bluuebunny/crossref_metadata_2025 huggingface dataset:
Steady-State and Transient Operation Of D.C. Machines and D.C. Motor Drives
Authors: Vas Peter
Published: November 2023

Although the d.c. machine is relatively complicated and thus expensive, especially in comparison with the squirrel-cage induction machine, it continues to be extensively used since it is relatively easy to control over wide ranges of speed and load. Due to the action of the commutator, the control of a d.c. drive is relatively simple, and the same basic control system can satisfy the requirements of most applications. The main disadvantages of the d.c. machine are that it requires periodic maintenance, there is a maximum speed limit where it can be safely operated, it is relatively unsuitable in hostile environments, and it is expensive. It should be noted that due to the rapid advance in the field of power electronics, in some applications d.c. drives have been replaced by variable-speed a.c. drives, for example, in servo drives, mill drives, and spindle drives. The stator of a d.c. machine is usually the stationary member and the rotor is the rotating member. The schematic of a four-pole d.c. generator is shown in Fig. 5.1.
Performance Evaluation By Test
Authors: Hendershot J R
Published: November 2023

Many performance issues have been dealt with of necessity within some of the previous chapters, in order to provide background and justification for the rotor and stator design methods. However, several important performance parameters must be considered more carefully in order to facilitate a proper design for a particular application. For example, the speed vs. torque curve has been mentioned, but a more detailed presentation is given. This treatment leads up to the issue of sizing a brushless motor at the outset before detailed design is performed. The problem of heating is also related to the sizing, materials used, and cooling methods. Temperature rise is a very difficult parameter to calculate unless the thermal time constant has been measured on an actual sample. Finally in this chapter, the so-called basic brushless motor constants will be summarized to illustrate how the design is summarized in terms of the performance specifications, why some of the motor constants are desired, and how they characterize a particular motor.
General aspects of the application of artificial intelligence in variable-speed drives
Authors: Vas Peter
Published: November 2023

So far the application of intelligent soft-computing based control methods have had the greatest impact in the aerospace industry, but it is most likely that this tendency will change in the near future. Although the numerous advantages of using artificial intelligence in drive systems will be discussed in detail in later chapters, it is important to note that in many cases their application leads to significantly reduced development times and can help to avoid mathematical difficulties in system development since they do not require the mathematical models of the system. Table 3.1 summarizes some of the main advantages offered by the application of artificial intelligence-based systems (controllers, estimators, etc.).
Application of artificial neural networks
Authors: Vas Peter
Published: November 2023

In the present chapter the fundamentals of artificial neural networks are described, these include static and dynamic neuron models, the backpropagation training algorithm, etc. Both supervised and unsupervised neural networks are discussed, e.g. the multi-layer feedforward backpropagation artificial neural network, the radial-basis function network and the Kohonen feature map. However, various neurocontrol systems are also described. In the present section the fundamentals of artificial neural networks (ANNs) are discussed in detail. For this purpose first a biological neuron model is given and this is followed by defining an artificial neuron. Hardware implementations of ANNs are also discussed briefly.
Fuzzy logic systems
Authors: Vas Peter
Published: November 2023

A fuzzy logic system is one type of approximate reasoning system. It can be considered as one type of (intelligent) non-linear function approximator (see also Section 4.4). In the past five years there has been a huge increase in the application of fuzzy logic systems. It is believed that this ‘revolution’ will continue. Therefore there is a strong need to have a good understanding of fuzzy systems.
Genetic algorithms
Authors: Vas Peter
Published: November 2023

In contrast to artificial neural networks, fuzzy logic systems and fuzzy-neural networks, which can be considered to be general non-linear function approximators (see Chapter 4), genetic algorithms (GAs) are optimization techniques [Goldberg, 1989), whose main features have been discussed in Section 3.5. In the present chapter details of GAs together with the necessary computational steps are given and it is also shown how GAs can be used for the tuning of membership functions in fuzzy logic systems and for the finding of the appropriate structure of a neural network.
Elementary viscous flow
Authors: Acheson D J
Published: November 2023

Steady flow past a fixed aerofoil may seem at first to be wholly accounted for by inviscid flow theory. The streamline pattern seems right, and so does the velocity field. In particular, the fluid in contact with the aerofoil appears to slip along the boundary in just the manner predicted by inviscid theory. Yet close inspection reveals that there is in fact no such slip. Instead there is a very thin boundary layer, across which the flow velocity undergoes a smooth but rapid adjustment to precisely zero —corresponding to no slip —on the aerofoil itself (Fig. 2.1). In this boundary layer inviscid theory fails, and viscous effects are important, even though they are negligible in the main part of the flow.
Very Viscous Flow
Authors: Acheson D J
Published: November 2023

The character of a steady viscous flow depends strongly on the relative magnitude of the terms (u · V)u and v V2u in the equation of motion

We are here concerned with the ‘very viscous’ case in which the (u • V)u term is negligible. There are two rather different ways in which this can happen.
Boundary Layers
Authors: Acheson D J
Published: November 2023

In August 1904 the Third International Congress of Mathematicians took place at Heidelberg, and Prandtl presented a paper ‘On the motion of fluids of very small viscosity’. He was no great figure at the time, and was given just ten minutes in the programme. The published version of his paper (1905) has 7^ pages of text and two pages of photographs.! At the heart of it Prandtl addresses the flow of a fluid of small viscosity past a solid body.
Instability
Authors: Acheson D J
Published: November 2023

The . . . experiments were made on three tubes .... The diameters of these were nearly 1 inch, ½ inch and ¼ inch. They were all about 4 feet 6 inches long, and fitted with trumpet mouthpieces, so that water might enter without disturbance. The water was drawn through the tubes out of a large glass tank [Fig. 9.1), in which the tubes were immersed, arrangements being made so that a streak or streaks of highly coloured water entered the tubes with the clear water.
Normal surfaces
Authors: Hemion Geoffrey
Published: November 2023

