unit 4 · 2008-02-26 · unit 4.2 c. elegans biology dr. nate szewczyk vocabulary: • apoptosis...
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UNIT 4.2
C. elegans Biology
Presented by: Dr. Nate Szewczyk
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UNIT 4.2 C. elegans Biology Dr. Nate Szewczyk Vocabulary:
• Apoptosis • Autosomal • Convergent • Gene • Prokaryotic
Purpose: The NASA Fundamental Space Biology Program has selected several model organisms to be used for future spaceflight research efforts. C. elegans is among the first models selected for near-term spaceflight opportunities. This workshop will provide an introduction to basic C. elegans biology and an overview of results from past flights. Objectives:
a) Describe basic C. elegans culture conditions.
b) Describe the basic life-cycle of C. elegans.
c) Explain why C. elegans is a model system.
d) Recall results from past C. elegans flights.
e) List sources of information on C. elegans.
f) Imagine C. elegans experiments consistent with NASA�s Research Goals.
g) Invent a hardware design for a C. elegans spaceflight experiment.
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Why? A NASA Vision
To improve life here, to extend life to there, to find life beyond
To prepare for and hasten the journey, the following questions must be answered through research:
• How can we assure survival of humans traveling from earth? • What must we know about how space changes life forms, so that humankind with
flourish? • What new opportunities can our research bring to expand understanding of the laws of
nature and enrich lives on Earth? • What technology must we create to enable the next explorers to go beyond where we
have been? • How can we educate and inspire the next generations to take the journey?
Spaceflight involves numerous stressors:
• High levels of noise • High levels of vibration
• High levels of CO2 • Variable temperature
• Variable pressure • Hyper-gravity
• Micro-gravity
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Spaceflight induces biological changes:
• Altered growth and metabolism: • Altered mammalian physiology: ◦ Prokaryotic: Increase in phage production (E. coli)
Increased resistance to high dose radiation (Salmonella, E. coli) Increased growth rate (P. vulgaris) Increased antibiotic resistance (E. coli)
◦ Mammalian cells: Decreased glucose utilization
(Human embryonic lung, Mouse osteoblasts) Increased size (HeLa) Reduced growth rate (Hybridoma) Altered cytoskeletal morphology (Mouse osteoblasts)
Reduced mRNA synthesis (Rat) Reduced growth rate in blood cells (Rat) Altered hormone levels (Human, Rat) Altered tubulin/cytoskeletal synthesis (Rat) Altered collagen distribution/secretion (Rat) Muscle atrophy (Human, Rat) Bone loss (Human, Rat) Altered immune response (Human, Rat) Fluid shift (Human)
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Why worms? Caenorhabditis elegans �the worm� is a model system for biology. Advantages:
• Established research community o Over 150 individual labs study C. elegans o Online resources
• Small o Adults are roughly 1 mm long
• Easy to grow and manipulate large numbers of worms o Need an incubator and agar plates with bacterial lawns o Self fertilize, thus easy to maintain genetic homozygotes
• Rapid life cycle o Egg to adult is roughly 2 days at 25°C
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Caenorhabditis elegans �the worm� is a model system for biology. Advantages:
• Genetically tractable o Males can be used to mate in or out genes of
interest o Has a well-defined genetic map
− Mutants readily available - CGC − Five pairs of autosomal and one pair of
sex chromosomes o Has a sequenced genome
− Available on-line − Allows �reverse� genetics
• Well studied o Most techniques can be done:
PCR Northerns IIF Southerns Transgenics RNA-i Westerns Drugs/Inhibitors
Essentially Invariant Cell Lineage
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Essentially Invariant Cell Lineage
Lineage studies led to the discovery of apoptosis 2002 Nobel prize in Physiology or Medicine
Studies also led to the discovery of vulval defects, which result from
alteration in signaling from the RAS pathway.
CED-4 ~ APAF-1 CED-9 ~ Bcl-2 CED-3 ~ Caspase
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�Wiring� of the Nervous System has been Mapped
Allows for Detection of �Silent� Mutations in the Nervous System
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Alternative �dauer� state found in the life cycle
Studies of the dauer Mutants led to the Discovery of TGF-β and Insulin-like Signaling in the Worm
Glucose based metabolism gene
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Multiple Receptors Control Protein Degradation in Muscles by Multiple Mechanisms
This is the only system for which we know this.
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History of Worms in Space Unique challenges of spaceflight experiments:
• Limited ability to oversee experiment • Use of non-standard laboratory equipment • Limited power • Limited size • Limited weight • Limited crew intervention
What are we doing?
