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• Title:Introduction to genomics / Arthur Lesk.
  
•    
• Author/Creator:Lesk, Arthur M., author.
  
• Published/Created:Oxford : Oxford University Press, [2017]
  

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  • Location:WOODWARD LIBRARY stacksWhere is this?
    
  • Call Number: QH447 .L47 2017
    
  • Number of Items:1
    
  • Status:Available
    

   
• Library of Congress Subjects:Genomics.
  
• Medical Subjects: Genomics.
  
• Edition:Third edition.
  
• Description:xxvii, 509 pages : illustrations (colour), maps (colour) ; 27 cm
  
• Summary:"Our genome is the blueprint for our existence: it encodes all the information we need to develop from a single cell into a hugely complicated functional organism. Yet it is more than a static information store: our genome is a dynamic, tightly-regulated collection of genes, which switch on and off in many combinations to give the variety of cells from which our bodies are formed. But how do we identify the genes that make up our genome? How do we determine their function? And how do different genes form the regulatory networks that direct the processes of life? Introduction to Genomics is the most up-to-date and complete textbook for students approaching the subject for the first time. Lesk's engaging writing style brings a narrative to a disparate field of study and offers a fascinating insight into what can be revealed from the study of genomes. The book covers: the similarities and differences between organisms; how different organisms evolved; how the genome is constructed and how it operates; and what our understanding of genomics means in terms of our future health and wellbeing."--Provided by publisher.
  
• Notes:Previous edition: 2012.
  Includes bibliographical references and index.
  
• ISBN:9780198754831 paperback
  0198754833 paperback
  
• Contents:Machine generated contents note: Learning goals
  Genomics: the hub of biology
  Phenotype = genotype + environment + life history + epigenetics
  Varieties of genome organization
  Chromosomes, organelles, and plasmids
  Genes
  scope and applications of genome sequencing projects
  Variations in genome sequences within species
  Mutations and disease
  Single-nucleotide polymorphisms
  Haplotypes
  clinically important haplotype: the major histocompatibility complex
  Populations
  Species
  biosphere
  Extinctions
  future?
  Genome projects and our current library of genome information
  High-throughput sequencing
  De novo sequencing
  Resequencing
  Exome sequencing
  What's in a genome?
  Some regions of the genome encode non-protein-coding RNA molecules
  Some regions of the genome contain pseudogenes
  Other regions contain binding sites for ligands responsible for regulation of transcription
  Repetitive elements of unknown function account for surprisingly large fractions of our genomes
  Dynamic components of genomes
  Genomics and developmental biology
  Genes and minds: neurogenomics
  Genetics of behaviour
  Proteomics
  Protein evolution: divergence of sequences and structures within and among species
  Mechanisms of protein evolution
  Organization and regulation
  Some mechanisms of regulation act at the level of transcription
  Some mechanisms of regulation act at the level of translation
  Some regulatory mechanisms affect protein activity
  On the web: genome browsers
  Genomics and computing
  Archiving and analysis of genome sequences and related data
  Databanks in molecular biology
  Programming
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  '...the end of the beginning'
  Human genome sequencing
  What makes us human?
  Comparative genomics
  Genomics and language
  human genome and medicine
  Prevention of disease
  Detection and precise diagnosis
  Genetic counselling-carrier status
  Discovery and implementation of effective treatment
  Tunable healthcare delivery: pharmacogenomics
  'Pop' applications of genome sequencing
  Genomics in personal identification
  DNA 'fingerprinting'
  Personal identification by amplification of specific regions has superseded the RFLP approach
  Mitochondrial DNA
  Analysis of non-human DNA sequences
  Parentage testing
  Inference of physical features, and even family name
  Ethical, legal, and social issues
  Databases containing human DNA sequence information
  Use of DNA sequencing in research on human subjects
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  Classical genetics as background
  What is a gene?
  Maps and tour guides
  Genetic maps
  Linkage
  Linkage disequilibrium
  Chromosome banding pattern maps
  Restriction maps
  Discovery of the structure of DNA
  DNA sequencing
  Frederick Sanger and the development of DNA sequencing
  DNA sequencing by termination of chain replication
  Maxam-Gilbert chemical cleavage method
  Automation of DNA sequencing
  Organizing a large-scale sequencing project
  Bring on the clones: hierarchical-or 'BAC-to-BAC'-genome sequencing
  Whole-genome shotgun sequencing
  Next-generation sequencing
  Roche 454 Life Sciences
  Illumina
  Ion Torrent/Personal Genome Machine (PGM)
  PacBio
  Oxford Nanopore
  10X Genomics
  Biohano Irys system
  Life in the fast lane
  How much sequencing power is there in the world?
