bluuebunny/crossref_metadata_2025 huggingface dataset:
Bounds on codes
Authors: Pretzel Oliver
Published: November 2023

In Parts 1 and 3 we have constructed codes that are designed to give a certain worst case performance. For such codes Shannon’s theorem is not an appropriate measure because it concerns the average performance of a code. In this chapter we shall prove some simple bounds on the worst-case performance of codes and compare our codes with them.
Movements of the hyperbolic plane
Authors: Hemion Geoffrey
Published: November 2023

The hyperbolic plane H is the universal covering space of any compact surface S whose Euler characteristic is less than zero. Let f : S → S be a homeomorphism of the surface onto itself. Then there is a mapping f*: H → H which is a ‘lifting’ off to the covering space. More specifically, the projection of H onto S is a mapping p : H → S. (It maps each copy of the fundamental region in H onto the single fundamental region of S.) Then the lifted mapping f* has the property that for each point x ϵ H we have f(p(x)) = p(f*(x)).
Matrix Eigenvalue Problems
Authors: Kockler Norbert
Published: November 2023

Characteristic properties of natural systems can often be described by eigenvalues of certain differential equations, see Chapter 8. If the differential equation is discretized, a matrix eigenvalue problem has to be solved. This kind of problem will be considered in this chapter. We will restrict ourselves to real matrices. But the eigenvalues of a real matrix may be complex numbers.
Initial Value Problems for Ordinary Differential Equations
Authors: Kockler Norbert
Published: November 2023

Ordinary differential equations (ODEs) are equations for functions of one independent variable. Each equation can depend on the unknown function and its derivatives up to a specified order.
Boundary Value and Eigenvalue Problems for Ordinary Differential Equations
Authors: Kockler Norbert
Published: November 2023

The mathematical theory for (two-point) boundary and eigenvalue problems for ordinary differential equations (ODEs) is not as standardized as that for initial value problems. But that does not mean that these problems do not play an important role for a lot of engineering and other applications. There are some problems of practical importance, where the mathematician cannot determine the question of existence or uniqueness of solutions, but they are regularly solved approximately with numerical methods.
Partial Differential Equations
Authors: Kockler Norbert
Published: November 2023

Partial differential equations (PDEs) are one of the most important subjects of applied mathematics, with innumerable applications in science and engineering. Accordingly numerical methods for their approximate solution are of some importance. In spite of these facts this chapter is short, because the field of partial differential equations is too large to be considered in detail within a general text on numerical methods like this one.
More About Paley-Wiener Spaces
Authors: Higgins J R
Published: November 2023

The four topics covered in this chapter are not directly concerned with sampling, but with various aspects of Paley-Wiener spaces. Since these spaces are typically collections of band-limited functions, and the notion of band-limitation in one form or another runs through all our work on sampling, this material has been included to provide some necessary background, and to lend perspective on these important spaces.For general reference it will be convenient to have at our disposal a collection of Paley-Wiener theorems.
Errors And Aliasing
Authors: Higgins J R
Published: November 2023

The act of expanding a function into a sampling series is fraught with the possibility of incurring errors of various kinds. These are to be seen as deviations from the desired goal and usually arise from an incomplete knowledge of all the parameters; this is often due to our incapacity to measure with complete accuracy. Sometimes errors are incurred deliberately, especially if there is some trade-off value in doing so. Let us recall that we are always dealing with the case in which functions require infinitely many samples for exact reconstruction.Several different kinds of error have been identified, and they have been studied intensively over the past few decades. The main ones are as follows.The truncation error arises if one ignores all the samples outside a finite interval; it always occurs in practice of course. The object function cannot be reconstructed exactly because there is insufficient information. A more general kind of error occurs if samples are missing from some locations; it is called the information loss error.
Multi-Dimensional Sampling
Authors: Higgins J R
Published: November 2023

Our previous work has largely been concerned with sampling theories in one dimension. Now we are going to extend matters to higher dimensions.
Ordered sets, lattices, and universal algebra
Authors: Blyth T S , Varlet J C
Published: November 2023

It is of course impossible to give a full account of ordered sets, lattices, and universal algebra in a few pages, so we refer the reader to the various books cited in the bibliography. Nevertheless, in order to make this monograph reasonably selfcontained, we shall summarise in this introductory chapter the fundamental notions that we shall use throughout. More specific concepts that we shall require will be defined as necessary. As far as notation is concerned, we provide an index of the various symbols that are used throughout.
Congruence relations
Authors: Blyth T S , Varlet J C
Published: November 2023

Let (L;f) be an Ockham algebra. Then an Ockham algebra congrnence (or, briefly, a congrnence) on L is an equivalence relation that has the substitution property for both the lattice operations and for the unary operation f. It follows that every congruence is in particular a lattice congrnence and it is essential to distinguish these two types. In order to do so, we shall use the subscript ‘lat’ to denote a lattice congruence.
Duality theory
Authors: Blyth T S , Varlet J C
Published: November 2023

Duality theory in the context of distributive lattice-ordered algebras has rather a long history. It was in 1933 that G. Birkhoff established his famous representation theorem for finite distributive lattices and, about three years later, M. H. Stone developed a representation theory for arbitrary boolean algebras, using topological methods. In the early seventies, H. A. Priestley provided an ingenious common generalisation of both these theories, thus allowing questions of a lattice-theoretic nature ‘to be translated into the language of ordered topological spaces’ and usually be resolved more easily, the dual space generally being simpler and more tractable than the algebra itself. Of course, it is impossible to give here a complete survey of the theory of duality; for this we refer the reader to [78], [79], and [63]. Here we shall simply introduce the concepts and results that we shall require.
The lattice of subvarieties
Authors: Blyth T S , Varlet J C
Published: November 2023

