Concluding Remarks

Volume 3 of the set of textbooks devoted to Circulatory and Ventilatory Sys- tems in the framework of Biomathematical and Biomechanical Modeling gives the basic knowledge on the first phases of signal transduction triggered by extracellular messengers. Signaling determines cell behavior. Numerous process can be modeled to quickly assess effects of parameters, all other agents remaining constant, once the mathematical model has been vali- dated. Advantage of mathematical models is to provide the complete quantity fields, whereas measurements are made in some points or corresponds to averages of exploration windows of the field of the investigated variable. Mathematical description of large, complex biochemical reaction networks, in which molecules are nodes, and modeling of the dynamics of interactions (scaffolding, reaction, transcription, etc.) relies on computational simulations. A biochemical reaction network is defined by: (1) a set of variables — the state variables — that define the state of the system and (2) rules of temporal changes and possible transport of involved variables. The network behavior can be analyzed in a single cells and extended to multicellular systems, especially in tumor models. Mathematical models of cascades of chemical reactions are aimed at describing evolution of molecular concentrations 1 using the mass action law or a reaction– diffusion equation set. A given reaction occurs with a certain probability. Stochastic models rely on a stochastic update of system variables. On the other hand, deterministic models are carried out in systems with a large number of molecules, the time and variable states uniquely defining the state at the next time step. In a deterministic continuous formulation based on the mass action formalism, 2 molecular reactions

1. Typical molecular concentrations, i.e., continuous variables related to the number of molecules per unit volume, range from 0.1 nmol to 1 μmol. 2. The law of mass action states that the rate of a given chemical reaction is proportional to the product of the concentrations of reactants with eventual exponents that are stoichiometric coefﬁcients for the reaction, in the absence of one-to-one stoichiometry. It is based on several assumptions: (1) well mixed media; and (2) low molecular concentrations; and (3) a probability of diffusing molecules to be available for the reaction proportional to the concentration.

M. Thiriet, Signaling at the Cell Surface in the Circulatory and Ventilatory Systems, 809 Biomathematical and Biomechanical Modeling of the Circulatory and Ventilatory Systems 3, DOI 10.1007/978-1-4614-1991-4, © Springer Science+Business Media, LLC 2012 810 Concluding Remarks are described by differential equations defining the rate of change of molecular concentrations. A rate constant (or affinity parameter) describes the occurrence rate of a reaction when reactants are close each other. In general, a mass action reaction can be written as: NR NP k f ∑ siRi −−−−→ ∑ s jPj, (11.1) i=1 j=1 where NR reactants Ri generate NP products Pj with a given stoichometry sk (relative quantities of reactants and products in the chemical reaction) with a forward rate 3 parameter k f (and a backward rate parameter kb when the reaction is reversible. The modeling procedure for a biochemical network incorporates several steps: (1) definition of the molecular players and their interactions; (2) description of the major molecular interactions by a mathematical model; (3) estimation of values of the model parameters (e.g., diffusion coefficients and reaction rates); and (4) analysis of the dynamical behavior. The dynamics of a continuous system can be described by a set of ordinary differential equations (ODE). In general, this ODE set cannot be solved analytically and, thus require numerical integrations. On the other hand, reaction–diffusion models are based on partial differential equations (PDE). For example, an activator (act)– inhibitor (inh) reaction-diffusion model (Gierer-Meinhardt model) in morphogenesis is given by:

∂ 2 cact cact 2 = p + pact − dact cact + Dact ∇ cact , ∂t cinh ∂ cinh 2 2 = pa + pinh − dinhcinh + Dinh∇ cinh, (11.2) ∂t

where cact is the concentration of a short-range, autocatalytic activator, cinh that of a long-range inhibitor, p the production rate, pact the production rate of the activator required to initiate the activator autocatalysis, pinh the low baseline production rate of the inhibitor, d the decay rate, and D the diffusion coefficient. Cells react to various types of external stimuli, in particular, mechanical stresses. In physiological systems associated with flows, the magnitude and direction of mechanical stresses applied by the flowing fluid on the wetted surface of conduit wall (i.e., vascular endothelium with its glycocalyx or respiratory epithelium with the mucus layer and periciliary fluid) as well as within the vessel wall varies during the cardiac and breathing cycles. The heart generates an unsteady flow with a given frequency spectrum in a network of blood vessels characterized by complicated ar- chitecture and variable geometry both in space and time. Vessel geometry varies over short distances. The vascular network of curved blood vessels is composed of successive geometrical singularities, mainly branchings. The thoracic muscular cage cyclically inflates and deflates, thereby lowering and heightening the intrathoracic pressure, and hence dilating and collapsing lung alveoli and airways to inhale and exhale air. The respiratory tract is characterized by a large wetted surface inside a

3. The reaction constant of a reversible reaction is the ratio k f /kb. Concluding Remarks 811 small volume, especially in the nose and thorax. In the nose, turbinates allows heat and water exchange, but renders air currents less simple. In addition, the laryngeal constriction, the aperture of which varies during the ventilatory cycle, provokes air jet. The bronchial tree is a network of successive branchings at inspiration, or junctions at expiration, between short, more or less curved pipes of corrugated walls in large bronchi due to the presence of partial or complete cartilaginous rings. Therefore, blood and air streams correspond to time-dependent, three-dimensional, developing, as they are conveyed in conduit entrance length, where boundary layer develop (Vol. 7). Moreover, blood vessels and airways are deformable. Changes in transmural pressure (the pressure difference between the pressure at the wetted surface of the lumen applied by the moving fluid on the deformable conduit wall and the pressure at the external wall side that depends on the activity on the neighbor organs) can also influence the shape of vessel cross-section, especially when it becomes negative. In addition, in the arterial compartment, the change in cross-section shape can result from taper. More generally, possible prints of adjacent organs with more or less progressive constriction and enlargment, and adaptation to branching (transition zone) also give rise to three-dimensional flows. These flows are commonly displayed by virtual transverse currents, even if the vessel is considered straight. Furthermore, geometrical singularities influence flow pattern both upstream and downstream from it. Local changes in the direction of stress components can also be caused by flow separation and flow reversal during the cardiac and respiratory cycles. Flow separation is set by an adverse pressure gradient when inertia forces and fluid vorticity are high enough, especially in branching segments. Due to its time-dependent feature, flow separation regions spread over a variable length during the flow cycle and can move. The location and variable size of the flow separation region depends on the flow distribution between branches that can vary during the flow cycle. Flow reversal occurs during the diastole of the left ventricle in elastic arteries, such as the aorta, and most of the muscular arteries, such as brachial and femoral arteries (but not in the carotid arteries), as well as during alternates from inspiratory decelerating flow phase and expiratory accelerating flow phase and conversely. In arteries, flow reversal can be observed either in a region near the wall, more or less wide with respect to the position of the local center of vessel curvature, or in the entire lumen. Consequently, the stress field experienced by the wall tissues are strongly variable both in time and space. Cellular sensors then process mechanical signals by ensemble averaging not only to raise the signal-to-noise ratio, but also to adequately adapt the local size of the conduit lumen, i.e., the local flow resistance to maintain either flow rate or pressure, only in the case of sustained, abnormal stress field. References

Introduction

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Chap. 1. Signal Transduction

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Chap. 5. Receptors of Cellular Trafﬁcking

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Chap. 6. Receptors

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Chap. 7. G-Protein-Coupled Receptors

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Chap. 9. Receptor Tyrosine Phosphatases

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Chap. 11. Receptors of the Immune System

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Aliases that designate different types of molecules as well as those that do not carry an obvious meaning are not used in the present text. For example, P35 is an alias for annexin-A1, brain syntaxin-1A, ﬁcolin-2, interleukin-12A, the cyclin-H assembly factor ménage á trois homolog-1, the regulatory subunit-1 of cyclin-dependent kinase CDK5, and uroplakin-3B, among others. It is substituted by AnxA1, Stx1a, Fcn2, IL12a, MAT1, CDK5R1, and UPK3B aliases, respectively. The P39 protein corresponds to the subunit D1 of the lysosomal V-type H+ ATPase (ATP6v0d1), Jun transcription factor, a component of the Activator protein AP1, and the regulatory subunit-2 of cyclin-dependent kinase CDK5 (CDK5R2). Extracellular signal- regulated protein kinases ERK1 and ERK2, members of the mitogen-activated protein kinase (MAPK) module (last tier), are also abbreviated P44 and P42 (also P40 and P41). However, both P42 and P44 correspond to the 26S protease regulatory AAA ATPase subunit (PSMC6). The alias P42 is also utilized for cyclin-dependent kinase CDK20, cyclin-dependent kinase-like protein CDKL1, and 43-kDa nucleoporin NuP43. The alias P44 can also refer to interferon-induced protein IFI44 (or microtubule-associated protein MTAP44) and androgen receptor cofactor P44 (a.k.a. methylosome protein MeP50 and WD repeat-containing protein WDR77). In the present text, P38 members (P38α–P38δ) of the mitogen-activated protein kinase modules (i.e., MAPK11–MAPK14) 1 are designated as P38MAPKs to avoid confusion with other molecules, the alias of which is also P38. 2

1. Protein P38α is also known as MAPK14, cytokine suppressive anti-inflammatory drug (CSAID)-binding protein CSBP, CSBP1, or CSBP2, and stress-activated protein kinase SAPK2a; P38β as MAPK11 and SAPK2b; P38γ as MAPK12, ERK6, and SAPK3; P38δ as MAPK13 and SAPK4. 2. Alias P38 is used for: (1) mitogen-activated protein kinase MAPK1, extracellular signal- regulated kinase ERK2, as well as P40, P41, and P42; (2) adaptor CRK (chicken tumor virus regulator of kinase, or v-crk sarcoma virus CT10 oncogene homolog); (3) growth factor receptor-binding protein GRB2-related adaptor protein GRAP2 (a.k.a. GRID, GADS, GRB2L, GRF40, GRPL, and Mona); (4) ubiquitin ligase ring finger protein RNF19a, or dorfin; (5) 38-kDa DNA polymerase-δ-interacting protein PolδIP2 (a.k.a. polymerase [DNA- directed] PDIP38 and PolD4); (6) activator of 90-kDa heat shock protein ATPase homo-

919 920 A Notation Rules: Aliases and Symbols A.1 Aliases for Molecules

Aliases include all written variants, i.e., any abbreviation 3 such as acronyms. An acronym corresponds to a word made from the initial letters or syllables of nouns that are pronounceable as a word. Acronyms are generally written with all letters in upper case. Yet, some acronyms are treated as words and written in lower case (e.g., laser [originally LASER] is an acronym for light amplification by stimulated emission of radiation, sonar [originally SONAR] for sound navigation and ranging). A substance name can derive from its chemical name (e.g., amphetamine: α-methylphenethylamine). Acronyms can give rise to molecule names by adding a scientific suffix such as “-in”, a common ending of molecule nouns (e.g., sirtuin, a portmanteau, that comes from the alias SIRT, which stands for silent information regulator-2 [two]). Other scientific prefixes and suffixes can be frequently detected throughout the present text. Their meaning is given in appendix Notations – Prefixes and Suffixes, particularly for readers from Asia. Many prefixes are used to specify position, configuration and behavior, quantity, direction and motion, structure, timing, frequency, and speed. A portmanteau is a word that combines initials and some inner letters of at least 2 words (e.g., calmodulin stands for calcium modulated protein; caspase, a cysteine- dependent aspartate-specific protease; chanzyme, an ion channel and enzyme; chemokine, a chemoattractant cytokine; 4 emilin, an elastin microfibril interfacer; en- dorphins and endomorphins, endogenous morphines; porin, a pore-forming protein; restin, a Reed-Steinberg cell-expressed intermediate filament-associated protein,an alias for cytoplasmic linker protein CLiP1 (or CLiP170); serpin, a serine protease inhibitor; siglec, a sialic acid-binding Ig-like lectin; transceptor, a transporter- related receptor; and Prompt, a promoter upstream transcript). 5 Initialisms are abbreviations that are formed from initial letters of a single long noun or several nouns and, instead of being pronounced like an ordinary word, are read letter-by-letter (e.g., DNA that stands deoxyribonucleic acid). Some abbreviations can give rise to alphabetisms that are written as new words (e.g., Rho-associated, coiled-coil-containing protein kinase [RoCK] that is also called Rho kinase). In biochemistry, multiple-letter abbreviations can also be formed from a single word that can be long (e.g., Cam stands for calmodulin, which is itself a portmanteau word, Trx for thioredoxin, etc.) as well as short (e.g., Ttn for titin, etc.). log AHSA1; and (7) aminoacyl tRNA synthase complex-interacting multifunctional protein AIMP2, or tRNA synthase complex component JTV1 [608]. 3. In general, abbreviations exclude the initials of short function words, such as “and”, “or”, “of”, or “to”. However, they are sometimes included in acronyms to make them pronounceable (e.g., radar [originally RADAR] for radio detection and ranging). These letters are often written in lower case. In addition, both cardinal (size, molecular weight, etc.) and ordinal (isoform discovery order) numbers in names are represented by digits. 4. Cytokines are peptidic, proteic, or glycoproteic regulators that are secreted by cells of the immune system. These immunomodulating agents serve as auto- or paracrine signals. 5. The upper case initial P in Prompt is used to avoid confusion with command-line inter- preter prompt or prompt book to direct precise timing of actions on theater stage. A.1 Aliases for Molecules 921

In addition, single-letter symbols of amino acids are often used to deﬁne a molecule alias (e.g., tyrosine can be abbreviated as Tyr or Y, hence SYK stands for spleen tyrosine kinase). Aliases use, in general, capital letters and can include hyphens and dots. Yet, as a given protein can represent a proto-oncogene 6 encoded by a gene that can give rise to an oncogene (tumor promoter) after gain- or loss-of-function mutations, 7 the same acronym represents 3 different entities. 8 Besides, a given abbreviation can designate distinct molecules without necessar- ily erroneous consequence in a given context (e.g., PAR: polyADPribose or protease- activated receptor and GCK: germinal center kinases or glucokinase; in the latter case, the glucokinase abbreviation should be written as GcK or, better, GK). In addition, a large number of aliases that designate a single molecule results from the fact that molecules have been discovered independently several times with possibly updated functions. Some biochemists uppercase the name of a given molecule, whereas others lowercase (e.g., cell division cycle guanosine triphosphatase of the Rho family CDC42 or Cdc42, adaptor growth factor receptor-bound protein GRB2 or Grb2, chicken tumor virus regulator of kinase CRK or Crk, guanine nucleotide-exchange factor Son of sevenless SOS or Sos, etc.). Acronyms are then not always capitalized. Printing style of aliases should not only avoid confusion, but also help one in remembering alias meaning. In the present textbook, choice of lower and upper case letters in molecule aliases is dictated by the following criteria.

6. In 1911, P. Rous isolated a virus that was capable of generating tumors of connective tissue (sarcomas) in chicken. Proteins were afterward identified, the activity of which, when uncontrolled, can provoke cancer, hence the name oncogene given to genes that encode these proteins. Most of these proteins are enzymes, more precisely kinases. The first oncogene was isolated from the avian Rous virus by D. Stéhelin and called Src (from sarcoma). This inves- tigator demonstrated that the abnormal functioning of the Src protein resulted from mutation of a normal gene, or proto-oncogene, which is involved in cell division. 7. Loss-of-function mutations cause complete or partial loss of function of gene products that operate as tumor suppressors, whereas gain-of-function mutations generate gene products with new or abnormal function that can then act as oncogenes. Typical tumor-inducing agents are enzymes, mostly regulatory kinases and small guanosine triphosphatases, that fa- vor proliferation of cells, which do normally need to be activated to exert their activities. Once their genes are mutated, these enzymes become constitutively active. Other oncogenes include growth factors (a.k.a. mitogens) and transcription factors. Mutations can also disturb signaling axis regulation, thereby raising protein expression. Last, but not least, chromosomal translocation can also provoke the expression of a constitutively active hybrid protein. 8. Like Latin-derived shortened expressions – as well as foreign words – that are currently written in italics, genes can be italicized. However, this usage is not required in scientific textbooks published by Springer. Italic characters are then used to highlight words within a text to easily target them. Proteins are currently romanized (ordinary print), but with a capital initial. Nevertheless, names (not aliases) of chemical species are entirely lowercased in most – if not all – scientific articles, except to avoid confusion with a usual word (e.g., hedgehog animal vs. Hedgehog protein and raptor [bird of prey] vs. Raptor molecule). 922 A Notation Rules: Aliases and Symbols

(1) An upper case letter is used for initials of words that constitute molecule nouns (e.g., receptor tyrosine kinase RTK). An alias of any compound takes into account added atoms or molecules (e.g., PI: phosphoinositide and PIP: phosphoinositide phosphate) as well as their number (e.g., PIP2: phosphatidylinositol bisphosphate and DAG: diacylglycerol). (2) A lower case letter is used when a single letter denotes a subfamily or an isoform when it is preceded by a capital letter (e.g., PTPRe: protein tyrosine phosphatase receptor-like type-E). Nevertheless, an upper case letter is used in an alias after a single or several lower case letters to distinguish the isoform type (e.g., RhoA isoform and DNA-repair protein RecA for recombination protein-A), but OSM stands for oncostatin-M, not osmole Osm 9 to optimize molecule identification. These criteria enable to use differently written aliases with the same sequence of letters for distinct molecules (e.g., CLIP for corticotropin-like intermediate peptide, CLiP: cytoplasmic CAP-Gly domain-containing linker protein, and iCliP: intramembrane-cleaving protease). As the exception proves the rule, current aliases, such as PKA and PLA that designate protein kinase-A and phospholipase-A, respectively, have been kept. Preceded by only 2 upper case letters, a lower case letter that should be used to specify an isoform can bring confusion with acronyms of other protein types (e.g., phospholamban alias PLb). Nouns (e.g., hormone-like fibroblast growth factor [hFGF] and urokinase-type plasminogen activator [uPA]) or adjectives (e.g., intracellular FGF isoform [iFGF]) that categorize a subtype of a given molecule correspond to a lower case letter to emphasize the molecule species. Hence, an upper case letter with a commonly used hyphen (e.g., I[R]-SMAD that stands for inhibitory [receptor-regulated] SMAD; V- ATPase for vacuolar adenosine triphosphatase; MT1-MMP for membrane type-1 matrix metalloproteinase; and T[V]-SNARE for target [vesicle-associated] soluble Nethylmaleimide-sensitive factor-attachment protein receptor) is then replaced by a lower case letter (e.g., i[r]SMAD, vATPase, mt1MMP, and t[v]SNARE), as is usual for RNA subtypes (mRNA, rRNA, snRNA, and tRNA for messenger, ribosomal, small nuclear, and transfer RNA, respectively). Similarly, membrane-bound and secreted forms of receptors and coreceptors that can derive from alternative mRNA splicing are defined by a lower case letter (e.g., sFGFR for secreted extracellular FGFR form and sFRP for soluble Frizzled-related protein), as well as eukaryotic translation elongation (eEF) and initiation (eIF) factors. (3) Although l, r, and t can stand for molecule-like, -related, and -type, respectively, when a chemical is related to another one, in general, upper case letters are used for the sake of homogenity and to clearly distinguish between the letter L and numeral 1 (e.g., KLF: Krüppel-like factor, CTK: C-terminal Src kinase (CSK)-type kinase, and SLA: Src-like adaptor). (4) An upper case letter is most often used for initials of adjectives contained in the molecule name (e.g., AIP: actin-interacting protein; BAX: BCL2-associated

9. Osmole: the amount of osmotically active particles that exerts an osmotic pressure of 1 atm when dissolved in 22.4 l of solvent at 0 ◦C. A.1 Aliases for Molecules 923

X protein; HIF: hypoxia-inducible factor; KHC: kinesin heavy chain; LAB: linker of activated B lymphocytes; MAPK: mitogen-activated protein kinase; and SNAP: soluble N-ethylmaleimide-sensitive factor-attachment protein); (5) Lower case letters are used when alias letters do not correspond to initials (e.g., Fox – not fox –: forkhead box), except for portmanteau words that are entirely written in minuscules (e.g., gadkin: γ1-adaptin and kinesin interactor). This rule applies, whether alias letters do correspond to successive noun letters (e.g., Par: partitioning defective protein and Pax: paxillin, as well as BrK: breast tumor kinase and ChK: checkpoint kinase, whereas CHK denotes C-terminal Src kinase [CSK]-homologous kinase) or not (e.g., Fz: Frizzled and HhIP: Hedgehog- interacting protein), 10 except for composite chemical species (e.g., DAG: diacylglycerol). However, some current usages have been kept for short aliases of chemical species name (e.g., Rho for Ras homolog rather than RHo). In any case, molecule (super)family (class) aliases as well as those of their members are written in capital letters, such as the IGSF (IGSFi: member i; immunoglobulin), KIF (KIFi; kinesin), SLC (SLCi; solute carrier), TNFSF (TNFSFi; tumor- necrosis factor), and TNFRSF (TNFRSFi; tumor-necrosis factor receptor) superfamily. Gene names are also written with majuscules when the corresponding protein name contains at least one minuscule, otherwise only the gene name initial is written with an upper case letter that is then followed by lower case letters. To highlight its function, substrate aliases (e.g., ARF GTPases) contained in a molecule alias are partly written with lower case letters (e.g., ArfRP, ArfGEF, Arf- GAP stand for ARF-related protein, ARF guanine-nucleotide exchange factor, and ARF GTPase-activating protein, respectively). Last, but not least, heavy and pedantic designation of protein isoforms based on roman numerals has been avoided and replaced by usual arabic numerals (e.g., angiotensin-2 rather than angiotensin-II), except for coagulation (or clotting) factors. Moreover, character I can mean either letter I or number 1 without obvious dis- crimination at first glance (e.g., GAPI that stands for Ras GTPase-activating protein GAP1, but can be used to designate a growth-associated protein inhibitor). Unnecessary hyphenation in aliases of substances (between an upper case letter, which can define the molecule function, and the chemical alias, or between it and assigned isotype number) has been avoided. In any case, the Notation section serves not only to define aliases, but also, in some instances, as disambiguation pages.

