bluuebunny/crossref_metadata_2025 huggingface dataset:
Hilbert Spaces, Bases And Frames
Authors: Higgins J R
Published: November 2023

Hilbert spaces of various types provide the natural setting for much of the sampling theory that we shall be studying.The reader is assumed to be familiar with the foundations of Hilbert and Banach spaces. We review here some of the important facts, mostly concerning Hilbert spaces, that will be needed throughout the text. Of particular importance is the rather more specialized topic of bases in Hilbert space. An elementary account can be found in the book by Higgins (1977). A very readable introduction to the theory of bases is in the book by Young (1980); the book of Marti (1969) has a more advanced treatment, while a vastly comprehensive treatment is to be found in the book of Singer (1970).Apart from the last section this chapter is intended as a review only, and almost no proofs are included. However, ample references to the texts mentioned above are given.
Finite Sampling
Authors: Higgins J R
Published: November 2023

In this chapter we consider the reconstruction of functions defined on domains with finite Lebesgue measure, from samples taken at finitely many points of the domain. We take our cue from the fact that finite interpolation problems arose first in the historical order of events as outlined in Chapter 1; but our emphasis from now on is going to be on sampling and reconstruction rather than interpolation.
Contour Integral Methods
Authors: Higgins J R
Published: November 2023

Contour integration has a variety of different uses in sampling theory, and three theorems and their proofs have been selected to iUustrate this classical technique. The first is the famous theorem of Paley and Wiener, one of sampling theory’s cornerstones. In §9.2 we take the first step towards another important principle of the subject, the equivalence of the sampling theorem with other basic theorems. Lastly, Theorem 9.4 has been included because it is a sampling theorem of some generality and variety (although by no means the most general of its kind; it has been extensively generalized by Hinsen (1993), whose methods are much more refined than those given here). Contour integration provides a powerful method for generating the correct form of the series, as a sum of residues, and of demonstrating the convergence in the symmetric partial sum mode.
Multi-Band Sampling
Authors: Higgins J R
Published: November 2023

Furthermore, these intervals are to be separated by gaps which a.re themselves intervals of positive length. It will be recalled from Definition 6.19 that such a function is called multi-band.
Campbell’s Generalized Sampling Theorem
Authors: Higgins J R
Published: November 2023

The main questions we want to ask here are concerned with the extent to which properties of the cardinal series persist in this more general form.
Modelling, Uncertainty And Stable Sampling
Authors: Higgins J R
Published: November 2023

The main goal of this chapter is to reach Landau’s theorem (Theorem 17.9) on the minimum stable sampling rate. Along the way we shall encounter several interesting aspects of signal modelling. The proof of Theorem 17.9, as presented in §17.5, is not fully complete and rests in some parts on heuristic arguments. A completely detailed proof would be too long for inclusion here, but we shall go as far as we can in order to get a feel for this important theorem. The complete proof, in the multi-dimensional case, can be found in Landau (1967b).
Introduction
Authors: Novick Peter
Published: November 2023

This section of the Guidebook will outline the components of the secretory machinery required for vesicular traffic through the Golgi apparatus and to the cell surface. Three approaches have been exploited to identify these components. One approach has been the biochemical reconstitution of vesicular traffic. This enabled the purification of a number of proteins required for transport through the Golgi apparatus1 and, more recently, for the Ca2+ triggered fusion of secretory granules with the plasma membrane. Another approach has been the genetic dissection of vesicular transport in yeast. This approach yielded many different genes whose products are required for transport at different stages of the secretory pathway. A third approach has been the purification of vesicular carriers and isolation of proteins associated with them. This has led to the identification of both peripherally associated coat proteins4, as well as membrane spanning components of the vesicular carriers5. Extensive convergence of these three approaches has begun to emerge.
MNT1
Authors: äusler A H , Robbins P W
Published: November 2023

A membrane-bound mannosyltransferase activity was purified to near homogeneity using an assay involving a,methylmannoside as acceptor and GDP-mannose as the mannose donor1. The activity fractionated with Golgi-like vesicles in sucrose density gradients2, and the product of this reaction has been shown to be exclusively in the a-1,2- linkage3. The purified enzyme activity corresponded to a 41 kDa soluble protein (see below). Internal amino acid sequences were determined and used in the design for primers in polymerase chain reactions with yeast genomic DNA.
Guanosine diphosphatase
Authors: Hirschberg B
Published: November 2023

The nucleotide sequence of the GDPase gene (GenBank accession# L79560) reveals a 1554 bp open reading frame encoding a polypeptide of 518 amino acids4. Three potential N-glycosylation sites are present in the sequence. Hydropathy plots suggest that it is a type II membrane proteins with a hydrophobic stretch of 16 amino acids close to the N-terminus that probably acts as a signal-anchor domain.
SNC1 and SNC2
Authors: Gerst J E
Published: November 2023

SNC1 was isolated as a multicopy suppressor of the CAP null phenotype in yeast possessing an activated allele of RAS26The CAP gene in 5. cerevisiae encodes a 526-residue protein that co-purifies with a RAS-responsive adenylyl cyclase complex and is required for full cellular responsiveness to activated RAS proteins7,8. Deletion analysis of CAP has shown that the CAP protein is bifunctional: 168 amino acids at the N-terminus are required for the penetrance of phenotypes associated with activated RAS (e.g., heatshock sensitivity)8, while 160 amino acids at the (-terminal are required for suppression of growth and morphology defects not associated with the RAS pathway8
ACT1
Authors: Novick P
Published: November 2023

