bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular mechanisms of DNA repair inhibition by caffeine.
Authors: Selby C P , Sancar A
Published: May 2006

Caffeine potentiates the mutagenic and lethal effects of genotoxic agents. It is thought that this is due, at least in some organisms, to inhibition of DNA repair. However, direct evidence for inhibition of repair enzymes has been lacking. Using purified Escherichia coli DNA photolyase and (A)BC excinuclease, we show that the drug inhibits photoreactivation and nucleotide excision repair by two different mechanisms. Caffeine inhibits photoreactivation by interfering with the specific binding of photolyase to damaged DNA, and it inhibits nucleotide excision repair by promoting nonspecific binding of the damage-recognition subunit, UvrA, of (A)BC excinuclease. A number of other intercalators, including acriflavin and ethidium bromide, appear to inhibit the excinuclease by a similar mechanism--that is, by trapping the UvrA subunit in nonproductive complexes on undamaged DNA.
Herpes simplex virus-infected cells disarm killer lymphocytes.
Authors: Confer D L , Vercellotti G M , Kotasek D , Goodman J L , Ochoa A , Jacob H S
Published: May 2006

Human endothelial cells or human foreskin fibroblasts infected with herpes simplex viruses (HSVs) potently inhibit the lytic activity of natural killer cells and interleukin 2-activated killer cells. The inhibition occurs after as little as 8 hr of viral infection and requires contact between effector cells and HSV-infected targets. Inhibition evidently stems from direct blockade of killer cell function because killer cells placed atop HSV-infected targets rapidly become incapable of lysing subsequently added HL-60 or K-562 cells. The impairment of killer cell function is prevented when protein glycosylation in HSV-infected cells is blocked with tunicamycin. These studies may be relevant for understanding the persistence of herpes simplex virus infections and, further, suggest a mechanism for failed immune surveillance.
Localization of a myosin heavy chain-like polypeptide to Drosophila nuclear pore complexes.
Authors: Berrios M , Fisher P A , Matz E C
Published: May 2006

Antibodies previously used for immunofluorescence localization of a myosin heavy chain-like polypeptide to the nuclear envelope in higher eukaryotic cells crossreact with both muscle and nonmuscle isoforms of Drosophila myosin heavy chain. Analyses of Drosophila tissue culture cells and premyogenic embryos suggest that it is the nonmuscle isoform that is associated with the nuclear envelope. Further immunofluorescence and immunoelectron microscopy indicate that this polypeptide is associated with nuclear pore complexes. These data support the hypothesis put forward previously that myosin or myosin-like molecules play a role in pore complex architecture.
Molecular cloning and expression of cDNA encoding the enzyme that controls conversion of high-mannose to hybrid and complex N-glycans: UDP-N-acetylglucosamine: alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I.
Authors: Sarkar M , Hull E , Nishikawa Y , Simpson R J , Moritz R L , Dunn R , Schachter H
Published: May 2006

UDP-GlcNAc:alpha-3-D-mannoside beta-1,2-N-acetylglucosaminyltransferase I (GnT I; EC 2.4.1.101) catalyzes an essential first step in the conversion of high-mannose N-glycans to hybrid and complex N-glycans. Cloning of the gene encoding this enzyme was carried out by mixed oligonucleotide-primed polymerase chain reaction amplification of rabbit liver single-stranded cDNA using sense and antisense 20- to 24-base-pair (bp) primers. A rabbit liver library in phage lambda gt10 yielded a 2.5-kilobase (kb) cDNA with a 447-amino acid coding sequence. None of the nine asparagine residues were in an Asn-Xaa-(Ser or Thr) sequence, indicating that the protein is not N-glycosylated. There is no sequence homology to other previously cloned glycosyltransferases, but GnT I appears to have a domain structure typical of these enzymes--i.e., a short amino-terminal domain, a transmembrane domain, a "neck" region, and a large carboxyl-terminal catalytic domain. RNA was transcribed off the 2.5-kb cDNA, and in vitro translation with rabbit reticulocyte lysate yielded a 52-kDa protein with GnT I activity.
A model for the quaternary structure of human placental insulin receptor deduced from electron microscopy.
Authors: Christiansen K , Tranum-Jensen J , Carlsen J , Vinten J
Published: May 2006

Electrophoretically pure and functionally intact human placental insulin receptor was studied by electron microscopy with negative-staining techniques. The quaternary structure of the detergent-solubilized receptor was determined. The receptor had the shape of a letter T approximately 24 nm in height and 18 nm in width with a thickness of the stem and the crossbar of 3-4 nm. No consistent change in ultrastructure of the receptor could be detected after the addition of insulin alone or insulin and Mn2+/Mg2+/ATP. After partial reduction of the alpha 2 beta 2 heterotetrameric receptor into alpha beta heterodimers, the electron micrographs showed a clear reduction in average size of the molecule with disappearance of the T profiles characteristic of the alpha 2 beta 2 heterotetramers. By incubation of the heterodimers in a phosphorylation medium containing insulin, a reassociation to molecules with molecular weights of the alpha 2 beta 2 heterotetramer took place judged from SDS/PAGE. Electron microscopy showed that the molecule formed larger aggregates, and only a few solitary T-shaped copies were seen.
Link homotopy.
Authors: Koschorke U
Published: May 2006

