bluuebunny/crossref_metadata_2025 huggingface dataset:
Large palindromes in the lambda phage genome are preserved in a rec+ host by inhibiting lambda DNA replication.
Authors: Shurvinton C E , Stahl M M , Stahl F W
Published: May 2006

A large palindrome carried by phage lambda has been shown to prevent growth of the phage on a rec+ strain of Escherichia coli. The phage do form plaques on recBC sbcB strains, but the palindrome is not stable--deletions that either destroy the palindrome or diminish its size overgrow the original engineered palindrome-containing phage. We have prepared stocks of lambda carrying a palindrome that is 2 X 4200 base pairs long. These phage stocks are produced by induction of a lysogen in which the two halves of the palindrome are stored at opposite ends of the prophage and are of sufficient titer (10(9) phage per ml) to enable one-step growth experiments with replication-blocked phage. We find that the large palindrome as well as a lesser palindrome of 2 X 265 base pairs are recovered intact among particles carrying unreplicated chromosomes following such an infection of a rec+ host. We propose that DNA replication drives the extrusion of palindromic sequences in vivo, forming secondary structures that are substrates for the recBC and sbcB gene products.
Identification of a peptide binding protein that plays a role in antigen presentation.
Authors: Lakey E K , Margoliash E , Pierce S K
Published: May 2006

The helper T-cell response to globular proteins appears, in general, to require intracellular processing of the antigen, such that a peptide fragment containing the T-cell antigenic determinant is released and transported to and held on the surface of an Ia-expressing, antigen-presenting cell. However, the molecular details underlying these phenomena are largely unknown. The means by which antigenic peptides are anchored on the antigen-presenting cell surface was investigated. A cell surface protein is identified that was isolated by its ability to bind to a 24-amino acid peptide fragment of pigeon cytochrome c, residues 81-104, containing the major antigenic determinant for B10.A mouse T cells. This peptide binding protein, purified from [35S]methionine-labeled cells, appears as two discrete bands of approximately equal to 72 and 74 kDa after NaDodSO4/PAGE. The protein can be eluted from the peptide affinity column with equivalent concentrations of either the antigenic pigeon cytochrome c peptide or the corresponding nonantigenic peptide of mouse cytochrome c. However, it does not bind to the native cytochromes c, either of pigeon or mouse, and thus the protein appears to recognize some structure available only in the free peptides. This protein plays a role in antigen presentation as evidenced by the ability of rabbit antibodies raised against it to block the activation of an antigen-specific T-cell hybrid by antigen-presenting cells and pigeon cytochrome c. Its expression is not major histocompatibility complex-restricted in that the blocking activity of the antisera can be absorbed on spleen cells from mice of different haplotypes. This peptide binding protein can be isolated from a variety of cell types, including B cells, T cells, and fibroblasts. The anchoring of processed peptides on the cell surface by such a protein may play a role in antigen presentation--facilitating the interaction of antigenic peptides with Ia and/or the T-cell receptor.
The gene encoding the epsilon subunit of the T3/T-cell receptor complex maps to chromosome 11 in humans and to chromosome 9 in mice.
Authors: Gold D P , van Dongen J J , Morton C C , Bruns G A , van den Elsen P , Geurts van Kessel A H , Terhorst C
Published: May 2006

The T3 complex is composed of three polypeptide chains that are both structurally and functionally associated with the receptor for antigen on the surface of human T lymphocytes. In a series of experiments utilizing both somatic cell hybrids and chromosomal hybridization in situ, the genes encoding two members of the human T3 complex, T3-delta and T3-epsilon, were found to reside on the long arm of chromosome 11 in band q23. The murine T3-epsilon gene was localized to chromosome 9. The location of the T3-delta and T3-epsilon genes with respect to the Hu-ets-1 gene, which is also located in 11q23, is discussed. Recent assignments of several genes, preferentially expressed in human cells of hematopoietic and neuroectodermal origins, to band q23 of human chromosome 11 and the murine equivalents to murine chromosome 9 may define a conserved gene cluster important in cell proliferation and differentiation.
The terminus region of the Escherichia coli chromosome contains two separate loci that exhibit polar inhibition of replication.
Authors: Hill T M , Henson J M , Kuempel P L
Published: May 2006

The terminus region of the chromosome of Escherichia coli contains two separate sites, called T1 and T2, that inhibit replication forks. T1 is located near 28.5 min, which is adjacent to trp, and T2 is located at 34.5-35.7 min on the opposite side of the terminus region, near manA. The sites act in a polar fashion, and replication forks traveling in a clockwise direction with respect to the genetic map are not inhibited as they pass through T1 but are inhibited at T2. Similarly, counterclockwise forks are not inhibited at T2 but are inhibited at T1. Consequently, forks are not inhibited until they have passed through the terminus region and are about to leave it. Studies with deletion strains have located T2 within a 58-kilobase interval, which corresponds to kilobase coordinates 387-445 on the physical map of the terminus region.
Neurons segregate clusters of membrane-bound acetylcholinesterase along their neurites.
Authors: Rotundo R L , Carbonetto S T
Published: May 2006