Temperature-sensitive, conditionally lethal act1 mutants were isolated by in vitro mutagenesis and gene replacement78. The act1-1 and act1-2 mutants are slowed, but not blocked in the export of the secreted protein invertase and accumulate 100 nm post-Golgi vesicles4. While the best characterized allele is act1-1, encoding a change of proline to leucine at position 32, many new alleles have been constructed and have not yet been characterized with regard to their effect on protein secretion8.
VPS10
Authors: Marcusson D , Horazdovsky, B , Emr S D
Published: November 2023

vps10 mutant cells grow at wild-type rates1 and exhibit normal vacuolar morphology3A, but exhibit a differential vacuolar protein sorting phenotype. Approximately 95% of the CPY is secreted from the cell as its Golgi modified p2 precursor form while the majority of proteinase A, proteinase B, and alkaline phophatase are matured normally5, presumably reflecting delivery to the vacuole.
VPS17
Authors: öhrcr J K , Emr S D
Published: November 2023

Haploid yeast cells carrying a vps17 gene are viable and do not show a temperature-sensitive growth defect4. However, vps17 null mutants exhibit differential defects in the sorting and processing of several vacuolar hydrolases. Carboxypeptidase Y (CPY) shows the most drastic defect with 90-95% being missorted and secreted as the Golgimodified precursor form (p2CPY). Proteinase A and proteinase B are only 40% missorted in the !wps17 mutant. The remaining 60% of these proteins are matured, indicative of their correct delivery to the vacuole.
VPS28
Authors: öhrer L K , Vida T A , Banta, L M , Emr S D
Published: November 2023

Haploid yeast cells carrying a disrupted vps28 gene are viable and do not show a temperature-sensitive growth defect4 The processing and delivery of CPY to the vacuole, however, is impaired in a vps28 null mutant strain. Approximately 20-30% of newly synthesized CPY is not processed to the mature form and much of this is secreted from the cell4 Interestingly, the Golgi-modified and mature forms of CPY detected in vps28t’l cells have a reduced mobility on SDS-polyacrylamide gels, relative to CPY expressed in wild-type cells. Endoglycosidase H treatment of immunoprecipitated CPY indicates that this reduced mobility is due to a distinct N-linked glycosylation defect that appears to affect all CPY molecules expressed in these mutant cells. The glycosylation defect most likely does not affect core glycosylation of CPY, since the mobility of the ER form of CPY (p1CPY) is not affected4  vps28 cells exhibit vacuole morphology typical of class E vps mutants5 [see VPS27 entry p. 240).
PEP4
Authors: Winther J , Raymond, C , Stevens T H
Published: November 2023

Encodes the 405 amino acid precursor of Pr A. The first 22 residues are typical of an ER signal sequence and include a consensus signal peptidase cleavage site. The following 54 residues constitute the ‘pro’ domain, and the mature Pr A is encoded in the carboxy-terminal 329 amino acids. Mature Pr A shares significant identity (-46% amino acid identity) with the human lysosomal enzyme cathepsin D1.
N-acetylglucosamine-1-phosphodiestcr —α, N-acety lglucosaminidase
Authors: Mullis J G
Published: November 2023

A Lebanese family that is heterozygous for uncovering enzyme has been identified. The cells of affected individuals contain ∼50% of the uncovering enzyme activity found in control individuals resulting in increased secretion of lysosomal enzymes, however, these individuals are clinically normal. Individuals homozygous for uncovering enzyme deficiency have not been identified.
Cation-independent mannose 6- phosphate/insulin-like growth factor-· II receptor
Authors: Canfield W M
Published: November 2023

No human disease has been shown to result from deficiency of the CI-M6P/IGF-II receptor. The CI-M6P/IGF-II receptor gene is imprinted in the mouse embryo being expressed only from the maternal chromosome 17. Embryos that inherit a deletion of the T-associated maternal effect (Tme) locus from their mother die at day 15 of gestation, in contrast inheritance of this locus from the father is benign3 The Tme mutation has been mapped to a deletion on chromosome 17, which includes the structural locus for the CI-M6P/IGF-II receptor4 These results suggest that the Tme mouse may be an animal model of CIM6P/IGF-II receptor deficiency although deletion of an adjacent locus or loci has not been excluded.
Clathrin heavy chain
Authors: Kirchhauscn T
Published: November 2023

The rat clathrin heavy chain is encoded by one gene, and there is no evidence for the existence of pseudogenes. Since the same single mRNA species is present in various tissues, it is believed that within the resolution of the RNA blots, clathrin heavy chain is not alternatively spliced. The sequence of the rat clathrin heavy chain, deduced from cDNA clones, contains 1675 amino acids and has a predicted molecular mass of 191,569 Daltons.
Clathrin light chains, LC:a and LCb
Authors: Plcy U , Parham P
Published: November 2023

LCa and LCb are coded for by separate genes present in single copies. In humans the LCa and LCb genes are located on different chromosomes. LCa genes of different species code for proteins of 213 to 218 amino acids in length, which are found in all tissues except neurons. In neurons differential splicing yields two forms of LCa, a minor neuron-specific form with an insertion of 18 amino acids about 2/3 towards the (-terminus and a major neuron-specific form with an insertion of 30 amino acids at the homologous site. This results in protein sizes of 231-236 amino acids for the minor neuronal form and 243-248 amino acids for the major neuronal form.
SEC2
Authors: Novick P
Published: November 2023

Temperature-sensitive, conditionally lethal sec2 mutants were isolated by a density enrichment protocol1. The sec2 mutants are blocked in the export of cell surface proteins and accumulate 100nm post-Golgi vesicles containing fully glycosylated secretory proteins23. The best characterized sec2 allele is sec2-59 which encodes an opal stop codon at amino acid 3752, truncating the protein at one half its normal length. Another temperature-sensitive allele, sec2-41 also encodes an opal stop codon4.
SEC4
Authors: Novick P
Published: November 2023