  Databanks in molecular biology
  Nucleic acid sequence databases
  Protein sequence databases
  Databases of genetic diseases-OMIM and OMIA
  Databases of structures
  Specialized or 'boutique' databases
  Expression and proteomics databases
  Databases of metabolic pathways
  Bibliographic databases
  Surveys of molecular biology databases and servers
  Computer programming in genomics
  Programming languages
  How to compute effectively
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  Evolution is exploration
  Biological systematics
  Biological nomenclature
  Measurement of biological similarities and differences
  Homologues and families
  Pattern matching-the basic tool of bioinformatics
  Sequence alignment
  Defining the optimum alignment
  Scoring schemes
  Varieties and extensions
  Approximate methods for quick screening of databases
  Pattern matching in three-dimensional structures
  Evolution of protein sequences, structures, and functions
  Evolution of protein structure and function
  Phylogeny
  Calculation of phylogenetic trees
  Short-circuiting evolution: genetic engineering
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  Evolution and phylogenetic relationships in prokaryotes
  Major types of prokaryotes
  Do we know the root of the tree of life?
  Genome organization in prokaryotes
  Replication and transcription
  Gene transfer
  Archaea
  genome of Methanococcus jannaschn
  Life at extreme temperatures
  Comparative genomics of hyperthermophilic archaea: Thermococcus kodakarensis and pyrococci
  Bacteria
  Genomes of pathogenic bacteria
  Genomics and the development of vaccines
  Viruses
  Nucleocytoplasmic large DNA viruses (or giant viruses)
  Viral genomes
  Recombinant viruses
  Viruses and evolution
  Influenza: a past and current threat
  'Ome, 'ome, on the range: metagenomics, the genomes in a coherent environmental sample
  Marine cyanobacteria-an in-depth study
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  origin and evolution of eukaryotes
  Evolution and phylogenetic relationships in eukaryotes
  yeast genome
  evolution of plants
  Arabidopsis thaliana genome
  Genomes of animals
  genome of the sea squirt (Ciona intestinalis)
  genome of the pufferfish (Tetraodon nigroviridis)
  genome of the chicken (Gallus gallus domesticus)
  genome of the platypus (Ornithorhynchus anatinus)
  genome of the dog
  Palaeosequencing-ancient DNA
  Recovery of DNA from ancient samples
  DNA from extinct birds
  High-throughput sequencing of mammoth DNA
  phylogeny of elephants
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  Introduction
  Unity and diversity of life
  Taxonomy based on sequences
  Sizes and organization of genomes
  Genome sizes
  Genome organization in eukaryotes
  Photosynthetic sea slugs: endosymbiosis of chloroplasts
  How genomes differ
  Variation at the level of individual nucleotides
  Duplications
  Duplication of genes
  Family expansion: G protein-coupled receptors
  Comparisons at the chromosome level: synteny
  What makes us human?
  Comparative genomics
  Genomes of chimpanzees and humans
  Genomes of mice and rats
  Model organisms for study of human diseases
  genome of Caenorhabditis elegans
  genome of Drosophila melanogaster
  Homologous genes in humans, worms, and flies
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  Introduction
  Some diseases are associated with mutations in specific genes
  Haemoglobinopathies-molecular diseases caused by abnormal haemoglobins
  Phenylketonuria
  Alzheimer's disease
  Identification of genes associated with inherited diseases
  Genome-wide association studies
  GWAS of sickle-cell disease
  GWAS of type 2 diabetes
  GWAS of schizophrenia
  human microbiome
  Treatment of abnormal microbiome composition
  Cancer genomics
  SNPs and cancer
  Whole-genome sequencing association studies of breast cancer
  Copy-number alterations in cancer
  Chromosomal aberrations
  Epigenetics and cancer
  microRNAs and cancer
  Immunotherapy for cancer
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  Ancestry of Homo sapiens
  Neanderthal genome
  Denisovan genome
  What do these data tell us?
  What have Neanderthals and Denisovans done for us lately?