Link homotopy considers systems of pairwise disjoint singular spheres up to deformations through such "link maps." In a large range of higher dimensions the resulting link homotopy groups are determined and described in the language of standard homotopy theory.
Interleukin 1 regulates heparin-binding growth factor 2 gene expression in vascular smooth muscle cells.
Authors: Gay C G , Winkles J A
Published: May 2006

The angiogenic polypeptide heparin-binding growth factor 2 (HBGF-2), or basic fibroblast growth factor, is a mitogen for vascular smooth muscle cells in vitro and in vivo. Smooth muscle cells also synthesize HBGF-2; thus, it may stimulate their proliferation in vivo by both autocrine and paracrine mechanisms. We report here that HBGF-2 gene expression in human saphenous vein smooth muscle cells is induced by interleukin (IL)-1 alpha and IL-1 beta, inflammatory cytokines produced by many cell types in response to a variety of signals. Maximal HBGF-2 mRNA levels are detected 2-4 hr after IL-1 treatment; induction may require de novo protein synthesis and does not occur if transcription is inhibited. Immunoprecipitation analysis indicates that IL-1-stimulated cells also express an increased amount of HBGF-2 protein. Interferon gamma and glucocorticoids, inhibitors of smooth muscle cell proliferation in vitro and in vivo, suppress the induction of HBGF-2 expression by IL-1. These results imply that cytokines released at sites of vascular injury or inflammation may regulate HBGF-2 production by smooth muscle cells. Increased HBGF-2 levels within the vessel wall could play a role in both the smooth muscle cell proliferation and the neovascularization associated with the development of atherosclerotic lesions.
Characterization of the alpha 4 integrin gene promoter.
Authors: Rosen G D , Birkenmeier T M , Dean D C
Published: May 2006

A cDNA for the alpha 4 chain of the alpha 4 beta 1 integrin was described previously [Takada, Y., Elices, M. J., Crouse, C. & Hemler, M. E. (1989) EMBO J. 8, 1361-1368]. Primer extension analysis indicated that alpha 4 mRNA extended well beyond the 5' end of this cDNA. To clone this 5' sequence, a primer extension cDNA library was constructed, and a cDNA extending an additional 660 base pairs was isolated. This cDNA hybridized to multiple mRNAs in both T and B lymphocytes, but no alpha 4 mRNA was found in different tissues or in adherent cell lines. A single alpha 4 gene was detected in a genomic Southern blot when hybridization was done at high stringency; however, additional bands were observed at lower stringency, indicating the presence of alpha 4-related genes. Some of the different mRNAs that hybridize to the alpha 4 cDNA may then be the products of these related genes. Analysis of the alpha 4 genomic sequence revealed a large first exon of 958 base pairs. Interestingly, translation of alpha 4 initiates from the second ATG in this exon (nucleotide + 744). The first ATG (nucleotide +21) is followed by a termination codon 21 amino acids downstream. Such upstream ATG codons have been implicated in translational control of protooncogenes. One major transcriptional start site was identified by using S1 nuclease and primer extension mapping. Consensus sequences for DNA regulatory elements were found upstream of the gene and in exon 1 and intron 1. The alpha 4 gene 5' flanking region acted as a promoter in transfection assays. Detailed characterization of the promoter should provide insight into molecular events regulating expression and tissue specificity of alpha 4.
Molecular cloning and identification of a serine/threonine protein kinase of the second-messenger subfamily.
Authors: Jones P F , Jakubowicz T , Pitossi F J , Maurer F , Hemmings B A
Published: May 2006

A partial cDNA was isolated that encoded a protein kinase, termed rac (related to the A and C kinases). This cDNA was subsequently used to screen libraries derived from the human cell lines MCF-7 and WI38 and led to the isolation of full-length cDNA clones. DNA sequence analysis identified an open reading frame of 1440 base pairs encoding a protein of 480 amino acids (Mr, 55,716). This result was supported by the synthesis of a Mr 58,000 protein in an in vitro translation system that used RNA transcribed from cloned cDNAs with SP6 RNA polymerase. The predicted protein contains consensus sequences characteristic of a protein kinase catalytic domain and shows 73% and 68% similarity to protein kinase C and the cAMP-dependent protein kinase, respectively. Northern (RNA) analysis revealed a single mRNA transcript of 3.2 kilobases that varied up to 300-fold between different cell lines. Specific antisera directed towards the carboxyl terminal of the rac protein kinase were prepared and used to identify that phosphorylated several substrates in immunoprecipitates prepared with the rac-specific antisera.
Transcription of a subset of human class II major histocompatibility complex genes is regulated by a nucleoprotein complex that contains c-fos or an antigenically related protein.
Authors: Ono S J , Bazil V , Levi B Z , Ozato K , Strominger J L
Published: May 2006

Transcriptional regulation of the human major histocompatibility complex class II genes requires at least two upstream elements, the X and Y boxes, located in the -50- to -150-base-pair region of all class II promoters. The DRA and DPB promoters contain phorbol ester-responsive elements overlapping the 3' side of their X boxes. Mutation of this sequence down-regulates the efficiency of the DRA promoter, suggesting that a positive regulator(s) binds to this site. In this report, anti-sense c-fos RNA and an anti-c-fos antibody were used to show that the product of the protooncogene c-fos or an antigenically related protein is a component of a complex that binds to the X box and is required for maximal transcription from the DRA and DPB promoters. As c-fos (or its related proteins) cannot bind alone to DNA, these results suggest that it may dimerize with other members of the JUN/AP-1 family, such as hXBP1, to participate in the activation of a subset of class II major histocompatibility complex genes.
Murine adenovirus infection of SCID mice induces hepatic lesions that resemble human Reye syndrome.
Authors: Pirofski L , Horwitz M S , Scharff M D , Factor S M
Published: May 2006