10. The Hedgehog gene was originally identiﬁed in the fruit ﬂy Drosophila melanogaster. It encodes a protein involved in the determination of segmental polarity and intercellular signaling during morphogenesis. Homologous gene and protein exist in various vertebrate species. The name of the mammal hedgehog comes from hecg and hegge (dense row of shrubs or low trees), as it resides in hedgerows, and hogg and hogge, due to its pig-like, long projecting nose (snout). The word Hedgehog hence is considered as a seamless whole. 924 A Notation Rules: Aliases and Symbols A.2 Symbols for Physical Variables

Unlike substances aliases, symbols for physical quantities are most often represented by a single letter of the Latin or Greek alphabet (i: current; J: flux; L: length; m: mass; p: pressure; P: power; T: temperature; t: time; u: displacement; v: velocity; x: space; λ: wavelength; μ: dynamic viscosity; ρ: mass density; etc.). These symbols are specified using sub- and superscripts (cp and cv: heat capacity at constant pressure and volume, respectively; DT : thermal diffusivity; Gh: hydraulic conductivity; GT: thermal conductivity; αk: kinetic energy coefficient; αm: momentum coefficient; etc.). A physical quantity associated with a given point in space at a given time can be: (1) a scalar uniquely defined by its magnitude; (2) a vector characterized by a magnitude, a support, and a direction represented by an oriented line segment defined by a unit vector; and (3) a tensor specified by a magnitude and a few directions. To ensure a straightforward meaning of symbols used for scalar, vectorial, and tensorial quantities, bold face upper (T) and lower (v) case letters are used to denote a tensor and a vector, respectively, whereas both roman (plain, upright)-style upper and lower case letters designate a scalar. List of Currently Used Prefixes and Suffixes

Prefixes (localization) by the body’s cells; endomembranes at organelle surfaces within the cell) “ep-” (variant “eph-”, or “epi-” [πι]): upon “ab-” (Latin) and “apo-” (Greek: απo): away (epigenetics refers to the inheritance from or off (abluminal: endothelial (“-genetic”: ability to procreate edge opposite to wetted surface; [γννητικoς]) of variations in gene apolipoproteins: lipid carriers that expression beyond ("epi-": on, upon, cause egress [also ingress] from above, close to, beside, near, toward, cells; aponeurosis (απoνυρωσις; against, among, beyond, and also) νυρoν: sinew, tendon) muscle sheath change in the DNA sequence. that limits radial motion and enhances “front-” and “pre-”: anterior or in front of axial contraction; and apoptosis: “post-”: behind separation [“-ptosis”: fall (πτωσiς): “infra-” and “sub-”: under or below as leaves fall away from a tree], a type “super-” and “supra-”: above of programmed cell death) “inter-”: between or among “acr-” (variant “acro-” [ακρoς]): top or apex “peri-” (πρι): around “ad-” (adfecto: to reach; adfio: to blow “tele-” (τλ): remote toward; adfluo: to flow toward): toward “trans-”: across (ad- becomes “ac-” before c, k, or q; “af-” before f [afferent]; “ag-” before Prefixes (composition) g [agglutination]; “al-” before l; “ap-” before p [approximation]; “as-” before “an-” and “aniso-” (ανισoς): unequal, s; and “at-” before t) uneven, heterogeneous παρα “cis-”, “juxta-”, and “para-” ( ): near, “iso-” (ισoς): equal, alike (isomer [μρoς: beside, or alongside part, portion] “contra-”: opposite side; “ipsi-” (ipse): same “mono-” (μoνoς) and “uni-” (unicus): single side; “latero-”: side; “oligo-” (oλιγoς): few, little, small “ecto-” (κτoς), “exo-” (ξo), and “extra-”: “multi-” (multus), “pluri-” (plus, plures), outside, outer, external, or beyond and “poly-” (πoλυς): many, much (exogenous chemicals produced by “ultra-”: in excess. an external source, or xenobiotics [“xeno-”: foreigner]) Prefixes (quantity) “endo-” (νδoν) and “intra-”: inside (endogenous substances synthesized “demi-” (dimidius) and “hemi-” (ημι): half

925 926 List of Currently Used Preﬁxes and Sufﬁxes

“sesqui-”: one and a half (half more) “macro-” (μακρoς): large, long, or big “di-”or“dis-”(δυo; δις)aswellas“bi-”or “mega-” (μγας): great, large “bis-”: 2, twice “meso-” (μσoς): middle “tri” (τρις, τρι-; tres, tria): 3 “micro-” (μικρoς): small “tetra-” (ττρα), “quadri-” (variant: “nano-” (νανoς): dwarf, tiny “quadr-” and “quadru-”): 4 “homo-” (oμo-): same (oμoλoγoς: agreeing, “penta-” (πντας; pentas), “quinqu-”, and corroborating; variant: “homeo-” “quint-”: 5 [homeostasis]) “hexa-” (ξ) and “sexa-”: 6 “hetero-” (τρo-): other “hepta-” (πτα): 7 “octa-” (oκτα): 8 Prefixes (timing) “nona-” (ννα): 9 (ninth part) “deca-” (δκα): 10 “ana-” (ανα): culminating (anaphase of “quadra-” (quadragenarius): 40 (elements) the cell division cycle), up, above “quinqua-” (quinquagenarius): 50 (ανoδoς: a way up, anode [positive “sexa-” (sexagenarius [sex: 6]: 60 electrode; oδoς; way, path, road, “septua-” (septuagenarius [septem: 7]): 70 track]) “nona-” (nonagenarius): 90 “ante-”: before “circa-”: approximately, around (circadian: Prefixes (motion and direction) approximately one day) “infra-”: below, shorter (infradian: rhythm “af-”: toward the center (single master with lower frequency than that of object); e.g., nerve and vascular circadian rhythm, not smaller period) afferents (ferre: to carry) to brain and “inter-”: among, between, during heart, respectively, rather than toward “meta-” (μτα): after, beyond, behind, any slave, supplied tissue from the set later; in the middle of (metaphase of of the body’s organs; also affector, the cell division cycle); as well as i.e., chemical messenger that brings connected to, but with a change of state a signal to the cell considered as the (metabolism) and about (metadata) object of interest, this exploration “post-”: after focus being virtually excised from the “pre-”: earlier organism with its central command “pro-” (πρo): preceding, first, before system, except received signals (prophase of the cell division cycle) “ef-” (effero: to take away): from the center “telo-” (τλoς): end, completion (efferent; effector, i.e., chemical “ultra-”: beyond, longer (ultradian: period transmitter recruited by the previous smaller than that of 24–28-hour cycle, mediator of a signaling cascade at a i.e., frequency greater than that of the given locus to possibly translocate to circadian rhythm) another subcellular compartment) “antero-” (anterior): before, in front of, Prefixes (functioning modality) facing, or forward “retro-”: behind or backward “auto-” (αυτoς): same, self “tropo-” (τρoπoς): duct direction; (tropa: “brady-” (βραδυς): slow (decelerate) rotation; celestial revolution); e.g., “tachy-” (ταχoς): rapid (accelerate) tropomyosin (μυς, musculus: muscle; “amphi-” (αμϕι): both (amphiphilic μυo-: refers to muscle [μυoτρωτoς: substances are both hydrophilic injured at a muscle]) and lipophilic; amphisomes are generated by both autophagosomes Prefixes (structure and size) and endosomes) List of Currently Used Prefixes and Suffixes 927

“ana-” : upward (anabolism) or against “-phob” (ϕoβια): repulsed (υδρoϕoβια, (anaphylaxis) hydrophobia [Latin]: horror of water) “cata-” (κατα): downward (catabolism, “-phore” (ϕρω): carrier (αμϕρω:to cathode [negative electrode; oδoς; bring up) way, path, road, track]) “-yl” denotes a radical (molecules with “anti-” (αντι): against unpaired electrons) “pro-”: favoring “-ploid” (πλoω): double, fold (diploid, “co-” (coaccedo: add itself to): together twofold; διπλoω: to double; “contra-”: adverse, against, beside, next to, διαπλoω: unfold) opposite “-emia”: in relation to flow (ανμια: “de-”: remove, reduce, separation after flatulence; υηνμια: fair wind), association (Latin de; e.g., deoxy-) particularly blood condition “dys-” (δυς): abnormal (δυσαης): “-genesis” (γνσις): cause, generation, ill-blowing) life source, origin, productive force “equi-” (æque): equal or alike “-iasis”: for diseased condition “hem-” or “hemat-” (αιμα: blood): related “-itis”: inflammation to blood “-lemma” (λμμα: skin): sheath “hypo-” (υπo): under, beneath, and low “-ole” and “-ule”: small (arteriole and “hyper-” (υπρ): above, beyond, and large venule; variant “-ula” [blastula] and “per-”: through (e.g., percutaneous) and “-ulum”) during (e.g., peroperative) “-plasma” (πλασμα): anything molded “pseudo-” (ψυδo): pretended, false (plasma: creature generated from silt “re-”; again of earth) “-plasia” (πλασια): formation, molding Scientific suffixes “-podium” (πoδoς: foot; podium [Latin]: “-ase”: enzyme (synthase, lipase, etc.) small knoll, small protuberance): “-ate”: salt of a base protrusion “-cyte” (κυτoς): cell (erythro- [ρυθρoς: “-poiesis” (πoιω): production red], leuko- [λυκoς: light, bright, “-soma” (σωμα): body clear, white], thrombo- [θρoμβoς: “-sclerosis” (σκλημα): hardness, induration lump, clot], adipo- [adeps: fat; “-stasis” (στασις): stabilization adipalis, adipatus, adipeus, adipinus: (απoκαταστασις: restoration; fatty], fibro- [fibra: fiber, filament], ανυπoστασις: migration) myo- [μυς: muscle, mouse, mussel], “-stomosis” (στoμα: mouth): equipped with myocardiocyte [κραδια: heart; an outlet cardiacus: related to heart, stomach; to “-taxy/tactic” (ταχυ: rapid; τακτικoς:to have heart trouble, stomach trouble], maneuver): related to motion (also etc.); prefix, i.e., ταχυκινησις: quick “-crine” (κρινω): to decide, to separate, and motion; ταχυνω: to accelerate; to secrete (e.g., endocrine regulator) and ταχυπνoια: short breath; not (υκρινω:keepinorder) [δια]ταξις: disposition, arrangement) “-elle”: small (organelle in a cell [like an “-trophy/trophic” (τρoϕις: well fed): related organ in a body]) to growth “-ium”, “-ion”, “-isk”, and “-iscus”: little “-oma”: tumor of (“-ium”: tissue interface and envelope, “-pathy” (παθoς, παθια): disease of such as endothelium and pericardium) “-tomy” (τoμια) and “-ectomy”: surgical “-phil” (ϕιλια): attracted (αϕιλια:wantof removal (απλoτoμια: simple incision; friends) ϕαûrhoυγγoτoμια: laryngotomy) List of Aliases

A ACK: activated CDC42-associated kinase ACP1: acid phosphatase-1, soluble A: Avogadro number (lmwPTP) ( ) A p : area–pressure relation ACTH: adrenocorticotropic hormone A: Almansi strain tensor Factin: filamentous actin A: cross-sectional area (Cav–actin: caveolin-associated Factin) A: actin-binding site Gactin: monomeric globular actin a: acceleration AcvR: activin receptor (TGFβ receptor a: major semi-axis superfamily) AA: arachidonic acid Ad: adrenaline AAA: ATPase associated with diverse ADAM: a disintegrin and metallopeptidase cellular activities (adamalysin) AAA: abdominal aortic aneurysm ADAMTS: a disintegrin and metallopepti- AAAP: aneurysm-associated antigenic dase with thrombospondin protein ADAP: adhesion and degranulation- AAK: adaptin-associated kinase promoting adaptor protein AATK: apoptosis-associated tyrosine kinase ABC: ATP-binding cassette transporter ADAP: ArfGAP with dual PH domains (transfer ATPase) ADF: actin-depolymerizing factor AbI: Abelson kinase interactor (cofilin-related destrin) Abl: Abelson leukemia viral proto-oncogene ADH: antidiuretic hormone (vasopressin) product (NRTK) ADMA: asymmetric dimethylarginine ABLIM: actin-binding LIM domain- ADP: adenosine diphosphate containing protein aDuSP: atypical dual specificity phosphatase ABP: actin-binding protein AE: anion exchanger AC: atrial contraction AEA: N-arachidonoyl ethanolamine ACAP: ArfGAP with coiled-coil, ankyrin (anandamide) repeat, PH domains AF: atrial fibrillation ACase: adenylate cyclase AFAP: ArfGAP with phosphoinositide- ACi: adenylate cyclase isoform i binding and PH domains ACAT: acylCoA–cholesterol acyltransferase aFGF: acidic fibroblast growth factor (FGF1) ACC: acetyl coenzyme-A carboxylase AGAP: ArfGAP with GTPAse, ankyrin ACE: angiotensin-converting enzyme repeat, and PH domains ACh: acetylcholine AGF: autocrine growth factor

929 930 List of Aliases

AGFG: ArfGAP with FG repeats ANT: adenine nucleotide transporter Ago: Argonaute protein Anx: annexin AGS: activator of G-protein signaling AOC: amine oxidase copper-containing AHR: aryl hydrocarbon receptor protein AIF: apoptosis-inducing factor AoV: aortic valve AIP: actin-interacting protein AP: (clathrin-associated) adaptor proteic AIRe: autoimmune regulator complex AKAP: A-kinase (PKA)-anchoring protein AP: Activator protein (transcription factor) ALE: arbitrary Eulerian Lagrangian AP: activating enhancer-binding protein ALIX: apoptosis-linked gene-2-interacting AP4A: diadenosine tetraphosphate protein-X APAF: apoptotic peptidase-activating factor ALK: anaplastic lymphoma kinase APAP: ArfGAP with PIx- and paxillin- ALKi: type-i activin receptor-like kinase binding domains (TGFβ receptor superfamily) APC: antigen-presenting cell ALOx5: arachidonate 5-lipoxygenase APC: adenomatous polyposis coli protein ALOx5AP: arachidonate 5-lipoxygenase (Ub ligase) activation protein APC/C: anaphase-promoting complex (or ALP: actinin-associated LIM protein cyclosome; Ub ligase) (PDLIM3) APH: anterior pharynx defective phenotype alsin: amyotrophic lateral sclerosis protein homolog (portmanteau) aPKC: atypical protein kinase C ALX: adaptor in lymphocytes of unknown APl: action potential function X Apn: adiponectin AMAP: A multidomain ArfGAP protein Apo: apolipoprotein AMBRA: activating molecule in beclin-1- ApoER: apolipoprotein-E receptor regulated autophagy protein APPL: adaptor containing phospho- AMHR: anti-Müllerian hormone receptor Tyr interaction, PH domain, and (TGFβ receptor superfamily) Leu zipper AMIS: apical membrane initiation site APS: adaptor with a PH and SH2 domain (lumenogenesis) Aqp: aquaporin AMP: adenosine monophosphate AR: adrenergic receptor (adrenoceptor) AMPAR: α-amino 3-hydroxy 5-methyl AR: androgen receptor (nuclear receptor 4-isoxazole propionic acid receptor NR3c4; transcription factor) AMPK: AMP-activated protein kinase AR: area ratio AMSH: associated molecule with SH3 ARAP: ArfGAP with RhoGAP, ankyrin domain (deubiquitinase) repeat, PH domains AmyR: amylin receptor Areg: amphiregulin (EGF superfamily Ang: angiopoietin member) AngL: angiopoietin-like molecule ARF: ADP-ribosylation factor Ank: ankyrin ArfRP: ARF-related protein ANP: atrial natriuretic peptide ARFTS: CKI2A-locus alternate reading ANPR (NP1): atrial natriuretic peptide frame tumor suppressor (ARF or receptor (guanylate cyclase) p14ARF ) ARE: activin-response element ARH: autosomal recessive hypercholes- ARE: androgen response element terolemia adaptor (low-density ARE: anti-oxidant response element lipoprotein receptor adaptor) ARNT: aryl hydrocarbon nuclear receptor ARH: aplysia Ras-related homolog translocator ArhGEF: RhoGEF ANS: autonomic nervous system ARL: ADP-ribosylation factor-like protein List of Aliases 931

ARNO: ARF nucleotide site opener BACE: β-amyloid precursor protein- ARP: absolute refractory period converting enzyme ARP: actin-related protein BAD: BCL2 antagonist of cell death ARPP: cAMP-regulated phosphoprotein BAF: barrier-to-autointegration factor Arr: arrestin BAG: BCL2-associated athanogene ART: arrestin-related transport adaptor (chaperone regulator) (α-arrestin) BAI: brain-specific angiogenesis inhibitor ART: adpribosyltransferase (adhesion-GPCR) Artn: artemin BAIAP: brain-specific angiogenesis ARVCF: armadillo repeat gene deleted in inhibitor-1-associated protein (insulin velocardiofacial syndrome receptor substrate) ARVD: arrythmogenic right ventricular BAK: BCL2-antagonist–killer dystrophy (i)BALT: (inducible) bronchus-associated AS: Akt (PKB) substrate lymphoid tissue ASAP: artery-specific antigenic protein BAMBI: BMP and activin membrane-bound ASAP: ArfGAP with SH3, ankyrin repeat, inhibitor homolog PH domains BAnk: B-cell scaffold with ankyrin repeats ASIC: acid-sensing ion channel Barkor: beclin-1-associated autophagy- ASK: apoptosis signal-regulating kinase related key regulator aSMC: airway smooth muscle cell BAT: brown adipose tissue ASP: actin-severing protein BATF: basic leucine zipper ATF-like AT: antithrombin transcription factor (B-cell-activating ATAA: ascending thoracic aortic aneurysm transcription factor) ATF: activating transcription factor BAX: BCL2-associated X protein AtG: autophagy-related gene product BBB: blood–brain barrier ATMK: ataxia telangiectasia mutated kinase BC: boundary condition ATn: angiotensin bCAM: basal cell adhesion molecule ATng: angiotensinogen (Lutheran blood group glycoprotein) AtOx: anti-oxidant protein (metallochaper- BCAP: B-cell adaptor for phosphatidylinosi- one) tol 3-kinase ATP: adenosine triphosphate BCAR: Breast cancer anti-estrogen ATPase: adenosine triphosphatase resistance docking protein ATR (AT 1/2): angiotensin receptor BCL: B-cell lymphoma (leukemia) protein ATRK: ataxia telangiectasia and Rad3- BCLxL: B-cell lymphoma extra-large related kinase protein AVN: atrioventricular node BCR: B-cell receptor AVV: atrioventricular valves BCR: breakpoint cluster region protein AW: analysis window Bdk: bradykinin BDNF: brain-derived neurotrophic factor B Becn, beclin: BCL2-interacting protein BEM: boundary element method B: Biot-Finger strain tensor Best: bestrophin B: bulk modulus bFGF: basic fibroblast growth factor (FGF2) B: bilinear form BFUe: burst-forming unit erythroid b: minor semi-axis BFUmeg: burst-forming unit megakaryocyte b: body force BGT: betaine–GABA transporter bˆ: unit binormal BH4: tetrahydrobiopterin (enzyme cofactor) B lymphocyte (B cell): bone marrow BID: BH3-interacting domain death agonist lymphocyte BIG: brefeldin-A-inhibited GEFs for ARFs 932 List of Aliases

BIK: BCL2-interacting killer c: stress vector BIM: BH3-containing protein BCL2-like 11 cτ:shear (BCL2L11) cw:wallshearstress BK: high-conductance, Ca++-activated, c: concentration voltage-gated K+ channel c(p):wavespeed BLK: B-lymphoid tyrosine kinase cp:isobarheatcapacity Blm: Bloom syndrome, RecQ DNA cv: isochor heat capacity helicase-like protein C1P: ceramide 1-phosphate BLnk: B-cell linker protein C-terminus: carboxy (carboxyl group BM: basement membrane COOH)-terminus BMAL: brain and muscle ARNT-like protein C/EBP: CCAAT/enhancer-binding protein (gene Bmal) CA: computed angiography BMAT: bone-marrow adipose tissue CAi: carbonic anhydrase isoform i BMF: BCL2 modifying factor Ca: calcium ++ BMP: bone morphogenetic protein (TGFβ CaV: voltage-gated Ca channel ++ superfamily) CaV1.x: L-type high-voltage-gated Ca BMPR: bone morphogenetic protein receptor channel ++ BNIP: BCL2/adenovirus E1B 19-kDa CaV2.x: P/Q/R-type Ca channel ++ protein-interacting protein CaV3.x: T-type low-voltage-gated Ca BNP: B-type natriuretic peptide channel BMX: bone marrow Tyr kinase gene in CAAT: cationic amino acid transporter chromosome-X product CABG: coronary artery bypass grafting BOC: brother of CDO Cables: CDK5 and Abl enzyme substrate BOK: BCL2-related ovarian killer CAK: CDK-activating kinase (pseudokinase) BORG: binder of Rho GTPase Cam: calmodulin (calcium-modulated BRAG: brefeldin-resistant ArfGEF protein) BrCa: breast cancer-associated (suscep- CamK: calmodulin-dependent kinase tibility) protein (tumor suppressor; cAMP: cyclic adenosine monophosphate DNA-damage repair; a.k.a. FancD1) CAP: adenylate cyclase-associated protein BrD: bromodomain-containing protein CAP: carboxyalkylpyrrole protein adduct BrK: breast tumor kinase CAP: chromosome-associated protein BrSK: brain-selective kinase (BrD4) BSEP: bile salt export pump CAPN: calpain gene BTF: basic transcription factor CaPON: carboxy-terminal PDZ ligand of BTK: Bruton Tyr kinase NOS1 (NOS1AP) BUB: budding uninhibited by benzimida- CAR: constitutive androstane receptor zoles (NR1i3) CaR: calcium-sensing receptor C CARP: cell division cycle and apoptosis regulatory protein C: stress tensor CAS: cellular apoptosis susceptibility C: compliance protein C: heat capacity CAS: CRK-associated substrate (or C: chronotropy P130CAS and BCAR1) Cx: type-x chemokine C (γ) CAs: cadherin-associated protein CD:dragcoefficient CASK: calcium–calmodulin-dependent Cf: friction coefficient serine kinase (pseudokinase) CL: lift coefficient CASL: CRK-associated substrate-related Cp: pressure coefficient protein (CAS2) List of Aliases 933

CASP: cytohesin-associated scaffold protein CeP: centrosomal protein caspase: cysteine-dependent aspartate- CEPC: circulating endothelial progenitor specific peptidase cell Cav: caveolin Cer: ceramide CBF: coronary blood flow CerK: ceramide kinase CBF: core-binding factor CerT: ceramide transfer protein CBL: Casitas B-lineage lymphoma adaptor CETP: cholesterol ester transfer protein and Ub ligase CFD: computational fluid dynamics CBLb: CBL-related adaptor CFLAR: caspase-8 and FADD-like apoptosis CBP: cap-binding protein regulator CBP: CREB-binding protein CFTR: cystic fibrosis transmembrane CBP: C-terminal Src kinase-binding protein conductance regulator β CBS: cystathionine -synthase (H2S CFU: colony-forming unit production) CFUb: CFU basophil (basophil-committed CCDC: coiled-coil domain-containing stem cells) protein ++ CFUc: CFU in culture (granulocyte CCICR: calcium channel-induced Ca precursors, i.e., CFUgm) release CFUe: CFU erythroid CCK4: colon carcinoma kinase 4 (PTK7) CFUeo: CFU eosinophil CCL: chemokine CC-motif ligand CFUg: CFU granulocyte CCN: CyR61, CTGF, and NOv (CCN1– CFUgm: CFU granulocyte–macrophage CCN3) family CFUgemm: CFU granulocyte–erythroid– Ccn: cyclin macrophage–megakaryocyte Ccnx–CDKi: type-x cyclin–type-i CFUm: CFU macrophage cyclin-dependent kinase dimer CFUmeg: CFU megakaryocyte CCPg: cell cycle progression protein CFUs: colony-forming unit spleen CCS: copper chaperone for superoxide (pluripotent stem cells) dismutase CG: chromogranin CCT: chaperonin containing T-complex cGK: cGMP-dependent protein kinase protein (protein kinase G) CCx: type-x chemokine CC (β) CCR: chemokine CC motif receptor cGMP: cyclic guanosine monophosphate CD: cluster determinant protein (cluster of CGN: cis-Golgi network differentiation) CGRP: calcitonin gene-related peptide CDase: ceramidase chanzyme: ion channel and enzyme CDC: cell division cycle protein chemokine: chemoattractant cytokine cDC: classical dendritic cell CHIP: C-terminus heat shock cognate-70- CDH: CDC20 homolog interacting protein Cdh: cadherin ChK: checkpoint kinase CDK: cyclin-dependent kinase CHK: CSK homologous kinase Cdm: caldesmon CHOP: CCAAT/enhancer-binding protein CDO: cell adhesion molecule-related/ homologous protein downregulated by oncogenes CHREBP: carbohydrate-responsive CE (CsE): cholesteryl esters element-binding protein CEC: circulating endothelial cell ChT: choline transporter CELSR: cadherin, EGF-like, LAG-like, and CI: cardiac index seven-pass receptor CICR: calcium-induced calcium release CenP: centromere protein Cin: chronophin CEP: carboxyethylpyrrole CIP: CDC42-interacting protein 934 List of Aliases