Immunocytochemical studies with a monoclonal antibody show that acetylcholinesterase (AcChoEase; EC 3.1.1.7) is distributed in clusters along the fibers of cultured sympathetic neurons but is essentially absent from cell bodies. Although tissue-cultured sympathetic neurons synthesize several oligomeric forms of AcChoEase, only the hydrophobic globular (G4) form of AcChoEase is present within these clusters. This G4 form is asymmetrically distributed within neurons and is transported preferentially into nerve fibers following its synthesis in the cell bodies. Thus G4 is found in clusters on neurons and is readily distinguishable from the hydrophilic forms on the surfaces of myotubes. The association of a specialized form of AcChoEase in densities on neurons in culture indicates that neurons and myotubes have distinct mechanisms for localizing AcChoEase molecules on their surfaces and suggests that these two types of electrically excitable cells have different requirements for organizing synaptic components on their plasma membranes.
Cerebellar GABAergic processes: evidence for critical involvement in a form of simple associative learning in the rabbit.
Authors: Mamounas L A , Thompson R F , Madden J
Published: May 2006

Converging evidence from electrophysiological recording and lesion studies suggests an essential role for the cerebellum in classical conditioning of the nictitating membrane response in the rabbit. The present study begins to delineate within this structure neurotransmitter systems that appear critical for the expression of this form of simple associative learning. Experiments reported here demonstrate that microinfusion of gamma-aminobutyric acid (GABA) antagonists (either bicuculline methiodide or picrotoxin) into specific areas of the medial dentate/lateral interpositus nuclei or into the cerebellar cortex of lobule HVI can selectively and reversibly abolish conditioned responding, while leaving the unconditioned reflex response intact. The results are consistent with the suggestion that GABAergic synapses play an essential role in the circuitry that mediates the conditioned response.
Occurrence in Saccharomyces cerevisiae of a gene homologous to the cDNA coding for the alpha subunit of mammalian G proteins.
Authors: Nakafuku M , Itoh H , Nakamura S , Kaziro Y
Published: May 2006

From cross-hybridization studies with cDNAs that code for the alpha subunits of rat brain guanine nucleotide-binding regulatory (G) proteins, we have isolated a gene from yeast Saccharomyces cerevisiae encoding an amino acid sequence that is highly homologous to the alpha subunit of the G protein that mediates inhibition of adenylate cyclase (Gi alpha) from rat brain. The gene, tentatively designated as GPA1, contains a contiguous, single open reading frame of 1416 nucleotides that codes for a protein of 472 amino acids with a calculated Mr of 54,075. The predicted amino acid sequence of the protein encoded by the GPA1 gene (tentatively designated as G protein 1 alpha or GP1 alpha) is remarkably homologous to the amino acid sequence of rat brain Gi alpha and the alpha subunit of the G protein of unknown function (Go alpha); the primary structure of the sites for GTP hydrolysis as well as GTP interaction are nearly identical. The main difference in the molecular sizes of yeast GP1 alpha (472 amino acids) and rat brain Gi alpha (355 amino acids) is due to the presence of a stretch of 110 extra amino acid residues in yeast GP1 alpha, which are inserted near the NH2-terminal one-third of mammalian Gi alpha. From blot-hybridization analysis, the size of the GP1 alpha mRNA was estimated as 1.7 kilobases.
Geometry of the antitumor drug ditercalinium bisintercalated into d(CpGpCpG)2 by 1H NMR.
Authors: Delbarre A , Delepierre M , Garbay C , Igolen J , Le Pecq J B , Roques B P
Published: May 2006

Rigid 7H-pyrido[4,3-c]carbazole dimers, such as Ditercalinium, are DNA bisintercalators that display high DNA affinity and strong antitumor properties. This activity appears crucially dependent on the geometry of their complexes with DNA. Therefore, structures of the complexes formed by the self-complementary tetranucleotide d(CpGpCpG) with Ditercalinium and with a related monomer were investigated in 0.1 M [2H]acetate buffer (pH 5.5) by using 400-MHz 1H NMR. In both cases, d(CpGpCpG) retained a right-handed duplex structure as shown by exchangeable-proton analysis and intramolecular nuclear Overhauser effect measurements. According to the large upfield shifts measured on the base protons (including the imino proton) and on the aromatic protons of the pyridocarbazole rings, the monomer appears to monointercalate and the dimer to bisintercalate into the tetranucleotide duplex. Ditercalinium dissociates from its complex about 100-1000 times slower than does the monomer. The negative intermolecular nuclear Overhauser effects observed on protons corresponding to the convex edge of the pyridocarbazole rings when the sugar protons are saturated suggest that both ligands intercalate with their chain oriented to the wide groove side of the helix, a situation mimicking that encountered with repressors. Antitumor activity of 7H-pyridocarbazole derivatives is discussed in terms of geometry of the intercalated complexes.
Functional analysis of a palindromic sequence required for normal replication of several staphylococcal plasmids.
Authors: Gruss A D , Ross H F , Novick R P
Published: May 2006

Most small multicopy antibiotic-resistance plasmids of Staphylococcus aureus contain a major axis of hyphenated dyad symmetry (palA) that is required for normal replication and stability, although located outside of the minimal replicon. Rearrangements affecting palA cause plasmid instability, a marked reduction in copy number, and the accumulation of large quantities of strand-specific circular single-stranded plasmid DNA. In view of the recent observation that pT181 initiates replication by a nick and 3'-extension mechanism (S. Khan, personal communication), it is suggested that these plasmids replicate by an asymmetric rolling-circle mechanism in which the displaced plus strand remains single stranded until palA is exposed, forming a hairpin that serves as the lagging strand origin.
Unusual conformational effect exerted by Z-DNA upon its neighboring sequences.
Authors: Kohwi-Shigematsu T , Manes T , Kohwi Y
Published: May 2006

