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Contents

Structure-function[edit]

Resolution (electron density): measure of the resolvability in the electron density map of a molecule. X-ray vs (cryo-)EM definition. X-ray crystallography: >4.0 Å - Individual coordinates meaningless.
Fourier shell correlation (FSC [Harauz & van Heel (1986)]; AKA: spatial frequency correlation function [Saxton & Baumeister (1982)]): measures the normalised cross-correlation coefficient between two 3D volumes over corresponding shells in Fourier space (i.e., as a function of spatial frequency); extension of the two-dimensional Fourier ring correlation (FRC) [van Heel (1982)].

Topology and structure[edit]

Linking number: e.g. DNA linking number in plasmids
Kissing number: e.g. materials science, chem, phys - dense packing of atoms: only two possibilities in 3D: FCC (face-centered cubic) and HCP (hexagonal close-packed) [or a hybrid of both]
Euler characteristic: topology, highly symmetrical (yet simple) viral coats

math, groups:

Coxeter group: abstract group that admits a formal description in terms of mirror symmetries.

math, graphs:

Coxeter–Dynkin diagram (Coxeter diagram, Coxeter graph): graph with numerically labeled edges (called branches) representing the spatial relations between a collection of mirrors (or reflecting hyperplanes). Dynkin diagrams: closely related objects, which differ from Coxeter diagrams in two respects: firstly, branches labeled "4" or greater are directed, while Coxeter diagrams are undirected; secondly, Dynkin diagrams must satisfy an additional (crystallographic) restriction, namely that the only allowed branch labels are 2, 3, 4, and 6.

Symmetry in (bio)molecules[edit]

Mathematical 2D and 3D group/symmetry notations[edit]
Symmetry group:
List of planar symmetry groups: what's the diff. with spherical symmetry groups? Plane vs sphere? Classes of discrete planar symmetry groups: 2 rosette groups (2D point groups) + 7 frieze groups (2D line groups) + 17 wallpaper groups (2D space groups)
List of spherical symmetry groups, spherical symmetry groups and point groups have the same notation. Are they qualitatively different? Or it's just the different way of putting graph theory (like binary vs. decimal, but still numbers)
Point group: group of geometric symmetries (isometries) that keep at least one point fixed; 1D, 2D, 3D, ..., 8D:
Point groups in two dimensions; point groups in 2D under crystallographic restriction theorem ⇒ wallpaper group (plane symmetry group or plane crystallographic group) [17]; frieze group
Point groups in three dimensions: 7 infinite families of axial (or prismatic groups), and 7 additional polyhedral (or Platonic groups) (Polyhedral group). Applying the crystallographic restriction theorem to these groups yields: 32 crystallographic point groups ((geometric) crystal classes)
Crystallographic point group (crystal class): tables: in Schoenflies [5*7=35, but 4 are forbidden and other 4 are the same as some others, so 35-4-4=27; add T, Td, Th, O and Oh [5]: 27+5=32], and in Hermann–Mauguin notations [32, table with empty (forbidden) spaces], and correspondence between different notations (crystal family & system, Hermann-Mauguin full & short symbols, Shubnikov, Schoenflies, orbifold, Coxeter, order) [32]
Notations for symmetry groups and point groups:
Coxeter notation (bracket notation): system of classifying symmetry groups, describing the angles between with fundamental reflections of a Coxeter group; uses a bracketed notation, with modifiers to indicate certain subgroups
Schoenflies notation (Schönflies notation): one of two conventions commonly used to describe Point groups; notation is used in spectroscopy (for molecular symmetry). Point group in the Schoenflies convention is completely adequate to describe the symmetry of a molecule; this is sufficient for spectroscopy. The Hermann–Maunguin notation is able to describe the space group of a crystal lattice, while the Schoenflies notation isn't. Thus the Hermann–Mauguin notation is used in crystallography.
Hermann–Mauguin notation (International notation (International Tables For Crystallography)): the other convention to commonly used to describe Point groups; used in crystallography (crystal symmetries in X-ray, neutron, electron, ...). Mirror plane (rotoinversion axis 2) is m, while the other rotoinversion axes are represented by the corresponding number with a macron, n1, 3, 4, 5, 6, 7, 8...
Orbifold notation (orbifold signature): system, invented by William Thurston (William Paul Thurston, of orbifold fame) and popularized by the mathematician John Conway, for representing types of symmetry groups in two-dimensional spaces of constant curvature. The advantage of the notation is that it describes these groups in a way which indicates many of the groups' properties: in particular, it describes the orbifold obtained by taking the quotient of Euclidean space by the group under consideration.
Fibrifold & fibrifold notation (in 3D): extension of orbifold notation for 3D space groups.
Schläfli symbol: notation of the form {p,q,r,...} that defines regular polytopes and tessellations (List of regular polytopes).
Wythoff symbol: first used by Coxeter, Longeut-Higgens and Miller in their enumeration of the uniform polyhedra.

Symmetries in 2D: tiling; crystallographic projections, molecule projections

Question: how is the symmetry number calculated?

Phys(chem(bio)): single molecules/particles, crystals & co[edit]
Crystal system: "In crystallography, the terms crystal system, crystal family, and lattice system each refer to one of several classes of space groups, lattices, point groups, or crystals. Crystal systems, crystal families, and lattice systems are similar but slightly different, and there is widespread confusion between them: in particular the trigonal crystal system is often confused with the rhombohedral lattice system, and the term "crystal system" is sometimes used to mean "lattice system" or "crystal family". Space groups and crystals are divided into 7 crystal systems according to their point groups, and into 7 lattice systems according to their Bravais lattices. Five of the crystal systems are essentially the same as five of the lattice systems, but the hexagonal and trigonal crystal systems differ from the hexagonal and rhombohedral lattice systems. The six crystal families are formed by combining the hexagonal and trigonal crystal systems into one hexagonal family, in order to eliminate this confusion." >>>See the table where "crystal system" from the left and "lattice system" from the right go into "point groups" on the left and into "bravais lattices" on the right and they meet as "space groups": see how "space groups" are split into 3 groups by this meeting from the left (trigonal/hexagonal crystal systems) and the right (rhombohedral/hexagonal lattice systems).
Crystal systems: table of 32 point groups
Lattice systems: table of 7 lattice systems subdivided into 14 Bravais lattices.
Template:Crystal systems: Crystallographic symmetries forbid quite some of the molecular symmetries and only 230 remain (in 3D) (i.e., although molecules have many possible symmetries, they can crystallize only in very few symmetries; everything else is not crystals):
Space group (in crystallography: crystallographic or Fedorov groups; in dimensions other than 3: Bieberbach groups):
Notation for space groups: number (in IUCr tables), International symbol or Hermann–Mauguin notation, Hall notation, Schoenflies notation, Shubnikov symbol, 2D:Orbifold notation and 3D:Fibrifold notation, Coxeter notation
Classification systems for space groups: see the table explaining how space groups are classified into classes (reminds of biological classification into species (correspond to crystallographic space groups), genuses, classes, families...) in 3D: (Crystallographic) space group types [230] ⇒ Affine space group types [219] ⇒ Arithmetic crystal classes [73] ⇒ ((geometric) Crystal classes [32] ⇒ Crystal systems [7] OR Bravais flocks [14] ⇒ Lattice systems [7]) ⇒ Crystal families [6]. Other classifications: Conway, Delgado Friedrichs, and Huson et al. (2001)::
Space groups in other dimensions: table of dimension, # lattice types (OEIS: A004030), # crystallographic point groups (OEIS: A004028), # crystallographic space group types (OEIS: A006227), # affine space group types (OEIS: A004029)
Table of space groups in 3 dimensions: table of: groupings international notation numbers, crystal systems [7], point groups (in international and Schoenflies notations) [32], crystallographic space groups (international short symbol) [230]. Also explanation how to obtain lattice systems from crystal systems (some of space group of the trigonal crystal systems have names beginning with "R" and are rhombohedral lattice systems; the other trigonal crystal systems belong to the hexagonal lattice system); Bravais lattices.
Molecular_symmetry, all symmetry elements applying to the molecules (only a subset of all 3D symmetries), infinite possibilities, limited only by (covalent) bond (number? and) strength, or there is no limitation of number of atoms bonded, as it could branch out more and more from the symmetry core to change the symmetry? Chiral: C_n, D_n, T, O, I.

Materials science, nanotechnology (bionanotech)[edit]

Category:Materials science
Category:Condensed matter physics
Category:Metallurgy
Category:Microtechnology: 10−4 to 10−7 m
Category:Nanotechnology
Category:Supramolecular chemistry
Category:Molecular machines
Category:Polymer chemistry
Category:Superconductivity {q.v. EECS::Superconductivity}
Category:Nanotechnology templates
Portal:Nanotechnology
Materials science: Materials in industry (Ceramics and glasses, Composite materials, Polymers, Metal alloys
Template:Nanotechnology (Template:Nanotech footer is the same) R
List of nanotechnology organizations: MRS (Materials Research Society)
Mechanosynthesis: chemical synthesis in which reaction outcomes are determined by the use of mechanical constraints to direct reactive molecules to specific molecular sites. In biology, the ribosome provides an example of a programmable mechanosynthetic device; diamond mechanosynthesis
Template:Molecular nanotechnology & Molecular nanotechnology (MNT): build structures to complex, atomic specifications by means of mechanosynthesis (reaction outcomes are determined by the use of mechanical constraints to direct reactive molecules to specific molecular sites). Combines physics, chemistry, life molecular machinery, and systems engineering of macroscale factories. Hard vs soft nanotech: hard would use vacuum and ~0 K to engineer stuff while the soft nanotech talks about wetness, stickness, brownian motion, high viscosity - biomimetic nanontech.
Molecular assembler: defined by K. Eric Drexler, is a "proposed device able to guide chemical reactions by positioning reactive molecules with atomic precision" (e.g. ribosome is a real molecular assembler in the liquids of the cell where the instruction is mRNA and the output in protein, while aa-tRNAs are used up). Nanofactories, self-replication. One molecular assembler, like a single ribosome, are slow, but when you have many of them, then you can produce in quantity (that's why cell produces ~2× ribosomes compared to the just-after-the-division point and only then divides into 2 daughter cells).
Drexler–Smalley debate on molecular nanotechnology: from wet/soft MNT (to bootstrap) to hard MNT? Quantum mechanics?
Molecular engineering: companies:
ZyvexZyvex Technologies (Zyvex Marine): works with carbon nanotubes embedded into resins to make several times lighter than alloys but as strong as alloys materials.
Template:Nanotechnology implications
Template:Nanomaterials
Template:Nanoelectronics
Dynamic random access memory
DNA origami: 2D/3D structures from DNA, the more complex the structure - the longer it takes to fold.

Research & design, companies[edit]

Infineon Technologies
National Physical Laboratory (United Kingdom)

Optics, Quantum Wave optics (diffraction) vs. particle scattering[edit]

Fraunhofer distance
Dynamical theory of diffraction: lots of red links and lots of citation from X-ray field
Eikonal equation: provides a link between physical (wave) optics and geometric (ray) optics
Optical aberration: R

Microscopes[edit]

Microscope: instrument used to see objects that are too small for the naked eye. Light, electron microscopes; scanning probe microscopes.

Photon, electron, atoms/ions: gallium, helium; mixed:

Scanning helium microscope
Transmission electron microscopy
High-resolution transmission electron microscopy (HRTEM)
Transmission Electron Aberration-Corrected Microscope (TEAM): a project between FEI and CEOS with the support of United States Department of Energy (DOE) and 4 US laboratories.
Transmission Electron Aberration-corrected Microscope
Scanning transmission electron microscopy
Energy filtered transmission electron microscopy (EFTEM)
Cryo-electron microscopy: cryoEM
Single particle analysis and Single Particle Reconstruction
Electron crystallography
Low Voltage Electron Microscopy
Scanning electron microscope
Electron diffraction
Electron beam induced deposition
X-ray microscope: see also Synchrotron X-ray tomographic microscopy (CT)
Staining: auxiliary technique used in microscopy to enhance contrast in the microscopic image. Stains and dyes are frequently used in biology and medicine to highlight structures in biological tissues for viewing, often with the aid of different microscopes. In vivo vs In vitro staining. Common biological stains: Acridine orange, Bismarck brown, Carmine, Coomassie blue, Cresyl violet, Crystal violet, DAPI, Eosin, Ethidium bromide, Acid fuchsine, Haematoxylin, Hoechst stains, Iodine, Malachite green, Methyl green, Methylene blue, Neutral red, Nile blue, Nile red, Rhodamine, Safranin.
Negative stain: contrasting a thin specimen with an optically opaque fluid; background is stained, leaving the actual specimen untouched, and thus visible. TEM: opaqueness to electrons is related to the atomic number; stains: ammonium molybdate, uranyl acetate, uranyl formate, phosphotungstic acid, osmium tetroxide, osmium ferricyanide and auroglucothionate.
Hardware[edit]
Camera (the "eye:retina"): Active pixel sensor vs. Charge-coupled device

Transfer functions and other blurs; their modeling[edit]

X-ray crystallography[edit]

X-ray crystallography
Crystal structure: Unit cell (Within the unit cell is the asymmetric unit, smallest unit the crystal can be divided into using the crystallographic symmetry operations of the space group. The asymmetric unit is also what is generally solved when solving a structure of a molecule or protein by X-ray crystallography.)
[1]: smallest unit of volume that contains all of the structural and symmetry information and that by translation can reproduce a pattern in all of space.
[2], [3]: smallest unit of volume that contains all of the structural information and that by application of the symmetry operations can reproduce the unit cell.
Biological unit (also, @Proteopedia: biological assembly, @PDB wiki: functional unit): smallest number of protein molecules which form a biologically active (e.g. catalytically active) unit (or biologically relevant as found in the cells). Functional form of the protein.
Structure solution methods:
Maximum entropy method
Crystallographic restriction theorem: rotational symmetries of a (3D) crystal are limited to 2-fold, 3-fold, 4-fold, and 6-fold (crystallography forbids 5 fold, 7 fold, and higher rotational symmetries).
But a phase in between the glass and crystal does exist:
Quasicrystal
Aperiodic tiling
Modified Bragg diffraction in quasicrystals

NMR spectroscopy[edit]

Nuclear magnetic resonance spectroscopy (NMR spectroscopy)
Nuclear magnetic resonance spectroscopy of proteins (Protein NMR)
Heteronuclear single quantum coherence

Electron paramagnetic resonance[edit]

Electron paramagnetic resonance (EPR; electron spin resonance (ESR))

Tomography[edit]

Different tomographies:

Electron tomography & Cryo-electron tomography (de:Kryoelektronentomographie)
Ultramicrotomy & Microtome:
Diamond knife: conventional hardest material used in microtomes
Nanoknife: a new development; carbon nanotube (like a wire) is used to cut materials
Photoacoustic tomography (PAT, or photoacoustic computed tomography (PACT)): reconstruction of an internal photoacoustic source distribution from measurements acquired by scanning ultrasound detectors over a surface that encloses the source under study. The PA source is the thermal expansion that results from a small temperature rise, which is caused by the absorption of externally applied radiation of pulsed electromagnetic (EM) waves.
Photoacoustic imaging in biomedicine, Photoacoustic spectroscopy
CT
(f)MRI
Ultrasound
many others

Signal processing[edit]

Typical signal processing examples: (adaptive) filtering, smoothing, spectrum analysis, digitization (from analog data), modulation, feature extraction, pattern recognition

Wavelet
Wavelet transform: used in JP(E)G; can be used in wavelet thresholding to remove random noise
Multiresolution analysis

Image processing[edit]

Category:Image processing
Category:Data clustering algorithms
Cluster analysis
Clustering high-dimensional data R?
Correlation clustering R?
k-means clustering
Principal component analysis R
Hierarchical clustering: agglomerative, divisive.
Fuzzy clustering r
Expectation-maximization algorithm r; maximum likelihood
Radon transform R; back projection lines, (common line theorem?)
Tomographic reconstruction
Algebraic reconstruction technique
Projection-slice theorem, aka Fourier slice theorem (aka projection theorem):
F_mP_m=S_mF_N.\,
  • Fm and FN: m- and N-dimensional Fourier transform operators
  • Pm: m-dimensional projection operator (which projects an N-D function onto a m-D line)
  • Sm: m-dimensional slice of the N-dimensional Fourier transform of a function (consisting of an m-dimensional linear submanifold through the origin in the Fourier space which is parallel to the projection submanifold, produced by Pm)
Sinogram: the mathematical term for Radon transform
X-ray transform: closely related to the Radon transform, and coincides with it in two dimensions. In higher dimensions, the X-ray transform of a function is defined by integrating over lines rather than over hyperplanes as in the Radon transform.
Structural similarity
Template:Noise (Noise (in physics and telecommunications)): Peak signal-to-noise ratio, Signal-to-noise ratio, Image noise

Modeling[edit]

Homology modeling (comparative modeling): constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template").