Two very important parts of the general plan are still missing. We hâve shown that ail knot spaces are sufficiently large; that is, they contain incompressible surfaces which we can use for our splitting purposes. But we hâve still not shown that there are only a finite number of possible such incompressible surfaces. Furthermore, we hâve not shown that the 3-dimensional pièces which result from a splitting along an incompressible surface are genuinely simpler than the original pièces. Both of these things are very essential for proving that the proposed algorithm is finite. With-out them, there is the danger that our overworked computer will descend into an endless recursion.
What to do in the difficult case
Authors: Hemion Geoffrey
Published: November 2023

Assuming that we are in the difficult case, then it must be that the 3-manifold M contains either (A) incompressible annuli which do not meet the boundary pattern of M, and/or (B) incompressible tori. Let us begin by thinking about case (B). If there are any incompressible tori which are not boundary parallel, then let T be one of them. Since ∂T= Ø, we have that the complexity of T is zero, not only according to the old definition of complexity, but also according to the new definition given in the previous chapter.
The conjugacy problem
Authors: Hemion Geoffrey
Published: November 2023

Our problem is to classify homeomorphisms of surfaces. Therefore it is natural that we confront ourselves with the basic question: what does it actually mean to classify the possible homeomorphisms of a topological space? At first sight the answer to this question might appear to be trivial.
Small conjugating homeomorphisms
Authors: Hemion Geoffrey
Published: November 2023

In the last chapter we have seen that a small, non-trivial, closed curve c exists in the interior of the surface S. The curve c is small with respect to both fundamental regions Δ and h(Δ), where h is some particular homeomorphism of the surface onto itself. Our task now is to show that this implies, in conjunction with a few ‘hidden’ assumptions which we are making, that the homeomorphism h is itself small. Let us begin by looking more closely at the curve c. We do not assume that c is necessarily simple. (That is to say it may have ‘singularities’—crossing over itself.) Nevertheless we can assume that c is piecewise linear, and that it crosses itself at most in a finite collection of isolated points.
Linear Optimization
Authors: Kockler Norbert
Published: November 2023

Optimization is itself a large area within the field of applied mathematics. It deals with the minimization and maximization of functions with or without constraints and has many different applications. A large number of these applications belong to the area of operations research within the economic sciences. Not surprisingly, there are some software packages for optimization. But methods for the solution of simple optimization problems may also be found in most textbooks on numerical mathematics. Mathematical software libraries always contain a chapter on optimization. In the NAG Fortran Library there are more than 40 routines in Chapter E04 and some routines on integer programming in Chapter H. Chapter 8 of the IMSL Library contains more than 30 routines on optimization.
Entering the secretory pathway
Authors: Rothblatt Jonathan , Novick Peter , Stevens Tom H
Published: November 2023

In prokaryotic and eukaryotic cells, specialized processes such as secretion and signal transduction, as well as the enzymatic reactions of intermediary metabolism, are organized into membranes and membrane-enclosed compartments. The unique biochemical make-up of each compartment and the specificity and directionality of the secretory process can be maintained only if mechanisms exist for selective targeting of newly-made proteins to their correct subcellular location, for their active transport across impermeant membrane barriers and for their covalent and conformational modification.
SRP-like complex in prokaryotes
Authors: Walter P
Published: November 2023

E. coli 4.5S RNA contains a highly conserved structural motif that is also found in the RNA subunit of mammalian SRP. Ffh binds to phylogentically conserved bases in this motif5-8. The primary structure of Ffh is highly similar over its entire length to that of SRP549-11 (see entry p. 29} and includes a central GTPase domain, an N-terminal domain of unknown function and a (-terminal methionine-rich domain that, for mammalian SRP54, was shown to contain both the RNA binding site and the signal sequence binding site.
SecA
Authors: Oliver D
Published: November 2023

Additional alleles of secA were isolated as suppressors, designated pr/D, of signal peptide defects in maltose-binding protein2and as mutants, designated azi, which confer resistance of growth to sodium azide, an inhibitor of SecA ATPase activity3.4.
SecY
Authors: Flower A M , Silhavy T J
Published: November 2023

The first alleles of secY were isolated as suppressors of signal sequence mutations and are designated prlA alleles4. Starting with a strain that was dextrin negative due to a mutation in the signal sequence of LamB (maltoporin), these suppressors were identified following selection for the ability to use dextrin as a carbon source.
PDI1
Authors: Tuite M F , Freedman R B
Published: November 2023

The S. cerevisiae POI-encoding gene (PD/1) is located on the left arm of chromosome Ill close to the GLK1 gene encoding glucokinase . The nucleotide sequence of the PD/1 gene has been independently reported by several laboratories.
ERN1
Authors: Mori K , Gething, M J , Sambrook J
Published: November 2023

em1 mutants were isolated using a genetic screen designed to identify genes involved in signalling the unfolded protein (UPR)4-7 response from the ER to the nucleus. They display wild-type levels of basal transcription from the UPR element in the promoter of the KAR2 (BiP) gene (see entry p. 41), but are impaired in the UPR response. The heat shock response is unaffected.
The ALG genes
Authors: Robbins P W
Published: November 2023

A [3H]mannose suicide selection was used to isolate yeast mutants which contain temperature sensitive defects in asparagine-linked glycosylation. Surviving cells were screened at the nonpermissive temperature for decreased ability to incorporate [3H]mannose, defects in glycosylation, and finally for synthesis in vivo of incomplete oligosaccharides linked to dolichol pyrophosphate.
Ribosome receptor
Authors: Savitz A J , Meyer D I
Published: November 2023