Supercoiled plasmid DNA harboring an insert of (dG-dC)16, a sequence known to form Z-DNA upon negative supercoiling, was reacted with chloroacetaldehyde. Chloroacetaldehyde, like bromoacetaldehyde, was found to be a specific probe for detecting unpaired DNA bases in supercoiled plasmid DNA. Under torsional stress (at bacterial superhelical density), chloroacetaldehyde reacted at multiple discrete regions within the neighboring sequences of the (dG-dC)16 insert. When the plasmid population was considered as a whole, the distribution of the chemically reactive bases exhibited a pattern of inversion symmetry with the center of inversion in the middle of the (dG-dC)16 insert. However, when a single supercoiled plasmid molecule was considered, chloroacetaldehyde reacted with only one of the neighboring sequences, either 5' or 3' of the (dG-dC)16 insert, but not with both. The possibility that the supercoiled plasmid DNA is in equilibrium with these two structural forms is discussed.
Porphyrins are endogenous ligands for the mitochondrial (peripheral-type) benzodiazepine receptor.
Authors: Verma A , Nye J S , Snyder S H
Published: May 2006

"Peripheral-type" benzodiazepine receptors are localized to the outer mitochondrial membrane. We have identified potent competitive inhibitors of these receptors and purified them from human blood and from several rat organs. TLC analysis of the purified inhibitor from erythrocytes displays a single peak of inhibitory activity with an absorbance spectrum identical to hemin. All of the inhibitory activity in extracts of several tissues can be accounted for by their porphyrin and metalloporphyrin content. Pure hemin and protoporphyrin IX competitively inhibit mitochondrial benzodiazepine binding with Ki values of 41 and 15 nM, respectively, and are less active by a factor of 1000 at central-type benzodiazepine receptors. Thus, porphyrins appear to be endogenous ligands for mitochondrial benzodiazepine receptors.
An enhancer responsible for activating transcription at the midblastula transition in Xenopus development.
Authors: Krieg P A , Melton D A
Published: May 2006

Transcripts from the Xenopus gene GS17 are absent from oocytes and first appear at the midblastula transition (MBT), about 8 hr after fertilization. Injection experiments with deletions of the GS17 gene and GS17-beta-globin hybrid genes show that a relatively short sequence of 74 base pairs is sufficient to activate, in cis, transcription at the MBT. This 74-base sequence is located about 700 bases upstream of the GS17 promoter and has the properties of an enhancer element.
Analysis of a cDNA clone expressing a human autoimmune antigen: full-length sequence of the U2 small nuclear RNA-associated B" antigen.
Authors: Habets W J , Sillekens P T , Hoet M H , Schalken J A , Roebroek A J , Leunissen J A , van de Ven W J , van Venrooij W J
Published: May 2006

A U2 small nuclear RNA-associated protein, designated B'', was recently identified as the target antigen for autoimmune sera from certain patients with systemic lupus erythematosus and other rheumatic diseases. Such antibodies enabled us to isolate cDNA clone lambda HB''-1 from a phage lambda gt11 expression library. This clone appeared to code for the B'' protein as established by in vitro translation of hybrid-selected mRNA. The identity of clone lambda HB''-1 was further confirmed by partial peptide mapping and analysis of the reactivity of the recombinant antigen with monospecific and monoclonal antibodies. Analysis of the nucleotide sequence of the 1015-base-pair cDNA insert of clone lambda HB''-1 revealed a large open reading frame of 800 nucleotides containing the coding sequence for a polypeptide of 25,457 daltons. In vitro transcription of the lambda HB''-1 cDNA insert and subsequent translation resulted in a protein product with the molecular size of the B'' protein. These data demonstrate that clone lambda HB''-1 contains the complete coding sequence of this antigen. The deduced polypeptide sequence contains three very hydrophilic regions that might constitute RNA binding sites and/or antigenic determinants. These findings might have implications both for the understanding of the pathogenesis of rheumatic diseases as well as for the elucidation of the biological function of autoimmune antigens.
The first external domain of the nonobese diabetic mouse class II I-A beta chain is unique.
Authors: Acha-Orbea H , McDevitt H O
Published: May 2006

The nonobese diabetic mouse is recognized as an important animal model for human insulin-dependent diabetes mellitus. One of the components of susceptibility to this disease has been mapped to the major histocompatibility complex. In this study, full-length cDNA clones encoding the I-A alpha and beta chains from the nonobese diabetic mouse have been isolated and sequenced. They are identical to the sequences previously determined from the H-2d haplotype except for the sequence encoding the first external domain, the leader peptide, and the 5' untranslated region of the I-A beta chain molecule. Most strikingly, there are five consecutive nucleotide substitutions which lead to two radical amino acid changes in a region that is conserved between human and mouse. We suggest that the unique structure of the first external I-A beta chain domain is a major determinant in the disease susceptibility that maps to the major histocompatibility complex of the nonobese diabetic mouse.
IgA antibody-producing cells in peripheral blood after antigen ingestion: evidence for a common mucosal immune system in humans.
Authors: Czerkinsky C , Prince S J , Michalek S M , Jackson S , Russell M W , Moldoveanu Z , McGhee J R , Mestecky J
Published: May 2006