Physics, Chemistry[edit]

Category:Applied and interdisciplinary physics
Category:Biophysics
Category:Materials science
Category:Physical chemistry
Lennard-Jones potential is an approximation:
V(r) = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^{6} \right],
Van der Waals force (London dispersion force is part of Van der Waals): r−6
Exchange interaction, aka Pauli exclusion: r−12
Spherical harmonics (Y_\ell^m): the angular portion of a set of solutions to Laplace's equation.
Parts-per notation: ppm (parts-per-million, 10–6), ppb (parts-per-billion, 10–9), ppt (parts-per-trillion, 10–12) and ppq (parts-per-quadrillion, 10-15). ppX arises from mol/mol, kg/kg, L/L etc. dimensionless quantities.
Interface and colloid science: intersection of branches of chemistry, physics, nanoscience and other fields dealing with colloids, heterogeneous systems consisting of a mechanical mixture of particles between 1 nm and 1000 nm dispersed in a continuous medium.
Double layer (interfacial) (DL; electrical double layer, EDL): structure that appears on the surface of an object when it is exposed to a fluid
Point of zero charge (pzc): physical chemistry: is a concept relating to the phenomenon of adsorption, and it describes the condition when the electrical charge density on a surface is zero; electrochemistry: electrode potential at the point of zero charge.
Zeta potential: electrokinetic potential in colloidal systems. In the colloidal chemistry literature, it is usually denoted using the Greek letter zeta (ζ), hence ζ-potential; electric potential in the interfacial double layer at the location of the slipping plane versus a point in the bulk fluid away from the interface
Debye length (Debye radius): measure of a charge carrier's net electrostatic effect in solution, and how far those electrostatic effects persist; Debye sphere is a volume whose radius is the Debye length, in which there is a sphere of influence, and outside of which charges are electrically screened
Particle aggregation: formation of clusters in a colloidal suspension and represents the most frequent mechanism leading to destabilization of colloidal systems

Instrumental analysis[edit]

Category:Instrumental analysis
Category:Mass spectrometry
Mass spectrometry: analytical technique that produces spectra of the masses of the atoms or molecules comprising a sample of material; used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical structures of molecules, such as peptides and other chemical compounds. Mass spectrometry works by ionizing chemical compounds to generate charged molecules or molecule fragments and measuring their mass-to-charge ratios. The use of the term mass spectroscopy is now discouraged due to the possibility of confusion with light spectroscopy.

Chemistry[edit]

Category:Chemistry

Nomenclature[edit]

International Union of Pure and Applied Chemistry (IUPAC; HQ=Zürich): international federation of National Adhering Organizations that represents chemists in individual countries; member of ICSU.
National Adhering Organizations: organizations that work as the authoritative power over chemistry in an individual country. Currently: 57 [2013].

Theoretical chemistry[edit]

Category:Chemistry
Category:Theoretical chemistry
Category:Quantum chemistry
Category:Medicinal chemistry
Category:Stereochemistry
Category:Molecules
Isostere. Classical isosteres: molecules or ions with the same number of atoms or the same number of valence electrons or both; later revised to include compounds with similarly reactive electron shells (e.g. H+ and F-; H+ and Na+; CO2 and N2O; Si and C). Non-Classical isosteres: do not obey the above classifications, but they still produce similar biological effects in vivo; may be made up of similar atoms, but their structures do not follow an easily-definable set of rules (e.g. methyl, amide, hydroxyl groups)
Bioisostere: substituents or groups with similar physical or chemical properties which produce broadly similar biological properties to a chemical compound; in drug design and pharmaceutical sciences, the purpose of exchanging one bioisostere for another is to enhance the desired biological or physical properties of a compound without making significant changes in chemical structure; used to reduce toxicity or modify the activity of the lead compound, and may alter the metabolism of the lead.
Isoelectronicity: several molecular entities (atoms, molecules, ions) are described as being isoelectronic with each other if they have the same number of electrons or a similar electron configuration and the same structure (number and connectivity of atoms), regardless of the nature of the elements involved. Valence isoelectronic: molecular entities have the same number of valence electrons or a similar electron configuration, but may have a different number of atoms or a different bonding. Amino acids selenocysteine, cysteine and serine are also considered (at least valence) isoelectronic.
Category:Molecular geometry
Isostructural chemical compounds have similar chemical structures; isomorphous when used in relation to crystal structures is essentially synonymous. E.g. benzene ~ borazine ("inorganic benzene"; BH and NH alternate in (BH)3(NH)3); indium(I) bromide ~ β-thallium(I) iodide: both have distorted rock salt structure; I-gold(I) bromide ~ gold(I) chloride.
Quantum chemistry[edit]
Category:Quantum chemistry
Molecular orbital theory (MO theory): method for determining molecular structure in which electrons are not assigned to individual bonds between atoms, but are treated as moving under the influence of the nuclei in the whole molecule
HOMO/LUMO: HOMO: highest occupied molecular orbital, LUMO: lowest unoccupied molecular orbital
Frontier molecular orbital theory: application of MO theory describing HOMO / LUMO interactions.

Periodic table[edit]

Template:Periodic table (metalloid) & Metalloid: chemical element with properties that are in between or a mixture of those of metals and nonmetals, and which is considered to be difficult to classify unambiguously as either a metal or a nonmetal; no standard definition of a metalloid nor is there agreement as to which elements are appropriately classified as such. Main metalloids: B, Si, Ge, As, Sb, Te; less commonly recognized metalloids: C, Al, Se, Po, At. On a standard periodic table all of these elements can be found in or near a diagonal region of the p-block, having its main axis anchored by boron at one end and astatine at the other. Metalloids and their compounds instead find common use in glasses, alloys and semiconductors.
Template:Periodic table (metalloid border) & Dividing line between metals and nonmetals (amphoteric line, metal-nonmetal line, metalloid line, semimetal line, staircase, Zintl border/line): can be found, in varying configurations, on some representations of the periodic table of the elements. Elements to the lower left of the line generally display increasing metallic behavior; elements to the upper right display increasing nonmetallic behavior.

Acid-base chemistry[edit]

Category:Acid-base chemistry
Category:Acids
Category:Superacids
Category:Bases
Category:Buffers
Acid–base reaction: Several concepts exist that provide alternative definitions for the reaction mechanisms involved and their application in solving related problems. Historic acid–base theories: Lavoisier's oxygen theory of acids, Liebig's hydrogen theory of acids. Common acid–base theories:
  • Arrhenius definition: an Arrhenius acid is a substance that dissociates in water to form H+; an Arrhenius base is a substance that dissociates in water to form OH.
  • Solvent system definition: limitations of the Arrhenius definition is its reliance on water solutions. Albert F. O. Germann, working with liquid COCl
    2
    , formulated the solvent-based theory in 1925, thereby generalizing the Arrhenius definition to cover aprotic solvents. Germann pointed out that in many solutions, there are ions in equilibrium with the neutral solvent molecules: solvonium: generic name for a positive ion. solvate: generic name for a negative ion.
  • Brønsted–Lowry acid–base theory: Brønsted acid is defined as being able to lose, or "donate" proton (H+) while a Brønsted base is defined as a species with the ability to gain, or "accept," a proton.
  • Lewis acids and bases: molecular entity (and the corresponding chemical species) that is an electron-pair acceptor and therefore able to react with a Lewis base to form a Lewis adduct, by sharing the electron pair furnished by the Lewis base.
Acid dissociation constant (Ka, acidity constant, acid-ionization constant): quantitative measure of the strength of an acid in solution
Acid strength: strong acid is one that completely ionizes (dissociates) in a solution; weak acid only partially dissociates in a solution.
Extremely strong acids (as protonators):
Magic acid: FSO3H-SbF5
Fluoroantimonic acid ({Chem|H|2|FSbF|6}}): protonates nearly all organic compounds.
Superacid: classical definition: acid with an acidity greater than that of 100% pure sulfuric acid
Leveling effect (solvent leveling): effect of solvent on the properties of acids and bases; strength of a strong acid is limited ("leveled") by the basicity of the solvent; strength of a strong base is leveled by the acidity of the solvent
Hammett acidity function (H0): measure of acidity that is used for very concentrated solutions of strong acids, including superacids
Category:Analytical chemistry
Category:Titration
Nonaqueous titration

Explosives[edit]

Category:Energetic materials
Category:Explosives
Explosive material (explosive; explosive charge): reactive substance that contains a great amount of potential energy that can produce an explosion if released suddenly, usually accompanied by the production of light, heat, sound, and pressure. Chemical energy: nitroglycerin or grain dust (grain elevator and grinding mill explosions); pressurized gas; nuclear energy. History: gunpowder (black powder; 9th c. China); nitroglycerin (1847); nitrocellulose, smokeless powder, dynamite, gelignite; WWI: TNT; WWII; modern explosives: C-4, others. Properties of explosive materials: Availability and cost; Sensitivity (impact, friction, heat); Sensitivity to initiation; Velocity of detonation; Stability (Chemical formula - kinetics, Temperature of storage, Exposure to sunlight, Electrical discharge); Power, performance, and strength; Brisance (shattering effect, rapidity with which an explosive reaches its peak pressure (power) is a measure of its brisance); Density; Volatility (vaporization); Hygroscopicity and water resistance; Toxicity; Explosive train; Volume of products of explosion; Oxygen balance (OB% or Ω); Chemical composition (mixture of explosive and clay, silica...); Chemically pure compounds; Mixture of oxidizer and fuel. Classification of explosive materials: By sensitivity: Primary explosive (extremely sensitive to stimuli such as impact, friction, heat, static electricity, or electromagnetic radiation), Secondary explosive (less sensitive than a primary explosive and require substantially more energy to be initiated; e.g. TNT, RDX), Tertiary explosive (blasting agents; so insensitive to shock that they cannot be reliably detonated by practical quantities of primary explosive, and instead require an intermediate explosive booster of secondary explosive); By velocity: low explosives (rate of decomposition proceeds through the material at less than the speed of sound), high explosives (detonate, explosive shock front passes through the material at a supersonic speed).
Chemical explosive
List of explosives used during World War II: mixtures of TNT, RDX or PETN.
Trinitrotoluene (TNT; 2,4,6-trinitrotoluene; 1863): explosive yield of TNT is considered to be the standard measure of strength of bombs and other explosives.
Pentaerythritol tetranitrate (PETN, PENT, PENTA, TEN, corpent, penthrite (de: nitropenta); 1891 (used by DE in WWI)): most well known as an explosive; one of the most powerful high explosives known, with a relative effectiveness factor of 1.66; mixed with a plasticizer forms a plastic explosive.
RDX ("Research Department Explosive"; cyclonite, hexogen, T4; chemical: cyclotrimethylenetrinitramine; 1898): developed as an explosive which was more powerful than TNT, saw wide use in WWII.

Amorphous phase (glass)[edit]

Glass transition temperature
Vitrification
Ice#Phases: Atmospheric pressure=105 Pa; Ic (cubic ice), Ih (hexagonal ice).
Amorphous ice: Low-density amorphous ice (LDA, vapor-deposited amorphous water ice, amorphous solid water (ASW), hyperquenched glassy water (HGW)) - density=0.94 g/cm3; High-density amorphous ice (HDA) - density=1.17 g/cm3; Very-high-density amorphous ice (VHDA) - density=1.26 g/cm3.

What is life? How cells and their contents work[edit]

Brownian motor: nano-scale or molecular devices by which thermally activated processes (chemical reactions) are controlled and used to generate directed motion in space and to do mechanical or electrical work
Fluctuation Theorem: (from statistical mechanics) relative probability that the entropy of a system which is currently away from thermodynamic equilibrium (i.e., away from maximum entropy) will increase or decrease over a given amount of time
Entropy and Gibb's free energy:
Entropy (statistical thermodynamics): statistical physics
Entropy and life
Microcanonical ensemble
Density of states: number of states per interval of energy at each energy level that are available to be occupied

Biology[edit]

Category:Branches of biology
Category:Biophysics
Category:Cell biology
Category:Molecular biology
Category:Structural biology
Biosafety level: all survival horror fans' beloved facilities in truth
Brain-computer interfacing
Biomimicry
Biological organisation (hierarchy of life, ecological organization): hierarchy of complex biological structures and systems that define life using a reductionistic approach; each level in the hierarchy represents an increase in organizational complexity, with each "object" being primarily composed of the previous level's basic unit; basic principle behind the organization is the concept of emergence—the properties and functions found at a hierarchical level are not present and irrelevant at the lower levels. A-cellular level and Pre-cellular level {atom/molecule} → biomacromolecular complexes {structural and machines} → Sub-cellular level {organelle} → Cellular level {cell} → Super-cellular level (Multicellular level) {tissue} → {organ → organ system → organism → population → biocoenosis/community → ecosystem → biosphere → [ecosphere (magnetosphere + atmosphere + biosphere + hydrosphere + pedosphere + geosphere)]}

Molecular Biology (Biochemistry) + Cellular Biology:

Wikipedia:WikiProject Molecular and Cellular Biology: aims to better organize information in articles related to molecular and cell biology on Wikipedia. {q.v. Gene Wiki; Portal:Gene Wiki}
Wikipedia:WikiProject Molecular and Cellular Biology/Style guide (gene and protein articles): scope of a gene/protein article is the human gene/protein (included all splice variants derived from that gene) as well as orthologs (as listed in HomoloGene) that exist in other species. If there are paralogs in humans (and by extension other species), then a gene family article in addition to the gene specific articles (see for example dopamine receptor) would be appropriate. Article name: if short, recommended UniProt protein name should be used as the article name; if verbose, either a widely used protein acronym or the official HUGO gene symbol, followed by "(gene)" if necessary to disambiguate. Abbreviations of genes are according to HUGO Gene Nomenclature Committee and written in italic font style, human gene names are written in capitals {q.v. Genetics::Gene nomenclature}

evo-devo:

Evolutionary developmental biology (evolution of development, informally: evo-devo): compares the developmental processes of different organisms to determine the ancestral relationship between them, and to discover how developmental processes evolved

Quantum mechanics and biology[edit]

Quantum biology, R ***
Quantum Aspects of Life, R

Biochemistry and Molecular Biology[edit]

Category:Molecular biology
Category:Biomolecules
Category:Biomolecules by type
Category:Biomolecules by physiological function
Category:Hormones
Hypothetical types of biochemistry

Transcription Translation

Trans-acting (trans-regulatory, trans-regulation; la: "across from"): "acting from a different molecule" (i.e., intermolecular). In the context of transcription regulation, a trans-acting element is usually a DNA sequence that contains a gene. This gene codes for a protein (or microRNA or other diffusible molecule) that will be used in the regulation of another target gene.
Cis-regulatory element (cis-element; la: "on the same side as"): region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA (often a chromosome). A cis-element may be located upstream of the coding sequence of the gene it controls (in the promoter region or even further upstream), in an intron, or downstream of the gene's coding sequence, either in the translated or untranscribed region.

Biochemical substances, pharmacy, pharmacology[edit]

Template:Phytochemical
Saponin=Sapogenin (key organic feature: steroid or other triterpene frameworks) +. :
  1. Quinoa saponins are classified as a mild eye and respiratory irritant and a low gastrointestinal irritant
  2. medicinal uses: e.g. digoxin (from Digitalis sp., cardiac glycoside: treat heart diseases), eleutheroside A (from Eleutherococcus senticosus, aka Siberian Ginseng), ginsenoside (Panax sp., aka ginseng; Rb1 group: Rb1, Rb2, Rc, Rd; Rg1 group: Rg1, Re, Rf, Rg2)

Proteins, enzymes[edit]

Category:Proteins
Category:Protein families
Category:Protein structure
Category:Protein domains

q.v. Structural biology; Biomacromolecular complexes

Template:Posttranslational modification: the enzymes and proteins involved: chaperons (heat shock or chaperonins); protein targeting - signal peptide; ubiquitin: E1, E2, E3, deubiquitinating enzymes; SUMO.
Template:Protein primary structure (Protein primary structure and posttranslational modifications): PTM modified amino acids: S/T, Y, C, D, E, N, Q, K, R, P, H, W. Disulfide bond (C-C), ...
Proteinogenic amino acid: 22 standard amino acids, but only 21 are found in eukaryotes. 21st and 22nd: selenocysteine and pyrrolysine are incorporated into proteins by distinctive biosynthetic mechanisms; other 20 are directly encoded by the universal genetic code.
PYLIS downstream sequence (PYLIS: pyrrolysine insertion sequence): stem-loop mRNA structure; causes the UAG (amber) stop codon to be translated to the amino acid pyrrolysine instead of ending the protein translation. In archaea the PYLIS downstream sequence is positioned straight after the UAG codon which is translated as pyrrolysine.
SECIS element (SECIS: selenocysteine insertion sequence): stem-loop mRNA structure of around 60 nts; translate UGA codons as selenocysteines. In bacteria the SECIS element appears soon after the UGA codon it affects. In archaea and eukaryotes, it occurs in the 3' UTR of an mRNA, and can cause multiple UGA codons within the mRNA to code for selenocysteine. In Methanococcus (archeon) it is located in the 5' UTR.
Posttranslational modification (PTM): chemical modification of a protein after its translation.
Protein phosphorylation: PTM of proteins in which S, T or Y is phosphorylated by a protein kinase by the addition of a covalently bound phosphate group. Regulation of proteins by phosphorylation is one of the most common modes of regulation of protein function, and is often termed "phosphoregulation". In almost all cases of phosphoregulation, the protein switches between a phosphorylated and an unphosphorylated form, and one of these two is an active form, while the other one is inactive, respectively. In mammals proteins are phosphorylated predominantly on S (86%), T (12%) and Y (2%).
Phosphatase: enzyme that removes a phosphate group from its substrate by hydrolysing phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group. This action is directly opposite to that of phosphorylases and kinases, which attach phosphate groups to their substrates by using energetic molecules like ATP. Protein phosphatases (PPs) can be grouped into three main classes based on sequence, structure and catalytic function: phosphoprotein phosphatase (PPP) family (contains also protein phosphatase Mg2+- or Mn2+-dependent (PPM) family); protein Tyr phosphatase (PTP) super-family; aspartate-based protein phosphatase group.
Metallothionein: family of cysteine-rich, 0.5 to 14 kDa proteins; localized to the membrane of the Golgi apparatus; bind both physiological (such as zinc, copper, selenium) and xenobiotic (such as cadmium, mercury, silver, arsenic) heavy metals through the thiol group of its cysteine residues, which represents nearly the 30% of its amino acidic residues
Engineered monoclonal antibodies.
Fragment antigen-binding (Fab): region on an antibody that binds to antigens. Composed of one constant and one variable domain of each of the heavy and the light chain.
Single-chain variable fragment (scFv): fusion protein of the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins, connected with a short linker peptide of ten to about 25 amino acids.
Protein families[edit]
Category:Protein families
Category:Protein structure
Category:Protein domains
DExD/H box proteins: refer to the DEAD box, DEAH, and the Ski families of proteins; quite distinct from one another and there is not one protein that belongs to more than one of these families; each family has a specific role in RNA metabolism
DEAD/DEAH box helicase: family of proteins whose purpose is to unwind nucleic acids. "DEAD box and DEAH box proteins NTPase activities become stimulated by RNA, but DEAD box proteins use ATP and DEAH does not" {from "DExD/H box proteins"}.
DEAD box: involved in an assortment of metabolic processes that typically involve RNAs, but in some cases also other nucleic acids; highly conserved in nine motifs and can be found in both prokaryotes and eukaryotes. "Involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression" {from "DEAD/DEAH box helicase"}.
Addictive substances, addiction[edit]
Drugs: addiction & lethal dose.
Alcohol belts in Europe: vodka, beer, wine (from "coldest" to the "warmest" climate EtOH containing drinks).
Nora Volkow: addiction science
Behavioral addiction
Compulsive buying disorder (CBD): found in 5.8% of the United States population, approximately 80% of those affected are female
Overeating & Binge eating
Problem gambling
Self-harm (SH) (deliberate self-harm (DSH), self-poisoning, self-mutilation): self-harm is found in 40–60% of suicides; generalising self-harmers to be suicidal is, in the majority of cases, inaccurate.
Sexual addiction
Workaholic: Workaholism is not the same as working hard. Despite logging in an extraordinary amount of hours and sacrificing their health and loved ones for their jobs, workaholics are frequently ineffective employees.
Computer & Internet:
Computer addiction
Internet addiction disorder (IAD)
Information addiction
Video game addiction
Delirium tremens (latin: "shaking frenzy"; "the horrors" or "the shakes"): acute episode of delirium that is usually caused by withdrawal from alcohol (or other sedative-hypnotics, such as benzodiazepines, or barbiturates), first described in 1813; can result in death. Withdrawal from other drugs which are not sedative-hypnotics such as caffeine, cocaine, etc. does not have major medical complications, and is not life-threatening.

