bluuebunny/crossref_metadata_2025 huggingface dataset:
Zoogeography, affinities and evolution, with special regard to the fish
Authors: Coulter G W
Published: November 2023

This chapter deals with a number of related subjects. In approaching these, the most difficult problem has been the choice of treatment. It was not possible in the space available to review exhaustively the ideas that have been put forward on the origins, affinities and evolution of the Tanganyika fauna. Nor is sufficient known about this very complex ecosystem to discuss it at any length in the light of current theories about community structure and evolutionary change, for example in terms of ‘equilibrium’, ‘stability’, ‘disturbance’, ‘patch dynamics’ and so on. No doubt many will find Tanganyika a fruitful field for research on such themes because of its evolutionary diversity and age. The approach chosen was to attempt to provide useful syntheses on various subjects some of which have attracted wide interest, such as the relationships of the Tanganyika fauna with those of other African lakes, or factors which have influenced evolution within the lake, where possible introducing new data. The reader should readily be able to find any further information that is available by reference to the Bibliography or to other chapters. The fish are prominent in this account because most research has been done on them.
Hydrodynamics
Authors: Coulter G W , Spigel R H
Published: November 2023

For the convenience of readers not concerned with the details of hydrodynamic data and theory contained in this chapter, a general summary is given first which outlines the physical regime and the main conclusions drawn from the data.
Basic Design Choices
Authors: Hendershot J R
Published: November 2023

Before a brushless motor design can begin, several important decisions must be made. The reasons for this should be obvious from previous discussion regarding the features of different types of brushless motors and the availability of different’ magnetic materials. The method of commutation is also an important issue which should be considered in making the basic decisions about the design. The choice of an interior rotor, exterior rotor, or an axial-gap motor must be made first, along with a rough idea of the correct magnet grade. Then the number of phases, the number of poles, the number of stator slots, and the winding configuration must be selected. The rotor and permanent magnet configuration is designed, then the stator and winding are determined. A step-by-step procedure is provided as a rough guide for a typical brushless DC motor design.
Electrical Design
Authors: Miller TfE
Published: November 2023

Now that we have reviewed the configuration of the motor and determined how to calculate the magnetic flux, we are in a good position to study the basic electrical operation. This chapter considers the windings in more detail: in particular, the factors affecting the layout of the windings and the calculation of the correct number of turns. This requires a simple explanation of the operation of the ideal brushless DC motor, describing how a squarewave EMF is generated and how this relates to the operation of the power electronic controller. Motors with 1,2, and 3 phases are considered, and there is a discussion of the use of wye and delta connections in three-phase motors. Although this chapter is mainly about squarewave motors, it deals with many fundamental points which are important for sinewave motors also (see Chapter 6).
Sinewave Motors
Authors: Miller TJE
Published: November 2023

We begin with a study of the properties of the ideal sinewave motor, developed initially from the basis of perfectly sine-distributed windings. This differs from the classical theory of AC machines, in which the fundamental winding element is the single concentrated full-pitch coil. In classical theory, the all-important fundamental flux, and the torque and EMF associated with it, can be extracted only after the harmonic winding factors are understood and applied, whereas in the present approach these essential parameters emerge without complication from simple integrals. The harmonic winding factors are developed afterwards, in order to characterize practical windings in terms of the ideal sine distributed windings.
sizing & computer-aided design
Authors: Miller TJE , Staton D A , Deodhar RP
Published: November 2023

The most usual situations which require a new brushless motor design include a set of performance specifications and a physical size or envelope. It is seldom that the performance requirement is given and the size is open. In many cases a new performance specification must be met through minor modifications to existing laminations and other components, in order to avoid additional tooling costs. When new designs are evolved from old ones, computer-aided design is valuable in two particular ways:
Conventional, fuzzy, neural, and fuzzy-neural function approximators
Authors: Vas Peter
Published: November 2023

It is the main goal of a function approximator that when a system is presented with new input data, and it is described by a function approximator, then it should give good predictions (correct output data). When conventional non-artificial intelligence-based systems are used, the function approximation is usually performed by using a mathematical model (equations) of the system under consideration. However, sometimes it is not possible to have an accurate mathematical model, or there may not exist any conventional type of model at all (which uses explicit mathematical models). In such a case mathematical model-free approximators are required and for this purpose artificial intelligence-based function approximators can be used. Sometimes a mathematical model-based system can work well when there is no noise on its inputs, but the same system may fail when the input data are noisy and uncertain. Furthermore, sometimes the implementation of mathematical-model-based function approximators is complicated and may lead to excessive computation times. However, these problems can be avoided by AI-based function approximators. Some other advantages of AI-based systems have also been described earlier in Chapter 3.
Artificial-intelligence-based steady-state and transient analysis of induction machines, estimators, control, design, condition monitoring, and diagnosis
Authors: Vas Peter
Published: November 2023

In the present chapter, first, the AI-based steady-state and transient analysis of slip-ring and squirrel-cage induction machines is discussed. For this purpose ANNs and fuzzy-neural networks are used and various networks are given which can be used to estimate the speed, position, electromagnetic torque and flux. This is followed by discussing AI-based condition monitoring, diagnosis, parameter determination and harmonic analysis. Thus various ANN-based, fuzzy-logic-based and fuzzy-neural network-based fault detection systems are also discussed which can be used to detect cage asymmetry, bearing and other faults in induction machines. However, unsupervised ANN-based fault diagnosis of a voltage source inverter and ANN-based current control of a voltage source inverter is also described.
Tensor algebra
Authors: d’Invemo Ray
Published: November 2023

