bluuebunny/crossref_metadata_2025 huggingface dataset:
Proofreading by the epsilon subunit of Escherichia coli DNA polymerase III increases the fidelity of calf thymus DNA polymerase alpha.
Authors: Perrino F W , Loeb L A
Published: May 2006

Addition of the 3'----5' proofreading exonuclease, epsilon subunit of Escherichia coli DNA polymerase III, to DNA polymerase alpha from calf thymus has been studied. Alone, calf thymus DNA polymerase alpha terminates in vitro DNA synthesis upon insertion of noncomplementary nucleotides. Upon addition of the epsilon subunit, DNA polymerase alpha elongates the newly synthesized DNA as a result of hydrolysis of the 3'-terminal mispair. The fidelity of DNA polymerase alpha in vitro is increased 7-fold by addition of the exonuclease. The functional interaction between DNA polymerase alpha and the epsilon subunit is independent of any detectable physical association. This suggests that a mechanism for proofreading could exist in mammalian cells involving sequential catalysis by DNA polymerase alpha excision of errors by a separate 3'----5' exonuclease, and further elongation onto correctly base-paired 3' termini by DNA polymerase alpha.
Molecular cloning of plant transcripts encoding protein kinase homologs.
Authors: Lawton M A , Yamamoto R T , Hanks S K , Lamb C J
Published: May 2006

Oligonucleotides, corresponding to conserved regions of animal protein-serine/threonine kinases, were used to isolate cDNAs encoding plant homologs in the dicot bean (Phaseolus vulgaris L.) and the monocot rice (Oryzae sativa L.). The C-terminal regions of the deduced polypeptides encoded by the bean (PVPK-1) and rice (G11A) cDNAs, prepared from mRNAs of suspension cultures and leaves, respectively, contain features characteristic of the catalytic domains of eukaryotic protein-serine/threonine kinases, indicating that these cDNAs encode plant protein kinases. The putative catalytic domains are most closely related to cyclic nucleotide-dependent protein kinases and the protein kinase C family, suggesting the plant homologs may likewise transduce extracellular signals. However, outside these domains, PVPK-1 and G11A exhibit no homology either to each other or to regulatory domains of other protein kinases, indicating the plant homologs are modulated by other signals. PVPK-1 corresponds to a 2.4-kb transcript in suspension cultured bean cells. Southern blots of genomic DNA indicate that PVPK-1 and G11A correspond to single copy genes that form part of a family of related plant sequences.
Structure and function of the Zn(II) binding site within the DNA-binding domain of the GAL4 transcription factor.
Authors: Pan T , Coleman J E
Published: May 2006

The transcription factor GAL4 from Saccharomyces cerevisiae contains a "zinc-finger"-like motif, Cys-Xaa2-Cys-Xaa6-Cys-Xaa6-Cys-Xaa2-Cys-Xaa6+ ++-Cys, within its DNA-binding domain. A GAL4 fragment consisting of residues 1-147 plus two additional residues from the cloning vector [denoted GAL4(149*)] has been cloned and overexpressed in Escherichia coli. This fragment includes the entire DNA-binding domain (residues 1-74). The homogeneous GAL4-(149*) protein contains 1-1.5 moles of Zn(II) per mole of protein. The GAL4(149*) protein binds tightly to the specific 17-base-pair palindromic DNA sequence found at GAL4 binding sites as shown by gel-retention assays using a 32P-labeled 23-mer containing this sequence. Removal of the intrinsic Zn(II) by EDTA at low pH abolishes binding to the 23-mer. The GAL4(149*) apoprotein can be reconstituted with Zn(II), Cd(II), or Co(II) with restoration of specific DNA binding. Titration of GAL4(149*) apoprotein with 113Cd(II) shows two 113Cd(II) binding sites on the molecule, one with delta of 707 ppm, suggesting coordination to four sulfur atoms, and one with delta of 669 ppm, suggesting coordination to three or four sulfur atoms. Because GAL4(149*) protein contains only six cysteine residues within its DNA-binding domain, the precise coordination of the two Cd(II) ions cannot be stated with certainty; one or more shared -S- ligands could exist. GAL4(149*) protein contains approximately 40% alpha-helix and approximately 20% beta-sheet, estimated from circular dichroism. Removal of the native Zn(II) ion causes limited unfolding of secondary structure, but less than one turn of alpha-helix. The binding of Zn(II), Cd(II), and, to a lesser extent, Co(II) to GAL4(149*) apoprotein protects the protein from proteolysis by trypsin, which produces a 13-kDa DNA-binding core.
Immunocytochemical localization of beta II subspecies of protein kinase C in rat brain.
Authors: Saito N , Kose A , Ito A , Hosoda K , Mori M , Hirata M , Ogita K , Kikkawa U , Ono Y , Igarashi K
Published: May 2006