Methods[edit]

Cross-link: cross-links in synthetic polymer chemistry; crosslinks in the biological sciences: protein-protein interaction, photo-reactive aa analogs (mass spectrometry); uses for crosslinked polymers: polyacrylamide gels for gel electrophoresis, rubber.

Biophysics, physical chemistry[edit]

Category:Biophysics
Category:Physical chemistry
Macromolecular crowding: alters the properties of molecules in a solution when high concentrations of macromolecules are present. Such conditions occur routinely in living cells, e.g., the cytosol of Escherichia coli contains about 300–400 mg/mL of macromolecules; these high concentrations of macromolecules reduce the volume of solvent available for other molecules in the solution, which has the result of increasing their effective concentrations

Structural biology[edit]

Category:Structural biology

q.v. Structure-function (esp. Microscopes, X-ray crystallography, Protein NMR, Tomography; Materials science, nanotechnology (bionanotech)...)

Template:Biomolecular structure & Biomolecular structure
Template:Protein structural analysis
Nucleic acid structure determination: Physical methods (X-ray, NMR, EM...); RNA sequencing; Chemical methods (Hydroxyl radical probing, DMS, CMCT, Kethoxal, Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE)); In-line probing; Nucleotide analog interference mapping
Nucleic acid design

Biomacromolecular complexes (bio, chem, phys, maths, CS/IT(dynamics(molecular,modeling,...)),...), which are sometimes (NOT always) called "-somes", from Greek soma->body[edit]

RNA containing complexes[edit]

q.v. Cell nucleus

Template:Post transcriptional modification
Ribonucleoprotein (RNP): nucleoprotein that contains RNA, i.e. protein + RNA.
Ribonucleoprotein particle: complex formed between RNA and RBPs. 'RNP foci' is used to denote an intracellular compartment involved in processing of RNA transcripts. RNP granules: stress granules, processing bodies, and exosomes in somatic cells; cell type and/or species specific.

RNAs:

Small nucleolar RNA (snoRNAs): primarily guide chemical modifications of other RNAs, mainly: rRNAs, tRNAs, snRNAs. Two main classes of snoRNA: the C/D box snoRNAs which are associated with methylation, and the H/ACA box snoRNAs which are associated with pseudouridylation. Commonly referred to as guide RNAs but should not be confused with the guide RNAs that direct RNA editing in trypanosomes.
Template:Small nucleolar RNA: J; MB; Me; psi; R, SNORA; SNORD; snR; TBR; U (e.g. U3; U2-19; U8); Z; other.
Small Cajal body-specific RNA (scaRNAs): specifically localise to the Cajal body, a nuclear organelle involved in the biogenesis snRNPs; guide the modification (methylation and pseudouridylation) of RNA polymerase II transcribed spliceosomal RNAs U1, U2, U4, U5 and U12.
RNA processing[edit]
transcriptosome:
Capping enzyme: addition of the cap occurs co-transcriptionally, after the growing RNA molecule contains about 30 nucleotides. The enzyme can only catalyze its reaction when bound to the phosphorylated carboxyl-terminal domain of RNA polymerase II; therefore it is specific to RNAs synthesized by this polymerase rather than those synthesized by RNA polymerase I or RNA polymerase III.
RNA polymerase (esp. RNA polymerase II)
transcription factors
splicing {q.v. Spliceosome, splicing}
RNA polymerase (RNAP, RANpol; DNA-dependent RNA polymerase)
RNA polymerase I (Pol I): in higher eukaryotes, the enzyme that only transcribes 18S, 5.8S, 28S rRNA (but not 5S rRNA, which is synthesized by RNA Polymerase III), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell. rDNA transcription is confined to the nucleolus where several hundreds of copies of rRNA genes are present, arranged as tandem head-to-tail repeats. Pol I transcribes one large transcript, encoding an rDNA gene over and over again; fastest-acting polymerase.
RNA polymerase II (RNAP II, Pol II): transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA; 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. Carboxy-terminal domain (CTD) of Pol II typically consists of up to 52 repeats of the sequence YSPTSPS.
RNA polymerase II holoenzyme: form of eukaryotic Pol II that is recruited to the promoters of protein-coding genes in living cells; consists of Pol II, a subset of general transcription factors, and regulatory proteins known as SRB proteins. CTD phosphorylation.
Mediator (coactivator) (Vitamin D Receptor Interacting Protein (DRIP) coactivator complex and the Thyroid Hormone Receptor-associated Proteins (TRAP)): multiprotein complex that functions as a transcriptional coactivator in all eukaryotes; required for the successful transcription of nearly all class II gene promoters in yeast. Human mediator complex: 26+ subunits, 1.2 MDa.
RNA polymerase III (Pol III): transcribes DNA to synthesize 5S rRNA, tRNA and other small RNAs
RNA polymerase IV: specific to plants genomes and is required for the synthesis of over 90% of 24-nt heterochromatic siRNA
RNA polymerase V: synthesizes RNAs involved in siRNA-directed heterochromatin formation in plants.
Post-transcriptional modification (co-transcriptional modification)
Non-coding RNA (ncRNA; sometimes: non-protein-coding RNA (npcRNA), non-messenger RNA (nmRNA), functional RNA (fRNA)): functional RNA molecule that is not translated into a protein; DNA sequence from which a non-coding RNA is transcribed is often called an RNA gene. tRNA, rRNA, snoRNA, microRNA, siRNA, snRNA, exRNA, piRNA, long ncRNA...
Long non-coding RNA (lncRNA {pronounced: lincRNA}): non-protein coding transcripts longer than 200 nucleotides:: somewhat arbitrary limit distinguishes lncRNAs from small regulatory RNAs: miRNAs, siRNAs, piRNAs, snoRNAs, and other short RNAs. Many well-described long ncRNAs, such as Air and Xist, are poorly conserved, suggesting that ncRNAs may be subject to different selection pressures; selection may conserve only short regions of long ncRNAs that are constrained by structure or sequence-specific interactions; selection act only over small regions of the long ncRNA transcript. Those conserved regions of the human genome that are subject to recent evolutionary change relative to the chimpanzee genome occurs mainly in non-coding regions, many of which are transcribed
Piwi-interacting RNAs (piRNAs)
Bacterial small RNA
Small hairpin RNA (short hairpin RNA (shRNA)): makes a tight hairpin turn that can be used to silence target gene expression via RNAi
Polyadenylation (addition of poly(A) tail): to RNA. In eukaryotes, polyadenylation is part of the process that produces mature mRNA for translation. Nuclear polyadenylation: Function, Mechanism.Cytoplasmic polyadenylation: germ line, early embryogenesis, post-synaptic sites of neurons. Tagging for degradation in eukaryotes. Evolution: polyadenylation is seen in almost all organisms, it is not universal.
RNA-binding protein (RBP): bind to the ds or ss RNA; contain RRMs.
Spliceosome, splicing[edit]
RNA splicing (splicing)
alternative splicing (differential splicing): regulated process during gene expression that results in a single gene coding for multiple proteins.
LSm several duplications: SmD1/LSm10 paralog pair and the SmD2/LSm11 paralog pair exist only in animals, fungi, and the amoebozoa; the SmB/SmN (neural tissue Sm) paralog pair is seen only in the placental mammals. SmB has alternatively spliced variant SmB'; very similar protein, SmN replaces SmB'/B in certain (mostly neural) tissues. LSm's are found in U1, U2, U4, U5, U6 as a ring around Sm motif in U1, U2, U4, U5, U6 RNAs.
Sm ring: SmG, SmD3, SmB/SmB'/SmN, SmD1, SmD2, SmF. + U1, U2, U4, U5, U11, U12, U4atac snRNAs.
Lsm2-8 ring: (Theorized order: LSm5, LSm7, LSm4, LSm8, LSm2, LSm3, LSm6.) ~20 times less abundant than the Sm rings. + U6, U6atac, snRNAs; + U8 snoRNA (for rRNA, tRNA processing in nucleolus).
Sm10/Sm11 ring: LSm10 replace SmD1 and LSm11 replaces SmD2. + U7 snRNA.
Lsm1-7 ring: same as Lsm2-8 except LSm1 replaces LSm8. Localizes in the cytoplasm where it assists in degrading messenger RNA in ribonucleoprotein complexes.
SMN complex: SMN + Gemins 2-8. Gemin 6 and Gemin7 have been discovered to have the LSm structure, and to form a heterodimer. PRMT5 complex stabilizes SmB+SmD3 dimer, SmD1+SmD2 dimer, and SmD1+SmD2+SmF+SmE+SmG pentamer by attaching pICln to these. The pentamer and SmB+SmD3 dimer are loaded onto the SMN complex, which in turn loads the Sm ring onto snRNAs. SnRNP#Assembly of core snRNPs in the SMN complex: involved in the assembly of snRNPs.
GEMINs 2-8: GEMIN8 (Gem-associated protein 8) + GEMIN7 + GEMIN6 + GEMIN5 + GEMIN4 + DDX20 (Probable ATP-dependent RNA helicase DDX20; aka GEMIN3) + Survival of motor neuron protein-interacting protein 1 (SIP1 gene; aka GEMIN2)
Survival of motor neuron (SMN1 gene): due to SMN1 deletion, (incomplete SMN complex?) results in widespread splicing defects, especially in spinal motor neurons, and is one cause of spinal muscular atrophy (SMA)
PRMT5 complex = Protein arginine methyltransferase 5 + CLNS1A (pICln) + WD repeat-containing protein 77 (Mep50)
LSm12-16 and other multi-domain LSm proteins: ataxin-2 is large protein and has N-terminal LSm domain.
Archaeal Sm rings: Sm1 (SmAP1) and Sm2 (SmAP2) form homoheptamer or homohexamer rings; reported to associate with RNase P RNA. Crenarchaeotes have Sm3.
Bacterial LSm rings: Hfq - homohexamer rings; YlxS (sometimes also called YhbC) - two-domain protein with a N-terminal LSm domain. MscS
SnRNPs (pronounced "snurps"; small nuclear ribonucleoproteins): U1, U2, U5, U5, U6 (in addition, in metazoans: U11 snRNA, U12 snRNA, U4atac snRNA, U6atac snRNA). Also: U7 snRNP, which processes 3′ loop of histone pre-mRNA. Biogenesis.
Small nuclear RNA (snRNA; U-RNA): found within the nucleus of eukaryotic cells; length of an average snRNA is approximately 150 nt
U7 snRNP = U7 small nuclear RNA + Sm10/Sm11 ring + ZPF100 + (HBP (aka SLBP) + Histone 3' UTR stem-loop). For histone 3' UTR stem-loop processing.
Histone 3' UTR stem-loop: involved in nucleocytoplasmic transport of the histone mRNAs, and in the regulation of stability and of translation efficiency in the cytoplasm; mRNAs of metazoan histone genes lack polyadenylation and a poly-A tail, instead 3' end processing occurs at a site between this highly conserved stem-loop and a purine rich region around 20 nucleotides downstream (the histone downstream element, or HDE).
SLBP (histone RNA hairpin-binding protein (HBP) or stem-loop binding protein):
Minor spliceosome: splices atypical class of spliceosomal introns (U12-type) from eukaryotic messenger RNAs in plant, insects, vertebrates and some fungi. U12-type introns represent less than 1% of all introns in human cells. However they are found in genes performing essential cellular functions.
Spliceosome and spliceosomal "subunits" and complexes (U1, U2 (SF3a + SF3b), U4/6&U5 (tri-snRNP) → U1+U2+U4/6&U5 (B) → U2/6&U5 (Bact, B*, C))
Introns + Exons = pre-mRNA; pre-mRNA-(Spliceosome)→mRNA
U1 snRNP = U1 spliceosomal RNA + SnRNP70 (aka, U1 small nuclear ribonucleoprotein 70 kDa) + Sm ring + U1-A
U2 snRNP = U2 spliceosomal RNA + PRPF8 {2335 AA} (YPrp8)
U4 snRNP = U4 spliceosomal RNA + (+ PRPF3)
U5 snRNP = U5 spliceosomal RNA + WDR57 (Y????)
U6 snRNP = U6 spliceosomal RNA + Lsm2-8 ring + (+ PRPF3)
U4/U6-U5 tri-snRNP = U4 + U6 + U5 + PRPF31
Splicing factor: protein involved in the removal of introns from pre-mRNA.
U2AF2 (U2 small nuclear RNA auxiliary factor 1): required for binding of U2 snRNP to pre-mRNA; PAP1 (RP9) interacts with U2AF
ASF/SF2 (SFRS1)
EFTUD2 (interacts with WDR57 and PRPF8)
SR protein: conserved family of proteins involved in RNA splicing; protein domain with long repeats of S and R aa; length of SR proteins: 50-300 aa; RS domain and at least one RRM domain; more commonly found in the nucleus than the cytoplasm, but several SR proteins are known to shuttle between the nucleus and the cytoplasm. Metazoans appear to have SR proteins and unicellular organisms lack SR proteins. Important in constitutive and alternative pre-mRNA splicing, mRNA export, genome stabilization, NMD, and translation. 9 human genes: SFRS1, SFRS2, SFRS3, SFRS4, SFRS5, SFRS6, SFRS7, SFRS9, SFRS11. mRNA export; Genomic stabilization; NMD; Translation. Diseases: Cancer; HIV-1; Spinal muscular atrophy.
RNA recognition motif (RRM, RNP-1): putative RNA-binding domain of about 90 aa that are known to bind single-stranded RNAs; found in many eukaryotic proteins
Kinases: Serine/threonine-protein kinases: SRPK1, SRPK2; CLK1
Heterogeneous ribonucleoprotein particle (hnRNP): present in the cell nucleus during gene transcription and subsequent post-transcriptional modification of pre-mRNA. Proteins involved in the hnRNP complexes are collectively known as heterogeneous ribonucleoproteins
Polypyrimidine tract-binding protein (PTB): plays a regulatory role in alternative splicing.
Protein K (gene expression); K-homology or KH domains
pre-mRNA structures:
Polypyrimidine tract: region of mRNA that promotes the assembly of the spliceosome. PTB and U2AF associate with polypyrimidine tract.
Exonic splicing enhancer (ESE): DNA sequence motif consisting of 6 bases within an exon that directs, or enhances, accurate splicing of hnRNA or pre-mRNA into mRNA.
Exonic splicing silencer (ESS): small region of an exon that inhibits or silences splicing of pre-mRNA.
Precursor mRNA (pre-mRNA is the major part of heterogeneous nuclear RNA (hnRNA)): immature single strand of mRNA. Processed pre-mRNA is called "mature mRNA" or simply "mRNA".
Splicing-associated genetic diseases:
Retinitis pigmentosa (RP): a group of genetic eye conditions that lead to incurable blindness. RPs linked to splicing: RP13=PRPF8, RP11=PRPF31, RP18=PRPF3, RP9=PAP1.
Exon junction complex (EJC): has major influences on translation, surveillance and localization of the spliced mRNA
Nonsense-mediated decay (NMD): surveillance pathway that exists in all eukaryotes. Its main function is to reduce errors in gene expression by eliminating mRNA transcripts that contain premature stop codons.
mRNA surveillance: mechanisms are pathways utilized by organisms to ensure fidelity and quality of mRNA; function at various steps of the mRNA biogenesis pathway to detect and degrade transcripts that have not properly been processed.
Trans-splicing & de:Transspleißen: special form of pre-mRNA processing in eukaryotes where exons from two different primary RNA transcripts are joined end to end and ligated.
Ribozymes[edit]
Ribosome
Processome: the "-some" which processes at least 16S rRNA of ribosome and assembles the small subunit of ribosome; made of U3 snoRNP, tUTP, bUTP, BMS1/RCL1.
RNase P: cleave off an extra, or precursor, sequence of RNA on tRNA molecules. Bacterial RNase P has two components: an RNA chain, called M1 RNA, and a polypeptide chain, or protein, called C5 protein (class A and B). Archaeal RNase P ribonucleoproteins consist of 4-5 protein subunits that are associated with RNA.
Nuclear RNase P: eukaryotic RNase P.
Intron
Spliceosomal introns: in nuclear protein-coding genes that are removed by spliceosomes
Introns in nuclear and archaeal transfer RNA genes that are removed by proteins (tRNA splicing enzymes)
Group I catalytic intron: large self-splicing ribozymes; catalyze their own excision from mRNA, tRNA and rRNA precursors in Eukaryota, Bacteria, Viruses.
Group II intron: large class of self-catalytic ribozymes as well as mobile genetic element found within the genes of all three domains of life. Self-splicing can occur under high-salt conditions in vitro; however, assistance from proteins is required for in vivo splicing.
Group III intron: found in mRNA genes of chloroplasts in euglenoid protists; have a conventional group II-type dVI with a bulged adenosine, a streamlined dI, no dII-dV, and a relaxed splice site consensus. Much shorter than other self-splicing intron classes, ranging from 95 to 110 nucleotides amongst those known to Christopher and Hallick, and identified in chloroplasts; conserved sequences proximal to the splicing sites have similarities to those of group II introns, but have fewer conserved positions; very A+T rich.