Temperature-sensitive, conditionally lethal sec4 mutants were isolated by a density enrichment protocol4 The best characterized sec4 allele is sec4-8. Within 5 min of a shift to the restrictive temperature, sec4-8 cells display a block in the transport of invertase, and accumulate 100 nm secretory vesicles containing fully processed cell surface proteins1A.
The Ras/Raf/ERK pathway
Authors: Marshall Chris
Published: November 2023

The Raf/ERK pathway consists of a serine protein kinase Rafthat phosphorylates and activates a dual-specificity MAPkinase kinase (Mek) that then phosphorylates and activatesthe MAP kinases (ERKs) (see Fig. 1). The MAP kinases(MAPK) form a distinctive class of serine/threonine proteinkinases that are activated by phosphorylation of a threonineand tyrosine residue separated by a single amino acidin kinase subdomain VIII ( Boulton et al. 1991).75
Bud2p
Authors: Park Hay-Oak , Chant John S
Published: November 2023

BUD2 was cloned from a yeast genomic DNA library by complementation of the bud-site selection defect of a bud2 mutant (Park et al. 1993). The BUD2 nucleotide sequence has the GenBank accession number L19162 (Park et al. 1993) and the EMBL database accession number X74130 (Cvrckova and Nasmyth 1993).
Rotund Rac-GAP
Authors: Guichard Annabel , Bergeret Evelyne , Griffin-Shea Ruth
Published: November 2023

The RnRac-GAP coding sequence, originally named pc1.7 and now renamed rnRac-GAP(l), was isolated (Agnel et al. 1989) by screening a cDNA library in Xgt10 prepared from pupae 5-7.5 days after egg laying (Poole etal. 1985) with a genomic fragment from the cloned rn region. Comparison of rnRac-GAP(l) with the corresponding genomic DNA showed the presence of a 482-bp intron at the 5’-end. Sequence and restriction map analysis of the insert of a second cDNA clone, originally named pc1.7d and now renamed rnRac-GAP(2), showed that the two inserts differed only at their 3’-ends.
The Interleukin-5 Receptor
Authors: Tavernier J
Published: November 2023

The nucleotide sequence of the human IL-5Ra cDNA (GenBank accession numbers M75914, M96651, M96652, X61176, X61177, X61178, and X62156) predicts a polypeptide of 420 amino acids (Fig. 1) (Tavernier et al. 1991, 1992; Murata et al. 1992). It is characterized by a 20 residue N-terminal signal peptide, followed by a 322-amino-acidlong extracellular domain, a membrane anchor spanning 20 residues, and a 58-amino-acid-long cytoplasmic tail.
Receptors for Interleukin-6 (IL-6)
Authors: Narazaki M , Kishimoto T
Published: November 2023

The human IL-6 receptor consists of 468 amino acids, including a signal peptide of 19 amino acids, an extracellular region of 339 amino acids, a membrane-spanning region of 28 amino acids, and a cytoplasmic region of 82 amino acids (Yamasaki et al. 1988) (GenBank accession numbers M20566, X12830). The predicted molecular weight of IL-GR is 50000 Da, although the observed molecular weight is 80000 Da due to N-glycosylation. In the amino terminus of the extracellular region, IL-GR has a domain of about 90 amino acids which fulfils the criteria for the constant 2 (C2) set of the immunoglobulin surpergene family.
Monocyte Chemoattractant Protein-1(MCP-1)
Authors: Yoshimura T , Leonard E J
Published: November 2023

MCP-1 was first described as lymphocyte-derived chemotactic factor (LDCF). Other names are tumour cell-derived chemotactic factor (TDCF), glioma-derived monocyte chemotactic factor (GDCF), smooth muscle cell-derived chemotactic factor (SMC-CF), monocyte chemotactic and activating factor (MCAF). The gene of the mouse homologue of MCP-1 was named JE.
Interleukin-13 (IL-13)
Authors: McKenzie A N J , Zurawski G
Published: November 2023

The mouse IL-13 cDNA (GenBank accession number M23504) encodes a protein of 131 amino acids (Brown eta/. 1989). The human IL-13 (hlL-13) cDNA (GenBank accession No L06801) encodes a protein of 132 amino acids (McKenzie et al. 1993a; Minty eta/. 1993). An alternative splicing event results in the inclusion/exclusion of a GLN residue at position 98 (McKenzie et al. 1993b). Cleavage of the leader peptide results in the mature protein starting at SER19 or GLY21 (Minty et al. 1993). The mouse and human cDNAs have 66 per cent sequence identity over the coding region and the proteins are 58 per cent identical (Fig. 1).
Tumour Necrosis Factor-P
Authors: Millet I , Rudd N H
Published: November 2023

Tumor necrosis factor-/] is also known as lymphotoxin, lymphotoxin-a, and cytotoxic factor. TNF/J is closely related and genetically linked to TNFa (Turetskaya et al. 1992) and LT/J (Browning et al. 1993). It has many of the same activities as TNFa. It is also related to CD40 ligand, CD27 ligand, and CD30 ligand. In contrast to the other family members it does not possess a transmembrane leader peptide and it is secreted. However, it can form a heteromeric membrane associated complex with LT/J (Fig. 1). TNF/J binds with high affinity to two different receptors, p55 TNF receptor and p75 TNF receptor.
Oncostatin M (OSM)
Authors: Rose T M , Bruce A G
Published: November 2023