The distribution of a subspecies of protein kinase C (PKC) encoded by the beta II sequence in rat central nervous tissue was demonstrated immunocytochemically by using antibodies raised against an oligopeptide having a partial sequence specific for the beta II PKC. The beta II PKC immunoreactivity was widely but discretely distributed in the brain. The distribution of the beta II PKC immunoreactivity differed from that of the beta I and gamma PKC subspecies. The beta II PKC immunoreactivity was found in the perikarya, dendrites, and axons of neuronal cells. Few if any glial cells were stained. Immunoreactive neurons were present in the anterior olfactory nucleus, olfactory tubercle, amygdaloid complex, caudate-putamen, accumbens nucleus, claustrum, dorsal part of the lateral septal nucleus, CA1 region of the hippocampus, subiculum, medial habenular nucleus, cerebral cortex, nucleus of the spinal tract of the trigeminal nerve, nucleus of the solitary tract, and substantia gelatinosa of the spinal cord. In these neurons, the beta II PKC immunoreactivity was seen mainly in the form of cytoplasmic dots and, in some cases, diffusely in the cytoplasm. Under electron microscopy, these immunoreactive large dots appeared to be associated with the Golgi complex, suggesting that the beta II PKC plays a specialized function at the Golgi complex in certain neuronal cell types.
B-type receptor for platelet-derived growth factor mediates a chemotactic response by means of ligand-induced activation of the receptor protein-tyrosine kinase.
Authors: Westermark B , Siegbahn A , Heldin C H , Claesson-Welsh L
Published: May 2006

Porcine aorta endothelial cells are devoid of receptors for platelet-derived growth factor (PDGF). We have transfected such cells with cDNA for the PDGF B-type receptor, both the wild-type receptor and a mutant form of the receptor (K634A), in which the putative nucleotide-binding lysine of the protein-tyrosine domain has been changed to alanine. Immunoprecipitation studies of metabolically labeled cells showed that both types of receptors were synthesized and processed to the mature form of Mr 190,000. In cells expressing the wild-type receptor, PDGF-BB, the natural ligand for the B-type receptor, induced membrane ruffling and reorganization of actin. Such a response has previously been seen in cells expressing the natural PDGF B-type receptor in response to PDGF-BB. No such effect was induced in nontransfected cells or in cells expressing the K634A mutant receptor. PDGF was also shown to be chemotactic for cells expressing the wild-type receptor, whereas no chemotactic response was elicited in control cells or in cells expressing the K634A mutant receptor. Our study thus provides formal evidence that the PDGF B-type receptor mediates a motility response including actin reorganization and chemotaxis. Furthermore, the results establish a role for the receptor-associated protein-tyrosine kinase in the transduction of the chemotactic signal.
Sequence analysis and DNA-protein interactions within the 5' flanking region of the Ca2+/calmodulin-dependent protein kinase II alpha-subunit gene.
Authors: Sunyer T , Sahyoun N
Published: May 2006

The 5' flanking region of the brain Ca2+/calmodulin-dependent protein kinase II alpha-subunit gene was identified and characterized. A total of 430 bases was sequenced upstream from the translation initiation codon, and the site of transcription initiation was located at -149 or -147 bases as determined by primer extension and S1 nuclease protection analysis, respectively. TATA and CAAT boxes were absent from their standard positions; however, the 5' flanking region was rich in G + C and contained a GGGCG and a TATATAA sequence 76 and 160 bases upstream from the transcription initiation site, respectively. Moreover, the sequence CAACGG was found 85 and 146 bases upstream from this site, indicating presumptive binding sites for the Myb protein. Gel-mobility shift assays revealed that a 120-base-pair fragment, which included the G + C-rich, TATA, and CAACGG sequences bound nuclear proteins specifically. DNA-protein complexes with similar gel mobilities were obtained with nuclear extracts from rat forebrain or cerebellum and from neonatal or adult brains. Extracts from rat liver, kidney, and spleen generated specific DNA-protein complexes with different electrophoretic mobilities, suggesting the occurrence of different nuclear proteins that bind to 5' regulatory elements of the Ca2+/calmodulin-dependent kinase II alpha-subunit gene.
Identification of heat shock protein hsp70 homologues in chloroplasts.
Authors: Marshall J S , DeRocher A E , Keegstra K , Vierling E
Published: May 2006

Cytoplasmic members of the heat shock protein hsp70 family have recently been implicated in the transport of proteins to the endoplasmic reticulum and mitochondria. In addition, other hsp70 homologues have been found in the endoplasmic reticulum and mitochondria and, at least for the endoplasmic reticulum hsp70 homologue, may be involved in the proper folding and assembly of newly transported proteins. Since chloroplasts are an important site of protein transport in plant cells, we were interested in determining whether hsp70 proteins might be located in this organelle. By using immunoblotting techniques and two antibody preparations against hsp70 proteins, we have identified three chloroplastic proteins of approximately 70 kDa that are related to hsp70 proteins. One of these proteins was tightly associated with the outer envelope membrane and was not exposed at the outer surface of the chloroplasts. The other two were soluble proteins located in the stroma. Steady-state levels of the chloroplastic hsp70 homologues did not change after heat stress nor were any additional hsp70 homologues detected in chloroplasts isolated from heat-stressed plants. We discuss the possible functions of these hsp70 homologues in the transport of proteins into and within chloroplasts.
Manganese(II) catalyzes the bicarbonate-dependent oxidation of amino acids by hydrogen peroxide and the amino acid-facilitated dismutation of hydrogen peroxide.
Authors: Berlett B S , Chock P B , Yim M B , Stadtman E R
Published: May 2006

