BioMEMS Class 0 CMEMS

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BioMEMS Class 0 - CMEMS

• Dr. Marc Madou
• Winter 2009

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Table of Content

• Fractals in Nature and Electrochemistry (borrowed
  design and material)
• Spinning Worms on a Compact Disc (modified
  animal)
• Responsive Drug Delivery (modified protein)
• Icarus Revisted-Conclusions

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Fractals

• The fundamental equation that describes scaling
  of various variables with relation to body mass
  is an allometric equation of the form VaMb
• An empirical observation that has perplexed
  scientists is the fact that the exponents (b) of
  many variables including cellular metabolism
  (b-1/4), heartbeat (b-1/4), maximal population
  growth (b-1/4), life-span (b1/4), blood
  circulation (b1/4), metabolic rates of entire
  organisms (b3/4), and cross-sectional areas of
  tree trunks (b3/4) are multiples of 1/4 instead
  of 1/3.

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Fractals

• Pure geometric scaling of area (2) and volume (3)
  leads to a scaling constant of 2/3, but as Max
  Kleiber discovered in the early 1930s, the
  metabolic rates of entire organisms (which should
  scale with area) scales with respect to body mass
  (which should scale with volume) with a scaling
  constant of 3/4. This relationship is now
  referred to as Kleiber's law.

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Fractals

• Why not S/V 0.67? One of the more inspiring
  explanations for Kleibers law came from
  ecologists Enquist and Brown and physicist West
  in 1997. These authors explain that the generic
  principle underlying Kleibers law is that
  nutrient supply networks in animals and plants
  form a branching fractal network? to reach all
  cells in an organism.
• By modeling the cardiovascular system as a
  fractal-like network that ends in terminal units
  (capillaries) of the same size, they have shown
  that minimizing the work that the heart performs
  in pulsatile systems leads to the proper scaling
  constants that are empirically observed (see also
  West et al 2005).
• G. B. West and J. H. Brown, Journal of
  Experimental Biology, 208, 1575-1592 (2005)

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Fractals in Electrochemistry

• Fractals are an optimal geometry for minimizing
  the work lost due to the transfer network while
  maximizing the effective surface area. In many
  electrochemical systems, it is advantageous to
  have a large surface to volume ratio, while
  needing to transfer the signal or power
  effectively to an electrical network.
  Electrochemical energy conversion devices such as
  fuel cells and some types of batteries as well as
  sensors such as glucose sensors are examples of
  such applications.

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Fractals in Electrochemistry
With Mr. Ben Park

• The resistance R of a bulk material scales with
• R V-1/3 (a) (1)
• when scaling isometrically and with R V -1
  (b) (2)
• when scaling area.
• The surface area and the scaling of the surface
  to volume ratios are as follows (assuming tltltlt l
  )

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Fractals in Electrochemistry
With Mr. Ben Park

• As can be seen in eqns (1), (2), (3), and (4), 2D
  scaling from a small fundamental building block
  results in lower internal resistance and higher
  effective area compared to an isometric 3D
  scaling approach.
• Indeed, commercial Li-ion batteries and fuel
  cells are composed of many layers of anode,
  cathode, and electrolyte that are rolled, folded,
  or stacked on top of each other

Fractals
Impossible in MEMS
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Fractals in Electrochemistry
With Mr. Ben Park

• The total current is proportional to the number
  of the smallest elements within the fractal
  network. Maximizing the number of small elements
  within a fractal structure is desired.
• The total resistance is the inversely
  proportional to the number of small elements and
  ensures that current is maximized, while the
  internal resistance is minimized.
• Comparing eq 7 to eq 2, it can be concluded that
  the resistance of fractal electrodes scale
  similar to a thinly layered structure, not to an
  isometrically scaled volumetric geometry.
• Comparing eq 8 to eq 4, the surface to volume
  ratio of a fractal electrode does not change as
  the volume changes, again he fractal geometry
  scales more like a layered film than a volumetric
  electrode.

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Carbon Fractals
C-MEMS
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Why Carbon?