OSM is a secreted glycoprotein monomer with a M, of 28 000 Da (Zarling et al. 1986). Nucleotide sequence analysis of OSM cDNA and genomic clones (human sequence-GenBank accession numbers M27286, M27287, M27288, M26966; Simian sequence-unpublished), determined that OSM was initially expressed as a 252-amino-acid precursor polypeptide (Malik et al. 1989) (Fig.1).
Ciliary Neurotrophic Factor (CNTF)
Authors: Yancopoulos G D
Published: November 2023

Genes or cDNAs encoding CNTF have been cloned from rat (GenBank accession number X17457) (Stockli et al. 1989), rabbit (GenBank accession number M29828} (Lin et al. 1989), and human (GenBank accession numbers 60477-8, 60542, 55889-90) (McDonald et al. 1991; Masiakowski et al. 1991). The rat and human CNTF proteins are 200 amino acids in length, while the rabbit protein is 199 amino acids long; the three proteins share 152 (-76 per cent) identically placed residues which include only a single conserved cysteine (Fig. 1). The rat, rabbit and human CNTF proteins do not contain consensus secretory signal peptides at their amino termini, and CNTF is not secreted but rather found in the cytoplasm of cells, such as astrocytes(Rudge et al. 1992) and schwann cells (Rende et al. 1992; Sendtner et al. 1992a; Friedman et al. 1992), which express CNTF; the mechanism by which CNTF may be released from cells remains unknown.
Erythropoietin Receptor
Authors: Hilton D J , Watowich S S
Published: November 2023

Epo receptors are detectable in binding experiments using 125I-epo. Primary erythroid progenitors in the yolk sac, fetal liver, bone marrow and spleen express small numbers of receptors, as do megakaryocytes (300-1000 per cell) (Youssoufian et al. 1993). Similar numbers of receptors are expressed on a variety of epo-responsive and epounresponsive cell lines. The equilibrium dissociation constant {K0) for the interaction between epo and its receptor is usually reported to be between 400 and 1000 pM (Youssoufian et al. 1993). In some instances, however, cells appear to express receptors with two affinities-a high affinity component with a K0of 100 pM and a second component with a K0of 600 pM. Epo receptors have also been described in some non-haemopoietic tissues, notably the placenta (Youssoufian et al. 1993).
Granulocyte Colony-Stimulating Factor (G-CSF)
Authors: Nagata S
Published: November 2023

The nucleotide sequences of human G-CSF cDNAs (Nagata et al. 1986a; Souza et al. 1986) (GenBank accession numbers X03655 and M13008) predict a protein of 204 amino acids containing a 30-amino-acid leader sequence (Fig. 1). A minor alternatively spliced form of the human G-CSF cDNA coding for 207 amino acids (GenBank accession number X03438) is also known (Nagata et al. 1986b). Mouse G-CSF cDNA (GenBank accession number M13926) codes for a protein of 208 amino acids with a 30-amino-acid leader sequence (Tsuchiya et al. 1986). Human and mouse G-CSFs are 73.6 per cent identical at the amino acid sequence level and fully cross-react both biologically and at receptor-binding level (Nicola et a/. 1985; Fukunaga et al. 1990). There is a significant sequence homology between G-CSF and interleukin-6 (Fig. 2).
The Epidermal Growth Factor (EGF) Family
Authors: Soler C , Carpenter G
Published: November 2023

Based on sequence similarity, mitogenic activity, and capacity to interact with the EGF receptor, there are five distinct mammalian gene products that can be identified as EGF-like molecules (EGF, transforming growth factor-a (TGFa), amphiregulin, heparin-binding EGF (HB-EGF), betacellulin) (Carpenter and Wahl 1990; Massague and Pandiella 1993; Shing et al.
Escherichia coli small heat shock proteins IbpA, IbpB
Authors: Gaestel M , Buchner J
Published: November 2023

The genes encoding IbpA, IbpB (GenBank accession number M94104) are organized in a common operon located at about 83 minutes in the chromosome (Allen etal., 1992; Chuang etal., 1993). The operon is controlled by a ^-dependent promoter. It contains a 110 bp gap between the coding sequences of IbpA, IbpB, a transcription terminator downstream from IbpB.
Mammalian calreticulin
Authors: Craig E A
Published: November 2023

The calreticulin cDNA sequence (GenBank accession numbers M84739, human; X53363, rat; L13462, bovine) predicts a soluble protein of c. 400 amino acids, with an N-terminal signal sequence, C-terminal tetrapeptide KDEL ER retrieval signal (Michalak etal., 1992).
PDI, thioredoxin-related proteins — an overview
Authors: Bardwell J C A
Published: November 2023

Strongly oxidizing catalysts such as DsbA from Escherichia coli tend to act as disulfide donors (Wunderlich, Glockshuber, 1993; Bardwell, 1994), while more reducing enzymes such as thioredoxin tend to remove disulfides from their substrates (Gleason, Holmgren, 1988). Protein disulfide isomerase, an endoplasmic reticulum (ER) protein of intermediate redox potential can catalyse the formation, isomerization, breakage of disulfides in a protein folding reaction (Freedman, 1995).
Mammalian protein disulfide isomerases
Authors: Freedman R B
Published: November 2023

PDI is readily purified from mammalian liver, or from other highly secretory tissues such as pancreas or placenta. [Here, in subsequent paragraphs where no specific citation is given see Freedman, Tuite (1994), Freedman etal., (1994, 1995), Freedman (1995) for pre-1994 references]. Purifications from bovine, rat, human tissues have been reported following basically similar procedures exploiting the enzyme’s abundance, acidic pl, thermostability. A current purification of PDI from bovine liver,, its derivation from earlier procedures, is described elsewhere (Freedman etal., 1995).
Mammalian Erp61
Authors: Marcus N , Green M
Published: November 2023

