13.09.2022 Views

Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

Create successful ePaper yourself

Turn your PDF publications into a flip-book with our unique Google optimized e-Paper software.

528 Chapter 8: Analyzing Cells, Molecules, and Systems

References

General

Ausubel FM, Brent R, Kingston RE et al. (eds) (2002) Short Protocols in

Molecular Biology, 5th ed. New York: Wiley.

Brown TA (2007) Genomes 3. New York: Garland Science Publishing.

Spector DL, Goldman RD & Leinwand LA (eds) (1998) Cells: A

Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor

Laboratory Press.

Watson JD & Berry A (2008) DNA: The Secret of Life. New York: Alfred

A Knopf.

Watson JD, Myers RM & Caudy AA (2007) Recombinant DNA: Genes

and Genomes – A Short Course, 3rd ed. Cold Spring Harbor, NY:

Cold Spring Harbor Laboratory Press.

Isolating Cells and Growing Them in Culture

Ham RG (1965) Clonal growth of mammalian cells in a chemically

defined, synthetic medium. Proc. Natl Acad. Sci. USA 53,

288–293.

Harlow E & Lane D (1999) Using Antibodies: A Laboratory Manual. Cold

Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Herzenberg LA, Sweet RG & Herzenberg LA (1976) Fluorescenceactivated

cell sorting. Sci. Am. 234, 108–116.

Milstein C (1980) Monoclonal antibodies. Sci. Am. 243, 66–74.

Purifying Proteins

de Duve C & Beaufay H (1981) A short history of tissue fractionation.

J. Cell Biol. 91, 293s–299s.

Laemmli UK (1970) Cleavage of structural proteins during the assembly

of the head of bacteriophage T4. Nature 227, 680–685.

Scopes RK (1994) Protein Purification: Principles and Practice, 3rd ed.

New York: Springer-Verlag.

Simpson RJ, Adams PD & Golemis EA (2008) Basic Methods in Protein

Purification and Analysis: A Laboratory Manual. Cold Spring Harbor,

NY: Cold Spring Harbor Laboratory Press.

Wood DW (2014) New trends and affinity tag designs for recombinant

protein purification. Curr. Opin. Struct. Biol. 26, 54–61.

Analyzing Proteins

Choudhary C & Mann M (2010) Decoding signalling networks by mass

spectrometry-based proteomics. Nat. Rev. Mol. Cell Biol.

11, 427–439.

Domon B & Aebersold R (2006) Mass spectrometry and protein

analysis. Science 312, 212–217.

Goodrich JA & Kugel JF (2007) Binding and Kinetics for Molecular

Biologists. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory

Press.

Kendrew JC (1961) The three-dimensional structure of a protein

molecule. Sci. Am. 205, 96–111.

Knight ZA & Shokat KM (2007) Chemical genetics: where genetics and

pharmacology meet. Cell 128, 425–430.

O’Farrell PH (1975) High resolution two-dimensional electrophoresis of

proteins. J. Biol. Chem. 250, 4007–4021.

Pollard TD (2010) A guide to simple and informative binding assays.

Mol. Biol. Cell 21, 4061–4067.

Wüthrich K (1989) Protein structure determination in solution by nuclear

magnetic resonance spectroscopy. Science 243, 45–50.

Analyzing and Manipulating DNA

Cohen S, Chang A, Boyer H & Helling R (1973) Construction of

biologically functional bacterial plasmids in vitro. Proc. Natl Acad.

Sci. USA 70, 3240–3244.

Green MR & Sambrook J (2012) Molecular Cloning: A Laboratory

Manual, 4th ed. Cold Spring Harbor, NY: Cold Spring Harbor

Laboratory Press.

International Human Genome Sequencing Consortium (2001) Initial

sequencing and analysis of the human genome. Nature 409,

860–921.

Jackson D, Symons R & Berg P (1972) Biochemical method for

inserting new genetic information into DNA of Simian Virus 40:

circular SV40 DNA molecules containing lambda phage genes and

the galactose operon of Escherichia coli. Proc. Natl Acad. Sci. USA

69, 2904–2909.