CIP2a: cancerous inhibitor of protein CntnAP: contactin-associated protein phosphatase-2A CO: cardiac output CIPC: CLOCK-interacting protein, circadian CoBl: Cordon-bleu homolog (actin CIS: cytokine-inducible SH2-containing nucleator) protein COLD: chronic obstructive lung disease CITED: CBP/P300-interacting transactivator COOL: Cloned out of library (RhoGEF6/7) with glutamic (E) and aspartic acid coSMAD: common (mediator) SMAD (D)-rich C-terminus-containing (SMAD4) protein COx: cyclooxygenase (prostaglandin CK: creatine kinase endoperoxide synthase) CK: casein kinase COx17: cytochrome-C oxidase copper CKI: cyclin-dependent kinase inhibitor chaperone CLAsP: CLiP-associated protein (microtu- CoP: coat protein bule binder) CoP: constitutive photomorphogenic protein ClASP: clathrin-associated sorting protein (Ub ligase) CLC: cardiotrophin-like cytokine COPD: chronic obstructive pulmonary ClC: voltage-gated chloride channel disease ClCa: calcium-activated chloride channel COUPTF: chicken ovalbumin upstream ClIC: chloride intracellular channel promoter transcription factor CLINT: clathrin-interacting protein located (NR2f1/2) in the trans-Golgi network CP4H: collagen prolyl 4-hydroxylase CLIP: corticotropin-like intermediate CPC: chromosomal passenger complex peptide CpG: cytidine-phosphate–guanosine CLiP: cytoplasmic CAP-Gly domain- oligodeoxynucleotide (motif) containing linker protein cPKC: conventional protein kinase C iCliP: intramembrane-cleaving peptidase Cpx: complexin (that clips) CR: complement component receptor CLK: CDC-like kinase Cr: creatine ClNS: Cl− channel nucleotide-sensitive cRABP: cellular retinoic acid-binding CLOCK: circadian locomotor output cycles protein kaput cRBP: cellular retinol-binding protein CLP: common lymphoid progenitor CRAC: Ca++ release-activated Ca++ CLS: ciliary localization signal channel Cmi: chylomicron CRACR: CRAC regulator CMLP: common myeloid–lymphoid Crb: Crumbs homolog polarity complex progenitor CRE: cAMP-responsive element CMP: common myeloid progenitor CREB: cAMP-responsive element-binding CMC: cardiomyocyte protein Col: collagen CRF: corticotropin-releasing factor (family) CoLec: collectin CRH: corticotropin-releasing hormone ColF: collagen ﬁber CRIB: CDC42/Rac interactive-binding CORM: carbon monoxide (CO)-releasing protein molecule CRIK: citron Rho-interacting, Ser/Thr CNG: cyclic nucleotide-gated channel kinase (STK21) CNS: central nervous system CRK: CT10 regulator of kinase CNT: connecting tubule CRK: chicken tumor virus regulator of CNTi: concentrative nucleoside transporter kinase (SLC28ai) CRKL: V-CRK avian sarcoma virus CT10 CNTF: ciliary neurotrophic factor homolog-like List of Aliases 935

CRL4: cullin-4A RING ubiquitin ligase CX3CLi: type-i CX3C (δ) chemokine ligand CRLR: calcitonin receptor-like receptor CX3CRi: type-i CX3C (δ) chemokine CRP: C-reactive protein receptor Crt: calreticulin cyCK: cytosolic creatine kinase CRTC: CREB-regulated transcription Cyld: cylindromatosis tumor suppressor coactivator protein (deubiquitinase USPL2) Cry: cryptochrome CyP: member of the cytochrome-P450 Cs: cholesterol superfamily CSBP: cytokine-suppressive anti- C3G: Crk SH3-binding GEF inflammatory drug-binding protein γ CSE: cystathionine -lyase (H2S production) D CSF: cerebrospinal fluid CSF: colony-stimulating factor CSF1: macrophage colony-stimulating D: dromotropy factor (mCSF) D: vessel distensibility CSF2: granulocyte–macrophage colony- D: diffusion coefficient stimulating factors (gmCSF and DT : thermal diffusivity sargramostim) D: deformation rate tensor CSF3: granulocyte colony-stimulating d: displacement vector factors (gCSF and filgrastim) D: flexural rigidity D CSK: C-terminal Src kinase : demobilization function (from prolifera- Csk: cytoskeleton tion to quiescence) d Csq: calsequestrin : death, decay, degradation rate CSS: candidate sphingomyelin synthase d: duration CT: cardiotrophin Dab: Disabled homolog CT: computed tomography DAD: delayed afterdepolarization CTBP: C-terminal-binding protein DAG: diacylglycerol CTen: C-terminal tensin-like protein DAPC: dystrophin-associated protein CTF: C-terminal fragment complex CTGF: connective tissue growth factor DAPK: death-associated protein kinase CTL: cytotoxic T lymphocyte DARC: Duffy antigen receptor for CTLA: cytotoxic T-lymphocyte-associated chemokine protein DAT: dopamine active transporter Ctn: catenin DAX: dosage-sensitive sex reversal, CTr: copper transporter adrenal hypoplasia critical region on CtR: calcitonin receptor chromosome X (NR0b1) CTRC: CREB-regulated transcription DBC: deleted in breast cancer protein coactivator DBP: albumin D-element binding protein Cul: cullin (PAR/b–ZIP family) CUT: cryptic unstable transcript DC: dendritic cell CVI: chronic venous insufficiency DCA: directional coronary atherectomy CVLM: caudal ventrolateral medulla DCAF: DDB1- and Cul4-associated factor CVP: central venous pressure DCC: deleted in colorectal carcinoma (netrin CVS: cardiovascular system receptor) Cx: connexin DCT: distal convoluted tubule CXCLi: type-i CXC (C-X-C motif; α) Dctn: dynactin chemokine ligand DDAH: dimethylarginine dimethyl- CXCRi: type-i CXC (C-X-C motif; α) aminohydrolase chemokine receptor DDB: damage-specific DNA-binding protein 936 List of Aliases

DDEF: development and differentiation- Dsc: desmocollin enhancing factor (ArfGAP) Dsg: desmoglein DDR: discoidin domain receptor Dsh: Disheveled (Wnt-signaling mediator) De: Dean number DSK: dual-specificity kinase DEC: differentially expressed in chondro- dsRNA: double-stranded RNA cytes (DEC1 and DEC2 are a.k.a Dst: dystonin bHLHe40 and bHLHe41, bHLHb2 DUb: deubiquitinase and bHLHb3, or HRT2 and HRT1) DUS: Doppler ultrasound DEC: deleted in esophageal cancer DuSP: dual-specificity phosphatase DEG: delayed-early gene DV: dead space volume deoxyHb: deoxyhemoglobin (deoxygenated Dvl: Disheveled (cytoplasmic phosphopro- hemoglobin) tein; other alias Dsh) DETC: dendritic epidermal γδ Tcell DVT: deep-vein thrombosis DH: Dbl homology dynactin: dynein activator DHET: dihydroxyeicosatrienoic acid DYRK: dual-specificity Tyr (Y) DHh: desert Hedgehog phosphorylation-regulated kinase Dia: Diaphanous DICOM: digital imaging and communication E for medicine ++ DICR: depolarization-induced Ca release E: strain tensor DISC: death-inducing signaling complex E: electric field Dkk: Dickkopf E: elastic modulus DLg: Disc large homolog E: elastance DLL: Delta-like (Notch) ligand E:energy { }3 DLx: distal-less homeobox protein eî i=1:basis DM: double minute e: strain vector DMM: DNA methylation modulator e: specific free energy DMPK: myotonic dystrophy-associated E-box: enhancer box sequence of DNA protein kinase E2: ubiquitin conjugase DMT: divalent metal transporter E3: ubiquitin ligase DN1: double-negative-1 cell EAAT: excitatory amino acid (glutamatee– DN2: double-negative-2 cell aspartate) transporter DN3: double-negative-3 cell EAD: early afterdepolarization DNA: deoxyribonucleic acid EAR: V-erbA-related nuclear receptor DNAPK: DNA-dependent protein kinase (NR2f6) DoC2: double C2-like domain-containing EB: end-binding protein protein EBCT: electron beam CT DOCK: dedicator of cytokinesis (GEF) EBF: early B-cell factor DOK: downstream of Tyr kinase docking EC: endothelial cell protein ECA: external carotid artery DOR: δ-opioid receptor ECF: extracellular fluid DPG: diphosphoglyceric acid ECG: electrocardiogram DRAM: damage-regulated modulator of ECM: extracellular matrix autophagy ED1L: EGF-like repeat- and discoidin-1-like DRF: Diaphanous-related formin (for domain-containing protein GTPase-triggered actin rearrange- EDGR: endothelial differentiation gene ment) receptor DRG: dorsal root ganglion EDHF: endothelial-derived hyperpolarizing Drl: Derailed factor List of Aliases 937

EDIL: EGF-like repeats and discoidin-1 EPDC: epicardial-derived cell (I)-like domain-containing protein Epgn: epigen (EGF superfamily member) EDV: end-diastolic volume EPH: erythropoietin-producing hepatocyte EEA: early endosomal antigen receptor kinase or pseudokinase eEF: eukaryotic translation elongation factor (EPHa10 and EPHb6) EEL: external elastic lamina ephrin: EPH receptor interactor EET: epoxyeicosatrienoic acid Epo: erythropoietin EFA6: exchange factor for ARF6 (ArfGEF) EPS: epidermal growth factor receptor EF-Tu: elongation factor Tu pathway substrate EGF: epidermal growth factor ER: endoplasmic reticulum EGFL: EGF-like domain-containing protein ERx: type-x estrogen receptor (NR3a1/2) EGFR: epidermal growth factor receptor eRas: embryonic stem cell-expressed Ras (or EGR: early growth response transcription hRas2) factor ErbB: erythroblastoma viral gene product B EHD: C-terminal EGFR substrate-15 (HER) homology domain-containing protein ERE: estrogen response element (DNA eIF: eukaryotic translation initiation factor sequence) EL: endothelial lipase Ereg: epiregulin (EGF superfamily member) ELAM: endothelial–leukocyte adhesion eRF: eukaryotic release factor molecules ERGIC: endoplasmic reticulum–Golgi ELCA: excimer laser coronary angioplasty intermediate compartment ELK: ETS-like transcription factor (ternary ERK: extracellular signal-regulated protein complex factor [TCF] subfamily) kinase ElMo: engulfment and cell motility adaptor ERK1/2: usually refers to ERK1 and ERK2 Eln: elastin ERM: ezrin–radixin–moesin ElnF: elastin ﬁber ERMES: endoplasmic reticulum– ELP: early lymphoid progenitor mitochondrion encounter structure EMI: early mitotic inhibitor ERP: effective refractory period EMR: EGF-like module-containing, ERR: estrogen-related receptor (NR3b1– mucin-like, hormone receptor-like NR3b3) protein ESCRT: endosomal sorting complex EMT: epithelial–mesenchymal transition required for transport ENA–VASP: Enabled homolog and ESL: E-selectin ligand vasoactive (vasodilator)-stimulated ESRP: epithelial splicing regulatory protein phosphoprotein family ESV: end-systolic volume ENaC: epithelial Na+ channel ET: endothelin EnaH: Enabled homolog ETP: early thymocyte progenitor endo-siRNA: endogenous small interfering ETR (ETA/B): endothelin receptor RNA ETS: E-twenty six (transcription fac- ENPP: ectonucleotide pyrophosphatase– tor; erythroblastosis virus E26 phosphodiesterase proto-oncogene product homolog) Ens: endosulﬁne ETV: ETS-related translocation variant ENT: equilibrative nucleoside transporter EVAR: endovascular aneurysm repair ENTPD: ectonucleoside triphosphate Exo: exocyst subunit diphosphohydrolase Ext: exostosin (glycosyltransferase) EPAC: exchange protein activated by cAMP EPAS: endothelial PAS domain protein F EPC: endothelial progenitor cell EPCR: endothelial protein-C receptor F: transformation gradient tensor 938 List of Aliases

F: function fraction of proliferating cells FHoD: formin homology domain-containing F: erythrocytic rouleau fragmentation rate protein (FmnL) f: surface force FIH: factor inhibiting HIF1α (asparaginyl fˆ: fiber direction unit vector hydroxylase) f : binding frequency FIP: focal adhesion kinase family-interacting fC: cardiac frequency protein fR: breathing frequency FIT: Fat-inducing transcript f : friction shape factor FKBP: FK506-binding protein fv: head loss per unit length FlIP: flice-inhibitory protein fi: molar fraction of gas component i FLK: fetal liver kinase FA: fatty acid fMLP: N-formyl methionyl-leucyl- FABP: fatty acid-binding protein phenylalanine FABP: filamentous actin-binding protein FN: fibronectin FACAP: F-actin complex-associated protein Fn: fibrin FAD: flavine adenine dinucleotide Fng: fibrinogen FADD: Fas receptor-associated death Fos: Finkel Biskis Jinkins murine osteosar- domain coma virus sarcoma proto-oncogene FAK: focal adhesion kinase product Fanc: Fanconi anemia protein Fox: forkhead box transcription factor FAN: Fanconi anemia-associated nuclease Fpn: ferroportin FAPP: phosphatidylinositol four-phosphate FR: flow ratio adaptor protein FRK: Fyn-related kinase Fas: death receptor (TNFRSF6a) FrmD: FERM domain-containing adaptor FasL: death ligand (TNFSF6) FRNK: FAK-related non-kinase FAST: Forkhead activin signal transducer FRS: fibroblast growth factor receptor FB: fibroblast substrate Fbln (Fibl): fibulin FSH: follicle-stimulating hormone Fbn: fibrillin FSI: fluid–structure interaction FBS: F-box, Sec7 protein (ArfGEF) FVM: finite volume method FBx: F-box only protein (ArfGEF) FXR: farnesoid X receptor (NR1h4) FC: fibrocyte Fz: Frizzled (Wnt GPCR) FCHO: FCH domain only protein FcαR: Fc receptor for IgA FcγR: Fc receptor for IgG G FcR: Fc receptor for IgE FCP: TF2F-associating C-terminal domain G: Green-Lagrange strain tensor phosphatase G: shear modulus FDM: finite difference method G : storage modulus FEM: finite element method G : loss modulus FERM: four point-1, ezrin–radixin–moesin G: Gibbs function domain G: conductance Fer: Fes-related Tyr kinase Gp: pressure gradient Fes: feline sarcoma kinase Ge: electrical conductivity FFA: free fatty acid Gh: hydraulic conductivity FGF: fibroblast growth factor GT: thermal conductivity FGFR: fibroblast growth factor receptor g: gravity acceleration FGR: viral feline Gardner-Rasheed sarcoma g: physical quantity oncogene homolog kinase g: detachment frequency FHL: four-and-a-half LIM-only protein g: free enthalpy List of Aliases 939

G protein: guanine nucleotide-binding GCN2: general control non-derepressible 2 protein (Gαβγ trimer) (pseudokinase) Gα: α subunit (signaling mediator) of gCSF: granulocyte colony-stimulating factor G protein (CSF3) Gαi (Gi): inhibitory Gα subunit GD: disialoganglioside Gαs (Gs): stimulatory Gα subunit GDP: guanosine diphosphate Gαt (Gt): transducin, Gα subunit of GDF: growth differentiation factor rhodopsin GDF: (Rab)GDI displacement (dissociation) GsXL: extra-large Gs protein factor Gαi/o (Gi/o): Gα subunit class GDI: guanine nucleotide-dissociation α α G q/11 (Gq/11): G subunit class inhibitor α α G 12/13 (G12/13): G subunit class GDNF: glial cell line-derived neurotrophic Gβγ: dimeric subunit (signaling effector) of factor G protein GEF: guanine nucleotide (GDP-to-GTP)- Ggust : gustducin, G protein α subunit (Gi/o) exchange factor of taste receptor GF: growth factor Gol f : G protein α subunit (Gs) of olfactory GFAP: glial fibrillary acidic protein receptor (intermediate filament) GAB: GRB2-associated binder GFL: GDNF family of ligands GABA: γ-aminobutyric acid GFP: geodesic front propagation − GABAA: GABA ionotropic receptor (Cl GFR: growth factor receptor channel) GFRαi: type-i GDNF family receptor-α GABAB: GABA metabotropic receptor GGA: Golgi-localized γ-adaptin ear- (GPCR) containing Arf-binding protein GABARAP: GABAA receptor-associated Ggust: (G protein) Gα subunit gustducin protein GH: growth hormone GaBP: globular actin-binding protein GHR: growth hormone receptor GADD: growth arrest and DNA-damage- GHRH: growth hormone-releasing hormone induced protein GIP: GPCR-interacting protein gadkin: γ1-adaptin and kinesin interactor GIRK: Gβγ-regulated inwardly rectifying GAG: glycosaminoglycan K+ channel GAK: cyclin G-associated kinase GIT: GPCR kinase-interacting protein Gal: galanin GKAP: G-kinase-anchoring protein GAP: GTPase-activating protein GKAP: glucokinase-associated phosphatase GAPDH: glyceraldehyde 3-phosphate (DuSP12) dehydrogenase GKAP: guanylate kinase-associated protein GAS: growth arrest-specific non-coding, GLK: GCK-like kinase single-stranded RNA GluK: ionotropic glutamate receptor (kainate GAT: γ-aminobutyric acid transporter type) GATA: DNA sequence GATA-binding GluN: ionotropic glutamate receptor protein (TF) (NMDA type) GBF: Golgi-associated brefeldin-A-resistant GluR: ionotropic glutamate receptor (AMPA guanine nucleotide-exchange factor type) GCAP: guanylate cyclase-activating protein GluT: glucose transporter GCC: Golgi coiled-coil domain-containing GlyCAM: glycosylation-dependent cell protein adhesion molecule GCK: germinal center kinase GlyR: glycine receptor (channel) GCKR: GCK-related kinase GlyT: glycine transporter GCNF: germ cell nuclear factor (NR6a1) GM: monosialoganglioside 940 List of Aliases gmCSF: granulocyte–monocyte colony- HAND: heart and neural crest derivatives stimulating factor (CSF2) expressed protein GMP: granulocyte–monocyte progenitor Hb: hemoglobin GMP: guanosine monophosphate HbSNO: Snitrosohemoglobin GnRH: gonadotropin-releasing hormone HBEGF: heparin-binding EGF-like growth GP: glycoprotein factor Gpc: glypican HCK: hematopoietic cell kinase GPI: glycosyl-phosphatidylinositol anchor HCLS: hematopoietic lineage cell-specific gpiAP: GPI-anchored protein Lyn substrate protein GPCR: G-protein-coupled receptor HCN: hyperpolarization-activated, cyclic GPx: glutathione peroxidase nucleotide-gated K+ channel GQ: quadrisialoganglioside HCNP: hippocampal cholinergic neurostim- GR: glucocorticoid receptor (NR3c1) ulatory peptide GRAP: GRB2-related adaptor protein (or HCT: helical CT GAds) HDAC: histone deacetylase complex GRB: growth factor receptor-bound protein HDL: high-density lipoprotein GRC: growth factor-regulated, Ca++- HDL–C: HDL–cholesterol permeable, cation channel (TRPV2) HDL–CE: HDL–cholesteryl ester GRE: glucocorticoid response element HDM: human double minute (Ub ligase) (DNA sequence) HEET: hydroxyepoxyeicosatrienoic GRK: G-protein-coupled receptor kinase hemin: heme oxygenase-1 inducer GRP: G-protein-coupled receptor phospha- HERG: human ether-a-go-go related gene tase HER: human epidermal growth factor GSH: reduced form of glutathione receptor (HER3: pseudokinase) GSK: glycogen synthase kinase HES: Hairy enhancer of split GSSG: oxidized form of glutathione HETE: hydroxyeicosatrienoic acid (glutathione disulfide) HEV: high endothelial venule GT: trisialoganglioside HGF: hepatocyte growth factor GTF: general transcription factor HGFA: hepatocyte growth factor activator GTP: guanosine triphosphate (serine peptidase) GTPase: guanosine triphosphatase HGFR: hepatocyte growth factor receptor GuCy: guanylate cyclase (CyG) HGS: HGF-regulated Tyr kinase substrate GWAS: genome-wide association study (HRS) HhIP: Hedgehog-interacting protein H HIF: hypoxia-inducible factor HIP: huntingtin-interacting protein H: height HIP1R: HIP1-related protein H : history function His: histamine H: dissipation Hjv: hemojuvelin h: head loss HK: hexokinase h: thickness HL: hepatic lipase h: specific enthalpy HMG: high mobility group protein hT: heat transfer coefficient HMGB: high mobility group box protein hm: mass transfer coefficient HMGCoAR: hydroxy methylglutaryl HA: hyaluronic acid coenzyme-A reductase HAD: haloacid dehalogenase HMT: histone methyl transferase HAP: huntingtin-associated protein HMWK: high-molecular-weight kininogen HAT: histone acetyltransferase HNF: hepatocyte nuclear factor (NR2a1/2) HAAT: heterodimeric amino acid transporter HNP: human neutrophil peptide List of Aliases 941 hnRNP: heterogeneous nuclear ribonucleo- ID: inhibitor of DNA binding protein IDL: intermediate-density lipoprotein HODE: hydroxy octadecadienoic acid IDmiR: immediately downregulated HOP: HSP70–HSP90 complex-organizing microRNA protein IDOL: inducible degrader of LDL receptor HotAIR: HOX antisense intergenic RNA (Ub ligase) (large intergenic non-coding RNA) IEG: immediate-early gene HOx: heme oxygenase IEL: internal elastic lamina Hox: homeobox DNA sequence (en- IEL: intra-epithelial lymphocyte codes homeodomain-containing IfIH: interferon-induced with helicase-C morphogens) domain-containing protein HPK: hematopoietic progenitor kinase Ifn: interferon (MAP4K) IfnAR: interferon-α/β/ω receptor hpRNA: long hairpin RNA IFT: intraflagellar transport complex hRas: Harvey Ras Ig: immunoglobulin HRE: hormone response element (DNA IGF: insulin-like growth factor sequence) IGFBP: IGF-binding protein HRM: hypoxia-regulated microRNA IgHC: immunoglobulin heavy chain hRNP: heterogeneous ribonucleoprotein IgLC: immunoglobulin light chain HRS: hepatocyte growth factor-regulated iGluR: ionotropic glutamate receptor Tyr kinase substrate IH: intimal hyperplasia HRT: Hairy and enhancer of Split-related IHh: indian Hedgehog transcription factor IK: intermediate-conductance Ca++- HS: heparan sulfate activated K+ channel HSC: hematopoietic stem cell IκB: inhibitor of NFκB HSC: heat shock cognate IKK: IκB kinase HSER: heat stable enterotoxin receptor (guanylate cyclase 2C) IL: interleukin HSP: heat shock protein (chaperone) ILC: innate lymphoid cell HSPG: heparan sulfate proteoglycan iLBP: intracellular lipid-binding protein Ht: hematocrit ILK: integrin-linked (pseudo)kinase HTR: high temperature requirement IMM: inner mitochondrial membrane endopeptidase IMP: Impedes mitogenic signal propagation INADl: inactivation no after-potential D I protein InCenP: inner centromere protein I: identity tensor InF: inverted formin i: current InsIG: insulin-induced gene product I: inotropy (ER anchor) IAP: inhibitor of apoptosis protein InsL: insulin-like peptide IBABP: intestinal bile acid-binding protein InsR (IR): insulin receptor IC: isovolumetric contraction InsRR: insulin receptor-related receptor ICA: internal carotid artery IP: inositol phosphate ICAM: intercellular adhesion molecule IP3: inositol (1,4,5)-trisphosphate ++ (IgCAM member) IP3R: IP3 receptor (IP3-sensitive Ca - IgCAM: immunoglobulin-like cell adhesion release channel) molecule IP4: inositol (1,3,4,5)-tetrakisphosphate ICF: intracellular fluid IP5: inositol pentakisphosphate ICliP: intramembrane-cleaving peptidase IP6: inositol hexakisphosphate 942 List of Aliases