Murine adenovirus type 1 (MAV-1) infection of CB-17 SCID mice (which are homozygous for the severe combined immunodeficiency mutation) induces hepatic histopathologic and ultrastructural features that are strikingly similar to human Reye syndrome. Gross pathologic examination of MAV-1-infected mice revealed only pale yellow liver tissue. Histopathologic studies of tissue from MAV-1-infected mice revealed diffuse hepatic injury manifested by microvesicular fatty degenerative changes of hepatocytes and electron microscopic evidence of focal mitochondrial swelling with disruption of cristae and depletion of glycogen. Serum aminotransferase activities increased markedly in the infected animals; however, plasma ammonia levels were not elevated at the times assayed. Although all mice infected with MAV-1 died, neutralizing anti-MAV-1 monoclonal antibodies provided a dose-dependent delay in the appearance of clinical disease and hepatic histopathologic findings. Other findings included rare viral inclusions with only minimal inflammation in spleen, adrenal, and liver of infected mice. Our findings indicate that MAV-1 infection of SCID mice may provide important insights into the pathogenesis of the hepatic lesions of Reye syndrome.
mShal, a subfamily of A-type K+ channel cloned from mammalian brain.
Authors: Pak M D , Baker K , Covarrubias M , Butler A , Ratcliffe A , Salkoff L
Published: May 2006

We have cloned and expressed a mouse brain cDNA, mShal, that encodes a transient, A-type K+ current. mShal, the vertebrate homolog of the Drosophila Shal gene, defines a distinct subfamily of voltage-gated K+ channels. The Shal deduced proteins are more highly conserved between mouse and Drosophila than other presently known K+ channels. mShal carries a "low-threshold" A-type current with a hyperpolarized steady-state inactivation midpoint. Marked similarity was observed between mShal and its Drosophila homolog, fShal, with regard to voltage sensitivity of activation, macroscopic inactivation, steady-state inactivation, and 4-aminopyridine sensitivity. Sequence conservation for Shal proteins is unusually high at the amino terminus, an area considered important for inactivation. Removal of conserved amino-terminal residues from mShal modifies macroscopic inactivation but the transient nature of the current is preserved. Underlying the very high conservation of mShal and fShal may be a role in the nervous system that is conserved in widely divergent species.
Reduced steady-state levels of rbcS mRNA in plants kept in the dark are due to differential degradation.
Authors: Fritz C C , Herget T , Wolter F P , Schell J , Schreier P H
Published: May 2006

When plants are placed in the dark, the level of the abundant mRNA encoding the small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS) declines rapidly. We present evidence demonstrating an active degradation of rbcS mRNA in the dark. Detailed analysis shows that transcripts originating from different members of the rbcS gene family are differentially affected by this degradation. This phenomenon is not common to all light-regulated plant genes since the mRNA for ST-LS1, another leaf-specific and light-induced gene, is not degraded in the dark within the same time scale.
Desmocollins form a distinct subset of the cadherin family of cell adhesion molecules.
Authors: Mechanic S , Raynor K , Hill J E , Cowin P
Published: May 2006

The desmosomal adhesive core is formed by four major components: desmoglein (Mr, 165,000), desmocollins I and II (Mr, 120,000 and 110,000, respectively), and a Mr 22,000 protein. Here, we report the cloning and sequencing of cDNAs encoding a bovine desmocollin. The open reading frame found in the longest cDNA, 5 kilobases, contains a region encoding a protein of 839 amino acids. The features of the deduced amino acid sequence imply that the mature 707-amino acid desmocollin is a type I transmembrane protein that is produced by proteolytic cleavage of an 810-amino acid precursor. The ectodomain of desmocollin contains repeats that show extensive sequence similarity to members of the cadherin family of calcium-dependent cell adhesion molecules. A comparison of the amino acid sequences of desmocollin, desmoglein, and the cadherins shows that although these intercellular junctional adhesion molecules share a consensus sequence in their adhesive domains that defines them as a family, several features, including the divergence in the sequence of their cytoplasmic tails, divide them into three distinct subtypes.
The major 85-kDa surface antigen of the mammalian-stage forms of Trypanosoma cruzi is a family of sialidases.
Authors: Kahn S , Colbert T G , Wallace J C , Hoagland N A , Eisen H
Published: May 2006

Trypanosoma cruzi, an intracellular protozoan parasite infecting a wide variety of vertebrates, is the agent responsible for Chagas disease in humans. An estimated 15-20 million people in South and Central America are infected with the parasite. Chagas disease often results in severe autoimmune and inflammatory pathology and is the major cause of heart failure in endemic areas. Nevertheless, little is known about the host-parasite interactions that lead to this pathology. We have previously cloned several members of a large gene family (SA85-1) and shown that these genes encode 85-kDa T. cruzi, mammalian-stage-specific, surface antigens. Here we report that members of the SA85-1 family possess sialidase activity and are shed by the parasite. We suggest that the sialidases may contribute to the pathology during T. cruzi infection by cleaving sialic acid from cells of the immune system.
Polymorphism in purified guanylate cyclase from vertebrate rod photoreceptors.
Authors: Hayashi F , Yamazaki A
Published: May 2006

