space filling branching patterns. In: Anon., Abstracts, The 39th Annual Symposium of The Society for Developmental Biology, Levels of Genetic Control in Development, Storrs: University of Connecticut, p. 5. • Gordon, R. (1980b. Numerical problems in simulating amorphous precipitation in diatoms. In Conference on Numerical Mathematics and Computing, October 2, 1980, Winnipeg University of Manitoba. • Gordon, R. (1981). The chemical basis for diatom morphogenesis: instabilities in diffusion-limited amorphous precipitation generate space filling branch patterns. Fed. Proc. 40, 827. • Witten Jr., T.A. & L.M. Sander (1981). Diffusion-limited aggregation, a kinetic phenomenon. Physical Review Letters47(19), 1400-1403. • Gordon, R. & R.W. Drum (1982). The chemical basis for diatom morphogenesis. I. Instabilities in diffusion-limited amorphous precipitation generate space filling branching patterns. In Anon., VII International Symposium on Recent and Fossil Diatoms, Abstracts, August 23, 1982, Philadelphia, Philadelphia Academy of Natural Sciences.

  12. Here’s a pennate diatom such as we’d like to simulate This & following from: Gordon, R. & R.W. Drum (1994). The chemical basis for diatom morphogenesis. Int. Rev. Cytol.150, 243-372, 421-422.

  13. Spatially distributed sources of silica: pennate diatom case Bumps stick out into a higher concentration and so grow faster: positive feedback

  14. Result is a fractal pattern, a bit reminiscent of costae, but frayed Moving boundary of the silicalemma Concentrationprofile This is a fractal pattern: looks the same if magnified, i.e, independent of scale: NOT like diatoms

  15. But, actually, not so bad, if one looks for an aberrant diatom that fits the simulation! by Ryan Drum

  16. Sintering smooths the structure,but it still doesn’t look good

  17. Sintering may occur via a bipedal walk as silica diffuses over precipitated silica, as hypothesized for water molecules moving over ice

  18. Let’s try this on a centric diatom

  19. DLA for a centric diatom, with a circular silicalemma

  20. Unconstrained DLA showing time coursehttp://www-personal.umich.edu/~lsander/

  21. Sintering is kind of lumpy Black/ white labelling shows “growth rings” Vicsek, T. (1992). Fractal Growth Phenomena, 2nd ed., Singapore World Scientific.

  22. But some centrics do have gentle bending of costaeCyclotella stelligera by Hedy Kling

  23. Others still mystify me with “crystalline” domains somehow made of amorphous silicaThalassiosira eccentrica by Gretha Hasle

  24. Puzzle:If DLA (diffusion limited aggregation) is necessary but not sufficient, what else is going on in diatom shell (valve) morphogenesis?The answer may be fundamental to deliberate control of silica precipitation needed for diatom nanotechnology.

  25. One common answer is:Prepatterns These are an intellectual nightmare, because they imply that a visible biological pattern just follows an invisible pattern of something else. At some point the regress must stop. That’s why I pushed the DLA approach as hard as possible, to see what silica can do on its own.

  26. John Parkinson steps in • Parkinson, J., Y. Brechet & R. Gordon (1999). Centric diatom morphogenesis a model based on a DLA algorithm investigating the potential role of microtubules. Biochim Biophys Acta1452(1), 89-102. • John is now at the Hospital for Sick Children, Toronto, heading Bioinformatics

  27. So we add a prepattern • We assume that there is a set of discrete sources for silica around the periphery of the silicalemma • Simulations were done for centric diatoms • Parameters are:temperature Tsurface tension Ksurface mobility X

  28. The droplet formation is a Rayleigh instability in which a cylinder breaks into a row of drops: try a strand of honey on a dish Rayleigh, L. (1879a). On the capillary phenomena of jets. Proc. Roy. Soc.29, 71-97. Rayleigh, L. (1879b). On the instability of jets. Proc. London Math. Soc.10, 4-13. Rayleigh, L. (1892). On the instability of a cylinder of viscous liquid under capillary force. Phil. Mag.34, 145-154.

  29. Next we let the discrete sites around the perimeter wander to various extents (Y), but stay a minimum distance apart (Z)

  30. Conclusions: A variety of patterns can be generated by altering the physicochemical conditions inside the silicalemma A so-called prepattern need not have the complexity of the pattern that results from its presenceA central disk of solid silica forms under some conditionsPores can result from nonequilibrium trapping of vacancies

  31. The sources around the perimeter of the silicalemma could represent movement of silica transport vesicles along microtubules to the growing perimeter of the silicalemma, if there is a microtubule organizing center (MTOC) centered on the silicalemma’s surface, just outside of it

  32. Hypothesized transport of silica vesicles along the inner face of the silicalemma by motor proteins attached to microtubules Silica particles are released by membrane fusion, and diffuse inside. The vesicle membrane contributes to growth of the silicalemma. Perpendicular microtubules may emanate from the MTOC through a hole in the donut shaped nucleus, where DNA synthesis is silica dependent MTOC

  33. Needed • A proper investigation of the relationship of microtubules to the silicalemma • An understanding of where and how silica enters a diatom • A full investigation of transport of silica within the cell to the silicalemma. Suggestions: Zurzolo, C. & C. Bowler (2001). Exploring bioinorganic pattern formation in diatoms. a story of polarized trafficking. Plant Physiol127(4), 1339-1345. • Note: while silica transport genes and silica binding proteins have been discovered, their relationship to valve morphogenesis still evades us. This is a spatial process that cannot be explained by scalar biochemistry.