IPCEF: interaction protein for cytohesin JNK: Jun N-terminal kinase (MAPK8– exchange factor MAPK10) IPOD: (perivacuolar) insoluble protein JNKBP: JNK-binding protein; deposit JNKK: JNK kinase IPP: inositol polyphosphate phosphatase JSAP: JNK/SAPK-associated protein IPP: ILK–PINCH–parvin complex Jun: avian sarcoma virus-17 proto-oncogene iPSC: induced pluripotent stem cell product (Japanese juunana: seventeen IQGAP: IQ motif-containing GTPase- [17]; TF) activating protein (IQ: first 2 amino JUNQ: juxtanuclear quality-control acids of the motif: isoleucine [I; compartment commonly] and glutamine [Q; invariably]). IR: isovolumetric relaxation K IRAK: IL1 receptor-associated kinase (IRAK2: pseudokinase) K: conductivity tensor IRE: irreversible electroporation K: bending stiffness IRES: internal ribosome entry site K: reflection coefficient IRF: interferon-regulatory protein (transcrip- Kd: dissociation constant (index of ligand– tion factor) target affinity: ([L][T])/[C]; [L], [T], IRFF: interferon-regulatory factor family [C]: molar concentrations of the IRP: iron regulatory protein ligand, target, and created complex, IRS: insulin receptor substrate respectively) ISA: intracranial saccular aneurysm KM: Michaelis constant (chemical reaction ISG: interferon-stimulated gene product kinetics) iSMAD: inhibitory SMAD (SMAD6 or Km: material compressibility SMAD7) k: cross-section ellipticity ITAM: immunoreceptor tyrosine-based kATP : myosin ATPase rate −23 activation motif kB: Boltzmann constant (1.38×10 J/K) Itch: Itchy homolog (Ub ligase) kc: spring stiffness Itg: integrin km: mass-transfer coefficient ITIM: immunoreceptor tyrosine-based kP: Planck constant inhibitory motif KR: resistance coefficient KaP: karyopherin ITK: interleukin-2-inducible T-cell kinase + ITPK: inositol trisphosphate kinase KATP : ATP-sensitive K channel IVC: inferior vena cava KCa1.x: BK channel IVP: initial value problem KCa2/3/4.x: SK channel KCa5.x: IK channel IVUS: intravascular ultrasound + KIR: inwardly rectifying K channel + KV: voltage-gated K channel J KAP: kinesin (KIF)-associated protein Kap: karyopherin J:flux KAT: lysine (K) acetyltransferase + − Jm: cell surface current density KCC: K –Cl cotransporter JAM: junctional adhesion molecule KChAP: K+ channel-associated protein JaK: Janus (pseudo)kinase KChIP: KV channel-interacting protein JIP: JNK-interacting protein (MAPK8IP1 KDELR: KDEL (Lys–Asp–Glu–Leu) and -2) endoplasmic reticulum retention JMy: junction-mediating and regulatory receptor protein KDR: kinase insert domain receptor List of Aliases 943

KHC: kinesin heavy chain Le: entry length KIF: kinesin family LEF: lymphoid enhancer-binding transcrip- KIR: killer cell immunoglobulin-like tion factor receptor LGalS: lectin, galactoside-binding, soluble KIT: cellular kinase in tyrosine (SCFR) cell adhesion molecule Kk: kallikrein LGIC: ligand-gated ion channel KLC: kinesin light chain LGL: lethal giant larva protein KLF: Krüppel-like factor LH: luteinizing hormone KLR: killer cell lectin-like receptor LIF: leukemia-inhibitory factor Kn: Knudsen number LIFR: leukemia-inhibitory factor receptor KOR: κ-opioid receptor LIMA: LIM domain and actin-binding kRas: Kirsten Ras protein Krt: keratin LIME: LcK-interacting molecule KSR: kinase suppressor of Ras (adaptor; LIMK: Lin1, Isl1, and Mec3 motif- pseudokinase) containing kinase LIMS: LIM and senescent cell antigen-like- L containing domain protein LiNC: linker of nucleoskeleton and L: velocity gradient tensor cytoskeleton L:inertance lincRNA: large intergenic non-coding RNA L: length LipC: hepatic lipase LA: left atrium LipD: lipoprotein lipase LAB: linker of activated B lymphocyte LipE: hormone-sensitive lipase LAd: LcK-associated adaptor LipG: endothelial lipase LANP: long-acting natriuretic peptide LipH: lipase-H LAP: leucine-rich repeat and PDZ liprin: LAR PTP-interacting protein domain-containing protein (4-member LIR: leukocyte immunoglobulin-like family) receptor LAP: latency-associated peptide (4 isoforms LIS: lissencephaly protein LAP1–LAP4) LKB: liver kinase-B LAP: nuclear lamina-associated polypeptide LKLF: lung Krüppel-like factor LAR: leukocyte common-antigen-related LLTC: large latent TGFβ complex receptor (PTPRF) LMan: lectin, mannose-binding LAT: linker of activated T lymphocytes LMO: LIM domain-only-7 protein LaTS: large tumor suppressor Lmod: leiomodin (actin nucleator) LAX: linker of activated X cells (both B and LMPP: lymphoid-primed multipotent T cells) progenitor LBR: lamin-B receptor LMR: laser myocardial revascularization LCA: left coronary artery Ln: laminin LCAT: lysolecithin cholesterol acyltrans- LOx: lipoxygenase ferase LP: lipoprotein LCC: left coronary cusp LPA: lysophosphatidic acid LCK: leukocyte-speciﬁc cytosolic LPase: lipoprotein lipase (non-receptor) Tyr kinase lpDC: lamina propria dendritic cell LCP: lymphocyte cytosolic protein (adaptor Lphn: latrophilin (adhesion-GPCR) SLP76) LPL: lysophospholipid LDL: low-density lipoprotein LPLase: lysophospholipase LDLR: low-density lipoprotein receptor LPP: lipid phosphate phosphatase LDV: laser Doppler velocimetry LPR: lipid phosphatase-related protein 944 List of Aliases

LPS: lipopolysaccharide MAIT: mucosal-associated invariant LQTS: long-QT syndrome T lymphocyte LRAT: lecithin–retinol acyltransferase MALT: mucosa-associated lymphoid tissue LRH: liver receptor homolog (NR5a2) MAO: monoamine oxidase LRO: lysosome-related organelle MAP: microtubule-associated protein LRP: LDL receptor-related protein MAP1LC3: microtubule-associated LRRTM: leucine-rich repeat-containing protein-1 light chain-3 (LC3) transmembrane protein mAP: mean arterial pressure LSK: Lin−,SCA1+,KIT+ cell MAPK: mitogen-activated protein kinase LST: lethal with Sec-thirteen MAP2K: MAPK kinase LSV: long saphenous vein MAP3K: MA2KP kinase LT (Lkt): leukotriene MAP3K7IP: MAP3K7-interacting protein LTBP: latent TGFβ-binding protein MAPKAPK: MAPK-activated protein ++ LTCC: L-type Ca channel (CaV1) kinase LTK: leukocyte tyrosine kinase MARCKS: myristoylated alanine-rich LUbAC: linear ubiquitin chain assembly C kinase substrate complex MaRCo: macrophage receptor with LV: left ventricle collagenous structure (ScaRa2) LVAD: left ventricular assist device MARK: microtubule affinity-regulating LX: lipoxin kinase LXR: liver X receptor (NR1h2/3) MASTL: microtubule-associated Ser/Thr LyVE: lymphatic vessel endothelial kinase-like protein hyaluronan receptor MAT: ménage à trois MATK: megakaryocyte-associated Tyr M kinase MAVS: mitochondrial antiviral signaling M: molar mass protein M : moment MBP: myosin-binding protein m: mass MBP: myeloid–B-cell progenitor Ma: Mach number MBTPSi: membrane-bound transcription MACF: microtubule-actin crosslinking factor peptidase site i factor MCAK: mitotic centromere-associated mAChR: acetylcholine muscarinic receptor kinesin (metabotropic; GPCR) MCAM: melanoma cell adhesion molecule MAD: mothers against decapentaplegic MCL1: BCL2-related myeloid cell leukemia homolog sequence protein-1 MAD: mitotic arrest-deficient protein MCLC: stretch-gated Mid1-related chloride MAdCAM: mucosal vascular addressin cell channel adhesion molecule MCM: minichromosome maintenance MAF: V-maf musculoaponeurotic fi- protein brosarcoma oncogene homolog MCP: monocyte chemoattractant protein (TF) mCSF: macrophage colony-stimulating MAGI: membrane-associated guanylate factor (CSF1) kinase-related protein with inverted MCT: monocarboxylate–proton cotrans- domain organization porter MAGP: microfibril-associated glycoprotein mDC: myeloid dendritic cell MAGuK: membrane-associated guanylate MDM: mitochondrial distribution and kinase morphology protein List of Aliases 945

MDR: multiple drug resistance (ABC MLKL: mixed lineage kinase-like transporter) pseudokinase MEF: myocyte enhancer factor MLL: mixed lineage [myeloid–lymphoid] megCSF: megakaryocyte colony-stimulating leukemia factor factor MLLT: mixed lineage leukemia translocated MEJ: myoendothelial junction protein MELK: maternal embryonic leucine zipper MLP: muscle LIM protein kinase mmCK: myoﬁbrillar creatine kinase MEP: megakaryocyte erythroid progenitor MME: membrane metalloendopeptidase MEP: myeloid–erythroid progenitor MMM: maintenance of mitochondrial MET: mesenchymal–epithelial transition morphology protein factor (proto-oncogene; HGFR) MMP: matrix metallopeptidase METC: mitochondrial electron transport MO: mouse protein chain Mo: monocyte metHb: methemoglobin MOMP: mitochondrial outer membrane MGIC: mechanogated ion channel permeabilization μ mGluR: metabotropic glutamate receptor MOR: -opioid receptor MGP: matrix Gla protein MP: MAPK partner MHC: major histocompatibility complex MPF: mitosis (maturation)-promoting factor MHC: myosin heavy chain (CcnB–CDK1 complex) MyHC or MYH: myosin heavy chain gene MPG: N-methylpurine (N-methyladenine)- DNA glycosylase miCK: mitochondrial creatine kinase MPO: median preoptic nucleus MiCU: mitochondrial calcium uptake protein Mpo: myeloperoxidase Mid: midline MP : membrane protein, palmitoylated MinK: misshapen-like kinase P MPP: multipotent progenitor miR: microRNA MR: mineralocorticoid receptor (NR3c2) miRNP: microribonucleoprotein mRas: muscle Ras (or rRas3) MiRP: MinK-related peptide MRCK: myotonic dystrophy kinase-related MIRR: multichain immune-recognition CDC42-binding kinase receptor MRI: (nuclear) magnetic resonance imaging MIS: Müllerian inhibiting substance mRNA: messenger RNA MIS: mini-invasive surgery mRNP: messenger ribonucleoprotein MIS: mitochondrial intermembrane space MRTF: myocardin-related transcription MIST: mastocyte immunoreceptor signal factor transducer MSC: mesenchymal stem cell MIT: mini-invasive therapy MSH: melanocyte-stimulating hormone MiV: mitral valve MSIC: mechanosensitive ion channel MIZ: Myc-interacting zinc ﬁnger protein MSSCT: multi-slice spiral CT MJD: Machado-Joseph disease protein MST: mammalian sterile-twenty-like kinase domain-containing peptidase (DUb) MSt1R: macrophage-stimulating-1 factor MKL: megakaryoblastic leukemia-1 fusion receptor (RON) coactivator MT: metallothionein MKP: mitogen-activated protein kinase MTM: myotubularin (myotubular myopathy- phosphatase associated gene product) MLC: myosin light chain mtMMP: membrane-type MMP (mtiMMP: MLCK: myosin light-chain kinase type-i mtMMP) MLCP: myosin light-chain phosphatase MTMR: myotubularin-related phosphatase MLK: mixed lineage kinase MTOC: microtubule organizing center 946 List of Aliases

MTP: myeloid–T-cell progenitor Ncdn: neurochondrin MTP: microsomal triglyceride transfer NCK: non-catalytic region of Tyr kinase protein adaptor MuRF: muscle-specific RING finger NCoA: nuclear receptor coactivator (Ub ligase) NCoR: nuclear receptor corepressor MuSK: muscle-specific kinase NCR: natural cytotoxicity-triggering MVB: multivesicular body receptor MVE: multivesicular endosome (MVB) ncRNA: non-coding RNA MVO2: myocardial oxygen consumption NCS: neuronal calcium sensor MWSS: maximal wall shear stress NCKX: Na+–Ca++–K+ exchanger MyB: V-myb myeloblastosis viral oncogene NCLX: Na+–Ca++–Li+ exchanger homolog (TF) NCX: Na+–Ca++ exchanger + − − MyC: V-myc myelocytomatosis viral NDCBE: Na -dependent Cl –HCO3 oncogene homolog (TF) exchanger MyHC: myosin heavy chain NecL: nectin-like molecule MyLC or MYL: myosin light-chain gene NEDD: neural precursor cell expressed, MyPT: myosin phosphatase targeting subunit developmentally downregulated MyT: myelin transcription factor NDFIP: NEDD4 family-interacting protein NeK: never in mitosis gene-A (NIMA)- N related kinase NES: nuclear export signal N: sarcomere number NESK: NIK-like embryo-specific kinase nˆ: unit normal vector nesprin: nuclear envelope spectrin repeat n: mole number protein n: PAM density with elongation x NeuroD: neurogenic differentiation protein n: myosin head density NF: neurofilament protein (intermediate NA: Avogadro number filament) N-terminus: amino (amine group NH2)- NF: neurofibromin (RasGAP) terminus NFAT: nuclear factor of activated T cells NAADP: nicotinic acid adenine dinucleotide NFe2: erythroid-derived nuclear factor-2 phosphate NFH: neurofilament, heavy polypeptide nAChR: acetylcholine nicotinic receptor NFκB: nuclear factor κ light chain enhancer (ionotropic; LGIC) of activated B cells NAD: nicotine adenine dinucleotide NFL: neurofilament, light polypeptide NADPH: reduced form of nicotinamide NFM: neurofilament, medium polypeptide adenine dinucleotide phosphate NGAL: neutrophil gelatinase-associated NAd: noradrenaline lipocalin NAF: nutrient-deprivation autophagy factor NGF: nerve growth factor NALT: nasal-associated lymphoid tissu Ngn: neogenin (netrin receptor) NAmPT: nicotinamide phosphoribosyltrans- NHA: Na+–H+ antiporter ferase NHE: Na+–H+ exchanger Nanog: ever young (Gaelic) NHERF: NHE regulatory factor NAP: NCK-associated protein (NCKAP) NHR: nuclear hormone receptor NAT: nucleobase–ascorbate transporter NIc: nucleoporin-interacting protein NAT1: noradrenaline transporter NIK: NFκB-inducing kinase + NaV voltage-gated Na channel NIK: NCK-interacting kinase + − NBC: Na –HCO3 cotransporters NIP: neointimal proliferation NCC: non-coronary cusp NK: natural killer cell NCC: Na+–Cl− cotransporter NKCC: Na+–Ka+–2Cl− cotransporter List of Aliases 947

NKG: NK receptor group NST: nucleus of the solitary tract NKT: natural killer T cell NT: neurotrophin NKx2: NK2 transcription factor-related NT5E: ecto-5-nucleotidase homeobox protein NTCP: sodium–taurocholate cotransporter NLR: NOD-like receptor (nucleotide- polypeptide binding oligomerization domain, NTF: N-terminal fragment Leu-rich repeat-containing) NTP: nucleoside triphosphate NLS: nuclear localization signal NTPase: nucleoside triphosphate hydrolase NMDAR: Nmethyl Daspartate receptor superfamily member NmU: neuromedin-U NTRK: neurotrophic tyrosine receptor NO: nitric oxide (nitrogen monoxide) kinase (TRK) NonO: non-POU domain-containing NTRKR: neurotrophic Tyr receptor octamer-binding protein kinase-related protein (ROR(RTK)) NOR: neuron-derived orphan receptor NTS: nucleus tractus solitarius (NR4a3) Nu: Nusselt number NOS: nitric oxide synthase NuAK: nuclear AMPK-related kinase NOS1: neuronal NOS NuP: nucleoporin (nuclear-pore complex NOS1AP: NOS1 adaptor protein protein) NOS2: inducible NOS NuRD: nucleosome remodeling and histone NOS3: endothelial NOS deacetylase NOx: NAD(P)H oxidase NuRR: nuclear receptor-related factor Noxa: damage (Latin) (NR4a2) NPAS: neuronal PAS domain-containing nWASP: neuronal WASP transcription factor NPC: nuclear-pore complex O NPC: Niemann-Pick disease type-C protein NPC1L: Niemann-Pick protein-C1-like OGlcNAc: βNacetyl Dglucosamine nPKC: novel protein kinase C OCRL: oculocerebrorenal syndrome of NPY: neuropeptide Y Lowe phosphatase NR: nuclear receptor Oct: octamer-binding transcription factor NRAP: nebulin-related actinin-binding ODE: ordinary differential equation protein OGA: OGlcNAcase nRas: neuroblastoma Ras (βNacetylglucosaminidase) NRBP: nuclear receptor-binding protein OMM: outer mitochondrial membrane NRF: nuclear factor erythroid-derived-2 ORC: origin recognition complex (NF-E2)-related factor ORF: open reading frame NRF1: nuclear respiratory factor-1 ORP: OSBP-related protein Nrg: neuregulin (EGF superfamily member) OSA: obstructive sleep apnea Nrgn: neuroligin OSBP: oxysterol-binding protein Nrp: neuropilin (VEGF-binding molecule; OSI: oscillatory shear index VEGFR coreceptor) OSM: oncostatin M NRPTP: non-receptor protein Tyr phospha- OSMR: oncostatin M receptor tase OSR (OxSR): oxidative stress-responsive NRSTK: non-receptor Ser/Thr kinase kinase NRTK: non-receptor Tyr kinase OTK: off-track (pseudo)kinase Nrxn: neurexin OTU: ovarian tumor superfamily peptidase NSCLC: non-small-cell lung cancer (deubiquitinase) NSF: N-ethylmaleimide-sensitive factor OTUB: otubain (Ub thioesterase of the OTU NSLTP: non-speciﬁc lipid-transfer protein superfamily) 948 List of Aliases

OVLT: organum vasculosum lamina PCMRV: phase-contrast MR velocimetry terminalis PCr: phosphocreatine oxyHb: oxyhemoglobin (oxygenated PCT: proximal convoluted tubule hemoglobin) PCTP: phosphatidylcholine-transfer protein PD: pharmacodynamics P pDC: plasmacytoid dendritic cell PdCD: programmed cell death protein P : permeability PdCD6IP: PdCD 6-interacting protein P:power PdCD1Lg: programmed cell death-1 ligand P: cell division rate PDE: phosphodiesterase p: production rate PDE: partial differential equation p:pressure PDGF: platelet-derived growth factor pi: partial pressure of gas component i PDGFR: platelet-derived growth factor PA: phosphatidic acid receptor PAAT: proton–amino acid transporter PDI: protein disulﬁde isomerase PACS: phosphofurin acidic cluster sorting PDK: phosphoinositide-dependent kinase protein Pe: Péclet number PAF: platelet-activating factor PE: pulmonary embolism PAFAH: platelet-activating factor acetylhy- PEBP: phosphatidylethanolamine-binding drolase protein PAG: phosphoprotein associated with PECAM: platelet–endothelial cell adhesion glycosphingolipid-enriched mi- molecule crodomains PEDF: pigment epithelium-derived factor PAH: polycyclic aromatic hydrocarbon (serpin F1) PAH: pulmonary arterial hypertension PEn2: presenilin enhancer-2 PAI: plasminogen activator inhibitor PEO: proepicardial organ PAK: P21-activated kinase Per: Period homolog PALR: promoter-associated long RNA PERK: protein kinase-like endoplasmic PALS: protein associated with Lin-7 reticulum kinase PAMP: pathogen-associated molecular PERP: P53 apoptosis effector related to pattern peripheral myelin protein PMP22 PAMP: proadrenomedullin peptide PET: positron emission tomography PAR: polyADPribose Pex: peroxin PAR: promoter-associated, non-coding RNA PF: platelet factor PARi: type-i peptidase-activated receptor PFK: phosphofructokinase Par: partitioning defective protein pFRG: parafacial respiratory group PARG: polyADPribosyl glycosidase PG: prostaglandin PARP: polyADPribose polymerase PGC: PPARγ coactivator PASR: promoter-associated short RNA pGC: particulate guanylate cyclase PATJ: protein (PALS1) associated to tight PGEA: prostaglandin ethanolamide junctions PGF: paracrine growth factor Pax: paxillin PGG: prostaglandin glycerol ester Paxi: paired box protein-i (transcription PGi2: prostacyclin regulator) PGP: permeability glycoprotein PBC: pre-Bötzinger complex (ventilation PGx: type-x (D, E, F, H, I) prostaglandin frequency) PGxS: type-x prostaglandin synthase PBIP: Polo box-interacting protein PH: pleckstrin homology domain PC: polycystin PHD: prolyl hydroxylase PC: protein C PhK: phosphorylase kinase List of Aliases 949

PHLPP: PH domain and Leu-rich repeat PK: pharmacokinetics protein phosphatase PK: protein kinase PI: phosphoinositide (phosphorylated PKA: protein kinase A phosphatidylinositol) PKB: protein kinase B PI(4)P: phosphatidylinositol 4-phosphate PKC: protein kinase C PI(i)PiK: phosphatidylinositol i-phosphate PKD: protein kinase D i-kinase PKG: protein kinase G PI(i,j)P2: phosphatidylinositol (i,j)- PKL: paxillin kinase linker bisphosphate (PIP2) PKMYT (MYT): membrane-associated PI(3,4,5)P3: phosphatidylinositol (3,4,5)- Tyr–Thr protein kinase trisphosphate (PIP3) PKN: protein kinase novel PI3K: phosphatidylinositol 3-kinase Pkp: plakophilin PI3KAP: PI3K adaptor protein PL: phospholipase PIiK: phosphatidylinositol i-kinase PLA2: phospholipase A2 PIAS: protein inhibitor of activated STAT PLC: phospholipase C (SUMo ligase) PLD: phospholipase D PIC: pre-initiation complex PLb: phospholamban PICK: protein that interacts with C-kinase PLd: phospholipid PIDD: P53-induced protein with a death PlGF: placental growth factor domain PLK: Polo-like kinase PIKE: phosphoinositide 3-kinase enhancer PLTP: phospholipid transfer protein (GTPase; ArfGAP) PMCA: plasma membrane Ca++ ATPase PIKK: phosphatidylinositol 3-kinase-related PML: promyelocytic leukemia protein kinase (pseudokinase) PMR: percutaneous (laser) myocardial PIM: provirus insertion of Molony murine revascularization leukemia virus gene product PMRT: protein arginine methyltransferase PIN: peptidyl prolyl isomerase interacting Pn: plasmin with NIMA Png: plasminogen PINCH: particularly interesting new PNS: peripheral nervous system Cys–His protein (or LIMS1) PoG: proteoglycan PInK: PTen-induced kinase PoM: pore membrane protein PIP: phosphoinositide monophosphate Pon: paraoxonase PIPiK: phosphatidylinositol phosphate POPx: partner of PIX i-kinase POSH: scaffold plenty of SH3 domains PIP2: phosphatidylinositol bisphosphate PP: protein phosphatase PIP3: phosphatidylinositol triphosphate PP3: protein phosphatase 3 (PP2b or PIPP: proline-rich inositol polyphosphate calcineurin) 5-phosphatase PPAR: peroxisome proliferator-activated PIR: paired immunoglobulin-like receptor receptor (NR1c1–3) piRNA: P-element-induced wimpy PPG: photoplethysmography testis-interacting (PIWI) RNA PPId: peptidyl prolyl isomerase-D PIRT: phosphoinositide-interacting regulator PPIP: monopyrophosphorylated inositol of TRP channels phosphate PITP: phosphatidylinositol-transfer protein (PP)2IP: bispyrophosphorylated inositol Pitx: pituitary (or paired-like) homeobox phosphate transcription factor PPK: PIP kinase PIV: particle image velocimetry PPM: protein phosphatase (magnesium- PIX: P21-activated kinase (PAK)-interacting dependent) exchange factor (Rho(Arh)GEF6/7) PPR: pathogen-recognition receptor 950 List of Aliases

