bluuebunny/crossref_metadata_2025 huggingface dataset:
Dark matter: theoretical perspectives.
Authors: Turner M S
Published: May 2006

I both review and make the case for the current theoretical prejudice: a flat Universe whose dominant constituent is nonbaryonic dark matter, emphasizing that this is still a prejudice and not yet fact. The theoretical motivation for nonbaryonic dark matter is discussed in the context of current elementary-particle theory, stressing that (i) there are no dark-matter candidates within the "standard model" of particle physics, (ii) there are several compelling candidates within attractive extensions of the standard model of particle physics, and (iii) the motivation for these compelling candidates comes first and foremost from particle physics. The dark-matter problem is now a pressing issue in both cosmology and particle physics, and the detection of particle dark matter would provide evidence for "new physics." The compelling candidates are a very light axion (10(-6)-10(-4) eV), a light neutrino (20-90 eV), and a heavy neutralino (10 GeV-2 TeV). The production of these particles in the early Universe and the prospects for their detection are also discussed. I briefly mention more exotic possibilities for the dark matter, including a nonzero cosmological constant, superheavy magnetic monopoles, and decaying neutrinos.
Differential antagonism of Ras biological activity by catalytic and Src homology domains of Ras GTPase activation protein.
Authors: Clark G J , Quilliam L A , Hisaka M M , Der C J
Published: May 2006

Ras p120 GTPase activation protein (GAP), a cytosolic protein, is a negative mediator and potential downstream effector of Ras function. Since membrane association is critical for Ras function, we introduced the Ras membrane-targeting signal (a 19-residue peptide ending in CAAX, where C = cysteine, A = aliphatic amino acid, and X = any amino acid) onto the GAP N-terminal Src homology 2 and 3 and the C-terminal catalytic domains (designated nGAP/CAAX and cGAP/CAAX, respectively) to determine the role of membrane association in GAP function. cGAP/CAAX and full-length GAP/CAAX, but not GAP or nGAP/CAAX, exhibited potent growth inhibitory activity. Whereas both oncogenic and normal Ras activity were inhibited by cGAP/CAAX, nGAP/CAAX, despite lacking the Ras binding domain, inhibited the activity of oncogenic Ras without affecting the action of normal Ras. Altogether, these results demonstrate that membrane association potentiates GAP catalytic activity, support an effector function for GAP, and suggest that normal and oncogenic Ras possess different downstream interactions.
Histones H1 and H5 interact preferentially with crossovers of double-helical DNA.
Authors: Krylov D , Leuba S , van Holde K , Zlatanova J
Published: May 2006

The interaction of the linker histones H1 and H5 from chicken erythrocyte chromatin with pBR322 was studied as a function of the number of superhelical turns in circular plasmid molecules. Supercoiled plasmid DNA was relaxed with topoisomerase I so that a population with a narrow distribution of topoisomers, containing from zero to five superhelical turns, was obtained. None of the topoisomers contained alternative non-B-DNA structures. Histone-DNA complexes formed at either 25 or 100 mM NaCl final concentration and at histone-DNA molar ratios ranging from 10 to 150 were analyzed by agarose gel electrophoresis. The patterns of disappearance of individual topoisomer bands from the gel were interpreted as an indication of preference of the linker histones for crossovers of double-helical DNA. This preference was observed at both salt concentrations, being more pronounced under conditions of low ionic strength. Isolated H5 globular domain also caused selective disappearance of topoisomers from the gel, but it did so only at very high peptide-DNA molar ratios. The observed preference of the linker histones for crossovers of double-helical DNA is viewed as a part of the mechanism involved in the sealing of the two turns of DNA around the histone octamer.
An electrostatic mechanism for substrate guidance down the aromatic gorge of acetylcholinesterase.
Authors: Ripoll D R , Faerman C H , Axelsen P H , Silman I , Sussman J L
Published: May 2006

Electrostatic calculations based on the recently solved crystal structure of acetylcholinesterase (acetylcholine acetylhydrolase, EC 3.1.1.7) indicate that this enzyme has a strong electrostatic dipole. The dipole is aligned with the gorge leading to its active site, so that a positively charged substrate will be drawn to the active site by its electrostatic field. Within the gorge, aromatic side chains appear to shield the substrate from direct interaction with most of the negatively charged residues that give rise to the dipole. The affinity of quaternary ammonium compounds for aromatic rings, coupled with this electrostatic force, may work in concert to create a selective and efficient substrate-binding site in acetylcholinesterase and explain why the active site is situated at the bottom of a deep gorge lined with aromatic residues.
von Willebrand factor mediates platelet adhesion to virally infected endothelial cells.
Authors: Etingin O R , Silverstein R L , Hajjar D P
Published: May 2006