In bicarbonate/CO2 buffer, Mn(II) and Fe(II) catalyze the oxidation of amino acids by H2O2 and the dismutation of H2O2. As the Mn(II)/Fe(II) ratio is increased, the yield of carbonyl compounds per mole of leucine oxidized is essentially constant, but the ratio of alpha-ketoisocaproate to isovaleraldehyde formed increases, and the fraction of H2O2 converted to O2 increases. In the absence of Fe(II), the rate of Mn(II)-catalyzed leucine oxidation is directly proportional to the H2O2, Mn(II), and amino acid concentrations and is proportional to the square of the HCO3- concentration. The rate of Mn(II)-catalyzed O2 production in the presence of 50 mM alanine or leucine is about 4-fold the rate observed in the absence of amino acids and accounts for about half of the H2O2 consumed; the other half of the H2O2 is consumed in the oxidation of the amino acids. In contrast, O2 production is increased nearly 18-fold by the presence of alpha-methylalanine and accounts for about 90% of the H2O2 consumed. The data are consistent with the view that H2O2 decomposition is an inner sphere (cage-like) process catalyzed by a Mn coordination complex of the composition Mn(II), amino acid, (HCO3-)2. Oxidation of the amino acid in this complex most likely proceeds by a free radical mechanism involving hydrogen abstraction from the alpha-carbon as a critical step. The results demonstrate that at physiological concentrations of HCO3- and CO2, Mn(II) is able to facilitate Fenton-type reactions.
Bialgebra cohomology, deformations, and quantum groups.
Authors: Gerstenhaber M , Schack S D
Published: May 2006

We introduce cohomology and deformation theories for a bialgebra A (over a commutative unital ring k) such that the second cohomology group is the space of infinitesimal deformations. Our theory gives a natural identification between the underlying k-modules of the original and the deformed bialgebra. Certain explicit deformation formulas are given for the construction of quantum groups--i.e., Hopf algebras that are neither commutative nor cocommutative (whether or not they arise from quantum Yang-Baxter operators). These formulas yield, in particular, all GLq(n) and SLq(n) as deformations of GL(n) and SL(n). Using a Hodge decomposition of the underlying cochain complex, we compute our cohomology for GL(n). With this, we show that every deformation of GL(n) is equivalent to one in which the comultiplication is unchanged, not merely on elements of degree one but on all elements (settling in the strongest way a decade-old conjecture) and in which the quantum determinant, as an element of the underlying k-module, is identical with the usual one.
Existence of two forms of rat liver arginyl-tRNA synthetase suggests channeling of aminoacyl-tRNA for protein synthesis.
Authors: Sivaram P , Deutscher M P
Published: May 2006

Arginyl-tRNA synthetase (arginine-tRNA ligase, EC 6.1.1.19) is found in extracts of mammalian cells both as a free protein (Mr = 60,000) and as a component (Mr approximately 72,000) of the high molecular weight aminoacyl-tRNA synthetase complex (Mr greater than 10(6). Several pieces of evidence indicate that the low molecular weight free form is not a proteolytic degradation product of the complex-bound enzyme but that it preexists in vivo: (i) the endogenous free form differs in size from the active proteolytic fragment generated in vitro, (ii) conditions expected to increase or decrease the amount of proteolysis do not alter the ratio of the two forms of the enzyme, and (iii) the free form contains an NH2-terminal methionine residue. A model is presented that provides a rationale for the existence of two forms of arginyl-tRNA synthetase in cells. In this model the complexed enzyme supplies arginyl-tRNA for protein synthesis, whereas the free enzyme provides arginyl-tRNA for the NH2-terminal arginine modification of proteins by arginyl-tRNA:protein arginyltransferase. This latter process targets certain proteins for removal by the ubiquitin-dependent protein degradation pathway. The necessity for an additional pool of arginyl-tRNA for the modification reaction leads to the conclusion that the arginyl-tRNA destined for protein synthesis (and/or protein modification) is channeled and unavailable for other processes. Other evidence supporting channeling in protein synthesis is discussed.
Long-range restriction map of the terminal part of the short arm of the human X chromosome.
Authors: Petit C , Levilliers J , Weissenbach J
Published: May 2006

The terminal part of the short arm of the human X chromosome has been mapped by pulsed-field gel electrophoresis (PFGE). The map, representing the distal two-thirds of Xp22.3 spans a total of 10,000 kilobases (kb) from Xpter to the DXS143 locus. A comparison with linkage data indicates that 1 centimorgan (cM) in this region corresponds to about 600 kb. CpG islands were essentially concentrated in the 1500 kb immediately proximal to the pseudoautosomal boundary. Several loci, including the gene encoding steroid sulfatase (STS) and the loci for the X-linked recessive form of chondrodysplasia punctata (CDPX) and for Kallmann syndrome (KAL) have been placed relative to the Xp telomere. CDPX is located between 2650 and 5550 kb from Xpter, and STS is located between 7250 and 7830 kb from Xpter. KAL maps to an interval of 350 kb between 8600 and 8950 kb from the telomere. The X-chromosomal breakpoints of a high proportion of XX males resulting from X-Y interchange cluster to a 920-kb region proximal and close to the pseudoautosomal boundary.
Monoclonal antibodies specific for the outer surface protein A (OspA) of Borrelia burgdorferi prevent Lyme borreliosis in severe combined immunodeficiency (scid) mice.
Authors: Schaible U E , Kramer M D , Eichmann K , Modolell M , Museteanu C , Simon M M
Published: May 2006

We have recently shown that viable Borrelia burgdorferi organisms induce a chronic infection associated with arthritis and carditis in severe combined immunodeficiency (scid) mice but not in immunocompetent mice. The disease is similar to that found in patients suffering from Lyme disease. We now show that B. burgdorferi-specific immune mouse sera as well as a monoclonal antibody to the spirochetal outer surface antigen A (31 kDa) but not monoclonal antibodies specific for the 41-kDa antigenic component of the periplasmic flagella are able to prevent (or mitigate) the development of the disease in scid mice when passively transferred at the time of the bacterial inoculation. The identification of a B. burgdorferi-associated protective antigen suggests that the corresponding spirochetal protein should be tested as a vaccine against Lyme disease.
Mitogenic stimulation of human tumor-infiltrating lymphocytes by secreted factor(s) from human tumor cell lines.
Authors: Packard B S
Published: May 2006