• Polymerizes better than Si
• All types of forms amorphous, graphite,
  nanotubes, etc
• Wide electrochemical stability window
• Biocompatibility
• Low cost
• Chemically inert
• Easy to derivatize
• Well known for its battery and sensor
  application
• Carbon nanotubes connect via C-MEMS?
• Carbon is natures building bloc!

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What is C-MEMS/C-NEMS?
Negative photoresist
Positive photoresist
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Spinning C elegans on a CD

• 1) Genetically tractable
• - Entire C. elegans genome sequenced.
• 2) More than 60 of human genes have homologs
  in C. elegans genome
• 3) Small and easy to culture
• - Adults are roughly 1 mm long.
• - Easy to grow and manipulate large numbers of
  worms
• - Self fertilize, thus easy to maintain genetic
  homozygotes
• - Rapid life span (birth to death 23 weeks)
• - Egg to adult is roughly 23 days at 25C

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Spinning C elegans on a CD
With Prof. Ji Sze
Loading s-medium(0.2ml) , E. coli (5micron) and
one nematode into CD _at_450 RPM
C. elegans in the cultivation chamber after 14days
Nutrient chamber
Cultivation chamber
waste chamber
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C. elegans Cultivation
With Prof. Ji Sze

• Worms are cultured in a liquid medium and fed
  with E. coli
• Each cultivation chamber can culture three
  generations, up to 1,000 worms
• Feeding and waste removal processes are achieved
  automatically using centrifugal force driven
  fluidics.

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C. elegans Cultivation
With Prof. Ji Sze

• The average of 1st, 2nd and 3rd experimental
  results with number of body bends per 10 seconds
  in CD-based cultivation system under unit gravity
  conditions (Data is presented as mean value and
  standard deviation for 6 worms).

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Physiology and Gene Expression in Hypergravity
With Prof. Ji Sze

• Worms can withstand 100G for at least 24 hours
• We use100G to investigate genetic basis
  underlying organism responses to altered
  gravitational force physiologically and
  genetically.
• The calculated acceleration (m/s2) and rotation
  speed (rpm)
• with various resultant gravities

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Tough Worms
With Prof. Ji Sze
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Muscle Structure and Feeding
With Prof. Ji Sze

• Feeding behavior under hypergravity for 3hrs,
  using E.coli bearing an RFP fusion reporter. The
  red fluorescence filled in both the pharynx and
  throughout the gut. There was no detectable
  difference in the intensity of red fluorescence
  between animals under 1G and 100G.
• Lethargic movement but no difference after 3 hrs
  at 100G in muscle structure , after 24 hrs
  sarcomere elongation but no hypercontraction as
  seen with the acetylcholinesterase inhibitor
  aldicarb GFP-tagged myosin heavy chain protein
  MYO-3 (MYO-3GFP) is used as a reporter

myo-3gfp expression
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Fat Accumulation
With Prof. Ji Sze

• Worms exposed to 100G for 24 hours showed an
  increase in fat contents in the intestine and
  hypodermis.
• This result is consistent with the observations
  that hypergravity exposure causes weight
  increases and fat deposit in rats (Smith et al.,
  1974 Bouet et al., 2004) and affects ageing in
  rats and Drosophila (Rattan, 2004 Bourg et al.,
  2004), and extends those works by demonstrating
  that gravity may cause metabolic shift to fat
  storage by inhibiting the pathway from the DAF-2
  insulin receptor to DAF-16 FOXO transcription
  factor.

Fat (Sudan black)
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Nuclear Localization
With Prof. Ji Sze

• Top DAF16GFP expressed in whole cell at 0hr
  at 100G
• After 1 hr at 100G
• After 2 hr at 100G
• After 3 hr at 100G
• Translocation of DAF-16 from the cytoplasm to the
  nuclei produces an increased resistance to
  environmental stressors and physiological
  challenges via changes in the expression of genes
  involved in postembryonic development,
  mitochondria function, and metabolic homeostasis

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Prozac Nation
With Prof. Ji Sze

• We used DAF-16GFP nuclear accumulation as a
  reporter to test the effects of serotonin and an
  antidepressant, the serotonin reuptake inhibitor
  (SSRI) fluoxetine. Applying serotonin or
  fluoxetine during their exposure to 100G
  significantly attenuated DAF-16GFP nuclear
  accumulation.
• These observations establish that serotonin
  modulates the response to mechanical stress, and
  that the drugs that increase serotonin signaling
  may alleviate stress responses to the changes in
  gravity.