  Ancient populations and migrations
  Western civilization? 'I think it would be a good idea'
  Domestication of the dog
  Domestication of the horse
  Domestication of crops
  Maize (Zea mays)
  Rice (Oryza sativa)
  Control of flowering time
  History of rice domestication
  Chocolate (Theobroma cacao)
  Theobroma cacao genome
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  Introduction
  Microarrays
  Microarray data are semiquantitative
  Applications of DNA microarrays
  Analysis of microarray data
  RNAseq
  RNAseq versus microarrays
  Expression patterns in different physiological states
  Sleep in rats and fruit flies
  Expression pattern changes in development
  Variation of expression patterns during the life cycle of Drosophila melanogaster
  Flower formation in roses
  Expression patterns in learning and memory: long-term potentiation
  Conserved clusters of co-expressing genes
  Evolutionary changes in expression patterns
  Applications of transcriptomics in medicine
  Development of antibiotic resistance in bacteria
  Childhood leukaemias
  Encyclopedia of DNA Elements (ENCODE)
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  Introduction
  Protein nature and types of proteins
  Contents note continued: Protein structure
  chemical structure of proteins
  Conformation of the polypeptide chain
  Protein folding patterns
  Domains
  Disorder in proteins
  Post-translational modifications
  Why is there a common genetic code with 20 canonical amino acids?
  Separation and analysis of proteins
  Polyacrylamide gel electrophoresis (Page)
  Two-dimensional Page
  Mass spectrometry
  Identification of components of a complex mixture
  Protein sequencing by mass spectrometry
  Quantitative analysis of relative abundance
  Measuring deuterium exchange in proteins
  Experimental methods of protein structure determination
  X-ray crystallography of proteins
  Interpretation of the electron density: model building and improvement
  How accurate are the structures?
  NMR spectroscopy in structural biology
  Protein structure determination by NMR
  Low-temperature electron microscopy (cryoEM)
  Classifications of protein structures
  SCOP
  SCOP2
  Protein complexes and aggregates
  Protein aggregation diseases
  Properties of protein-protein complexes
  Stoichiometry-what is the composition of the complex?
  Affinity-how stable is the complex?
  How are complexes organized in three dimensions?
  Multisubunit proteins
  Many proteins change conformation as part of the mechanism of their function
  Conformational change during enzymatic catalysis
  Motor proteins
  Allosteric regulation of protein function
  Allosteric changes in haemoglobin
  Conformational states of serine protease inhibitors (serpins)
  Protein structure prediction and modelling
  Homology modelling
  Secondary structure prediction
  Prediction of novel folds: ROSETTA
  Available protocols for protein structure prediction
  Structural genomics
  Directed evolution and protein design
  Directed evolution of subtilisin E
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  Introduction
  Classification and assignment of protein function
  Enzyme Commission
  Gene Ontology[™] Consortium protein function classification
  Comparison of EC and GO classifications
  Metabolic networks
  Databases of metabolic pathways
  EcoCyc
  Kyoto Encyclopedia of Genes and Genomes
  Human Metabolome Database
  Evolution and phylogeny of metabolic pathways
  Alignment and comparison of metabolic pathways
  Comparing linear metabolic pathways
  Reconstruction of metabolic networks
  Comparing non-linear metabolic pathways: the pentose phosphate pathway and the Calvin-Benson cycle
  Metabolomics in ecology
  Dynamic modelling of metabolic pathways
  Looking forward
  Recommended reading
  Exercises and problems
  Learning goals
  Introduction
  Regulatory mechanisms
  Two parallel networks: physical and logical
  Networks and graphs
  Robustness and redundancy
  Connectivity in networks
  Dynamics, stability, and robustness
  Protein complexes and aggregates
  Protein interaction networks
  Protein-DNA interactions
  DNA-protein complexes
  Structural themes in protein-DNA binding and sequence recognition
  Bacteriophage T7 DNA polymerase
  Some protein-DNA complexes that regulate gene transcription
  Regulatory networks
  Structures of regulatory networks
  Structural biology of regulatory networks
  Gene regulation
  transcriptional regulatory network of Escherichia coli
  genetic switch of bacteriophage X
  Regulation of the lactose operon in Escherichia coli
  genetic regulatory network of Saccharomyces cerevisiae
  Adaptability of the yeast regulatory network
  Looking forward
  Recommended reading
  Exercises and problems
  Prologue: Preliminaries
  0.1. Signpost: Uncertainty
  0.2. Discrete Probability Distributions
  0.2.1. probability distribution summarizes our knowledge about an uncertain situation
  0.2.2. Conditional probability quantifies the degree to which events are correlated
  0.2.3. random variable can be partially described by its expectation and variance
  0.2.4. Joint distributions
  0.2.5. Some explicit discrete distributions
  0.3. Dimensional Analysis
  0.4. Continuous Probability Distributions
  0.4.1. Probability density functions
  0.4.2. Some explicit continuous distributions
  0.5. More Properties of, and Operations on, Probability Distributions
  0.5.1. Transformation of a probability density function
  0.5.2. sample mean of many independent, identically distributed random variables has lower variance than any one of its constituents
  0.5.3. Count data are typically Poisson distributed
  0.5.4. difference of two noisy quantities can have greater relative standard deviation than either by itself
  0.5.5. convolution of two distributions describes the sum of their random variables
  0.6. Thermal Randomness
  Big Picture
  Key Formulas
  Problems
  ch. 1 What Is Light?