  34. Parkinson, J., Y. Brechet & R. Gordon (1999). Centric diatom morphogenesis a model based on a DLA algorithm investigating the potential role of microtubules. Biochim Biophys Acta1452(1), 89-102.

  35. One role for diatomists: Learning the fundamental cell biology of diatom morphogenesis • Where and how does the silica enter the cell? We know from Volcani and his collaborators that most of it comes into the cell during valve construction, not in advance. • How and in what form is it transported to the silicalemma? Does this involve the SDVs (silica deposition vescicles)? • Is it transported to specific sites on the silicalemma, as by an MTOC (microtubule organizing center)?

  36. How does the silica enter the silicalemma? Is membrane fusion involved? How much prepattern is in/on the silicalemma, and what does it consist of? How is that prepattern constructed? What are the physicochemical conditions inside the silicalemma, and do they vary between species?

  37. Example: salt in the silicalemma Gordon, R. & G.W. Brodland (1990). On square holes in pennate diatoms. Diatom Res.5(2), 409-413. Therefore we can alter the chemistry inside the silicalemma via the medium the cells are grown in. We also have available: *temperature *pressure *choice of species *genetic manipulation via mutagens and genetic engineering

  38. Needed: isolated or artificial silicalemmas Microvesicles can be made from bilayer lipid membranes. Perhaps we can learn how to make them produce specific structures. Material nucleating silica precipitation Or an open system would allow easier chemical access:

  39. Do diatoms age? There is accumulating evidence that ageing in mammals may not be caused by telomere shortening: Holliday, R. (2001). Senescence of dividing somatic cells. In Marshak, D.R., R.L. Gardner & D. Gottlieb, Stem Cell Biology, Cold Spring Harbor, New York Cold Spring Harbor Laboratory Press, p. 95-109. Diatoms “age” in culture too: Estes, A. & R.R. Dute (1994). Valve abnormalities in diatom clones maintained in long-term culture. Diatom Res.9(2), 249-258. Could diatoms be a useful model for ageing of cells? How do we prevent aberrations when we want reproducible nanotechnology?

  40. “Although diatoms might not tell us how legs and arms and brains of vertebrates are put together, bridging the intellectual gap from the genome to diatom shell structure would be a great accomplishment.”Drum, R.W. & R. Gordon (2003). Star Trek replicators and diatom nanotechnology. TibTech (Trends in Biotechnology)21(8), 325-328.

  41. The Multicellular Morphogenesis Problem ? 1,000,000 µm = 1 meter Egon Schiele Kneeling Male Nude (Self-Portrait). 1910. http://www.moma.org/exhibitions/schiele/artistwork.html How did your spherically symmetrical egg turn into a highly asymmetrical shape? We’re not even bilaterally symmetric, if you consider the brain your internal organs, and your left or right handedness! Nikas, G., T. Paraschos, A. Psychoyos & A.H. Handyside (1994). The zona reaction in human oocytes as seen with scanning electron microscopy. Hum. Reprod.9(11), 2135-2138.

  42. Some diatoms are left/right asymmetric Nitzschia sp. BGSU Center for Algal Microscopy and Image Digitization http://www.bgsu.edu/departments/biology/facilities/algae/SEM/nitz1.gif

  43. How far can we push diatoms to make structure we want? • This is a fundamental question in evodevo = “evolution & development” • It is the question of developmental constraints • It is the question of so-called Darwinian gradualism vs Stephen J. Gould’s punctuated equilibrium

  44. Darwin was not a Gradualist • "But I must here remark that I do not suppose that the process ever goes on so regularly as is represented in the diagram, though in itself made somewhat irregular, nor that it goes on continuously; it is far more probable that each form remains for long periods unaltered, and then again undergoes modification." • Darwin, C. (1872). Origin of Species by Means of Natural Selection or the Preservation of Favored Races in the Struggle for Life, 6th, reprinted ed., New York Modern Library. • This is a clear statement of stasis and punctuated equilibrium in evolution.

  45. Novick, A. & L. Szilard (1950). Experiments with the chemostat on spontaneous mutations of bacteria. Proc. Natl. Acad. Sci. USA36, 708-719. Chemostat • http://www.ibri.org/Books/Pun_Evolution/Chapter3/3.2.htm Basically works like a stomach

  46. Compustat • Gordon, R. (1996). Computer controlled evolution of diatoms design for a compustat. Nova Hedwigia112(Festschrift for Prof. T.V. Desikachary), 213-216. • Computer controlled microscope and laser checks each diatom in a growth chamber and zaps the one’s furthest from the desired shape or pattern. The remaining ones are allowed to grow, perhaps in the presence of a mutagen. Then repeat. This is forced evolution, otherwise known as domestication Design your own

  47. Motility • Autonomous movement used to be one of the definitions of life • Müller (1783) called Bacillaria paradoxa the “peg animal” • Because of the rigidity of diatoms, we have a much simpler system to investigate than that of animal cells: for the most part, diatoms need only execute forward, stop, or reverse, at normal or escape velocities • Thus diatoms could provide a breakthrough in understanding the control of eukaryotic cell motility

  48. Two testable theories for diatom motility • Actin bundles transport the raphe fluid using motor molecules that attach through the cell membrane to raphe fibers and detach at raphe pore, then return to the other end. • Capillarity: raphe fluid wets the inner hydrophobic walls of the raphe, reacts with water, becomes hydrated and hydrophilic, comes out of the raphe and sticks to a surface. Actin bundles control release of the raphe fluid. raphe Diatom trail Actin Surface diatom glides on

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