DNA

The Story of the Genetic Revolution

James D Watson, Beaverton Library, 576.5 WAT 2017

• p8-10 Gregor Mendel peas, careful statistics, and math 1856-1868 (yellow dominant) died 1884

  • "Versuche über Pflanzenhybriden" ("Experiments on Plant Hybridization") published in 1866 in Verhandlungen des naturforschenden Vereines in Brünn, referenced three times in 35 years

• p11-13 Thomas Hunt Morgan Columbia U. fruit flies 1901- , crossover
• p37 Oswald Avery identified DNA as "transforming principle", denied Nobel because Swedish chemist Einar Hammarsten believed genes were proteins
• p40 Maurice Wilkins from nuclear physics to X-ray diffraction of DNA
• p42 23yo Watson postdoc at Cambridge under Max Perutz and Lawrence Bragg, shared lab with 35yo ex-physicist Francis Crick
• p43 31yo physical chemist Rosalind Franklin, mountaineer, high society, impatient with fools.
• p45 Watson at first confused "unit cell" with "assymetric unit", DNA crystals water rich.
• p46 Erwin Chargaff found A/T and G/C ratios close to unity
• p47 Franklin's "photograph 51" B type, more water, taken by her student Raymond Gosling
• p48 density measurements favored two chain rather than three chain
• p49 February 28, 1953, base molecules pair edge to edge with hydrogen bonds, two for A=T, three for G≡C (purine to pyrimidine). Appeared in Nature April 25 p737.
• p57 Meselson-Stahl experiment with heavy/light nitrogen isotopes and centrifugation showed hybrid (half weight) first generation, light and hybrid second generation.
• p57 Nobel physiology-or-medicine 1962 to Crick, Wilkins, and Watson; Franklin died of ovarian cancer in 1958, age 37
• p58 Watson speculates if she had lived, Franklin would have shared the Chemistry prize with Wilkins in 1962
  • Watson: Franklin refused for a long time ... DNA was a helix, data from her work was absolutely critical.

• p63 1941 Beadle and Tatum mutated red mold Nerosposa Crassa, found strain 299 that couldn't synthesize something from minimum medium, but could if vitamin B₆ added. → thus "one gene, one enzyme"

• p67 Watson and George Gamow RNA Tie Club. 20 members, one for each amino acid. Gamow had ALA tie pin, Watson PRO, Teller LEU, Feynman GLY, Chargaff LYS, Crick TYR, Delbrück TRY, Brenner VAL, Orgel THR, others I haven't heard of (yet).
• p69 Crick proposes adapter molecules
• p73 Nirenberg and Mathaei make "UUUUUU" RNA, which synthesizes chains of polyphenylalanine, hence codon UUU. Khorana figured out much of the rest. They shared the 1968 Nobel Prize for Physiology or Medicine.

• p93 Abraham Lincoln High School science club run by stockroom supervisor Miss Sophie Wolfe. Students Arthur Kornberg (1936), Paul Berg (1943), and Jerome Karle (1933) are Nobel laureates.

• p95 1974 Science Moratorium letter, February 1975 Asilomar conference, led to modified K-12 variant of E. coli requiring artificial nutrients.

• p104 Sanger sequencing: solution of bases with a few modifed "dideoxy" bases that terminate chains. Sort the segments by mass (hence length) with electrophroresis, then measure which dideoxy base terminates the segment. So, position on the gel is position on the chain.

• p110 Herb Boyer and Bob Swanson start Genentech to make human insulin (51 amino acid) genes inserted into bacteria (but without the human introns, thus bypassing regulations and moratorium rules. Licensed to Lilly, IPO brought in $38M, share value to $66M to each founder.

• p124 Novartis Gleevec against chronic myeloid leukemia (CML) blood cancer
• p127 Martin Shkreli's Turing Pharmaceuticals generic toxoplasmosis drug Daraprim hiked price from $13.50 to $750 per tablet. Rival Imprimis manufactured a Daraprim generic for a dollar.

• p142 Bacillis thuringiensis Bt bacteria toxin against lepidopteran caterpillars, beetle and fly larvae, now added to Bt crops (corn, potato, cotton, soybean) ... massive pesticide reduction.

• p145 Bruce Ames quote: "There are more rodent carcinogens in one cup of coffee than pesticide residues you get in a year."
• p151 Starlink corn approved for feed, not people, but cross contamination made that impossible.
• p165 Max Hoffman Foundation pledged $36M for $75M UC telescope, other donors balked. W.M. Keck Foundation paid entire project (now the Keck Telescope on Mauna Kea), so Hoffman money redirected in 1985 to a UC Santa Cruz -based Human Genome Project. Funding from NIH and DOE (for radiation mutations) supplanted that. Conference at Cold Springs Harbor Lab in 1986, estimated $3B for 3B base pairs with Sanger sequencing; $3B= $200M/year for 15 years.
  • Celera/Venter claimed $300M for whole genome.