PPRE: PPAR response element (DNA PtdSer (PS): phosphatidylserine sequence) PtdIns (PI): phosphatidylinositol PR: progesterone receptor (NR3c3) PTen: phosphatase and tensin homo- PRC: protein regulator of cytokinesis log deleted on chromosome ten PRC: Polycomb repressive complex (phosphatidylinositol 3-phosphatase) Prdx: peroxiredoxin PTFE: polytetraﬂuoroethylene pre-cDC: pre-classical dendritic cell PTH: parathyroid hormone pre-miR: precursor microRNA PTHRP: parathyroid hormone-related preBotC: pre-Bötzinger complex protein preKk: prekallikrein PTK: protein Tyr kinase PREx: PIP3-dependent Rac exchanger PTK7: pseudokinase (RTK) (RacGEF) PTP: protein Tyr phosphatase PRG: plasticity-related gene product PTPni: protein Tyr phosphatase non-receptor PRH: prolactin-releasing hormone type i pri-miR: primary microRNA PTPR: protein Tyr phosphatase receptor PRL: phosphatase of regenerating liver PTRF: RNA polymerase-1 and transcript Prl: prolactin release factor PrlR: prolactin receptor PUFA: polyunsaturated fatty acid PRMT: protein arginine (R) N- PUMA: P53-upregulated modulator of methyltransferase apoptosis Prompt: promoter upstream transcript PuV: pulmonary valve Protor: protein observed with Rictor PVF: PDGF- and VEGF-related factor PROX: prospero homeobox gene PVNH: paraventricular nucleus of Prox: PROX gene product (transcription hypothalamus factor) PVR: pulmonary vascular resistance PrP: processing protein PWS: pulse wave speed PRPK: P53-related protein kinase Px: pannexin PRR: pattern recognition receptor PXR: pregnane X receptor (NR1i2) PRR: prorenin and renin receptor PYK: proline-rich tyrosine kinase PS: presenilin P2X: purinergic ligand-gated channel PS: protein S P53AIP: P53-regulated apoptosis-inducing PSC: pluripotent stem cell protein PSD: postsynaptic density adaptor p75NtR: pan-neurotrophin receptor PsD: postsynaptic density PSEF: pseudo-strain energy function Q PSer: phosphatidylserine PSGL: P-selectin glycoprotein ligand Q: material quantity PSKh: protein serine kinase H Qe: electric current density Psm: proteasome subunit QT: thermal energy (heat) PSTPIP: Pro–Ser–Thr phosphatase- qT: transfer rate of thermal energy (power) interacting protein q:ﬂowrate PTA: plasma thromboplastin antecedent Ptc: Patched receptor (Hedgehog signaling) R PTCA: percutaneous transluminal coronary angioplasty R: resistance PtcH: Patched Hedgehog receptor R : local reaction term PTCRA: PTC rotational burr atherectomy Rh: hydraulic radius PtdCho (PC): phosphatidylcholine Rg: gas constant PtdEtn (PE): phosphatidylethanolamine RR: respiratory quotient List of Aliases 951

R: recruitment function (from quiescence to REDD: regulated in development and proliferation) DNA-damage response gene product r:cellrenewalrate Rel: reticuloendotheliosis proto-oncogene r: radial coordinate product (TF; member of NFκB) RA: right atrium REP: Rab escort protein RAAS: renin–angiotensin–aldosterone ReR: renin receptor (PRR) system restin: Reed-Steinberg cell-expressed Rab: Ras from brain intermediate filament-associated Rab11FIP: Rab11 family-interacting protein protein (CLiP1) Rac: Ras-related C3-botulinum toxin ReT: rearranged during transfection substrate (receptor Tyr kinase) RACC: receptor-activated cation channel RevRE: reverse (Rev)-ErbA (NR1d1/2) RACK: receptor for activated C-kinase response element (DNA sequence) RAD: recombination protein-A (RecA)- RFA: radiofrequency ablation homolog DNA-repair protein RGL: Ral guanine nucleotide dissociation Rad: radiation sensitivity protein stimulator-like protein (GEF) Rag: Ras-related GTP-binding protein RGS: regulator of G-protein signaling Ral: Ras-related protein RHEB: Ras homolog enriched in brain RAlBP: retinaldehyde-binding protein RHS: equation right-hand side RalGDS: Ral guanine nucleotide-dis- Rho: Ras homologous sociation stimulator RIAM: Rap1-GTP-interacting adaptor RAMP: (calcitonin receptor-like) receptor- RIBP: RLK- and ITK-binding protein activity-modifying protein RICH: RhoGAP interacting with CIP4 Ran: Ras-related nuclear protein homolog RANTES: regulated upon activation, normal RICK: receptor for inactive C-kinase T-cell expressed, and secreted product Rictor: rapamycin-insensitive companion of (CCL5) TOR RAP: receptor-associated protein RIF: Rho in filopodium Rap: Ras-proximate (Ras-related) protein RIn: Ras and Rab interactor (RabGEF) Raptor: regulatory associated protein of RIN: Ras-like protein expressed in neurons TOR (GTPase) RAR: retinoic acid receptor (NR1b2/3) RIP: regulated intramembrane proteolysis Ras: rat sarcoma viral oncogene homolog (small GTPase) RIPK: receptor-interacting protein kinase RasA: Ras p21 protein activator RISC: RNA-induced silencing complex rasiRNA: repeat-associated small interfering RIT: Ras-like protein expressed in many RNA (PIWI) tissues RASSF: Ras interaction/interference protein RKIP: Raf kinase inhibitor protein RIN1, afadin, and Ras association RlBP: retinaldehyde-binding protein domain-containing family protein RLC: RISC-loading complex RB: retinoblastoma protein RLK: resting lymphocyte kinase (TXK) RBC: red blood cell (erythrocyte) RNA: ribonucleic acid RBP: retinoid-binding protein RNABP: RNA-binding protein RC: ryanodine calcium channel (RyR) RNase: ribonuclease RCA: right coronary artery RnBP: renin-binding protein RCan: regulator of calcineurin RNF2: RING finger protein-2 (Ub ligase) RCC: right coronary cusp RNP: ribonucleoprotein RCC: regulator of chromosome condensation Robo: roundabout Re: Reynolds number ROC: receptor-operated channel 952 List of Aliases

RoCK: Rho-associated, coiled-coil- s: sarcomere length containing protein kinase s: evolution speed ROI: region of interest SAA: serum amyloid A − + ROMK: renal outer medullary potassium SACCl(K): stretch-activated Cl (K )- channel selective channel ROR: RAR-related orphan receptor SAc: suppressor of actin domain-containing (NR1f1–NR1f3) 5-phosphatase ROR(RTK): receptor Tyr kinase-like orphan sAC: soluble adenylate cyclase receptor SACCNS: stretch-activated cation non- ROS: reactive oxygen species selective channel Ros: V-ros UR2 sarcoma virus proto- SACM1L: suppressor of actin mutation-1- oncogene product (RTK) like RPIP: Rap2-interacting protein SAH: subarachnoid hemorrhage RPS6: ribosomal protein S6 SAIC: stretch-activated ion channel RPTP: receptor protein Tyr phosphatase SAN: sinoatrial node rRas: related Ras SAP: SLAM-associated protein rRNA: ribosomal RNA SAP: stress-activated protein RSA: respiratory sinus arrhythmia SAPi: synapse-associated protein i RSE: rapid systolic ejection SAPK: stress-activated protein kinase RSK: P90 ribosomal S6 kinase (MAPK) RSKL: ribosomal protein S6 kinase-like SAR: secretion-associated and Ras-related (pseudokinase) protein rSMAD: receptor-regulated SMAD SBE: SMAD-binding element (SMAD1–SMAD3, SMAD5, and SBF: SET-binding factor SMAD9) Sc: Schmidt number RSMCS: robot-supported medical and SCA: stem cell antigen surgical system SCAMP: secretory carrier membrane protein RSpo: R-spondin SCAP: SREBP cleavage-activating protein RSTK: receptor Ser/Thr kinase (SREBP escort) RTK: receptor Tyr kinase SCAR: suppressor of cAMP receptor RTN: retrotrapezoid nucleus (WAVe) Rubicon: RUN domain and Cys-rich ScaR: scavenger receptor domain-containing, beclin-1- SCF: SKP1–Cul1–F-box Ub-ligase complex interacting protein SCF: stem cell factor Runx: Runt-related transcription factor SCFR: stem cell factor receptor (KIT) RV: right ventricle Scgb: secretoglobin RVF: rapid ventricular ﬁlling SCLC: small-cell lung cancer RVLM: rostral ventrolateral medulla scLC: squamous-cell lung cancer (NSCLC RVMM: rostral ventromedial medulla subtype) RXR: retinoid X receptor (NR2b1–NR2b3) SCN: suprachiasmatic nucleus RYK: receptor-like Tyr (Y) kinase SCO: synthesis of cytochrome-C oxidase (pseudokinase) SCP (CTDSP): small C-terminal domain RyR: ryanodine receptor (ryanodine- (CTD)-containing phosphatase ++ sensitive Ca -release channel) Scp: stresscopin (urocortin 3) Scrib: Scribble polarity protein S Sdc: syndecan SDF: stromal cell-derived factor S: Cauchy-Green deformation tensor SDPR: serum deprivation protein response s:entropy SE: systolic ejection List of Aliases 953

SEF: strain-energy function SIP: steroid receptor coactivator-interacting SEF: similar expression to FGF genes protein (inhibitor of RTK signaling) siRNA: small interfering RNA SEK: SAPK/ERK kinase SiRP: signal-regulatory protein Sema: semaphorin (Sema, Ig, trans- SIRT: sirtuin (silent information regulator-2 membrane, and short cytoplasmic [two]; histone deacetylase) domain) SIT: SHP2-interacting transmembrane SERCA: sarco(endo)plasmic reticulum adaptor calcium ATPase SK: small conductance Ca++-activated K+ serpin: serine peptidase inhibitor channel SerT: serotonin transporter SKi: sphingosine kinase-i SF: steroidogenic factor (NR5a1) SKIP: sphingosine kinase-1-interacting SFK: SRC-family kinase protein SFO: subfornical organ SKIP: skeletal muscle and kidney-enriched SFPQ: splicing factor proline and inositol phosphatase glutamine-rich SKP: S-phase kinase-associated protein sFRP: secreted Frizzled-related protein SLA: Src-like adaptor SftP (SP): surfactant protein SLAM: signaling lymphocytic activation sGC: soluble guanylate cyclase molecule SGK: serum- and glucocorticoid-regulated SLAMF: SLAM family member kinase SLAP: Src-like adaptor protein SGlT: Na+–glucose cotransporter (SLC5a) SLC: solute carrier class member Sgo: shugoshin (Japanese: guardian spirit) SLCO: solute carrier organic anion class SH: Src homology domain transporter Sh: Sherwood number SLK: Ste20-like kinase SH3P: Src homology-3 domain-containing Sln: sarcolipin adaptor protein SLPI: secretory leukocyte peptidase inhibitor Shank: SH3 and multiple ankyrin repeat SLTC: small latent TGFβ complex domain-containing protein SM: sphingomyelin SHAX: SNF7 (VSP32) homolog associated SMA: smooth muscle actin with ALIX SMAD: small (son of, similar to) mothers SHB: Src homology-2 domain-containing against decapentaplegia homolog adaptor SMAP: Small ArfGAP protein, stromal SHC: Src-homologous and collagen-like membrane-associated GTPase- substrate activating protein SHC: Src homology-2 domain-containing SMase: sphingomyelinase transforming protein SMC: smooth muscle cell SHh: sonic Hedgehog Smo: Smoothened SHIP: SH-containing inositol phosphatase SMPD: sphingomyelin phosphodiesterase SHP: SH-containing protein Tyr phosphatase SMRT: silencing mediator of retinoic acid (PTPn6/11) and thyroid hormone receptor SHP: small heterodimer partner (NR0b2) SMS: sphingomyelin synthase shRNA: small (short) hairpin RNA SMURF: SMAD ubiquitination regulatory SIAH: Seven in absentia homolog (Ub factor ligase) SNAAT: sodium-coupled neutral amino acid siglec: sialic acid-binding Ig-like lectin transporter SIK: salt-inducible kinase SNAP: soluble N-ethylmaleimide-sensitive SIn: stress-activated protein kinase- factor-attachment protein interacting protein SnAP: synaptosomal-associated protein 954 List of Aliases

SNARE: SNAP receptor SREBP: sterol regulatory element-binding SNF7: sucrose non-fermenting (VPS32) protein SNIP: SMAD nuclear-interacting protein SRF: serum response factor snoRNA: small nucleolar RNA SRM/SMRS: Src-related kinase lacking snoRNP: small nucleolar ribonucleoprotein regulatory and myristylation sites SNP: single-nucleotide polymorphism SRP: stresscopin-related peptide (uro- snRNA: small nuclear RNA cortin 2) snRNP: small nuclear ribonucleoprotein SRPK: splicing factor RS domain-containing SNx: sorting nexin protein kinase SOC: store-operated Ca++ channel SRY: sex-determining region Y SOCE: store-operated Ca++ entry SSAC: shear stress-activated channel SOCS: suppressor of cytokine signaling SSE: slow systolic ejection protein Ssh: slingshot homolog phosphatase SOD: superoxide dismutase SSI: STAT-induced STAT inhibitor SorbS: sorbin and SH3 domain-containing ssRNA: single-stranded RNA adaptor Sst: somatostatin SOS: Son of sevenless (GEF) SSV: short saphenous vein Sost: sclerostin St: Strouhal number SostDC: sclerostin domain-containing STAM: signal-transducing adaptor molecule protein STAMBP: STAM-binding protein (Ub SOX: sex-determining region Y (SRY)-box isopeptidase) gene StAR: steroidogenic acute regulatory protein Sox: SOX gene product (transcription factor) StART: StAR-related lipid transfer protein SP1: specificity protein (transcription factor) STAT: signal transducer and activator of SPARC: secreted protein acidic and rich in transduction cysteine STEAP: six transmembrane epithelial SPC: sphingosylphosphorylcholine antigen of the prostate SPCA: secretory pathway Ca++ ATPase STICK: substrate that interacts with SPECT: single photon emission CT C-kinase Sph: sphingosine StIM: stromal interaction molecule SphK: sphingosine kinase STK: protein Ser/Thr kinase SPI: spleen focus-forming virus (SFFV) STK1: stem cell protein Tyr kinase receptor proviral integration proto-oncogene STLK: Ser/Thr kinase-like (pseudo)kinase product (transcription factor) Sto: Stokes number SPInt: serine peptidase inhibitor StRAd: STe20-related adaptor SPN: supernormal period STRAP: Ser/Thr kinase receptor-associated SPP: sphingosine phosphate phosphatase protein SpRED: Sprouty-related protein with an StRAP: stress-responsive activator of P300 EVH1 domain Stx: syntaxin (SNAREQ) SPURT: secretory protein in upper SUMo: small ubiquitin-related modifier respiratory tract SUn: Sad1 and Unc84 homology protein SQTS: short-QT syndrome SUR: sulfonylurea receptor SR: sarcoplasmic reticulum SUT: stable unannotated transcript SR: Arg/Ser domain-containing protein SV: stroke volume (alternative splicing) SVC: superior vena cava SRA: steroid receptor RNA activator SVCT: sodium-dependent vitamin-C SRC: steroid receptor coactivator transporter Src: sarcoma-associated (Schmidt-Ruppin SVF: slow ventricular filling A2 viral oncogene homolog) kinase SVP: synaptic vesicle precursor List of Aliases 955

SVR: systemic vascular resistance TACE: tumor-necrosis factor-α-converting SW: stroke work enzyme (ADAM17) SwAP70: 70-kDa switch-associated protein TACE: transarterial chemoembolization (RacGEF) TAF: TBP-associated factor SYK: spleen tyrosine kinase TAK: TGFβ-activated kinase (MAP3K7) Synj: synaptojanin TALK: TWIK-related alkaline pH-activated Syp: synaptophysin K+ channel Syt: synaptotagmin TANK: TRAF family member-associated S1P: sphingosine 1-phosphate NFκB activator S6K: P70 ribosomal S6 kinase (P70RSK) TASK: TWIK-related acid-sensitive K+ channel T TASR: terminus-associated short RNA TAP: transporter associated with antigen T: extrastress tensor processing (ABC transporter) T: transition rate from a cell cycle phase to Taz: taffazin the next TBC1D: Tre2 (or USP6), BUB2, CDC16 T: temperature domain-containg RabGAP T lymphocyte (T cell): thymic lymphocyte TBCK: tubulin-binding cofactor kinase TC: cytotoxic T lymphocyte (CD8+ effector (pseudokinase) T cell; CTL) TBK: TANK-binding kinase TC1: type-1 cytotoxic T lymphocyte TBP: TATA box-binding protein (subclass- TC2: type-2 cytotoxic T lymphocyte 4F transcription factor) TCM: central memory T lymphocyte TBx: T-box transcription factor TConv: conventional T lymphocyte TC: thrombocyte (platelet) TEff: effector T lymphocyte TCA: tricarboxylic acid cycle TEM: effector memory T lymphocyte TCF: T-cell factor TFH: follicular helper T lymphocyte TCF: ternary complex factor TH: helper T lymphocyte (CD4+ effector TcFi: type-i transcription factor T cell) TCP: T-complex protein THi: type-i helper T lymphocyte TCR: T-cell receptor (i = 1/2/9/17/22) TEA: transluminal extraction atherectomy TH3:TGFβ-secreting TReg lymphocyte TEC: Tyr kinase expressed in hepatocellular TL: lung transfer capacity (alveolocapillary carcinoma membrane) TEF: thyrotroph embryonic factor TR1: type-1, IL10-secreting, regulatory (PAR/b–ZIP family) T lymphocyte TEK: Tyr endothelial kinase TReg: regulatory T lymphocyte TEM: transendothelial migration hi aTReg: CD45RA−, FoxP3 , activated Ten: tenascin TReg cell TF: transcription factor iTReg: inducible TReg lymphocyte Tf: transferrin nTReg: naturally occurring (natural) TFPI: tissue factor pathway inhibitor TReg lymphocyte TfR: transferrin receptor low rTReg: CD45RA+, FoxP3 , resting TG: triglyceride (triacylglycerol) TReg cell TGF: transforming growth factor tˆ: unit tangent TGFBR: TGFβ receptor gene t: time TGFβRAP: TGFβ receptor-associated TβRi: type-i TGFβ receptor protein TAA: thoracic aortic aneurysm TGN: trans-Golgi network TAB: TAK1-binding protein THETE: trihydroxyeicosatrienoic acid 956 List of Aliases

THIK: tandem pore-domain halothane- TP: thromboxane-A2 Gq/11-coupled inhibited K+ channel receptor THR: thyroid hormone receptor (NR1a1/2) TP53I: tumor protein P53-inducible protein TIAM: T-lymphoma invasion and tPA: tissue plasminogen activator metastasis-inducing protein (RacGEF) Tpo: thrombopoietin TICE: transintestinal cholesterol efﬂux TPPP: tubulin polymerization-promoting TIE: Tyr kinase with Ig and EGF homology protein domains (angiopoietin receptor) TPST: tyrosylprotein sulftotransferase TIEG: TGFβ-inducible early gene product TR: testicular receptor (NR2c1/2) TIGAR: TP53-inducible glycolysis and TRAAK: TWIK-related arachidonic apoptosis regulator acid-stimulated K+ channel TIM: T-cell immunoglobulin and mucin TRADD: tumor-necrosis factor receptor- domain-containing protein associated death domain adaptor Tim: timeless homolog TRAF: tumor-necrosis factor receptor- TIMM: translocase of inner mitochondrial associated factor membrane TRAM: TRIF-related adaptor molecule TIMP: tissue inhibitor of metallopeptidase transceptor: transporter-related receptor TIRAP: Toll–IL1R domain-containing TRAP: TNF receptor-associated protein adaptor protein (HSP75) tiRNA: transcription initiation RNA TraPP: transport protein particle TJ: tight junction TRAT: T-cell receptor-associated transmem- TKR: Tyr kinase receptor brane adaptor TLC: total lung capacity Trb: Tribbles homolog (pseudokinase) TLR: Toll-like receptor TRE: TPA-response element (AP1/CREB- TLT: TREM-like transcript binding site on promoters) TLX: tailless receptor (NR2e1) TRE: trapped in endoderm TM: thrombomodulin TREK: TWIK-related K+ channel TMi: transmembrane segment-i of TREM: triggering receptor expressed on membrane protein myeloid cells TMC: twisting magnetocytometry TRESK: TWIK-related spinal cord K+ TMePAI: transmembrane prostate androgen- channel induced protein TRF: TBP-related factor TMy: tropomyosin TRH: thyrotropin-releasing hormone Tnn (TN): troponin TRIF: Toll–IL1R domain-containing adaptor Tn: thrombin inducing Ifnβ TNF: tumor-necrosis factor TRIM: T-cell receptor-interacting molecule TNFαIP: tumor-necrosis factor-α-induced TRIP: TGFβ receptor-interacting protein protein (eIF3S2) TNFR: tumor-necrosis factor receptor TRK: tropomyosin receptor kinase (NTRK) TNFRSF: tumor-necrosis factor receptor tRNA: transfer RNA superfamily member TRP: transient receptor potential channel TNFSF: tumor-necrosis factor superfamily TRPA: ankyrin-like transient receptor member potential channel TNK:TyrkinaseinhitorofNFκB TRPC: canonical transient receptor potential Tns: tensin channel TOR: target of rapamycin TRPM: melastatin-related transient receptor TORC: target of rapamycin complex potential channel TORC: transducer of regulated CREB TRPML: mucolipin-related transient activity (a.k.a. CRTC) receptor potential channel List of Aliases 957

