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
• Supported by:
National Institute of Biomedical Imaging
and Bioengineering (NIBIB) at the
U.S. National Institutes of Health
• 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.
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, 47 Nov.1988, New Orleans, LA, USA , New
York: Institute of Electrical and Electronics
Engineers, 10 , p. 273-274.
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.
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.
Actually,
diatom
nanotech
is 140
years old,
started by
Max
Schultze
(18251874) in
1863.
Last cited
1876.
Max Schultze’s diatom papers
Max 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 Anatomie 1, 376-402.
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.
Physics 34(2), 323-329.
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.
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 Letters 47(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.
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, 421422.
Spatially distributed sources of
silica: pennate diatom case
Bumps stick out into a
higher concentration
and so grow faster:
positive feedback
Result is a fractal pattern, a bit
reminiscent of costae, but frayed
Moving
boundary of
the
silicalemma
Concentration
profile
This is a
fractal
pattern: looks
the same if
magnified,
i.e,
independent
of scale: NOT
like diatoms
But,
actually,
not so bad,
if one looks
for an
aberrant
diatom that
fits the
simulation!
by Ryan Drum
Sintering smooths
the structure,
but it still doesn’t
look good
Sintering may occur
via a bipedal walk as
silica diffuses over
precipitated silica, as
hypothesized for
water molecules
moving over ice
Let’s try this on a centric diatom
DLA for a
centric
diatom, with
a circular
silicalemma
Unconstrained DLA showing
time course
http://www-personal.umich.edu/~lsander/
Sintering is kind of lumpy
Black/ white
labelling shows
“growth rings”
Vicsek, T.
(1992). Fractal
Growth
Phenomena, 2nd
ed., Singapore
World Scientific.
But some centrics do have gentle
bending of costae
Cyclotella stelligera by Hedy Kling
Others still mystify me with
“crystalline” domains somehow made
of amorphous silica
Thalassiosira eccentrica by Gretha Hasle
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.
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.
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 Acta 1452(1), 89102.
• John is now at the Hospital for Sick
Children, Toronto, heading
Bioinformatics
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 T
surface tension K
surface mobility X
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.
Next we let
the discrete
sites
around the
perimeter
wander to
various
extents (Y),
but stay a
minimum
distance
apart (Z)
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 presence
A central disk of solid silica forms under some
conditions
Pores can result from nonequilibrium trapping of
vacancies
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
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.
MTOC
Perpendicular
microtubules
may emanate
from the MTOC
through a hole
in the donut
shaped nucleus,
where DNA
synthesis is
silica dependent
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 Physiol 127(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.
•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 Acta 1452(1), 89-102.
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)?
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?
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
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:
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.
1) Could diatoms be a useful model for ageing of cells?
2) How do we prevent aberrations when we want reproducible
nanotechnology?
“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.
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
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.
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!
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
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
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.
Novick, A. & L. Szilard
(1950). Experiments with
the chemostat on
spontaneous mutations of
bacteria. Proc. Natl. Acad.
Sci. USA 36, 708-719.
Chemostat
Basically works
like a stomach
•
http://www.ibri.org/Books/Pun_E
volution/Chapter3/3.2.htm
Compustat
• Gordon, R. (1996). Computer controlled evolution of
diatoms design for a compustat. Nova Hedwigia
112(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
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
Two testable theories for diatom motility
1. 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.
2. 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
Actin
Surface diatom glides on
Diatom
trail
Motility Models
• Gordon, R. & R.W. Drum (1970). A capillarity mechanism
for diatom gliding locomotion. Proceedings of the National
Academy of Sciences of the United States of America 67,
338-344.
• Edgar, L.A. & J.D. Pickett-Heaps (1983). The mechanism
of diatom locomotion. I. An ultrastructural study of the
motility apparatus. Proc. Roy. Soc. Lond. B218, 331-343.
• Gordon, R. (1987). A retaliatory role for algal projectiles,
with implications for the mechanochemistry of diatom
gliding motility. J. Theor. Biol. 126, 419-436.
• Wolgemuth, C., E. Hoiczyk, D. Kaiser & G. Oster (2002).
How myxobacteria glide. Curr Biol 12(5), 369-377. Same
model as Gordon & Drum (1970).
Diatom Motility for Nanotech
• Diatoms with raphes can lift 1000x their own weight, so there might
be ways to put this talent to work for us:
Harper, M.A. & J.T. Harper (1967). Measurements of diatom adhesion
and their relationship with movement. Br. Phycol. Bull. 3(2), 195-207.
• Diatoms can be led around by their noses:
Cohn, S.A., T.P. Spurck & J.D. Pickett-Heaps (1999). High energy
irradiation at the leading tip of moving diatoms causes a rapid change
of cell direction. Diatom Res. 14(2), 193-206.
• As their motility depends on adhesion to a surface, we might be able
to create spatial arrays by allowing them to move on patterned
surfaces
Chiu, D.T., N.L. Jeon, S. Huang, R.S. Kane, C.J. Wargo, I.S. Choi, D.E.
Ingber & G.M. Whitesides (2000). Patterned deposition of cells and
proteins onto surfaces by using three-dimensional microfluidic systems.
Proc Natl Acad Sci U S A 97(6), 2408-2413.
• The relationship between
cell shape and
differentiation is coming
to the fore for animal
cells by plating cells onto
cell-sized patterned
surfaces
• Chen, C.S., C.