• Developed a new culture system for worms in flight • Have been using the system to look at the effects of hyper gravity on earth • Attempting to use the system in flight to:
o Establish baseline behavioral data for C. elegans in-flight o Establish baseline gene expression data for C. elegans in-flight o Examine the use of C. elegans as a model for space flight atrophy
• Working with SSBRP to establish C. elegans as a model system in space Why the Culture System?
• Traditional method of growing worms subjects them to surface tension forces of 10,000-100,000xG. (masks microG?)
• Traditional method requires frequent astronaut intervention. • New culture system avoids issue of surface tension and allows automation.
o Animals grow for at least four weeks in unchanged media. Technical Issues with Worms Grown in Cemm:
• Tested ability to perform standard lab protocols ○ Dauer formation/recovery ○ Freezing ○ Manipulation of animals ○ Synchronizing populations (bleaching, gravity) ○ Mating • Tested differences in form of medium (liquid vs. solid) • Examined ability of animals to �condition� the medium
○ pH change ○ Accumulation of shed cuticle and dead animals • Biocompatibility of various equipment with animals in medium
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Biocapatibility Material: Manufacturer:
Tubes
1 ml Eppendorf 15 ml conical Falcon 50 ml conical Falcon
Dishes 60 mm petri Falcon 100 mm petri Falcon 60 mm tissue culture Falcon 100 mm tissue culture Falcon 24 well tissue culture Corning 96 well tissue culture Corning
Flasks 25 cm2 cell culture Corning 75 cm2 cell culture Corning
Membranous devices 10 mm membrane tubing Spectrapor Opticell� BioCrystal FEP bag American Fluoroseal
How do worms grown in CeMM compare to those on NGM?
Developmental profile Growth Rate
Larval Stages
Effects on metabolism General appearance
Lipid stores Protein stores
Reproductive profile Brood Size
Egg Laying period
Gene expression Microarray
Life span
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Effects on Metabolism
Lipid Stores
Protein Stores & General Appearance
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Gene Expression
Microarray
a) Downregulated in CeMM versus on NGM Decrease
(Fold log2)
Genepairs Name
Encodes or predicted to encode 2.12 ± 0.16 F59A1.10 Diacylglycerol acyltransferase 2 2.09 ± 0.17 C18C4.5 Myosin/CLIP-190 like 2.06 ± 0.07 T21B10.3 Nuclear protein 2.23 ± 0.16 F42H10.7 DGCR14/ES2 like 2.31 ± 0.22 K05C5.5 UTP4 like 2.23 ± 0.06 ZK856.9 Zinc finger 2.58 ± 0.15 ZC395.9 C2H2 Zinc finger 2.82 ± 0.23 T10F2.3 Ulp1 protease family 2.96 ± 0.29 ZK593.5 dnc-1 2.36 ± 0.15 F22B7.5 dnj-10 2.07 ± 0.12 Y46H3C.D DNA gyrase/topoisomerase 3.21 ± 0.32 T07A9.6 daf-18 2.70 ± 0.15 Y39A1A.12 AAA ATPase 2.27 ± 0.11 F49E8.2 Glutaredoxin 2.39 ± 0.16 ZC317.7 Dynactin interacting protein like 2.78 ± 0.17 T02B5.1 Carboxylesterase 2.44 ± 0.22 ZK1320.9 Acetyl-CoA hydrolase/transferase 3.90 ± 0.28 F25D1.1 Protein Phosphatase 2 C 3.88 ± 0.35 F56A6.1 PAZ, Piwi , & ncoil domains 2.46 ± 0.18 C55B7.1 glh-2 2.41 ± 0.20 C10H11.1 ncoil and villin headpiece domains 2.74 ± 0.15 K07D8.1 mup-4 4.90 ± 0.20 T22B7.7 Long-chain acyl-CoA thioester hydrolase 3.82 ± 0.38 F59D8.C vit-3 3.01 ± 0.24 C47B2.6 NAD dependent epimerase/dehydratase 3.63 ± 0.32 F02A9.5 Carboxyl transferase
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Gene Expression
Microarray
b) Upregulated in CeMM versus on NGM Increase
(Fold log2)
Genepairs Name