TRPN: no mechanoreceptor potential C Ucn: urocortin TRPP: polycystin-related transient receptor UCP: uncoupling protein potential channel UDP: uridine diphosphate-glucose TRPV: vanilloid transient receptor potential UK: urokinase channel ULK: uncoordinated-51-like kinase TrrAP: transactivation (transforma- (pseudokinase) tion)/transcription domain-associated Unc: uncoordinated receptor protein (pseudokinase) uPA: urokinase-type plasminogen activator TrV: tricuspid valve (urokinase) TRx: thioredoxin uPAR: uPA receptor TRxIP: thioredoxin-interacting protein uPARAP: uPAR-associated protein TSC: tuberous sclerosis complex (CLec13e) TSH: thyroid-stimulating hormone UPR: unfolded protein response TSLP: thymic stromal lymphopoietin UPS: ubiquitin-proteasome system Tsp: thrombospondin UP4A: uridine adenosine tetraphosphate Tspan: tetraspanin Uro: urodilatin TsPO: translocator protein of the outer US: ultrasound mitochondrial membrane USC: unipotential stem cell tSNARE:targetSNARE USF: upstream stimulatory factor tsRNA: tRNA-derived small RNA USI: ultrasound imaging tssaRNA: transcription start site-associated USP: ubiquitin-specific peptidase (deubiqui- RNA tinase) Ttn: titin (pseudokinase) UTP: uridine triphosphate TUT: terminal uridine transferase UTR: untranslated region TWIK: tandem of P domains in a weak UVRAG: ultraviolet wave resistance- inwardly rectifying K+ channel associated gene product TxA2: thromboxane A2 (thromboxane) TxB2: thromboxane B2 (thromboxane V metabolite) TXK: Tyr kinase mutated in X-linked V:leftstretchtensor agammaglobulinemia V: volume TxaS: thromboxane-A synthase Vq: cross-sectional average velocity TyK: tyrosine kinase Vs: specific volume T3: tri-iodothyronine v: velocity vector T4: thyroxine v: recovery variable + TP: plus-end-tracking proteins V1(2)R: type-1(2) vomeronasal receptor V1A/1B/2: type-1a/1b/2 arginine vasopressin U receptor VAAC: volume-activated anion channel − + U: right stretch tensor VAC Cl(K): volume-activated Cl (K )- u: displacement vector selective channel u: electrochemical command VACamKL: vesicle-associated CamK-like u: specific internal energy (pseudokinase) Ub: ubiquitin VAC C NS: volume-activated cation UbC: ubiquitin-conjugating enzyme non-selective channel UbE2: E2 ubiquitin conjugase VAChT: vesicular acetylcholine transporter UbE3: E3 ubiquitin ligase VAIC: volume-activated ion channel UbL: ubiquitin-like protein VAMP: vesicle-associated membrane protein UCH: ubiquitin C-terminal hydrolase (DUb) (synaptobrevin) 958 List of Aliases

VanGL: Van Gogh (Strabismus)-like protein VVO: vesiculo-vacuolar organelle VAP: VAMP-associated protein vWF: von Willebrand factor VASP: vasoactive stimulatory phosphoprotein W VAT: vesicular amine transporter vATPase: vesicular-type H+ ATPase W: vorticity tensor VAV: ventriculoarterial valve W : strain energy density Vav: GEF named from Hebrew sixth letter W: work, deformation energy VC: vital capacity w: weight VCAM: vascular cell adhesion molecule w: grid velocity VCt: vasoconstriction WASH: WASP and SCAR homolog VDAC: voltage-dependent anion channel WASP: Wiskott-Aldrich syndrome protein (porin) WAT: white adipose tissue VDACL: plasmalemmal, volume- and WAVe: WASP-family verprolin homolog voltage-dependent, ATP-conductive, WBC: white blood cell large-conductance, anion channel WDR: WD repeat-containing protein VDCC: voltage-dependent calcium channel Wee: small (Scottish) VDP: vesicle docking protein WHAMM: WASP homolog associated with VDt: vasodilation actin, membranes, and microtubules VEGF: vascular endothelial growth factor WIP: WASP-interacting protein VEGFR: vascular endothelial growth factor WIPF: WASP-interacting protein family receptor protein VF: ventricular ﬁbrillation WIPI: WD repeat domain-containing VF: ventricular ﬁlling phosphoinositide-interacting protein VGAT: vesicular GABA transporter WNK: with no K (Lys) kinase VGC: voltage-gated channel Wnt: wingless-type VgL: Vestigial-like protein WPWS: Wolff-Parkinson-White syndrome VGluT: vesicular glutamate transporter WNRRTK: Wnt and neurotrophin VHL: von Hippel-Lindau Ub ligase receptor-related receptor Tyr kinase VIP: vasoactive intestinal peptide (ROR(RTK)) VLDL: very-low-density lipoprotein WSB: WD-repeat and SOCS box-containing VLDLR: very-low-density lipoprotein protein (Ub ligase) receptor WSS: wall shear stress VMAT: vesicular monoamine transporter WSSTG: WSS transverse gradient VN: vitronectin WWTR: WW domain-containing transcrip- VPO: vascular peroxidase tion regulator VPS: vacuolar protein sorting-associated kinase X VR: venous return VRAC: volume-regulated anion channel X : trajectory VRC: ventral respiratory column X: reactance VRK: vaccinia-related kinase X: Lagrangian position vector VS: vasostatin x: position vector vSMC: vascular smooth muscle cell {x,y,z}: Cartesian coordinates vSNARE: vesicular SNAP receptor XBE: X-factor-binding element (SNARE) XBP: X-box-binding protein (transcription VSOR: volume-sensitive outwardly factor) rectifying anion channel XIAP: X-linked inhibitor of apoptosis VSP: voltage-sensing phosphatase (Ub ligase) List of Aliases 959

Y ZnF: zinc finger protein ZO: zonula occludens Y: admittance coefficient YAP: Yes-associated protein Miscellaneous YBP: Y-box-binding protein (transcription factor) 2-5A: 5-triphosphorylated, (2,5)- YY: yin yang (transcriptional repressor) phosphodiester-linked oligoadenylate Z 2AG: 2-arachidonyl glycerol 3DR: three-dimensional reconstruction Z: impedance 3BP2: Abl Src homology-3 domain-binding ZAP70: ζ-associated protein 70 adaptor ZBTB: zinc finger and BTB (Broad 4eBP1: inhibitory eIF4e-binding protein complex, Tramtrack, and bric-à-brac) 5HT: serotonin domain-containing transcription factor 7TMR: 7-transmembrane receptor (GPCR) Complementary Lists of Notations

Greek Letters κo: osmotic coefficient κs: size ratio {κ }9 α: volumic fraction k k=1: tube law coefficients α: convergence/divergence angle κe: correction factor α: attenuation coefficient Λ: head loss coefficient λ αk: kinetic energy coefficient L: Lamé coefficient λ αm: momentum coefficient : stretch ratio β: inclination angle λ: wavelength 2 λ {βi} : myocyte parameters A: area ratio 1 λ βT : coefficient of thermal expansion a: acceleration ratio Γ: domain boundary λL: length ratio λ ΓL: local reflection coefficient q: flow rate ratio λ ΓG: global reflection coefficient t : time ratio γ: heat capacity ratio λv: velocity ratio γ: activation factor μ: dynamic viscosity γg: amplitude ratio (modulation rate) of g μL: Lamé coefficient ν γs: surface tension : kinematic viscosity γ˙:shearrate νP: Poisson ratio δ: boundary layer thickness Π: osmotic pressure ρ T : emissivity (thermal energy radiation) : mass density τ e: electric permittivity : time constant ε: strain Φ: potential ε: small quantity φ(t): creep function ζ: singular head loss coefficient ϕ: phase ζ: transmural coordinate χ: Lagrangian label 3 {ζ j} : local coordinate chii: molar fraction of species i 1 χ η: azimuthal spheroidal coordinate i: wetted perimeter θ: circumferential polar coordinate ψ(t): relaxation function Ψ θ: (eˆx,tˆ) angle : porosity κ:wallcurvature ω: angular frequency Ω κc: curvature ratio : computational domain κd:dragcoefficient κh: hindrance coefficient Dual Notations

961 962 Complementary Lists of Notations

Bϕ: basophil s: solute Eϕ: eosinophil s: serial Lϕ: lymphocyte s: systolic Mϕ: macrophage t: stream division aaMϕ: alternatively activated macrophage T:total caMϕ: classically activated macrophage t: turbulence Nϕ: neutrophil t: time derivative of order 1 Σc: sympathetic tt: time derivative of order 2 pΣc: parasympathetic tis: tissue V: ventricular Subscripts v: venous w:wall A: alveolar, atrial w: water (solvent) Ao: aortic Γ: boundary a: arterial θ: azimuthal app: apparent +: positive command atm: atmospheric −: negative command b: blood ∗: at interface c: contractile 0: reference state (·0: unstressed or low shear c: center rate) c: point-contact ∞: high shear rate D: Darcy (filtration) d: diastolic Superscripts dyn: dynamic a E: expiration, Eulerian : active state e e: external : elastic f e: extremum :fluid h eff:effective : hypertensive n f:fluid : normotensive p g:grid : passive state p I: inspiration :power s i: internal : solid T inc: incremental : transpose v L: Lagrangian : viscoelastic l: limit :scale ∗ : line-contact : complex variable M: macroscopic · : first component of complex elastic and m:mean shear moduli max: maximum · : second component of complex elastic m: muscular, mouth and shear moduli met: metabolic : static, stationary, steady variable μ: microscopic P: pulmonary Mathematical Notations p: parallel p: particle T: bold face capital letter means tensor q: quasi-ovalization v: bold face lower case letter means vector r: radial S, s: upper or lower case letter means scalar rel: relative Δ•: difference S: systemic δ•: increment Complementary Lists of Notations 963 d • /dt: time gradient kinase, and corresponding gene and ∂t : first-order time partial derivative oncogene product, respectively) • ∂tt: second-order time partial derivative : radical (unpaired electron[s]) ΔNT ∂i: first-order space partial derivative with : truncated form without the N-terminal respect to spatial coordinate xi domain ∇ ΔCT : gradient operator : truncated form without the C-terminal ∇u: displacement gradient tensor domain ∇ ( ) v: velocity gradient tensor D L X: D (L)-stereoisomer of amino ∇· : divergence operator acids and carbohydrates (chirality ∇2 : Laplace operator prefixes for dextro- [dexter: right] || +: positive part and levorotation [lævus: left]), i.e., || −: negative part dextro(levo)rotatory enantiomer • ˙: time derivative GX: globular form of X molecule • ¯: time mean F(G)actin: polymeric, filamentous (mono- • ˘: space averaged meric, globular) actin • : ensemble averaged X: carboxy (carboxyl group COOH • C ˜: dimensionless [C])-terminal cleaved part of molecule •+ ∈ [ , ] : normalized ( 0 1 ) X •ˆ:peakvalue NX: amino (amine group NH2 [N])-terminal •∼: modulation amplitude cleaved part of molecule X det(•): determinant X: cytosolic molecule cof(•): cofactor c X: membrane-bound molecule tr(•): trace m tX: truncated isoform X X Cranial Nerves i: type-i isoform of the receptor of ligand (i: integer) I: olfactory nerve (sensory) XRi: receptor isoform i of ligand X (i: II: optic nerve (sensory) integer) X+: molecule X expressed (X-positive) III: oculomotor nerve (mainly motor) + IV: trochlear nerve (mainly motor) X : cation; also intermediate product X of V: trigeminal nerve (sensory and motor) oxidation (loss of electron) from a VI: abducens nerve (mainly motor) reductant (or reducer) by an oxidant VII: facial nerve (sensory and motor) (electron acceptor that removes VIII: vestibulocochlear (auditory-vestibular) electrons from a reductant) nerve (mainly sensory) X−: molecule X absent (X-negative) − IX: glossopharyngeal nerve (sensory and X : anion; also intermediate product X of motor) reduction (gain of electron) from an X: vagus nerve (sensory and motor) oxidant (or oxidizer) by a reductant XI: cranial accessory nerve (mainly motor) (electron donor that transfers electrons XII: hypoglossal nerve (mainly motor) to an oxidant) XA: activator form of molecule X Chemical Notations Xa: active form of molecule X XECD: soluble fragment correponding to [X]: concentration of X species the ectodomain of molecule X after X (x): upper and lower case letters cor- extracellular proteolytic cleavage respond to gene and corresponding and shedding (possible extracellular protein or conversely (i.e., Fes, messenger or sequestrator) FES, and fes designate protein, a X(ER): endoplasmic reticulum type of proto-oncogene product that acts as a molecule X 964 Complementary Lists of Notations small GTPaseGTP(GDP): active (inactive) iX: inhibitory mediator (e.g., iSMAD) or form of small (monomeric), regulatory intracellular (e.g., iFGF) or inducible guanosine triphosphatase (e.g., iNOS) isoform XGTP(GDP): GTP (GDP)-loaded molecule X kX: renal type (kidney) molecule X XICD: soluble fragment correponding to ksX: kidney-specific isoform of molecule X intracellular domain of molecule lX: lysosomal molecule X X after intracellular proteolytic l,acX: lysosomal, acidic molecule X cleavage (possible messenger and/or mX: mammalian species or membrane- transcription factor; e.g., NotchICD: associated molecule X (e.g., mTGFβ) intracellular Notch fragment) mtX: mitochondrial type of molecule X XM: methylated molecule X nX: neutral X; neuronal type (e.g., nWASP) XMT: mitochondrial type of molecule X oxX: oxidized molecule X (e.g., oxLDL) XP: phosphorylated molecule X plX: plasmalemmal type of molecule X pAA: phosphorylated amino acid (pSer, pThr, rX: receptor-associated mediator or receptor- and pTyr) like enzyme; also regulatory type of XPM: plasmalemmal type of molecule X molecular species (e.g., rSMAD) XR: repressor form of molecule X sX: secreted, soluble form of molecule X XS: soluble form s,acX: secreted, acidic molecule X XSNO: Snitrosylated molecule X skX: skeletal myocyte isoform (e.g., XU: ubiquitinated protein X skMLCK) smcX: smooth muscle cell isoform (e.g., X : alternative splice variant alt smcMLCK) X : full-length protein X FL tX: target type of X (e.g., tSNARE); tissue X : high (low, mid)-molecular-weight h(l,m)MW type (e.g., tPA) isotype tmX: transmembrane type of X X : long (short) isoform (splice variants) L(S) vX: vesicle-associated (e.g., vSNARE) or X : catalytic subunit c vacuolar (e.g., vATPase) type of X X X P: palmitoylated molecule GPX: glycoprotein (X: molecule abbreviation Xi: number of molecule or atom (i: integer, or assigned numeral) often2or3) Xx:(x: single letter) splice variants (X1–X2)i: oligomer made of i complexes X1: human form (ortholog) constituted of molecules X1 and X2 Xi: isoform type i (paralog or splice variant; (e.g., histones) i: integer) a, c, nX: atypical, conventional, novel Xi/j: (i,j: integers) refers to either both molecule X (e.g., PKC) isoforms (i.e., Xi and Xj,suchas acX: acetylated molecule X (e.g., acLDL) ERK1/2) or heterodimer (i.e., Xi–Xj, al, ac, nX: alkaline, acidic, neutral molecule such as ARP2/3) X (e.g., sphingomyelinase) X1/X2: molecular homologs or commonly asX: alternatively spliced molecule X (e.g., used aliases (e.g., contactin-1/F3) asTF) PI(i)P, PI(i,j)P2,PI(i,j,k)P3: i,j,k (inte- cX: cellular, cytosolic, constitutive (e.g., gers): position(s) of phosphorylated cNOS), or cyclic (e.g., cAMP and OH groups of the inositol ring of cGMP) molecule X phosphatidylinositol mono-, bis-, and caX: cardiomyocyte isoform (e.g., caMLCK) trisphosphates dX: deoxyX eX: endothelial isoform (e.g., eNOS and Amino Acids eMLCK) hX: human form (ortholog); heart type (e.g., Ala (A): alanine hFABP); hormone-like isoform (FGF) Arg (R): arginine Complementary Lists of Notations 965

Asn (N): asparagine OH−: hydroxide anion − Asp (D): aspartic acid PO3 : phosphate anion − 4 AspCOO : aspartate 2− SO4 : sulfate anion CysH (C): cysteine Zn++: zinc cation (common oxidation state) Cys: cystine Gln (Q): glutamine Inhaled and Signaling Gas Glu (E): glutamic acid − CO: carbon monoxide (or carbonic oxide; GluCOO : glutamate signaling gas and pollutant) Gly (G): glycine CO : carbon dioxide (cell waste) His (H): histidine 2 H S: hydrogen sulﬁde (signaling gas) Iso, Ile (I): isoleucine 2 He: helium (inert monatomic gas) Leu (L): leucine N : nitrogen (inert diatomic gas) Lys (K): lysine 2 NO: nitric oxide (or nitrogen monoxide; Met (M): methionine signaling gas and pollutant) Phe (F): phenylalanine NO : nitrogen dioxide (air pollutant) Pro (P): proline 2 O : oxygen (cell energy producer) Ser (S): serine 2 SO : sulfur dioxide (air pollutant) Thr (T): threonine 2 Trp (W): tryptophan Tyr (Y): tyrosine Nitric Oxide Derivatives Val (V): valine NO•: free radical form + Ions NO : nitrosyl or nitrosonium cation NO−: nitroxyl or hyponitrite anion Asp−: aspartate (carboxylate anion of (inodilator) aspartic acid) HNO: protonated nitroxyl anion − 3 HNO2: nitrous acid ADP : ADP anion − 4− ATP : ATP anion NO2 : nitrite anion ++ − Ca : calcium cation NO3 : nitrate anion Cl−: chloride anion Reactive Oxygen and Nitrogen Species Co++: cobalt cation Cu+: copper monovalent cation H2O2: hydrogen peroxide Cu++: copper divalent cation N2O3: dinitrogen trioxide Fe++: ferrous iron cation • NO2: nitrogen dioxide Fe3+: ferric iron cation − − O2 : superoxide Glu : glutamate (carboxylate anion of O=C(O•)O−: carbonate radical glutamic acid) • + OH : hydroxyl radical (hydroxide ion H : hydrogen cation (proton) neutral form) + − H3O : hydronium (oxonium or hydroxo- ONOO : peroxynitrite nium) cation − HCO3 : bicarbonate anion 2− Time Units HPO4 : hydrogen phosphate anion K+: potassium cation ++ d: day Mg : magnesium cation h: hour Mg 2− ATP : ATP anion mn: minute Mn++: manganese cation + s: second Na : sodium cation wk: week Ni++: nickel cation (common oxidation state) SI-Based and Non-SI Units of Quantity 966 Complementary Lists of Notations mmol, nmol, μmol: milli-, nano-, (osm: number of moles of a osmotically micromoles active chemical compound) (amount of a chemical species, one mole kDa: kiloDalton containing about 6.02214078×1023 (Da: atomic or molecular mass unit) molecules) ppm: parts per million mosm: milliosmole l: liter Index

Symbols adenomatous polyposis coli...... 732 ADPribose ...... 41, 121, 172 adenosine ...... 17, 85, 86, 225, 300, 474 ADPribosylhydrolase...... 41 adenosine receptor ...... 229, 262, 474 Nacetylglucosaminyltransferase ...... 40 adenylate cyclase16, 248, 310, 409, 532, 543 (pro)renin receptor ...... 413, 742 adhesionGPCR...... 428 βNacetylglucosaminidase...... 40 adipocyte 314, 315, 397, 420, 500, 502, 534, β-glycan (TβR3) ...... 665, 669 739 14-3-3 protein ...... 40, 653, 737 adiponectin ...... 352, 419, 492 adiponectin receptor ...... 419, 492 A adiposetissue...... 213, 336, 419, 420, 589 α-actinin...... 251 ADP . . 85, 86, 262, 299, 453, 483, 485, 490, α-adrenergic receptor 83, 297, 415, 493, 502 491 α2-antiplasmin...... 415 adrenaline ...... 296, 298, 366, 499, 500 AATyKkinase...... 641 ABC transporter . . 16, 81, 96, 228, 265, 285, adrenocorticotropic hormone ...... 555 315, 393, 399, 403, 405, 537 adrenomedullin...... 513 acetylation...... 37 adrenomedullin receptor...... 514 acetylcholine . . . . 82, 83, 225, 279, 290, 366, aging ...... 183, 750 415, 470 agmatine...... 414 acetylglucosamination...... 40 agrin ...... 471, 645, 646 ACh muscarinic receptor...... 226, 470 airwayepithelium...... 81, ACh nicotinic receptor ...... 140, 365, 613 88, 106, 131, 132, 176, 202, 257, 259, actin 158, 229, 263, 265, 313, 654, 708, 731, 262, 263, 266, 267, 288, 301, 308, 751, 753 319, 344, 380, 412, 488, 619, 643 actin depolymerizing factor ...... 471 airway smooth muscle cell . . . 176, 263, 426, action potential ...... 215, 364 452, 472, 527, 584 activating transcription factor (ATF) . . . . 683 airwaysurfaceﬂuid...... 328 Activator protein-1 . 126, 387, 389, 436, 794 AKAP.29, 32, 102, 145, 170, 174, 177, 227, activin...... 668 254, 263, 264, 466 acylCoA–cholesterol acyltransferase. . . .403 albumin...... 343 adamlysin . 57, 553, 613, 619, 627, 656, 660, aldosterone ...... 202, 226, 391, 525 706, 750, 780 ALK receptor S/T kinase (TGFRSF) . . . 662, adaptor ...... 29, 788, 792 671, 675, 676, 679 ADAPadaptor...... 788 ALKreceptorYkinase...... 645