von Willebrand factor is an adhesive glycoprotein critical to normal hemostasis. It is stored in the Weibel-Palade body of endothelial cells and upon release may mediate platelet adhesion. Herpesvirus-infected endothelium is known to be prothrombotic and to support enhanced platelet adherence. We previously identified P-selectin as a monocyte receptor that is translocated from the Weibel-Palade body to the endothelial cell surface in response to the local generation of thrombin on herpesvirus infected cells. In this study, we show that viral injury to vascular endothelial cells induces secretion of von Willebrand factor which mediates enhanced platelet adhesion to these cells.
Azamacrolides: a family of alkaloids from the pupal defensive secretion of a ladybird beetle (Epilachna varivestis).
Authors: Attygalle A B , McCormick K D , Blankespoor C L , Eisner T , Meinwald J
Published: May 2006

Defensive droplets from glandular hairs of the pupa of the Mexican bean beetle, Epilachna varivestis, contain a group of structurally novel alkaloids, the azamacrolides. The major constituent of this secretion, epilachnene, is shown to be (5Z)-11-propyl-12-azacyclotetradec-5-en-14-olide. The secretion also contains an epilachnadiene and trace amounts of three closely related components.
Specific defect in N-acetylglucosamine incorporation in the biosynthesis of the glycosylphosphatidylinositol anchor in cloned cell lines from patients with paroxysmal nocturnal hemoglobinuria.
Authors: Hillmen P , Bessler M , Mason P J , Watkins W M , Luzzatto L
Published: May 2006

Paroxysmal nocturnal hemoglobinuria (PNH) is a clonal disorder arising in a multipotent hemopoietic stem cell. PNH manifests clinically with intravascular hemolysis resulting from an increased sensitivity of the red cells belonging to the PNH clone to complement-mediated lysis. Numerous studies have shown that surface proteins anchored to the membrane via a glycosylphosphatidylinositol (GPI) anchor (including proteins protecting the cell from complement) are deficient on the cells of the PNH clone, leading to the notion that GPI-anchor biosynthesis may be abnormal in these cells. To investigate the biochemical defect underlying PNH we have used lymphoblastoid cell lines (LCLs) with the PNH phenotype obtained by Epstein-Barr virus immortalization of lymphocytes from nine patients with PNH. By labeling cells with myo-[3H]inositol we have found that PNH LCLs produce phosphatidylinositol normally. By contrast, PNH LCLs fail to incorporate [3H]mannose into GPI anchor precursors. When cell-free extracts of PNH LCLs and normal LCLs obtained from the same patients (and expected therefore to be isogeneic except for the PNH mutation) were incubated with uridine diphospho-N-acetyl[3H]glucosamine (UDP-[3H]GlcNAc), we observed complete failure or marked reduction in the production of N-acetylglucosaminyl(alpha-1,6)phosphatidylinositol and glucosaminyl(alpha-1,6)phosphatidylinositol by the PNH LCLs in all cases. These findings pinpoint the block in PNH at an early stage in the biosynthesis of the GPI anchor, suggesting that the defective enzyme is UDP-GlcNAc:phosphatidylinositol-alpha-1,6-N- acetylglucosaminyltransferase. The existence of PNH type III cells and type II cells is probably explained by the transferase deficiency being total or partial, respectively.
CD4 down-regulation by nef alleles isolated from human immunodeficiency virus type 1-infected individuals.
Authors: Mariani R , Skowronski J
Published: May 2006

PCR was used to clone isolates of the human immunodeficiency virus type 1 (HIV-1) nef gene directly from peripheral blood leukocytes of HIV-1-infected individuals. A transient expression system with human CEM T cells was used to assess the effect of nef on CD4 antigen expression on the cell surface. We show that CD4 down-regulation is a frequent property of primary HIV-1 nef alleles. Mutations in conserved amino acid motifs of Nef disrupted CD4 down-regulation. Our observations strongly suggest that CD4 down-regulation reflects a conserved function of nef, which is selected in vivo in human HIV-1 infection. Methodology described here provides quantitative assays to establish whether alterations in nef correlate with the dynamics of disease progression in human AIDS.
Formins: phosphoprotein isoforms encoded by the mouse limb deformity locus.
Authors: Vogt T F , Jackson-Grusby L , Rush J , Leder P
Published: May 2006