A subclass of a variety V which is also a variety is called a subvariety of V. The subvarieties of V form a lattice which we denote by ∧(V). In this, the meet A I\ B of two subvarieties A, B is their intersection, and the join A ∨ B is the equational closure of their union, i.e. the smallest subvariety of V that contains A∪ B. A celebrated theorem of B. Jönsson [15] states that if Vis a variety every algebra of which has a distributive congruence lattice then ∧ (V) is distributive. Applying this to the variety O of Ockham algebras, we thus have that ∧(O) is distributive.
Fixed points
Authors: Blyth T S , Varlet J C
Published: November 2023

In an Ockham algebra (L;f) the notion of a fixed point f was introduced in Chapter 2 as an element a ∈L such that f(a) = a. Dually, we say that an element x of an Ockham space (X;g) is a fixed point of g if g(x) = x. We shall denote by Fix L [resp. Fix X] the subset of L [resp. X] formed by the fixed points f [resp. g].
Fixed point separating congruences
Authors: Blyth T S , Varlet J C
Published: November 2023

If (L;f} is an Ockham algebra and x,y are distinct elements of L then we shall say that a congruence ,  ϑ on L separates x and y if (x, y) ∉ , ϑ. By a fixed point separating congrnence on L we shall mean a congruence that separates every pair of fixed points of L. We shall denote by :  ℱ (L) the set of fixed point separating congruences on L. We let Fix L = { αi ; i∈I} be the set of fixed points of (L;/), and we shall assume throughout this chapter that I Fix LI ≥ 2. All of the results that follow appear in [56].
Congruences on K1,1-algebras
Authors: Blyth T S , Varlet J C
Published: November 2023

We now take a close look at congruences on a K,11-algebra L. We begin by characterising the principal congruences.
The dual space of a finite simple Ockham algebra
Authors: Blyth T S , Varlet J C
Published: November 2023

We recall that an n-crown (with n;  ≥2) is an ordered set C with 2n elements x  1, ... , x2n whose only comparabilities are

An n-crown C is connected, has length 1, |Max 𝒞|𝒞; = |Min 𝒞|= n, every minimal element is covered by two maximal elements, and every maximal element covers two minimal elements; so all vertices of 𝒞 have degree 2. There have been some attempts to generalise this notion. We mention two of these. In [93], W. T. Trotter, Jr. defines a crown  Snk as follows : for n ≥ 3 and k ≥ :0, Snk is an ordered set of length 1 with n +; k minimal elements a1, ... , an+k and n + k maximal elements b1, ... , bn+k each a;I being incomparable with bi, ... , bi;+k and being covered by the remaining n - l maximal elements. Here, of course, the subscripts have to be interpreted cyclically. For example, the graph of S42 is as follows :
Relative Ockham algebras
Authors: Blyth T S , Varlet J C
Published: November 2023

In Chapter 1 we gave an affirmative answer to the question of whether every bounded distributive lattice L can be made into an Ockham algebra (L; ∼). If the subvariety V of O to which (L; ∼) has to belong is prescribed, then the answer is far from being affirmative, even when L is finite. For example, as we observed in [41], the 5-element distributive lattice with Hasse diagram [ufig] cannot be made into an M1-algebra since otherwise we would have [ueq] whence either ∼a= l or ∼b = l, so that either ∼2a = 0 or ∼2b = 0 from which it follows by axiom (1) that either a = 0 or b = 0, a contradiction.
Double MS-algebras
Authors: Blyth T S , Varlet J C
Published: November 2023

The notion of a double Stone algebra is well known. This is an algebra (L;  ∨  ∧ *,+0,1)of type (2, 2, 1, 1, 0, 0) such that both (L; *) and (L0P; +) are Stone algebras with the unary operations a ⟼a*and a ⟼a+ linked by the properties [ueq] Our objective now is to consider the following natural generalisation.
Subdirectly irreducible double MS-algebras
Authors: Blyth T S , Varlet J C
Published: November 2023

In order to determine the subdirectly irreducible double MS-algebras we can extend the discussion given in Chapter 4 for MS-algebras. Corresponding to the notion of a g-subset in the dual space (X;g) of an MS-algebra (L; 0), we define a {g, h}-subset in the dual space (X; g, h) of a double MS-algebra (L; 0, +) to be a subset of X that is both a g-subset and an h-subset. Such a subset, for example, is gw{x} ∪ hw{ x}. Working with this we see that, corresponding to Corollary 1 of Theorem 4.6, a finite double MS-algebra (L; 0, +) is subdirectly irreducible if and only if there exists x ∈ X such that X = gw{x} ∪ hw{x}.
Singles and Doubles
Authors: Blyth T S , Varlet J C
Published: November 2023

In Chapter 5 we showed that every variety of MS-algebras is characterised by adjoining to the basic axioms of MS at most three from a list of ten identities. If a double MS-algebra (L;0, +) is such that (L;0) satisfies some of these identities then it is natural to ask when (L0P;+) satisfies the same identities. More particularly, if (L;0, +} ∈ DMS and V(L;0) =R, what are the possible subvarieties V(L0P; +)?
A history of the hmneobox
Authors: Walter J. Gehring
Published: November 2023

Almost ten years have passed since the discovery of the homeobox and it seems appropriate to tell the “homeo box story”, how it happened and what advances were made in this field over the past decade. Of course, such accounts are quite subjective and the same events are seen differently by different observers. The discovery of the homeobox was only possible in the congenial atmosphere of a laboratory in which a group of creative and hardworking young scientists made a concerted effort to elucidate the mechanisms of development.
Sec B
Authors: Kumamoto C
Published: November 2023

The first mutations affecting the sec B locus were isolated by selecting for increased activity of a hybrid protein containing the N-terminal portion of maltose binding protein (MBP) fused to-galactosidase. A null mutation was subsequently constructed by insertion of Tn S.
Leader peptidase
Authors: Dalbey R E
Published: November 2023