  1.1. Signpost: Photons
  1.2. Light Before 1905
  1.2.1. Basic light phenomena
  1.2.2. Light displays wavelike behavior in many situations
  1.3. Light Is Lumpy
  1.3.1. discrete aspect of light is most apparent at extremely low intensity
  1.3.2. photoelectric effect
  1.3.3. Einstein's proposal
  1.3.4. Light-induced phenomena in biology qualitatively support the Einstein relation
  1.4. Background: Poisson Processes
  1.4.1. Poisson process can be defined as a continuous-time limit of repeated Bernoulli trials
  1.4.2. Blip counts in a fixed interval are Poisson distributed
  1.4.3. Waiting times are Exponentially distributed
  1.5. New Physical Model of Light
  1.5.1. Light Hypothesis, part 1
  1.5.2. spectrum of light can be regarded as a probability density times an overall rate
  1.5.3. Light can eject electrons from individual molecules, inducing photochemical reactions
  1.6. Fluorescence and Photoisomerization Can Occur after Photon Absorption
  1.6.1. Electron State Hypothesis
  1.6.2. Atoms have sharp spectral lines
  1.6.3. Molecules: fluorescence
  1.6.4. Molecules: photoisomerization
  1.7. Transparent Media Are Unchanged by the Passage of Light, but Slow It Down
  Big Picture
  Key Formulas
  1.3.1. Quantum randomness is distinct from classical chaos
  1.3.3.a. reality of photons
  1.3.3.b. Light also carries momentum
  1.3.3.c. thermal radiation spectrum
  1.3.3.d. role of frequency
  1.4. Corrections to Poisson emission and detection
  1.5.1.a. Gamma rays
  1.5.1.b. More about the Light Hypothesis
  1.5.3. Mechanism of DNA photodamage
  1.6.1. Dense media
  1.6.2.a. More about atoms and light
  1.6.2.b. Cauchy distribution in physics
  1.6.3.a. Born-Oppenheimer approximation
  1.6.3.b. Classical approximation for nuclear motion
  1.6.3.c. Debye relaxation
  1.6.4. Fast conformational changes
  Problems
  ch. 2 Photons and Life
  2.1. Signpost: Seeing and Touching
  2.2. Light-Induced DNA Damage
  2.3. Fluorescence as a Window into Cells
  2.3.1. Fluorescence can discriminate healthy from diseased tissue during surgery
  2.3.2. Fluorescence microscopy can reduce background and specifically show only objects of interest
  2.4. Background: Membrane Potential
  2.4.1. Electric currents involve ion motion
  2.4.2. ion imbalance across the cell membrane can create a membrane potential
  2.4.3. Ion pumps maintain a resting electric potential drop across the cell membrane
  2.4.4. Ion channels modulate the membrane potential to implement neural signaling
  2.4.5. Action potentials can transmit information over long distances
  2.4.6. Creation and utilization of action potentials
  2.4.7. More about synaptic transmission
  2.5. Optogenetics
  2.5.1. Brains are hard to study
  2.5.2. Channelrhodopsin can depolarize selected neurons in response to light
  2.5.3. Halorhodopsin can hyperpolarize selected neurons in response to light
  2.5.4. Other methods
  2.6. Fluorescent Reporters Can Give Real-Time Readout of Cellular Conditions