To work effectively in Newtonian theory, one really needs the language of vectors. This language, first of all, is more succinct, since it summarizes a set of three equations in one. Moreover, the formalism <lfvectors helps to solve certain problems more readily, and, most important of all, the language reveals structure and thereby offers insight. In exactly the same way, in relativity theory, one needs the language of tensors. Again, the language helps to summarize sets of equations succinctly and to solve problems more readily, and it reveals structure in the equations. This part of the book is devoted to learning the formalism of tensors which is a pre-condition for the rest of the book. The approach we adopt is to concentrate on the technique of tensors without taking into account the deeper geometrical significance behind the theory. We shall be concerned more with what you do with tensors rather than what tensors actually are. There are two distinct approaches to the teaching of tensors: the abstract or index-free (coordinate-free) approach and the conventional approach based on indices. There has been a move in recent years in some quarters to introduce tensors from the start using the more modem abstract approach (although some have subsequently changed their mind and reverted to the conventional approach). The main advantage of this approach is that it offers deeper geometrical insight. However, it has two disadvantages. First of all, it requires much more of a mathematical background, which in turn takes time to develop. The other disadvantage is that, for all its elegance, when one wants to do a real calculation with tensors, as one frequently needs to, then recourse has to be made to indices. We shall adopt the more conventional index approach, because it will prove faster and more practical. However, we advise those who wish to take their study of the subject further to look at the index-free approach at the first opportunity.
Special relativity revisited
Authors: d’Invemo Ray
Published: November 2023

As we saw in Chapter 2, special relativity discards the old Newtonian picture in which absolute time is split off from three-dimensional Euclidean space. Instead, we introduce a four-dimensional continuum called space-time in which an event has coordinates (t, x, y,z) and where the square of the infinitesimal interval dsbetween infinitesimally separated events satisfies the Minkowski line element (2.13). The essence of special relativity lies in the special Lorentz transformations, and the significance of the Minkowski line element is that it is invariant under such transformations. We now use the language of Part B to formulate this more precisely.
The field equations of general relativity
Authors: d’Invemo Ray
Published: November 2023

The considerations of the last chapter led us to conclude that, locally, i.e. neglecting variations in the gravitational field, we can regain special relativity. However, in a non-local situation, we require a non-flat metric which may be thought of as the potentials of the gravitational field. Correspondence with Newtonian theory then suggests that we require second-order field equations in these potentials, and, moreover, from the principle of covariance, these equations must be tensorial in character. In this chapter, we shall pursue the Newtonian correspondence further and reformulate Newtonian theory in such a way that it leads naturally to the particular set of field equations of general relativity.
General relativity from a variational principle
Authors: d’Invemo Ray
Published: November 2023

since partial derivative commutes with variation and is equivalent to covariant derivative in geodesic coordinates. Now both δRa  bcd,being the difference of two tensors, and the quantities on the right-hand side of the last equation are tensors, and so by our fundamental result (if a tensor equation holds in one coordinate system it must hold in all coordinate systems) we can deduce the Palatini equation Many tensor identities are best derived using the technique of geodesic coordinates, where we choose an arbitrary point P at which r?c = 0. Then, in particular, covariant derivatives reduce to ordinary derivatives at the point P.
The Schwarzschild solution
Authors: d’Invemo Ray
Published: November 2023

We now turn our attention to solving the vacuum field equations in the simplest case, namely, that of spherical symmetry. As a preliminary, in the next two sections we make clear the distinction between stationary and static solutions. In simple terms, solution is stationary if it is time-independent. This does not mean that the solution is in no way evolutionary, but simply that the time does not enter into it explicitly. On the other hand, the stronger requirement that a solution is static means that it cannot be evolutionary. In such a case, nothing would change if at any time we ran time backwards, i.e. static means time-symmetric about any origin of time. Think of the motion of a gas in a pipe (Fig. 14.1). If it is being pumped by some time-dependent device, then the motion Will be non-stationary. If the gas travels with constant velocity at each point in the pipe, then the motion is stationary. If the gas velocity is zero everywhere, then the system is static.
Non-rotating black holes
Authors: d’Invemo Ray
Published: November 2023

In this chapter, we are going to make an effort to understand the Schwarz-schild vacuum solution. The solution (14.47) is exhibited in a particular coordinate system. In general, if we wish to write down a solution of the field equations, then we need to do so in some particular coordinate system. But what, if any, is the significance of any particular coordinate system? For example, take the Schwarzschild solution and apply as complicated a coordinate transformation as you can imagine, labelling the new coordinates x′a.
Introduction
Authors: Acheson D J
Published: November 2023

Take a shallow dish and pour in salty water to a depth of 1 cm. Make a model wing with a length and span of 2 cm or so, ensuring that it has a sharp trailing edge. (One method is to cut the wing out of an india rubber with a knife.) Dip the wing vertically in the water and turn it to make a small angle of attack a with the direction in which it is to be moved. Put a blob of ink or food colouring around the trailing edge; a thin layer of this should then float on the salt water.
Hamming codes and the binary Golay codes
Authors: Pretzel Oliver
Published: November 2023

In the previous chapter we saw that a binary linear code C can correct all single errors if and only if its check matrix H has distinct columns. In Chapter 3 it was shown that the rank of C is bounded by the number of columns of H minus the rank of H. If H has a sufficiently large set of columns, then its rank is just the length of the columns. So to make the rank of the code maximal we must choose as many distinct columns for H as possible. This leads us to define a class of single error-correcting binary codes by choosing the check matrix to have all possible non-zero columns of length k. These are the celebrated Hamming codes, which we shall denote by Ham(k).
The construction of fields
Authors: Pretzel Oliver
Published: November 2023