A temperature-sensitive amber mutation in the leader peptidase gene was isolated after localized mutagenesis. Strain IT41 bearing this mutation accumulates precursor proteins rapidly after a temperature shift to 42°C. Another chromosomal mutation has been constructed in strain H560/pRD9, in which the normal constitutive promoter of the leader peptidase gene is replaced with the inducible arabinose promoter2 Four hours after transfer of this strain to arabinose-free media, precursor proteins begin to accumulate. Protease-mapping and osmotic shock experiments indicated that the precursor to the maltose binding protein is translocated across the plasma membrane and is anchored to the outer surface of the inner membrane. The physiological role of leader peptidase is to release exported proteins from the outer surface of the inner membrane so they can move into the periplasm or to the outer membrane.
KAR2
Authors: Rose M , Vogel J P
Published: November 2023

kar2-1 and all other temperature sensitive (ts·) alleles of KAR2 exhibit defects in nuclear fusion5·8. The ts· mutants can be placed into two classes based on their viability and effects on secretion at the restrictive temperature. Class I alleles (e.g. kar2-159) block translocation of secretory proteins into the lumen of the ER and exhibit a corresponding rapid loss in cell viability at the restrictive temperature. Class II alleles (e.g. kar2-1) do not block secretion but instead result in a variety of post-translocational defects. In contrast to the class I mutants, class II mutants remain viable at the restrictive temperature. Surprisingly, the class II mutant phenotypes are most consistent with a defect in secretory protein processing in the Golgi.
FKB2
Authors: Sykes K
Published: November 2023

The nucleotide sequence of FKB2, isolated from the yeast Saccharomyces cerevisiae, predicts a protein of 135 amino acids, including an N-terminal hydrophobic region that may constitute a 16 (or 17) residue signal sequence12 The mature yeast Fkb2 protein and human FKBP-13 proteins share 55% amino acid sequence identity, and the yeast Fkb2 protein is 52% identical with the yeast cytosolic Fkb1 protein.
SPC18
Authors: Shelness G
Published: November 2023

The nucleotide sequence of SPC 18 cDNA2 (GenBank accession number J05466) encodes a 179 amino acid polypeptide with a calculated molecular mass of 20,626 Da. SPC 18 and SPC 21 (seep. 90) are products of separate genes, yet their amino acid sequences are strikingly similar. In a 176 amino acid region of overlap between the two proteins, no insertions or deletions are present and identity exists at 143 or 81% of amino acid positions. The most dramatic primary structure differences between the two proteins exist at the amino terminus where the SPC 21 primary translation product possesses 11 additional amino acids not present in SPC 18, and in an internal region of the protein where 4 acidic residues in SPC 21 appear as neutral or basic amino acids in SPC 18 (Asp117 to Gin105, Asp120 to His108, Glu131 to Ala119, and Glu140 to Gln128).
α-Glucosidase II
Authors: Trimble R , Morcmcn, K , Herscovics A
Published: November 2023

a-Glucosidase II from rat1 and calf2 liver microsomes and from yeast3 was initially shown to catalyze the specific removal of both glucose residues from Glc2Man9GlcNAc2 Removal of the innermost glucose residue is much slower than that of the terminal glucose. The mannose residues on the upper a-1,6-mannosyl branch of the oligosaccharide are required for enzyme activity3.4. The enzyme readily cleaves aryl a-glucosides and is strongly inhibited by dNJ, N-Me-dNJ, castanospermine, and related compounds5·7 Inhibition by these agents of further processing of oligosaccharides to complex structures is incomplete, in part owing to the ability of some cells to transfer non-glucosylated oligosaccharides to protein8, and in part owing to the action of an endo-a-mannosidase9 (see entry p. 190).
Ca2+ -dependent a-1,2-mannosidase
Authors: Trimble R , Herscovics K Moremen,and A
Published: November 2023

A calcium-activated a-1,2-mannosidase was first partially purified from rabbit liver microsomes and shown to require nonionic detergent or specific phospholipids for activity12. The enzyme removes a-1,2-linked mannose residues from glycoprotein and oligosaccharide substrates. It does not act on aryl a-mannoside, and is inhibited by 1- deoxymannojirimycin (dMNJ) but not by swainsonine3 The purified enzyme is a glycoprotein that migrates on SDS-PAGE as a 52 kDa species. Antibodies have not yet been prepared for immunolocalization studies.
SEC20
Authors: Pelham H
Published: November 2023

Three temperature-sensitive, conditionally-lethal mutant alleles of 5EC20 have been identified. The best characterized of these is sec20-1, which was isolated using a density enrichment screen. At the non-permissive temperature (37°C), this mutant shows a block in secretion at the ER to Golgi step with accumulation of ER and 50nm vesicles2.
SEC7
Authors: Franzusoff A
Published: November 2023

Temperature-sensitive, conditionally lethal sec7 mutants were isolated by a density enrichment protocoI5 Two alle-les, secl-1 and secl-4, appear to exert different effects in disrupting vesicular traffic in the yeast secretory pathway2·6. The accumulation of heterogeneous populations of glycoprotein intermediates in the pathway was observed, ranging from ER to late Golgi forms of the secreted proteins invertase and o:-factor2·. The transport of both soluble and membrane-bound vacuolar enzymes is also disrupted in sec7 yeast at the non-permissive temperature2· s-10_ Multiple species of glycoprotein intermediates were identified (i.e. “leaky” phenotype) even after shifting the cells to 38°C for longer periods before initiating pulse-chase experiments.
KEX2
Authors: Fuller B
Published: November 2023

The DNA sequence of the KEX2 gene (GenBank accession # M24201} predicts an 814 residue polypeptide (90.1 kDa) (see Figure 1) that contains an N-terminal signal peptide and a single transmembrane spanning domain near the Cterminus1A,17. Like subtilisin, the predicted Kex2 polypeptide has the structure of a pre-pro-protein, with a pro-segment of about 90 residues preceding the region of homology to mature subtilisin.
STE13
Authors: Flanagan C A , Thorner J
Published: November 2023