  2.6.1. Voltage-sensitive fluorescent reporters
  2.6.2. Split fluorescent proteins and genetically encoded calcium indicators
  2.7. Two-Photon Excitation Permits Imaging Deep within Living Tissue
  2.7.1. problem of imaging thick samples
  2.7.2. Two-photon excitation depends sensitively on light intensity
  2.7.3. Multiphoton microscopy can excite a specific volume element of a specimen
  2.8. Fluorescence Resonance Energy Transfer
  2.8.1. How to tell when two molecules are close to each other
  2.8.2. physical model for FRET
  2.8.3. Some forms of bioluminescence also involve FRET
  2.8.4. FRET can be used to create a spectroscopic "ruler"
  2.8.5. Application of FRET to DNA bending flexibility
  2.8.6. FRET-based indicators
  2.9. Glimpse of Photosynthesis
  2.9.1. It's big
  2.9.2. Two quantitative puzzles advanced our understanding of photosynthesis
  2.9.3. Resonance energy transfer resolves both puzzles
  Big Picture
  Key Formulas
  2.4.3. More about membrane potentials
  2.4.5. Other uses for the resting potential
  2.7.2. beta-squared rule
  2.7.3. More about two-photon imaging
  2.8.1. About FRET and its efficiency
  2.8.4. Other experimental tests of FRET
  2.8.5. Why reported FRET efficiencies sometimes exceed 100%
  2.9.3. More details about the photosynthesis apparatus in plants
  Problems
  ch. 3 Color Vision
  3.1. Signpost: A Fifth Dimension
  3.2. Color Vision Confers a Fitness Payoff
  Contents note continued: 3.3. Newton's Experiments on Color
  3.4. Background: More Properties of Poisson Processes
  3.4.1. Thinning property
  3.4.2. Merging property
  3.4.3. Significance for light
  3.5. Combining Two Beams Corresponds to Summing Their Spectra
  3.6. Psychophysical Aspects of Color
  3.6.1. R+G looks like Y
  3.6.2. Color discrimination is many-to-one
  3.6.3. Perceptual matching follows quantitative, reproducible, and context-independent rules
  3.7. Color from selective absorption
  3.7.1. Reflectance and transmittance spectra
  3.7.2. Subtractive color scheme
  3.8. Physical Model of Color Vision
  3.8.1. color-matching function challenge
  3.8.2. Available wetware in the eye
  3.8.3. trichromatic model
  3.8.4. trichromatic model explains why R+a~,Y
  3.8.5. Our eyes project light spectra to a 3D vector space
  3.8.6. mechanical analogy for color matching
  3.8.7. Connection between the mechanical analogy and color vision
  3.8.8. Quantitative comparison to experimentally observed color-matching functions
  3.9. Why the Sky Is Not Violet
  3.10. Direct Imaging of the Cone Mosaic
  Big Picture
  Key Formulas
  3.5.a. Flux, irradiance, and spectral flux irradiance
  3.5.b. Combining spectra is a linear operation
  3.6.3.a. Variation of color matching
  3.6.3.b. Colorblindness
  3.6.3.c. Tetrachromacy
  3.7. Perceptual color
  3.8.3.a. Determination of sensitivity functions
  3.8.3.b. Contrast to audition
  3.8.4.a. Enhancement of color contrast in autofluorescence endoscopy
  3.8.4.b. Spectral analysis can discriminate many fluorophores and their combinations