ERp61 has also been identified as Grp58 (Lee, 1981), HIP- 70 (Mobbs et al., 1990), Q-2 (Srivastava et al., 1991), a thiol protease of 60 kDa (Urade et al., 1992), a 54 kDa carnitine medium/long chain acyltransferase (Murthy, Pande, 1993), a protein covalently associated with a metabolite of halothane (Martin et al., 1991) and, incorrectly, as form I phosphoinositide-specific phospholipase C (Bennett etal., 1988).
Saccharomyces cerevisiae Cpr6
Authors: Chang H -C J , Lindquist S
Published: November 2023

Cpr6 was isolated in a search for proteins that bind to Hsp90 in 5. cerevisiae (Chang and Lindquist, 1994). Nickel-affinity chromatography was employed to isolate histidine-tagged Hsp90 as well as Hsp90-associated proteins (Chang and Lindquist, 1994). Histidine-tagged Hsp90 possessed wild-type function in vivo, and, hence, the associated protein complexes are expected to be functionally relevant. Cpr6, a 45 kDa protein, was one of four proteins identified in this manner (Chang and Lindquist, 1994).
Mammalian cydophilin C
Authors: Trahey M , Weissman I L
Published: November 2023

CypC was originally identified as an IL-1-induced transcript from a murine bone marrow stromal cDNA library (GenBank accession number M74227; Friedman and Weissman, 1991). The human cDNA was subsequently isolated from a kidney cDNA library (GenBank accession number S71018; Schneider et al., 1994). A complex of CypC and the immunosuppressant drug CsA was shown to bind to and inhibit the calcium and calmodulin-regulated serine/threonine phosphatase activity of calcineurin (Friedman and Weissman, 1991; Liu etal., 1991). In T cells, this block of calcineurin activity results in an inhibition of IL-2 transcription which is a key element in the immunosuppressive effect of CsA (Clipstone and Crabtree, 1992; O’Keefe etal., 1992).
Mammalian cydophilin 40 (Cyp40)
Authors: Hoffman K , Handschumacher R E
Published: November 2023

Estrogen receptor binding cyclophilin (ERBC; Ratajczak etal., 1993).

The open reading frame in a human pancreatic islet cell Cyp40 cDNA clone (Kieffer et al., 1993; GenBank acces number L11667) is 1110 nucleotides in length. Alignments of the deduced amino acid sequence reveal two structural domains (Fig. 1). The N-terminal region (amino acid residues 9-185) shares about 60% identity with Cyp18, the cyclophilin prototype, and includes the postulated CsA binding and isomerase activity sites.
Escherichia coli trigger factor
Authors: Moerschell R , Kandror O , Goldberg A L , Fischer G , Rahfeld J -U
Published: November 2023

In Escherichia coli cells trigger factor (TF) is a 42 kDa molecular chaperone which also has peptidyl-prolyl cis-trans isomerase (PPIase) activity that is not inhibited by the immunosuppressants cyclosporin A and FK506. Thus, trigger factor is not an immunophilin. Its protein sequence shares only 18.2 and 28.3% overall identity with the conserved region of the amino acid sequences of cyclophilins and FKBPs, respectively. However, the enzymatic properties of trigger factor resemble those of the FKBPs. Trigger factor is found in E. coli as a free protein, in association with the 50S ribosome or in complexes with the molecular chaperone, GroEL. It was first discovered by its ability to bind to secreted proteins and facilitate their translocation into isolated membrane vesicles. When associated with GroEL, trigger factor can stimulate GroEL binding to many unfolded proteins in vitro. Formation of the TF-GroEL-substrate complex is also the rate-limiting step in the degradation of certain polypeptide substrates. In the ribosome, trigger factor is bound to nascent polypeptide chains. The relationship between the cochaperone function and PPIase activity is unclear at present.
Mammalian FKBP52
Authors: Toft D O , Faber L E
Published: November 2023

FKBP59 (Tai et al., 1992), FKBP51 (Wiederrecht et al., 1992), Hsp56 (Sanchez, 1990), p59 (Tai etal., 1986), p50 (Smith et al., 1993), HBI (HSP-binding immunophilin) (Chambraud etal., 1993).

Nucleotide sequences encoding FKBP52 proteins from the rabbit (Lebeau et al., 1992; GenBank accession number M84474) and the human (Peattie et al., 1992; M88279) reveal an acidic protein of 459 amino acid residues with a molecular weight of 51 810 Da (human). A domain with homology to FKBP12 exists at the N-terminus.
Escherichia coli SurA
Authors: Gross C , Connolly L , Rouviere P
Published: November 2023

SurA is a periplasmic protein with two tandem domains that exhibit similarity to the entire sequence of parvulin, the founding member of a family of peptidyl-prolyl isomerases (PPIases) . Purified SurA has low peptidyl-prolyl isomerase activity with synthetic substrates. Cells lacking SurA are defective in assembly and production of some outer membrane porins.

