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Contemporary Concepts in

Cellular and Molecular Biology for the

Medical Physicist

Barry S. Rosenste in, Ph.D.Mount Sinai School of Medicine

NYU School of Medicine

www.chem.ucsb. edu/.../images/WatsonCrick.j

pg

Albert s et al. Molec ular Biology of the Cell, 1994

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Alber ts et al. Molec ularBio logy of the Cell , 1994 Alberts et al. Molecular Biology of the Cell , 1994

Alber ts et al.Molecular

Bio logy of theCell , 1994 Alberts et al. Molecular Biology of the Cell, 1994

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Alberts et al. Molecular Biology of the Cell , 1994

Alberts et al.Molecul ar

Biology of theCell 1994

Lewin , GenesV, 1994

Hall, Radiobiology forthe Radiologist , 2000

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Lewin , GenesV, 1994 Lewin, Genes V, 1994

Alb erts et al. MolecularBiology of the Cell,

1994

RESTRICTIONENDONUCLEASES

VECTORS

•Self -repl icati ng DNA molecule that hasthe abil ity to carry another foreign DNAmolecule into a host cell.

•Purpose - insert a fragment of DNA intoa vect or so that it can be replicated andgrown into quantities suitable for study.

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PLASMID

Alberts et al. Molec ular Biology of the Cell , 1994

Alb erts et al.Molecular Biologyof the Cell , 1994

REPORTERGENE

ASSAYS

Hall and Giaccia ,Radiobiology for the

Radiol ogist , 2006

COMMONLY USED REPORTER GENES

• Chlorampheni col Acet ylt rans ferase (CAT)• Firefly Luciferase• ββββ-Galactosi dase• Secreted Alkaline Phosp hatase (SEAP)• Human Growth Hormone (hGH)• ββββ-Glucuronid ase (GUS)• Green Fluores cent Prote in (GFP)

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LIBRARIESGENOMIC LIBRARY

Compil ation of DNA fragments thatmake up the entir e genome.

athen a.bioc.uvic .ca/.../copy13_of_samp le/phage

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cDNA LIBRARY

DNA comple mentary to mRNA - onlythe expre ssed genes of a particula rcell.

8e.devbio.c om/images/ch04/0405fig2.jpg

http: //fig.c ox.miami.e du/~cmal lery/150/gene/sf16x5.jpg

EXPRESSIONLIBRARY

Albert s et al. MolecularBiology of the Cell , 1994

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GEL ELECTROPHORESIS

Hall andGiaccia,

Radiobi ology for the

Radiolo gist ,2006

www.cbs.dtu.dk/sta ff/dav e/roan oke/fig5_33.j pg

http://www .mun.ca/biol ogy/s carr/Lab_5_gel_1 999.gifHall and Giaccia, Radio biology for the

Radiolo gis t, 2006

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SDS POLYACRYLAMI DE GELELECTROPHORESIS

http://fig.cox .miam i.edu/~cmallery/255/255tech/mcb3.32 .SDS.elect .jpg

Hall and Giacc ia, Radiobiology for the Radiolog ist ,2006

POLYMERASECHAIN

REACTION

Albert s et al. MolecularBiology of the Cell , 1994

Albert s et al. Molecular Biology of the Cell, 1994

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REVERSE TRANSCRIPTASE PCRRT PCR

qPCR Using Real-Time PCR

https://ww w.finnzymes.fi/realtime_qpcr/dyna mo_capillary_sy br_green_qpcr_kit.html

Sout hern Blot ting – DNANort hern Blott ing – RNA

Alb erts et al. Molecular Biology of the Cell , 1994 http:/ /www .mcm aster.ca/inabis98 /higuchi/n oda0326/ f3small. gif

NORTHEN BLOT

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http ://ww w.bseinquiry.gov. uk/report/v olu me2/fig1_8.htm

WESTERNBLOT

FAR-WESTERN BLOTTING

http:// www.bio on.com/experiment/Upload Files/200408/2004080313192 9294.gif

EXPRESSION MICROARRAYS

www.Af fymetrix.com www.Affy metrix.com

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www.Affym etrix.com

www.Affyme trix .com

ww w.Affymetrix .com www.Aff yme trix .com

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ww w.Affymetrix. c

om Hall and Giaccia, Radiobi ology for the Radiolo gist , 2006

http:/ /www.ogt. co.uk/ima ges/hu man -gene-expre ssion.gifBru chova . Leukem ia

Res.28:1,2004

SINGLENUCLEOTIDE

POLYMORPHISM

SNP

www.seq.u bc .ca/decode.ne-icelands -dna/

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PERSONALIZED MEDICINE

The use of detailed in formation about a patient'sgenotype in order to select a medication, thera py orpreventative measu re that is par ticularl y suite dspeci fic ally to that pati ent.

www. san ger.ac .uk

SNP ASSAYS

SINGLE-STRANDED CONFORMATIONPOLYMORPHISM

SSCP

National.diagnost ics.combined /images/2_3_2/gi f

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Clin ical Scienc eClin ical Sciencewww.cl in sci.orgwww.cl in sc i.org .. ClinClin ..SciSci . (2005) 109, 365. (2005) 109, 365--379379

5’ NucleaseTaqManAss ay

MOLECULAR BEACONS

www. ebiotrade.com/ ,,,/fig.molecular_be

acons. gif

IlluminaAffy metrix

SNP/CNP (Genotyping ) Arrays

www.Aff yme trix .com

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http:/ /www .access excellence. org/RC/VL/GG/transgen ic.php http://www.b iken.osa ka-u.ac.jp/act /act_o kabe_e.php

KNOCKOUTMICE

http ://www.nia aa.nih.gov/Resources/Gr aphicsGalle ry/Genetics/homa

n.htm

Enzyme-Lin ked ImmunoSorbent Assay

http://64 .202.120.86/upl oad/image /articles/2 006/biopen/biop en-elisa -sch ematic.jpg

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Electrophoretic Mobility Shift AssayEMSA

www.biochem.arizona .edu/.../Am64./8a.gif

IMMUNOPRECIPITATION

www.mo lecularst ation.com

CHROMATIN IMMUNOPRECIPITATIONChIP

www. vinicib iochem.it /images/chip_fl ow. jpg

ChIP-on-chip

http:/ /en.wik iped ia.org/wiki/ ChIP-on -chip

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DNase IFootprintin g

Alber ts et al. MolecularBio logy of the Cell , 1994 Albert s et al. Molec ular Biology of the Cell, 1994

www.scq.ubc .ca/wp-cont ent/siR NA.gif

siRNA miRNA

www.mi crorna .ic.cz/obr/ image0 03.png

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DNA STRAND BREAKASSAYS

PULSED FIELD GELELECTROPHORESIS

Hersc hleb et al., Nature Protocols2: 677, 2007

Burdak-Rothkamm Oncogene 26: 993, 2007

COMET ASSAY

www.scie lo.br/img/f bpe/gmb/ v23n1/2339f1.jp g

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http:// jamescbender.com/bendersblo g/Default.aspx