The first allele isolated, ste13-1, was an a-specific sterile mutation that displayed temperature-sensitive mating5  MATa ste13-1 cells were found to secrete, even at 30°C, primarily pro-a-factor containing the -X-Ala- repeats of the spacer sequence2 This aberrant form of secreted pheromone (“a-factor*”) was not biologically active on normal MATa cells, but could be detected using MATa sst2 mutants, which are hypersensitive to pheromone.
DSS4
Authors: Roberts D , Novick P
Published: November 2023

dss4-1 suppresses the growth defect, the block in invertase secretion, and the accumulation of 100 nm secretory vesicles seen in sec4-8 cells at the restrictive temperature1. Suppression is seen at 35°C, but not at 37°C whether dss4-1 is present in single copy or overexpressed. dss4-1 can not suppress a deletion of SEC4 and can not suppress the growth defect of ypt1-1 (seep. 121). dss4-1 has no effect on wild-type SEC4 cells.
A. Protein Translocation And Maturation In The Yeast Er
Authors: Rothblatt J
Published: November 2023

Genetic selections for 5accharomyces cerevisiae mutants exhibiting temperature-sensitive conditional defects in the targeting and translocation of secretory and membrane proteins1 have proved a powerful technique for identifying yeast proteins involved in these processes. in vitro studies of protein import into yeast microsomes initially provided few clues as to the identity of key components. However, such studies did reveal that protein translocation in yeast, by contrast to the situation in mammalian cells, could occur by both co-translational and post-translational mechanisms.
GP-2
Authors: Rindler M J
Published: November 2023

Sequence analysis of a cDNA encoding rat pancreatic GP-2 revealed a protein of 530 amino acids with a predicted 24 residue N-terminal signal sequence and eight potential Nglycosylation sites. The sequence of the canine form is essentially similar. A stretch of 21 hydrophobic amino acids at the (-terminus contains a consensus sequence for attachment of a GPI anchor. The protein is remarkably cysteine-rich, with 28 cysteines present in the mature protein. (GenBank accession nos. M58716, X53935, M37032).
p145
Authors: martin T J f. , Walent J H , Porter B W , Hay J C
Published: November 2023

The regulated exocytotic release of secretory granule constituents from neural, endocrine and exocrine cells has been studied in cells permeabilized by a variety of methods5. Secretion from permeable cells is ATP-dependent and stimulated by Ca2+ over the range of 0.1-10 M. Permeabilization methods that generate large plasma membrane lesions result in a progressive loss of ATPdependent, Ca2+-activated secretion, indicating that regulated secretion requires soluble macromolecular factors5.
VPS5
Authors: Horazdovsky B F , Emr S D
Published: November 2023

could correspond to a signal sequence or to membrane spanning domains. A comparison of the deduced amino acid sequence of the VP55 gene product with sequences of other known proteins revealed no significant similarities. Gene disruption experiments have shown that the VPS5 gene product is not essential for cell viability1. However, cells carrying the null allele exhibit differential defects in vacuolar protein sorting. Greater than 95% of carboxypeptidase Y (CPY) is secreted from these cells in its Golgi modified p2 precursor form.
VPS8
Authors: Raymond C K , Stevens T H
Published: November 2023

vps8 null mutants are viable and exhibit growth characteristics indistinguishable from wild-type cells. The vps8 mutant cells secrete approximately 65% of their newly synthesized CPY.
VPS27
Authors: Raymond C K , Stevens T H
Published: November 2023

Strains bearing mutations within the VPS27 gene share phenotypic characteristics in common with mutants representing at least twelve other vps complementation groups1. These mutants secrete modest amounts (30-60%) of the newly synthesized soluble vacuolar protein carboxypeptidase Y (CPY). Proteolytic processing of the intracellular proCPY is normal1·3 Similarly, visual inspection and/or vacuolar vital staining of these mutant strains suggests they assemble a relatively normal vacuolar compartment.
VPS35
Authors: Horazdovsky B , Par,ivicini, G , Enu S D
Published: November 2023

““ “ p - _-

Cells carrying a null allele of VPS35 exhibit a differential vacuolar protein sorting defect. The sorting of CPY is drastically affected in !wps35 mutant cells; >95% of CPY is secreted in its Golgi modified p2 precursor form. However, the vast majority of two other soluble vacuolar proteases, proteinase A (Pr A) and proteinase B (PrB) are retained and matured in these mutants, indicating delivery to the vacuole. These results suggest that CPY sorting is completely dependent on the presence of functional Vps35p. Yet the sorting and processing of other soluble hydrolases (PrA and PrB), as well as the vacuolar membrane protein alkaline phosphatase can occur in a Vps35p-independent manner. Apparently only a subset of soluble vacuolar proteins, like CPY, require Vps35p for their efficient sorting to the vacuole. It is possible that CPY and Pr A may utilize different receptor complexes for their sorting and/or delivery to the vacuole.
PEP7
Authors: Zhang J Q , Webb, C C , Jones E W
Published: November 2023

hole contents by the bud is profoundly impaired in these mutants; however, vacuoles do eventually form. In addition, intervacuole communication in zygotes14 is greatly diminished. Whereas lack of the VAC1/PEP7 gene has a profound effect on vacuole segregation, the accurate segregation of the nucleus, mitochondria and Golgi apparatus does not require VAC7/PEP7function.
VMA13
Authors: Ho M N , Stevens T H
Published: November 2023

Mutant phenotypes associated with vma13 cells are identical to those found for vma2 mutants (see VMA2 entry p. 261)1,3_ However, deletion of the VMA13 gene in yeast results in strains that are deficient for vacuolar acidification12. The remaining vacuolar H+-ATPase subunits (Vma1p, Vma2p, Vma3p, Vma4p, Vma5p, and Vph 1p) continue to associate with the vacuolar membrane in the absence of Vma13p. This is surprising given that several of the remaining subunits, including the Vma1, Vma2, Vma4, and Vma5 polypeptides, are hydrophilic proteins that are thought to peripherally associate with the vacuolar membrane only when the H+-ATPase is fully assembled45. These results suggest that although Vma13p is essential for the activity of the vacuolar W-ATPase, it is not required for some level of enzyme assembly onto the vacuolar membrane.
CLC1
Authors: Silveira L , Schekman R
Published: November 2023