This chapter will show you how to use a Euclidean domain D to construct a field. The most important case is when D is the set of polynomials over a small field that you already know. The construction is used in algebra to analyse the solutions of algebraic equations, but that is not our main purpose. For us, the important fact is that if the little field we start with is finite, the result will be another larger finite field. Later it will turn out that all possible finite fields can be constructed by this method.
BCH error correction: (2) an algorithm
Authors: Pretzel Oliver
Published: November 2023

In this chapter we present an efficient algorithm for solving the fundamental equation for BCH codes. It can be used as the basis of a practical error processor for BCH codes. The existence of such processors is the principal reason for the pre-eminence of the BCH family among block codes in practical use.
Reed-Solomon codes and burst error correction
Authors: Pretzel Oliver
Published: November 2023

If you look through the previous two chapters you will notice that in dealing with BCH codes all calculations take place in GF(16). We only check at the end that the answers lie in GF(2) = B. So why not drop that final condition? Then we obtain a linear code with an alphabet of elements of GF(16). This code is called a Reed-Solomon code. The arguments of the last two chapters can easily be adapted to show that this code also corrects up to t errors in a word, but now each error affects a symbol from GF(16).
Introduction
Authors: Hemion Geoffrey
Published: November 2023

People have always found knots to be fascinating and frustrating. A ‘knotty problem’ is difficult to solve. If we allow ourselves to become entangled in the intricacies of such a problem, then we will be ‘tied in a knot’. One way out may be to follow the example of Alexander in his conquest of Asia. He simply drew his sword and slashed through the Gordian knot, reducing things to the level of mere destruction! Knots, along with pyramids and pendulums, have formed the basis of obscure speculations in the realms of the occult. Organic chemists claim that their molecules may form knots or links. Mathematical physicists have declared that physical space is of a stringy nature. As far as pure mathematics is concerned, knot theory has been studied seriously for more than a hundred years. Hundreds of papers have been published during that time. Many strange and delightful facts have been uncovered. But surely the main mathematical question concerns the classification of knots. If Alexander had been a philosopher then he would have attempted to determine whether or not the Gordian knot could be unknotted; that is, shown to be equivalent to the trivial knot. Slightly more general is the problem of comparing two arbitrary knots with one another.
Numerical Methods and Scientific Computing
Authors: Kockler Norbert
Published: November 2023

The book covers the whole range of numerical mathematics from linear equations to ordinary differential equations with short sections on the calculus of errors and on partial differential equations. It attempts to give a unified approach of theory, algorithms, applications and use of software. Therefore it contains only a few proofs but many examples and applications. This book is appearing simultaneously with the problem-solving environment PAN. The PAN system contains an enlarged hypertext version of the text, together with all the programs described in the text, help systems, and utility tools. PAN is licensed public domain software. This parallel appearance of paper and electronic versions including additional useful software is unique. There are four appendices, which describe PAN, the programs written for PAN that are used in the text for examples and applications, and the NAG Fortran and NAG Graphics Libraries used by the programs.
Irregular Sampling
Authors: Higgins J R
Published: November 2023

A sampling process employing sample points that are not equidistantly spaced is usually called irregular, or sometimes non-uniform. Irregular sampling arises mathematically by simply asking the question “What is special about equidistantly spaced sample points?”; and then finding, as we shall in this chapter, that the answer is “Within certain limitations, nothing at all”.In practice it is often said that irregular sampling is the norm rather than the exception. For example, sample points are likely to be disturbed by “noise”, meaning any random influences beyond our control. Again, it might he convenient to reconstruct a function from the locations of its zeros, or places where it crosses some datum function. Such points are, of course, intrinsic to the object function.Again, sample points might be required to have a deterministic distribution, and then we ask if all functions of a given class can be reconstructed from their samples at these points. This is the only kind of irregular sampling we shall discuss here. A review of the applied aspects of irregular sampling can be found in Marvasti (1993), and there are many interesting studies on this theme in the Conference Proceedings of the 1995 workshop on sampling theory and applications, Jurmala, Latvia, 1995, published by the Institute of Electronics and Computer Science, Riga, Latvia.
A comprehensive classification of homeobox genes
Authors: Burglin Thomas R
Published: November 2023

The homeodomain was originally described as a highly conserved protein motif of 60 to 63 amino acids, encoded by a short DNA fragment, the horneobox, that was found in Drosophila developmental control genes (McGinnis et al., 1984; Scott and Weiner, 1984). As more and more homeobox-containing genes were isolated it became obvious that for closely related homeodomains the sequence similarity could be extended upstream and/or downstream of the core 60 amino acids (for a previous compilation, see Scott et al., 1989). In contrast, highly divergent homeodomain sequences have been identified for which the sequence similarity is shorter than the orig inally defined 60 amino acids. The definition of the homeodomain used here is based on the canonical 60 amino acid core as it is most often used.
SEC67
Authors: Feldheim D A
Published: November 2023

Sec67p was identified as a 23 kDa protein that co-precipitated in an immune complex with Sec62p when radiolabeled, detergent solubilized membrane proteins were immunoprecipitated with anti-Sec62p antibodies under non-denaturing conditions1. Subsequently it was shown that anti-Sec63p antibodies also co-immunoprecipitate Sec67p2 Sec67p was purified in quantities suitable for microsequencing using large-scale immunoprecipitation.
SEC72
Authors: Green N
Published: November 2023