Mutations at the mouse limb deformity (ld) locus result in defects of growth and patterning of the limb and kidney during embryonic development. The gene responsible for this phenotype is large and complex, with the capacity to generate a number of alternatively spliced messenger RNA transcripts encoding nuclear protein isoforms called "formins." We have made polyclonal antibodies to specific formin peptides and have confirmed the authenticity of the antibodies' reactivity, using cell lines derived from mice with molecularly defined mutations at the ld locus. In addition, we have used these antibodies to detect and characterize polypeptides encoded by both wild-type and mutant ld alleles. In so doing, we show that a formin isoform (i) is modified by posttranslational phosphorylation at serine and threonine residues and (ii) when present in a crude nuclear extract, is retained by DNA-cellulose.
Unusual charge configurations in transcription factors of the basic RNA polymerase II initiation complex.
Authors: Karlin S
Published: May 2006

A systematic analysis of the primary sequences of the polymerase II initiation complex has revealed unusual charge features in the TFII family proteins. In particular, the proteins TFIIA alpha, TFIIE alpha, and TFIIF carry multiple charge clusters and hyper charge runs, sequence features occurring in < 4% of all (available) eukaryotic proteins. Possible implications for these charge structures are discussed in relation to the assembly and function of the polymerase II transcriptional complex.
Yeast calmodulin and a conserved nuclear protein participate in the in vivo binding of a matrix association region.
Authors: Fishel B R , Sperry A O , Garrard W T
Published: May 2006

Chromatin becomes reorganized during mitosis each cell cycle. To identify genes potentially involved in these supramolecular events, we have used a colony-color assay to screen temperature-sensitive mutants of Saccharomyces cerevisiae. When a sequence that mediates attachment to the nuclear matrix in vitro was inserted into the GAL1 promoter of a lacZ fusion gene, beta-galactosidase synthesis was inhibited. This observation permitted screening for temperature-sensitive-inducible mutants on 5-bromo-4-chloro-3-indolyl beta-D-galactoside plates. Only 1 of 20 complementation groups of newly isolated mutants exhibited temperature-sensitive inducibility for the matrix association region but not for control CEN3 or STE6 inserts--a cmd1 mutant in which the last 7 amino acids of calmodulin were truncated by an ochre termination codon. Another mutant (smi1) exhibited a rare phenotype at the nonpermissive condition, which included S phase and budding arrest. We cloned and sequenced the SMI1 gene, which encodes a 57-kDa polypeptide with evolutionarily conserved epitope(s) found in mammalian cell nuclei. Thus, we provide evidence for involvement of calmodulin and another conserved protein in the in vivo binding of a matrix association region.
Nucleic acid binding proteins in highly purified Creutzfeldt-Jakob disease preparations.
Authors: Sklaviadis T , Akowitz A , Manuelidis E E , Manuelidis L
Published: May 2006

The nature of the infectious agent causing human Creutzfeldt-Jakob disease (CJD), a slowly progressive dementia, is controversial. As in scrapie, no agent-specific proteins or nucleic acids have been identified. However, biological features of exponential replication and agent strain variation, as well as physical size and density data, are most consistent with a viral structure--i.e., a nucleic acid-protein complex. It is often assumed that nuclease treatment, which does not reduce infectious titer, leaves no nucleic acids of > 50 bp. However, nucleic acids of 500-6000 bp can be extracted from highly purified infectious complexes with a mass of approximately 1.5 x 10(7) daltons. It was therefore germane to search for nucleic acid binding proteins that might protect an agent genome. We here use Northwestern blotting to show that there are low levels of nonhistone nucleic acid binding proteins in highly purified infectious 120S gradient fractions. Several nucleic acid binding proteins were clearly host encoded, whereas others were apparent only in CJD, but not in parallel preparations from uninfected brain. Small amounts of residual host Gp34 (prion protein) did not bind any 32P-labeled nucleic acid probes. Most of the minor "CJD-specific" proteins had an acidic pI, a characteristic of many viral core proteins. Such proteins deserve further study, as they probably contribute to unique properties of resistance described for these agents. It remains to be seen if any of these proteins are agent encoded.
Expression of a gene encoding a unique protein-tyrosine kinase within specific fetal- and adult-derived hematopoietic lineages.
Authors: Choi K , Kennedy M , Keller G
Published: May 2006