In most strain backgrounds, haploid yeast cells lacking 93% of the CLC1 coding region are viable, but grow -2-3 times more slowly than wild-type cells. Upon propagation, fastergrowing variants arise. Cells lacking both clathrin light chain and clathrin heavy chain (encoded by CHC1 - see CHC1 entry p. 267) are also viable but slow-growing. Clathrin heavy chain is less stable in c/c1 cells than in wildtype cells4. Vesicles isolated from clc1 cells do not contain detectable clathrin heavy chain, even if prepared from cells overproducing clathrin heavy chain5 It has not been determined whether clathrin heavy chain coats on these vesicles are unstable to isolation or whether they are never formed. Light-chain-deficient cells, like cells lacking clathrin heavy chain6, secrete a heterogeneous high molecular weight form of the mating pheromone a-factor4, presumably due to the mislocalization of the processing protease Kex2p.
END2
Authors: Hamburger C , Egerton, M , Riezman H
Published: November 2023

The end2 mutant was isolated by screening a bank of ethanemethanesulfonate mutagenized yeast cells for their ability to accumulate lucifer yellow CH in the vacuole. The original mutant allele, end2-1, is temperature-sensitive for growth showing only slight growth at 37°C. Lucifer yellow CH accumulation in the vacuole is also thermosensitive with significant, but less than wild-type accumulation at 24°C. cx.-factor pheromone, an endocytic marker, is internalized normally at 37°C in the mutant. Pheromone degradation is strongly inhibited at this temperature indicating that transport of internalized cx.-factor to the vacuole is blocked. Vacuole morphology and maturation of the vacuolar enzyme, carboxypeptidase Y, are nearly the same as in wild-type cells. lnvertase secretion is also normal. Haploid cells carrying a disrupted open reading frame in END2 are inviable2
RENZ
Authors: Davis O G , Sprague,Jr. G F
Published: November 2023

The ren1 mutation was isolated by virtue of its defect in receptor endocytosis . The yeast pheromone receptors, members of the rhodopsin/j3--adrenergic receptor family, are subject to endocytosis, which proceeds rapidly and constitutively in the absence of cognate pheromoneligand. This constitutive endocytosis has been well established for the a-factor receptor. Internalized receptors are delivered to the vacuole where they are hydrolysed in a PEP4-dependent process1 (see PEP4 entry p. 247). The halflife of the receptor is about 20 min in wild-type cells; in pep4 cells receptor half-life increases to much greater than 2 hr. Moreover, when degradation is blocked in pep4cells, the a-factor receptor visualized by indirect immunofluorescence microscopy is found to accumulate in the vacuole1. The a-factor receptor also appears to be subject to constitutive endocytosis.
UDP-N-acety lglucosamine : ly sosomal enzyme N-acetylglucosaminc 1-phosphotransfcrase
Authors: Ketcham D M
Published: November 2023

Fibroblasts from patients with I-cell disease (mucolipidosis II) contain little or no detectable GlcNAc-phosphotransferase, whereas pseudo-Hurler (mucolipidosis Ill) fibroblasts are characterized by residual low levels of GlcNAc-phosphotransferase. Three complementation groups have been identified by cell fusion experiments5-7. Fibroblasts from all three groups are deficient in lysosomal enzyme phosphorylation, but group IIIC fibroblasts retain the ability to phosphorylate a-methylmannoside. While group IIIA and 111B mutant enzymes show decreased activities towards a-methylmannoside as well as lysosomal enzymes, the apparent Km values are normal. Group IIIC fibroblasts therefore contain a normal level of GlcNAcphosphotransferase that is deficient in the specific recognition of lysosomal enzymes, while group IIIA and 111B deficiencies may be due to decreased synthesis or instability of the enzyme, or possibly synthesis of an enzyme with a defective catalytic domain4 7-9.
Dynamin (shibire)
Authors: Vallee R B
Published: November 2023

Dynamin was initially isolated from calf brain tissue by microtubule co-purification1 In this procedure microtubules are assembled from cytosolic extracts using taxol, washed, and dynamin is extracted with GTP. AMPPNP is included in this step to prevent extraction of kinesin. The dynamin is subsequently rebound to microtubules, reextracted, and further purified by DEAE-Sepharose chromatography.
SSS1
Authors: é E K épe
Published: November 2023

The 5551 gene (for “Sec Sixty-one Suppressor”) was isolated as a strong multicopy suppressor of the sec61-2 mutation that affects protein translocation. A conditional expression mutant was constructed by expressing the 5551 gene under the control of a galactose-inducible promoter on a plasmid, while disrupting the chromosomalrnpy of the gene. One or two generations after a shift to restrictive growth conditions, the mutant cells start accumulating precursor forms of several secretory or vacuolar proteins on the cytosolic aspect of intracellular membranes, presumably at the site of translocation/insertion. These accumulated proteins include the soluble proteins prepro-a-factor, invertase, carboxypeptidase Y, and the membrane protein dipeptidylaminopeptidase B1.
End5
Authors: Draper R K
Published: November 2023

Mutant 42.2, selected for resistance to diphtheria toxin, represents the End5 complementation group12 42.2 cells are temperature-sensitive for viability and accumulate less transferrin than normal at the restrictive temperature. Endosomal and lysosomal acidification are apparently unimpaired. 42.2 cells are not defective in secreti.
SEC1
Authors: Novick P
Published: November 2023

