Biomarkers: distinct indicators that help define the physiology or state of a living system
Biomarkers are not just ANY indicator
Marcelle uses his fingers as an indicator of how close we came to shit-creek. But that’s not a biomarker
Chris uses a YSI probe to measure dissolved oxygen. But that’s not a biomarker.
Biomarkers represent the complexity of life
When hypoxia sets in, a yawn indicates the homeostatic mechanism to increase oxygen uptake AKA the Boopathy Biomarker
Biomarkers include
Any indicator of a biological phenomenon:
Microbiological biomarkers to indicate cloning ampicillin resistance
Expression markers for biosynthesis/ trafficking gfp protein tagging
Genetic biomarkers of disease in humans
Induced biomarkers as evidence of abnormality
2002 Nobel Laureate: Sydney Brenner
Genetic Biomarkers
Caenorhabditis elegans, Apoptosis model
A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes.
AUTHORS: The Huntington's Disease Collaborative Research Group
aka
MCDONALD,M., AMBROSE,C.M., DUYAO,M.P., MYERS,R.H., LIN,C.S., SRINIDHI,J., BARNES,G., TAYLOR,S.A., JAMES,M., GROOT,N., MCFARLANE,H., JENKINS,B., ANDERSON,M.A., WEXLER,N.S., GUSELLA,J.F., BATES,G.P., BAXENDALE,S., HUMMERICH,H., KIRBY,S., NORTH,M., YOUNGMAN,S., MOTT,R., ZEHETNER,G., SEDLACEK,Z., POUSTKA,A., FRISCHAUF,A.-M., LEHRACH,H., BUCKLER,A.J., CHURCH,D., DOUCETTE-STAMM,L., O'DONOVAN,M.C., RIBA-RAMIREZ,L., SHAH,M., STANTON,V.P., STROBEL,S.A., DRATHS,K.M., WALES,J.L., DERVAN,P., HOUSMAN,D.E., ALTHERR,M., SHIANG,R., THOMPSON,L., FIELDER,T., WASMUTH,J.J., TAGLE,D., VALDES,J., ELMER,L., ALLARD,M., CASTILLA,L., SWAROOP,M., BLANCHARD,K., COLLINS,F.S., SNELL,R., HOLLOWAY,T., GILLESPIE,K., DATSON,N., SHAW,S. and HARPER,P.S.
… I count 58 authors in all
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qpllpqpqpp ppppppppgp avaeeplhrp kkelsatkkd rvnhcltice nivaqsvrns
pefqkllgia melfllcsdd aesdvrmvad eclnkvikal mdsnlprlql elykeikkng
aprslraalw rfaelahlvr pqkcrpylvn llpcltrtsk rpeesvqetl aaavpkimas
fgnfandnei kvllkafian lksssptirr taagsavsic qhsrrtqyfy swllnvllgl
Poly-glutamine stretch of huntingtin coded for by CAG repeats
POLYGLUTAMINE EXPANSION LEADS TO ELEVATED SUSCEPTIBILITY TO APOPAIN
CLEAVAGE AND LIKELY RESULTS IN ACCELERATED NEURONAL APOPTOSIS
Table 1
No. of CAGrepeats
Outcome
< 28 Normal range; individual will not develop HD
29-34Individual will not develop HD but the nextgeneration is at risk
35-39Some, but not all, individuals in this range willdevelop HD; next generation is also at risk
> 40 Individual will develop HD
Huntington’s Disease Repeats
Human ortholog of ced 3 is caspase 3
Huntingtin is cleaved by caspase 3, and this change is associated with neuronal death
Genetic Biomarkers
Allow the elimination of imperfect embryos
Plus…
Potential for both
Germline or Somatic Gene Therapy
Woody Guthrie
1930’s
Woody and Arlo, 1950’s
Arlo still performing in 2002
Woody, Krisna, Abe Guthrie
Rachel Carsonpublished Silent Spring 1962 raising concerns on DDTHeptachlorDieldrin
Advocating integrated pest management, she referred to work by Henry Long who reported that heptachlor used to treat fire ants had INCREASED cane borer damage.
Only a small modification b/w estrogen and testosterone
Conventional Intracellular receptor MOA
Several environmental pollutants have been defined as estrogenic:
Endocrine disruptors
Estrogen imparts a 3 layered effect
Transcription of Primary genes
Transcription of Secondary genes
A stabilization of cytoplasmic mRNA
Final Result:
A gradual and long lasting cell response such as synthesis of vitellogenin by liver
The Endocrine Disruptor Hypothesis
Compounds from a variety of sources, once thought to be safe, are having a non-lethal but devastating impact on normal biological signaling
1. Human Medicine
2. Vertebrate Metamorphosis
3. Invertebrate Sex determination
4. Vetebrate Sex determination
1950 – 1970s DES prescribed to prevent miscarriages
DES mothers with 30% higher breast cancer 1980’s
DES daughters with 9x ectopic preg, 2x miscarriage, 5x premature delivery, 2x pre-cancerous dysplasia, 3-5x cervical cancer , vaginal cancer ages 14-22.
John McLachlan DES studies, NIEHS, Tulane biomarkers: transferrin, uterine cancer
Methoprene inhibits mosqui pupation
but bd products disrupt vertebrate ret acid signalling
Tyrone Hayes: Atrazine effects biormarker: frog gonadal abnormalities
Lou Guillette and Lake Apopka: 1992 feminization of gators
2002 Lou says DDE is still in water; gator sexes still confused
Biomarker: steroid levels
Chain of Causation:•Chemical spill in 1992 contained DDT, DDE and more
• Juvenile alligator population has decreased
•females have elevated levels of estradiol
•males have depressed levels of testo
•Females have altered aromatase activity
•Males have poorly organized testes
•Males have reduced penis size
•Testes have elevated estradiol production
•Females have poyovular follicles
•Many contaminants bind to alligator est receptors
biomarkers in certain species have become useful as indicators of environmental health
Biomarkers for estrogen induction can be applied to test for normal reproductive health
As well as Environmental Stress such as Endocrine Disruption
By far the most famous endocrine disruption biomarker is the yolk protein precursor, vitellogenin made by the liver under estrogen induction, transported by the blood and stored in the oocyte
Primers designed against F. heteroclituscDNAs were used to amplify orthologous mRNA from a group of other teleosts.
ApproachF. grandis (sw)
F. chrysotus (fw)
Gambusia affinis (fw)
VITELLOGENINS AND CHORIOGENINS
Biomarkers 2005
Expect to teach me what YOU learn
A semester-long biomarker study design of biomarker experimental induction
assay and publication
A survey of biomarker techniques from our department and the literature