The interaction of ribosomes with the membrane of the endoplasmic reticulum (ER) has been shown to be sensitive to puromycin and high salt1-4 as well as proteases1,5. This implies that protein-protein interactions, beyond that of the nascent chain with the translocation machinery, mediate ribosome binding. Rough microsomes, from which ribosomes have been removed (stripped), are able to rebind ribosomes, under the appropriate conditions, to pre-stripped levels5-7. To measure this rebinding, radiolabeled ribosomes are added to stripped membranes, and bound ribosomes are separated from free ribosomes by flotation of the membranes in a sucrose gradient7 In this way, the rebinding reaction can be quantified and characterized.
Mammalian Sec61p
Authors: Hartmann E , Rapoport T A
Published: November 2023

The mammalian homolog of SecYp/Sec61p is an integral non-glycosylated membrane protein of 476 amino acids with an apparent molecular weight in SOS-gels of 40 kDa1 Highly homologous sequences were obtained by cDNA cloning from MOCK (canine) cells and from rat liver tissue. They are available in the GenBank under the accession numbers M96629 and M96630, repectively1.
Calrcticulin
Authors: Koch H L E
Published: November 2023

The nucleotide sequences of cDNAs encoding calreticulins from mouse3, rat3, rabbit9 and nematode10 (GenBank accession numbers X14926, X53363, J05138, X59589) each reveal an open reading frame encoding a protein of approximately 400 amino acids including an N-terminal signal sequence and the (-terminal tetrapeptide KDEL (HOEL in the nematode protein) associated with ER retrieval11, The murine and nematode proteins display 61% sequence identity.
N-Acetylglucosaminyl phosphate transferase
Authors: Krag S S
Published: November 2023

The isolation of the cDNA for this enzyme was facilitated by two tools - first, tunicamycin-resistant Chinese hamster ovary (CHO) cells6·8, which had amplified the target gene89, and second, the ALGl gene from yeast10 (seep. 58), which confers tunicamycin resistance to yeast and which is presumably the gene encoding the yeast N-acetylglucosaminyl phosphate transferase.
Oligosaccharyltransferase complex
Authors: Gilmore R
Published: November 2023

Glycosylation of proteins on asparagine residues (N-linked glycosylation) occurs during or shortly after the nascent polypeptide is translocated across or integrated into the membrane of the rough ER. The mannose-rich oligosaccharide moiety is transferred en block from the lipid-linked oligosaccharide donor Glc3Man9GlcNAc2-P-P-dolichol to Nlinked carbohydrate acceptor sites by the enzyme oligosaccharyltransferase.
SEC31
Authors: Salama N
Published: November 2023

Sec31p was identified as a 150 kDa protein that copurified with the functional form of Sec13p using an in vitro budding reaction to assess activity. Sec31p was dissociated from Sec13p using 2 M urea and purified to homogeneity using gel filtration chromatography to obtain material for microsequencing and antibody production. The cloned gene for p150 complemented sec31-1, a mutation isolated in a screen for mutants that accumulate unprocessed alpha factor2.
ARFl and ARF2
Authors: Stearns T , Kahn R A
Published: November 2023

ARF1 was cloned by homology with a mammalian ARF gene1; ARF2 was cloned by hybridization with ARF7. Null mutations have been constructed in each of the genes by gene disruption. arf1 mutants grow more slowly than wild-type, are cold-sensitive, and are hyper-sensitive to fluoride ion in the medium. At all temperatures, invertase in arf7 null mutants is only partially glycosylated relative to wild-type, and there is some intracellular accumulation of the protein3 arf2 mutants are indistinguishable from wildtype for all phenotypes. In a strain that has both chromosomal copies of ARF deleted and a plasmid bearing ARF1 under control of the GAL1 promoter, depletion of ARF protein by shifting carbon source results in accumulation of core-glycosylated invertase, and is lethal after approximately 8 hours. Overexpression of ARF1 using this GAL1 promoter construct in wild-type ARF1 ARF2 cells is also lethal.
BET1
Authors: Ferro-Novick S
Published: November 2023

bet1 is a conditional-lethal secretory mutant that was isolated by a 3H-mannose suicide selection. At 37°C, this mutant blocks the secretion of invertase, pro-a-factor, and acid phosphatase. It also fails to transport carboxypeptidase Y to the vacuole. The glycosylation state of the precursor protein that accumulates in bet1 at 37°C is consistent with a block in ER to Golgi transport. Thin section electron microscopy revealed that, at the restrictive growth temperature, bet1 accumulates an extensive network of dilated ER and small vesicles.
SEC22
Authors: Ferro-Novick S
Published: November 2023

Mutations in sec22 were isolated by a density enrichment protocol. Although proteins continue to be synthesized in the sec22 mutant at 37°C, cell surface growth is blocked and the cells become dense. sec22 is temperature-sensitive for growth and pleiotropically blocks protein transport. The glycosylation state of the precursor protein that accumulates when secretion is blocked is consistent with a defect in ER to Golgi transport.
SEC18
Authors: Graham T , Emr S
Published: November 2023

sec18 mutant cells were originally described to exhibit a temperature-sensitive block in protein transport from the ER to the Golgi complex and to accumulate ER and small vesicles12. The phenotype of double sec mutants (e.g. sec18 sec23) suggests that Sec18p is not required to form transport vesicles from the ER, but is required for the targeting and/or fusion of these transport vesicles with an early Golgi compartment3. Further studies indicate that the sec18 mutant exhibits a temperature-sensitive block at most, if not all, intercompartmental transport steps along the secretory pathway4. Sec18p is required in vivo for protein transport between at least three Golgi compartments (containing an a-1,3-mannosyltransferase and the Kex2 endopeptidase) from the Golgi to the cell surface but not for protein transport from a late Golgi compartment to the yeast vacuole.
ERGIC-53
Authors: Hauri H -P
Published: November 2023