Temperature-sensitive, conditionally lethal sec1 mutants were isolated by a density enrichment protocol2,3. The sec1 mutants are blocked in the export of cell surface proteins and accumulate 100 nm post-Golgi vesicles containing fully glycosylated secretory proteins23,78. The best characterized sec1 allele is sec1-1.
CAAX farnesyl transferase
Authors: Seabra Miguel C , Brown Michael S , Goldstein Joseph L
Published: November 2023

Tase is composed of two tightly coupled subunits, designated a and p (Reiss et al. 1990). Mammalian cDNAs forboth subunits were cloned initially from a rat brain cDNA library using oligonucleotides encoding peptides present in the purified protein (Chen et al. 1991a,b). cDNAs for both subunits were subsequently cloned from bovine brain (Kohl eta/. 1991; Omer et al. 1993), human placenta (Omer et al. 1993), and human retina (Andres et al. 1993a). GenBank accession numbers for the a-subunit are M81225 (rat), M74083 (bovine), and L10413 (human). GenBank accession numbers for the P-subunit are M69056 (rat),L00633 (bovine), and L10414 (human). The genes for a andsubunits of human FTase have been mapped to chromosomes 8p22-q11 and 14q23-q24, respectively., USA
Rab escort proteins (REP1 and REP2)
Authors: Seabra Miguel C , Goldstein Joseph L , Brown Michael S
Published: November 2023

Two different Rab escort proteins, designated REP1 (also known as choroideremia gene product (CHM) or Component A of Rab GGTase) and REP2 (also known as choroideremia-like gene product (CHML)), have been identified. The gene for human REP1 was originally isolated by positional cloning techniques as a candidate gene for choroideremia, a retinal degeneration disease (Cremers et al. 1990). Later, the cDNA for rat REP1 was cloned from a brain library (Andres et al. 1993) based on sequences of tryptic peptides derived from REP1 purified from rat brain (Seabra et al. 1992). The cDNA for REP2 was cloned by crosshybridization with probes for REP1 (Cremers et al. 1992). USA.
Cal1p/Cdc43p
Authors: Ohya Yoshikazu , Anraku Yasuhiro , Trueblood Cynthia E
Published: November 2023

ca/1-1 was originally identified as a mutation resulting in aCa2+-dependent phenotype (Ohya et al. 1984). The mutantexhibits a homogeneous terminal phenotype at 37°C witha G2/M nucleus and a small bud (Ohya et al. 1984).Independent screening of the yeast cell cycle mutants thataccumulated enlarged unbudded cells identified cdc43-2-cdc43-7 (Adams et al. 1990). The complete nucleotidesequence of Cal1/Cdc43 was determined by Johnson et al.(1990, correction appeared in 1991) and Ohya eta/. (1991).The GenBank accession numbers are M29471 and M31114.Note that another group temporarily used CAL 1 as thename of a gene encoding chitin syntase isozyme(Valdivieso et al. 1991), which is now called CHS3 (Shaw etal. 1991).59.
Bet4p
Authors: Ferro-Novick Susan
Published: November 2023

The BET4 gene was originally isolated on a fragment ofDNA that complements the benomyl-sensitivity of themad2-1 mutant (described in Li and Murray 1991). TheGenBank accession number is M73821.
K-Ras
Authors: McCormick Frank
Published: November 2023

K-RasA and B are P01116 and P01118; for mouse K-RasA and B they are P32883 and P08643. The nucleotide sequence is shown in Fig. 1.I ProteinsViral K-Ras, transduced by the Kirsten sarcoma virus, corresponds to the splicing variant designated K-Ras 4A. This protein, when fully processed, consists of 186 amino acids and has a (-terminus modified by farensylation as well as palmitolylation.
N-Ras
Authors: McCormick Frank
Published: November 2023

Swiss-Prot accession numbers for human, mouse and guinea-pig N-Ras are P10301, P10833 and P08556, respectively; the nucleotide sequence of N-Ras is shown in Fig. 1.
RalB
Authors: Chardin Pierre
Published: November 2023

RalB was isolated from a human pheochromocytoma cDNA library using a simian RalA probe at moderate stringency (Chardin and Tavitian 1989; GenBank accession number X15015), and later from a human retina cDNA library (Hsieh et al. 1990; GenBank accession number M35416), a rat pheochromocytoma cDNA library (Wildey et al. 1993; GenBank accession number L19699), and a marine ray electric lobe cDNA library (Ngsee et al. 1991; GenBank accession number M38394).
Sos
Authors: Downward Julian
Published: November 2023

Drosophila Sos was cloned due to the effect of mutations in the son of sevenless locus on the development of photoreceptor cell R7 (Bonfini etal. 1992; Simon etal. 1991). Two murine Sos cDNAs, Sos1 and Sos2, were cloned by low stringency hybridization to Drosophila Sos probes (Bowtell et al. 1992). Human Sos1 was cloned by a similar method (Chardin et al. 1993). GenBank accession numbers: human Sos1, L13857; murine Sos1, Z11574; murine Sos2, Z11664; Drosophila Sos, M83931.
Cdc25 Mm (Dpd-GEF)
Authors: Martegani Enzo , Vanoni Marco , Zippel Renata , Sturani Emmapaola , Alberghina Lilia
Published: November 2023

CDC25Mm was identified by screening a mouse brain cDNA expression library (constructed in the yeast expression vector pGR56) by functional complementation of a Saccharomyces cerevisiae strain carrying the cdc25 temperature sensitive mutation (Martegani etal. 1992). Two clones were isolated, CDC25Mm12, encoding a protein of 287 aa, and a longer one, CDC25Mm17, encoding a protein of 472 aa (Accession number X59868). By taking advantage of the CDC25Mm12 sequence, Cen et al.
Smg-GDS
Authors: Kaibuchi Kozo , Takai Yoshimi
Published: November 2023