The finding that ingestion of antigens results in the selection induction of IgA antibodies in external secretions suggests that antigen sensitizes Peyer's patch lymphoid cells, which migrate to mucosal sites and generate local secretory IgA (S-IgA) antibody responses. Evidence for a common mucosal immune system in humans has been scanty because of the difficulty in demonstrating migratory behavior of Peyer's patch cells. In the present study, peripheral blood mononuclear cells (PBMC) from human volunteers who had ingested capsules containing killed Streptococcus mutans were assayed for spontaneous antibody-producing cells. Four of five volunteers exhibited circulating IgA-producing cells within 7 days and reached maximum responses by days 10-12. One IgA-deficient subject exhibited IgM responses with identical kinetics. Pokeweed-mitogen-stimulated PBMC produced anti-S. mutans antibodies predominantly of the IgA isotype. Significant S-IgA anti-S. mutans antibodies were detected in saliva and tears by day 14, and the antibodies reached maximum titers by 3 weeks. No changes in serum anti-S. mutans antibodies were noted. The IgA-deficient subject produced salivary secretory IgM antibodies. These results suggest that, after antigen ingestion, peripheral blood contains antigen-specific precursors of IgA plasma cells and that their presence precedes the appearance of S-IgA antibodies in external secretions. Therefore, these experiments provide further support for the existence of a common mucosal immune system in humans.
Human peroxisomal 3-oxoacyl-coenzyme A thiolase deficiency.
Authors: Schram A W , Goldfischer S , van Roermund C W , Brouwer-Kelder E M , Collins J , Hashimoto T , Heymans H S , van den Bosch H , Schutgens R B , Tager J M
Published: May 2006

We investigated the peroxisomal beta-oxidation system in liver from a patient with clinical features similar to those in the cerebrohepatorenal (Zellweger) syndrome and with elevated levels in body fluids of very-long-chain fatty acids and intermediates in the biosynthesis of bile acids. The peroxisomal beta-oxidation of fatty acids, measured as the cyanide-insensitive formation of [14C]acetyl units from [14C]palmitoyl-CoA, was very low in the patient (less than 10% of the values in control subjects). Immunoblotting experiments using antibodies to peroxisomal beta-oxidation enzymes indicated that peroxisomal 3-oxoacyl-CoA thiolase (acyl-CoA:acetyl-CoA C-acyltransferase, EC 2.3.1.16) was deficient. Addition of purified rat-liver peroxisomal 3-oxoacyl-CoA thiolase to a reaction mixture containing liver homogenate from the patient restored peroxisomal beta-oxidation. We conclude that the deficiency of peroxisomal 3-oxoacyl-CoA thiolase is responsible for the very low peroxisomal beta-oxidation activity and for the accumulation of very-long-chain fatty acids and intermediates in the biosynthesis of bile acids. Furthermore, the finding that both very-long-chain fatty acids and abnormal bile acids accumulate in this patient suggests that a single peroxisomal 3-oxoacyl-CoA thiolase is involved in the oxidative chain shortening of both very-long-chain fatty acids and the coprostanoic acids.
Acetylcholine receptor channels on adult mouse skeletal muscle are functionally identical in synaptic and nonsynaptic membrane.
Authors: Brehm P , Kullberg R
Published: May 2006

It has been proposed that acetylcholine receptor channels exhibit a functionally distinct "junctional" form at the region of synaptic contact between nerve and muscle. As a direct test of this idea, we compared acetylcholine-activated single-channel currents from the synaptic membrane to those obtained from nonsynaptic sites on freshly dissociated adult mouse toe muscle. We observed, at locations along the entire length of the cell, openings by a channel with a high conductance (70 pS) and brief open time (approximately 2 msec), characteristic of the classical "junctional type" of acetylcholine receptor. In 8 out of 10 synaptic and in 9 out of 19 nonsynaptic recordings, we also observed infrequent openings by a low-conductance (45-pS) channel traditionally associated only with nonsynaptic regions. In these recordings the low-conductance acetylcholine receptor channel averaged only 3% of the total channel openings. Comparisons of synaptic and nonsynaptic patches indicated no trend toward an increased proportion of low-conductance channel openings with increased distance from the synapse. These findings support the view that the functional properties of the acetylcholine receptor channel do not depend on proximity to the synapse in innervated mouse skeletal muscle.
Spontaneous assembly of double-stranded helicates from oligobipyridine ligands and copper(I) cations: structure of an inorganic double helix.
Authors: Lehn J M , Rigault A , Siegel J , Harrowfield J , Chevrier B , Moras D
Published: May 2006

Two oligobipyridine ligands containing two and three 2,2'-bipyridine subunits separated by 2-oxapropylene bridges have been synthesized and some of their complexation properties with metal ions have been investigated. In particular, with copper(I) they form, respectively, a dinuclear and a trinuclear complex containing two ligand molecules and two or three Cu(I) ions. In view of the pseudotetrahedral coordination geometry of Cu(I) X bis(bipyridine) sites and of NMR data indicating that the present complexes are chiral, one may assign to these dinuclear and trinuclear species a double-helical structure in which two molecular strands are wrapped around two or three Cu(I) ions, which hold them together. These complexes may thus be termed "double-stranded helicates." Determination of the crystal structure of the trinuclear species has confirmed that it is indeed an inorganic double helix, possessing characteristic features (helical parameters, stacking of bipyridine bases) reminiscent of the DNA double helix. This spontaneous formation of an organized structure by oligobipyridine ligands and suitable metal ions opens ways to the design and study of self-assembling systems presenting cooperativity and regulation features. Various further developments may be envisaged along organic, inorganic, and biochemical lines.
Neural BC1 RNA: cDNA clones reveal nonrepetitive sequence content.
Authors: DeChiara T M , Brosius J
Published: May 2006