• p173 PCR now uses DNA polymerase derived from Thermus aquaticus from Yellowstone Hot Springs, which isn't destroyed at 95C

• p175 Applied Biosystems Inc. Mike Hunkapiller, capillary tubes, up to half a million base pairs per day.
• p176 cDNA: DNA copy made with reverse transcriptase from RNA, without the introns
• p177 NIH head Bernadine Healy forces Watson to resign in 1992 after 4 years heading HGP
• p178 Venter with William Hazeltine: HGS Human Genome Sciences (business arm), TIGR The Institute for Genome Research (nonprofit research)

• p181 C. elegans nematode worm, 97M base pairs, 20K genes.

• p183 1998 Venter forms Celera Genomics using 300 sequencers (ABI PRISM 3700) and huge computation, WGS, Whole Genome Shotgun sequencing

• p184 1996 [ https://en.wikipedia.org/wiki/Bermuda_Principles | Bermuda Principles: ]] sequence data should be released promptly.

  • Venter would defer by three months
• Eric Lander, Jim Kent public project. Kent "borrowed" 100 UC instruction computers for sequence assembly, finishing June 22.
• p189 Celera finishd June 25, public announcement with President Clinton June 26, 2000
• p196 Jonathan Rothberg 454 Life Sciences, Project Jim, Watson's genome, blood sample late 2006, presentation May 2007, cost $1M
  • APOE4 omitted, Watson's aunt had Alzheimers
• p204 Illumina !HiSeqX: 3 days oer run, 6 G reads per run, run length 300, Reagents $7/GB, 1800 Gbases/run

  • Oxford Nanopore MiniIon, 48 hours, 4.4 M reads per run, run length 10K, Reagents $1K/GB, 900 Mbases/run

• p207 November 2007: !23andMe [ https://en.wikipedia.org/wiki/Anne_Wojcicki | Anne Wojcicki], !deCODE Genetics Kári Stephánson in Iceland, SNP tests

• p215 June 13, 2013 Supreme Court overturns gene patents.
• p217 2008 Genetic Information Nondiscrimination Act GINA
• p224 "Moore's Law" vs sequencing graph: $100M 2001, $10M 2007, 10K 2011, $6K 2014, $1200 2015
  • 2017 Illumina Nova Seq, $100 genome in a few years
• p233 more genes for highly varying environments, E. coli 4000, humans 21000 , mustard plant 27000.

• p236 Humans 3.2G base pairs, Onions 18G, Amoeba dubia 670G

• p262 DNA can survive up to 50,000 years if corpse dries fast enough.
• p264 Mitochondria 16600 base pair loop, 500 to 1000 per cell
• p265 humans differ from Neanderthal 5% out of 379 base pairs confirmed by two labs
• p265 5 cm Neanderthal bone from Vindija cave in Croatia 1980 , 40kya, 1 million bases, 55% of Neanderthal genome 2010 Science Pääbo.
• p286 most recent common human ancestor 150 kya, not much variation time
• p288 "Nilotic form" tall skinny facilitates heat loss, "Pygmy form" short, minimum calory needs
• p289 Lactose intolerance after weaning, diarrhea, gas, abdominal bloating
• p296 Alec Jeffreys DNA fingerprinting, individual patterns in noncoding DNA, 1985 reunited wrongfully deported Andrew Sarbah with mother in England
• p310 DNA fingerprinting identified Romanovs, discredited Anastasia pretender Anna Anderson
• p315 King Richard III skeleton discovered, !mtDNA match to 20th-generation descendants of sister
• p327-365 disease gene discovery Huntington's (HD), beta thasselimia, Duchene's muscular dystrophy (DMD), cystic fibrosis (CF)
  • BRCA1, PKU. Fragile X, Cystic fibrosis, medium chain acyl-!CoA dehydrogenase deficience (MCAD), Tay Sachs

• restriction fragment length polymorphisms (RFLP)

• p356 Anne Morriss and Lee Silver GenePeeks

• p357 Allen Roses at Duke APOE4
• p366 CRISPR clustered regularly interspaced short palindromic repeats

• p401 Decoding Annie Parker 2013 film about Mary-Claire King and BRCA1

• p401 550 thousand US Americans died of malignant cancers, 1 in 3
• much about cancer and the ethics of germ line modification