Protein complexes[edit]

Category:Protein complexes
Multiprotein complex (protein complex): group of two or more associated polypeptide chains; distinct from a multienzyme polypeptide, in which multiple catalytic domains are found in a single polypeptide chain. Unfortunately, many of the techniques used to break open cells and isolate proteins are inherently disruptive to such large complexes, so their protein complexes within the cell may be even more widespread than can be detected. Obligate vs non-obligate protein complex; Transient vs permanent/stable protein complex; Fuzzy complex.
Protein–protein interaction (PPI): two or more proteins bind together, often to carry out their biological function
Proteasome: the center for protein and peptide degradation:
20S: core of proteasome; lids: 19S (10-protein base and 9-protein lid); 11S
19S+20S=26S
11S+20S=PA28/REG (11S is induced by interferon gamma; responsible for the generation of peptides for MHC)
Anaphase-promoting complex (cyclosome; APC/C): E3 ubiquitin ligase that marks target cell cycle proteins for degradation by the 26S proteasome.
Nuclear pore complex (NPC)
Rhodopsin = Opsin + retinal
Cap binding complex (CBC): DE version has structures [12/02/09]
Origin recognition complex (ORC): multi-subunit DNA binding complex (6 subunits: ORC1-ORC6); binds in all eukaryotes to origins of replication in ATP-dependent manner. Serves as foundation for assembly of pre-replication complex (pre-RC; complex of Cdc6, Tah11 (aka Cdt1), Mcm2-Mcm7).
Cdc6 (Cell Division Cycle 6, in S. cerevisiae): essential regulator of DNA replication and plays important roles in the activation and maintenance of the checkpoint mechanisms in the cell cycle that coordinate S phase and mitosis. In humans: CDC6 (cell division control protein 6 homolog).
Segrosome: ensure accurate segregation (partitioning) of plasmids or chromosomes during bacterial cell division; "minimalist spindles".
SMC protein (Structural Maintenance of Chromosomes): large family of ATPases that participate in many aspects of higher-order chromosome organization and dynamics. Any relation between SMCs and segrosome?
Oxidative phosphorylation#Organization of complexes: "respirasomes"
Template:Hemeproteins
Globins: related family of proteins, which are thought to share a common ancestor.
Myoglobin: iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals.
Hemoglobin (Hb): iron-containing oxygen-transport metalloprotein in the red blood cells of all vertebrates as well as the tissues of some invertebrates.
Hemocyanins: respiratory proteins in the form of metalloproteins containing two copper atoms that reversibly bind a single oxygen molecule.

Microtubule organizing center (MTOC): structure found in eukaryotic cells from which microtubules emerge; two main functions: the organization of eukaryotic flagella and cilia and the organization of the mitotic and meiotic spindle apparatus, which separate the chromosomes during cell division. Centriole: usually 9*3 MTs; absent in higher plants and fungi. D. melanogaster embryos: 9*2; C. elegans sperm cells and early eambryos: 9*1; crabs maybe 9*2.

Centrosome: organelle that serves as the main MTOC of the animal cell as well as a regulator of cell-cycle progression; composed of two orthogonally arranged centrioles surrounded by an amorphous mass of protein termed PCM.
Pericentriolar material (PCM): amorphous mass of protein which makes up the part of the animal centrosome that surrounds the two centrioles.
Basal body (basal granule, kinetosome): organelle formed from a centriole, and a short cylindrical array of microtubules. Found at the base of a eukaryotic undulipodium and serves as a nucleation site for the growth of the axoneme microtubules; 9*3 helicoidal configuration forms a hollow cylinder.
Undulipodium (9+2 organelle): eukaryotic flagella and cilia; extension of the cell membrane containing both cytoplasm and a regular arrangement of microtubules known as an axoneme.
Axoneme: inner core of the undulipodium. Motile cilia/flagela: 9*2+2 axoneme; non-motile/primary cilia: no dynein arms are found, 9*2+0 (sometimes 9*2+1), (sensory functions?).

Tubulin: most common members of the tubulin family are α-tubulin and β-tubulin (αβ dimers make up microtubules). FtsZ is a prokaryotic homolog of eukaryotic tubulins. γ-tubulin important in the nucleation and polar orientation of microtubules, found in centrosomes. Tubulin/FtsZ family, GTPase domain - evolutionary conserved protein domain.

Microtubule nucleation (γ-tubulin ring complex (γ-TuRC)): cap of the (−) end while microtubule growth continues towards the (+) direction; found typically in MTOC.
Microtubules (MTs): component of the cytoskeleton; outer diameter of microtubule is ~25 nm. Kinesins are motor proteins binding MTs; katanin severs MTs & co.
Inositol trisphosphate receptor (InsP3R; IP3R; type = 1,2,3): membrane glycoprotein complex acting as a Ca2+ channel activated by IP3; very diverse among organisms, and is necessary for the control of cellular and physiological processes including cell division, cell proliferation, apoptosis, fertilization, development, behavior, learning and memory; strong evidence suggesting that IP3R plays an important role in the conversion of external stimuli to intracellular Ca2+ signals characterized by complex patterns relative to both space and time; (e.g. Ca2+ waves and oscillations). Rat cerebellum IP3R is type 1 (IP3R1).
Ryanodine receptors (RyRs): form a class of intracellular calcium channels in various forms of excitable animal tissue like muscles and neurons; major cellular mediator of calcium-induced calcium release (CICR) in animal cells. In the muscle cells RyRs are in the membrane of sarcoplasmic reticulum. Similar to IP3R. Small amount of Ca2+ in the cytosol near RyR will cause it to release even more Ca2+ (CICR).
Calcium-induced calcium release (CICR)
Calcium (Ca2+) sparks
Template:ATPase & ATPase (EC 3.6.1.3; adenylpyrophosphatase, ATP monophosphatase, triphosphatase..., ATP hydrolase...): cation(s) pump vs ATP. Cations: H+; Na+/K+; H+/K+; Ca++; Mg++; Cu++.
ATP synthase (EC 3.6.3.14; TCDB 3.A.2 (F-type, V-type and A-type ATPase (sometimes just F-ATPase) superfamily))
F-ATPase: bacterial plasma membranes, in mitochondrial inner membranes, and in chloroplast thylakoid membranes. F0 + F1
V-ATPase: vacuoles and other intracellular organelles of eukaryotes and in bacteria. V0 + V1
A-ATPase: found in archaea.
E-ATPase: cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.

Genetics[edit]

Gene Wiki: project that facilitates transferring information on human genes to Wikipedia article stubs with the goal of promoting collaboration and expansion of the articles.
Portal:Gene Wiki: dedicated to the goal of applying community intelligence to the annotation of gene and protein function. {http://genewikiplus.org/wiki/Main_Page} mirror of the Gene Wiki project on Wikipedia, running on top of the Semantic Mediawiki framework.
Portal:Gene Wiki/Other Wikis
genome sizes for the various groupings of organisms.
Genome
Genome size: 1 pg = 978 Mb; 1991 Drake proposed a rule: that the mutation rate within a genome and its size were inversely correlated.
C-value: amount, in picograms, of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism; in polyploids the C-value may represent two or more genomes contained within the same nucleus.
C-value enigma (C-value paradox): observation that genome size does not correlate with organismal complexity.
List of sequenced eukaryotic genomes: all the eukaryotes known to have publicly available complete nuclear and organelle genome sequences that have been assembled, annotated and published; draft genomes are not included, nor are organelle-only sequences.
Phylogenetic tree shows the relationship between the best-documented instances of paleopolyploidy in eukaryotes.
Polyploid: containing more than two paired (homologous) sets of chromosomes; most eukaryotic species are diploid, meaning they have two sets of chromosomes — one set inherited from each parent, however polyploidy is found in some organisms and is especially common in plants.
Paleopolyploidy: result of genome duplications which occurred at least several mya; most paleopolyploids, through evolutionary time, have lost their polyploid status through a process called diploidization, and are currently considered diploids.
Gene–environment interaction (genotype–environment interaction, G×E)
Genomic imprinting: certain genes are expressed in a parent-of-origin-specific manner; inheritance process independent of the classical Mendelian inheritance. Forms of genomic imprinting have been demonstrated in insects, mammals and flowering plants. Epigenetic process that involves DNA methylation and histone methylation in order to achieve monoallelic gene expression without altering the genetic sequence; epigenetic marks are established in the germline and are maintained throughout all somatic cells of an organism. At least 80 imprinted genes in humans and mice, many of which are involved in embryonic and placental growth and development [~2005-2006]. Mouse: ~80% of imprinted genes are found in clusters such as these, called imprinted domains, suggesting a level of co-ordinated control [2001]. In the developing sperm (during spermatogenesis), a paternal imprint is established, whereas in developing oocytes (oogenesis), a maternal imprint is established. Majority of imprinted genes in mammals have been found to have roles in the control of embryonic growth and development, including development of the placenta. Beckwith–Wiedemann syndrome (BWS); Silver–Russell syndrome (SRS; Silver–Russell dwarfism; Russell–Silver syndrome (RSS)); Angelman syndrome (AS); Prader–Willi syndrome (P.W.S)
Experiments on Plant Hybridization (1865; de: Versuche über Pflanzen-Hybriden): by Mendel; result after years spent studying genetic traits in pea plants; Mendel discovered that one inheritable trait would invariably be dominant to its recessive alternative.
Bacterial genetic nomenclature: standards were proposed in 1966 by Demerec et al. Each bacterial gene is denoted by a mnemonic of three lower case letters which indicate the pathway or process in which the gene-product is involved, followed by a capital letter signifying the actual gene; in some cases, the gene letter may be followed by an allele number; all letters and numbers are underlined or italicised
Gene nomenclature: scientific naming of genes, the units of heredity in living organisms; international committee published recommendations for genetic symbols and nomenclature in 1957. For many genes and their corresponding proteins, an assortment of alternate names is in use across the scientific literature and public biological databases, posing a challenge to effective organization and exchange of biological information. HGNC is responsible for providing human gene naming guidelines and approving new, unique human gene names and symbols (short form abbreviations); research communities of vertebrate model organisms have adopted guidelines whereby genes in these species are given, whenever possible, the same names as their human orthologs. Human: italicised, with all letters in uppercase (e.g. SHH); proteins not italicised, first letter uppercase and the rest lowercase (e.g. Shh/SHH). Mouse and rat: similar to human (Shh and SHH). Chicken (Gallus sp.): the same as humans (SHH and SHH). Frog (Xenopus sp.): shh and Shh. Zebrafish: shh and Shh.

Epigenetics[edit]

Dutch famine of 1944: hildren of pregnant women exposed to famine were more susceptible to diabetes, obesity, cardiovascular disease, microalbuminuria...; children of the women who were pregnant during the famine were smaller, as expected. However, surprisingly, when these children grew up and had children those children were also smaller than average. These data suggested that the famine experienced by the mothers caused some kind of epigenetic changes that were passed down to the next generation.

Transcription factors[edit]

Category:Transcription factors
Category:Forkhead transcription factors
FOX proteins (Forkhead box): family of transcription factors that play important roles in regulating the expression of genes involved in cell growth, proliferation, differentiation, and longevity. Many FOX proteins are important to embryonic development. Founding member and namesake of the FOX family is the fork head transcription factor in Drosophila, discovered by Detlef Weigel and Herbert Jäckle.
Fork head domain: 80-100 aa; binds DNA; "winged helix".
FOXP1
FOXP2
FOXP2 and human evolution: ability of humans to communicate in complex ways through speech and language is unique to this species, where our closest relatives the chimpanzee show a more primitive level of communication

Human genetics[edit]

Human chromosomes (Template:Chromosomes)
Pseudoautosomal region, PAR1 and PAR2: homologous sequences of nucleotides on the X and Y chromosomes
Human accelerated regions (HARs): set of 49 segments of the human genome that are conserved throughout vertebrate evolution but are strikingly different in humans; named according to their degree of difference between humans and chimpanzees (HAR1 showing the largest degree of human-chimpanzee differences). Several of the HARs encompass genes known to produce proteins important in neurodevelopment. HAR1 sequence is found (and conserved) in chickens and chimpanzees but is not present in fish or frogs that have been studied. HAR2 includes HACNS1 a gene enhancer "that may have contributed to the evolution of the uniquely opposable human thumb, and possibly also modifications in the ankle or foot that allow humans to walk on two legs"; of the 110,000 gene enhancer sequences identified in the human genome, HACNS1 has undergone the most change during the evolution of humans following the split with the ancestors of chimpanzees.
Ultra-conserved element (UCE): region of DNA that is identical in at least two different species
UCbase: 100% identity among human, mouse and rat = 481 UCEs have been identified in the human genome longer than 200 nt
Human genetic clustering: ~85% of genetic variation is found within groups, ~6–10% between groups within the same continent and ~6–10% is found between continental groups (e.g. Human Genome Project states: "two random individuals from any one group are almost as different [genetically] as any two random individuals from the entire world.", 85% vs 15%). The more markers are used the better one can cluster the individuals into "subgroups", but these "subgroups" depend a bit on the classification/clustering methods used. Heavy statistics and models.
"Human genetic diversity: Lewontin's fallacy" (scientific paper)
Template:Human genetics:
Human genetic engineering
Human genetic clustering
Human genetic variation
Human geneology:
Human Y-chromosome DNA haplogroup: male line (father to son), so the longer ago in history, the smaller the portion of contribution (besides Y chromosome, which has its own doubts), i.e. 1/2 for father, 1/4 for paternal grandfather, for 10 generations back, (\frac{1}{2})^{10}
Template:Y-chromosome haplogroups by populations:
Y-DNA haplogroups in European populations
Category:Genetic genealogy projects
Human Genome Diversity Project (HGDP): was started by Stanford University's Morrison Institute and a collaboration of scientists around the world; many years of work by Luigi Cavalli-Sforza. Some NGOs, human rights organizations, indigenious communities objected to the project; concern about misuse of the gathered data (also: insurance and genetic sequencing).
Genographic Project: Indigenous Peoples Council on Biocolonialism (IPCB) protested against the project because of the connections with HGDP
List of haplogroups of historical and famous figures
Template:Human group differences
Genetic studies on Jews
Sequencing and interpretation of human genomes[edit]
Human Genome Organisation (HUGO): Human Genome Project (HGP); HGNC is the hugest subgroup of HUGO (bio nomenclature).
Knome: sells human whole genome and exome (exons) analysis and sequencing services to researchers and consumers.
1000 Genomes Project: launched 2008.01; international research effort to establish by far the most detailed catalogue of human genetic variation. Scientists plan to sequence the genomes of at least 1000 anonymous participants from a number of different ethnic groups till 2012[???], using newly developed technologies which are faster and less expensive. In late 2010: production phase with a target - upwards of 2000 individuals. UK (Wellcome Trust Sanger Institute), PRC (Beijing Genomics Institute, Shenzhen), USA (NHGRI).
Personal Genome Project: long term, large cohort study which aims to sequence and publicize the complete genomes and medical records of 100,000 volunteers, in order to enable research into personalized medicine.
Hendrikje van Andel-Schipper#Genome: senility research; old-age disease research (cardiovascular; various dementias)
Beijing Genomics Institute (BGI): one of the world’s premier genome sequencing centers

Sequencing DNA, RNA[edit]

DNA sequencing:
gel (microfluidic: :Sanger method and its comparison to other methods in 2009 Feb.)
pyrosequencing (454)
Polony sequencing: multiplex sequencing technique
Ion semiconductor sequencing (aka: ion torrent sequencing, pH-mediated sequencing, silicon sequencing, or semiconductor sequencing): detection of hydrogen ions that are released during the polymerization of DNA. Released Feb., 2010.
future: sequencing by hybridization, mass spectrometry, electron microscopy, AFM, ...
RNA[edit]
Wikipedia:WikiProject RNA
Wikipedia:Wikiproject RNA/external links: number of good databases for RNA that might be consulted for further information: Rfam, The noncoding RNA database, RNAdb: mammalian noncoding RNA database, fRNAdb: functional RNA database, miRBase: microRNA database, methylation guide snoRNA database, snoRNAbase: human H/ACA and C/D box snoRNA database, tRNA database, tmRDB: database of tmRNA sequences, ...

q.v. RNA containing complexes; RNA processing

Gender, sex, reproductive biology[edit]

Sex-determination system (sex chromosomes (gonosomes)): biological system that determines the development of sexual characteristics in an organism. Determination genetically is generally through chromosome combinations of XY, ZW, XO, ZO, or haplodiploid.
Heterogametic sex (digametic sex): sex of a species in which the sex chromosomes are not the same, e.g. human and Drosophila males have an X and a Y sex chromosome, while birds' and some reptiles' females have one Z and one W chromomose. The opposite is referred to as the homogametic sex (females for humans and Drosophila, while males for birds and some reptiles).
Reproductive isolation (mechanisms of reproductive isolation; hybridization barriers): collection of mechanisms, behaviors and physiological processes that prevent the members of two different species that cross or mate from producing offspring, or which ensure that any offspring that may be produced is not fertile; maintain the integrity of a species over time, reducing or directly impeding gene flow between individuals of different species, allowing the conservation of each species’ characteristics.