BC1 is a small developmentally regulated RNA that is prevalent in nervous tissue. In order to determine if BC1 RNA represents the transcriptional by-product of various repetitive brain identifier (ID) elements or the independent transcript of a single or a few genes, we compared the sequences of a population of cDNA clones derived from in vitro C-tailed BC1 RNA. Each of 10 randomly selected clones revealed a 5' domain that was identical in sequence to the ID element, followed by an internal region of poly(A). In 8 of the clones, we found an identical, nonrepetitive sequence domain located at the 3' end of each molecule. An oligonucleotide of 30 residues complementary to this section identified only BC1 RNA in blot-hybridization analysis. Our results strongly suggest that BC1 RNA is transcribed specifically from the BC1 gene(s) and is not a highly heterogeneous population of ID-containing RNA polymerase III transcripts. Moreover, the availability of a unique BC1 RNA sequence will facilitate studies on tissue- and stage-specific gene regulation and will help in clarifying the role of this small RNA in the brain.
Three-dimensional structure of flavocytochrome b2 from baker's yeast at 3.0-A resolution.
Authors: Xia Z X , Shamala N , Bethge P H , Lim L W , Bellamy H D , Xuong N H , Lederer F , Mathews F S
Published: May 2006

The structure of flavocytochrome b2 from baker's yeast was solved at 3.0-A resolution by the multiple isomorphous replacement method combined with solvent leveling procedures, using data collected from an area detector. The tetramer of Mr 230,000 has 4-fold symmetry. Each subunit contains a cytochrome domain consisting of the first 100 residues, a flavin-binding domain containing the next 386 residues, and an extended C-terminal tail of 25 residues. The cytochrome domain closely resembles microsomal cytochrome b5, whereas the flavin-binding domain contains a parallel beta 8/alpha 8 barrel motif similar to glycolate oxidase and trimethylamine dehydrogenase. Two of the four cytochrome domains are disordered in the crystals. The flavin ring and heme group are separated by about 16 A between their centers, and their planes are inclined by about 17 degrees to each other.
Segment-specific and common nucleotide sequences in the noncoding regions of influenza B virus genome RNAs.
Authors: Stoeckle M Y , Shaw M W , Choppin P W
Published: May 2006

The nucleotide sequences of the 3' noncoding regions of all eight segments of influenza B virus RNA and the sequences of the 5' noncoding regions of segments 4-8 were determined in virus strains isolated over a period of 40 years. Nearly complete conservation of the noncoding sequences was found. Nine nucleotides at the 3' termini and 11 nucleotides at the 5' termini were common to all segments examined. In the region immediately adjacent to the common 3' terminal region, the nucleotides were specific for each segment and these segment-specific sequences were conserved in all strains examined. In each of the five segments in which both termini were examined, the segment-specific 3' sequences exhibited perfect inverted complementarity to a segment-specific sequence adjacent to the common 5' terminus. In addition, in the 3' noncoding region of RNA segments 1-3, which encode proteins involved in RNA synthesis, a single nucleotide substitution at position 10 was found that distinguishes these segments from segments 4-8. Comparison of these data with published reports has revealed that some of the features found in the noncoding regions of influenza B virus are also present in influenza A and C virus RNAs. In the RNAs of all three virus types, there is a segment-specific sequence of nucleotides near the 3' terminus that shows inverted complementarity to a sequence near the 5' terminus. This segment-specific sequence may play a role in the transcription of individual segments or in sorting of segments during virion assembly.
A chemical model for the cooperation of sulfates and carboxylates in calcite crystal nucleation: Relevance to biomineralization
Authors: Addadi L. , Moradian J. , Shay E. , Maroudas N. G. , Weiner S.
Published: May 2006

Acidic matrix macromolecules involved in regulation of biological crystal growth often contain aspartic acid-rich domains and covalently bound sulfated polysaccharides. We propose that sulfates and β-sheet structured carboxylates cooperate in oriented calcite crystal nucleation. The sulfates concentrate calcium, creating the supersaturation necessary for nucleation on the structured carboxylate domains. An artificial model, composed of sulfonated polystyrene surfaces and adsorbed β-sheet poly(aspartate), demonstrates that the two components indeed act cooperatively with respect to two independent assays, both by induction of calcite nucleation off the (001) plane and by calcium association. Evidence is presented that a purified organic matrix acidic glycoprotein from mollusk shells may behave
in vitro
in a similar way.
Limited cleavage of cellular fibronectin by plasminogen activator purified from transformed cells.
Authors: Quigley J P , Gold L I , Schwimmer R , Sullivan L M
Published: May 2006

The substrate specificity and direct catalytic activity of plasminogen activator (PA) was examined under conditions where its natural substrate, plasminogen, was missing or inhibited. PA, purified from cultures of transformed chicken fibroblasts, was incubated with purified preparations of potential substrates. The adhesive glycoprotein fibronectin, isolated from normal chicken fibroblast extracellular matrix, underwent limited but specific cleavage by PA in the absence of plasminogen. Analysis of the cleavage products by polyacrylamide gels under both reducing and nonreducing conditions indicated that PA-mediated cleavage occurred near the carboxyl terminus of fibronectin but on the amino-terminal side of the interchain disulfide bridge, thus disrupting the native dimeric fibronectin molecule. Under the identical conditions, chicken ovalbumin was not cleaved while the established substrate, chicken plasminogen, was extensively converted to plasmin. A monoclonal antibody, directed against avian PA and shown to inhibit plasminogen-free, cell-mediated matrix degradation, specifically inhibited the fibronectin cleavage. A human PA, urokinase, also cleaved fibronectin under plasminogen-free conditions yielding a limited number of high molecular weight cleavage products.
Evolutionary origin of cholinergic macromolecules and thyroglobulin.
Authors: Mori N , Itoh N , Salvaterra P M
Published: May 2006