Guanylate cyclase from rod photoreceptors of amphibian (toad, Bufo marinus, and frog, Rana catesbeiana) and bovine retinas was solubilized and purified by a single chromatography step on a GTP-agarose column. Silver staining of purified amphibian enzymes in SDS/polyacrylamide gels disclosed a doublet band (110 and 115 kDa), while the bovine enzyme appeared as a singlet band (110 kDa). The identification of these guanylate cyclases was confirmed using three chromatography systems with the purified enzymes. Specific binding to Con A-Sepharose suggested that rod guanylate cyclase is a glycoprotein. Two-dimensional gel electrophoresis of purified toad, frog, and bovine enzymes resolved two, three, and five variants, respectively, that differed in isoelectric point. Two variants of toad guanylate cyclase showed differences in various characterizations. These data suggest multiple mechanisms for regulation of guanylate cyclase activity in vertebrate rod photoreceptors.
Organization of the gene for human erythrocyte membrane protein 4.2: structural similarities with the gene for the a subunit of factor XIII.
Authors: Korsgren C , Cohen C M
Published: May 2006

Human erythrocyte band 4.2 is a major membrane-associated protein with an important, but still undefined, role in erythrocyte survival. We previously sequenced the complete cDNA for band 4.2 and showed that the protein has a strong sequence identity with the transglutaminase family of proteins but lacks transglutaminase activity. Here we have analyzed the genomic organization of band 4.2. The band 4.2 gene is approximately 20 kilobases, consisting of 13 exons and 12 introns. Reticulocytes contain two different sized messages for band 4.2, and our results show that the major, smaller, message is produced by alternative splicing within band 4.2 exon I. The upstream region of the gene has several prospective promoter elements arranged in a pattern similar to that of two other erythroid genes, beta-globin and porphobilinogen deaminase. Alignment of the band 4.2 amino acid sequence with that of the a subunit of human coagulation factor XIII and division of the sequences into exons reveal a remarkable correspondence, and in most cases identity, in the sizes of the paired exons. Moreover, each corresponding intron of the two genes is of an identical splice junction class. These and other similarities suggest that the gene for band 4.2 is closely related to and possibly derived from that for the a subunit of factor XIII and that the proteins may share common structural and functional properties.
Mixed nicotinic and muscarinic features of cholinergic receptor coupled to secretion in bovine chromaffin cells.
Authors: Shirvan M H , Pollard H B , Heldman E
Published: May 2006

Acetylcholine evokes release from cultured bovine chromaffin cells by a mechanism that is believed to be classically nicotinic. However, we found that the full muscarinic agonist oxotremorine-M (Oxo-M) induced a robust catecholamine (CA) secretion. By contrast, muscarine, pilocarpine, bethanechol, and McN-A-343 did not elicit any secretory response. Desensitization of the response to nicotine by Oxo-M and desensitization of the response to Oxo-M by nicotine suggest that both nicotine and Oxo-M were acting at the same receptor. Additional experiments supporting this conclusion show that nicotine-induced secretion and Oxo-M-induced secretion were similarly blocked by various muscarinic and nicotinic antagonists. Moreover, secretion induced by nicotine and Oxo-M were Ca2+ dependent, and both agonists induced 45Ca2+ uptake. Equilibrium binding studies showed that [3H]Oxo-M bound to chromaffin cell membranes with a Kd value of 3.08 x 10(-8) M and a Hill coefficient of 1.00, suggesting one binding site for this ligand. Nicotine inhibited Oxo-M binding in a noncompetitive manner, suggesting that both ligands bind at two different sites on the same receptor. We propose that the receptor on bovine chromaffin cells that is coupled to secretion represents an unusual cholinergic receptor that has both nicotinic and muscarinic features.
Fundamental theorem of natural selection under gene-culture transmission.
Authors: Findlay C S
Published: May 2006

A generalized fundamental theorem of natural selection is derived for populations incorporating both genetic and cultural transmission. The phenotype is determined by an arbitrary number of multiallelic loci with two-factor epistasis and an arbitrary linkage map, as well as by cultural transmission from the parents. Generations are discrete but partially overlapping, and mating may be nonrandom at either the genotypic or the phenotypic level (or both). I show that cultural transmission has several important implications for the evolution of population fitness, most notably that there is a time lag in the response to selection such that the future evolution depends on the past selection history of the population.
Iron-independent induction of ferritin H chain by tumor necrosis factor.
Authors: Miller L L , Miller S C , Torti S V , Tsuji Y , Torti F M
Published: May 2006