Bioengineering[edit]

Biological engineering (biotechnological engineering, engineering (including biological systems engineering))
BioBrick standard biological parts: DNA sequences of defined structure and function; they share a common interface and are designed to be composed and incorporated into living cells such as E. coli to construct new biological systems.
International Genetically Engineered Machine (iGEM) competition: worldwide Synthetic Biology competition aimed at undergraduate university students.

Population[edit]

Topics in population genetics (Template:Popgen):
Founder effect

Genetic diseases[edit]

Rare disease (orphan disease): a window to human mutations (mainly) and some extremely rare pathogens (seldom); lots of discoveries into human biology and genetics.
Finnish disease heritage
Organizations:
European Organization for Rare Diseases (EURORDIS, non-governmental patient-driven alliance of patient organizations and individuals active in the field of rare diseases)
National Organization for Rare Disorders (NORD, American non-profit organization aiming to provide support individuals with rare diseases)
Orphan drug: politics and economics of rare disease treatment
Gene therapy[edit]
Jesse Gelsinger (1981.06.18-1999.09.17): first person publicly identified as having died in a clinical trial for gene therapy. 1999.09.13 he was injected with adenoviral vector carrying corrected gene to test the safety of the procedure; died 4d. later apparently having suffered a massive immune response.
Alipogene tiparvovec (Glybera): gene therapy treatment that compensates for lipoprotein lipase deficiency (LPLD), which can cause severe pancreatitis. In 2012.07, the European Medicines Agency recommended it for approval, the first recommendation for a gene therapy treatment in either Europe or US.

Politics[edit]

The Race Question: UNESCO statement issued on 18 July 1950 following World War II. No "race", only "ethnic groups". In the current scientific light: "ethnic groups" as everything non-hereditary (culture, language, religion...) while human genetic groups (in the older times called "races") as everything hereditary (genes and from genotypes coming phenotypes).

Cell biology[edit]

Category:Cell biology
Category:Cell anatomy
Subcellular localization: eukaryotes vs prokaryotes
Protein subcellular localization prediction
Pseudo amino acid composition
Low-frequency collective motion in proteins and DNA: solitons

Cell nucleus[edit]

q.v. RNA processing; Spliceosome, splicing

Template:Nucleus
Cell nucleus: membrane-enclosed organelle found in eukaryotic cells; contains most of the cell's genetic material, organized as multiple long linear DNA molecules in complex with a large variety of proteins, such as histones, to form chromosomes. Nuclear envelope; Nuclear pores; Nuclear lamina; Chromosomes; subnuclear bodies: Nucleolus; Cajal bodies and gems; RAFA and PTF domains; PML bodies; Paraspeckles; Splicing speckles (At the fluorescence-microscope level they appear as irregular, punctate structures, which vary in size and shape, and when examined by electron microscopy they are seen as clusters of interchromatin granules). Nuclear transport; Assembly and disassembly. Anucleated and multinucleated cells.
Cajal body (CB): spherical sub-organelles of 0.3-1.0 µm in diameter found in the nucleus of proliferative cells like embryonic cells and tumor cells, or metabolically active cells like neurons (hence the finding by Santiago Ramón y Cajal in 1903: nucleolar accessory bodies); largely consisting of proteins and RNA. Rediscovered by electron microscopists and named coiled bodies, according to their appearance as coiled threads on EM images, and later renamed after their discoverer. Marker protein: p80/coilin. Implicated in RNA-related metabolic processes such as snRNP biogenesis, maturation and recycling, histone mRNA processing and telomere maintenance
Nuclear dots ("Nuclear bodies", "nuclear domains", "PML bodies")
Paraspeckle: irregularly shaped, 0.2-1 μm in size, found in the nucleus' interchromatin space; "para" is short for parallel and the "speckle" refers to the splicing speckles to which they are always in close proximity; function not known [2013], but they may localize proteins in the nucleus; in the absence of RNA polymerase II transcription the paraspeckle disappears

Developmental bio[edit]

X-inactivation: random in placental mammals, inactivation in marsupials applies exclusively to the paternally derived X chromosome
Anencephaly: cephalic disorder that results from a neural tube defect that occurs when the rostral (head) end of the neural tube fails to close, usually between the 23rd and 26th day of conception, resulting in the absence of a major portion of the brain, skull, and scalp. With very few exceptions, most babies with this disorder do not survive.
Baby K (1992-1995): was an anencephalic baby who became the center of a major U.S. court case and a debate among bioethicists; kept alive much longer than most anencephalic babies.

Neuroscience[edit]

Neuroscience Information Framework (NIF): repository of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/genomic resources and provides many authoritative links throughout the neuroscience portal of wikipedia.
NeuroLex: dynamic lexicon of neuroscience concepts; structured as a semantic wiki, using Semantic MediaWiki

Soliton vs Hodgin-Huxley model:

Hodgkin–Huxley model: mathematical model (a type of scientific model) that describes how action potentials in neurons are initiated and propagated. It is a set of nonlinear ordinary differential equations that approximates the electrical characteristics of excitable cells such as neurons and cardiac myocytes.
Soliton model: proposes that the signals travel along the cell's membrane in the form of certain kinds of sound (or density) pulses known as solitons.
Mirror test: animals that have passed the mirror test: mainly mammals: all great apes, 3*Gibbons, Bottlenose dolphins, orcas, elephants, and:
European Magpie (Pica pica): the most intelligent bird, one of the most intelligent animals. The pairs are monogamous, and remain together for the duration of their lives. Should one of the two die, the widow or widower will find a new partner from the stock of yearlings. Possible subspieces or neighboring species: Korean Magpie (Asian, Chinese Magpie), Yellow-billed Magpie (California), Black-billed Magpie (N. America)
Encephalization quotient (EQ, encephalization level): measure of relative brain size defined as the ratio between actual brain mass and predicted brain mass for an animal of a given size, which is hypothesized to be a rough estimate of the intelligence of the animal. More refined than raw brain-to-body mass ratio by taking allometric effects. Ew(brain) = 0.12w(body)2/3. EQ(human)=7.44, EQ(tucuxi dolphin)=4.56, EQ(bottlenose dolphin)=4.14, EQ(chimp)=2.49, EQ(dog)=1.17, EQ(cat)=1.00, EQ(mouse)=0.5
Deep brain stimulation (DBS): surgical treatment involving the implantation of a medical device called a brain pacemaker, which sends electrical impulses to specific parts of the brain. Possible therapeutic benefits for chronic pain, Parkinson's, tremor, dystonia; sexual arousal; tested on patients with post-tramatic coma; could change behavior drastically. Despite the long history of DBS, its underlying principles and mechanisms are still not clear.
Wirehead (science fiction): when fiction meets DBS.
Behavioral contagion: propensity for certain behavior exhibited by one person to be copied by others either in the vicinity of the original user, or who have been exposed to media coverage describing the behavior of the original actor.
Neural top down control of physiology: direct regulation by the brain of physiological functions (in addition to smooth muscle and glandular ones). Regulation occurs through the sympathetic and parasympathetic system (the autonomic nervous system), and their direct innervation of body organs and tissues that starts in the brainstem. There is also a noninnervation hormonal control through the hypothalamus and pituitary (HPA). These lower brain areas are under control of cerebral cortex ones. Pavlovian conditioning shows that brain control over basic cell level physiological function can be learnt.
Mind uploading (whole brain emulation, mind transfer): hypothetical process of transferring or copying a conscious mind from a brain to a non-biological substrate by scanning and mapping a biological brain in detail and copying its state into a computer system or another computational device. The computer would have to run a simulation model so faithful to the original that it would behave in essentially the same way as the original brain, or for all practical purposes, indistinguishably.
Blue Brain Project (BBP): attempt to create a synthetic brain by reverse-engineering the mammalian brain down to the molecular level. Simulation of rat neocortical column (2 mm tall, 0.5 mm in diameter, 108 synapses) was completed in 2006.12.
Human Brain Project (HBP): research project which aims to simulate (with supercomputers) and better understand the human brain. EU gave >1 bln € to this project.

Neurotransmitters[edit]

Category:Neurotransmitters
Monoamine neurotransmitter: contain one amino group that is connected to an aromatic ring by a two-carbon chain (-CH2-CH2-); derived from aromatic amino acids like phenylalanine, tyrosine, tryptophan, and the thyroid hormones by aromatic amino acid decarboxylase enzymes; function of monoamine is not clear but it is thought to trigger crucial components such as emotion, arousal, and cognition; drugs used to increase the effect of monoamine may be used to treat patients with psychiatric disorders, including depression, anxiety, and schizophrenia.

Vision and brain[edit]

Blindsight: defined as the ability of people who are cortically blind due to lesions in their striate cortex, also known as primary visual cortex or V1, to respond to visual stimuli that they do not consciously see. There is signal processing all the way from the retinal ganglions to the visual cortex. Damage to visual cortex only leaves the other signal processing intact and the cortically blind can "see". Exact mechanism unknown.
Optical illusions[edit]
Spinning Dancer

Intelligence, IQ[edit]

Heritability of IQ: IQ is a polygenic trait, however, certain single gene genetic disorders can severely affect intelligence, with phenylketonuria as an example. Estimates of heritability vary from below 0.5 to as high as 0.9.
Environment and intelligence: environmental influences: family, peer group, education, training and interventions, environmental enrichment; bio influences: nutrition, exposure to toxic chemicals and other substances (lead, Fetal alcohol spectrum disorder), birth complications (perinatal factors); development of genius; training: musical (Mozart effect: listening to classical music boosts IQ scores in specific area), chess (boosts math and comprehension performance).
''g'' factor ("general factor"): construct developed in psychometric investigations of cognitive abilities. g is highly heritable; g's biological correlates: brain size.
Genetic Studies of Genius (Terman Study of the Gifted): Terman: "At any rate, we have seen that intellect and achievement are far from perfectly correlated". Longitudinal study begun in 1921.
Flynn effect: substantial and long-sustained increase in intelligence test scores measured in many parts of the world.
Fertility and intelligence: Other correlates of IQ include income and educational attainment, which are also inversely correlated with fertility rate, and are to some degree heritable.

Sleep[edit]

Category:Sleep
Category:Sleep physiology
Sleep (non-human): nematode C. elegans is the most primitive organism in which sleep-like states have been observed. Sleep in fish is not extensively studied; EEG pattern in reptilian sleep differs from what is seen in mammals and other animals; significant similarities between sleep in birds and sleep in mammals, which is one of the reasons for the idea that sleep in higher animals with its division into REM and NREM sleep has evolved together with warm-bloodedness (opinions partly differ about sleep in migratory birds); mammals: daily need for sleep is highest in carnivores, lower in omnivores and lowest in herbivores. Unihemispheric sleep: birds, some aquatic mammals, maybe certain species of lizards. Eared seals and whales show unihemispheric sleep; earless seals sleep bihemispherically like most mammals.
Torpor: umbrella-term used to categorize a state of regulated metabolic suppression in animals, typically to levels below what are normally essentially the minimum, so-called, basal metabolic rate (BMR); this does not exclude the possibility that torpor can be triggered from an elevated metabolic position and may terminate before reaching below BMR (e.g. diving).

Model organisms[edit]

Template:Model Organisms:

Schizosaccharomyces pombe (fission yeast) & Saccharomyces cerevisiae (budding yeast):
Schizosaccharomyces pombe#Comparison with budding yeast (Saccharomyces cerevisiae)
  • diverged 300-600 mya
  • cerevisiae: 250 introns; pombe: ~5000
  • cerevisiae: 16 chromosomes; pombe: 3
  • cerevisiae: often diploid; pombe: often haploid
  • cerevisiae: in G1 phase (cell cycle) for an extended period (G1-S transition tightly controlled); pombe: in G2 (G2-M transition tightly controlled)
  • both share genes with higher eukaryotes that they do not share with each other: pombe: RNAi machinery genes; cerevisiae has greatly simplified heterochromatin compared to pombe; cerevisiae has well-developed peroxisomes, while pombe does not
  • cerevisiae: small point centromere of 125 bp, and sequence-defined replication origins of about the same size; pombe: large, repetitive centromeres (40–100 kb) more similar to mammalian centromeres, and degenerate replication origins of at least 1kb
Saccharomyces Genome Database

Human medicine and human biology[edit]

All drugs prevent something, but also bring something; everything is drug: even food and water (too much water can kill you! [drowning]):
Triple-negative breast cancer#Oral contraceptive a risk factor: any breast cancer that does not express the genes for estrogen receptor (ER), progesterone receptor (PR) or Her2/neu
Template:Reproductive physiology (Human physiology and endocrinology of sexual reproduction)
Template:Menstrual cycle
Ovarian follicle atresia
Menopause:
Maternal age effect
Grandmother hypothesis
Template:Pregnancy
Prenatal:
Procedures:
Chorionic villus sampling (CVS): determine chromosomal or genetic disorders in the fetus; usually with FISH or PCR.
Amniocentesis (amniotic fluid test, AFT): chromosomal abnormalities and fetal infections, and also used for Sex Determination in which a small amount of amniotic fluid, which contains fetal tissues, is sampled from the amnion or amniotic sac surrounding a developing fetus, and the fetal DNA is examined for genetic abnormalities.
Template:Medicinal herbs & fungi (Medicinal herbs and fungi)
Template:Traditional Medicine
Alternative medicine
Traditional Chinese medicine
Chinese classic herbal formula
Kampo: Japanese study and adaptation of Traditional Chinese medicine
Kampo herb list
Kampo list
Patent medicine: medical compounds of questionable effectiveness sold under a variety of names and labels. E.g. "snake oil".
Information-theoretic death: destruction of the information within a human brain (or any cognitive structure capable of constituting a person) to such an extent that recovery of the original person is theoretically impossible by any physical means; distinct from clinical death and legal death.
Placebo: simulated or otherwise medically ineffectual treatment for a disease or other medical condition intended to deceive the recipient. Sometimes patients given a placebo treatment will have a perceived or actual improvement in a medical condition, a phenomenon commonly called the placebo effect. Expectancy and classical conditioning; placebo and brain → brain and body
Program in Placebo Studies (Beth Israel Deaconess Medical Center and the Harvard Medical School; 2011-): placebo response and the impact of medical ritual, the patient-physician relationship and the power of imagination, hope, trust, persuasion, compassion and empathic witnessing in the healing process.
Institute for Health Metrics and Evaluation (IHME): global health statistics and evaluation; core grant funding from the Bill & Melinda Gates Foundation and the state of Washington.
List of causes of death by rate

Human (mammal?) hormones[edit]

Category:Hormones
Category:Hormones by functional axis
Category:Hormones of the hypothalamus-pituitary axis
Category:Hormones of the hypothalamus-pituitary-adrenal axis
Category:Hormones of the hypothalamus-pituitary-gonad axis
Category:Hormones of the hypothalamus-pituitary-thyroid axis
Category:Hormones of the somatotropic axis: Growth-hormone-releasing hormone, Somatostatin, Tesamorelin
Category:Human homeostasis
Endocrine system
Hypothalamic–pituitary–adrenal axis (HPA or HTPA axis; limbic-hypothalamic-pituitary-adrenal axis (LHPA axis), hypothalamic-pituitary-adrenal-gonadotropic axis): Stress and disease: mood disorders.
Hypothalamic–pituitary–gonadal axis (HPG axis): Function: Reproduction, Life cycle, Sexual dimorphism and behavior
Hypothalamic–pituitary–thyroid axis (HPT axis)
Thyroid hormone: triiodothyronine (T3) and thyroxine (T4); tyrosine-based hormones produced by the thyroid gland that are primarily responsible for regulation of metabolism; iodine is necessary for the production of T3 and T4; T4:T3=20:1 released into the blood; T4 → T3 (by deiodinases (5'-iodinase) inside the cells), T3 is 3-4× more potent than T4. These are further processed by decarboxylation and deiodination to produce iodothyronamine (T1a) and thyronamine (T0a); all three isoforms of the deiodinases are selenium-containing enzymes, thus dietary selenium is essential for T3 production.
Renin–angiotensin system (RAS; renin-angiotensin-aldosterone system (RAAS)): hormone system that regulates blood pressure and water (fluid) balance.