The nucleotide sequence of ERGIC-53 (EMBL accession number X71661) cloned from human liver and placenta cDNA libraries2 predicts a type 1 transmembrane protein of 510 amino acid residues with a cleavable signal sequence of 30 amino acids, a large luminal domain, a putative transmembrane domain of 18 amino acids and a cytoplasmic domain of 12 amino acids. The (-terminus of ERGIC-53 carries a KKXX (-Lys-Lys-X-X) motif known to be required for the retention of the adenovirus protein E3/19K and some other transmembrane proteins in the ER. The ERGIC-53 sequence lacks consensus sites for N-glycosylation and shows no homology to any known protein.
Rab1
Authors: Balch W E
Published: November 2023

Rab1A and rab1B were initially identified in a search for ras-related homologues in mammalian cells. Clones are available encoding the mouse, dog and human isoforms 4·11. The protein is ubiquitously distributed in all tissues types indicative of its central role in the function of the secretory pathway.
Lipoprotcin signal peptidase
Authors: Isaki L , Wu H C
Published: November 2023

The essential nature of lipoprotein signal peptidase has been demonstrated by the isolation of a conditionally lethal mutation1 and by the cell’s sensitivity to globomycin2. Two mutant phenotypes have been reported134 A partial revertant of a temperature-sensitive globomycin-resistant mutant of E coli was isolated after nitrosoguanidine mutagenesis, followed by introduction of an IPTG-inducible Ipp (lipoprotein structural gene)carrying plasmid. Induction with IPTG resulted in accumulation of a large amount of modified prolipoprotein in the envelope leading to cell death.
P115
Authors: Waters M G
Published: November 2023

p115 is a polypeptide required for cis to medial transport through the Golgi apparatus in vitro. It was discovered and purified based on a cell-free transport assay utilizing Golgi that had been stripped of peripheral membrane components by extraction with high salt concentration 1,  2 In addition to NSF, SNAPs, and p115, at least two other high molecular weight components are also required for activity in this system. p115 has a subunit molecular mass of 115 kDa, but hydrodynamic measurements indicate that it is a non-globular homo-oligomer in its native state.
Synapsin protein family
Authors: Jahn R , Südhof T C
Published: November 2023

Synapsin I and synapsin II are the products of two different genes, with the a and b forms resulting from alternative splicing4 (GenBank accession numbers la: M27812, lb: M27924, Ila: M27925, and lib: M27926). They generate proteins of 704, 668, 586 and 479 amino acids for rat synapsin la, lb, Ila and lib, respectively. Sequence comparison of the four synapsins revealed a characteristic structure consisting of a mosaic of common and individual domains. All four proteins share a large homologous N-terminal globular domain that can be divided into three subdomains. The most N-terminal subdomain is short and contains a phosphorylation site common to all synapsins.
Synaptophysin protein family
Authors: Jahn R , Südhof T C
Published: November 2023

cDNAs encoding synaptophysin have been sequenced from several mammalian species (GenBank accession number for rat cDNA: X06177) and from Torpedo1·5They encode a protein of approximately 34,000 Daltons with four predicted transmembrane segments and the C- and N-termini facing the cytoplasm124·5. No signal sequence is observed, similar to all other synaptic vesicle membrane proteins cloned so far. The sequence contains two potential glycosylation sides and four cysteine residues, all located in the luminal loops. The cytoplasmic tail contains 10 copies of a unique pentapetpide repeat with the consensus sequence Tyr-Gly-Pro(Gln)-Gln-Gly. Sequence comparison reveals a high degree of conservation in the mammalian species. However, the synaptophysin sequence from Torpedo is more divergent, with more than a third of the amino acid residues being different5 Interestingly, the (-terminal tail which is highly conserved in mammals is the most divergent part. It nevertheless has a similar overall amino acid composition (i.e. rich in Tyr, Gin, Pro, Gly). Thus, synaptophysin is less well conserved in evolution than synaptobrevin, synaptotagmin or rab3.
GDI
Authors: Novick P
Published: November 2023

Essential gene from Saccharomyces cerevisiae has been identified which shares 50% identity with bovine GDl10, GDI was first purified from bovine brain cytosol1. Two assays were used in the purification. The first measured the inhibition of GDP dissociation from rab3A (also known as smg p25A, see entry p. 205). The second assay was based on the observation that GDI will prevent GDPbound rab3A from binding to Advantech A045A304D membrane filters. A protein homologous to GDI has also been purified from Drosophila embryos based on a charge shift in the quartet mutant5 The nature of the modification that results in this charge shift is not yet known.
SEC65
Authors: Stirling B J
Published: November 2023

sec65-1 was isolated using a procedure designed to select for mutants defective in the assembly of integral membrane proteins into the ER membrane. sec65-1 is temperature sensitive for growth at 37°C, and following a one hour temperature shift to 37°C, mutant cells accumulate unglycosylated, unprocessed, cytoplasmic forms of various translocation precursors, including prepro-a-factor, invertase, and the integral membrane proteins dipeptidylaminopeptidase B, and Kex2p.
VPS33
Authors: Banta M M , Emr S D
Published: November 2023

Cells carrying a mutation in VPS33 secrete multiple vacuolar hydrolases5 and exhibit extreme defects in vacuole morphology. These cells lack a compartment resembling a wild-type vacuole but accumulate many small vesicles and other aberrant membranous structures, typical of Class C vps mutants36.  vps33 null mutants and most spontaneous vps33 mutants are unable to grow at 37°C but exhibit defects in vacuole protein localization and morphology even at permissive temperature. One vps33 temperature-sensitive mutant contains a missense mutation that results in a conditional phenotype; this strain contains normal-looking vacuoles at the permissive temperature but lacks vacuoles specifically in the buds at the non-permissive temperature.
VAC2
Authors: Shaw J , Wiclrner W
Published: November 2023