Iron increases the synthesis of the iron-storage protein, ferritin, largely by promoting translation of preexisting mRNAs for both the H and L ferritin isoforms (H, heavy, heart, acidic; L, light, liver, basic). We have recently cloned and sequenced a full-length cDNA to murine ferritin H and identified ferritin H as a gene induced by tumor necrosis factor alpha (TNF-alpha, cachectin). Using primary human myoblasts, we have now examined the relationship between TNF-alpha and iron in regulating ferritin. Four lines of evidence suggest that TNF-alpha regulates ferritin independently of iron. First, evaluation of mRNA showed that TNF-alpha increased ferritin H chain specifically, provoking no change in steady-state levels of ferritin L mRNA; iron, in contrast, increased the mRNA of both isoforms. Second, the increase in ferritin H protein synthesis observed during TNF-alpha treatment was dependent on an increase in ferritin H mRNA: actinomycin D blocked the TNF-alpha-induced changes in ferritin H but did not inhibit the translational induction of ferritin seen with iron treatment. Third, equal ferritin mRNA induction was observed in iron-loaded cells and in cells depleted of iron by a permeant chelator, 2,2'-dipyridyl. Fourth, ferritin H induction by TNF-alpha and iron was additive over the entire range of iron concentrations, even at TNF-alpha doses known to maximally stimulate ferritin H mRNA levels. Nonetheless, the role of iron in translational regulation of ferritin was retained in TNF-alpha-treated cells; effective biosynthesis of TNF-alpha-induced, H-subunit-predominant ferritin protein required iron and could be enhanced by treatment of the cells with additional iron or blocked by 2,2'-dipyridyl. Finally, we observed that the TNF-alpha-mediated increase in ferritin synthesis peaked at 8 hr and was followed by a decrease in both H and L isoferritin synthesis; the addition of iron, however, reversed the late-occurring depression in ferritin synthesis. This suggests that TNF-alpha-induced synthesis of H-rich ferritin may reduce the regulatory pool of intracellular iron, secondarily inhibiting iron-mediated translation of ferritin mRNA. We conclude that TNF-alpha acts independently of iron in its induction of ferritin H mRNA but requires the presence of iron for this effect to be fully expressed at the protein level.
An additional function for bacteriophage lambda rex: the rexB product prevents degradation of the lambda O protein.
Authors: Schoulaker-Schwarz R , Dekel-Gorodetsky L , Engelberg-Kulka H
Published: May 2006

The rex operon of bacteriophage lambda excludes the development of several unrelated bacteriophages. Here we present an additional lambda rexB function: it prevents degradation of the short-lived protein lambda O known to be involved in lambda DNA replication. We have shown that it is the product of rexB that is responsible for the stabilization of lambda O: when a nonsense mutation is present in rexB, lambda O protein is labile; suppression of the mutation by the corresponding nonsense suppressor causes partial restabilization of lambda O. lambda rexB also stabilizes lambda O in trans. We discuss our results in relation to the function of rexB in lambda DNA replication and its role in the protein degradation pathways of bacteriophage lambda.
From one gene to two proteins: the biogenesis of cytochromes b and c1 in Bradyrhizobium japonicum.
Authors: Thöny-Meyer L , James P , Hennecke H
Published: May 2006

Genes coding for polyproteins that are cleaved posttranslationally into two or more functional proteins are rarely found in prokaryotes. One example concerns the biogenesis of the Bradyrhizobium japonicum cytochromes b and c1, two of the three constituent subunits of ubiquinol-cytochrome-c reductase (ubiquinol:ferricytochrome-c oxidoreductase, EC 1.10.2.2); the respective apoproteins for these subunits are encoded by the 5' and 3' halves of a single gene, fbcH. These two halves are linked by an extra piece of DNA encoding a characteristic signal peptide for protein translocation across the cytoplasmic membrane. Processing of the fbcH gene product is shown to occur at a typical signal peptidase recognition site. This reaction is reminiscent of that catalyzed by the regular bacterial signal peptidase that normally cleaves off presequences from the N termini of translocated proteins. Mutational alteration of the signal peptidase recognition site within FbcH results in the appearance of an uncleaved bc1 fusion protein in the membrane. Additionally, a functional heme-binding site in the apocytochrome c1 section of FbcH is shown to be a necessary prerequisite for the formation of the bc1 complex.
Microtubule destabilization and neurofilament phosphorylation precede dendritic sprouting after close axotomy of lamprey central neurons.
Authors: Hall G F , Lee V M , Kosik K S
Published: May 2006

Axotomy of giant lamprey (Petromyzon marinus) central neurons (anterior bulbar cells) close to their somata results in ectopic axon-like sprouting from the dendritic tips. Such sprouts first appear as swellings at the tips of a small subset of dendrites 2-3 weeks after "close" axotomy. We report here that immunocytochemical examination of these swellings reveals a structure and composition that differs from that of conventional growth cones; incipient sprouts contain many highly phosphorylated neurofilaments (NFs), little tubulin, and virtually no stable (acetylated) microtubules (MTs). The dendrites of anterior bulbar cells after close axotomy also show pronounced changes in NF protein and tubulin staining patterns prior to the emergence of sprouts from the dendrites. The amount of tyrosinated tubulin increases greatly; this rise is tightly coupled to the appearance of highly phosphorylated NFs and the loss of nonphosphorylated NFs in the dendrites. Acetylated tubulin is generally reduced after close axotomy and is selectively lost from dendrites that gave rise to sprouts. These changes indicate that an invasion of the dendrites by phosphorylated NFs may be linked to the destabilization of dendritic MTs, and in some dendrites this may lead to a marked loss of stable MTs, which is correlated with the emergence of NF-filled sprouts from the dendritic tips.
Infection of polarized MDCK cells with herpes simplex virus 1: two asymmetrically distributed cell receptors interact with different viral proteins.
Authors: Sears A E , McGwire B S , Roizman B
Published: May 2006

Herpes simplex virus 1 attaches to at least two cell surface receptors. In polarized epithelial (Madin-Darby canine kidney; MDCK) cells one receptor is located in the apical surface and attachment to the cells requires the presence of glycoprotein C in the virus. The second receptor is located in the basal surface and does not require the presence of glycoprotein C. Exposure of MDCK cells at either the apical or basal surface to wild-type virus yields plaques and viral products whereas infection by a glycoprotein C-negative mutant yields identical results only after exposure of MDCK cells to virus at the basal surface. Multiple receptors for viral entry into cells expand the host range of the virus. The observation that glycoprotein C-negative mutants are infectious in many nonpolarized cell lines suggests that cells in culture may express more than one receptor and explains why genes that specify the viral proteins that recognize redundant receptors, like glycoprotein C, are expendable.
Isoenthalpic and isoentropic temperatures and the thermodynamics of protein denaturation.
Authors: Lee B
Published: May 2006