  3.8.5.a. Photoisomerization rate regarded as an inner product
  3.8.5.b. Correction to predicted color matching due to absorption
  3.8.8.a. Relative versus absolute sensitivity
  3.8.8.b. Simplified color space
  Problems
  ch. 4 How Photons Know Where to Go
  4.1. Signpost: Probability Amplitudes
  4.2. Summary of Key Phenomena
  4.3. Probability Amplitude
  4.3.1. Reconciling the particle and wave aspects of light requires the introduction of a new kind of physical quantity
  4.4. Background: Complex Numbers Simplify Many Calculations
  4.5. Light Hypothesis, part 2
  4.6. Basic Interference Phenomena
  4.6.1. Two-slit interference explained via the Light Hypothesis
  4.6.2. Newton's rings illustrate interference in a three-dimensional setting
  4.6.3. objection to the Light Hypothesis
  4.7. Stationary-Phase Principle
  4.7.1. Fresnel integral illustrates the stationary-phase principle
  4.7.2. probability amplitude is computed as a sum over all possible photon paths
  4.7.3. Diffraction through a single, wide aperture
  4.7.4. Reconciliation of particle and wave aspects
  Big Picture
  Key Formulas
  4.2. On philosophically repugnant theories
  4.5.a. More about the Light Hypothesis
  4.5.b. More about uniform media
  4.6.1. Which slit?
  4.6.2. More about reflection
  4.6.3. More objections
  4.7.2.a. neighborhood of the stationary-phase path
  4.7.2.b. Nonuniform media
  Problems
  ch. 5 Optical Phenomena and Life
  5.1. Signpost: Sorting and Directing
  5.2. Structural Color in Insects, Birds, and Marine Organisms
  5.2.1. Some animals create color by using nanostructures made from transparent materials
  5.2.2. extension of the Light Hypothesis describes reflection and transmission at an interface
  5.2.3. single thin, transparent layer reflects with weak wavelength dependence
  5.2.4. stack of many thin, transparent layers can generate an optical bandgap
  5.2.5. Structural color in marine organisms
  5.3. Ray-optics Phenomena
  5.3.1. reflection law is a consequence of the stationary-phase principle
  5.3.2. Transmission and reflection gratings generate non-ray-optics behavior by editing the set of allowed photon paths
  5.3.3. Refraction arises from the stationary-phase principle applied to a piecewise-uniform medium
  5.3.4. Total internal reflection provides another tool to enhance signal relative to noise in fluorescence microscopy
  5.3.5. Refraction is generally wavelength dependent
  Big Picture
  Key Formulas
  5.2.2. Transmission and reflection in classical electromagnetism
  5.3.1. Fine points about reflection and refraction
  5.2.4. More complicated layers
  Problems
  ch. 6 Direct Image Formation
  6.1. Signpost: Bright Yet Sharp
  6.2. Image Formation Without Lenses
  6.2.1. Shadow imaging
  6.2.2. Pinhole imaging suffices for some animals
  6.3. Addition of a Lens Allows Formation of Bright, Yet Sharp, Images
  6.3.1. focusing criterion relates object and image distances to lens shape
  6.3.2. more general approach
  6.3.3. Formation of a complete image
  6.3.4. Aberration degrades image formation outside the paraxial limit
  6.4. Vertebrate Eye
  6.4.1. Image formation with an air-water interface
  6.4.2. Focusing powers add in a compound lens system
  6.4.3. deformable lens implements focal accommodation
  6.5. Light Microscopes and Related Instruments
  6.5.1. "Rays of light" are a useful idealization in the ray-optics regime
  6.5.2. Real and virtual images
  6.5.3. Spherical aberration
  6.5.4. Dispersion gives rise to chromatic aberration
  6.5.5. Confocal microscopy suppresses out-of-focus background light
  6.6. Darwin's Difficulty
  6.7. Background: Angles and Angular Area
  6.7.1. Angles
  6.7.2. Angular area
  6.8. Diffraction Limit
  6.8.1. Even a perfect lens will not focus light perfectly
  6.8.2. Three dimensions: The Rayleigh criterion
  6.8.3. Animal eyes match their photoreceptor size to the diffraction limit
  Big Picture
  Key Formulas
  6.4. retinal pigment epithelium
  6.8.2. Abbe criterion
  Problems
  ch. 7 Imaging as Inference
  7.1. Signpost: Information
  7.2. Background: On Inference
  7.2.1. Bayes formula tells how to update a probability estimate
  7.2.2. Inference with a Uniform prior reduces to likelihood maximization
  7.2.3. Inferring the center of a distribution
  7.2.4. Parameter estimation and credible intervals
  7.2.5. Binning data reduces its information content
  7.3. Localization of a Single Fluorophore
  7.3.1. Localization is an inference problem
  7.3.2. Formulation of a probabilistic model
  7.3.3. Maximum-likelihood analysis of image data
  7.3.4. Results for molecular motor stepping
  7.4. Localization Microscopy
  7.5. Defocused Orientation Imaging