Medicinal ethics and law[edit]

Futile medical care: continued provision of medical care or treatment to a patient when there is no reasonable hope of a cure or benefit. One could say that it is impossible to reach a firm definition of futile medical care, because this would depend upon universal agreement about the point at which there is no further benefit to intervention, and different involved parties may always disagree about the amount and type of benefit under discussion. For instance, a cancer patient may be willing to undergo yet more chemotherapy with a very expensive medication for the benefit of a few weeks of life, while medical staff, the insurance company, and close relatives may all feel otherwise, for different reasons.
Baby Doe Law (Baby Doe Amendment; 1984): set forth specific criteria and guidelines for the treatment of seriously ill and/or disabled newborns, regardless of the wishes of the parents.
Template:Medical ethics cases:
David Vetter ("David, the bubble boy"; 1971.09.21-1984.02.22): severe combined immunodeficiency; a few months after unmatched bone marrow transplant from his sister Katherine, he died from Burkitt's lymphoma due to the dormant Epstein-Barr virus in the donor bone marrow.

Surgery[edit]

Invasiveness of surgical procedures
The future surgeries are the least invasive, e.g.:
High-intensity focused ultrasound (HIFU, or sometimes FUS): highly precise medical procedure using high-intensity focused ultrasound to heat and destroy pathogenic tissue rapidly through ablation. Clinical HIFU is image-guided: Magnetic Resonance-guided Focused Ultrasound (MRgHIFU or MRgFUS); Ultrasound-guided Focused Ultrasound (USgFUS). Limited by the precision of imaging (MRI or US), by the precision of HIFU lenses and how HIFU travels and gets distorted in the tissues, and by the computational models how HIFU travels from the source to the destination (e.g. breathing/moving patient).

Medical research[edit]

Category:Medical research
Category:Animal testing
Great ape research ban: severe restrictions on the use of non-human great apes in research, is currently in place in NL, NZ, UK, SE, DE, AT.

Brave New World[edit]

Intracytoplasmic sperm injection ++
Designer baby
Reprogenetics
Human enhancement +
Transhumanism#Dehumanization (Frankenstein argument) +

Evolution[edit]

Evolution as a process during which the fidelity of replication increased several folds of magnitude (RNA world, RNP world / DNA world, protein (the machines, hardware) & DNA (the code, software) world; next step (non-bio): human literature → computer programs & digital storage (copying errors are extremely small compared to human genome replication in digital world))

Speed of reactions catalyzed by these molecules (from the slowest to the fastest): RNA (RNA world) → RNP (early protein + RNA world) → protein (current world of proteins as machines, DNA as storage, mRNA as intermediate remaining as relic & more from the previous "ages")

Age-of-Man-wiki.jpg
Modern evolutionary synthesis: 20th c. union of ideas from several biological specialties which provides a widely accepted account of evolution
Evolution: The Modern Synthesis (1942): book by Julian Huxley, one of the most important books of the modern evolutionary synthesis.
Evolution as theory and fact
Punctuated equilibrium: is it a tiny part of the modern evolution synthesis or a huge one? What could tiny/huge mean in terms of genetics and evo-devo?
Arsenic-based life
GFAJ-1: isolated from the shore of Mono Lake, California, USA {highest natural concentrations of arsenic in the world (200 μM)}. On the tree of life, according to the results of 16S rRNA sequencing, the rod-shaped GFAJ-1 nestles in among other salt-loving bacteria in the family Halomonadaceae. When starved of phosphorus, GFAJ-1 can instead incorporate arsenic into its metabolites and macromolecules and continue growing.

Human evolution and extant "cousins"[edit]

Category:Human evolution
Template:Apes:
Neanderthal Genome Project
Chimpanzee genome project
Genes of humans vs the other apes:
SRGAP2: protein twice duplicated in human genome as compared to chimps and other extant apes. First duplication 3.4 mya, next 2.4 mya (this duplication allows neurons to migrated faster in the human brain).
Baculum: penis bone; absent in humans but present in nearest extant relative the chimpanzee
Population bottleneck: Humans (Toba; 'long bottleneck')
Recent African origin of modern humans: supposition - archaic Homo sapiens evolved to anatomically modern humans solely in Africa, between 200 ka and 150 ka, that members of one branch of Homo sapiens left Africa by between 125 ka and 60 ka, and that over time these humans replaced earlier human populations such as Neanderthals and Homo erectus without interbreeding with them.
Toba catastrophe theory: between 69 ka and 77 ka at Lake Toba (Sumatra, Indonesia); supposed bottleneck in human evolution
Multiregional origin of modern humans: less probable explanation (esp. considering Toba), but maybe the synthesis of both (with majority of modern humans coming from Africa 125 ka - 60 ka, while very small amount survived Toba from the migrations as far back as 2Ma?) is also possible
Template:Human Evolution
Anatomically modern humans vs Archaic ''Homo sapiens'' (includes Homo heidelbergensis, Homo rhodesiensis, Homo neanderthalensis and sometimes Homo antecessor):
Omo remains: 198 ± 14 ka (geologic layer below the fossil), 104 ± 7 ka (geologic layer above the fossil)
Homo sapiens idaltu: ~160 ka
Skhul and Qafzeh hominids: 80 - 120 ka; a few Neanderthal features, but huge resemblance to modern humans
Denisova hominin: ~41 ka mtDNA and genome sequenced; between 4% and 6% of the genome of Melanesians derives from a Denisovan population; mtDNA of the Denisova hominin is distinct from the mtDNAs of Neanderthals and modern humans
Homo erectus soloensis, aka Solo Man: While most subspecies of Homo erectus disappeared from the fossil record roughly 400,000 years ago, H. e. soloensis persisted up until 50,000 years ago in regions of Java and was possibly absorbed by a local Homo sapiens population at the time of its decline.
Researchers: Svante Pääbo

Evolutionary biology, chemistry[edit]

Category:Biological evolution
Category:Evolutionary biology {also q.v. Category:Phylogenetics}
Homology (biology): relationship between a pair of structures, or genes, due to having shared ancestry. Anatomical homology. Sequence homology: Orthology - homologous sequences are orthologous if they are inferred to be descended from the same ancestral sequence separated by a speciation event: when a species diverges into two separate species, the copies of a single gene in the two resulting species are said to be orthologous (orthologs, or orthologous genes); Paralogy - homologous sequences are paralogous if they were created by a duplication event within the genome. Homology between sexes and forms.
Deep homology: growth and differentiation processes are governed by genetic mechanisms that are homologous and deeply conserved across a wide range of species.
Abiogenesis (biopoesis): "how biological life arises from inorganic matter through natural processes, and the method by which life on Earth arose". Early life on earth: at high temperature(?), at high pressure (?), at which concentrations of simple "bio-molecules"? "Primordial soup": Miller–Urey experiment (nowadays: reducing atmosphere, monomer formation); deep sea vent theory; Fox's experiments; Eigen's hypothesis: self-replicating hypercycle; iron–sulfur world theory; radioactive beach hypothesis; RNA world hypothesis...
Last universal ancestor (LUA; last universal common ancestor (LUCA), cenancestor): most recent organism from which all organisms now living on Earth descend; MRCA of all current life on Earth. LUA is estimated to have lived some 3.5-3.8 bya. LUA was a small, single-cell organism; had a cell wall and a ring-shaped coil of DNA floating freely within the cell, like modern bacteria; genetic code was based on DNA; genetic code was expressed via RNA intermediates, which were single-stranded; genetic code was expressed into proteins; proteins were assembled from free amino acids by translation of an mRNA by ribosomes, tRNA and a group of related proteins; ATP was used as an energy intermediate; several hundred protein enzymes which catalyzed chemical reactions that extract energy from fats, sugars, and amino acids, and that synthesize fats, sugars, amino acids, and nucleic acid bases using arbitrary chemical pathways; inside the cell, the concentration of sodium was lower, and potassium was higher, than outside; cell multiplied by duplicating all its contents followed by cellular division.
Evolutionary arms race: prey vs predator, parasite vs host, within the species.
Sexual conflict (sexual antagonism):
Penis fencing: flatworms
Traumatic insemination (hypodermic insemination): bed bugs
Sexual coercion
Sexual cannibalism: primarily by members of arachnid orders as well as several insect orders (mantis).
Love dart (gypsobelum)
Error threshold (evolution): "mutation process places a limit on the number of digits a molecule may have. If a molecule exceeds this critical size, the effect of the mutations become overwhelming and a runaway mutation process will destroy the information in subsequent generations of the molecule." (Eigen, 1971)

Zoology[edit]

Animals[edit]

Humans are animals too, but q.v. Human medicine and human biology.

Animal sexual behaviour:
Monogamy: social monogamy (90% of bird species are socially monogamous) vs sexual monogamy vs genetic monogamy (very few species show 100% genetic monogamy; out of 180 different species of socially monogamous songbirds, only 10% are sexually monogamous).
Polygamy: polygyny: when a new alpha male arrives, the current embryos and the young are killed/aborted in one of several ways: competitive infanticide (lions, hippopotamuses, some monkeys), harassment to miscarriage (horses, baboons), pheromone based spontaneous abortion (some rodents (e.g. mice): Bruce-Parkes effect).
Promiscuity: chimpanzees and bonobos.
Against Nature?

Ecology[edit]

Buffer strip: area of land maintained in permanent vegetation that helps to control air, soil, and water quality, along with other environmental problems, dealing primarily on land that is used in agriculture. Buffer strips trap sediment, and enhance filtration of nutrients and pesticides by slowing down runoff that could enter the local surface waters.
Riparian buffer: vegetated area near a stream, usually forested, which helps shade and partially protect a stream from the impact of adjacent land uses. It plays a key role in increasing water quality in associated streams, rivers, and lakes, thus providing environmental benefits.
Windbreak

Microbiology[edit]

Category:Microbiology
Category:Archaea
Category:Bacteriology
Category:Microorganisms
Category:Phytopathology
Category:Prokaryotes
Category:Virology

Bacteriology, bacteria[edit]

Mycobacterium: aerobic and nonmotile bacteria (except: Mycobacterium marinum, which has been shown to be motile within macrophages); characteristically acid-alcohol-fast; lack of an outer cell membrane; all share a characteristic cell wall, thicker than in many other bacteria, which is hydrophobic, waxy, and rich in mycolic acids. Adapt readily to growth on very simple substrates, using ammonia or amino acids as nitrogen sources and glycerol as a carbon source in the presence of mineral salts. Some species can be very difficult to culture, have extremely long reproductive cycles — M. leprae, may take more than 20 days to proceed through one division cycle; availability of genetic manipulation techniques still lags far behind that of other bacterial species
Tuberculosis: common, and in many cases lethal, infectious disease caused by various strains of mycobacteria, usually Mycobacterium tuberculosis; typically attacks the lungs, but can also affect other parts of the body; most infections are asymptomatic and latent, but about one in ten latent infections eventually progresses to active disease which, if left untreated, kills more than 50% of those so infected; classic symptoms of active TB infection are a chronic cough with blood-tinged sputum, fever, night sweats, and weight loss (the latter giving rise to the formerly prevalent term "consumption"); multiple drug-resistant tuberculosis (MDR-TB) infections. 1/3rd of the world's population is thought to have been infected with M. tuberculosis, with new infections occurring in about 1% of the population each year. ~80% of the population in many Asian and African countries test positive in tuberculin tests, while only 5–10% of USA population tests positive. More people in the developing world contract tuberculosis because of compromised immunity, largely due to high rates of HIV infection and the corresponding development of AIDS.
Mycobacterium tuberculosis: most recent common ancestor of the M. tuberculosis complex evolved ~40,000 years ago.
Multi-drug-resistant tuberculosis
Extensively drug-resistant tuberculosis
Totally drug-resistant tuberculosis
Lipoarabinomannan (LAM): glycolipid, and a virulence factor associated with M. tuberculosis; inactivate macrophages and scavenge oxidative radicals
Mycolic acid: long fatty acids found in the cell walls of Mycobacterium sp.; major component of the cell wall
Leprosy (Hansen's disease (HD)): left untreated, leprosy can be progressive, causing permanent damage to the skin, nerves, limbs and eyes. Contrary to folklore, leprosy does not cause body parts to fall off, although they can become numb or diseased as a result of secondary infections; these occur as a result of the body's defenses being compromised by the primary disease
Mycobacterium leprae (Hansen’s coccus spirilly): intracellular, pleomorphic, acid-fast bacterium; culture takes several weeks to mature; obligate intracellular parasite; longest doubling time of all known bacteria, and has thwarted every effort at culture in the laboratory
Mycobacterium lepromatosis: discovered in 2008; species is distinct from Mycobacterium leprae; causes diffuse Lepromatous leprosy (DLL)
Leprosy stigma
Leper colony (leprosarium, lazar house): in 2001, government-run leper colonies in Japan came under judicial scrutiny, leading to the determination that the Japanese government had mistreated the patients, and the District Court ordered Japan to pay compensation to former patients
National Hansen's Disease Museum (Japan)
Bacterial microcompartment
Carboxysome: bacterial microcompartments that contain enzymes involved in carbon fixation; made of polyhedral protein shells about 80 to 140 nm in diameter; thought to concentrate carbon dioxide to overcome the inefficiency of RuBisCO; found in all cyanobacteria and many chemotrophic bacteria that fix carbon dioxide

Borderline life[edit]

Category:Borderline life
Category:Prions
Ultramicrobacteria (0.3-0.2 µm): many, if not all, of these small bacteria are dormant forms of larger cells that allow survival under starvation conditions
Nanobe: tiny filamental structure first found in some rocks and sediments.
Template:Subviral agents
Viroid
Virusoid
Virophage
Sputnik virophage
Prion: in the Scrapie form (PrPSc) is an infectious agent composed of protein in a misfolded form; the central idea of the Prion Hypothesis, which remains debated. This would be in contrast to all other known infectious agents (virus/bacteria/fungus/parasite) which must contain nucleic acids (either DNA, RNA, or both).
PRNP (Major prion protein; PrP): the only known example of a prion protein. In humans, it is encoded by the PRNP gene.

Virology[edit]

Non-cellular life: term presumes the phylogenetic scientific classification of viruses as lifeforms
Viral evolution: many viruses, in particular RNA viruses, have short generation times and relatively high mutation rates (on the order of one point mutation or more per genome per round of replication for RNA viruses). Studies at the molecular level have revealed relationships between viruses infecting organisms from each of the three domains of life, and viral proteins that pre-date the divergence of life and thus the last universal common ancestor; genomes of most vertebrate species contain hundreds to thousands of sequences derived from ancient retroviruses
Paleovirology (viral fossils): regions of genomes that originate from ancient germline integration of viral genetic material
Endogenous viral element (EVE): DNA sequence derived from a virus, and present within the germline of a non-viral organism; may be entire viral genomes (proviruses), or fragments of viral genomes.
Endogenous retrovirus (ERV; HERV: Human Endogenous Retrovirus): can play an active role in shaping genomes; long terminal repeat (LTR) sequences that flank ERV genomes frequently act as alternate promoters and enhancers, often contributing to the transcriptome by producing tissue-specific variants. 64% of known LTR-promoted transcription variants are expressed in reproductive tissues. Retroelements in general are largely prevalent in rapidly evolving, mammal-specific gene families whose function is largely related to the response to stress and external stimuli: class I & class II MHC genes. Majority of ERVs that occur in vertebrate genomes are ancient, inactivated by mutation, and have reached genetic fixation in their host species. HERVs comprise: 98,000 ERV elements; fragments make up nearly 8%; no HERVs capable of replication had been identified [2005], containing major deletions or nonsense mutations. HERV-K (HML2) family of viruses has been active since the divergence of humans and chimpanzees; makes up less than 1% of HERV elements but is one of the most studied; has even been active in the past few hundred thousand years, e.g., some human individuals carry more copies of this virus family than others; two members of HERV-K(HML2), HERV-K106 and HERV-K116, were active in the last 800,000 years and that HERV-K106 may have infected modern humans 150kya; absence of known infectious members of the HERV-K(HML2) family, and the lack of elements with a full coding potential within the published human genome sequence, suggests to some that the family is less likely to be active at present
ERVWE1 (HERV-W_7q21.2 provirus ancestral Env polyprotein; syncytin; enverin): in humans, and other mammals, intact env proteins called syncytins are responsible for the formation and function of syncytiotrophoblasts; been suggested that the selection and fixation of these proteins for this function have played a critical role in the evolution of viviparity. Distinct, syncytin-like genes have been identified in primates, rodents, lagomorphs, carnivores, and ungulates, with integration dates ranging from 10-85 million years ago. Syncytins: retroviral envelope proteins have been exapted to produce a protein that is expressed in the placental syncytiotrophoblast, and is involved in fusion of the cytotrophoblast cells to form the syncytial layer of the placenta; syncytiotrophoblast: responsible for maintaining nutrient exchange and protecting the developing fetus from the mother's immune system
Virology: study of viruses; structure, classification and evolution, their ways to infect and exploit host cells for reproduction, their interaction with host organism physiology and immunity, the diseases they cause, the techniques to isolate and culture them, and their use in research and therapy; virology is considered to be a subfield of microbiology or of medicine.
RNA virus: mutation rate about 106 times faster than DNA viruses, "because viral RNA polymerases lack the proof-reading ability of DNA polymerases". ssRNA, sometimes dsRNA. Ribovirus: explicitly excludes retroviruses (DNA intermediate).

Very large viruses:

Mimivirus (genome: 1,181,404 bp)
Pandoravirus (genome: 1.9-2.5 Mb)
Megavirus (genome: 1,259,197 bp)
HIV[edit]

HIV-1:

HIV Rev response element (RRE): highly structured, ~350 nucleotide RNA segment present in the Env coding region of unspliced and partially spliced viral mRNAs; in the presence of the HIV-1 accessory protein Rev, HIV-1 mRNAs that contain the RRE can be exported from the nucleus to the cytoplasm for downstream events such as translation and virion packaging.