The standard enthalpy or entropy change upon transfer of a small nonpolar molecule from a nonaqueous phase into water at a given temperature is generally different for different solute species. However, if the heat capacity change is independent of temperature, there exists a temperature at which the enthalpy or the entropy change becomes the same for all solute species within a given class. Similarly, the enthalpy or the entropy change of protein denaturation, when extrapolated to high temperature assuming a temperature-independent heat capacity change, shows a temperature at which its value becomes the same for many different globular proteins on a per weight basis. It is shown that the existence of these temperatures can be explained from a common formalism based on a linear relationship between the thermodynamic quantity and a temperature-independent molecular property that characterizes the solute or the protein. For the small nonpolar molecule transfer processes, this property is the surface area or the number of groups that are brought in contact with water. For protein denaturation, it is suggested that this property measures the polar/nonpolar mix of the internal interaction within the protein interior. Under a certain set of assumptions, this model leads to the conclusion that the nonpolar and the polar groups of the protein contribute roughly equally to the stability of the folded state of the molecule and that the solvent-accessible surface area of the denatured form of a protein is no more than about two-thirds that of the fully extended form.
Phosphorylation of protein 4.1 on tyrosine-418 modulates its function in vitro.
Authors: Subrahmanyam G , Bertics P J , Anderson R A
Published: May 2006

Protein 4.1 was initially characterized as a protein that regulates cytoskeletal assembly in erythrocytes. However, recent studies have shown that protein 4.1 is ubiquitous in mammalian cells. Here, we show that protein 4.1 is phosphorylated on tyrosine by the epidermal growth factor receptor (EGFR) tyrosine kinase. The phosphorylation site has been localized to the 8-kDa domain, which has one tyrosine, tyrosine-418. The 8-kDa region is required for the assembly of the spectrin/actin complex, and phosphorylation by EGFR reduced the ability of protein 4.1 to promote the assembly of the spectrin/actin/protein 4.1 ternary complex. Immunoblotting with anti-phosphotyrosine antibodies showed that purified protein 4.1 contained phosphorylated tyrosine, and this increased upon phosphorylation by EGFR. This suggests that tyrosine phosphorylation of protein 4.1 occurs in vivo and may be functionally significant. The tyrosine phosphorylation site is in the center of a sequence motif that is expressed by a differentiation-specific splicing mechanism.
Ancestral facial morphology of Old World higher primates.
Authors: Benefit B R , McCrossin M L
Published: May 2006

Fossil remains of the cercopithecoid Victoria-pithecus recently recovered from middle Miocene deposits of Maboko Island (Kenya) provide evidence of the cranial anatomy of Old World monkeys prior to the evolutionary divergence of the extant subfamilies Colobinae and Cercopithecinae. Victoria-pithecus shares a suite of craniofacial features with the Oligocene catarrhine Aegyptopithecus and early Miocene hominoid Afropithecus. All three genera manifest supraorbital costae, anteriorly convergent temporal lines, the absence of a postglabellar fossa, a moderate to long snout, great facial height below the orbits, a deep cheek region, and anteriorly tapering premaxilla. The shared presence of these features in a catarrhine generally ancestral to apes and Old World monkeys, an early ape, and an early Old World monkey indicates that they are primitive characteristics that typified the last common ancestor of Hominoidea and Cercopithecoidea. These results contradict prevailing cranial morphotype reconstructions for ancestral catarrhines as Colobus- or Hylobates-like, characterized by a globular anterior braincase and orthognathy. By resolving several equivocal craniofacial morphocline polarities, these discoveries lay the foundation for a revised interpretation of the ancestral cranial morphology of Catarrhini more consistent with neontological and existing paleontological evidence.
DNA bending induced by Cro protein binding as demonstrated by gel electrophoresis.
Authors: Lyubchenko Y , Shlyakhtenko L , Chernov B , Harrington R E
Published: May 2006

We report an approach for studying protein-induced DNA bends in solution that is based on measuring the sizes of circular DNA molecules by using two-dimensional gel electrophoresis. These circular fragments are obtained by ligating short synthetic oligonucleotides containing a protein-recognition region in the presence of protein. Oligonucleotides 21-base-pairs-long containing the OR3 recognition site were synthesized and ligated in both the presence and the absence of the Cro repressor from lambda phage. We show that in the presence of Cro protein, circular DNA molecules are formed with substantial frequency. No circular molecules are observed in the DNA samples ligated in the absence of Cro. These experiments clearly demonstrate that DNA bending is induced by Cro in this operator site. The sum of inherent plus Cro-induced bending is estimated as 45 degrees.
Cloning of a phospholipase A2-activating protein.
Authors: Clark M A , Ozgür L E , Conway T M , Dispoto J , Crooke S T , Bomalaski J S
Published: May 2006