Cells harboring the vac2-1 allele exhibit a temperaturesensitive defect in vacuole inheritance. At 37°C, vac2-1 mother cells produce buds and daughter cells that lack wild-type vacuoles. Daughter cells that lack a vacuole appear to assemble this organelle via a separate pathway that requires little or no inheritance of maternal vacuolar contents. The vac2-1 strain is not temperature-sensitive for growth on rich medium but grows poorly at 37°C on solid, minimal praline medium. Haploid vac2-1 cells grown at 37°C do not mislocalize the soluble vacuolar proteins carboxypeptidase Y (CPY) or proteinase A (PrA). In addition, newly synthesized precursors of CPY and PrA are converted to mature forms with similar kinetics in vac2-1 and wild-type cells. Although vac2-1 mother cells produce large buds that lack wild-type vacuoles, these buds do inherit both nuclei and mitochondria normally.
VMA1
Authors: Ho N N , Stevens T H
Published: November 2023

The DNA sequence of the VMA1 gene (GenBank accession # J05409) predicts a protein of 1071 amino acids (118.6 kDa)6. The VMA1 locus has been mapped to the left arm of chromosome IV. The 5’ and 3’ thirds of the gene encode the 69 kDa Vma1 protein, which share 73% and 77% identity, respectively, with the catalytic subunit of the Neurospora crassa vacuolar H+-ATPase. Vma1p shows similar identity to the ‘70 kDa’ catalytic subunits of the vacuolar H+-ATPase from several organisms35. Vma1p contains a nucleotide binding sequence that is proposed to be involved in ATPase hydrolysis5 The central third of the VMA1 gene encodes the 50 kDa Vma1 spacer protein, which has no homology to any known vacuolar ATPase subunit, but is 33.5% identical to one region of the HO endonuclease.
VMA4
Authors: Ho M N , Stevens T H
Published: November 2023

Vma4p has an apparent molecular weight of 27 kDa on denaturing gels3 Internal peptide sequences of the 27 kDa subunit of the vacuolar W-ATPase match the predicted sequence of the VMA4 gene, indicating that Vma4p is an authentic subunit of the vacuolar H+-ATPase2 The Vma4p is essential for the activity and assembly of the vacuolar H+ATPase enzyme onto the vacuolar membrane as evidenced by the fact that the enzyme is disassembled and inactive in cells deleted for the VMA4 gene1,2.
TC21/R-Ras2
Authors: Graham Suzanne M , Der Channing J , Cox Adrienne D , Drivas George T , Rush Mark G , D’Eustachio Peter
Published: November 2023

R-Ras2 was identified by screening a human teratocarcinoma cDNA library using degenerate oligonucleotides corresponding to the conserved sequence DTAGQE shared by all members of the Ras superfamily of proteins (Drivas et al. 1990). The gene was originally named TC21 due to its derivation from a teratocarcinoma cell line. However, due to its high sequence conservation with R-Ras (approximately 70% amino acid identity), we have suggested that R-Ras be renamed R-Ras1 and that TC21 be renamed R-Ras2 (Graham etal. 1994). The DNA sequence is shown in Fig. 1 (Drivas et al. 1990). The GenBank accession number is M31468.
RasD
Authors: Louis Sharon A , Weeks Gerald , Spiegelman George B
Published: November 2023

RasD, the first ras gene characterized in Dictyostelium discoideum, was isolated from a pseudoplasmodial-stage Xgt11 cDNA library (Reymond etal. 1984). The rasD gene is 3.2 kb in length and contains three introns. The sequence is approximately 85% A+T as is characteristic of the Dictyostelium genome. Originally called Ddras, the name was changed to rasD after the isolation of a second Dictyostelium ras gene (rasG), that was maximally expressed during growth and early development (Robbins etal. 1989). The nucleotide sequence for the rasD cDNA is shown in Fig. 1. The genomic sequence for rasD has three accession numbers in GenBank: Z11804, K02114 and X58190.
Rho of Aplysia californica
Authors: Madaule Pascal
Published: November 2023

Aplysia rho cDNA was isolated by very low stringency screening of a library, using as a probe a human cDNA coding for the a subunit shared by the hormones thyroidstimulating hormone (TSH), luteinizing hormone (LH), and follicle-stimulating hormone (FSH). Random homology was responsible for the hybridization signal, but significant homology was observed with Ras proteins (Madaule and Axel 1985). Southern blot analysis of the Aplysia genome suggested that Aplysia rho belongs to a small family of closely related genes. High-stringency Northern blots indicated that Aplysia rho gene is transcribed in various tissues, resulting usually in two mRNA of distinct size. Aplysia rho cDNA is a reliable probe for moderate-stringency hybridization, since it allowed isolation of rho-related sequences from yeast, insects, and mammals (Madaule and Axel 1985). The GenBank accession number for Aplysia rho cDNA is M10078.
RhoA
Authors: Hall Alan
Published: November 2023

Rho sequences were originally isolated from an Aplysia cDNA library and used to identify three distinct, but highly homologous human sequences (Madaule and Axel 1985). The complete sequence of one of these, RhoA (originally called clone 12) (Yeramian et al. 1987), is shown in Fig. 1. The GenBank accession number is X05026.
RhoG
Authors: Fort Philippe
Published: November 2023