We have compared the amino acid sequences of proteins that are involved in acetylcholine (AcCho) metabolism and cholinergic neurotransmission: choline acetyltransferase (ChoAcTase), acetylcholinesterase (AcChoEase), and a neuronal alpha subunit of nicotinic AcCho receptor (AcChoR). A comparison of Drosophila ChoAcTase and rat neuronal alpha subunit of AcChoR shows a limited segmental type homology, which may suggest a similar acetylcholine binding site in the two proteins evolving by convergence. We note a global homology of 21-44% identity between Drosophila ChoAcTase and Torpedo AcChoEase. Six homologous segments of 40-60 amino acids cover 38% and 54% of the sequences, raising the possibility of a common evolutionary origin. We also note that mammalian thyroglobulin (TG), the precursor for thyroid hormones, contains an AcChoEase-like sequence at its carboxyl end. This homology raises the possibility that the gene for TG has evolved by gene fusion or condensation (i.e., recruiting a preexisting redundant copy of a gene for AcChoEase during vertebrate evolution). Our results demonstrate that the record of evolutionary history for nervous system proteins can be read across the boundaries of separation between vertebrates and invertebrates. They also provide molecular evidence for the common evolutionary origins of the nervous and endocrine systems in vertebrates--both evolving to make intercellular communication possible.
Developmentally regulated expression of the nerve growth factor receptor gene in the periphery and brain.
Authors: Buck C R , Martinez H J , Black I B , Chao M V
Published: May 2006

Nerve growth factor (NGF) regulates development and maintenance of function of peripheral sympathetic and sensory neurons. A potential role for the trophic factor in brain has been detected only recently. The ability of a cell to respond to NGF is due, in part, to expression of specific receptors on the cell surface. To study tissue-specific expression of the NGF receptor gene, we have used sensitive cRNA probes for detection of NGF receptor mRNA. Our studies indicate that the receptor gene is selectively and specifically expressed in sympathetic (superior cervical) and sensory (dorsal root) ganglia in the periphery, and by the septum-basal forebrain centrally, in the neonatal rat in vivo. Moreover, examination of tissues from neonatal and adult rats reveals a marked reduction in steady-state NGF receptor mRNA levels in sensory ganglia. In contrast, a 2- to 4-fold increase was observed in the basal forebrain and in the sympathetic ganglia over the same time period. Our observations suggest that NGF receptor mRNA expression is developmentally regulated in specific areas of the nervous system in a differential fashion.
Absence of three secreted proteins and presence of a 57-kDa protein related to irreversible arrest of cell growth.
Authors: Ching G , Wang E
Published: May 2006

Two subsets of proteins from the conditioned medium of normal human diploid fibroblasts were detected by NaDodSO4/polyacrylamide gel electrophoresis analysis; the presence of these subset is related to the nonproliferative state of in vitro aged cells. One subset consists of three proteins (molecular mass from 80 to 87 kDa) secreted by replicating cells in sparse cultures, as well as by quiescent cells in confluent or serum-starved cultures of young fibroblasts. These proteins disappear from the medium when cultures reach the state of senescence. The other subset consists of a single protein of 57 kDa, detected only in conditioned medium of senescent fibroblast cultures. The results suggest that when human fibroblasts reach senescence, they secrete the 57-kDa protein and concomitantly stop secreting the other three proteins normally found in the culture medium of young fibroblasts. Therefore, the alternative secretion of these protein subsets could specifically signify irreversible arrest of cell growth during in vitro cellular aging.
Developmentally regulated expression by Trypanosoma cruzi of molecules that accelerate the decay of complement C3 convertases.
Authors: Rimoldi M T , Sher A , Heiny S , Lituchy A , Hammer C H , Joiner K
Published: May 2006

We recently showed that culture-derived metacyclic trypomastigotes (CMT), but not epimastigotes (Epi), of the Miranda 88 strain of Trypanosoma cruzi evade lysis by the human alternative complement pathway because of inefficient binding of factor B to complement component C3b on the parasite surface. These results suggested that CMT and tissue-culture-derived trypomastigotes (TCT), which also activate the alternative pathway poorly, might produce a molecule capable of interfering with factor B binding to C3b. We now demonstrate that CMT and TCT lysates, as well as molecules spontaneously shed from CMT and TCT but not Epi, accelerate decay of 125I-labeled factor Bb from the alternative-pathway C3 convertase (C3bBb) assembled on zymosan or Epi and also accelerate decay of the classical-pathway C3 convertase (C4b2a) on sheep erythrocytes. Parasites metabolically labeled with [35S]methionine spontaneously shed a limited number of radioactive components ranging in molecular mass from 86 to 155 kDa for trypomastigotes and 25 to 80 kDa for Epi. Decay-accelerating activity within supernatants is inactivated by papain and is coeluted with 35S-containing polypeptides on FPLC anion-exchange chromatography, suggesting that the active constituents are protein molecules. Molecules with decay-accelerating activity may explain the developmentally regulated resistance to complement-mediated lysis in infective and vertebrate stages of the T. cruzi life cycle.
Further properties of random walks on diagrams (graphs) with and without cycles.
Authors: Hill T L
Published: May 2006