SurA was originally identified in a search for Escherichia coli genes essential for survival in stationary phase. A Tn10 insertion in surA leads to a pronounced loss in the viability of stationary phase cells; hence the name surA (Tormo et al., 1990).
Saccharomyces cerevisiae Sti1
Authors: Johnson J L
Published: November 2023

STI1 was isolated as a transactivator of the promoter of SSA4, one of the cytosolic hsp70 genes in Saccharomyces cerevisiae. STI1 mRNA levels increase approximately tenfold upon heat induction. Cells carrying a disruption of the STU gene grow like wild-type cells at 30°C, but show impaired growth at higher and lower temperatures (Nicolet and Craig, 1989).
Proteinase A and its propeptide
Authors: Hazel J R Winther H B van den
Published: November 2023

ProPrA is encoded by the PEP4 gene in Saccharomyces cerevisiae with a 22 residue signal peptide, a 54 residue propeptide and an enzyme part of 329 residues (Ammerer et al., 1986; Woolford et al., 1986; GenBank accession numbers M13358 and M13632). The signal sequence fulfils the conventional requirements (hydrophobicity, etc.) for directing the protein across the endoplasmic reticulum membrane, and the mature part of the protein is very similar to that of other aspartic proteases (e.g. 46% sequence identity to human cathepsin D). The propeptide, however, is not homologous to those of even closely related aspartic proteases (Ammerer et al., 1986; Jarai et al., 1995). PrA is modified with N-linked glycosylation at two positions in the enzyme part. Of these, one site is not always used, frequently giving rise to doublet bands on SDS-PAGE (Pedersen and Biedermann, 1993; Sorensen etal., 1994).
Signalling of the unfolded protein response from the endoplasmic reticulum to the nucleus
Authors: McNees C , Gething M -J
Published: November 2023

In eukaryotic cells, the accumulation of misfolded polypeptides in the ER lumen results in the transcriptional up-regulation of many of the genes that encode ER-resident chaperones and folding catalysts. This cellular response is called the ‘unfolded protein response’ (UPR). The transduction of the UPR signal to its final destination in the nucleus must proceed through a number of obligatory stages, when it is considered that even though their membrane surfaces are contiguous, the ER and the nucleus are distinct membrane bounded organelles. These stages include: the detection of the presence of unfolded proteins in the ER lumen, the transduction of this signal across the ER membrane, the transmission of this signal to the transcriptional machinery in the nucleus, and finally the activation of transcription of genes encoding UPR-regulated ER-resident proteins. In recent years a number of the components of the UPR signalling pathway in yeast have been identified and promoter elements involved in the transcriptional control of UPR-regulated genes have been defined in both yeast and mammalian cells.
Thermosome
Authors: Waldmann T , Lupas A , Baumeister W
Published: November 2023

TF55/TF56 (thermophilic factor of 55 kDa) (Trent et al., 1991; GenBank accession number L34691). Archaebacterial, eukaryotic cytosolic chaperonins have been termed ‘group II chaperonins’ (Kubota etal., 1995).
Escherichia coli CIpA
Authors: Gottesman S , Wickner S , Maurizi M R
Published: November 2023

The dpA nucleotide sequence from E. coli (GenBank accession number M31045) predicts a protein of 758 amino acids, containing sequences that are highly conserved between CIpA, CIpB,, other HSP100 family members (Gottesman et al., 1990b, 1996; Squires, Squires, 1992; see also the overview of HSP100/Clp proteins, p. 231). The first highly conserved domain (amino acids 183-415) contains an ATP-binding site consensus; the second highly conserved domain (amino acids 421-608) contains a second consensus ATP-binding site motif (Gottesman etal., 1990b, 1996).
Escherichia coli CIpB
Authors: Squires C L , Squires C
Published: November 2023

ClpB93 has also been called F84.1, E89 (VanBogelen etal., 1992; Fuge, Farr, 1993). ClpB79 has been called E72, F68.5,, ClpBz(Squires etal., 1991). The Escherichia coli CIpB heat shock protein (NCBI sequence identification number 147365) (Kitagawa etal., 1991; Squires et al., 1991) is a member of a recently discovered family (Gottesman et al., 1990; Squires, Squires, 1992), which has been referred to as the HSP100 family (Parsell et al., 1994). E. coli CIpB, other members of this family share two distinct ATP-binding regions (each about c. 200 amino acids in length) that possess very high sequence similarity.
Synechococcus sp. PCC 7942 CIpB
Authors: Clarke A K , Eriksson M -J
Published: November 2023

Two clpB genes exist in the unicellular cyanobacterium Synechococcus sp. PCC 7942. The first, clpB1 (GenBank accession number U20646), consists of an uninterrupted 2649 bp open reading frame coding for a polypeptide of 883 amino acids (92 kDa). The second gene, clpB2 (Genbank accession number U97124), is 2685 bp, codes for a predicted protein of 94 kDa.
Ammodytoxins (Vipera ammodytes ammodytes)
Authors: Gubenšek F , Križaj I
Published: November 2023

Ammodytoxins (atx) A, B, and C (PIR accession numbers A00768, A25806, and 506853) and ammodytin (atn) L (PIR, S19570) are group II secretory phospholipases A2 (PLA2), having 122 amino acids and molecular weights around 13 800 Da. The protein (Ritonja and Gubensek 1985; Ritonja et al. 1986; Križaj et al. 1989) and cDNA sequences (Pungercar et al. 1991) of atx A, B, and C (EMBL accession numbers: X53471, X52241, and X15138) exhibit over 97 and 99 per cent indentity, respectively. Atn L (EMBL accession number: X53036) being less similar to atx A, exhibits only 74 per cent identity on the protein and 90 per cent identity on the DNA level (Krizaj et al. 1991; Pungercar et al. 1991). It is enzymatically inactive since Asp 49, essential for binding of Ca2+, is substituted by Ser.
Introduction
Authors: Chiamulera C , Ferraguti F
Published: November 2023

