A genome is the complete set of genetic information under discussion. For a cellular organism it is encoded in DNA, including genes and other sequences. Specify whether a comparison concerns a nuclear genome, a mitochondrion's genome or all cellular genetic material: the cell nucleus does not contain every DNA sequence in a typical eukaryote. See NHGRI: genome.

Replica plating transfers samples from corresponding biological colonies or patches to several growth conditions while preserving their spatial arrangement. A master plate makes it possible to relate growth or failure at one location to the same source population on another plate.

The master preserves the source biological colonies; each replica tests a sample of their biological cells. A fabric carrier takes one spatial impression from the master and deposits samples onto fresh plates. Different cell culture medium formulations can then reveal different growth phenotypes at corresponding sites. The carrier copies locations, not a guaranteed number of biological cells. Replica plating spatial correspondence therefore lets an investigator connect a readout to a recoverable source without treating every empty replica site as a missing master biological colony.

The useful trick is that a destructive or growth-restricting test can interrogate one sample while another remains available. In indirect selection of bacterial mutants, the replica supplies information about which source to recover. This also makes a failure-to-grow phenotype accessible: a missing replica biological colony cannot be picked, but its source may still be present on the master. Matching positions is the bridge between testing and retrieval.

Genetic transformation introduces DNA into recipient biological cells. It can change their genotype and sometimes their phenotype; the yeast cross-species complementation experiment separates detecting introduction of a plasmid from detecting its functional effect.

A plasmid is an extrachromosomal DNA replicon: genetic material maintained by DNA replication separately from the host's main chromosomes. Separate copying does not mean independence of the host's enzymes or resources. Many plasmids are circular, but naturally occurring linear plasmids also exist.^[ref]

Engineered plasmids can carry genes for genetic transformation and functional complementation. Typical laboratory plasmids combine an origin of replication, a selectable marker and a plasmid insert. These are engineering roles, not requirements that every natural plasmid carry an experimentally chosen selectable marker or plasmid insert.^[ref]

The useful separation is between keeping a DNA fragment, finding its carriers and testing its function. Molecular cloning uses propagation to recover more copies for study. Plasmid restriction mapping tests a proposed arrangement, while DNA sequencing examines its letters. A successful genetic transformation or a biological colony showing antibiotic resistance answers neither question completely. The yeast cross-species complementation experiment goes a step further by separating plasmid selection from a test of functional complementation.

Online text: www.ncbi.nlm.nih.gov/books/NBK26884/

Online text: www.ncbi.nlm.nih.gov/books/NBK26854/

Online text: www.ncbi.nlm.nih.gov/books/NBK26840/

Online text: www.ncbi.nlm.nih.gov/books/NBK26822/

Cited passages: Alberts and colleagues (2002), Signaling through Enzyme-Linked Cell-Surface Receptors: receptor catalytic activity and insulin receptor signaling.

Online text: www.ncbi.nlm.nih.gov/books/NBK26813/

Cited passages: Alberts and colleagues, Molecular Biology of the Cell, 4th edition (2002), General Principles of Cell Communication, Figure 15-15 and intracellular signaling proteins: local channel regulation, intracellular mediators and relay components.

Cited passages: Alberts and colleagues: local signaling and transmitter removal; Alberts et al., Molecular Biology of the Cell, 4th edition: Figure 15-24 and cellular sensitivity; Alberts et al., Molecular Biology of the Cell, 4th edition: general principles of cell communication; Alberts et al., Molecular Biology of the Cell: Cells Can Adjust Their Sensitivity to a Signal.

Online text: www.ncbi.nlm.nih.gov/books/NBK26910/

Cited passages: Alberts and colleagues, Molecular Biology of the Cell, 4th edition (2002), Ion Channels and the Electrical Properties of Membranes: acetylcholine-gated channels and ionic driving forces.

Cited passages: Alberts and colleagues, Molecular Biology of the Cell: chemical synaptic transmission; Alberts and colleagues: chemical synaptic transmission; Alberts and colleagues: graded postsynaptic signals and integration; Alberts and colleagues: propagation of action potentials; Alberts et al., Molecular Biology of the Cell, 4th edition (2002): ion channels and membrane electrical properties.