Three problems are considered. The first is the relation between ensemble-averaged state probabilities in a random walk with absorption and time-averaged state probabilities in the corresponding closed diagram. The second problem is concerned with random walks on diagrams with cycles in which the cycle completion rates and probabilities may depend on the "remainder" after the previously completed cycle. The final topic is a study of cycle completions prior to absorption for diagrams that involve both cycles and absorption (e.g., a cycling enzyme that binds a dead-end inhibitor or poison in one of its states).
Positional variations in germinal cell growth in pigment-chimeric eyes of Xenopus: posterior half of the developing eye studied in genetic chimerae and in computer simulations.
Authors: Hunt R K , Bodenstein L , Cohen J S , Sidman R L
Published: May 2006

Growth of germinal cells at different angular positions within the posterior portion of the embryonic frog eye has been examined by orthotopically transplanting small groups of germinal cells from pigmented (stage 30-38) donor embryos into albino (stage 28-36) hosts and then serially photographing the polyclonal-cell progeny domain (typically a black sector) in the pigmented retinal epithelium of the living, growing eye. Far-ventral (6 o'clock) germinal cells formed a narrow sector along the ventral fissure, but ventral germinal cells at a position just posterior to the fissure (7 o'clock on a right eye) were seen to expand rapidly their angular territory on the germinal zone and formed huge sectors that widened toward the front of the older larval eye. Posterior (8, 9, and 10 o'clock) germinal cells were seen to shift their angular positions gradually toward dorsal and formed sectors that appeared to veer dorsalward nearing the front of the older eye. Dorsal (11 o'clock) germinal cells showed attenuative growth, forming sectors that narrowed approaching the front of the older eye. A simulation model of the growth dynamic was used to examine how expansive growth ventrally drives the positional variations in growth. When far-ventral germinal cells were programmed to retain the 6 o'clock position and ventral (7 o'clock) germinal cells were programmed to divide symmetrically at a high probability to produce two daughter germinal cells, not only were the observed ventral chimeric patterns simulated, but also simulated were the attenuative growth of dorsal transplants and the dorsal displacement and veering seen in the growth of posterior transplants.
Sequences of 12 monoclonal anti-dinitrophenyl spin-label antibodies for NMR studies.
Authors: Leahy D J , Rule G S , Whittaker M M , McConnell H M
Published: May 2006

Eleven monoclonal antibodies specific for a spin-labeled dinitrophenyl hapten (DNP-SL) have been produced for use in NMR studies. They have been named AN01 and AN03-AN12. The stability constants for the association of these antibodies with DNP-SL and related haptens were measured by fluorescence quenching and ranged from 5.0 X 10(4) M-1 to greater than 1.0 X 10(8) M-1. cDNA clones coding for the heavy and light chains of each antibody and of an additional anti-DNP-SL monoclonal antibody, AN02, have been isolated. The nucleic acid sequence of the 5' end of each clone has been determined, and the amino acid sequence of the variable regions of each antibody has been deduced from the cDNA sequence. The sequences are relatively heterogeneous, but both the heavy and the light chains of AN01 and AN03 are derived from the same variable-region gene families as those of the AN02 antibody. AN07 has a heavy chain that is related to that of AN02, and AN09 has a related light chain. AN05 and AN06 are unrelated to AN02 but share virtually identical heavy and light chains. Preliminary NMR difference spectra comparing related antibodies show that sequence-specific assignment of resonances is possible. Such spectra also provide a measure of structural relatedness.
Nucleoside adducts are formed by cooperative reaction of acetaldehyde and alcohols: possible mechanism for the role of ethanol in carcinogenesis.
Authors: Fraenkel-Conrat H , Singer B
Published: May 2006

The exocyclic amino groups of ribonucleosides and deoxyribonucleosides react rapidly at ambient temperature with acetaldehyde and alcohols to yield mixed acetals [--NH--CH(CH3)OR]. Nucleotides and nucleoside di- and triphosphates also react. Depending on the nucleoside used and on the relative amounts of aldehyde, alcohol, and water, preparative reactions reach equilibrium with yields up to 75% in a few hours. The structures have been confirmed by fast atom bombardment MS and proton NMR. Half-lives at 37 degrees C have been determined, and maximum stability is in the pH range of 7.5-9.5. In the absence of alcohol, acetaldehyde-nucleoside adducts could be isolated at 4 degrees C, but these were too unstable to characterize except for their UV spectra, also at 4 degrees C. Ethanol is often present in human blood and tissues, and acetaldehyde is its initial metabolic product, as well as being formed by many other metabolic processes. Both chemicals have separately been implicated in carcinogenic and other cytopathologic processes, but no cooperative mechanism has been proposed. The reactions reported here are of biological concern because they also occur in dilute aqueous solution. These findings supply a mechanism by which ethanol can be covalently bound to nucleic acids under physiological conditions.
Anti-endothelial cell antibodies: detection and characterization in sera from patients with autoimmune hypoparathyroidism.
Authors: Fattorossi A , Aurbach G D , Sakaguchi K , Cama A , Marx S J , Streeten E A , Fitzpatrick L A , Brandi M L
Published: May 2006