  Big Picture
  Key Formulas
  7.3.2.a. Airy point spread function
  7.3.2.b. Anisotropic point spread function
  7.3.2.c. Other tacit assumptions
  7.3.3. Advantages of the maximum likelihood method
  7.3.4. Background estimation
  7.4. Interferometric PALM imaging
  7.5. More about anisotropy
  Problems
  ch. 8 Imaging by X-Ray Diffraction
  8.1. Signpost: Inversion
  8.2. It's Hard to See Atoms
  8.3. Diffraction Patterns
  8.3.1. periodic array of narrow slits creates a diffraction pattern of sharp lines
  8.3.2. Generalizations to the setup needed to handle x-ray crystallography
  8.3.3. array of slits with substructure gives a diffraction pattern modulated by a form factor
  8.3.4. 2D "crystal" yields a 2D diffraction pattern
  8.3.5. 3D crystals can be analyzed by similar methods
  8.4. Diffraction Pattern of DNA Encodes Its Double-Helical Character
  8.4.1. helical pitch, base pair rise, helix offset, and diameter of DNA can be obtained from its diffraction pattern
  8.4.2. Accurate determination of size parameters led to a breakthrough on the puzzle of DNA structure and function
  Big Picture
  Key Formulas
  8.3.3. Factorization of amplitudes
  8.4.1.a. How to treat fiber samples of DNA
  8.4.1.b. phase problem
  Problems
  ch. 9 Vision in Dim Light
  9.1. Signpost: Construction
  9.2. Edge of Vision
  9.2.1. Many ecological niches are dimly lit
  9.2.2. single-photon challenge
  9.2.3. Measures of detector performance
  9.3. Psychophysical Measurements of Human Vision
  9.3.1. probabilistic character of vision is most evident under dim-light conditions
  9.3.2. Rod cells must be able to respond to individual photon absorptions
  9.3.3. eigengrau hypothesis states that true photon signals are merged with a background of spontaneous events
  9.3.4. Forced-choice experiments characterize the dim-light response
  9.3.5. Questions raised by psychophysical experiments
  9.4. Single-Cell Measurements
  9.4.1. Vertebrate photoreceptors can be monitored via the suction pipette method
  9.4.2. Determination of threshold, quantum catch, and spontaneous signaling rate
  9.4.3. Direct confirmation that the rod cell imposes no threshold
  9.4.4. Additional single-cell results
  9.4.5. Questions raised by the single-cell measurements
  Big Picture
  Key Formulas
  9.4.2.a. fraction of light absorbed by a sample depends exponentially on thickness
  9.4.2.b. quantum yield for rod signaling
  9.4.2.c. Quantum catch for a single human rod cell under axial illumination
  9.4.2.d. whole-retina quantum catch is the product of several factors
  Problems
  ch. 10 Mechanism of Visual Transduction
  10.1. Signpost: Dynamic Range
  10.2. Photoreceptors
  10.2.1. Photoreceptors are a specialized class of neurons
  10.2.2. Each rod cell simultaneously monitors one hundred million rhodopsin molecules
  10.3. Background: Cellular Control and Transduction Networks
  Contents note continued: 10.3.1. Cells can control enzyme activities via allosteric modulation
  10.3.2. Single-cell organisms can alter their behavior in response to environmental cues, including light
  10.3.3. two-component signaling pathway motif
  10.3.4. Network diagrams summarize complex reaction networks
  10.3.5. Cooperativity can increase the sensitivity of a network element
  10.4. Photon Response Events Localized to One Disk
  10.4.1. Step 1: photoisomerization of rhodopsin in the disk membrane
  10.4.2. Step 2: activation of transducin in the disk membrane
  10.4.3. Steps 3-4: activation of phosphodiesterase in the disk membrane, and hydrolysis of cyclic GMP in the cytosol
  10.5. Events Elsewhere in the Rod Outer Segment
  10.5.1. Ion pumps in the rod cell plasma membrane maintain nonequilibrium ion concentrations
  10.5.2. Step 5: ion channel closing in the plasma membrane
  10.6. Events at the Synaptic Terminal
  10.6.1. Step 6: hyperpolarization of the plasma membrane
  10.6.2. Step 7: modulation of neurotransmitter release into the synaptic cleft
  10.7. Summary of the Visual Cascade
  Big Picture
  Key Formulas
  10.2.2. Higher light intensities
  10.3.3.a. More about two-component signaling pathways
  10.3.3.b. Phototaxis
  10.3.4. More about adaptation in chemotaxis
  10.4.1. Cone and cone bipolar cells
  10.4.3. Recently discovered vertebrate photoreceptors
  10.6. Glutamate removal
  10.7.a. Termination of the photoreceptor response
  10.7.b. Negative feedback implements adaptation and standardizes signals from rod cells
  10.7.c. Recycling of retinal
  Problems
  ch. 11 First Synapse and Beyond
  11.1. Signpost: False Positives
  11.2. Transmission at the First Synapse
  11.2.1. synapse from rod to rod bipolar cells inverts its signal via another G protein cascade