RhoG was isolated from a differential screening of a hamster lung fibroblast cDNA library, using probes derived from resting or growth-stimulated cells (Vincent et al. 1992,1993). The human homologous full-length cDNA was isolated from a HeLa cDNA library. Genbank accession numbers for human and hamster sequences are X61587 and X61588, respectively.
Rho-GDI
Authors: Tanaka Kazuma , Kikuchi Akira , Kaibuchi Kozo , Sasaki kuya , Takai Yoshimi
Published: November 2023

Rho-GDI was first purified from bovine brain and its cDNA was cloned based on the amino acid sequences (Ueda etal. 1990; Fukumoto etal. 1990). The cDNA for human Rho-GDI was also cloned and sequenced (Maeda etal., unpublished results). Recently, a closely related homolog of Rho-GDI, D4 (Lelias etal. 1993) or Ly-GDI (Scherle etal. 1993), has been cloned from human hematopoietic cell lines. D4 and Ly-GDI encode the same protein.
Dbl
Authors: Cerione Richard
Published: November 2023

Proto-Dbl encodes a 115-kDa protein (925 amino acids) that is predicted to be very hydrophilic and contains an amino terminal domain (497 amino acids) that was deleted in the generation of oncogenic Dbl and contains a secondary structure similar to the rod domain of several structural proteins, especially the intermediate filament protein, vimentin (Evaand Aaronson 1985; Ron etal. 1988).
The Chimaerin and Ber familes
Authors: Settleman Jeffrey
Published: November 2023

The following section combines family members n-chimaerins and wice are primarily GTPase-activating porteins(GAPS) for Rac and separate family members,BCr andAbrmwhose chimaterin-related Gap domain acts on both rac and Cdec42 this combination allows convenient co,parisons of the realtionships between different family members and beteween the different families.
Rho 1p
Authors: Madaule Pascal , Johnson Joni , McCaffrey Mary , Boquet Patrice , Myers Alan
Published: November 2023

RHO1 was identified by a low stringency screen of a Saccharomyces cerevisiae genomic library, using as a probe a Rho cDNA from Aplysia californica (Madaule and Axel, 1985; Madaule etal. 1987). RHO1 is an essential gene adjacent to MRP2, which codes for a ribosomal protein of the mitochondrion. The two genes are convergently transcribed, with 281 base pairs separating their termination codons, and their transcripts overlap by at least 111 base pairs (Peterson and Myers, 1993). This gene locus has been mapped physically to chromosome XVI (Myers et al. 1987). The GenBank accession number for RHO1 is M15189.
Rab22
Authors: Olkkonen Vesa M
Published: November 2023

The sequence was first identified in the PCR study of Chavrier et al. (1992). Here, Rab/Rho-related sequences were amplified from adult mouse kidney cDNA using degenerated oligonucleotides corresponding to two of the conserved sequence stretches of Rab/Rho GTPases as primers. The PCR-Rab14 sequence was used for probing an MDCK li cell cDNA library. The sequence of the complete open reading frame (ORF) obtained (Fig. 1) was renamed Rab22 (Olkkonen etal. 1993). The EMBLdatabase/GenBank accession number of the sequence is Z22820.
Rab-GDI
Authors: Sasaki Takuya , Kikuchi Akira , Kaibuchi Kozo , Takai Yoshimi
Published: November 2023

Rab-GDI was purified from bovine brain cytosol and its cDNA was cloned based on the amino acid sequences (Sasaki et al. 1990; Matsui et al. 1990). Human Rab-GDI cDNA was isolated from a human brain cDNA library by use of bovine Rab-GDI cDNA as a probe (Asada et al., unpublished results). Recently, a closely related homolog of Rab- GDI has been cloned from Drosophila ovary (Zahner and Cheney, 1993). Two closely related homologs of Rab-GDI have also been cloned from rat brain (Nishimura et al. 1994).
Sec4p
Authors: Novick Peter
Published: November 2023

Temperature-sensitive, conditionally lethal sec4 mutants were isolated by a density enrichment protocol (Novick et al. 1980). The best characterized sec4 allele is sec4-8. Within 5 min of a shift to the restrictive temperature, sec4-8 cells display a block in the transport of invertase, and accumulate 100-nm secretory vesicles containing fully processed cell surface proteins (Novick et al. 1981; Salminen and Novick 1987).
Betlp/Slyl2p
Authors: Ferro-Novick Susan
Published: November 2023

DNA sequence analysis of the BET1 gene predicts a protein (142 amino acids) that is serine-rich at its amino-terminus. The BET1 sequence also predicts the presence of a 131-bp intron that contains a non-conserved 5*-splice site (GTATGA). BET1 shares certain structural features with BOS1. Both genes contain introns and encode small proteins that have a hydrophobic stretch of amino acids at or near their COOH-termini (Dascher eta/. 1991; Shim etal. 1991; Newman etal. 1992).
Slylp
Authors: Schmitt Hans Dieter , Dascher Christiane , Gallwitz Dieter
Published: November 2023

The dominant SLY1-20 mutant allele of S. cerevisiae was isolated from a genomic library made with DNA from a SLY1-20 mutant strain (Dascher et al. 1991). The genomic yeast DNA had been partially digested with Taql and inserted into the C/a/ site of the centromer vector YCp50. Galactose-dependent GAL10-YPT1 cells containing the SLY1-20 allele on a plasmid can grow on glucose-contain- ing media. As the original SLY1-20 mutant, the cloned allele enables the cell to survive the deletion of the YPT1 gene.
Ypt5 (Schizosaccharomyces pombe)
Authors: Armstrong John
Published: November 2023

The ypt5 gene was isolated by hybridizing a S. pombe genomic library with mixed oligonucleotides encoding the conserved sequence DTAGQE (Fawell et al. 1992, Armstrong etal. 1993). The sequence, which includes seven introns, is shown in Fig. 1(A). The positions of the introns were confirmed by isolation and sequencing of cDNA. The EMBL accession number Z22220.
Interleukin-la, Interleukin-ip, and Interleukin-1 Receptor Antagonist (IL-la, IL-1 p, and IL-lra)
Authors: Dower S K , Sims J E
Published: November 2023