In a previous report, we described antibodies in autoimmune hypoparathyroidism (AHP) that are cytotoxic for cultured bovine parathyroid cells. In the present study, we show that sera from six AHP patients, but not from 26 patients with other autoimmune diseases or from 7 healthy subjects, react with bovine endothelial cells in culture (by flow cytometry and fluorescence microscopy) and in tissue sections (by immunohistology). We found uniformly that the immunoglobulin class reacting is IgM. Adsorption experiments showed that the antigenic determinants reacting with AHP sera were similar on bovine cultured endothelial cell membranes and in tissue sections of bovine parathyroid glands. The AHP sera also reacted with endothelial cells cultured from bovine adrenal medulla and pulmonary artery. Immunoblot analysis showed antibody binding to two major bands of 200 and 130 kDa solubilized from the membrane fraction of bovine parathyroid endothelial cells. Only one AHP serum consistently recognized endothelium-related structures on frozen sections of three different human parathyroid adenomas; two other sera reacted with one adenoma each; and three did not react with human adenomas. This indicates that human material is less suitable than bovine in detecting endothelium-related immune phenomena in AHP sera. The anti-endothelium IgM antibodies appear to be disease-specific but are not organ- or species-specific. The identification of endothelial cells as the target for antibodies in AHP raises the possibility that the endothelium subserves an important local function for endocrine epithelium.
Cloning and sequencing of the cDNA encoding a core protein of the paired helical filament of Alzheimer disease: identification as the microtubule-associated protein tau.
Authors: Goedert M , Wischik C M , Crowther R A , Walker J E , Klug A
Published: May 2006

Screening of cDNA libraries prepared from the frontal cortex of an Alzheimer disease patient and from fetal human brain has led to isolation of the cDNA for a core protein of the paired helical filament of Alzheimer disease. The partial amino acid sequence of this core protein was used to design synthetic oligonucleotide probes. The cDNA encodes a protein of 352 amino acids that contains a characteristic amino acid repeat in its carboxyl-terminal half. This protein is highly homologous to the sequence of the mouse microtubule-associated protein tau and thus constitutes the human equivalent of mouse tau. RNA blot analysis indicates the presence of two major transcripts, 6 and 2 kilobases lon g, with a wide distribution in normal human brain. Tau protein mRNAs were found in normal amounts in the frontal cortex from patients with Alzheimer disease. The proof that at least part of tau protein forms a component of the paired helical filament core opens the way to understanding the mode of formation of paired helical filaments and thus, ultimately, the pathogenesis of Alzheimer disease.
Insulin growth factors regulate the mitotic cycle in cultured rat sympathetic neuroblasts.
Authors: DiCicco-Bloom E , Black I B
Published: May 2006

While neuronal mitosis is uniquely restricted to early development, the underlying regulation remains to be defined. We have now developed a dissociated, embryonic sympathetic neuron culture system that uses fully defined medium in which cells enter the mitotic cycle. The cultured cells expressed two neuronal traits, tyrosine hydroxylase [L-tyrosine, tetrahydropteridine:oxygen oxidoreductase (3-hydroxylating); EC 1.14.16.2] and the neuron-specific 160-kDa neurofilament subunit protein, but were devoid of glial fibrillary acidic protein, a marker for non-myelin-forming Schwann cells in ganglia. Approximately one-third of the tyrosine hydroxylase-positive cells synthesized DNA in culture, specifically incorporating [3H]thymidine into their nuclei. We used this system to define factors regulating the mitotic cycle in sympathetic neuroblasts. Members of the insulin family of growth factors, including insulin and insulin-like growth factors I and II, regulated DNA synthesis in the presumptive neuroblasts. Insulin more than doubled the proportion of tyrosine hydroxylase-positive cells entering the mitotic cycle, as indicated by autoradiography of [3H]thymidine incorporation into nuclei. Scintillation spectrometry was an even more sensitive index of DNA synthesis, revealing a 4-fold insulin stimulation with an ED50 of 100 ng/ml. Insulin-like growth factor I was 100-fold more potent than insulin, whereas insulin-like growth factor II was less potent, suggesting that insulin growth factor type I receptors mediated the mitogenic responses. In contrast, the trophic protein nerve growth factor exhibited no mitogenic effect, suggesting that the mitogenic action of insulin growth factors is highly specific. Our observations are discussed in the context of the detection of insulin growth factors and receptors in the developing brain.
Applications of quantitative measurements for assessing glutamate neurotoxicity.
Authors: Finkbeiner S , Stevens C F
Published: May 2006

The role of the N-methyl-D-aspartate receptor channel in glutamate neurotoxicity was investigated in cultured hippocampal neurons of the CA1 region. An equation, the survival function, was developed to quantify the effects of putative modulators of neurotoxicity. 2-Amino-5-phosphonovaleric acid (30 microM) reduced the neuronal sensitivity to glutamate by a factor greater than 20, whereas glycine (1 microM) enhanced it by a factor of 7.5 +/- 2.5. Neurons were protected by increasing Mg2+ concentrations in a predictable way based on the ion's ability to block the N-methyl-D-aspartate channel. These findings provide a quantitative basis for the assessment of various neuroprotective agents and add further support to the hypothesis that the N-methyl-D-aspartate channel is central to glutamate neurotoxicity.
Molecular decoys: ligand-binding recombinant proteins protect mice from curarimimetic neurotoxins.
Authors: Gershoni J M , Aronheim A
Published: May 2006

Mimic ligand-binding sites of the nicotinic acetylcholine receptor bind d-tubocurarine and alpha-bungarotoxin in vitro. Injection of such binding sites into mice could act as molecular decoys in vivo, providing protection against toxic ligands. This hypothesis of molecular "decoyance" has been tested in greater than 250 mice. Bacterially produced cholinergic binding sites provided a 2-fold increase in the survival rate of animals challenged with curarimimetic neurotoxins. Possible considerations for decoy designs and their applications are discussed.