Brangwynne & D.E.
Ingber (1999). Pictures in
cell biology squaring up
to the cell-shape debate.
Trends Cell Biol 9(7),
283.
• The geometry of diatoms may act for
their cytoskeleton as patterned
substrates do for animal cells
• For example, as some diatoms get
smaller in successive generations,
they cross a threshold where they can
no longer sexually reproduce, and
perhaps die
• This may be a model for apoptosis
• Chen, C.S., M. Mrksich, S. Huang,
G.M. Whitesides & D.E. Ingber
(1997). Geometric control of cell life
and death. Science 276(5317), 14251428.
The Axolotl
Ambystoma mexicanum
A rare piebald axolotl, 23 cm long, showing its external gills.
Tensegrity Toy
A model for the cytoplasm:
stiff components are
microtubules, themselves
supported by intermediate
filements:
Brodland, G.W. & R. Gordon
(1990). Intermediate
filaments may prevent
buckling of compressivelyloaded microtubules. J.
Biomech. 112(3), 319-321.
Contractile microfilements
(actin bundles) keep them in
tension
Ingber, D.E., L. Dike, H. Liley, L. Hansen, S. Karp, H. Liley, A.J.
Maniotis, H. McNamee, D. Mooney, G. Plopper, J. Sims & N. Wang
(1994). Cellular tensegrity exploring how mechanical changes in the
cytoskeleton regulate cell growth, migration, and tissue pattern during
morphogenesis. Int. Rev. Cytol. 150, 173-224.
MF
MT
IF
Contraction Wave
B
Nucleus
ve
MF =
microfilament ring
A
Wa
nsion
Expa
The Cell State
Splitter
Cell state splitter
MT =
annular apical
microtubule mat
IF =
intermediate
filament ring
Signal
transduction
C
Signal
transduction
The Unstable (Bistable) Mechanical Equilibrium
between the Microfilament Ring and the
Microtubule Mat in the Cell State Splitter
MF ring is a torus of radius r and cross sectional area A,
empirically of constant volume V
Force F  A
V = 2rA, so
F 1/r, a hyperbola
Gordon, R.,
N.K. Björklund
& P.D.
Nieuwkoop
(1994).
Dialogue on
embryonic
induction and
differentiation
waves. Int.
Rev. Cytol.
150, 373-420.
A Peculiar Trajectory: Why the Contraction Wave
doesn’t Turn the Whole Ectoderm into Brain
Head end
Gordon, R., N.K.
Björklund & P.D.
Nieuwkoop (1994).
Dialogue on
embryonic induction
and differentiation
waves. Int. Rev.
Cytol. 150, 373-420.
Tail end
The result is the
neural plate,
which later forms
the brain and
spinal cord
Gordon, R. & A.G. Jacobson (1978). The shaping of tissues in embryos. Scientific
American 238(6), 106-113.
Back to the silicalemma
This form of cell state splitter is found
in sea urchin ectoderm, and looks like
a silicalemma*. Therefore the
silicalemma may be attached to a
cytoskeletal tensegrity apparatus that
is bistable. This could produce:
Buckling phenomena and shaping of
the diatom shell
Changes in precipitation of silica and
costal branching patterns
Gordon, R. & G.W. Brodland (1987). The cytoskeletal mechanics of brain morphogenesis. Cell
state splitters cause primary neural induction. Cell Biophys 11, 177-238.
*Pickett-Heaps, J.D., D.H. Tippit & J.A. Andreozzi (1979). Cell division in the pennate diatom
Pinnularia. IV. - Valve morphogenesis. Biol. Cellulaire 35(2), 199-203.
Evolutionary Shaping of Diatoms
• Diatoms adhering in running water are long
and narrow, as if responding (by evolution)
to the shear
Sheared fluid drops
Artificial
streams
Gordon, R., N.K. Björklund, G.G.C.
Robinson & H.J. Kling (1996). Sheared
drops and pennate diatoms. Nova
Hedwigia 112(Festschrift for Prof. T.V.
Desikachary), 287-297.
Shear flow molds diatom
shape via its genome
In Summary
• Diatoms are superb organisms for studying some
of the most general and fundamental, outstanding
questions about life, and the major contribution of
diatomists to nanotech may prove to be solving
these problems
• How is the diatom shell formed?
• Exactly what is the relationship between the
diatom’s genome and its morphogenesis?
• What are the morphological limits to the evolution
of diatoms?
• What is the mechanism of motility and how is it
controlled?
The Opportunity
• This is a precious moment in diatom nanotech
• No one has produced anything useful yet
• Everyone is still open and talking, not hiding
behind patents and intellectual property rights
• The diatom nanotechies need your help, to
understand the vast potential of diatoms and how
on earth they pull it off
• It’s time to cooperate and collaborate, and have
the time of your life doing so
Announcements
• Diatom nanotech business meeting Thursday, 8–
8:30pm, immediately after NADS auction, to
discuss next diatom nanotech meeting
• Tutorial on diatoms during Microscopy Session, 3–
5PM Friday, by Eugene Stoermer & Jeff Johanson
with Charlie Reimer as TA
• Needed: tutorial PowerPoint slides, etc., for this
session. Please offer if you’ve brought some
• If your poster is nanotech related, and not covered
by an article submitted for the special issue of
Journal of Nanoscience and Nanotechnology on
diatom nanotechnology, please send it to me by e–
mail for possible inclusion