A mutant allele (sec72-1) was isolated based on its inability to insert into the membrane of the ER a membrane-bound fusion protein consisting of the N-terminal 255 residues of arginine permease and the complete histidinol dehydrogenase sequence encoded by the HIS4C region of H/5412 The histidinol dehydrogenase portion of the fusion protein was poorly translocated across the ER membrane in sec72-1 mutant cells. This mutant was also defective in translocation of the dehydrogenase when it was placed behind only the N-terminal 189 residues of the permease and in the insertion of another membrane-bound fusion protein containing an N-terminal segment of Sec63p fused to invertase, a glycosylated reporter protein.
EUG1
Authors: Ekena K , LaMantia, M , Steven T
Published: November 2023

EUG1 (I;R protein necessary for growth under standard laboratory conditions) was named for its observed mutant phenotype. Overproduction or deletion of the EUG1 gene appears to have no effect on cell viability or function. Yeast cells deleted for EUG1 grow with wild-type rates on rich or minimal media at temperatures from 18°( to 40°( and can grow anaerobically. Sporulation is not affected in homozygous eug1t,, cells, nor is the transport of vacuolar and secreted proteins through the secretory pathway. Finally, eug1 cells do not exhibit any increased sensitivity or requirement for calcium.
SHR3
Authors: Ljungdahl P O , Fink G R
Published: November 2023

Spontaneous yeast mutants resistant to 30 mM histidine were isolated1· Genetic analysis indicates that super high histidine resistant (shr} mutants resulted from recessive mutations in single genes defining nine complementation groups. Mutations in the SHR3 gene confer resistance to high concentrations of histidine by pleiotropically inhibiting the functional expression of the general amino acid permease (GAP1} and at least 10 specific high affinity amino acid permeases.
WBP1
Authors: Aebi M , Heescn S te
Published: November 2023

The Wbp1 protein was purified by virtue of its binding to the lectin wheat germ agglutinin (Wbp1 = heat germ agglutinin _binding Qrotein 1) and the monoclonal antibody RL112. Oligonucleotide probes were designed using N-terminal and internal peptide sequences of the protein and used to screen a plasmid library of yeast genomic DNA.
PMR1
Authors: Antebi A , Fink G R
Published: November 2023

PMR1 encodes a non-essential secretory protein whose absence neither leads to inviability nor impedes secretory transport. In fact, the original mutant (previously called ssc1-1) was isolated as one of two complementation groups having “supersecretor” activity, the ability to secrete yeast/mammalian heterologous proteins which in wild-type strains remain trapped within the ceI11. The acquisition of the gene and the construction by molecular genetic techniques of strains carrying a pmr1 deletion allele confirmed that the original ssc1 phenotype represents pmr1 loss of function2. This ability does not reflect an overall increase in the rate of normal secretory transit, as the half-time of secretion of the endogenous yeast protein, invertase, is approximately the same for mutant and wildtype strains (4 and 5 minutes respectively)3.
SEC14
Authors: Bankaitis V
Published: November 2023

Mutants harboring conditional-lethal mutations were isolated using a Ludox density enrichment method and found to exhibit a terminal phenotype of exaggerating intracellular toroid structures interpreted to represent dysfunctional yeast Golgi9 Indeed, within 15 min of shift to a restrictive temperature, sec14rs mutants display a secretory block and accumulate fully-glycosylated secretory proteins within the ce11.
KtX1
Authors: Cooper A , Bussey H
Published: November 2023

kex1 mutants were originally isolated due to their reduced production of active K1 killer toxin (killer expression). In addition, such mutants, although not sterile for yeast mating, produce a partially processed form of a-factor pheromone with less biological activity than mature a-factor produced by KEX1 strains1 Cellular extracts prepared from kex1 strains lack a membrane-bound carboxypeptidase activity specific for basic residues2 The growth rate of strains containing disruptions of the KEX1 locus are not significantly different from those of the wild-type KEX1 strain1.
SEC15
Authors: Novick P
Published: November 2023

Temperature-sensitive, conditionally lethal sec15 mutants were isolated by a density enrichment protocol3 The best characterized sec15 allele is sec15-1. Within a 10 min shift to the restrictive temperature, sec15-1 cells accumulate 100 nm secretory vesicles.
SNAP
Authors: Brunner M , Whiteheart S W
Published: November 2023

SNAP proteins purified from bovine brain tissue were digested by proteases3. Amino acid sequence analyses of SNAP peptides were used to design degenerate oligonucleotide primers and SNAP specific probes were then amplified from a bovine brain cDNA library using the polymerase chain reaction. These probes were then used to screen a ).,gt10 library3 and clones encoding a-, 13-, and y-SNAPS were obtained. The cDNA clones contain open reading frames of 885, 894 and 984 nucleotides, encoding proteins with predicted M,s of 33 kDa, 34 kDa and 36 kDa, respectively, for a-, 13-, and y-SNAPS. a- and 13-SNAP are identical to each other and 34% and 33% identical, respectively, to 5.
V1PS18/PEP3
Authors: Robinson K S , Emr S D
Published: November 2023