Recently we have described the isolation and biochemical characterization of a phospholipase A2-activating protein (PLAP). We have cloned this protein and found it to be expressed as a 2.5-kilobase mRNA. The steady-state levels of PLAP mRNA are induced in smooth muscle and endothelial cells following treatment with leukotriene D4. The increased message levels coincide with increased amounts of PLAP. Synthetic antisense DNA was used to block the synthesis of PLAP and this treatment effectively blocked the activation of phospholipase A2 and the increased generation of prostanoids in smooth muscle and endothelial cells treated with leukotriene D4.
GTPase domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families, and functional sites.
Authors: Valencia A , Kjeldgaard M , Pai E F , Sander C
Published: May 2006

GTPase domains are functional and structural units employed as molecular switches in a variety of important cellular functions, such as growth control, protein biosynthesis, and membrane traffic. Amino acid sequences of more than 100 members of different subfamilies are known, but crystal structures of only mammalian ras p21 and bacterial elongation factor Tu have been determined. After optimal superposition of these remarkably similar structures, careful multiple sequence alignment, and calculation of residue-residue interactions, we analyzed the two subfamilies in terms of structural conservation, sequence conservation, and residue contact strength. There are three main results. (i) A structure-based alignment of p21 and elongation factor Tu. (ii) The definition of a common conserved structural core that may be useful as the basis of model building by homology of the three-dimensional structure of any GTPase domain. (iii) Identification of sequence regions, other than the effector loop and the nucleotide binding site, that may be involved in the functional cycle: they are loop L4, known to change conformation after GTP hydrolysis; helix alpha 2, especially Arg-73 and Met-67 in ras p21; loops L8 and L10, including ras p21 Arg-123, Lys-147, and Leu-120; and residues located spatially near the N and C termini. These regions are candidate sites for interaction either with the GTP/GDP exchange factor, with a GTPase-affected function, or with a molecule delivered to a destination site with the aid of the GTPase domain.
CD3 stimulation causes phosphorylation of phospholipase C-gamma 1 on serine and tyrosine residues in a human T-cell line.
Authors: Park D J , Rho H W , Rhee S G
Published: May 2006

The human T-cell line Jurkat was found to contain at least two immunologically distinct isoforms of inositol phospholipid-specific phospholipase C (PLC), PLC-beta 1 and PLC-gamma 1. Treatment of Jurkat cells with antibody to CD3 led to phosphorylation of PLC-gamma 1 but not of PLC-beta 1. The phosphorylation of PLC-gamma 1 occurred rapidly and transiently on both serine and tyrosine residues; tyrosine phosphorylation reached a maximum level less than 1 min after stimulation and decreased rapidly, both in the presence and in the absence of orthovanadate. Two-dimensional phosphopeptide map analysis revealed that the major sites of tyrosine and serine phosphorylation in PLC-gamma 1 from activated Jurkat cells are the same as those in PLC-gamma 1 from cells treated with peptide growth factors such as epidermal growth factor and platelet-derived growth factor. Previously, it has been shown that multiple phosphorylation of PLC-gamma 1 by the growth factor receptor tyrosine kinases leads to activation of PLC-gamma 1. Thus, the current data suggest that inositol phospholipid hydrolysis triggered by the T-cell antigen receptor-CD3 complex is due, at least in part, to activation of PLC-gamma 1 and that the mechanism by which this activation is achieved involves phosphorylation of multiple tyrosine residues on PLC-gamma 1 by a nonreceptor tyrosine kinase coupled to the T-cell antigen receptor-CD3 complex.
Rescue of a foreign gene by Sendai virus.
Authors: Park K H , Huang T , Correia F F , Krystal M
Published: May 2006

A simple protocol for the rescue of a synthetic genome into a paramyxovirus has been developed. First, a synthetic Sendai virus-like RNA, containing the antisense coding region of the chloramphenicol acetyltransferase gene replacing the coding region of the Sendai virus genome, was transcribed from a cDNA. When introduced into cells that are infected with Sendai virus, this RNA construct was transcribed, replicated, and packaged into infectious virions. The addition of infected cell extract to the RNA prior to transfection markedly enhanced levels of chloramphenicol acetyltransferase expression and rescue. However, this enhancement is not due to encapsidation of the RNA into nucleocapsids as the RNA remains nuclease-sensitive. Uninfected cell extract also enhances expression and rescue efficiency, implying involvement of a cellular factor(s) with the synthetic viral-like RNA construct that allows for enhanced polymerase recognition. This system should allow for the dissection of the various cis-acting RNA signals within the paramyxovirus genome.
G alpha 12 and G alpha 13 subunits define a fourth class of G protein alpha subunits.
Authors: Strathmann M P , Simon M I
Published: May 2006

Heterotrimeric guanine nucleotide-binding regulatory proteins (G proteins) are central to the signaling processes of multicellular organisms. We have explored the diversity of the G protein subunits in mammals and found evidence for a large family of genes that encode the alpha subunits. Amino acid sequence comparisons show that the different alpha subunits fall into at least three classes. These classes have been conserved in animals separated by considerable evolutionary distances; they are present in mammals, Drosophila, and nematodes. We have now obtained cDNA clones encoding two murine alpha subunits, G alpha 12 and G alpha 13, that define a fourth class. The translation products are predicted to have molecular masses of 44 kDa and to be insensitive to ADP-ribosylation by pertussis toxin. They share 67% amino acid sequence identity with each other and less than 45% identity with other alpha subunits. Their transcripts can be detected in every tissue examined, although the relative levels of the G alpha 13 message appear somewhat variable.
Stimulation of a Ca(2+)-dependent protein kinase by GM1 ganglioside in nerve growth factor-treated PC12 cells.
Authors: Hilbush B S , Levine J M
Published: May 2006