967 968 Index allergen...... 302 arterial tortuosity syndrome...... 315 allostery...... 28 asbestos...... 619 alveolar macrophage ...... 340, 353 asthma...... 762 alveolus ...... 267, 322 atherosclerosis 332, 341, 352, 359, 406, 439, ALXadaptor...... 789 516, 645 AMP...... 85 ATP...... 80,81,85,87, amphetamine...... 585 89, 123, 133, 150, 159, 167, 173, 176, amphiregulin ...... 605 177, 179, 183, 187, 189, 193, 227, AMPK ...... 42, 419, 492 228, 259–262, 266, 289, 299, 308, amylin...... 513 379, 409, 483, 485, 487, 490, 491, 799 amyloid precursor protein ...... 340, 347 ATPsynthase...... 269 anandamide ...... 116, 129, 132 ATPanion...... 81,260 anaphylatoxin...... 519 autoregulation...... 480 androgenreceptor...... 388 autotaxin...... 550 aneurysm...... 506 axin...... 732 angiogenesis...... 79, Axl (RTK) ...... 596, 642, 803 85, 283, 398, 432, 478, 480, 509, 529, 548, 550, 553, 563, 566, 573, 582, B 619, 621, 626, 636, 653, 658, 660, β-adrenergic receptor51, 461, 466, 479, 481, 693, 700, 703, 715, 720, 739, 746, 769 493, 512 angiopoietin ...... 660, 693, 715 B-cellreceptor...... 58,783 angiotensin . . . 131, 134, 185, 243, 287, 344, BACEprotease...... 57 413, 420, 504, 530, 618, 619 Bardet-Biedl syndrome protein...... 742 angiotensin-converting enzyme 39, 506, 511, baroreceptor...... 200 513 baroreflex ...... 475, 496 angiotensin receptor . . . . . 238, 464, 487, 504 basalcell...... 326 ankyrin ...... 158, 177, 179, 211, 229 BCAR/CAS docker ...... 417, 645 annexin ...... 418, 546 BCL2 protein ...... 178, 530 anoctamin...... 259 bestrophin ...... 259 antiporter...... 91 Bezold-Jarischreflex...... 117 aortic body...... 365 biasedsignaling...... 500 APCUbligase...... 737 bicarbonate ...... 153, 266 apelin ...... 419, 508 biglycan...... 625, 736 apelin receptor ...... 419, 508 bile acid ...... 392, 402, 510 apolipoprotein . 321, 332, 352, 405, 672, 674 bilitranslocase ...... 303 apolipoprotein-E receptor ...... 349 biomarker...... 259 apoptosis ...... 113, 774 birth...... 530 APSadaptor...... 790 bistability ...... 676 aquaporin ...... 305, 328, 587 BK channel ...... 181, 220, 226, 244 arachidonic acid82, 129, 132, 133, 234, 516, BLnkadaptor...... 790 517, 524, 544 blood–brain barrier.312, 323, 325, 431, 541, ARFGTPase...... 404 543, 765 arginine...... 414 bloodpressure...... 202 Argosome...... 736 bloodvolume...... 202 arrestin . . 131, 459, 462, 490, 577, 578, 612, BMP ...... 345, 668, 674, 713 707, 726, 740 bombesin ...... 510 arrhythmogenic right ventricular dysplasia Bowditch/Treppeeffect...... 189 667 bradykinin...... 415, 510 artemin...... 651 bradykinin receptor ...... 510 Index 969 brain . 90, 121, 198, 213, 282, 286, 315, 322, cardiac frequency ...... 365, 521 328, 336, 419 cardiomyocyte...... 39, 51, BrCa1Ubligase...... 50 91, 135, 161, 167, 171, 174, 175, 181, breathing frequency ...... 365, 576 183, 196, 197, 206, 208, 210, 213, bronchoconstriction . . . . . 452, 472, 473, 544 214, 229, 237, 242, 249, 252, 260, bronchodilation ...... 452, 499 261, 266, 284, 293, 308, 313, 389, brush cell ...... 207, 258, 323, 365 409, 412, 419, 463, 464, 471, 480, 492, 499, 506, 507, 509, 515, 527, C 530, 532, 563, 565, 567, 582, 602, C-reactiveprotein...... 765 612, 619, 709, 744, 752, 790 C/EBP factor ...... 396, 397 cardiomyopathy...... 284, 481 C1qTNFSF...... 148 cardiotonicsteroid...... 214 Ca++-induced Ca++ release. .180, 185, 186 cardiotrophin...... 767 Ca++ 2-porechannel...... 172 carotid body ...... 201, 247, 365 CaV channel . . 132, 164, 167, 169, 240, 248, CARP2(RFFL1)Ubligase...... 782 308, 409, 452, 487, 523, 535, 543, casein kinase. .127, 251, 388, 473, 646, 653, 560, 745 720, 724, 732, 740 cadherin ...... 492, 645, 697 caspase ...... 178, 627, 775, 781, 797 cADPR ...... 161, 185 catenin ...... 346, 696, 697, 728, 730 calcitonin...... 513 cathepsin ...... 420, 568 calcitonin gene-related peptide . 83, 117, 513 caveola ...... 214, 355, 356, 515, 612 calcium ...... 32, 42, 65–67, 80, 81, 83, caveolin . . . . 39, 49, 117, 176, 201, 229, 244, 89–91, 111, 113, 116, 119, 121, 123, 265, 313, 389, 572, 614, 633, 666 126, 127, 130–133, 147, 157, 160, CBLbadaptor...... 790 173, 179, 244, 287, 308, 341, 343, CBL Ub ligase 601, 603, 607, 630, 633, 639, 365, 414, 491, 496, 514, 524, 532, 720 788, 805 calcium-sensingreceptor...... 514 CBP (HAT)...... 379, 381 calciumblip...... 180 CCPgadaptor...... 790 calcium oscillation ...... 179 CD36...... 537 calcium puff ...... 173, 175, 180 CDC25 phosphatase ...... 41 calcium spark...... 175, 181, 187, 248 cellulin...... 605 calciumtransient...... 126 cell cycle ...... 41, 239, 667, 749 calcium wave ...... 180, 181 cell migration . 293, 319, 341, 342, 434, 630 calmodulin . . . 102, 119, 171, 178, 183, 250, cellpolarity...... 637 251, 467, 582 central nervous system . . 140, 291, 419, 474, calmodulin-dependent kinase . . . 35, 80, 144, 522, 746 171, 172, 178, 183, 184, 189, 199, cerebellin ...... 148 226, 233, 237, 240, 501, 507, 681, 747 cerebrospinal fluid ...... 365, 578 calpain...... 42,178 ceruloplasmin...... 284 calreticulin ...... 340, 341 CE transfer protein ...... 350, 406 calsequestrin...... 189 CFTR channel. . .81, 96, 155, 258, 262, 265, Cam2K...... 493 319, 326, 498, 552 cAMP . . 16, 32, 80, 133, 266, 308, 326, 388, cGMP...... 17,133 411, 490, 497, 543 chemerin...... 420 cancer ...... 530, 717 chemerinreceptor...... 420 cannabinoid receptor ...... 116, 515 chemokine ...... 341, 359 carbonic anhydrase ...... 153, 268 chemokine receptor ...... 517 carbon dioxide ...... 253, 333, 365 chemotaxis ...... 420, 518–520, 545, 584 carbon monoxide ...... 202, 247, 399 Chibby...... 736 970 Index chloride . . 81, 85, 88, 95, 139, 141, 149, 157 creatinekinase...... 415 cholecystokinin...... 520 CREB factor ...... 16, 168, 192, 198, 384 cholesterol. . . .237, 321, 350, 352, 392, 393, CRK adaptor ...... 349, 626 399, 402, 403, 537 crosstalk 40, 71, 79, 389, 456, 458, 503, 513 cholesterol ester transfer protein...... 402 Cryptic ...... 605, 665, 671 choline...... 290 CSF2...... 332 cholinetransporter...... 290 CSF3...... 564 chondroitin sulfate proteoglycan . . . 691, 698 CSF receptor ...... 640 choriogonadotropin ...... 539 CTDSP/SCP phosphatase ...... 681 chromogranin ...... 178 cubilin...... 344 chylomicron ...... 350, 403 cullin Ub ligase...... 737 chymase...... 420 cyclin-dependent kinase . 178, 460, 641, 724, chymotrypsin ...... 568 763 cIAPUbligase...... 798 cyclooxygenase132, 390, 515, 565, 567, 747 ciliary beat frequency . . . 132, 133, 365, 634 cysticfibrosis...... 88 ciliary neurotrophic factor ...... 767 cytochrome-Coxidase...... 283 ciliated cell ...... 326 cytochromeC...... 178 circadian rhythm ...... 401, 408, 542, 579 cytochrome P450 ...... 372, 402 cis-actingfactor...... 59 cytokinesis...... 41 Cl−–H+ antiporter...... 255 cytokinereceptor...... 370 Cl−–H+ exchanger ...... 155, 255, 258 cytotoxicTcell...... 324 − − Cl –HCO3 exchanger . . 155, 265, 268, 327, 328 D Clara cell...... 400, 534 Dab adaptor...... 339, 343, 349, 665, 672 clathrin...... 49,614 DAPKkinase...... 147 clathrin-coated pit ...... 285, 343, 464, 611 DDRkinase...... 642 claudin...... 305 decorin...... 423, 625 ClCa channel ...... 181, 262, 265, 327, 487 DeltexUbligase...... 707 ClC channel...... 81, 156, 255 demethylase...... 43 ClICchannel...... 263 dendritic cell ...... 123, 280, 496, 641, 800 ClNSchannel...... 82,265 dermatansulfate...... 625 CNG channel ...... 136, 216, 252 DGKkinase...... 616 coagulationfactor...... 420 diabetes...... 799 cofilin...... 471 diacylglycerol . 110, 120, 244, 464, 505, 567 collagen...... 354, 643 Dickkopf...... 739 collectin...... 353 diffusion...... 268 complement ...... 366, 519 Disheveled . . . . 465, 646, 728, 730, 736, 741 connexin ...... 89 Dispatched ...... 719, 720 connexon ...... 89 distal-less homeobox (DLx) ...... 564 contactin ...... 691, 696 divalentmetaltransporter...... 285 copper ...... 283 DLg adaptor . . 144, 145, 223, 227, 239, 240, copper ATPase ...... 270, 283 343, 498, 576 copper transporter ...... 283 DM2Ubligase...... 463 cortactin...... 235 DOCKGEF...... 417 corticosterone...... 402 DOK adaptor . 639, 646, 651, 660, 665, 789, corticotropin-releasing hormone...... 521 805 cortisol...... 390 dopamine . . 84, 141, 225, 296, 310, 522, 578 CRACchannel...... 162 dopamine receptor ...... 265, 522 creatine...... 414 dynamin ...... 719 Index 971 dynein ...... 674, 685 epidermal growth factor . . 73, 248, 389, 602, dynorphin ...... 509, 524, 559 724 dystroglycan...... 36 epigen...... 605 dystrophin ...... 196 epiregulin ...... 605, 620 epithelial–mesenchymal transition ...... 626 E epithelium...... 206 E2Ffactor...... 38,683 epsin...... 607 EAATtransporter...... 292 ERK . . . 23, 72, 81, 124, 201, 202, 214, 273, ecto-5-nucleotidase ...... 17, 87, 474 286, 297, 341, 358, 389, 390, 399, ecto-alkaline phosphatase...... 87 413, 417, 419, 421, 422, 439, 462, ectonucleotidase ...... 87 487, 496, 501, 503, 506, 507, 510, ectoproteinkinase...... 485 518, 522, 526, 527, 532, 533, 545, EET ...... 90, 132, 255 548, 552, 561, 572, 574, 578, 579, EGF-like domain-containing protein . . . . 619 581, 588, 601, 606, 609, 612, 616, EGFRpathwaysubstrate...... 607 619, 628, 630, 635, 645, 661, 667, EGF receptor . 249, 381, 417, 507, 532, 602, 680, 685, 771, 773, 794 711 erythrocyte . . . 81, 85, 86, 90, 216, 249, 266, eicosanoid...... 129, 301 320, 580 elastase ...... 201, 420 ESCRT...... 59,604, 615 electrolyte...... 93 estrogen...... 503, 531, 612, 696 embryo/fetus...... 175 estrogen-relatedreceptor...... 392 ENaC channel . 200, 226, 262, 265, 287, 327 estrogenGPCR...... 531, 540 endocannabinoid ...... 129, 225, 515 excitatory postsynaptic potential . . . 142, 145 endocytosis ...... 630 exercise...... 490 endoglin ...... 665, 669, 672, 678 exporter ...... 91 endomorphin ...... 225, 560 ezrin–radixin–moesin ...... 206, 265, 628 endophilin ...... 498 endoplasmic reticulum ...... 113 F endoplasmic reticulum stress...... 195 farnesoidXreceptor...... 392 endorphin ...... 559 fatty acid ...... 301, 330, 398, 532 endosome ...... 21, 59, 125, 258, 356, 629 fattyacid-bindingprotein...... 301 endothelin134, 175, 185, 243, 325, 506, 526, fatty acid transport protein ...... 637 619 Fcreceptor...... 784 endothelin receptor ...... 526 feedback...... 19, 21, 25, 32, 65, endothelium ...... 45, 79, 71, 119, 132, 151, 166, 170, 171, 179, 84, 131, 132, 206, 230, 249, 262, 266, 186, 192, 245, 260, 263, 289, 349, 303, 312, 353, 356, 357, 389, 397, 385, 393, 397, 399, 413, 416, 421, 399, 410, 419, 473, 478, 490, 492, 441, 467, 491, 499, 509, 555, 598, 507, 509, 527, 528, 541, 564, 580, 602, 607, 608, 613, 628, 644, 656, 582, 628, 637, 658, 672, 678, 695, 679, 680, 707, 711–713, 719, 725 697, 708, 709, 739, 746, 752, 753 feedforward ...... 162, 608 ENDPKkinase...... 87,88 ferritin...... 285 enkephalin ...... 509, 524, 559 FGF receptor ...... 621, 771 ENPP ectonucleotidase ...... 16, 87 fibrin...... 415 ENTPD ectonucleotidase . . 86, 87, 474, 490 fibrinogen...... 491 EpCAM...... 750 fibroblast ...... 206, 410, 506, 507, 570 ephrin...... 653, 713 fibroblast growth factor ...... 249, 410, 691 EPH receptor ...... 593, 653 fibronectin...... 738 epican(CD44)...... 627 fibrosis...... 645, 745 972 Index

filamin...... 666 glucocorticoid receptor ...... 145, 390 flavonoid ...... 303 glucose ...... 358, 522 FLK2 (CD135) ...... 640 glucose transporter . 313, 398, 420, 630, 633 flotillin ...... 633 glutamate ...... 84, 142, 414, 521, 538 foam cell ...... 332, 336, 358 glutamate–aspartate transporter ...... 292 focal adhesion ...... 505, 739 glutamate channel ...... 142, 521, 747 focal adhesion kinase . . . 381, 504, 645, 650, glutamate receptor ...... 538 657, 699, 789 glutathione...... 46 follicle-stimulating hormone ...... 539 GLUT enhancer factor (GEF) ...... 313 Fos factor ...... 181, 388, 516, 522 glycan...... 38 FoxCfactor...... 715 glycerol...... 308 FoxGfactor...... 718 glycinechannel...... 149 FoxH factor ...... 666, 682 glycogen synthase kinase206, 543, 667, 681, FoxOfactor...... 661 724, 732 Frizzled ...... 346, 465, 535, 728 glycoprotein hormone receptor ...... 539 functionalhyperemia...... 539 glycosaminoglycan ...... 47 functionalselectivity...... 500 glycosylation ...... 38, 139, 150, 260 furin ...... 201, 339, 705 glypican...... 39 Fyn kinase ...... 178, 349, 358, 633, 640 goblet cell ...... 488 Golgi body ...... 258, 283 G gonadotropin-releasing hormone ...... 540 GABA ...... 84, 141, 225, 291 GPCR...... 463 GABAA channel...... 141 GPCR kinase ...... 459, 473, 490, 578 GABAB receptor ...... 226, 535 GPCR phosphatase ...... 460 GAB adaptor . . 527, 617, 618, 626, 699, 788 GPIanchor...... 39 GAds/GRAP2adaptor...... 788 GRB adaptor . . . . 32, 40, 507, 526, 603, 631, galanin...... 536 651, 788, 789 galanin-likepeptide...... 536 Gregg’s phenomenon ...... 528 ganglioside ...... 601, 604 Grouchofactor...... 743 gapjunction...... 90 growth factor...... 366, 601, 747 gastrin...... 520 growth hormone-releasing hormone399, 537 gastrin-releasingpeptide...... 510 gutflora...... 532 gastransporter...... 333 Gprotein...... 61 GATAfactor...... 709 G protein-coupled receptor ...... 366 GDF...... 668 GDNF ...... 650 H gelsolin...... 549 H+–K+ ATPase ...... 269, 328 general transcription factor GTF2 . 378, 392, H+ ATPase . . . 254, 258, 268, 269, 298, 328, 682 413, 742 ghrelin...... 537 HV channel ...... 106, 267 ghrelin receptor ...... 399, 537 HBEGF...... 248 girdin...... 620 HCKkinase...... 763 GIRK channel...... 216, 223, 410 HCN channel ...... 137, 409, 452, 543 − glialcell...... 260 HCO3 transporter...... 153, 254 Glifactor...... 722 HDL...... 332, 350, 352, 405 glucagon ...... 503, 537 Headactivator...... 347 glucagon-like peptide ...... 537 heart 117, 121, 130, 282, 286, 293, 315, 322, glucagonreceptor...... 537 328, 336, 419, 527, 589, 649, 674, glucocorticoid...... 202, 237, 322, 402, 521 698, 780 Index 973 heartfailure...... 240 I heat-gated ion channel . . 112, 123, 124, 128, iKACh current...... 216 130 IDL...... 350 heat shock protein...... 202, 387, 796, 799 IDOL Ub ligase ...... 337, 394 HECWUbligase...... 737 IGF2Rreceptor...... 416 Hedgehog ...... 344, 464, 624, 709, 718 IGF receptor ...... 632 helperTcell...... 151 IKchannel...... 249 heme ...... 202, 247 imidazolinereceptor...... 414 heme oxygenase ...... 201, 202, 247, 399 immunoglobulin ...... 366 heparan sulfate proteoglycan ...... 39, importer ...... 91 64, 340, 341, 344, 594, 623, 625, 636, infarction...... 532 657, 688, 736, 739 inflammasome ...... 797, 799 heparin ...... 341, 625, 736 inflammation ...... 399, 765 inhibin...... 668 hepatocyte ...... 321, 328, 332, 393 initiation factor ...... 331 hepatocytegrowthfactor...... 762 inositol trisphosphate67, 161, 172, 173, 244, hepcidin...... 675 496, 567 hepsin...... 624 inotropy...... 493 HER receptor ...... 503, 592, 593, 610 InsRRreceptor...... 632 HESfactor...... 708 insulation...... 72 HETE ...... 129, 171, 398 insulin . . . 130, 206, 308, 312, 313, 321, 389, HETEE ...... 129 415, 422, 473, 496, 500, 503, 521, HGFactivator...... 625 534, 593, 653, 695, 697, 739 HGF receptor ...... 624, 803 insulin-like growth factor130, 286, 389, 724, histamine...... 410, 541 745 histaminereceptor...... 541 insulin-likepeptide...... 573 histone deacetylase ...... 604, 613 insulin receptor ...... 40, 423, 631 HODE...... 398 insulin receptor substrate . . . . . 618, 632, 739 Homerscaffold...... 179, 185, 192, 539 integrin...... 14, hormone...... 106, 215, 362, 366, 576 64, 224, 261, 262, 265, 297, 358, 362, hormone response element...... 387 417, 517, 627, 643, 645, 689, 738, 788 HPETE...... 129 intercalateddisc...... 206 HPETEE ...... 129 interferon...... 330 HRS (ZFYVE8) ...... 604, 607 interferonregulatoryfactor...... 797 HRT factor ...... 708, 715 interleukin ...... 90, 297, 332, 747, 799 intermediatefilament...... 613 HUNK kinase ...... 616 intimal hyperplasia ...... 134, 249 HUWE1(ArfBP1)Ubligase...... 401 intracellular hormone receptor ...... 363 hydrogen ...... 90, 147, 153, 173 intramembrane-cleaving protease ...... 57 hydrogen ion control ...... 94, 207, 412 inversin...... 742 hydrogenperoxide...... 411 ioncarrier...... 66 hydrogensulfide...... 230 ion pump ...... 108 hydronium ion ...... 204, 266 IP3 receptor ...... 214, 539 hydroxylation ...... 42 IQGAP ...... 68 hypertension...... 135, 183, 214, 565 IRAK (pseudo)kinase ...... 758, 793 hypertrophy ...... 617, 619 iron...... 285 hypothalamus...... 509, 586 ischemic preconditioning ...... 411, 480 hypoxia . . . 90, 167, 202, 230, 480, 567, 748 Itch Ub ligase ...... 131, 607, 616 hypoxia-inducible factor ...... 43, 747 ITKkinase...... 788 974 Index

J LDL...... 350 JadeUbligase...... 748 LDLR-related protein . . . 339, 416, 706, 728 JAMMmetalloprotease...... 52 LDLRAPadaptor...... 339 Janus kinase . . 421, 436, 504, 507, 563, 658, LDLR receptor 335, 336, 355, 407, 416, 728 694, 763, 803 lecithin–cholesterol acyltransferase 350, 406 JNK 125, 358, 436, 501, 508, 572, 581, 588, lectin ...... 353, 359, 422, 643, 800 616, 628, 635, 645, 656, 671, 674, leptin ...... 421, 521, 534, 555 681, 730, 739–741, 747, 777, 794, 798 leptinreceptor...... 421 junctin...... 190 leucyl–cystinyl aminopeptidase ...... 312 junctophilin ...... 191 leukemiainhibitoryfactor...... 767 Jun factor ...... 388, 516 leukocyte ...... 106, 420, 491, 619, 755 K leukotriene ...... 129, 398, 544, 547 K+–H+ exchangingATPase...... 155 leukotriene receptor ...... 544 LGR(GPCR)...... 739 K1P channel...... 217 LIMK kinase ...... 471, 685 K2P channel...... 217, 218, 253 KATP channel ...... 227, 329, 411, 415 lipocalin...... 302 KCa (BK) channel ...... 478, 539 lipoprotein ...... 366 KCa (SK)channel...... 543 lipoprotein lipase ...... 350 KCa channel ...... 116, 132, 216, 220, 244 lipoxin ...... 544 KIR channel . . 158, 222, 260, 318, 319, 327, lipoxygenase ...... 129, 341, 545 329, 409, 452, 478, 487, 516, 535, liprin ...... 688, 695, 696, 699 539, 556, 560 liver 121, 282, 299, 302, 314, 315, 328, 329, KNa channel ...... 220, 252 336, 343, 419, 420, 527 KV channel39, 219, 230, 327, 487, 543, 690, liverkinase-B...... 493 695 liver X receptor ...... 321, 323, 332, 393 kallidin ...... 510 long-QT syndrome...... 243 kallikrein ...... 512 long-term potentiation...... 143 KCCcotransporter...... 262 LPA receptor ...... 551 kidney . . 54, 81, 92, 108, 111, 120, 123, 130, LTKkinase...... 645 131, 164, 202, 207, 255, 282, 286, lung 107, 116, 117, 121, 164, 174, 176, 198, 288, 290, 293, 299, 302, 305, 309, 213, 286, 299, 302, 305, 311, 314, 311, 314, 315, 322, 328, 336, 412, 315, 320–322, 336, 353, 400, 419, 419, 522, 524, 589, 596, 643, 653, 420, 527, 558, 572, 589, 596, 643, 671, 674, 698, 780 645, 653, 671, 674, 688, 695, 697, kinesin ...... 721, 726 698, 718, 720, 762, 780, 781, 792 kinin...... 510 luteinizing hormone...... 539 kininogen ...... 510 kisspeptin...... 543 lymphangiogenesis ...... 553, 636, 638, 658 Klotho ...... 622, 750 lymphatic ...... 661 Kremenreceptor...... 739 lymphocyte . . . 108, 162, 172, 236, 249, 260, 280, 357, 487, 534, 580, 583, 641, L 777, 787 lamellipodium...... 635 Lyn kinase ...... 131, 358, 616, 786 larynx...... 262 lysophosphatidic acid . . . 398, 410, 465, 548, latrophilin GPCR ...... 544 550 LATadaptor...... 788 lysophospholipid ...... 548 LcK kinase ...... 694, 772, 789 lysosomalprotein...... 356 LCP2adaptor...... 788 lysosome ...... 113, 125, 259, 356 Index 975

