Ginger Armbrust

1
Ginger Armbrust Deirdre Meldrum University of
Washington
Ecogenomic Sensors
2
What are ecogenomic sensors?
A dream!

• Biological sensors that detect
• Who is there
• What are they doing

3
(No Transcript)
4
Global Carbon Cycle
Global Carbon Cycle
Gas Exchange Between Air and Ocean
Land Use Changes
Combustion
Gas Exchange Between Air and Ocean
Net Accumulation in Ocean
Photosynthesis Respiration
Net Accumulation in Ocean
Photosynthesis Respiration
Geological Reserve
Circulation
Circulation
5
http//www.gsfc.nasa.gov/gsfc/earth/environ/carbon
/carbon.htm
6
(No Transcript)
7
(No Transcript)
8
(No Transcript)
9
(No Transcript)
10
The Environmental Sample Processor (ESP)
Chris Scholin, MBARI

• Autonomous collection of samples and timed
  application of multiple reagents in situ,
  subsurface
• Two-way communication

11
Biological Sensors
12
Biological Sensors
13
Biological Sensors
14
What are we able to do now?

• Nitrogen fixation at some level, coming on line
• Bioavailable Fe at some level, coming on line
• Toxin production not yet, but not far away
• Phylochip pertinent markers for specific
  biochemical pathways will provide understanding
  of who/when/where/why toxins are produced
• Cyanobacterial ecology possibly much later
• What regulates the assemblage? Right now we can
  only count the cells
• Are there different strains seasonally? Are they
  physiologically different?

15
What are we able to do now?

• Samples can assess the abundance of specific
  organisms (small finite number)
• Approach is very dependent upon scale abundance
• Limited temporal scales
• Low throughput
• Relate abundance of specific microbial community
  composition to physical chemical factors
• Probe for specific DNA, RNA, protein
• Limited number of samples, size of sample, level
  of detection

16
What are we able to do now?

• Broad scale diversity arrays who is there at a
  very coarse scale
• Sample archiving but not very satisfying in
  real-time sense
• Proteomics in the lab
• Single cell assays in the lab

17
Where are future technologies headed?

• Smaller, cheaper, faster, more accurate
• Automated for simultaneous measurements
• Fast, cheap, sequencing (1000 genome)
• E.g. pyrosequencing, nanopores, sequencing by
  hybridization, sequencing by synthesis
• No cloning steps
• From single cell

18
1000 Genome 10 years out

• e.g., Nanopore Sequencing
• Use native DNA
• DNA translocates under electric potential
  difference
• Detector in pore translates physical/chemical
  properties to into electrical signature
• Potential for 1000 bases per second

Mark Akeson, UC Santa Cruz
19
Where are future technologies headed?

• Miniaturization, including nanorobots
• Single cell analyses
• Monitor complex assemblages
• Flow through systems
• New hybridization detection technologies
• Imaging
• Mass spectrometry
• Metabolic sensors
• Sensors at different scales
• 4D arrays (space, time)
• Time series
• Standards for collection and storage of metadata
• Adaptive sampling

20
Where are future technologies headed?

• Sensors and sensor platforms for continuous
  real-time measurements in time and space

21
NIH NHGRICenters of Excellence in Genomic
Science (CEGS)

• Microscale Life Sciences Center (MLSC)
• University of Washington
• Fred Hutchinson Cancer Research Center
• Started August 2001

Goal Develop microscale modules to measure
multiple parameters in living cells in real time
to correlate cellular events with genomic
information
Life-on-a-chip
22
Multiparameter MeasurementsPhysiological,
genetic, genomic, proteomic, transcriptomic
H2O
O2
2. Multiwavelength fluorescence --membrane
potential --membrane integrity
--ion gradients --substrate utilization
--DNA content --surface markers
23
General Configuration
O2 Sensor
MediaCells
T 37 C 5 CO2
Media
Lid
MediaA
Lid control
MediaB
Rinse Buffer
Waste
IB(ti), IC(ti), IG(ti) IY(ti),
IR(ti),V(ti) t?t0, tf ? tf j j?1, Nchamber
Microwell Array
Feature Vector
z(t)
y(t)
x(t)
Multispectral and Time-domain Imaging
Stage/Focus Control
Database
Storage
24
Microwell Sensor Array Chip
25
Core technologysubsystem test Chamber Seal
Impressions in Au barrier
Microscopy platform
Microwell array with seal in test setup
Seal-ridge microwell array
26
Microwell Array OxygenConsumption Measurement
27
Initial Tests on the R/V Thompson
28
(No Transcript)
29
(No Transcript)
30
Sensorbot Scenario
John R. Delaney, UW School of Oceanography
31
Sensorbot Swarms

• Mooring delivers power and Gb/sec bandwidth
  connectivity from/to land-based power control
  system
• Sensorbot power on-board is from rechargeable
  batteries (initially) serviced at charging
  stations near moorings
• Communication with sensorbot swarm by optical
  modem with acoustic backup via comm/nav modules
  (blue)
• Sensorbots make simultaneous measurements in time
  and controlled space
• Sensorbots can adjust their buoyancy

32
Future for Sensorbots

• Full suite of plug-and-play sensors
• Chemical
• Physical
• Ecogenomic
• Sensorbot buoyancy
• Motion control and propulsion systems
• Compact, efficient power systems
• Next generation packaging
• Interactive via NEPTUNE
• and more!

33
Show Animation of Sensorbots