Tumor-infiltrating lymphocytes (TILs) have shown in vivo antitumor efficacy in both animal and human studies. Functions thought necessary for antitumor activity include cytolysis, homing, and proliferation at tumor sites. TILs, which are T lymphocytes grown ex vivo directly from tumors, bear interleukin 2 (IL-2) receptors capable of transducing the IL-2 mitogenic signal. However, IL-2 is not normally synthesized by solid tumor cells. This study was aimed at exploring the possible presence of T-cell mitogens of tumor origin. To this end four TIL lines derived from four melanoma patients were studied for their ability to use the environments of cultured tumor cell lines as mitogenic sources. The presence of four irradiated cultured human tumor cell lines, three of which were derived from the same melanoma patients as the TILs, were found to stimulate proliferation of human TILs in the absence of IL-2. Further investigation showed that the observed proliferative stimulation by the fourth tumor line was due to secreted factor(s) as mitogenic activity was present in the serum-free tumor cell supernatant. Both immunologic analyses of this medium and proliferative assays in which TILs were stimulated with recombinant lymphokine standards suggest the presence of a yet uncharacterized T-cell mitogen.
Muscarinic and beta-adrenergic depression of the slow Ca2(+)-activated potassium conductance in hippocampal CA3 pyramidal cells is not mediated by a reduction of depolarization-induced cytosolic Ca2+ transients.
Authors: Knöpfel T , Vranesic I , Gähwiler B H , Brown D A
Published: May 2006

Combined intracellular and microfluorometric recording techniques were used to evaluate whether the inhibition by cholinergic or adrenergic transmitters of the Ca2(+)-activated potassium current (IAHP) in hippocampal CA3 pyramidal cells was mediated by an alteration of depolarization-induced change in cytosolic free Ca2+ concentration [(Ca2+]i). Low concentrations of isoproterenol (1-10 microM) and muscarine (0.25-1 microM) reversibly abolished IAHP without affecting concomitant Ca2+ transients or the steady-state [Ca2+]i. Only after application of higher concentrations of muscarine, [Ca2+]i increased; in the presence of potassium channel blockers, muscarine depressed Ca2+ currents and concomitant Ca2+ transients. These observations provide direct evidence that the inhibition of IAHP by isoproterenol and muscarine are not mediated by an alteration of Ca2+ dynamics.
Effect of genetic modification of tyrosine-185 on the proton pump and the blue-to-purple transition in bacteriorhodopsin.
Authors: Jang D J , el-Sayed M A , Stern L J , Mogi T , Khorana H G
Published: May 2006

The retinylidene chromophore mutant (Y185F) of bacteriorhodopsin, in which Tyr-185 is substituted by phenylalanine, is examined and compared with wild-type bacteriorhodopsin expressed in Escherichia coli; both were reinstituted similarly in vesicles. The Y185F mutant shows (at least) two distinct spectra at neutral pH. Upon light absorption, the blue species (which absorbs in the red) behaves as if "dead"--i.e., neither its tyrosine nor its protonated Schiff base undergoes deprotonation nor does its tryptophan fluorescence undergo quenching. This result is unlike either the purple species (which absorbs in the blue) or wild-type bacteriorhodopsin expressed in E. coli. As the pH increases, both the color changes and the protonated Schiff base deprotonation efficiency suggest a blue-to-purple transition of the Y185F mutant near pH 9. If this blue-to-purple transition of Y185F corresponds to the blue-to-purple transition of purple-membrane (native) bacteriorhodopsin (occurring at pH 2.6) and of wild-type bacteriorhodopsin expressed in E. coli (occurring at pH 5), the protein-conformation changes of this transition as well as the protonated Schiff base deprotonation may be controlled not by surface pH alone, but rather by the coupling between surface potential and the general protein internal structure around the active site. The results also suggest that Tyr-185 does not deprotonate during the photocycle in purple-membrane bacteriorhodopsin.
A Schistosoma mansoni epitope recognized by a protective monoclonal antibody is identical to the stage-specific embryonic antigen 1.
Authors: Ko A I , Dräger U C , Harn D A
Published: May 2006

In infections with the parasitic trematode Schistosoma mansoni, a component of the host defense is directed against the invading larval form, and carbohydrates on the surface of these larvae are targets for the immune attack during the early stages of infection. To identify such carbohydrate epitopes, which may be suitable for immunization against schistosomiasis, we have previously generated monoclonal antibodies to surface antigens; some of these confer protection to naive mice when passively administered. Here we show that one of the protective antibodies recognizes a determinant present in both the parasite and its mammalian hosts. The immunohistochemical distribution of this determinant in the head of embryonic mice was found to be identical to the stage-specific embryonic antigen 1 (SSEA-1), an epitope abundant in pre-implantation embryos, several adult tissues, and malignant tumors. Oligosaccharides containing the SSEA-1 trisaccharide Gal beta 1-4(Fuc alpha 1-3)GlcNAc inhibit antibody binding to parasite antigen. SSEA-1 antibodies generated from mice immunized with rodent neural antigens bind to the surface of the schistosome larvae and mediate antibody-dependent cellular cytotoxicity. SSEA-1 antibodies are also elicited during human schistosomiasis infection, and this autoantibody response may be involved in the development of the natural immunity against the parasite.
Liquid crystal domains and thixotropy of filamentous actin suspensions.
Authors: Kerst A , Chmielewski C , Livesay C , Buxbaum R E , Heidemann S R
Published: May 2006