Additional cited passages: resting potential and potassium leak channels; slow decay after stopping the sodium–potassium pump; Figure 11-22 caption, small interfacial charge separation. Whole-book authorship and the 2002 edition date apply; no separate section author or revision date is credited.

By K. P. Burr, T. R. Akylas, C. C. Mei.

Online text: web.mit.edu/fluids-modules/www/highspeed_flows/ver2/bl_Chap2/node10.html

Cited passages: Momentum Integral, equations (89)-(93), specialized to constant outer velocity and zero wall-normal velocity.

By K. P. Burr, T. R. Akylas, C. C. Mei.

Online text: web.mit.edu/fluids-modules/www/highspeed_flows/ver2/bl_Chap2/node7.html

Cited passages: Boundary-layer Thickness, Skin friction, and Energy dissipation, discussion before equation (79): asymptotic edge and experimental sensitivity of a 99% criterion; Equation (79) and following interpretation of the volume-flux deficit; Equation (80) and interpretation of the momentum-defect flux; Equation (82), dimensional wall shear definition; the coefficient here follows the numerically checked Blasius equation in the stated normalization.

By K. P. Burr, T. R. Akylas, C. C. Mei.

Online text: web.mit.edu/fluids-modules/www/highspeed_flows/ver2/bl_Chap2/node4.html

By K. P. Burr, T. R. Akylas, C. C. Mei.

Online text: web.mit.edu/fluids-modules/www/highspeed_flows/ver2/bl_Chap2/node2.html

Cited passages: Boundary Layer Governing Equations, equations (13)-(23): inertia-viscosity balance, normal pressure balance, and dimensional equations.

Online text: ocw.mit.edu/courses/8-13-14-experimental-physics-i-ii-junior-lab-fall-2016-spring-2017/7c85fcf2432fca75c26f9f78b6c8cb18_MIT8_13-14F16-S17expIII.pdf

This is a laboratory protocol, not a dataset demonstrating the new gas-cell curve.

Cited passages: MIT Department of Physics, Optical Interferometry, sections III–V: calibrated actuator, two-channel readout and wavelength inference.

Cited passages: MIT Department of Physics, Optical Interferometry laboratory guide, §§II–IV: apparatus and visibility measurement.

Online text: ocw.mit.edu/courses/2-71-optics-spring-2014/ecd8b4c1c7717a31e961837de299879b_MIT2_71S14_lec25_notes.pdf

Cited passages: Nick Fang, Review for Optics, 12 May 2014, pp. 7–8, §E(a–b): coherent field and incoherent intensity imaging; Review for Optics, p. 8, §E(b): OTF as Fourier transform of intensity PSF and pupil autocorrelation; Review for Optics, pp. 6–8, §§D(c), E: lens Fourier transform and pupil transfer function.

Online text: ocw.mit.edu/courses/2-71-optics-spring-2014/d558a4fabb2cc2eee8f864d3928b31f6_MIT2_71S14_lec2_notes.pdf

The notes also use a nondispersive travel-time interpretation; this enrichment limits that interpretation explicitly rather than applying it to arbitrary dispersive media.

Cited passages: Nick Fang, Lecture Notes on Geometrical Optics, page 4, equation 1: optical path integral.

Cited passages: Nick Fang, MIT Lecture Notes on Geometrical Optics, 2014, introduction and §H; Nick Fang, MIT Lecture Notes on Geometrical Optics, 2014, §J: Composite lenses; Nick Fang, MIT Lecture Notes on Geometrical Optics, §H: Magnification; Nick Fang, MIT Lecture Notes on Geometrical Optics, §J: Composite lenses; Nick Fang, MIT Lecture Notes on Geometrical Optics, §§E–G; Nick Fang, MIT: Geometrical optics; Nick Fang, MIT: Geometrical optics, pages 1-3.

Online text: www.ocw.mit.edu/courses/2-71-optics-spring-2014/13134562742a242caad5fd92fcb27dfa_MIT2_71S14_lec10_notes.pdf

Course is Spring 2014; PDF itself bears the date string 03/11/13. Author identified as Nick Fang in PDF and Nicholas X. Fang on course page.

Cited passages: Nick Fang, Optics lecture 10, pages 1–3: eikonal equation, optical path integral and ray direction.