Catabolin, endogenous pyrogen (EP), osteoclast activating factor (OAF), lymphocyte activating factor (LAF), epidermal cell derived thymocyte activating factor (ETAF), serum amyloid A inducer or hepatocyte stimulating factor (HSF), leucocyte endogenous mediator (LEM), fibroblast activating factor (FAF), B cell activating factor (BAF), proteolysis inducing factor (PIF), haemopoietin-1 (H-1).
Interleukin-2 (IL-2)
Authors: Greene M A Goldsmith ,W C
Published: November 2023

IL-2 is a 15.5 kDa glycoprotein secreted primarily by activated T lymphocytes. The mature human IL-2 protein contains 133 amino acid residues, while the homologous proteins in other species contain 133 to 149 amino acids. The IL-2 primary translation product undergoes several post-translational processing steps that include removal of an Nterminal signal peptide, glycosylation at Thr 3, and disulphide linkage of Cys 58 and Cys 105. Glycosylation appears to be dispensable for IL-2 function, but formation of the disulphide bond is critical for bioactivity of the resultant molecule (Robb et al. 1983). IL-2 appears to be a very stable protein, exhibiting resistance to both heat and acidic pH. An X-ray crystallographic study of human IL-2 demonstrated that it is a largely helical molecule, with a-helices representing approximately 67 per cent of the entire protein (Brandhuber et al. 1987). A proposed structure derived from these studies contains six distinct helical domains involving 89 amino acids (Fig. l(a)). However, an alternative three-dimensional structure was subsequently described which appeared to accommodate the carbon backbone data provided by the above analysis and simultaneously to incorporate the results of mutational studies defining the site of ligand-receptor binding (Bazan 1992).
Interleukin 8 and Related Chemokine a Family Members
Authors: Taub D D , Oppenheim J J
Published: November 2023

The chemokine a family members from mouse and man exhibit a great deal of homology in their amino acid sequences (Fig. 1) (Oppenheim et al. 1991; Schall 1991). The cDNAs code for a precursor protein which contains a leader sequence. This presumably enables the chemokines to be secreted and enzymatically cleaved to yield a mature form. The mature form of all chemokine a proteins contains four cysteine residues which form two disulphide bridges. The first two cysteines in this subfamily are separated by only one amino acid. Members of this family are typically secreted as non-glycosylated dimers and tetramers containing between 66 and 80 amino acids in their mature monomeric protein form (Oppenheim et al. 1991; Schall 1991; Matsushima et al. 1992).
Interferon-Gamma (IFNy)
Authors: Gray P W
Published: November 2023

The human IFNycDNA (GenBank accession number X13274) encodes a 143-amino-acid mature protein with a 23 residue signal sequence (Gray et al. 1982). The activity of IFNy is species specific due to the low level of homology between different species sequences. Mouse IFNy only contains 40 per cent identical residues (Gray and Goedde/ 1983). The mouse cDNA (GenBank K00083) encodes a 133 residue mature protein with a 22 amino acid signal sequence (Gray and Goedde/ 1983).
Receptor for Granulocyte Colony-Stimulating Factor (G-CSF)
Authors: Nagata S
Published: November 2023

The nucleotide sequences of mouse and human G-CSF receptor cDNAs (GenBank accession numbers M58288 and M59820) predict a protein of 837 (mouse) or 836 (human) amino acids each containing a 25- or 23-amino-acid leader sequence (Fukunaga et al. 1990a, 1990b; Larsen et al. 1990). Human and mouse G-CSF receptors have marked homology (62.5 per cent) at the amino acid sequence level, and the two G-CSF receptors cross-react in their G-CSF binding and signal transducing activities. The G-CSF receptor has a significant overall similarity with the gpl30 (the interleukin 6 receptor signal transducer) and leukaemia inhibitory factor receptor (Fig. 1) (Nagata and Fukunaga 1991, 1993).
Insulin-like Growth Factors (IGFs)
Authors: LeRoith D , Roberts C T
Published: November 2023

The nucleotide sequences encoding IGF-1 and IGF-II have been characterized for most major vertebrate species. The mammalian IGF-1 genes are large, spanning over 90 kb of chromosomal DNA [GenBank accession numbers X57025 (cDNA) and X03419 (gene)]. The human IGF.
Vascular Endothelial Growth Factor (VEGF)
Authors: Ferrara N , Park J E
Published: November 2023

VEGF purified from conditioned media of normal and neoplastic cells is a glycoprotein of -45000 kDa (Ferrara and Henzel 1989). It is inactivated by reducing agents but it is heat- and acid-stable. By alternative splicing of RNA, VEGF may exist in four different homodimeric isoforms (Leung et al. 1989; Houck et al. 1991; Tisher et al. 1991). Following signal sequence cleavage, human VEGF monomers are expected to have 121, 165, 189, and 206 amino acids, respectively (VEGF121, VEGF165, VEGF189, VEGF206). Rodent or bovine VEGF monomers are shorter by one amino acid.
Endothelin and Its Receptors
Authors: Luscher T F
Published: November 2023

Endothelins are products of three distinct genes [GenBank accession numbers (AC): Y00749 (Endothelin-1), M65199 and X55177 (Endothelin-2), and X52001 (Endothelin-3)]. 2.2 kb human preproendothelin messenger RNA is encoded on chromosome 6 in five exons which are distributed over nearly 7 kb of the genome. The 5’ flanking region contains several response elements which confer inducibility of transcription by phorbol esters (e.g. fos/jun complex inducibility), nuclear factor-1 (responsible for transforming growth factor beta-induced expression) and hexanucleotide sequence elements, which may be involved in induction byacute physical stress.
The small heat shock proteins — an overview
Authors: Buchner J , Gaestel M , Vierling E
Published: November 2023