The thixotropic properties of filamentous actin suspensions were examined by a step-function shearing protocol. Samples of purified filamentous actin were sheared at 0.2 sec-1 in a cone and plate rheometer. We noted a sharp stress overshoot upon the initiation of shear, indicative of a gel state, and a nearly instantaneous drop to zero stress upon cessation of shear. Stress-overshoot recovery was almost complete after 5 min of "rest" before samples were again sheared at 0.2 sec-1. Overshoot recovery increased linearly with the square root of rest time, suggesting that gel-state recovery is diffusion limited. Actin suspensions subjected to oscillatory shearing at frequencies from 0.003 to 30 radians/sec confirmed the existence of a 5-min time scale in the gel, similar to that for stress-overshoot recovery. Flow of filamentous actin was visualized by polarized light observations. Actin from 6 mg/ml to 20 mg/ml showed the "polycrystalline" texture of birefringence typical for liquid crystal structure. At shear rates less than 1 sec-1, flow occurred by the relative movement of irregular, roughly ellipsoidal actin domains 40-140 microns long; the appearance was similar to moving ice floes. At shear rates greater than 1 sec-1, domains decreased in size, possibly by frictional interactions among domains. Eventually domains flow in a "river" of actin aligned by the flow. Our observations confirm our previous domain-friction model for actin rheology. The similarities between the unusual flow properties of actin and cytoplasm argue that cytoplasm also may flow as domains.
cDNA cloning, sequence, and expression of carbonic anhydrase in Chlamydomonas reinhardtii: regulation by environmental CO2 concentration.
Authors: Fukuzawa H , Fujiwara S , Yamamoto Y , Dionisio-Sese M L , Miyachi S
Published: May 2006

cDNA clones for the periplasmic carbonic anhydrase (CA; carbonate hydro-lyase, EC 4.2.1.1) of Chlamydomonas reinhardtii cells were isolated and characterized. The fact that the cloned cDNA fragments encoded a 377-amino acid polypeptide (41,626 Da) consisting of an NH2-terminal hydrophobic signal peptide of 20 amino acids, a large (35,603 Da) subunit polypeptide, and a small (4144 Da) subunit polypeptide indicates that the two subunits are cotranslated as a precursor polypeptide. The amino acid sequence of mature subunits deduced from the nucleotide sequence showed 20-22% homology with human CA isozymes (CAI, CAII, and CAIII). Three zinc-liganded histidine residues and those forming a hydrogen-bond network to zinc-bound solvent molecules were highly conserved in the plant and animal enzymes. Three possible asparagine-linked glycosylation sites were found in the large subunit. Northern blot analysis was carried out using the cDNA fragment as a probe. The level of 2.0-kilobase CA mRNA increased within 1 hr when CO2 concentration of the bubbling gas was changed from 5% to 0.04% (air level) in the presence of light. On the other hand, CA mRNA did not accumulate when CO2 concentration was lowered in the dark. Experiments using 3-(3,4-dichlorophenyl)-1,1-dimethylurea showed that photosynthesis is absolutely required for the accumulation of CA mRNA. These results indicate that CA biosynthesis is regulated by changes in environmental CO2 concentration as well as light at the level of mRNA abundance.
Interaction of immunoactive monokines (interleukin 1 and tumor necrosis factor) in the bivalve mollusc Mytilus edulis.
Authors: Hughes T K , Smith E M , Chin R , Cadet P , Sinisterra J , Leung M K , Shipp M A , Scharrer B , Stefano G B
Published: May 2006

Mytilus edulis has been the subject of recent studies to determine whether the relationship between the immune and neuroendocrine systems seen in vertebrates also exists in invertebrates. The effects of mammalian monokines were studied in Mytilus immunocytes previously shown to produce and react to opioid peptides. These invertebrate cells respond to interleukin 1 (IL-1) and tumor necrosis factor (TNF), both in vitro and in vivo, in a manner similar to that of human granulocytes. As in the mammalian monokine network, the effect of IL-1 on the immunocytes is brought about, at least in part, by its stimulatory effect on the formation of TNF. In addition, the presence of immunoreactive IL-1 and TNF in Mytilus hemolymph was demonstrated.
Tyrosine phosphorylation is a signal for the trafficking of pp85, an 85-kDa phosphorylated polypeptide associated with phosphatidylinositol kinase activity.
Authors: Cohen B , Yoakim M , Piwnica-Worms H , Roberts T M , Schaffhausen B S
Published: May 2006

A family of 85/86-kDa (85K/86K) polypeptides closely linked to phosphatidylinositol kinase activity is found in polyoma middle-sized tumor antigen (MTAg)/pp60c-src complexes. MTAg and the 85-kDa phosphoprotein (pp85) could be reassociated in solution, or on blots, after denaturation with SDS. Results from such experiments focus attention on phosphorylation in controlling intracellular sorting and activation of pp85. Tyrosine phosphorylation seems important for recruitment of pp85 from cytosol to membrane. By blotting, pp85 is substantially cytosolic, whereas that recognized by anti-phosphotyrosine antibody is almost exclusively in membranes. Tyrosine phosphorylation also determined association of pp85 with MTAg. Manipulation of MTAg tyrosine phosphorylation, for example, by expressing MTAg using baculovirus vectors in the absence or presence of pp60c-src, dramatically affects reassociation. Finally, tyrosine phosphorylation appears to be involved in release of pp85 from MTAg, since vanadate increased its rate of dissociation.
Isolation and expression of the gene for a major surface protein of Giardia lamblia.
Authors: Gillin F D , Hagblom P , Harwood J , Aley S B , Reiner D S , McCaffery M , So M , Guiney D G
Published: May 2006