M mineralocorticoid receptor ...... 145, 391 macrophage . . 280, 283, 321–323, 332, 350, MISTadaptor...... 790 397, 399, 537, 564, 640, 644, 739, mitochondrial Ca++ uptake protein. . . . .162 747, 787, 802 mitochondrion 162, 198, 262, 283, 299, 315, magnesium . . . 111, 133, 134, 147, 152, 153, 384 182, 183, 187, 251, 261, 271, 285, mitoferrin...... 285 287, 586 mitofusin...... 710 maltosetransporter...... 318 mitogen- and stress-activated kinase . . . . 792 manganese...... 196 mitosignalosome...... 797 mannose 6-phosphate receptor. . . . .412, 416 MJD deubiquitinase ...... 52 MAPK ...... 19, 29, 30, 35, 68, 69, MMP . . . . . 57, 415, 553, 565, 570, 622, 628, 73, 264, 293, 388, 460, 487, 492, 496, 643–645, 769 504, 510, 527, 543, 564, 602, 656, monocarboxylate transporter ...... 155, 281 681, 724, 758, 763, 797 monocyte ...... 564 mastocyte 123, 176, 421, 454, 553, 584, 625, motilin ...... 556 639 mRNA...... 59 MATKkinase...... 639 mucin...... 488 matriptase...... 624 mucociliary clearance ...... 203, 262, 488 Maxianionchannel...... 82,259 mucus ...... 203, 263 mechanogatedchannel...... 107 multidrug resistance transporter ...... 323 mechanosensitive channel. . . .107, 110, 119, multivesicular body ...... 61, 735 134, 156 MuSK kinase ...... 471, 646 mechanosome...... 12 MyB transcription factor ...... 196, 199 mechanotransduction 86, 201, 308, 435, 454, MycBP2Ubligase...... 401 462, 659 MyC transcription factor . 264, 667, 682, 749 Mediator complex ...... 381 MyD88 adaptor ...... 757, 792, 793 melanin-concentrating hormone ...... 554 myocardin ...... 390 melanocortinreceptor...... 554 myocardium ...... 578 melanocyte-stimulating hormone . . 554, 555 myocyte enhancer factor (MEF) ...... 313 melatonin...... 556 myogenic differentiation factor (MyoD).683 membrane raft ...... 39, 63, 332, 633 myogenic response ...... 134 Mer(RTK)...... 596, 616, 642, 803 myosin...... 313, 567 mesenchymal–epithelial transition ...... 634 myosin light-chain kinase ...... 494 metallothionein...... 284 myristoylation ...... 45, 247, 444 metastasis...... 262, 626 myristoyltransferase...... 45 methylation...... 43 methyltransferase...... 43 N Mg++ ATPase...... 271 Na+–Ca++–K+ exchanger...... 197 Mg++ transporter...... 285 Na+–Ca++–Li+ exchanger...... 197 MibUbligase...... 706 Na+–Ca++ exchanger . . 135, 158, 166, 175, Mical...... 752 186, 195, 196, 213, 420, 509, 526, 530 microphthalmia transcription factor (MiTF) Na+–Cl− cotransporter...... 92 259 Na+–H+ antiporter...... 155 microRNA . 21, 77, 321, 338, 395, 397, 499, Na+–H+ exchanger 153, 155, 206, 254, 268, 607, 609, 737 328, 343, 420, 499, 507, 509, 523, microtubule ...... 211, 666 524, 526, 530, 552, 562, 734 + − microtubule-associated protein ...... 132 Na –HCO3 symporter ...... 155, 262 microvillus...... 265 Na+–K+ ATPase . . 158, 197, 200, 212, 226, midkine...... 691 269, 292, 296, 523 976 Index

NaV channel ...... 39, 158, 208, 561, 693 neurotrophin RTK ...... 646 NAADP...... 161, 172 neurturin...... 651 NAADP receptor ...... 172 neutrophil . 85, 283, 357, 433, 487, 546, 564 NAD+ ...... 172 nexin ...... 569, 674 NADPH oxidase . . . 185, 268, 303, 307, 505, NFκB...... 25,45, 635, 779 50, 341, 387, 398, 464, 465, 487, 628, natriuretic peptide . . . 17, 310, 407, 506, 507 717, 736, 758, 773, 792, 797, 805 natriuretic peptide receptor . . . 407, 409, 556 NFκB-inducing kinase ...... 798 NCK adaptor ...... 381, 788 NFAT factor ...... 199, 487, 530, 787, 805 NCoAcoactivator...... 379 NHERF...... 562 NCoRcorepressor...... 377 nicotine ...... 140, 192 NDPKkinase...... 88 nicotinicacid...... 559 neddylation ...... 56, 607 Niemann-Pick type-C protein ...... 403 NEDD Ub ligase. . .202, 235, 261, 288, 607, nitricoxide...... 17,45,83, 616 84, 132, 133, 178, 183, 184, 254, 305, nephron. .199, 202, 207, 226, 253, 286, 288, 310, 333, 356, 390, 407, 411, 414, 291, 343 473, 490, 491, 506, 512, 526, 598 nervegrowthfactor...... 73 nitric oxide synthase 45, 124, 183, 196, 266, nervoussystem...... 527 303, 325, 390, 399, 487, 506, 507, nestin...... 613 530, 661 neuralizedUbligase...... 706 nitrosylation...... 45,487 neuregulin ...... 610, 613 NKCCcotransporter...... 641 neurite growth-promoting factor...... 691 NKx2-5factor...... 400 neurogenic differentiation factor (NeuroD) NMDA receptor ...... 226 389 nociceptin...... 560 neurokinin...... 584 NOD-like receptor ...... 796 neuromedinB...... 510 Nodal...... 665 neuromedinC...... 510 nodal cell ...... 261, 409 neuromedinN...... 558 non-receptorTyrkinase...... 457 neuromedin receptor ...... 556 noradrenaline . . . . 82, 83, 170, 251, 296, 500 neuromedinS...... 557 nose ...... 262, 424 neuromedinU...... 556 Notch ...... 619, 623, 703, 720, 727 neuromuscular junction ...... 82, 471, 646 Notumpectinacetylesterase...... 39 neuron ...... 213, 260, 422 NRFfactor...... 709 neuropeptideB...... 557 nuclear estrogen receptor...... 24, 388 neuropeptideEI...... 554 nuclear respiratory factor (NRF1) ...... 384 neuropeptideFF...... 543 nucleobinding (calnuc) ...... 345, 348 neuropeptideGE...... 554 nucleoside...... 474, 482 neuropeptideK...... 584 nucleotide ...... 474, 482 neuropeptideS...... 557 neuropeptideW...... 557 O neuropeptide Y ...... 422, 554, 556, 557 obesity...... 421 neurophysin...... 588 occludin...... 306 neuropilin ...... 636, 751 octopamine...... 585 neuroregulin ...... 602, 713 omentin...... 422 neurotensin ...... 347, 369, 524, 525, 558 oncostatin...... 767 neurotransmitter . . . 106, 215, 225, 362, 366, opioid...... 559 576 Orai Ca++ channel...... 163 neurotrophin ...... 646 ORCC Cl− channel ...... 265, 327 Index 977 orexin...... 562 phosphatidic acid ...... 505, 550 osmoreceptor...... 131 phosphodiesterase ...... 16, 535 osmoticpressure...... 81,107 phosphoinositide ...... 113, 234 osteoclast...... 802 phospholamban...... 194 osteoprotegerin...... 780 phospholipase A . . . 132, 133, 505, 543, 550, OTU deubiquitinase...... 52 578 oxidative stress ...... 42, 56, 315, 353, 741 phospholipase C91, 113, 115–117, 125, 153, oxygen...... 247, 253, 333, 365 162, 176, 226, 229, 244, 262, 409, oxysterol ...... 726 420, 475, 480, 486, 493, 505, 509, oxytocin ...... 83, 586, 587 511, 523, 543, 556, 572, 578, 598, 623, 626, 637, 788, 789 P phospholipase D ...... 33, 505, 578, 581 P-typeATPase...... 160 phospholipid ...... 548 P1receptor...... 482 phosphorylation ...... 20, 21, 31, 34, 150 P21-activated kinase ...... 381, 471, 609 PI3K202, 214, 341, 419, 460, 527, 532, 579, P2X channel ...... 80, 82, 90, 150, 260, 482 598, 612, 615, 626, 633, 637, 656, P2Y GPCR ...... 80, 133, 260, 262, 482 763, 789 P300 (HAT) ...... 379, 381 PIASSUMoligase...... 765 P38MAPK . . . 358, 419, 460, 501, 508, 516, Piezo (Fam38) ...... 107 561, 581, 588, 606, 614, 628, 641, pituitary ACase-activating peptide ...... 588 671, 685, 773, 777, 794, 798 PKMytkinase...... 41 P53 transcription factor . . 33, 38, 41, 43, 44, plasmerosome ...... 117, 164, 213, 214 264, 699 plasmin ...... 201, 415, 420, 624 P70 ribosomal S6 kinase (S6K) . . . . 419, 685 plasminogen ...... 415 pacemaker...... 101, 137 platelet . . 178, 249, 265, 297, 320, 354, 357, palmitoylation ...... 46, 233, 389, 444 453, 491, 553, 642, 643, 803 pannexin...... 90,487 platelet-activatingfactor...... 563 parasympathetic...... 83, 650 platelet-derived growth factor . . . . . 410, 746 parathyroid hormone ...... 562 pleiotrophin ...... 645, 691 parathyroid hormone-related peptide. . . .562 plexin...... 628, 650, 751, 752 Patched ...... 719, 725 PLuNC...... 201 paxillin ...... 650, 657, 699, 789 PMCA pump ...... 186, 195 PDGF receptor...... 417, 634 pneumocyte ...... 322, 343, 344, 400 PDK1kinase...... 633 Polo-likekinase...... 749 Peli1Ubligase...... 794 polyADPribosylglycosidase ...... 41 pepducin...... 518 polyADPribosylpolymerase...... 41 peptidase...... 339 polyadpribosylation...... 41 peptidase-activated receptor ...... 568 Polycomb chromatin repressor ...... 779 peptideYY...... 534 polycystin ...... 125, 434 pericyte...... 658 polysialyltransferase...... 39 peripheralnervoussystem...... 140 pore...... 91 perivascularnerve...... 85 potassium...... 81,157 peroxisome ...... 329, 330, 384 PP1 . . 40, 172, 177, 184, 225, 233, 246, 527, persephin...... 651 609, 672 PGCfactor...... 382 PP2 . . 44, 172, 177, 225, 251, 259, 410, 461, pH . . 204–206, 247, 253, 275, 281, 294, 300, 512, 609, 672, 681, 724, 737 308, 328, 365, 439 PP3 ...... 196, 233, 237, 410, 530, 564, 787 phagocytosis...... 268, 804 PPAR factor ...... 301, 323, 352, 395, 419 phosphacan ...... 700 PPM1 ...... 264, 410, 681 978 Index pre-Bötzinger complex ...... 576 PTPRc ...... 694, 764 pregnancy...... 512 PTPRd...... 694 prenylation...... 46,444 PTPRe ...... 695, 764 presenilin ...... 611, 750 PTPRf ...... 627, 696 primary cilium . . . . . 126, 435, 447, 720, 742 PTPRg...... 696 prion...... 340 PTPRh...... 696 prokineticin...... 563 PTPRj ...... 627, 696 prokineticinreceptor...... 563 PTPRk...... 697 prolactin-releasingpeptide...... 543 PTPRm...... 697 prolyl hydroxylase ...... 43 PTPRn...... 697 prostacyclin...... 132, 398, 490, 565, 567 PTPRn2...... 697 prostaglandin . . 309, 310, 328, 398, 512, 565 PTPRo ...... 656, 698 prostanoid receptor ...... 248, 565 PTPRq...... 698 proteasome...... 49,460 PTPRr...... 698 proteinC...... 568 PTPRs...... 699 protein domain ...... 28 PTPRt...... 699 protein kinase A80, 129, 144, 171, 177, 183, PTPRu...... 699 184, 225, 243, 246, 266, 289, 309, PTPRv...... 699 327, 389, 452, 466, 543, 609, 720, PTPRz1...... 700 721, 724 pulmonary hypertension . 120, 297, 530, 685 protein kinase B . . . 178, 206, 422, 460, 506, purine...... 474, 482 510, 532, 543, 564, 582, 609, 628, pyrimidine...... 482 633, 661, 667, 717, 724, 752, 773, 803 proteinkinaseC...... 73, R 80, 120, 129, 144, 171, 183, 185, 226, R-spondin ...... 739 229, 244, 246, 262, 266, 325, 336, Rab GTPase ...... 61, 314, 464, 719, 749 420, 473, 480, 496, 509, 530, 609, Rac GTPase . . . 501, 572, 630, 730, 739, 740 629, 633, 639, 681, 763, 805 Rafkinase...... 609 protein kinase D ...... 286, 473 RAMP...... 514 protein kinase G . . . 171, 177, 246, 266, 411, RapGEF...... 349 676, 681 rapsyn...... 646 protein S ...... 803, 804 Rap GTPase ...... 349, 645 proteoglycan...... 725 RasA GAP ...... 626, 628 proteolysis...... 57 RasGAP...... 598 proton-sensingGPCR...... 551 Ras GTPase ...... 507, 616, 656, 680 pseudogene ...... 109 RE1-silencing transcription factor (REST) pseudokinase ...... 591, 654 248 PTen phosphatase ...... 578, 633 reactive oxygen species . . 58, 171, 185, 206, PTK7 kinase ...... 593, 650, 742 254, 268, 283, 315, 411, 505, 508, PTPn1...... 422, 615, 627, 764 516, 529, 619, 635, 688, 779, 799 PTPn11/SHP2 206, 421, 511, 527, 626, 628, receptor-operated channel . . . . 133, 134, 163 633, 634, 637, 639, 764, 786, 789, receptor for activated C kinase ...... 348 803, 805 receptor Ser/Thr kinase ...... 366, 662 PTPn2...... 627, 764 receptor Tyr kinase ...... 366, 457, 593 PTPn4...... 148 receptor Tyr phosphatase...... 366, 687 PTPn6/SHP1 . 598, 637, 639, 653, 764, 786, recepzyme ...... 362 796, 803, 805 recoverin...... 460 PTPRa...... 689 reduction–oxidation ...... 58 PTPRb...... 260, 601, 646, 661, 691 reelin ...... 335, 349 Index 979 reelinreceptor...... 349 Schnurritranscriptionfactor...... 264 refractoryperiod...... 186 sclerostin...... 345 regulator of G-protein signaling . . . 226, 436, secretase...... 336, 611, 613, 627, 706 458, 466, 473, 511 secreted Fz-related protein ...... 738, 746 relaxin...... 573 secretin ...... 537, 589 renin ...... 289, 412, 524 Sefinhibitor...... 624 repressilator...... 66 selenoprotein...... 192 repulsive guidance molecule ...... 675 semaphorin...... 628, 649, 650, 751 resistin...... 423 senescence...... 750 resistinreceptor...... 423 SERCA pump ...... 156, 186, 193 respiratoryepithelium...... 634 serotonin ...... 84, 225, 243, 296, 399, 574 respiratoryneuron...... 253 serotonin 5HT3 channel...... 149 retinaldehyde-binding protein ...... 303 serotonin5HTreceptor...... 297 retinoic acid ...... 301, 400 serotonintransporter...... 297 retinoic acid-binding protein ...... 302 serpin ...... 339, 415, 711 retinoic acid-related orphan receptor . . . . 401 serumamyloid-A...... 546 retinoic acid receptor ...... 301, 400, 676 Ser protease ...... 201, 204 retinoid...... 301 SGK kinase ...... 203, 226, 288 retinoid X receptor...... 301, 321, 400 SH3BP2adaptor...... 789 retinol-binding protein ...... 301 SHBadaptor...... 790 retromer...... 347 SHC adaptor . . . 40, 341, 507, 526, 603, 626, ReTreceptor...... 650 644, 651 RhoGEF...... 752 shear...... 86 Rho GTPase . . 153, 501, 572, 730, 739, 749, SHIP phosphatase ...... 633, 787, 805 752 SIAH Ub ligase ...... 378, 790 RIBPadaptor...... 789 sialidase...... 39 RIPkinase...... 798 sialylation...... 39,328 RNA-bindingprotein...... 60 siglec...... 770 RNAoperon/regulon...... 60 signalingspecificity...... 68 RoCK kinase ...... 494, 567 signalingrobustness...... 64 ROMK channel ...... 226, 266, 287, 327 sinoatrial node ...... 138 RON (MSt1R) kinase ...... 595, 634, 803 sirtuin...... 708, 740 ROR (RTK) ...... 535, 741 SITadaptor...... 789 Roskinase...... 653 SK channel ...... 220, 225, 249 Runxtranscriptionfactor...... 683 SLAMreceptor...... 804 ryanodine receptor ...... 180, 248, 264 SLAadaptor...... 790 RYK kinase ...... 535, 651, 652, 741 SLC transporter ...... 155, 266, 274, 393 SMAD factor.34, 38, 79, 299, 344, 378, 678 S Smoothened ...... 464, 719, 722 S100 protein ...... 189, 418 smooth muscle cell...... 83, 84, SAPadaptor...... 804 91, 108, 125, 130–132, 167, 171, 181, sarcolipin...... 194 185, 187, 196, 198, 199, 206, 213, SARMadaptor...... 792 230, 238, 243, 248, 249, 315, 341, SARGTPase...... 403 390, 413, 417, 452, 473, 490, 492, scaffoldprotein...... 28,73,144 506, 508, 528, 532, 563, 570, 619, scavenger receptor . 350, 399, 403, 405, 407, 644, 709, 739, 765 537 SMURF Ub ligase ...... 616, 666, 671, 672 SCF receptor ...... 638 Snail homolog (Snai) ...... 683 SCF Ub ligase ...... 379, 666, 732, 799 SOCS...... 422, 639, 762, 803 980 Index sodium ...... 81, 125, 157, 266 sympathoexcitatory reflex ...... 512 solubleadenylatecyclase...... 412 symporter ...... 92 solubleguanylatecyclase...... 410 synaptojanin...... 658 somatostatin ...... 225, 579 synaptotagmin...... 314 sorcin...... 191 syndecan ...... 625, 645 SOS GEF . . 32, 33, 527, 601, 604, 606, 628, syntaxin...... 266 633, 788 syntrophin ...... 196 Soxtranscriptionfactor...... 743 SP1transcriptionfactor...... 299 T SPCA pump ...... 156, 196 T-cellfactor(TCF)...... 743 spectrin...... 666 tachykininreceptor...... 584 sphingomyelinase ...... 779 TAM receptor ...... 803 sphingosine 1-phosphate . . . . . 320, 410, 580 TATA box-binding protein (TBP)...... 743 spindle checkpoint ...... 52, 749 TCRreceptor...... 805 spinophilin ...... 466 tenascin...... 691 Sprouty ...... 601, 624 testicularreceptor...... 391 SPURTsensor...... 204 tetraspanin ...... 615, 639, 772 Src kinase . 58, 147, 178, 208, 214, 226, 237, TGF receptor...... 662 349, 381, 389, 390, 417, 460, 503, thermosensitive ion channel . . 112, 127, 131 504, 526, 527, 609, 614, 616, 619, thioredoxin ...... 46, 120 623, 626, 653, 656, 685, 689, 694, thioredoxin-interacting protein ...... 799 695, 789, 802 thrombin ...... 568, 625 SREBP factor...... 321, 393 thrombospondin ...... 341, 354, 356, 706 STAMBP deubiquitinase ...... 609 thromboxane ...... 243, 248, 491, 565, 567 STAMadaptor...... 604 thrombus...... 178 STAT factor51, 322, 421, 436, 611, 616, 626, thymosin ...... 563 629, 639, 658, 694, 709, 762, 763, 803 thyroid-stimulating hormone ...... 539 Stefan-Maxwellequation...... 268 thyroid hormone...... 202, 386, 555 stemcell...... 206 thyroid transcription factor (TTF) ...... 322 stemcellfactor...... 638 thyrotropin-releasing hormone ...... 555 steroid ...... 363, 386 TIAMGEF...... 628, 630 sterol regulatory element-binding pro- TIE receptor ...... 660, 693 tein(SREBP)...... 322 tightjunction...... 306 StIM Ca++ sensor ...... 110, 163 TIRAPadaptor...... 792 STK39/SPAKkinase...... 287 tissue factor ...... 568, 573 store-operated channel . . 113, 119, 134, 162, tissue plasminogen activator ...... 415 163, 187 TNFαIPDUb/Ubligase...... 52 stretch-activated ion channels ...... 107 TNFRSF...... 30,630, 773 substance P ...... 83, 117, 369, 524, 584 TNFSF...... 630 sulfation...... 46 Toll-like receptor ...... 358, 790, 804 SUMo ...... 54, 237, 253, 632 traceamine...... 585 sumoylation...... 54,671 trachea ...... 262, 263 SUMo sentrin-specific protease ...... 54 tracheobronchialtree...... 262 superoxide dismutase ...... 85, 283, 284 TRAF Ub ligase . 30, 50, 644, 671, 758, 771, surfactant ...... 320, 322 773, 777, 778, 780, 781, 794, 795 surfactant protein ...... 322, 400 TRAMadaptor...... 792 Swi–SNF chromatin-remodeler ...... 379 trans-actingfactor...... 59 SYK kinase ...... 694, 786, 789, 802 transceptor...... 273 sympathetic ...... 83, 533, 650 transcriptionfactor...... 61,372 Index 981 transducisome...... 27 vascular endothelial growth factor . 249, 398, transferrin...... 285 636, 650 transferrin receptor ...... 285 vascular smooth muscle cell . . . 85, 120, 131, transforming growth factor . . . 248, 264, 299, 134, 166, 176, 211, 213, 230, 237, 344, 508, 662 259, 297, 342, 419, 479, 509, 527, transmembrane electric potential difference 619, 657, 658 94 vascular tone . . 113, 237, 243, 245, 248, 522 transporter...... 92 vasculogenesis ...... 548, 635, 700 transthyretin...... 302 vasoactive intestinal peptide . . . 83, 546, 588 transversetubule...... 260 vasoactive stimulatory phosphoprotein . . 411 TRATadaptor...... 789 vasoconstriction 85, 119, 120, 134, 185, 246, Trbadaptor...... 685 248, 297, 451, 473, 496, 506, 529, TREMreceptor...... 801 530, 544, 557, 567, 570, 586, 587 triadin...... 190 vasodilation . . . . 84, 113, 116, 132, 187, 213, tricarboxylic acid cycle...... 162 230, 243, 244, 246, 249, 356, 389, TRIFadaptor...... 792 410, 411, 420, 451, 474, 506, 512, triglyceride...... 350 524, 529, 530, 539, 567, 586, 701 TRIMUbligase...... 683 vasopressin 83, 108, 202, 309, 420, 509, 586 troponin ...... 188 vATPase ...... 155, 269 TRP channel . . . 42, 108, 172, 248, 308, 348, Vav GEF ...... 788, 789, 805 410, 434, 564 VDACchannel/porin...... 262 trypsin ...... 204, 568 VEGF receptor ...... 636 tryptase ...... 420, 455 vesicle...... 31,61 tubulin...... 211 vesicular ACh transporter ...... 291, 298 tumor-necrosis factor ...... 297, 325, 331 vesicularcalciumchannel...... 162 tumor cell . . . . . 439, 603, 622, 630, 751, 796 vesicularGABAtransporter...... 291 Tweety homolog channel ...... 260 vesicular glutamate transporter ...... 291 TyK2kinase...... 563 vesicular monoamine transporter . . 291, 298 tyramine...... 585 VHLUbligase...... 43 TyrO3 (RTK) ...... 596, 642, 803 visfatin...... 423 tyrosylprotein sulfotransferase ...... 47 vitamin-A ...... 301, 343, 372, 377, 400 vitamin-B ...... 319, 343, 344, 559 vitamin-C ...... 301, 315 U vitamin-D ...... 343, 344, 372, 377, 726 ubiquitin ...... 59, 61, 63, 615, 737 vitamin-E ...... 343, 344 ubiquitination . . . . 21, 47, 463, 671, 708, 738 vitronectin...... 417 UCH deubiquitinase ...... 52 VLDL...... 350 UCKkinase...... 616 VLDLRreceptor...... 349 uniporter...... 92 voltage-gated channel ...... 103, 199 uPAreceptor...... 342 volume-activated anion channel ...... 82 urmylation...... 56 volume-activated ion channels ...... 107 urocortin...... 521 von Willebrand factor ...... 491 urodilatin...... 408 VRAC channel ...... 261, 265 urokinase...... 342, 415 VSORchannel...... 81 urotensin...... 586 USP deubiquitinase . . 52, 463, 609, 615, 738 W Willis circle ...... 710 V wine polyphenol ...... 389 VangL...... 741 WNK kinase ...... 120, 226, 286, 287 982 Index

Wnt.345, 346, 399, 413, 650–652, 699, 727, ZBTBfactor...... 413 750 ZEBfactor...... 78 ZFYVE anchor ...... 665, 667, 672, 679 Y zinc ...... 116, 147, 149, 152, 267, 304, 720 Yeskinase...... 358 ZnFadaptor...... 790 Z zonula occludens protein ...... 564 ZAP70 kinase ...... 593, 789 zwitterion ...... 294