Encodes or predicted to encode 2.11 ± 0.11 R13H8.1a daf-16 2.33 ± 0.19 T20D3.6 Transmembrane protein 2.27 ± 0.16 F31E3.6 Transmembrane protein 3.95 ± 0.29 F35A5.2 Transmembrane protein 3.58 ± 0.10 C18A11.2 Transmembrane protein 2.46 ± 0.17 C39D10.2 Cytochrome c binding 2.31 ± 0.19 M03E7.4 LD-lipoprotein receptor 3.92 ± 0.36 T08G5.10 mtl-2 3.80 ± 0.21 7T10B10.6 Heavy metal binding 3.15 ± 0.09 F32H5.3 Transmembrane protein 2.15 ± 0.14 C25E10.8 Trypsin inhibitor like 2.85 ± 0.27 K11G9.6 mtl-1 2.14 ± 0.18 F18E9.2 nlp-7 7.64 ± 0.18 F36D3.9 Cysteine endo-peptidase 2.37 ± 0.20 F54E7.2 rps-12 2.28 ± 0.16 F37C12.9 rps-14 2.60 ± 0.20 F37C12.11 rps-21 2.10 ± 0.15 F39B2.6 rps-26 2.47 ± 0.16 B0414.4 rps-29 2.49 ± 0.12 Y48B6A.2 rpl-43 2.53 ± 0.13 F28F8.3 SNRNP-E like 2.84 ± 0.11 Y46G5.Z Unknown
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History of Worms in Space
STS-95 (E. Moss), Suspended in liquid: Animals died (of hypoxia?)
STS-42 (G. Nelson), Grown on NGM: Males mate Undergo two generations in-flight No gross morphologic defects Increased rate of mutation
STS-76 (G. Nelson), Suspended in M9: Radiation, not microgravity, key factor in increased rate of mutation
STS-107 (C. Conley), Grown on NGM and CeMM: CeMM supported animals in flight Animals survived Columbia breakup
STS-65 (S. Nagaoka), Grown on ground: Free flow electrophoresis of DNA successful
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Actual Design
HOBO: Autonomous temperature recorder, temperature logged every 30 minutes
LiOH: Used to �soak up� CO2
N2: Weight on NGM
CC1 Weight on CeMM
ms: Mixed Stage
Can 1 Can 2 Can 3 Can 4 Can 5 Can 6 HOBO HOBO 500ms CC1 LiOH HOBO LiOH
500 CC1 LiOH 500ms CC1 500ms CC1 10 N2 10 N2
10 N2 500ms CC1 500ms CC1 500ms CC1 10 N2 10 N2
100 CC1 10 N2 500ms CC1 500ms CC1 10 N2 10 N2
100 N2 100 CC1 500ms CC1 500ms CC1 100 N2 10 N2
10 CC1 100 N2 500ms CC1 500ms CC1 10 N2 10 N2
500 N2 10 CC1 500ms CC1 500ms CC1 500N2 10 N2
500ms CC1 500 N2 500ms CC1 500ms CC1 10 N2 10 N2
500ms CC1 500ms CC1 10 N2
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Reference Materials Papers on Worms in Space: Johnson, T.E., and Nelson, G.A. Caenorhabditis elegans: A model system for space biology studies. Experimental Gerontology 26:299-309 1991 Nelson, G.A., et al. Nematode radiobiology and development in space. Results from IML-1. Proceedings of the Fifth European Symposium on Life Sciences Research in Space. 187-91 1994 Nelson, G.A., et al. Radiation effects in nematodes: Results from IML-1 experiments. Adv. Space Res. 14: 87-91 1994 Nelson, G.A., Schubert, W.W., Kazarians, G.A., and Richards, G.F. Development and chromosome mechanics in nematodes: Results from IML-1. Adv. Space Res. 14: 209-14 1994 Hartman, P.S., et al. A comparison of mutations induced by accelerated iron particles versus those induced by low earth orbit space radiation in the FEM-3 gene of Caenorhabditis elegans. Mutation Research 474: 47-55 2001 Books on Worms: The Nematode Caenorhabditis elegans Wood, W.B., Ed. Cold Spring Harbor Laboratory Press 1988 C. elegans II Riddle, D.L., Blumenthal, T., Meyer, B., and Priess, J.R., Eds. Cold Spring Harbor Laboratory Press 1997 Caenorhabditis elegans: modern biological analysis of organism (Methods in Cell Biology , Vol 48) Epstein, H.F. and Shakes, D.C., Eds. Academic Press 1995 C. elegans (A practical approach) Hope, I.A., Ed. Oxford University Press 1999 Online Resources:
http://elegans.swmed.edu http://www.wormbase.org
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