Haploid yeast strains in which the entire open reading frame of the VPS18 gene has been deleted are viable12. Such vps1B!l cells have only a slight growth defect at lower temperatures but cannot divide at 37°C. The mutant cells mislocalize and secrete (>95%) the precursor form of the soluble vacuolar hydrolase carboxypeptidase Y (CPY) even at lower temperatures (20°C and 30°(). Precursors of other soluble vacuolar hydrolases are also mislocalized.
VPS34
Authors: Stack J H , Herman, P K , Emr S D
Published: November 2023

vps34 mutants exhibit a temperature-sensitive growth defect and are sensitive to osmotic stress. Deletion of the VPS34 gene results in a ts growth defect, indicating that the VPS34 gene is required for vegetative growth only at elevated temperatures1. vps34 mutants exhibit a defect in bud vacuole inheritance as indicated by the fact that no vacuolar structures were observed in the newly emerging bud in 80% of dividing vps34 cells1. Such a vacuole segregation defect is typical of class D vps mutants5  vps34 cells are defective in the proper sorting of a variety of yeast vacuolar proteins, including proteinase A, proteinase B, and carboxypeptidase Y13 >95% of the newly synthesized carboxypeptidase Y is mislocalized and secreted from vps34 cells as a Golgi-modified precursor form.
PEP8
Authors: Bachhawat A K , Jones F W
Published: November 2023

Haploid yeast cells possessing a disruption allele of the PEPB gene are viable and have apparently normal vacuoles as visualized by light microscopy. Pep B mutants are deficient in carboxypeptidase Y (CPY) activity. pepB mutants also secrete the precursor forms of protease A and CPY.
MVP1
Authors: Ekena K , Stevens T H
Published: November 2023

MVP1 is a nonessential gene of S. cerevisiae. Cells carrying a deletion in the MVP1 open reading frame are viable and grow at a rate indistinguishable from wild-type cells at 30°C.
VMA2
Authors: Ho M N , Stevens T H
Published: November 2023

Cells carrying the vma2 null allele are viable, however, these cells are devoid of vacuolar H+-ATPase activity2,5. Vacuoles in vma2 cells are not acidified relative to the cytoplasm as determined by a flow cytometric pH assay2. vma2 strains are defective for growth in medium buffered at a neutral pH, and have a slowed growth rate relative to wild-type cells in acidic medium2·5. vma2 cells grow poorly on medium containing elevated levels of calcium and are unable to grow on non-fermentable medium such as glyceroI2,5,6.
VMAS
Authors: Ho M N , Stevens T H
Published: November 2023

The DNA sequence of the VMA5 gene (GenBank accession # M77143) encodes a hydrophilic protein of 373 amino acids with a predicted molecular mass of 42 kDa. The amino acid sequence of Vma5p shares 37% identity with subunit C of the vacuolar H+-ATPase isolated from bovine kidney microsomes6 The amino acid sequence of Vma5p does not contain an amino-terminal signal sequence or a membrane spanning domain.
VMA11
Authors: Ohya Y , Umemoto, N , Anraku Y
Published: November 2023

Cells carrying the vma11 null allele grow normally in yeast extract-polypeptone-glucose (YPD) medium, however, these cells are devoid of vacuolar H+-ATPase activity1-2  vma11 mutants show a Pet” Cls- (£alcium-2ensitive) phenotype as they cannot utilize nonfermentable carbon sources such as glycerol, lactate and succinate, and cannot grow in YPD-100 mM CaCl2 medium. In YP-glycerol medium, vma11 cells cannot grow (generation time>16 hrs), but most cells are viable even after 16 hr of incubation. More than 80% of the mutant cells die within 2 hr in YPD-100 mMCaCl2 medium.
YPT7
Authors: Wichmann I , Hengst L , Callwitz D , Schmiiller, F , Riezman H
Published: November 2023

Cells carrying a disruption in the YPTl gene exhibit a strong defect in vacuole biogenesis resulting in abnormal fragmentation of that compartment. The maturation of both soluble and membrane-bound vacuolar proteins is extremely delayed in the mutant. Three soluble vacuolar hydrolases, carboxypeptidase Y and proteinases A and B, need up to two hours for complete maturation whereas alkaline phosphatase, a membrane-bound vacuolar enzyme is only partially matured within the same time range. Unlike the vps mutants with fragmented vacuoles, carboxypeptidase Y is not secreted by yptl null mutants1
Cation-dependent mannose 6-phosphatereceptor
Authors: Johnson K F
Published: November 2023

The human, bovine and murine CD-MPR cDNAs (GenBank accession numbers: bovine, #M17025; human, #J02937; mouse, #M63286) all predict a protein of approximately 31 kDa with five potential N-linked glycosylation sites, four of which are utilized1·3. The 67 amino acid cytoplasmic tail is absolutely conserved in the human, bovine, and murine receptors3 There is some amino acid heterogeneity in the extracytoplasmic and transmembrane domains of the CDMPR in these three species. The CD-MPR shows some sequence identity with the cation-independent mannose 6-phosphate receptor (CI-MPR). The entire extracytoplasmic domain of the CD-MPR has 14 to 28% identity with each of the 15 contiguous repeats in the extracytoplasmic domain of the CI-MPR. The two MPRs have potential serine phosphorylation sites and stretches of acidic residues in their cytoplasmic domains.
GTP-binding proteins in plants
Authors: Terryn Nancy , Montagu Marc Van , Inze Dirk
Published: November 2023

Full length cDNAs of small GTP-binding proteins were inserted into PGEM1 under the control of the T7 promotor as described previously (Chavrier et al. 1990; Huber et al. 1993). GTP-binding proteins were then transiently expressed in BHK 21 cells with the T7 RNA polymeraserecombinant vaccinia virus system (Fuerst et al. 1986; Chavrier et al. 1990; Huber et al. 1993, 1994b). Cells were scraped and fractionated 5 hours after infection/transfection and membrane fractions applied to high resolution 2D-gel electrophoresis. After renaturing transfer to nitrocellulose the blots were overlaid with [a-32P] GTP and the GTP-binding profiles visualized by autoradiography.
Dictyastelium discoideum Rab- and Rho-related proteins
Authors: Bush John , Cardelli James
Published: November 2023