Smg-GDS was purified from bovine brain cytosol and its partial amino acid sequences were determined (Yamamoto et al. 1990). Bovine Smg-GDS cDNA was isolated from a bovine brain cDNA library using oligonucleotide probes designed from its partial amino acid sequences (Kaibuchi et al. 1991). Human Smg-GDS cDNA was isolated from a human brain cDNA library by use of bovine Smg-GDS cDNA as a probe (Kikuchi etal. 1992). The nucleotide sequence of the bovine Smg-GDS cDNA and its deduced amino acid sequence are shown in Fig. 1. GenBank accession numbers are M63325 (Bovine Smg-GDS) and X63465 (Human SmgGDS).
Rap-GAP
Authors: McCormick Frank
Published: November 2023

Rap-GAP is a protein of 88 kDa, comprising 663 amino acids (Rubinfeld etal. 1991). Of these, 75 to 516 are necessary for Rap-GAP activity (Rubinfeld et al. 1992). An alternative splice variant has been cloned that contains an additional 26 amino acids These residues make up a repeat of similar sequence adjacent to the splice point (Rubinfeld et al.
Extracellular signal-regulated kinases (ERKs)
Authors: vers Sally Lee , Marshall Chris
Published: November 2023

A partial cDNA for rat ERK1 (Boulton et al. 1990) and full length cDNA for rat ERK2 (Boulton et al. 1991) were the first ERK-encoding cDNAs isolated. More recently, full length human sequences encoding ERK1 (Charest et al. 1993) and ERK2 (Owaki etal. 1992) have been isolated (Fig. 1).
Ira1p
Authors: Powers Scott
Published: November 2023

The Ira1 gene was cloned from a yeast DNA expression library by complementation of the heat-shock sensitivity of an ira1-1 mutant (Tanaka etal. 1989). The ira1-1 mutation was isolated by virtue of its ability to counteract the growth inhibitory effect of a temperature-sensititive cyr2/cdc25 mutation (Tanaka etal. 1989). The ira1-1 mutation was originally termed ppd1-1 (Tanaka etal. 1989). The GenBank accession number is M24378.
SP-Ras
Authors: Kaziro Yoshito
Published: November 2023

The S. pombe ras1 gene was identified by Southern blotting of S. pombe DNA with S. cerevisiae RAS1/RAS2 (Fukui and Kaziro 1985). The coding sequence for 219 amino acids is interrupted by an intron of 67 bp between codons 2 and The sequences GTAAGT and TAG were found as splice donor and acceptor sequences, respectively, and a sequence AACTAATCA which is similar to the splice consensus sequence TACTAACA for S. cerevisiae was present in the intron. The DNA sequence of S.pombe ras1 is shown in Fig. 1. GenBank accession number is X02331. The cloning and characterization of a gene allelic to ras1 from S.pombe was also reported by Nadin-Davis et al. (1986). The GenBank accession number of the latter authors’ sequence is X03771.
RhoB
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, human rhoB (originally clone 6), (Chardin et al. 1988) is shown in Fig. 1. The GenBank accession number is X06820.
RhoC
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, human RhoC (originally clone 9) (Chardin etal. 1988), is shown in Fig. 1. The GenBank accession number is X06821.
Cdc42Hs
Authors: Cerione Richard
Published: November 2023

Cdc42Hs was identified by screening a human placental cDNA library (Shinjo et al. 1990) and a human fetal brain library (Munimetsu etal. 1990) using degenerate oligonucleotide probes from peptide sequences generated from the purified GTP-binding protein isolated from human platelets and human placenta (Polakis et al. 1989). This GTP-binding protein was originally named Gp because of its apparent high abundance in platelets and placenta (Evans etal. 1986) and then later named G25K because of its mobility on some sodium dodecyl sulfate (SDS) gel systems (Polakis et al. 1989).
Rho-GAP
Authors: Hall Alan
Published: November 2023

A full-length Rho-GAP clone has been isolated from a human fibrosarcoma cDNA library (Lancaster eta/. 1994). A single mRNA of approximately 3600 nucleotides encodes a protein of 50 kDa. The nucleotide sequence of human p50 Rho-GAP and its deduced amino acid sequence are shown in Fig. 1. The GenBank accession number is Z23024.
Rho-p21-associated protein kinases
Authors: Manser Edward , Leung Thomas , Lim Louis
Published: November 2023

A human partial ACK cDNA was isolated by expression screening of a hippocampal library with (732P]GTP-labelled recombinant Cdc42. Subsequent screening of the library by DNA hybridization yielded a full-length cDNA of 4545 nucleotides (Manser et al. 1993). The human cDNA encodes a protein of molecular mass 119 kDa with 1091 amino acid residues and contains 450 nt of 5’ non-coding sequence and 819 nt of 3’ non-coding sequence (Fig. 1).
RhoSp
Authors: Matsui Yasushi , Imai Jun , Toh-e Akio
Published: November 2023

Several DNA fragments were amplified by polymerase chain reaction using yeast genomic DNA as a template and convergent degenerated olignucleotides corresponding to the sequences GXXXV/CGKT/S and DTAGQE, conserved in members of Ras-, Rho-, and Rab-type GTPases (Barbacid 1987). RHOB was identified by sequencing such DNA fragments, and clones carrying the full-length RHOB gene were isolated by screening a yeast Saccharomyces cerevisiae genomic DNA library using the amplified DNA fragment as a probe (Matsui and Toh-e 1992a).
Rho4p
Authors: Matsui Yasushi , Toh-e Akio
Published: November 2023

Several DNA fragments were amplified by polymerase chain reaction using yeast genomic DNA as a template and using convergent degenerated olignucleotides corresponding to the sequences GXXXV/CGKT/S and DTAGQE, conserved in members of Ras-, Rho-, and Rab-type GTPases (Barbacid 1987). RHO4 was identified by sequencing these DNA fragments, and clones carrying the full-length RHO4 gene were isolated by screening a yeast Saccharomyces cerevisiae genomic DNA library using the amplified DNA fragment as a probe (Matsui and Toh-e 1992). The DNA and deduced amino acid sequences of RHO4 are shown in Fig. 1. GeneBank accession number is D10007.
Rabla, b
Authors: Balch William E
Published: November 2023