Kosuri S & Church GM (2014) Large-scale de novo DNA synthesis:

technologies and applications. Nat. Methods 11, 499–507.

Maniatis T, Hardison RC, Lacy E et al. (1978) The isolation of structural

genes from libraries of eucaryotic DNA. Cell 15, 687–701.

Mullis KB (1990) The unusual origin of the polymerase chain reaction.

Sci. Am. 262, 56–61.

Nathans D & Smith HO (1975) Restriction endonucleases in the analysis

and restructuring of DNA molecules. Annu. Rev. Biochem.

44, 273–293.

Saiki RK, Gelfand DH, Stoffel S et al. (1988) Primer-directed enzymatic

amplification of DNA with a thermostable DNA polymerase. Science

239, 487–491.

Sanger F, Nicklen S & Coulson AR (1977) DNA sequencing with chainterminating

inhibitors. Proc. Natl Acad. Sci. USA 74, 5463–5467.

Shendure J & Lieberman Aiden E (2012) The expanding scope of DNA

sequencing. Nat. Biotechnol. 30, 1084–1094.

Studying Gene Expression and Function

Botstein D, White RL, Skolnick M & Davis RW (1980) Construction of

a genetic linkage map in man using restriction fragment length

polymorphisms. Am. J. Hum. Genet. 32, 314–331.

DeRisi JL, Iyer VR & Brown PO (1997) Exploring the metabolic and

genetic control of gene expression on a genomic scale. Science

278, 680–686.

Esvelt KM, Mali P, Braff JL et al. (2013) Orthogonal Cas9 proteins for

RNA-guided gene regulation and editing. Nat. Methods

10, 1116–1121.

Fellmann C & Lowe SW (2014) Stable RNA interference rules for

silencing. Nat. Cell Biol. 16, 10–18.

Mello CC & Conte D (2004) Revealing the world of RNA interference.

Nature 431, 338–342.

Nüsslein-Volhard C & Wieschaus E (1980) Mutations affecting segment

number and polarity in Drosophila. Nature 287, 795–801.

Palmiter RD & Brinster RL (1985) Transgenic mice. Cell 41, 343–345.

Weigel D & Glazebrook J (2002) Arabidopsis: A Laboratory Manual.

Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Wilson RC & Doudna JA (2013) Molecular mechanisms of RNA

interference. Annu. Rev. Biophys. 42, 217–239.

Mathematical Analysis of Cell Functions

Alon U (2006) An Introduction to Systems Biology: Design Principles of

Biological Circuits. Boca Raton, FL: Chapman & Hall/CRC.

Alon U (2007) Network motifs: theory and experimental approaches.

Nat. Rev. Genet. 8, 450–461.

Ferrell JE Jr (2002) Self-perpetuating states in signal transduction:

positive feedback, double-negative feedback and bistability. Curr.

Opin. Cell Biol. 14, 140–148.

Ferrell JE Jr, Tsai TY & Yang Q (2011) Modeling the cell cycle: why do

certain circuits oscillate? Cell 144, 874–885.

Gunawardena J (2014) Models in biology: ‘accurate descriptions of our

pathetic thinking’. BMC Biol. 12, 29.

Lewis J (2008) From signals to patterns: space, time, and mathematics

in developmental biology. Science 322, 399–403.

Mogilner A, Allard J & Wollman R (2012) Cell polarity: quantitative

modeling as a tool in cell biology. Science 336, 175–179.

Novak B & Tyson JJ (2008) Design principles of biochemical oscillators.

Nat. Rev. Mol. Cell Biol. 9, 981–991.

Silva-Rocha R & de Lorenzo V (2008) Mining logic gates in prokaryotic

transcriptional regulation networks. FEBS Lett. 582, 1237–1244.

Tyson JJ, Chen KC & Novak B (2003) Sniffers, buzzers, toggles and

blinkers: dynamics of regulatory and signaling pathways in the cell.

Curr. Opin. Cell Biol. 15, 221–231.

Hooray! Your file is uploaded and ready to be published.

Saved successfully!

Ooh no, something went wrong!