We have isolated seven new rho-like cDNAs (Table I; Bush et al. 1993a), five of which encode proteins that are at least 70 percent identical in amino acid sequence to the human Rac1 protein (Drivas eta/. 1990).
Receptors for Interleukin-2 (IL-2)
Authors: Voss S D , Robb R J
Published: November 2023

The a chain (p55, Tac) of the human IL-2 receptor, encoded by a single gene on chromosome 10, p14--15 (Leonard et al. 1985a), is produced as a 272 amino acid (aa) precursor with a 21 aa signal sequence (GenBank accession number K63122) (Leonard et al. 1985b). The mature protein contains a 219 aa extracellular domain, a 19 aa membranespanning region, and an intracellular, carboxy-terminal domain of 13 residues (Fig. 1) (Leonard et al. 1984, 1985b). The difference between the observed molecular weight of 55 000 Oa (SOS-PAGE) and the predicted molecular weight of 28437 Oa is due to N-(Asn 49 and 68) and 0-linked glycosylation and sulphation (Leonard et al. 1985c). The a chain is characterized by an internal repeat of - 65 residues corresponding to exons 2 and 4 of the gene (Leonard et al. 1985b). These segments have 25 per cent homology with each other and limited homology to the Ba fragment of complement factor B. Exon 4 is deleted in a fraction of a chain mRNA (Leonard et al. 1984).
Interleukin-3 (IL-3)
Authors: Schrader J W
Published: November 2023

Multi-lineage colony-stimulating factor, persisting (P)-cellstimulating factor, mast-cell growth factor, burst-promoting activity, Thy-1-stimulating activity, Histamine-producing cell stimulating activity, haemopoietic cell growth factor, multilineage haemopoietic growth factor, CFUsstimulating activity, stem cell-activating factor, haemopoietin-2, synergistic activity, pan specific haemopoietin, and CSF-2a and -2/J.
Receptors for Interleukin-3 (IL-3)
Authors: Ogorochi T , Miyajima A
Published: November 2023

The murine and human IL-3R o. subunit cDNAs (GenBank accession numbers X64534 and M74782) encode a protein of 396 and 378 amino acids including a putative signal peptide of 16 and 18 amino acids, an extracellular domain of 315 and 288 amino acids, a single transmembrane spanning segment of 24 and 20 amino acids, and a cytoplasmic domain of 41 and 52 amino acids, respectively (Fig. 1). The sequence identity between these two a. subunits is 47 per cent at the DNA level and 30 per cent at the amino-acid level. The deduced molecular weights of the murine and human IL-3R a subunits are 41215 Da and 41254 Da, respectively. The observed molecular weights on SOS-PAGE are 60-70 kDa due to glycosylation at several of the predicted five N-glycosylation sites. The extracellular domains contain common features of the class I cytokine receptor family that include four conserved cysteine residues and the WSXWS motif near the transmembrane domain. There is a short strech of amino acid sequence that is conserved among the a subunits ofthe fl-3, IL-5, and GM-CSF receptors (Kitamura eta/. 1991; Hara and Miyajima 1992).
Interleukin-10 (IL-10)
Authors: Nicola N A
Published: November 2023

The nucleotide sequences of interleukin-10 cDNAs cloned from mouse and man (GenBank accession numbers M37897 and M57627, respectively) predict proteins of 178 (human) or 175 (mouse) amino acids each including an amino-acid leader sequence (Moore et al. 1990; Vieira et al. 1991).
Interleukin-12 (IL-12)
Authors: Wolf S F , Nickbarg E
Published: November 2023

cDNAs for human and murine IL-12 subunits have been cloned (Wolf et al. 1991; Gubler et al. 1991; Schoenhaut et al. 1992). The nucleotide sequences of the p40 subunit from man and mouse (GenBank accession numbers M65292, M65272, and M86671) predict polypeptides of 328 and 335 amino acids, respectively. Both include amino terminal sequences, 22 amino acids in length, which are characteristic of hydrophobic signal peptides. At the amino acid level, the p40 subunits are 70 per cent identical and 79 per cent similar.
High Molecular Weight R Cell Growth Factor (Interleukin-14)
Authors: Blumenthal D E , Ford R J , Ambrus J L
Published: November 2023

50-60 kDa forms of IL-14 have been identified in supernatants of normal human Tcells, T-ALLcells, B cell lines, and B cell lymphomas after stimulation with phytohemagglutinin (PHA), and in ascites and pleural fluid from patients with B cell lymphomas (Ambrus and Fauci 1985; Ford et al. 1992). Purified 60 kDa IL-14 from PHA-stimulated Namalva cells or T-ALL cells is glycosylated, and its apparent molecular weight does not change under reducing conditions. lsoelectric focusing reveals that the 60 kDa band can be resolved into two distinct proteinsat pl 6.7 and 7.8, both of which demonstrate B cell growth factor activity (Ambrus and Fauci 1985; Ambrus et al. 1985).
Erythropoietin
Authors: Goldwasser M Gupta ,E
Published: November 2023