AMPA-kainate receptors generally conduct monovalent cations, however, glutamate in certain neuronal cells can trigger the activation of Ca2+-permeable AMPA-kainate receptors. The different ionic selectivity depends on the combination of different subunits, and in particular on the presence of the GluR2 subunit. This subunit contains an arginine residue within the second transmembrane segment, whereas the other three subunits carry a glutamine residue at the corresponding position. This difference confers a very weak Ca2+ permeability thus determining the channel conductance and Ca2+ permeation (Verdoorn et al. 1991).
Conantokins (Conus spp.)
Authors: Olivera B M , Steel D J
Published: November 2023

The conantokins are peptides from the venom of fishhunting cone snails which interact with and inhibit the N-methyl-D-aspartate (NMDA) receptor, a subset of the glutamate receptor family (Olivera et al. 1990). Two conantokins have been described (Table 1), conantokin-G from Conus geographus venom (Rivier et al. 1987) and conantokin-T from Conus tulipa venom (Haack et al. 1990).
Applications and Extensions of Malecot’s Work in Human Genetics
Authors: Morton Newton E
Published: November 2023

Malecot profoundly influenced population genetics in the generation of Cockerham, Sved, Falconer, Kimura, Crow, and Nagylaki. His influence on human genetics was especially great in population structure, forensic use of DNA, and linkage disequilibrium. These contributions are described, together with recent developments that use his probabilistic approach.
Recent Applications of Diffusion Theory to Population Genetics
Authors: Stephan Wolfgang , Kim Yuseob
Published: November 2023

Since the 1930s, diffusion theory has been used to find approximate mathematical solutions for a number of population genetic problems. The work of Wright, Malecot, and Kimura laid the foundation of theoretical population genetics. In this chapter, three examples are discussed that show how the theory of diffusion approximations has been expanded in the past decade by applying it to problems in molecular population genetics. These examples are typically multi allele or multi-locus models, for which approximate solutions can only be found if the underlying processes occur on different time scales such that dimensionality can be reduced. We focus on Muller’s ratchet, an infinite-allele model, and two 2-locus models: (i) the background selection model; and (ii) the model of genetic hitch-hiking.
The Travelling World
Authors: Higgins Peter M
Published: November 2023

Dusk is the time when we are reminded that our world is adrift in space. As the sun sets, the brightest stars appear as faint and distant points of light piercing the twilight sky. As darkness settles the stars brighten, mysteriously they seem to draw nearer and, especially if the night sky is clear and without the moon, we are left standing beneath a heavenly sphere glowing with thousands of stars, gloriously bright. Away from city lights it is the most sublime sight in nature and in witnessing it we can understand why peoples the world over have imagined the night sky as the home of the gods.

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The Human Geography of Europe: A Prehistoric Perspective
Authors: Sherratt A
Published: November 2023

The cartographic images that confront us on the pages of a modem atlas give the Earth’s surface an impression of permanence; but it is a deceptive one. It is not just the brightly coloured political maps whose boundaries periodically change, but also the more subtly toned and naturally coloured maps of the physical landscape which alter over time. Between the last two editions of the Oxford Atlas, for instance, the Caspian Sea has altered its outline, and the .Aral Sea all but disappeared—the latter under human influence, to irrigate the cotton crops of Kazakhstan. Maps of settlement-distributions and popufation density require constant updating; but so, too, should ‘natural’ vegetation and coastlines, and on a longer timescale even the reassuring averages of precipitation and annual temperature. Every map represents only a sample snapshot, extracted from patterns which are continuously changing, each at its own characteristic ( though variable) rate. A historical geography is therefore an account of processes operating over a defined timescale, themselves encompassing briefer, event-like changes, and all set within longer and (on a human timescale) barely perceptible alterations which set the stage but do not interact in the way that human and natural processes have int1uenced each other over the last ten thousand years. To place these later phenomena in perspective, it is instructive to begin with the deep-seated rhythms of the Earth itself.
Geographical Knowledge and the Expansion of the European World after 1490
Authors: Butlin R A
Published: November 2023

The historical geography of Emope has never been self-contained: in prehistoric times and for most of its history it has had links with Asia, and North and South America, and in later periods with the more distant lands of Australasia and the remoter Arctic and Antarctic wastes. The processes whereby these links were initiated and modified were exceedingly complex, comprising kaleidoscopic mixe of cultures, racial attitudes, geographical knowledge and broader belief systems or cosmographies, geopolitical ambitions and failures, scientific understandings through experiment and ambition, and changing processes of resource evaluation and realization.
The Changing Political Map: Geography, Geopolitics, and the Idea of Europe since 1500*
Authors: Heffernan M
Published: November 2023

The political geography of Europe has been in a constant state of flux over the past 500 years. The continent’s borders and frontiers have changed so frequently that a substantial (and probably rather tedious) volume would be required to provide even a crude outline of the major events. Conceptually, such a project would be extremely challenging, for the idea of ‘Europe’ and the broader notion of ‘political space’ are not universal, transcendent concepts; rather, they are complex ideas whose meanings have changed enormously over the past half-millennium. The assumption that the political map of Europe in 1500 can be regarded simply as a different version of the comparable map today is thus ilieoretically and historically absurd.
Rural Europe since 1500: Areas of Innovation and Change*
Authors: Clout H
Published: November 2023