Classification, taxonomy, systematics[edit]

Category:Scientific classification
Category:Morphology
Category:Morphology (biology)
Category:Nomenclature
Category:Classification systems
Category:Taxonomy
Category:Borderline life
Category:Phylogenetics {also q.v. Category:Evolutionary biology}
Template:Taxonomic ranks: Main ones: Domain, Kingdom, Phylum/Division, Class, Order, Family, Tribe, Genus, Species.
Taxonomy (biology): academic discipline of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups; groups created through this process are referred to as taxa (singular taxon). Father of modern taxonomy: Carolus Linnaeus. Taxonomic descriptions; Classifying organisms: Phylogenetics and cladistics, Phenetics.
Biological classification (scientific classification in biology): method of taxonomy used to group and categorize organisms into groups such as genus or species
Systematics: study of the diversification of living forms, both past and present, and the relationships among living things through time; used to understand the evolutionary history of life on Earth.
Synonym (taxonomy): scientific name that applies to a taxon that (now) goes by a different scientific name, although zoologists use the term somewhat differently. Differences between zoology and botany.
Monophyly: "A satisfactory and comprehensive cladistic definition of a species or genus is in fact impossible, and reflects the impossibility of seamlessly impressing a gradualistic model of continual change over the 'quantum' Linnean model, where species have defined boundaries, and intermediaries between species cannot be accommodated". Then comes paraphyly, polyphyly... Quantum physics vs classical physics; (mathematical) logics vs complete & consistent
Gene Ontology
Structural Classification of Proteins: SCOP, manual classification
CATH: CATH Protein Structure Classification

Organizations and nomenclature:

International Code of Zoological Nomenclature (ICZN or ICZN Code): Principles: Principle of Binominal Nomenclature, Principle of Priority, Principle of Coordination, Principle of the First Reviser, Principle of Homonymy (name of each taxon must be unique), Principle of Typification.
International Commission on Zoological Nomenclature (ICZN)
ZooBank: open access website intended to be the official ICZN (Commission) registry of zoological nomenclature; proposed: 2005; live: 2006.08.10 :: 1.5 mln species. LSIDs
International Code of Nomenclature for algae, fungi, and plants (ICN; before 2011.07: International Code of Botanical Nomenclature (ICBN))

Encyclopedias:

ARKive: "promoting the conservation of the world's threatened species, through the power of wildlife imagery"; locating and gathering films, photographs and audio recordings of the world's species into a centralised digital archive
Wikispecies
Encyclopedia of Life (EOL; 2008.02.26-): free, online collaborative encyclopedia intended to document all of the 1.9 million living species known to science
Biodiversity Heritage Library (BHL; 2005-): consortium of natural history and botanical libraries that cooperate to digitize and make accessible the legacy literature of biodiversity held in their collections and to make that literature available for open access and responsible use as a part of a global “biodiversity commons". Since 2009, the BHL has expanded globally.
Integrated Taxonomic Information System (ITIS): partnership designed to provide consistent and reliable information on the taxonomy of biological species
Catalogue of Life: started in 2001.06 by ITIS and Species 2000; planned to become a comprehensive catalogue of all known species of organisms on Earth
Species 2000: federation of database organizations across the world

Biological classification[edit]

Species problem: mixture of difficult, related questions that often come up when biologists define the word "species". E.g. what works well for some organism (e.g., birds) will be useless for others (e.g., bacteria). When to recognize a new species, for example when new data indicate that one previously described species actually may include two or more separately evolving groups, each of which could possibly be recognized as a separate species. Jody Hey: "result of two conflicting motivations by biologists: 1) to categorize and identify organisms; 2) to understand the evolutionary processes that give rise to species".
Ring species: connected series of neighboring populations, each of which can interbreed with closely sited related populations, but for which there exist at least two "end" populations in the series, which are too distantly related to interbreed, though there is a potential gene flow between each "linked" species. Such non-breeding, though genetically connected, "end" populations may co-exist in the same region thus closing a "ring". Formally, the issue is that interfertile ("able to interbreed") is not a transitive relation – if A can breed with B, and B can breed with C, it does not follow that A can breed with C – and thus does not define an equivalence relation.
Template:Mammal hybrids: some are through natural and some through artificial insemination.
Template:Eukaryota:
Bikont ("two flagella")
Plants+HC+SAR megagroup (AH/SAR)
Plants+HC clade
Archaeplastida (Plantae sensu lato): Red algae (Rhodophyta), Glaucophytes (glaucocystophytes), Plantae
Hacrobia (cryptomonads-haptophytes assemblage; CCTH (standing for Cryptophyta, Centrohelida, Telonemia and Haptophyta); "Eukaryomonadae"): proposed monophyletic grouping of chromalveolata that are not included in the SAR supergroup
SAR supergroup
Halvaria
Heterokont (stramenopiles ("S")): major line of eukaryotes currently containing more than 100,000 known species: algae (kelp - diatoms (plankton)), oomycetes (generally parasitic)
Alveolate
Rhizaria: vary considerably in form, but for the most part they are amoeboids with filose, reticulose, or microtubule-supported pseudopods; many produce shells or skeletons, which may be quite complex in structure, and these make up the vast majority of protozoan fossils. Nearly all have mitochondria with tubular cristae.
Excavate (Excavata): major subgroup of unicellular eukaryotes: Discoba or JEH (Euglenozoa, Heterolobosea (Percolozoa), Jakobea), Metamonada or POD (Preaxostyla, Fornicata, Parabasalia)
Apusozoa: comprising several genera of flagellate protozoa; occur in soils and aquatic habitats, where they feed on bacteria; grouped together based on the presence of an organic shell or theca under the dorsal surface of the cell.
Unikont: have a single emergent flagellum, or are amoebae with no flagella
Amoebozoa: pseudopodia are characteristically blunt and finger-like, called lobopodia
Opisthokont (ὀπίσθιος (opísthios) = "rear, posterior" + κοντός (kontós) = "pole" i.e. "flagellum"; "Fungi/Metazoa group")
Holozoa: includes animals and their closest single-celled relatives, but excludes fungi
Mesomycetozoea (DRIP clade, or Ichthyosporea): small group of protists, mostly parasites of fish and other animals
Filozoa: monophyletic grouping; include animals along with their nearest unicellular relatives (those organisms which are more closely related to animals than to fungi or Mesomycetozoa)
Filasterea
Choanoflagellate
Metazoa or "Animalia"
Holomycota
Fungus (pl.: fungi or funguses)
Nucleariid: group of amoebae with filose pseudopods, known mostly from soils and freshwater; distinguished from the superficially similar vampyrellids mainly by having mitochondria with discoid cristae.
Unclassified
Animal (Animalia, Metazoa)
Parazoa {subkingdom}: Sponge (phylum=Porifera) Placozoa (phylum; "flat animals")

Primates[edit]

Primate (order Primates): with the exception of humans, who inhabit every continent, most primates live in tropical or subtropical regions of the Americas, Africa and Asia. Primates are characterized by large brains relative to other mammals, as well as an increased reliance on stereoscopic vision at the expense of smell, the dominant sensory system in most mammals. These features are more developed in monkeys and apes and noticeably less so in lorises and lemurs. Three-color vision has developed in some primates.
Haplorhini ("dry-nosed" primates): all lost the function of the terminal enzyme which manufactures vitamin C; haplorhine upper lip, which has replaced the ancestral rhinarium found in strepsirrhines, is not directly connected to their nose or gum, allowing a large range of facial expressions. Their brain to body ratio is significantly greater than the strepsirrhines, and their primary sense is vision.
Simian (infraorder Simiiformes, Anthropoidea): "higher primates"
Catarrhini: catarrhines (from Ancient Greek kata-, "down" and rhin-, "nose") have nostrils which face downwards; never have prehensile tails, and have flat fingernails and toenails, a tubular ectotympanic (ear bone), 2.1.2.32.1.2.3
Ape (Hominoidea; hominoids): Old World anthropoid mammals; apes are native to Africa and SE Asia; the largest primates and the orangutan, an ape, is the largest living arboreal animal. Except for gorillas and humans, hominoids are agile climbers of trees. Their diet is best described as vegetarian or omnivorous, consisting of leaves, nuts, seeds and fruits, including grass seeds, and in most cases other animals, either hunted or scavenged (or farmed in the case of humans), along with anything else available and easily digested.
Hominidae (great apes): 4 genera:
Chimpanzee (chimp; genus Pan): Common chimpanzee (Pan troglodytes; W. + C. Africa) + Bonobo (Pan paniscus; DR Congo)
Gorilla: DNA of gorillas is highly similar to that of a human, from 95–99% depending on what is counted, and they are the next closest living relatives to humans after the bonobo and common chimpanzee.
Homo: genus is estimated to be about 2.3 to 2.4 mya.
Orangutan (Pongo): Bornean orangutan (P. pygmaeus) and the Sumatran orangutan (P. abelii); both species had their genomes sequenced and they appear to have diverged around 400,000 years ago. Orangutans diverged from the rest of the great apes 15.7 to 19.3 mya; most arboreal of the great apes and spend most of their time in trees. Most solitary of the great apes, with social bonds occurring primarily between mothers and their dependent offspring, who stay together for the first two years
Old World monkey (Superfamily: Cercopithecoidea; Family: Cercopithecidae): most have tails (the family name means "tailed ape"); tails are never prehensile; distinction of Old World monkeys from apes depends on dentition (the number of teeth is the same in both, but they are shaped differently)

Tech and ethics[edit]

Technological singularity

Experiments, research[edit]

Category:Experiments
Category:Research
In vitro
In vivo
In silico: "performed on computer or via computer simulation"
Laboratory (lab)
Wet laboratory (wet lab)
Lab-on-a-chip

Software, internet, databases[edit]

Academic, research, science games:

NanoMission: serious game by PlayGen for Wellcome Trust and FEI in order to teach the player about the world of nanomedicine. Advergame

Software[edit]

Category:Computational chemistry software
Category:Bioinformatics software: PyMOL, UCSF Chimera
List of molecular graphics systems
Molecular design software: polymers, peptides, nucleic acids, solvents, partial charges, docking, optimization, molecular mechanics, quantum mechanics, Force Fields
Category:Molecular modelling software: PyMOL, UCSF Chimera, Coot (program)
List of software for nanostructures modeling: more material sciences
List of software for molecular mechanics modeling: MD simulations
Structural alignment software: structure-function
List of sequence alignment software
Biopython
b:Software Tools For Molecular Microscopy: molecular microscopy or cryo-electron microscopy (cryoEM)

Computations, CS, IT, bioinformatics (BioInfo), computational biology (Comp Bio)[edit]

Critical Assessment of Prediction of Interactions
Critical Assessment of Techniques for Protein Structure Prediction
PHYLIP ((PHYLogeny Inference Package)): free computational phylogenetics package of programs for inferring evolutionary trees (phylogenies).
Open Bioinformatics Foundation: BioPython
Bioconductor: based on statistical R programming language

Bioinformatics[edit]

Category:Bioinformatics
Category:Phylogenetics
Multiple sequence alignment (MSA): sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.
Clustal: widely used MSA program. ClustalW: command line; ClustalX: GUI; Clustal Omega: increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours (command line, protein-only).
Stockholm format: MSA format used by Pfam and Rfam to disseminate protein and RNA sequence alignments

molecular dynamics & molecular modeling (MD)[edit]

Finite element method, FEM, aka finite element analysis (FEA): numerical technique for finding approximate solutions of partial differential equations (PDE) as well as of integral equations.
Gaussian network model, also elastic network models (ENM): representation of a biological macromolecule as an elastic mass-and-spring network to study, understand, and characterize mechanical aspects of its long-scale dynamics.
Anisotropic Network Model: essentially an Elastic Network Model for the Cα atoms with a step function for the dependence of the force constants on the inter-particle distance.

Databases (DBs), classification: phys, chem, bio, ...[edit]

Biocurator (scientific curators, data curators or annotators): professional scientist who collects, annotates, and validates information that is disseminated by biological and model organism databases. Employ shared biomedical ontologies; consistent use of nomenclatures (e.g. HUGO, IUBMB: EC number). International Society for Biocuration (ISB) was founded in 2008.
Bioinformatic Harvester: uses many DBs to gather bio/chem/(phys) data
Enzyme Commission number (EC number; enzyme nomenclature): numerical classification scheme for enzymes, based on the chemical reactions they catalyze; every EC number is associated with a recommended name for the respective enzyme. Strictly speaking, EC numbers do not specify enzymes, but enzyme-catalyzed reactions, if different enzymes (for instance from different organisms) catalyze the same reaction, then they receive the same EC number; through convergent evolution, completely different protein folds can catalyze an identical reaction and therefore would be assigned an identical EC number.
Entrez: federated search engine over many DBs: PubMed (Medline, PubMed Central), OMIM & OMIA, (Nucleotide (SNP, Gene, HomoloGene, Genome), Taxonomy, Protein, Structure), many other
Mendelian Inheritance in Man: OMIM; diseases with genetic component (nature vs. nurture), links to genes in human genome
BLAST: Basic Local Alignment Search Tool. Bio-sequences: protein, nucleotides (DNA (genomic), RNA). Algorithm, scoring matrix, "training" the algorithm.
UniProt (Universal Protein resource; launched in 2003.12): comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. In 2002, these joined forces as UniProt Consortium: European Bioinformatics Institute (EBI (UK), @EMBL) + the Swiss Institute of Bioinformatics (SIB) + Protein Information Resource (PIR (US)). SIB: ExPASy; PIR (@Georgetown University Medical Center in Washington, DC, USA): Margaret Dayhoff's Atlas of Protein Sequence and Structure, first published in 1965.
UniProtKB (UniProt Knowledgebase):
UniProtKB/Swiss-Prot: contains reviewed, manually annotated entries by biocurators. Aim: to provide all known relevant information about a particular protein.
UniProtKB/TrEMBL: contains unreviewed, automatically annotated entries; introduced in response to increased dataflow resulting from genome projects, as the time- and labour-consuming manual annotation process of UniProtKB/Swiss-Prot could not be broadened to include all available protein sequences.
UniParc (UniProt Archive): comprehensive and non-redundant database, which contains all the protein sequences from the main, publicly available protein sequence databases. Identical sequences are merged, regardless of whether they are from the same or different species. Each sequence is given a stable and unique identifier (UPI), making it possible to identify the same protein from different source databases. UniParc contains only protein sequences, with no annotation.
UniRef (UniProt Reference Clusters): consists of three databases of clustered sets of protein sequences from UniProtKB and selected UniParc records: UniRef100 (identical sequences, 100% sequence identity), UniRef90 (at least 90%), UniRef50 (at least 50% sequence identity). This clustering of sequences enables faster sequence searches and reduces DB size.
UniMes (UniProt Metagenomic and Environmental Sequences): metagenomic and environmental data.
Other UniProt related:
ExPASy: proteomics: sequence (domains), structure (functional sites), protein families, 2D gel electrophoresis analysis. By SIB; collaborates with EMBL-EBI.
NeXtProt: knowledge platform on human proteins; comprehensive resource that provides a variety of types of information on human proteins, such as their function, subcellular location, expression, interactions and role in diseases. Major part of the information obtained from the UniProt Swiss-Prot database, but gradually being complemented by data originating from high-throughput studies with an emphasis on proteomics
BRENDA (BRaunschweig ENzyme DAtabase): enzymes
International HapMap Project: human genomes, SNPs
HUGO Gene Nomenclature Committee (HGNC) {http://www.genenames.org/}: approves a unique and meaningful name for every known human gene based on a query of experts. In addition to a long name, the HGNC also assigns an abbreviation (referred to as symbol) to every gene.
Information Hyperlinked over Proteins: (iHOP) genes, proteins, RNA as hyperlinks in PubMed abstracts
KEGG: collection of DBs: genomes, enzymatic pathways , biological chemicals ("pathway intermediates")
Protein Information Resource: PIR; bioinfo DB: genomic and proteomic (+RNA?)
Ensembl: the ultimate resource to genomes, genomics and genetics. Retrieval of genomic information
Vertebrate and Genome Annotation Project: annotated genomes of human, mouse, zebrafish, pig, dog. Built upon Ensembl
Protein Data Bank (PDB): 3D structural data repository of large (bio)molecules, e.g. DNA, RNA, protein, sugars, lipids (small inorganics are excluded). X-ray, NMR, EM, hybrid data. File format. Classification projects: Gene Ontology, SCOP, CATH.
EM Data Bank (Electron Microscopy Data Bank (EMDB)): from 2011.12.20 EMDB joined PDB archive.
Worldwide Protein Data Bank (wwPDB): organization that maintains the archive of macromolecular structure; mission: to maintain a single PDB Archive of macromolecular structural data that is freely and publicly available to the global community. 4 members: Research Collaboratory for Structural Bioinformatics Protein Database (RCSB PDB), Protein Data Bank in Europe (PDBe), Protein Data Bank Japan (PDBj), Biological Magnetic Resonance Data Bank (BMRB).
Orientations of Proteins in Membranes database (OPM) {http://opm.phar.umich.edu/}: spatial positions of membrane protein structures with respect to the lipid bilayer. However, structures of many membrane-associated proteins are not included in the database if they can not be computationally predicted.
Ki Database: binding affinities (Ki) of chemical compounds for biomacromolecules (proteins: receptors, transporters, ion channels, enzymes)
OvidSP: health science DBs search interface
InterPro {http://www.ebi.ac.uk/interpro/}: database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them; signatures consist of models (simple types, such as regular expressions or more complex ones, such as Hidden Markov models) which describe protein families, domains or sites.
Pfam: database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. q.v. TrEMBL
PRINTS: collection of so-called "fingerprints"; provides both a detailed annotation resource for protein families, and a diagnostic tool for newly-determined sequence.
TIGRFAMs: database of protein families designed to support manual and automated genome annotation.
SUPERFAMILY {http://supfam.org/SUPERFAMILY/}: database of structural and functional annotation for all proteins and genomes
PROSITE {http://prosite.expasy.org/}: entries describing the protein families, domains and functional sites as well as amino acid patterns, signatures, and profiles in them; manually curated by a team of the Swiss Institute of Bioinformatics and tightly integrated into Swiss-Prot protein annotation
Transporter Classification database (TCDB): IUBMB approved classification system for membrane transport proteins including ion channels; designed to be analogous to the EC number system for classifying enzymes, but it also uses phylogenetic information.
GeneCards: database of human genes that provides genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes; developed and maintained by the Crown Human Genome Center at the Weizmann Institute of Science.
Comprehensive Microbial Resource (CMR): data on publicly available prokaryotic genomes; searches for similarities and differences between genomes.