Epo was purified from the urine of anaemic patients(Miyake et al. 1977), and the amino acid sequence derived from the purified protein {Lai et al. 1986) led to the cloning of the human epo gene {Lin et al. 1985; Jacobs et al. 1985). Epo is a secreted glycoprotein containing 193 amino acids(human) or 192 amino acids (monkey and mouse) including a hydrophobic leader sequence of 27 amino acids. Approximately 40 per cent of the human recombinant matureprotein is composed of carbohydrate. It has one site (Ser 126) with O-linked glycosylation and three sites {Asn 24, 38,83) with N-linked glycosylation.
The Macrophage Colony-Stimulating Factor (M-CSF) Receptor
Authors: Rohrschneider L R
Published: November 2023

The M-CSF receptor (Fms) is a member of the class Ill family of tyrosine kinase growth factor receptors and is most highly related to the PDGF receptors, c-kit, kdr/flk1 (vascular endothelial cell growth factor receptor), the torso gene product, flt1, flt3/flk2, and flt4. The cDNAs for feline, murine, and human c-fms genes have been cloned (Rohrschneider and Woolford 1991) (GenBank accession numbers J03149, X06368, and X03663, respectively). The predicted amino acid sequences exhibit the general structural features shown in Fig. 1. For the murine receptor, the extracellular, M-CSF-binding domain is composed of 510 amino acids (512 amino acids for human Fms), with a 26-aminoacid transmembrane sequence, and a 440 amino acid cytoplasmic domain (434 amino acids for human Fms). The primary translation product contains a hydrophobic leader sequence of which the N-terminal 19 amino acids are cleaved. N-linked glycosylation is added at up to nine potential sites in murine Fms, 10 sites in feline Fms, and 11 in the human Fms. Seven ofthese sites are common among all three Fms proteins and no O-linked glycosylation is detectable on Fms.
Kit (Stem Cell or Steel Factor) Receptor
Authors: Bernstein A , Motro B
Published: November 2023

The human c-kit receptor gene encodes a 972-amino-acid precursor protein with a predicted 24-amino-acid leader sequence (GenBank accession number X06182) (Yarden et al. 1987). A single predicted transmembrane domain of 23 amino acids divides the protein into two major domains. The amino terminal extracellular 487 amino acids form the ligand-binding domain and are composed of five immunoglobulin-like loops. The predicted molecular weight of the receptor is 109000 but the observed molecular weight on SDS-PAGE gels is 145-160000 due to N-glycosylation at several of the nine potential glycosylation sites. The (terminal intracellular439-amino-acids domain contains the phosphotyrosine kinase domain. The kinase domain is split by a 68-amino-acid kinase insert domain between the ATP binding site and the catalytic phosphotransferase domain.
Hepatocyte Growth Factor (HGF) Receptor
Authors: Comoglio P M , Graziani A
Published: November 2023

The HGF receptor was identified as the product of the proto-oncogene c-Met, the pl 90Met protein (Bottaro et al. 1991; Naldini et al. 1991a,b). p190Met is composed of a 50 kDa (a) chain disulphide linked to a 145 kDa (/J) chain in an apcomplex of 190 kDa (GenBank accession number X54559) (Giordano et al. 1989a; Ponzetto et al. 1991). Both the a chain and the p chain are exposed at the cell surface; the pchain contains a 23-amino-acid membrane-spanning segment and an intracellular region containing the tyrosine kinase domain.
Transforming Growth Factor-O (TGFB)
Authors: Gitelman S E , Derynck R
Published: November 2023

The TGF/3 superfamily may be divided into subfamilies according to sequence homology. One group consists of the closely related TGF/31, -2, and -3. cDNAs described previously as chicken TGF/34 and Xenopus TGF/35 are now thought to represent TGF/31 cDNAs. The other subfamilies include the inhibins and activins, Mullerian inhibitory substance, and the decapentaplegic/Vg1/BMP group, which has been referred to as DVR (Lyons et al. 1991). This latter group includes Vg1 from Xenopus laevis, a maternally inherited transcript localized to the vegetal pole of embryos. The bone morphogenetic proteins (BMPs) were originally characterized as osteoinductive factors purified from demineralized bone, and there are now at least eight such related factors (Wozney 1992). BMPs-2 and -4 bear closest homology to the decapentaplegic complex protein, a Drosophila protein mediating dorsal/ventral axis specification. BMPs-5, -6 (also known as vgr-1), -7, and -8 most closely resemble Drosophila protein 60A.
Receptors for Transforming Growth Factor-B (TGFB)
Authors: Knaus P I , Lodish H F
Published: November 2023

The cDNA for the TGF/3 type Ill receptor was first isolated from A10 cells (rat vascular smooth muscle cell line) by expression cloning in COS 7 cells (Wang et al. 1991) (GenBank accession number M 80784) and from rat fetal tissue by a peptide-sequencing-PCR approach (Lopez-Casillias et a/. 1991) (GenBank accession number M 77809). The human and pig cDNAs encoding the type Ill receptor have since been isolated (Moren et al. 1992). The encoded receptor is an 853-amino-acid protein (Fig. 1) with a single hydrophobic transmembrane domain, a 43-amino-acid-long cytoplasmic tail with no obvious signalling motif and a large N-terminal extracellular domain containing at least two sites for glycosaminoglycan addition and six consensus sites for N-linked glycosylation (Wang et al. 1991; Lopez-Casillias et al. 1991).
The Hsp70 family - an overview
Authors: Miao B , Davis J , Craig E A
Published: November 2023

hsp70 genes were first visualized as puffs on polytenechromosomes isolated from salivary glands upon exposureof Drosophila larvae to high temperature orchemicals (Ritossa, 1962). More than a decade later it wasdetermined that the major gene being transcribed andtranslated upon exposure to stress encoded a 70 kDaprotein (reviewed in Ashburner, Bonner, 1979; Craig,1985)). Proteins related to the Drosophila HSP70s havenow been identified in all organisms examined (Fig. 1).
Plant small heat shock proteins (sHSPs)
Authors: Vierling E , Lee GJ
Published: November 2023