As in earlier times, Europe remained an emphatically rural continent in the age of the great discoveries. Human life was threatened by pestilence, war, and famine, hence the key imperative was to produce enough food for its population to survive. This meant ensuring a supply of grain for daily bread, since meat was a luxury for all except the urban elite (Braudel, 1981: 104). Agricultural systems varied according to physical circumstances, social organization, local traditions, and access to urban markets and trade routes. Despite important regional differences, cereal yields were low, with seed: yield averages for both wheat and rye standing at 1:4, and four-fifths of the workforce was involved, to a greater or lesser degree, in food production (Pounds, 1990: 225). Much of the landscape would have appeared relatively untamed to our eyes, with stretches of waste or forest surrounding cultivated areas (Darby, 1957: 20). More land was worked when population pressures increased, but the margin of cultivation retreated, and settlements declined or were abandoned when population numbers declined. As a result, the cultivated area had expanded between 1100 and 1300, then retreated until the sixteenth century when moors, marshes, heaths, and woods were reclaimed, only to contract in the seventeenth century, and be replaced by expansion from 1750 to 1850 (Grigg, 1980: 32). Towards the end of the nineteenth century the amount of cultivated land declined again, largely because cereals from the New World could be imported more easily than ever before. Such pulsations in land use were rein-forced by price fluctuations, with reclamation taking place especially when cereal prices were high, as during the sixteenth century and from 1750 to 1850 (Slicher van Bath, 1963: 199).
Changing Patterns of Trade a Interaction since 1500
Authors: Walton J R
Published: November 2023

In 1500 European trade was about to undergo a sea-change, both literally and metaphorically. Between 1460, ‘when the death of Prince Henry closed a chapter in Portugal’s tentative exploration of the West African coast, and Magellan’s achievement of the first global circumnavigation during the years 1519—22, European seafarers discovered the existence of continuous sea passages from ocean to ocean around the world, that ‘all the seas of the world are one’ (Parry, 1981; Boorstin, 1983; Living-stone, 1992). The discovery of the sea, largely by Iberians or by Iberian-sponsored expeditions, over such a short period of time is a measure of the extent of Europe’s existing level of development. Financial and business institutions, shipbuilding and military technology, and navigation science had already progressed, within a European frame of reference, to the point where they were capable of supporting European adventures overseas (Cipolla, 1965; Parker, 1988). The major lure was the prospect of profit from trade. Unlike E’xplorers of the late nineteenth and early twentieth Europeans of the age of reconnaisance did not seek unknown lands, but new and more profitable sea routes to known markets and known sources of tradable commodities.
Towards an Environmental History of Europe
Authors: Simmons G
Published: November 2023

To attempt an account of the last 10,000 years of the history of the European environment from Scandinavia to the Mediterranean and from the Dingle peninsula to the Urals, some broad generalizations of both time and space must be made. For the former, time with be divided according to the pre-dominant human economies which have occupied the European space and which are set out in Table 16.1. Each phase has left some traces of its existence in today’s landscapes but only in pockets are there functioning examples. For example, remnants of non-agricultural economies persisted until very recently in reindeer-herding cultures such as the Saami. In the case of solar-based agriculture, a fewpockets exist in the poorer parts of Europe, but all have to some extent been affected by access to industriai products and knowledge.
Inequality
Authors: Kingston Paul W , Holian Laura M
Published: November 2023

Matters of inequality go to the very heart of the argument for American exceptionalism. In much American public lore and some scholarly arguments America is above all the land of equality. Tocqueville, early on, famously noted the spirit of equality that permeated American life. Since then, stories of rags to riches have been commonly invoked, emblematic of the belief that in America social origins have little impact on economic achievements—and that the impact of individual talent and hard work is decisive. Even if the disparities between the successful and unsuccessful can be stark, this is often viewed as the price to be paid for having a dynamic system that generates great aggregate wealth and wide opportunities for individual success. This egalitarianism presumably flowed from America’s origins as the ‘first new nation’, unshackled by the weight of a feudal past with rigid hierarchies and social distinctions (Lipset 1979a).
Politics and Institutional Architectures
Authors: Martinelli Alberto
Published: November 2023

There are several studies comparing the political system of the United States with one or more nation-states of Europe which show significant diﬀerences both between the countries on the two sides of the Atlantic and great interstate diversity within Europe. These include diﬀerent types of electoral systems (majority vs. pro-portional), diﬀerent rates of voting behavior and political participation, diﬀerent forms of organized interests representation and pressure politics, diﬀerent party systems and diﬀerent party ideologies and organizational structures, diﬀerent institutional architectures in the form of the state (centralized vs. federal) and in the mechanisms of democratic accountability (parliamentary, semi-presidential, and presidential), diﬀerences in policymaking and policy implementation, diﬀerences in the structure and function of the judiciary, and diﬀerences in the role of the media.
Value change
Authors: Forse Michel , Parodi Maxime
Published: November 2023

Shared values are part of what is needed to make up a society. Constituting a society certainly implies the establishment of collective institutions and norms but they would have little political, social, or moral legitimacy if they were not based on shared values. To take this into account, it is necessary to focus on the actors and their reasons; for example it is clear that there is no democracy in a country with no democrats. If we examine the social foundations of Europe in this way while allowing that it is not a society like, say, the United States, we can ask ourselves if Europe actually amounts to a society, or is at least on its way to becoming one.
Cities
Authors: Galès Patrick Le , Zagrodzki Mathieu
Published: November 2023

From the integrated medieval European cities surrounded by walls, to the colonial Boston or the rapidly growing Phoenix, Las Vegas, or South East London, the category ‘city’ comprises diﬀerent densities, borders, and dimensions; for instance: the material city of walls, squares, houses, roads, lights, utilities, buildings, waste, and physical infrastructure; the cultural city in terms of imagination, diﬀerence, representations, ideas, symbols, art, texts, senses, religion, and aesthetics; the politics and policies of the city in terms of domination, power, government, mobilization, welfare, and education; the social city of riots, ethnic, economic, or gender inequalities, everyday life and social movements; the economy of the city: division of labor, scale, production, consumption, trade Urban areas are robust beasts.