To study the interactions between the parasitic protozoan Giardia lamblia and its environment, we have cloned the gene that encodes the two major surface-labeled trophozoite protein species. Sequence analysis of this gene reveals a single open reading frame specifying a hydrophilic, cysteine-rich (11.8%) protein of 72.5-kDa molecular mass with an amino-terminal signal peptide and a postulated hydrophobic membrane-spanning anchor region near the carboxyl terminus. Most of the cysteine residues (58 of 84) are in the motif Cys-Xaa-Xaa-Cys, which is dispersed 29 times throughout the sequence. Antibodies against the recombinant protein react with the entire surface of live trophozoites, including flagella and adhesive disc. These antibodies inhibit trophozoite attachment, prevent growth, and immunoprecipitate the major approximately 66- and 85-kDa proteins from surface-labeled live trophozoites. The recombinant Escherichia coli also expresses polypeptides of approximately 66- and 85-kDa molecular mass, which are not fusion proteins. This suggests that the processing and/or conformational changes that lead to production of these two peptide species in E. coli reflect those that occur in Giardia. The abundance of cysteine residues suggests that the native proteins on the parasite surface may contain numerous disulfide bonds, which would promote resistance to intestinal fluid proteases and to the detergent activity of bile salts and would help to explain the survival of Giardia in the human small intestine.
Transcriptional activation by Sp1 as directed through TATA or initiator: specific requirement for mammalian transcription factor IID.
Authors: Smale S T , Schmidt M C , Berk A J , Baltimore D
Published: May 2006

Transcription of mammalian genes by RNA polymerase II often begins at a specific nucleotide, whose location is determined either by an upstream DNA element known as a TATA box or by an element positioned at the transcription start site called an initiator (Inr). By in vitro analysis of synthetic promoters, we demonstrate here that the TATA and Inr elements are functionally similar and that the Inr is contained between nucleotides -3 and +5 relative to the initiation site. Moreover, we found that a mammalian transcription factor IID (TFIID) protein fraction is required for transcriptional stimulation by an Sp1-dependent activating element placed upstream of either TATA or Inr elements. However, in these assays, the yeast TATA-binding protein, which previously was shown to function similarly to mammalian TFIID, could not efficiently substitute for the mammalian TFIID fraction. These results demonstrate that mammalian TFIID is functionally distinct from the yeast TATA-binding protein and may contain additional subunits or domains that are important for transcriptional activation from some promoters.
Central nervous system neurons migrate on astroglial fibers from heterotypic brain regions in vitro.
Authors: Gasser U E , Hatten M E
Published: May 2006

In different regions of the developing mammalian brain, neurons follow the processes of radial glial cells over very different trajectories to reach their destinations in specific neuronal layers. To investigate whether the movement of neurons along glial fibers is specified by glia in a given region or whether glia provide a permissive substrate for migration in different brain regions, we purified neurons and astroglial cells from developing cerebellum and hippocampus and analyzed neuronal migration on heterotypic glial fibers with time-lapse, video-enhanced differential interference microscopy in vitro. Granule neurons purified from early postnatal rat cerebellum migrated on astroglial processes of glia purified from late embryonic or early postnatal rat hippocampus with a cytology, neuron-glial relationship, and dynamics of movement that were indistinguishable from those of mouse granule cells migrating on cerebellar astroglial processes in vitro [Edmondson, J. C. & Hatten, M. E. (1987) J. Neurosci. 7, 1928-1934]. In the reciprocal combination, hippocampal neurons migrated on cerebellar glial processes in a manner that was also remarkably similar to migration along homotypic, hippocampal glial fibers [Gasser, U. E. & Hatten, M. E. (1990) J. Neurosci. 10, 1276-1285]. In all cases, migrating neurons had a characteristic appearance, apposing their cell soma against the glial fiber and extending in the direction of migration a motile, leading process that enfolded the glial fiber with short filopodia and lamellipodia. As seen by video microscopy, neurons moved along homotypic and heterotypic glial processes by translocation of the soma and were not "pulled" forward by the leading process. As the neuron moved, the nucleus remained in the posterior portion of the cell and cytoplasmic vesicles moved forward from the soma into the leading process. The dynamics of the movement of neurons along heterotypic glial substrates, including the speed and periodicity of motion, was identical to that of neurons migrating along homotypic glial substrates. These experiments suggest that the mechanism of movement of neurons along glial fibers is conserved in these two brain regions during development.
Endothelins are more sensitive than sarafotoxins to neutral endopeptidase: possible physiological significance.
Authors: Skolovsky M , Galron R , Kloog Y , Bdolah A , Indig F E , Blumberg S , Fleminger G
Published: May 2006

Incubation of endothelins (ETs) with bovine kidney neutral endopeptidase (NEP) resulted in a selective two-step degradation with loss of biochemical activity. The Km of the enzyme indicated high-affinity binding, and hydrolysis was completely inhibited by phosphoramidon. The first step was nicking of the Ser5-Leu6 bond, followed by cleavage at the amino side of Ile19. The nicked peptide exhibited biochemical activities comparable to those of the intact peptide--i.e., binding to the ET receptor, induction of inositol phospholipid hydrolysis, and toxicity. The twice-cleaved product was inactive. The sarafotoxins (SRTXs) were more resistant than the ETs to NEP: for example, the half-time for ET-1 was approximately 1 hr, while it was approximately 4 hr for SRTX-b and even higher for SRTX-c. These in vitro findings may indicate a regulatory role of NEP (or similar enzymes) in the physiological inactivation of ETs. They might also help to explain why under certain physiological conditions ETs may be less toxic than SRTXs.
The bulk of the peripheral B-cell pool in mice is stable and not rapidly renewed from the bone marrow.
Authors: Förster I , Rajewsky K
Published: May 2006