Rabla and 1 b isoforms have been identified by the screening of cDNA libraries from mouse, rat, human and canine sources using oligonucleotide probes specific to Rasrelated proteins (Haubruck etal. 1987; Touchot etal. 1987; Wagner eta/. 1987; Tachibana etal. 1988; Vielh eta/. 1989; Wichmann etal. 1989; Zahraoui etal. 1989; Chavrier eta/. 1990, 1992). The nucleotide sequence of the rat Rabla (Touchot et al. 1987) and the rat Rablb (Wichmann et al. 1989) isoforms are shown in Fig. 1. GenBank accession numbers are J02998 (Rabla) and X13905 (Rablb).
Rab5a
Authors: Kikuchi Akira , Takai Yoshimi
Published: November 2023

Rab3a cDNA was isolated by two methods. In the first, the small GTPase with an Mr of 24 kD was purified from bovine brain membranes (Kikuchi et al. 1988). Its partial amino acid sequences were determined and bovine Rab3a cDNA was isolated from a bovine brain cDNA library using oligonucleotide probes designed from its partial amino acid sequences (Matsui etal. 1988). In the second method, rat Rab3a cDNA was isolated by screening a rat brain cDNA library using oligonucleotide probes synthesized according to the sequences corresponding to the consensus sequences of the GDP/GTP-binding domains (Zahraoui et al. 1988).
Rab4a
Authors: Mellman Ira
Published: November 2023

Rab4a was identified by screening a rat brain (Touchot et al. 1987) and human pheochromocytoma cDNA libraries (Zahraoui etal. 1989) with an oligonucleotide corresponding to the amino acid sequence WDTAGQE, which is shared by members of the Rab and Rho protein subfamilies (Valencia etal. 1991). The GenBank accession numbers are J03001 and M28211.
Rab5a
Authors: Zerial Marino
Published: November 2023

Rab5a was identified by screening a cDNA library (Zahraoui et al. 1989; Chavrier et al. 1990) using degenerated oligonucleotides corresponding to the sequence WDTAGQE shared by members of the Ypt1/Sec4/Rab subfamily (Valencia et al. 1991). It was originally named Rab5 before the identification of the Rab5b and Rab5c proteins (Chavrier eta/. 1992). Rab5 is now renamed Rab5a. The DNA sequence of canine Rab5a (Chavrier etal. 1990) is shown in Fig. 1. The GenBank accession number is M35520 for canine Rab5a and M28215 for human Rab5a.
Rab5b and Rab5c
Authors: Bucci Cecilia , Liitcke Anne , Dupree Paul , Zerial Marino
Published: November 2023

Rab5b and Rab5c were identified by Chavrier etal. (1992), using a PCR approach to amplify Rab proteins from embryonic day 17 mouse kidney cDNA. The two oligonucleotides used corresponded to the GXXXXGKS/T and to the WDTAGQE conserved regions. Using modified RACE protocols (Frohman et al. 1988; Walker et al. 1992), cDNA clones encoding Rab5b and Rab5c from mouse kidney RNA were identified. Rab5b was also independently cloned from a human endothelial cDNA library (Wilson and Wilson 1992).
Rabll
Authors: Urbe Sylvie , Parton Robert G
Published: November 2023

Rab11 was identified by screening a Madin-Darby canine kidney (MDCK)-cell cDNA library (Chavrier eta/. 1990) using degenerate oligonucleotides corresponding to the sequence WDTAGQE shared by members of the Ypt1/Sec4/Rab subfamily (Valencia et al. 1991). A human homologue termed YL8 (Drivas and Rush 1991) was cloned from two human cDNA libraries by a polymerase chain reaction (PCR)-approach based on oligonucleotide primer pairs specific to the four highly-conserved coding domains of the ras genes. Furthermore, a PCR approach based on oligonucleotides derived from the amino acid sequences of a rat homologue referred to as 24K G has led to the cloning of a homologous gene from a rat liver cDNA library (Sakurada etal. 1991).
Rabl6
Authors: Elferink Lisa A , Schellers Richard H
Published: November 2023

Rab16 was originally identified from a rat brain cDNA library, during a screen for GTPases involved in membrane trafficking and regulated secretion (Elferink et al. 1992). The nucleotide and deduced amino acid sequence of Rab16 is presented in Fig. 1. The GenBank accession number is M83681.
Rabl8
Authors: Lutcke Anne , Zerial Marino
Published: November 2023

Like Rab17 and Rab20, the Rab18 cDNA was isolated from an embryonic day 17 mouse kidney cDNA library using a polymerase chain reaction (PCR) fragment identified by Chavrier et al. (1992) as a probe. As expected from the size of the mRNA on Northern blots (-2.4 kb), the longest clone obtained (∼1.9 kb) was still lacking the first four nucleotides from the 5’-end. As these nucleotides were contained within the partial clone isolated by Chavrier et al. (1992), a full-length clone was constructed by PCR. The nucleotide and deduced amino acid sequences are shown in Fig. 1 and can be obtained from the EMBL/GenBank/DDB under the accession number X80333.
Rab19
Authors: Liitcke Anne , Zerial Marino
Published: November 2023

A 1.1 -kb cDNA clone spanning the region from the 5’-end of the Rabi 9 coding region to the poly A tail was obtained by 3’RACE (Frohman etal. 1988; Walker etal. 1992) based on a PCR fragment identified by Chavrier etal. (1992). The nucleotide and deduced amino acid sequences of Rab19 are shown in Fig. 1 and can be obtained from the EMBL/GenBank/DDB under the accession number X80473. By Northern blot, a corresponding mRNA of ∼1.6 kb could be detected in a subset of mouse tissues (Fig. 2) Lutcke etal. (1995).