bluuebunny/crossref_metadata_2025_split huggingface dataset:
Instability
Authors: Acheson D J 
Published: November 2023

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

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

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

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

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

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

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

Abstract
The first alleles of secY were isolated as suppressors of signal sequence mutations and are designated prlA alleles4. Starting with a strain that was dextrin negative due to a mutation in the signal sequence of LamB (maltoporin), these suppressors were identified following selection for the ability to use dextrin as a carbon source.
ERN1
Authors: Mori K , Gething, M J , Sambrook J 
Published: November 2023

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Abstract
RhoG was isolated from a differential screening of a hamster lung fibroblast cDNA library, using probes derived from resting or growth-stimulated cells (Vincent et al. 1992,1993). The human homologous full-length cDNA was isolated from a HeLa cDNA library. Genbank accession numbers for human and hamster sequences are X61587 and X61588, respectively.