Wikis[edit]

Proteopedia: Wiki of proteins, RNA, DNA and other molecules. All PDB entries.

Dedicated search engines of published papers[edit]

List of academic databases and search engines: representative list of major databases and search engines useful in an academic setting for finding and accessing articles in academic journals, repositories, archives, or other collections of scientific and other articles.
ArXiv {physics, mathematics, CS, nonlinear sciences, quantitative bio, statistics}
CiteSeer: replaced by CiteSeerX.
Google scholar
JSTOR: originally containing digitized back issues of academic journals, it now also includes books and primary sources, and current issues of journals;
LexisNexis {law}
Science.gov: gateway to US government scientific and technical information and research
Scopus (SciVerse Scopus, @Elsevier): bibliographic database containing abstracts and citations for academic journal articles.
Pubget: by Copyright Clearance Center (CCC).
PubMed (1996.01): free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at NIH maintains the database as part of the Entrez information retrieval system. Indexed with MeSH.
PubMed identifier (PMID): unique number assigned to each PubMed record; there is a similar PMCID (PMC). Assignment of a PMID or PMCID to a publication tells the reader nothing about the type or quality of the content. PMIDs are assigned to letters to the editor, editorial opinions, op-ed columns, and any other piece that the editor chooses to include in the journal, as well as peer-reviewed papers. The existence of the identification number is also not proof that the papers have not been retracted for fraud, incompetence, or misconduct. The announcement about any corrections to original papers may be assigned a PMID.
MEDLINE (Medical Literature Analysis and Retrieval System Online, or MEDLARS Online): bibliographic database of life sciences and biomedical information. MEDLARS (Medical Literature Analysis and Retrieval System) is a computerised biomedical bibliographic retrieval system, launched by NLM in 1964.
United States National Library of Medicine (NLM): operated by USA federal government is world's largest medical library
Index Medicus
GoPubMed: mashup; Gene Ontology (GO) and Medical Subject Headings (MeSH) serve as "Table of contents" in order to structure the millions of articles of the MEDLINE database.
PubMed Central: free digital database of full-text scientific literature in biomedical and life sciences. It grew from the online Entrez PubMed biomedical literature search system. PubMed Central was developed by NLM as an online archive of biomedical journal articles.
Europe PubMed Central (Europe PMC; till 2012.11.01: UK PubMed Central): launched in 2007 as the first ‘mirror’ site to PMC
PubMed Central Canada (PMC Canada; 2009-)
Zasshi Kiji Sakuin (雑誌記事索引, "Japanese Periodicals Index"): searchable database of scholarly articles in Japanese
Japanese Historical Text Initiative (JHTI): Japanese historical documents and English translations. It is part of the Center for Japanese Studies at the University of California at Berkeley.
ISI Web of Knowledge: search engine, citation index, who is highly cited and why ("popular research")
Scirus (2001.04.1): comprehensive science-specific search engine

Technical writing styles[edit]

Technical writing:
Style guide R
Template:Styles : writing, formatting, citing, other examples according to defined "standard" styles
Wikipedia:Manual of Style: q.v. Wikipedia::Manual of Style
Punctuation

Citation, references, SW, reference management[edit]

See also: \Books_EECS : "Reference management"

Wikipedia:Citing sources: q.v. Wikipedia::Templates
Parenthetical referencing and Wikipedia:Parenthetical referencing: "author-date" and "author-title"
Comparison of reference management software:
Internet browser integration
Zotero (AGPL; by Roy Rosenzweig Center for History and New Media (CHNM)): Firefox (original add-on); Zotero Standalone can be integrated into Google Chrome, Safari.
Mendeley (on ~2013.04 Elsevier bought): proprietary; main competitor to Zotero. Based on Qt, runs on Windows, Mac, Linux, iOS (iPhone, iPad).
Papers (software) (on ~2012.11 Springer bought): initially only Mac OS X and iOS (iPhone, iPad), in 2012.02.14 on Windows. iTunes-like look & feel.
Social bookmarking of papers/articles: CiteULike, Connotea (NPG)
No integration into Internet browser:
EndNote (Thomson Reuters): the granddaddy of all current reference management software.
Aigaion, JabRef, RefDB, Refbase, BibDesk (Mac OS X)
Template:Reference management software: web-based reference management (OS independent, only browser is needed)
Comparison of notetaking software: Evernote, Microsoft OneNote
Citavi: reference management program for MS Windows. Popular in DE.
Citation Style Language: open XML-based language to describe the formatting of citations and bibliographies. Used by Zotero, Mendeley, Papers.

Publishers (groups), journals, information management[edit]

Category:Academic publishing
Category:Academic journals
Category:Technical communication
Category:Peer review
IMRAD (introduction, methods, results, and discussion)
Academic journal
Review journal
Review article: attempt to summarize the current state of understanding on a topic; analyze or discuss research previously published by others, rather than reporting new experimental results.
Journals and publishing groups:
Template:Reed Elsevier:
Elsevier
ScienceDirect
Cell Press: imprint of Elsevier
Trends (journals)
Science (journal)
Georg von Holtzbrinck Publishing Group (also: Die Zeit (50%), Handelsblatt, Der Tagesspiegel.):
Nature Publishing Group (NPG)
Macmillan Publishers Ltd (The Macmillan Group)
Proceedings of the National Academy of Sciences (PNAS): by USA NAS
Public Library of Science & Template:PLoS:
Plos one - multidisciplinary, comparable to Nature, Science, PNAS...
Annual Reviews (publisher): reviews of particular topics
Annual Review of Biochemistry: sets the standard for review articles in biological chemistry and molecular biology.
Wiley-Blackwell: Microscopy Research and Technique
Cold Spring Harbor Laboratory Press (1933-): CSH monographs, CSH perspectives
RNA (journal) (1995.03-2003: Cambridge University Press; 2003-: CSHL Press): published on behalf of the RNA Society.
Cambridge University Press (1534- granted letters patent by Henry VIII): world's oldest publishing house, and the second largest university press in the world.
Template:Thomson Reuters: business data provider and was created by the Thomson Corporation's purchase of Reuters Group on 17 April 2008. Owned 53% by Thomson family. Thomson Reuters is Canada's "leading corporate brand".
Thomson Scientific & Healthcare: split in 2006: Thomson Healthcare + Thomson Scientific. In 2008 both were renamed due to the merger and in 2009 both were merged back into Healthcare & Science unit of the Professional Division of Thomson Reuters, now [12/02/09] called IP & Science (includes also: Legal and Tax & Accounting).
Wolters Kluwer: global information services and publishing company. In 1987 formed by friendly merger of Kluwer Publishers and Wolters Samson (to defend against hostile takeover by Elsevier).
Health & Pharma Solutions: Ovid Technologies: access to online (health science) bibliographic databases, journals and other products; once produced MEDLINE; new DB search interface OvidSP in 2007. SilverPlatter (SilverPlatter Information, Inc.): produced commercial reference databases on CD-ROMs; now part of Ovid.
other: Financial & Compliance Services; Legal & Regulatory; Tax & Accounting.
Journal of Visualized Experiments (JoVE; 2006-): publishing biological, medical, chemical, and physical research in video format.
Aggregators:
Faculty of 1000: recent research papers evaluated by "over 2000 biological researchers by interestingness"

Plagiarism:

VroniPlag Wiki & (2011.03.28-): wiki at Wikia that examines and documents the extent of plagiarism in German theses (Doctoral, MD, Master, Law...).
for Karl-Theodor zu Guttenberg's '

Bibliometrics[edit]

Category:Bibliometrics
Scientometrics: science of measuring and analysing science. In practice, scientometrics is often done using bibliometrics which is a measurement of the impact of (scientific) publications. Fathers of scientometrics: Derek J. de Solla Price and Eugene Garfield. One significant finding in the field is a principle of cost escalation to the effect that achieving further findings at a given level of importance grow exponentially more costly in the expenditure of effort and resources. However, new methods in search, machine learning and data mining are showing that is not the case for many information retrieval and extraction based problems (what about robotization?).
Impact factor (IF): measure reflecting the average number of citations to articles published in science and social science journals. Frequently used as proxy for the relative importance of a journal within its field, with journals with higher impact factors deemed to be more important than those with lower ones. Devised by Eugene Garfield, the founder of ISI (now part of Thomson Reuters). Spoofs of IF: "A short history of SHELX" (by University of Göttingen crystallographer George Sheldrick); reviews have much higher per article IF than an article/letter about original research. Articles providing new tools (e.g. software (esp. FOSS), new biochemical method (e.g. SDS-PAGE, Bradford assay)) have much higher IFs than articles about new phys/chem/bio phenomena.
Bibliometrics: set of methods to quantitatively analyze scientific and technological literature. Citation analysis and content analysis. Trying to make automatic tools to make citation indexes and to use these to distribute scientific funding, grant tenures...
Altmetrics: new metrics proposed as an alternative to the widely used Journal Impact Factor; covers not just citation counts, but also other aspects of the impact of a paper, such as how many data and knowledge bases refer to the article, article views, downloads, or mentions in social media and news media.

Be objective[edit]

Jan Hendrik Schön
Bogdanov Affair
Template:Pseudoscience

Scientific wikis[edit]

Scholarpedia: English-language online wiki-based encyclopedia that uses the same MediaWiki software as Wikipedia, but has features more commonly associated with open-access online academic journals. Articles are written by invited expert authors and are subject to peer review. Scholarpedia lists the real names and affiliations of all authors, curators and editors involved in an article, however, the peer review process (which can suggest changes or additions, and has to be satisfied before an article can appear) is anonymous. Focus fields: computational neuroscience, dynamical systems, computational intelligence, physics and astrophysics.

Openness and competition[edit]

Open notebook science
Openwetware

Presentation(s)[edit]

Edward Tufte#Criticism of PowerPoint: PowerPoint - useful or not? Handouts and reading vs. only speaking? Q&A session?

Other DBs: arts, humanities, ...[edit]

EServer.org

Funding (agencies), companies, government, politics, scientific societies[edit]

Science policy
List of wealthiest charitable foundations (charitable foundations, private foundations and other charitable organizations):
Howard Hughes Medical Institute (HHMI) (endowment=16.1 bln USD)
Janelia Farm Research Campus (opened in 2006)

United States of America[edit]

National Institutes of Health (NIH): agency of United States Department of Health and Human Services; primary agency of the United States government responsible for biomedical and health-related research (Main provider of funds for biomedical research).
National Science Foundation (NSF); fundamental research and education in all the non-medical fields of science and engineering
National Institute of Standards and Technology (NIST): agency of United States Department of Commerce. Very few funds to keep measurement standards.
Non-money giving organization:
United States National Academy of Sciences (NAS): corporation in the United States whose members serve pro bono as "advisers to the nation on science, engineering, and medicine." Publishes PNAS.
American Association for the Advancement of Science (AAAS): council of AAAS has some elected delegates where at least 2 are from US NAS.

European Union[edit]

EU: European Research Area (ERA) ⇒ European Research Council (ERC) similar to NSF: Framework Programmes for Research and Technological Development funds research in ERA.
European Molecular Biology Laboratory (EMBL): established in 1974 by many EU members at that time (Western part of current EU); the main Laboratory in Heidelberg, and Outstations in Hinxton (EBI), Grenoble, Hamburg, and Monterotondo near Rome.
European Bioinformatics Institute (EBI; 1992-): lots of DBs
European Science Foundation (ESF; 1974-): association of 72 member organizations devoted to scientific research in 30 European countries; independent, non-governmental, non-profit organisation that facilitates cooperation and collaboration in European research and development, European science policy and science strategy. Together represent €25 bln funding.
Central European Institute of Technology (CEITEC; Brno, Czech Republic): European centre of excellence in the fields of life sciences and advanced materials and technologies; nanotechnologies and microtechnologies, structural biology, genomics and proteomics going into advanced materials and medicine.
de:Kategorie:Begabtenförderungswerk
Alfried Krupp von Bohlen und Halbach Foundation & de:Alfried Krupp von Bohlen und Halbach-Stiftung
de:Fonds der Chemischen Industrie
Boehringer Ingelheim Fonds

Germany[edit]

DE: de:Deutsche Forschungsgemeinschaft (DFG):
Fraunhofer Society: 1/3rd from gov, 2/3rds from contract work, either for government sponsored projects or from industry
Max Planck Society (Max-Planck-Gesellschaft zur Förderung der Wissenschaften Eingetragener Verein, MPG): federal and state (Länder) gov. funding
Forschungszentrum Jülich: Ernst Ruska-Centre does HRTEM (FEI Titan, JEOL TEMs)
Helmholtz Association of German Research Centres:
German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)
DESY (Deutsches Elektronen Synchrotron), collaborates in International Linear Collider (ILC, under planning/building, 2010), European x-ray free electron laser (Eu XFEL) (being built, 2010)
Alfred-Wegener-Institut für Polar- und Meeresforschung (AWI), German Center for Neurodegenerative Diseases (DZNE) [being built, 2010], Max Delbrück Center for Molecular Medicine Berlin-Buch (MDC), Forschungszentrum Dresden-Rossendorf (FZD)
de:Aula der Georg-August-Universität
de:Studentenkarzer (Göttingen)
Göttingen Academy of Sciences and Humanities (de:Akademie der Wissenschaften zu Göttingen): second oldest of the seven academies of sciences in Germany.
AnimalBase (de:AnimalBase) {public domain}: brought to life in 2004 and is maintained by the University of Göttingen; special focus on literature and names published prior to 1800.
Göttingen State and University Library (de:Niedersächsische Staats- und Universitätsbibliothek Göttingen): library for Göttingen University as well as the central library for the German State of Lower Saxony (with its central catalogue), and the library for the Göttingen Academy of Sciences
Center for Retrospective Digitization (de:Göttinger Digitalisierungszentrum): one of the largest libraries in Germany, the Göttingen SUB houses some 4½ million volumes as well as 13,000 holographs and other manuscripts and 350 Nachlässe

United Kingdom[edit]

Template:Science and technology in the United Kingdom
UK Research councils: Arts and Humanities Research Council (AHRC), Biotechnology and Biological Sciences Research Council (BBSRC), Economic and Social Research Council (ESRC), Engineering and Physical Sciences Research Council (EPSRC), Medical Research Council (MRC), Natural Environment Research Council (NERC), Particle Physics and Astronomy Research Council (PPARC), Science and Technology Facilities Council (STFC)
Royal Society of Chemistry (RSC): learned society (professional association) in UK with the goal of "advancing the chemical sciences." Formed in 1980.

Canada[edit]

Category:Canada Research Chairs
Canada Research Chair (CRC; 2000-): prestigious Canadian university research professorships created through the Canada Research Chairs Program; created to attract world best scholars in various disciplines to be part of CA university system. $300 million is spent annually to attract and retain outstanding scholars and scientists. Tier 1 Chairs – tenable for seven years and renewable indefinitely, are for outstanding researchers acknowledged by their peers as world leaders in their fields; Tier 2 Chairs – tenable for five years and renewable once, are for exceptional emerging researchers, acknowledged by their peers as having the potential to lead in their field.

Middle East, Western Asia[edit]

King Abdullah University of Science and Technology (KAUST): public research university located in Thuwal, Saudi Arabia; built and operated for the first three years by Saudi Aramco. Focuses exclusively on graduate education and research, using English as the official language of instruction. Biological and Environmental Sciences and Engineering; Computer, Electrical, and Mathematical Sciences and Engineering; and Physical Sciences and Engineering

Scientific societies[edit]

International:

International Association of Academies (IAA; 1899-1913): was an academy designed for the purpose of linking the various Academies around the world, of which the first meeting was held in Paris, FR, in 1900.
Template:International Council for Science (ICSU, formerly International Council of Scientific Unions): formed in 1931; international co-operation in the advancement of science. One of the oldest non-governmental organizations in the world and represents the evolution and expansion of two earlier bodies known as the IAA (1899-1913/14) and the International Research Council (IRC; 1919-1931). Members are national scientific bodies (e.g. academy of science of country X), and international scientific unions.

The international scientific unions (also members of ICSU; [member since]):

IUPAC (1922)
International Astronomical Union (IAU; [1922])
International Mathematical Union (IMU; [1922])
(IUGS; [1922])
International Union of Biological Sciences (IUBS; founded in 1919; [1925]): promotes the biological sciences internationally.
International Union of Crystallography (IUCr; [1947])
International Union of Biochemistry and Molecular Biology (IUBMB; formed as International Union of Biochemistry in [1955])
EU
European Molecular Biology Organization (EMBO); publications: Molecular Systems Biology, EMBO Journal, EMBO Reports
European Life Scientist Organisation (ELSO) absorbed by EMBO, end 2008
Federation of European Biochemical Societies (FEBS); publications: FEBS Journal, FEBS Letters and Molecular Oncology

Companies[edit]

Pharma (according to size {human count}):
  1. Bayer: chemical and pharmaceutical
  2. Hoffmann–La Roche (aka Roche): pharmaceuticals and diagnostics; holding company: Roche Holding AG
  3. Boehringer Ingelheim