We have investigated the ability of exogenous gangliosides to modulate nerve growth factor (NGF) signal transduction in PC12 cells. The effects of exogenous ganglioside GM1 on multiple protein kinase activities were assayed by analyzing site-specific serine phosphorylation of tyrosine hydroxylase (TyrOHase) by two-dimensional phosphopeptide mapping. In the presence of NGF, exogenous GM1 (1-10 microM) increased 32P incorporation into TyrOHase phosphopeptide T2, a Ca2+/calmodulin-dependent protein kinase substrate whose phosphorylation is not normally affected by NGF treatment. In the absence of NGF, GM1 treatment had no significant effects on TyrOHase phosphorylation. The removal of extracellular Ca2+ or blockade of dihydropyridine-sensitive Ca2+ channels prevented the GM1-induced increases in 32P incorporation into phosphopeptide T2. Exogenous GM1 also potentiated K+ depolarization-induced increases in the phosphorylation of TryOHase. These results suggest that the stimulatory effects of exogenous GM1 ganglioside on NGF actions may be due to its ability to potentiate a Ca(2+)-dependent signaling pathway.
Normal serum immunoglobulins participate in the selection of peripheral B-cell repertoires.
Authors: Freitas A A , Viale A C , Sundblad A , Heusser C , Coutinho A
Published: May 2006

In B-cell development, expression of immunoglobulin heavy-chain variable-region (VH) gene repertoires is determined by genetic mechanisms that favor rearrangement of the most D-proximal genes, resulting in overutilization of the VH7183 gene family early in ontogeny and in differentiating B cells of the adult bone marrow. Maturation of the immune system is accompanied by a decreased expression of VH7183 genes in the peripheral immunocompetent B-cell pool of adult animals. By comparing VH gene family expression in the bone marrow (emergent) and peripheral (available and actual) B-cell repertoires of germ-free and conventionally raised BALB/c mice, we found that peripheral selection of VH gene family utilization does not occur in germ-free animals. Reconstitution of germ-free mice with normal serum immunoglobulins purified from syngeneic donors reestablishes selection of VH7183-expressing B cells. Our results indicate that preimmune B-cell repertoires are selected in normal animals by environmental antigens and serum immunoglobulins.
Binary-liquid phase separation of lens protein solutions.
Authors: Broide M L , Berland C R , Pande J , Ogun O O , Benedek G B
Published: May 2006

We have determined the coexistence curves (plots of phase-separation temperature T versus protein concentration C) for aqueous solutions of purified calf lens proteins. The proteins studied, calf gamma IIIa-, gamma IIIb-, and gamma IVa-crystallin, have very similar amino acid sequences and three-dimensional structures. Both ascending and descending limbs of the coexistence curves were measured. We find that the coexistence curves for each of these proteins and for gamma II-crystallin can be fit, near the critical point, to the function /(Cc-C)/Cc/ = A [(Tc - T)/Tc]beta, where beta = 0.325, Cc is the critical protein concentration in mg/ml, Tc is the critical temperature for phase separation in K, and A is a parameter that characterizes the width of the coexistence curve. We find that A and Cc are approximately the same for all four coexistence curves (A = 2.6 +/- 0.1, Cc = 289 +/- 20 mg/ml), but that Tc is not the same. For gamma II- and gamma IIIb-crystallin, Tc approximately 5 degrees C, whereas for gamma IIIa- and gamma IVa-crystallin, Tc approximately 38 degrees C. By comparing the published protein sequences for calf, rat, and human gamma-crystallins, we postulate that a few key amino acid residues account for the division of gamma-crystallins into low-Tc and high-Tc groups.
CD4 peptide-protein conjugates, but not recombinant human CD4, bind to recombinant gp120 from the human immunodeficiency virus in the presence of serum from AIDS patients.
Authors: Ghetie V , Slaughter C , Wheeler H T , Uhr J W , Vitetta E S
Published: May 2006

Sera from human immunodeficiency virus-positive (HIV+; Walter Reed stage 6) individuals inhibit the interaction between recombinant human CD4 and recombinant gp120 from HIV (rCD4 and rgp120, respectively), thereby interfering with the ability of soluble rCD4 to block infection with HIV or rCD4-toxin conjugates to kill HIV-infected cells. In this report we demonstrate that the inhibitory activity of such sera is caused primarily by anti-gp120 antibodies that do not recognize the CD4 interaction site on gp120. To circumvent the problem of inhibition, we have generated a construct containing a peptide of CD4 (residues 41-84) conjugated to ovalbumin (three to five peptides per molecule). This multivalent conjugate binds to rgp120 and binding is not inhibited by antibodies in HIV+ sera.
Specificity of the Mnt protein determined by binding to randomized operators.
Authors: Stormo G D , Yoshioka M
Published: May 2006

The relative binding affinities of Mnt protein from bacteriophage P22 are determined for each possible base pair at position 17 of the operator. These are determined from the partitioning of randomized operators into bound and unbound fractions; quantitation is provided by restriction enzyme analysis. Mnt protein is found to have an unusual specificity at this position: a C.G base pair (the wild-type operator) has the highest affinity, a G.C base pair has the lowest affinity, and both orientations of A.T base pairs are intermediate and nearly equivalent. A specific binding constant and specific binding free energy are defined and shown to be directly related to the information content of the operator sequences bound to the protein, taking into account the quantitative differences in binding affinities.