  11.2.2. first synapse also rejects rod signals below a transmission breakpoint
  11.3. Synthesis of Psychophysics and Single-Cell Physiology
  11.3.1. Why does vision require several captured photons?
  11.3.2. Review of the eigengrau hypothesis
  11.3.3. Single-rod measurements constrain the fit parameters in the eigengrau model
  11.3.4. Processing beyond the first synapse is highly efficient
  11.4. Multistep Relay Sends Signals on to the Brain
  11.4.1. classical rod pathway implements the single-photon response
  11.4.2. Other signaling pathways
  11.4.3. Optogenetic retinal prostheses
  11.5. Evolution and Vision
  11.5.1. Darwin's difficulty, revisited
  11.5.2. Parallels between vision, olfaction, and hormone reception
  Big Picture
  Key Formulas
  11.2.2.a. Instrumental noise
  11.2.2.b. Quantal release noise
  11.2.2.c. Mechanism of discrimination at the first synapse
  11.2.2.d. Why discrimination at the first synapse is advantageous
  11.2.2.e. Thresholding at later stages of processing
  11.3.4. Psychophysics with single photon stimuli
  11.4.1.a. ON and OFF pathways
  11.4.1.b. Image processing in the retina
  11.5.1. Rhabdomeric photoreceptors
  Problems
  ch. 12 Electrons, Photons, and the Feynman Principle
  12.1. Signpost: Universality
  12.2. Electrons
  12.2.1. From paths to trajectories
  12.2.2. action functional singles out classical trajectories as its stationary points
  12.2.3. Feynman principle expresses probability amplitudes as sums over trajectories
  12.2.4. States and operators arise from partial summation over trajectories
  12.2.5. Stationary states are invariant under time evolution
  12.2.6. confined-electron problem
  12.2.7. Light absorption by ring-shaped molecules
  12.2.8. Schrodinger equation emerges in the limit of an infinitesimal time step
  12.3. Photons
  12.3.1. action functional for photon trajectories
  12.3.2. special case of a monochromatic light source reduces to our earlier formulation
  12.3.3. Vista: reflection, transmission, and the index of refraction
  Big Picture
  ch. 13 Field Quantization, Polarization, and the Orientation of a Single Molecule
  13.1. Signpost: Fields
  13.2. Single Molecule Emits Photons in a Dipole Distribution
  13.3. Classical Field Theory of Light
  13.4. Quantization Replaces Field Variables by Operators
  13.5. Photon States
  13.5.1. Basis states can be formed by applying creation operators to the vacuum state
  13.5.2. Coherent states mimic classical states in the limit of large occupation numbers
  13.6. Interaction with Electrons
  13.6.1. Classical interactions involve adding source terms to the field equations
  13.6.2. Electromagnetic interactions can be treated perturbatively
  13.6.3. dipole emission pattern
  13.6.4. Electrons and positrons can also be created and destroyed
  13.7. Vistas
  13.7.1. Connection to the approach used in earlier chapters
  13.7.2. Some invertebrates can detect the polarization of light
  13.7.3. Invertebrate photoreceptors have a different morphology from vertebrates
  13.7.4. Polarized light must be used for single photoreceptor measurements
  13.7.5. Some transitions are far more probable than others
  13.7.6. Lasers exploit a preference for emission into an already occupied state
  13.7.7. Fluorescence polarization anisotropy
  Big Picture
  ch. 14 Quantum-Mechanical Theory of FRET
  14.1. Signpost: Decoherence
  14.2. Two-state Systems
  14.2.1. FRET displays both classical and quantum aspects
  14.2.2. isolated two-state system oscillates in time
  14.2.3. Environmental effects modify the behavior of a two-state system in solution
  14.2.4. density operator summarizes the effect of the environment
  14.2.5. Time development of the density operator
  14.3. FRET
  14.3.1. weakly coupled, strongly incoherent limit displays first-order kinetics
  14.3.2. Forster's formula arises in the electric dipole approximation
  14.3.3. More realistic treatment of the role of FRET in photosynthesis
  Big Picture
  A.1. Mathematical Notation
  A.2. Network Diagrams
  A.3. Named Quantities
  B.1. Base Units
  B.2. Dimensions Versus Units
  B.3. About Graphs
  B.3.1. Arbitrary units
  B.3.2. Angles
  B.4. Payoff
  C.1. Fundamental Constants
  C.2. Optics
  C.2.1. Index of refraction for visible light
  C.2.2. Miscellaneous
  C.3. Eyes
  C.3.1. Geometric
  C.3.2. Rod cells
  C.3.3. Cone cells
  C.3.4. Beyond photoreceptors
  C.4. B-Form DNA.