11 kDa-late embryogenesis abundant protein, 14 kDa- Myobacterium tuberculosis antigen, 18 kDa-M. leprae antigen, 25 kDa-growth-related protein, 25 kDa-inhibitor of actin polymerization, aB-crystallin, a-crystallin B-chain, AV25 protein, C14B9.1 protein, estrogen-regulated ‘24K’ protein, estrogen receptor-related protein, Hsp16, Hsp16.3, Hsp16.9, Hsp17, Hsp17.1, Hsp17.3, Hsp17.4, Hsp17.5, Hsp17.6, Hsp17.7, Hsp17.8, Hsp17.9, Hsp18, Hsp18.1, Hsp18.2, Hsp18.5, Hsp18.6, Hsp20, Hsp21, Hsp22, Hsp22.3, Hsp22.5, Hsp22.7, Hsp23, Hsp23.5, Hsp23.9, Hsp25, Hsp26, Hsp26.6, Hsp27, Hsp30, Hsp42, IbpA, IpbB, low molecular weight/mass Hsp, IAP-25, p25, p27, pPf203.
Small heat shock protein Hsp25 from mouse, rat
Authors: Gaestel M , Buchner J
Published: November 2023

Rodent/murine low molecular weight heat shock protein (Arrigo, Landry, 1994); mouse Hsp27/28 (Zantema etal., 1992); rat Hsp27/28 (Uoshima etal., 1993); 25 kDa growth-related protein p25 (Benndorf et al., 1988; Oesterreich etal., 1990).
Escherichia coli thioredoxin
Authors: Nakamura H , Bjornstedt M , Holmgren A
Published: November 2023

Escherichia coli B thioredoxin was originally purified to homogeniety from a neutralized pH 5.0 supernatant by heat treatment to 85°C, followed by chromatography on DEAE-cellulose, Sephadex G-50 (Holmgren, Reichard, 1967). A source of E. coli thioredoxin is the K12 strain, SK 3981 (Lunn, et al., 1984), which contains a derivative of the plasmid pBR325 (pBHK8) into which- a 3 kb Pvu II fragment of E. coli DNA containing the thioredoxin gene was inserted.
Synechococcus TxIA
Authors: Grossman A , Collier J
Published: November 2023

The nucleotide sequence of the txlA gene was determined (Collier, Grossman, 1995) from a genomic clone isolated from the cyanobacterium Synechococcus sp. strain PCC7942 (GenBank accession number U05044). The sequence predicts a protein of 191 amino acids, with an isolelectric point of 4.2. While the N-terminal 37 amino acids, the C-terminal 44 amino acids show no homology to sequences in the GenBank database, the central sequence of 110 amino acids is similar to a number of protein disulfide oxidoreductases, including thioredoxins (Buchanan, 1991), protein disulfide isomerases (Bardwell, Beckwith, 1993).
BS2: Trypanosoma brucei protein disulfide isomerase homologue
Authors: Bangs J D
Published: November 2023

African trypanosomes of the T. brucei species (Order Kinetoplastida) are parasitic protozoa that are the causative agents of African trypanosomiasis (African sleeping sickness) in humans, Nagana in cattle (Vickerman et al., 1993). Analyses of 18S rRNA sequence homologies indicate that these organisms comprise one of the most ancient of all eukaryotic lineages, being as distant phylogenetically from yeast as they are from humans (Sogin et al., 1989).
Saccharomyces cerevisiae Scc3/Cpr4
Authors: Contreras R , Demolder J
Published: November 2023

The genomic sequence of the SCC3 gene (Accession numbers: EMBL: X59720; PIR: S26658; HSSP: PO5092; PROSITE: PS00170) was originally identified during the sequencing of chromosome III in the overlap of the insert of phages PM5307 and PM6589 (Franco etal., 1991). SCC3 corresponds to the third cyclophilin gene from 5. cerevisiae. It is present as a single copy in the genome. Analysis of the 5’ non-coding region of SCC3 shows a TATA box at -135, a putative CAAA (at -78) and a CAPyACA (at -64) promotor motif. No upstream activating sequences are detected, which is reflected in Northern analysis which indicates that SCC3 renders an abundant 1.2 kb transcript during exponential growth. The 3’ non-coding region of SCC3 shows a potential sequence (i 111 lATA) at +1054 for polyadenylation.
Three-dimensional structure of FKBPs
Authors: Liang J , Clardy J
Published: November 2023

The mammalian cytosolic FKBP12 protein was discovered through its ability to bind the immunosuppressive agents FK506 (tacrolimus) and rapamycin (sirolimus) (Harding et al., 1989; Siekierka et al., 1989). The FKBP family, for FK506 binding proteins, is growing rapidly, and the best characterized members are the mammalian proteins FKBP12, FKBP13 (Jin et al., 1991), FKBP25 (Galat et al., 1992), and FKBP59 (Tai et al., 1992).
Escherichia coli FkpA
Authors: Raina S , Missiakas D
Published: November 2023

In Escherichia coli, misfolded proteins accumulating in the cell envelope, that is the periplasm or the outer membrane, induce a stress response that is controlled at the transcriptional level by the Er/ polymerase (Mecsas et al., 1993; Raina etal., 1995; Missiakas etal., 1996a). Unfolding of proteins is quite pronounced in strains lacking major periplasmic catalysts such as the Dsb proteins, which are involved in the formation of disulfide bonds of exported proteins (Bardwell, 1994; see entries on the Dsb proteins, pp. 318–328).