We have reevaluated the in vivo lifespan of B lymphocytes based on incorporation of the thymidine analogue 5-bromo-2'-deoxyuridine into the DNA of dividing cells. To exclude potential alterations in the turnover of B-lineage cells due to the bromodeoxyuridine incorporation, we performed pulse-chase experiments comparing the appearance and disappearance of bromodeoxyuridine-labeled cells over long periods of time. The data consistently show that more than two-thirds of splenic B cells in adult (greater than 2 months old) mice have a lifetime of several weeks or months, whereas a more rapid turnover takes place in young (4 week old) mice. Thus, the peripheral B-cell pool is only slowly renewed after it has been initially built up early in life.
Identification and characterization of an enhancer in the coding region of the genome of human immunodeficiency virus type 1.
Authors: Verdin E , Becker N , Bex F , Droogmans L , Burny A
Published: May 2006

Transcription of human immunodeficiency virus type 1 (HIV-1) is regulated by cis-acting DNA elements located in the viral long terminal repeats, by viral transregulatory proteins, and by cellular transcription factors acting in concert to modulate the degree of viral expression. We demonstrate that a DNA fragment corresponding to the central portion of the HIV-1 genome exhibits enhancer activity when cloned upstream of the thymidine kinase promoter of herpes simplex virus. This enhancer is inducible by phorbol 12-myristate 13-acetate in HeLa cells and is independent of its position and orientation with respect to the promoter. We have mapped the activity of the enhancer to two independent domains encompassing nucleotides 4079-4342 (end of the pol gene) and nucleotides 4781-6026 (vif gene and first coding exon of tat). This intragenic enhancer and its subdomains demonstrate cellular specificity because they are only active in specific cell lines. The presence of similar intragenic enhancer elements in other retroviruses suggests that they might be a conserved feature of this family of viruses.
Role of the intradiscal domain in rhodopsin assembly and function.
Authors: Doi T , Molday R S , Khorana H G
Published: May 2006

The role of the intradiscal polypeptide loops in bovine rhodopsin has been investigated by deletions in the N-terminal tail and in loops B-C, D-E, and E-F as well as by single amino acid substitutions in the D-E loop. Mutants with three types of phenotypes were observed. Type I mutants showed a rhodopsin-like chromophore and glycosylation. Type II mutants did not regenerate the chromophore and showed abnormal glycosylation. Type III mutants showed poor chromophore regeneration and abnormal glycosylation. Reduced transducin activation was shown by some type I and III mutants. Single amino acid substitutions in the D-E loop gave mostly type I mutants. Deletions in loops B-C, D-E, and F-G gave type II mutants, whereas deletions in the N-terminal tail produced type III mutants. Systematic deletions of two adjacent amino acids in loop D-E indicated that the amino acid sequences 171-182 and 189-192 were essential to rhodopsin structure. Immunofluorescence double-staining and transmission electron microscopy of one type II mutant (with residues 189 and 190 deleted) showed that it was mostly in the endoplasmic reticulum, whereas the wild-type protein was in the plasma membrane. We conclude that the first step in the assembly of the rhodopsin molecule is the formation of a three-dimensional structure in the intradiscal domain involving the bulk of the out-of-the-membrane polypeptide segments followed by the linkage of Cys-110 and Cys-187 through a disulfide bond.
Modifications of protein-DNA interactions in the proximal promoter of a cell-growth-regulated histone gene during onset and progression of osteoblast differentiation.
Authors: Owen T A , Holthuis J , Markose E , van Wijnen A J , Wolfe S A , Grimes S R , Lian J B , Stein G S
Published: May 2006

A temporal sequence of interrelated cellular, biochemical, and molecular events which occurs during the progressive expression of the differentiated osteoblast phenotype in primary cultures of fetal rat calvarial cells results in the development of a bone-tissue-like organization. This ordered developmental sequence encompasses three periods: proliferation, matrix maturation, and mineralization. Initially, the cells actively proliferate and synthesize type I collagen. This is followed by a period of matrix organization and maturation and then by a period of extracellular matrix mineralization. At the completion of proliferation, when expression of osteoblast phenotype markers such as alkaline phosphatase is observed, the cell-cycle-related histone genes are down-regulated transcriptionally, suggesting that a key signaling mechanism at this transition point involves modifications of protein-DNA interactions in the regulatory elements of these growth-regulated genes. Our results demonstrate that there is a selective loss of interaction of the promoter binding factor HiNF-D with the site II region of an H4 histone gene proximal promoter that regulates the specificity and level of transcription only when the down-regulation of proliferation is accompanied by modifications in the extracellular matrix that contribute to progression of osteoblast differentiation. Thus, this specific loss of protein-DNA interaction serves as a marker for a key transition point in the osteoblast developmental sequence, where the down-regulation of proliferation is functionally coupled to the appearance of osteoblast phenotypic properties associated with the organization and maturation of an extracellular matrix that becomes competent to mineralize.
Cytotoxic T lymphocytes recognize a reconstituted class I histocompatibility antigen (HLA-A2) as an allogeneic target molecule.
Authors: Elliott T J , Eisen H N
Published: May 2006