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From Worm to Man
With Prof. Ji Sze
A signaling pathway conserved from worm to man
insulin receptor to FOXO transcription factors
Fat accumulation Increase antioxidants, Increase
innate immunity Longevity
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Whole Cell Sensing
With Prof. Sylvia Daunert

• A few strains of bacteria are resistant to
  arsenite, arsenate and antimonite. When such a
  bacterial cell is exposed to any of these toxic
  species, it synthesizes a protein pump that
  removes arsenite and antimonite.
• The genes that code for the pump are grouped
  together on the DNA in what is known as the ars
  operon. These genes are expressed together when
  arsenate, arsenite or antimonite is present. Two
  genes in the ars operon, arsA and arsB, code for
  proteins that associate to form the pump. A third
  gene, arsC, codes for the enzyme arsenate
  reductase that converts arsenate to arsenite.

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With Prof. Sylvia Daunert
Whole Cell Sensing

• The ars operon expression is controlled by a
  regulatory protein, ArsR, which is the product of
  the arsR gene. In the absence of toxic metals,
  ArsR is bound to a region of the bacterial DNA
  immediately in front of the ars operon.

• This region is called a promoter-operator. When
  ArsR is bound to the promoter-operator region,
  expression of the ars genes is prevented.
  Arsenite and antimonite can induce expression of
  the ars operon by binding to ArsR and promoting
  its release from the promoter-operator.

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Whole Cell Sensing
With Prof. Sylvia Daunert

• A biosensor can be made by linking the ars
  promoter-operator region with a reporter gene.
  The reporter gene codes for an enzyme whose
  activity produces a signal that can be readily
  detected.

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Whole Cell Sensing
With Prof. Sylvia Daunert
Signal
Reporter protein
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With Prof. Sylvia Daunert
Whole Cell Sensing

• Low power and space requirements
• Less reagent and sample consumption
• Easy disposal
• Short analysis time
• Integrate washing, sample preparation,
• and calibration

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With Prof. Sylvia Daunert
Reporter GFP
Whole Cell Sensing
Arsenic Detection
In this study, Escherichia coli cells containing
plasmid pSD10 were engineered to sense arsenite
and antimonite. The biosensing system takes
advantage of the recognition of the regulatory
protein, ArsR, for arsenite and antimonite to
produce the reporter protein, which in this case
is GFP.
Anal Biochem. 2005 Jul 1342(1)11-9. Epub 2004
Dec 7
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Response Drug Delivery
With Prof. Daunert
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Response Drug Delivery
With Prof. Daunert
Monitoring, repair, construction and control of
human biological systems at the molecular level
using engineered nanodevices and nanostructures
Nanomedicine
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With Prof. Daunert
Responsive Drug Delivery
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Responsive Drug Delivery
With Prof. Daunert
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Responsive Drug Delivery
With Prof. Daunert
Dose-response curve at 37 C after 60 days
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With Prof. Daunert
Responsive Drug Delivery
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Response Drug Delivery
With Prof. Daunert
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Biomimetics Icarus Revisted?

• Nature and mankind have developed competitive
  manufacturing methods on the macro level (e.g.,
  steel versus bone)
• Biomimetics on the macro-level mostly failed.
  Background reading Cats Paws and Catapults by
  Steven Vogel (Efficiency of mechanical systems in
  biology and human engineering in the
  macro-world).
• On the nanoscale nature is outperforming us by
  far (perhaps because nature has had more time
  working towards biological molecules/ cells than
  towards making larger organisms such as trees and
  us).
• NEMS might be inspired by biology but will most
  likely be different again -- the drivers for
  human and natural manufacturing techniques are
  very different.

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Conclusion

• Fractal electrodes might solve miniaturization
  issues in micro-power devices
• New animal assay platform
• Bacteria as sensor
• Back to in-vivo sensing
• Biomimetics in the nanoworld more warranted as we
  have not been able to achieve similar complexity
  at those length scales