Plants synthesize sHSPs belonging to five,, possibly more, nuclear-encoded gene families (Waters et al., 1996). There are over 50 plant sHSP gene sequences available in current databases. The plant sHSPs are categorized according to amino acid sequence similarity, immunological cross-reactivity, intracellular localization. The five best characterized families comprise two classes of cytosolic proteins (class I, II), three families of organelle-localized proteins, which have been shown to be targeted to the endoplasmic reticulum, chloroplast or mitochondrion.
Escherichia coli DsbB
Authors: Bardwell J C A
Published: November 2023

dsbB null mutants in E. coli have a severe, general defect in disulfide bond formation within the periplasm. The pleiotropic phenotypes associated with this defect are very similar to those of dsbA mutants (see entry p. 318). dsbB mutants have been isolated based on these phenotypes (Bardwell et al., 1993.
Escherichia coli DsbE
Authors: Missiakis D , Raina S
Published: November 2023

One of the genetic approaches that has led to the identification of genes whose products are involved in thiol-disulfide exchange reactions was based on the rationale that if such activities existed they should be inhibited in vivo by reducing agents such as dithiothreitol (DTT) (Missiakas etal., 1993).
Bacillus brevis Bdb
Authors: Udaka S
Published: November 2023

bdb was cloned from Bacillus brevis as a gene that complements the Escherichia coli dsbA mutation,, encodes an 118 amino acid precursor with a signal sequence of 27 amino acids (Ishihara et al., 1995) (GenBank accession number D37936).
Saccharomyces cerevisiae protein disulfide isomerase (PDI)
Authors: Tuite M F , Dunn A
Published: November 2023

Thioredoxin-related glycoprotein (TRG) (Gunther et al., 1991); glycosylation site binding protein (GSBP) (LaMantia etal., 1991).

Protein disulfide isomerase (PDI; EC 5.3.4.1) is the archetypal member of a family of sequence-related proteins located in the lumen of the endoplasmic reticulum (ER) of eukaryotic cells (Freedman et al., 1994). These proteins contain one or more copies of the -CGHC- motif which is related to the thioredoxin active site sequence -WCGPCK-.
Saccharomyces cerevisiae Mpdlp, Mpd2p
Authors: Tachikawa H , Mizunaga T
Published: November 2023

The MPD1, MPD2 genes were identified as multicopy suppressors of a pdi1 deletion mutant (Tachikawa et al., 1995). Unlike the PDI1 gene (see entry on S. cerevisiae PDI, p. 335), neither MPD1 nor MPD2 is essential for viability. The MPD1 gene encodes a polypeptide of 318 amino acids (GenBank accession number D34633), which is a member of the PDI family. While PDI has two disulfide isomerase active site sequences, mammalian PDI related proteins have two or three of those sites (Freedman et al., 1994).
Saccharomyces cerevisiae cydophilin A /Cpr1/Cyp1
Authors: Haendler B
Published: November 2023

CPH (Haendler etal., 1989); Cpr1 (Heitman et al., 1991); Cyp1 (Koser etal., 1991). CypA was isolated from a S. cerevisiae cell-free lysate using dye-ligand chromatography, isoelectric focusing and gel filtration (Haendler etal., 1989). The cDNA sequence predicts a protein of 162 amino acids (Haendler et al., 1989; Dietmeier and Tropschug, 1990; GenBank accession number X17505). Comparison with the protein sequence of other soluble cyclophilins from yeast or higher eukaryotes shows the existence of a highly conserved central region and of specific N- and C-terminal parts.
Saccharomyces cerevisiae Cpr7
Authors: Chang H -C J , Lindquist S
Published: November 2023

Cpr7 was isolated in a two-hybrid screen for proteins that interact with Rpd3, a yeast homolog of histone deacetylase (Duina etal., 1996a; Taunton etal., 1996). CPR7 was also identified in the yeast genome sequencing project (Zagulski etal., 1995).

The CPR7 gene (GenBank accession number U48868), located on chromosome X, encodes a protein of 393 amino acids with a predicted molecular weight of 45 kDa. The primary amino acid sequence of Cpr7 shares 38% amino acid identity with Cpr6, a Cyp40 homolog (Duina et al., 1996a). A search of the complete genomic sequence of S. cerevisiae indicates that Cpr6 and Cpr7 are the only two cyclophilins in the Cyp40 subfamily.
Saccharomyces cerevisiae CYPD/Cpr5
Authors: Frigerio G
Published: November 2023

The genomic CYPD sequence is part of cosmid 9740 from chromosome IV (GenBank accession number U28374; Johnston et al., unpublished entry). The open reading frame of a previously isolated cDNA (EMBL accession number X73142; Frigerio and Pelham, 1993), predicts a protein of 225 amino acids with a 22 residue N-terminal hydrophobic signal sequence and the C-terminal ER retrieval signal HDEL (Pelham, 1990). The 162 amino acid cyclophilin core domain defined with regard to cytoplasmic cyclophilins has up to 62% amino acid identity with other 5. cerevisiae cyclophilins. Sequence similarity is highest with a second cyclophilin found in the secretory pathway followed by the mitochondrial and the cytoplasmic form.