Recent findings suggest that peptide fragments of newly synthesized proteins may associate intracellularly with nascent chains of class I histocompatibility antigens (termed MHC-I proteins because they are encoded by genes of the major histocompatibility complex) and that these peptide adducts may be required for the folding or stability and perhaps even the transport of these proteins to the cell surface. To determine whether these proteins can be reconstituted from their separated subunits into ostensibly native molecules in the absence of added peptides, we denatured a purified human MHC-I protein (HLA-A2) with 4 M NaSCN, separated its heavy (alpha) and light (beta 2-microglobulin) chains by gel filtration, and then mixed them in the presence of a 3-fold molar excess of beta 2-microglobulin and absence of added peptides. The reconstituted protein, recovered in 10% yield, was indistinguishable from native A2 in its reactivity with a monoclonal antibody (BB7.7) and its ability to specifically activate A2-specific CD8+ T cells. Inasmuch as the reconstituted A2 contained no detectable peptide adducts (we estimate less than 1 per 100 on a molar basis, assuming peptides of 2-5 kDa), the results suggest that peptide-free A2 can be recognized by CD8+ T cells and that peptide adducts are not essential for the MHC-I protein to maintain an ostensibly native structure.
Cell division in higher plants: a cdc2 gene, its 34-kDa product, and histone H1 kinase activity in pea.
Authors: Feiler H S , Jacobs T W
Published: May 2006

The mitotic cell cycle of yeast and animal cells is regulated by the cdc2 gene and its product, the p34 protein kinase, and by other components of the MPF or histone H1 kinase complex. We present evidence that cdc2, p34, and a histone H1 kinase also exist in higher plants. Protein extracts from 10 plant species surveyed display a 34-kDa component recognized by a monoclonal antibody directed against an evolutionarily conserved epitope of fission yeast p34. Nondenatured protein extracts of mitotic Pisum sativum (garden pea) tissues were fractionated by gel filtration, electrophoretically separated under denaturing conditions, and immunoblotted. p34 crossreactive material was apparent in both low and high molecular mass fractions, indicating that pea p34 occurs as both a monomer and as part of a high molecular mass complex. Histone H1 kinase activity was found predominantly in the higher molecular mass fractions, those to which the least phosphorylated form of pea p34 was confined. We also report the cloning of the pea homologue of cdc2 by polymerase chain reaction. DNA sequence analysis reveals perfect conservation of the hallmark "PSTAIR" sequence motif found in all cdc2 gene products analyzed to date.
Subcellular localization of low-abundance human immunodeficiency virus nucleic acid sequences visualized by fluorescence in situ hybridization.
Authors: Lawrence J B , Marselle L M , Byron K S , Johnson C V , Sullivan J L , Singer R H
Published: May 2006

Detection and subcellular localization of human immunodeficiency virus (HIV) were investigated using sensitive high-resolution in situ hybridization methodology. Lymphocytes infected with HIV in vitro or in vivo were detected by fluorescence after hybridization with either biotin or digoxigenin-labeled probes. At 12 hr after infection in vitro, a single intense signal appeared in the nuclei of individual cells. Later in infection, when cytoplasmic fluorescence became intense, multiple nuclear foci frequently appeared. The nuclear focus consisted of newly synthesized HIV RNA as shown by hybridization in the absence of denaturation and by susceptibility to RNase and actinomycin D. Virus was detected in patient lymphocytes and it was shown that a singular nuclear focus also characterizes cells infected in vivo. The cell line 8E5/LAV containing one defective integrated provirus revealed a similar focus of nuclear RNA, and the single integrated HIV genome was unequivocally visualized on a D-group chromosome. This demonstrates an extremely sensitive single-cell assay for the presence of a single site of HIV transcription in vitro and in vivo and suggests that it derives from one (or very few) viral genomes per cell. In contrast, productive Epstein-Barr virus infection exhibited many foci of nuclear RNA per cell.
Protein database searches for multiple alignments.
Authors: Altschul S F , Lipman D J
Published: May 2006

Protein database searches frequently can reveal biologically significant sequence relationships useful in understanding structure and function. Weak but meaningful sequence patterns can be obscured, however, by other similarities due only to chance. By searching a database for multiple as opposed to pairwise alignments, distant relationships are much more easily distinguished from background noise. Recent statistical results permit the power of this approach to be analyzed. Given a typical query sequence, an algorithm described here permits the current protein database to be searched for three-sequence alignments in less than 4 min. Such searches have revealed a variety of subtle relationships that pairwise search methods would be unable to detect.
Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus.
Authors: Churchill M E , Tullius T D , Klug A
Published: May 2006

The zinc finger protein TFIIIA, a positive transcription factor of the 5S RNA gene, binds to an internal control region of 50 nucleotides. Two modes of binding have been considered for the TFIIIA-DNA complex, one of which has been proposed on the basis of nuclease and chemical protection experiments and the other on model building. Since then, evidence has accumulated on the structures of individual components of the complex--for example, zinc finger polypeptides studied by NMR and a segment of the binding site analyzed by x-ray crystallography, but no high-resolution structural data on the TFIIIA-DNA complex itself are available. Probes used previously to study the TFIIIA-DNA complex do not react with every nucleotide of DNA, unlike hydroxyl radical, which cleaves DNA at every backbone position. We describe here the quantitative analysis of high-resolution hydroxyl radical footprints and suggest how the array of zinc fingers might interact with the double helix.