A gene encoding a unique protein-tyrosine kinase was isolated by PCR from undifferentiated embryonic stem (ES) cells. The gene, Emsk (embryonic stem cell kinase), is expressed in a number of different lymphoid and myeloid hematopoietic lineages and has been shown to be identical to the recently isolated focal adhesion-associated kinase gene (Fadk). Within the nonlymphoid lineages analyzed, Emsk/Fadk was found to be expressed in primitive and definitive erythroid cells but not in mast cells or macrophages. All CD5+ (B-1a) B cells tested, as well as freshly isolated conventional (B-2) B cells, expressed readily detectable levels of Emsk/Fadk. Within the T-cell lineage, Emsk/Fadk was expressed in V gamma 5 gamma/delta cells as well as in immature alpha/beta cells found within the thymus. As the alpha/beta T-cell population matures and exits the thymus, expression of Emsk/Fadk appears to be down regulated. The expression pattern outlined here suggests a role for Emsk/Fadk in multiple stages of hematopoietic development and raises the possibility that the kinase encoded by this gene has a broader spectrum of activities than was initially suggested.
Proline isomerases function during heat shock.
Authors: Sykes K , Gething M J , Sambrook J
Published: May 2006

The cyclophilins (CYPs) and FK506 binding proteins (FKBPs) are two families of distinct proline isomerases that are targets for a number of clinically important immunosuppressive drugs. Members of both families catalyze cis/trans isomerization of peptidyl-prolyl bonds, which can be a rate-limiting step during protein folding in vitro and in vivo. We demonstrate in Saccharomyces cerevisiae that heat shock causes a 2- to 3-fold increase in the level of mRNA encoded by the major cytoplasmic CYP gene, CYP1. The cloned CYP1 promoter confers heat-inducible expression upon a reporter gene, and transcriptional induction is mediated through sequences similar to the consensus heat shock response element. Disruption of CYP1 decreases survival of cells following exposure to high temperatures, indicating that CYP1 plays a role in the stress response. A second CYP gene, CYP2, encodes a cyclophilin that is located within the secretory pathway. Its expression is also stimulated by heat shock, and cells containing a disrupted CYP2 allele are more sensitive than wild-type cells to heat. By contrast, expression of the FKB1 gene, which encodes a cytoplasmic member of the yeast FKBP family, is neither heat responsive nor necessary for survival after exposure to heat stress.
Interleukin 4 suppresses interleukin 2 and interferon gamma production by naive T cells stimulated by accessory cell-dependent receptor engagement.
Authors: Tanaka T , Hu-Li J , Seder R A , Fazekas de St Groth B , Paul W E
Published: May 2006

Interleukin 2 (IL-2) and interferon gamma (IFN-gamma) production by CD4+ T cells and IFN-gamma production by CD8+ T cells from naive mice in response to soluble anti-CD3 and antigen-presenting cells (APCs) were strikingly inhibited by culture in the presence of IL-4. IL-4 decreased IL-2 and IFN-gamma mRNA levels after 15-24 hr but gave relatively little decrease in these mRNAs at 6-12 hr after stimulation with soluble anti-CD3. A 16-hr preculture of T cells with anti-CD3, APCs, and IL-4 was sufficient to inhibit subsequent production of IL-2 and IFN-gamma in response to restimulation in the absence of IL-4. Furthermore, IL-4 treatment of T cells purified 24 hr after stimulation inhibited their capacity to subsequently produce IL-2 in response to anti-CD3 and APCs, indicating that T cells were targets of IL-4-mediated inhibition. IL-4 blocked acute IL-2 production in response to a cytochrome c peptide of T cells derived from transgenic mice expressing T-cell receptors specific for cytochrome c but it did not block IL-2 production by such cells after they had been primed in vitro. Nor did IL-4 inhibit production of IFN-gamma by cloned T cells in response to antigen and APCs or production of IL-2 and IFN-gamma by naive T cells in response to phorbol ester and calcium ionophore. These results indicate that IL-4 strikingly inhibits IL-2 and IFN-gamma production by naive T cells in response to accessory cell-dependent, receptor-mediated stimulation (i.e., soluble anti-CD3 and APCs or antigen and APCs) but does not inhibit accessory cell-independent stimulation of naive T cells or accessory cell-dependent receptor-mediated stimulation of recently primed T cells or cloned T-cell lines.
Cloning from the thyroid of a protein related to actin binding protein that is recognized by Graves disease immunoglobulins.
Authors: Leedman P J , Faulkner-Jones B , Cram D S , Harrison P J , West J , O'Brien E , Simpson R , Coppel R L , Harrison L C
Published: May 2006

Human actin binding protein (ABP) links specific membrane glycoproteins to cytoskeletal actin microfilaments. In human platelets and leukocytes, ABP directly links, respectively, the membrane glycoproteins GPIb and the high-affinity Fc receptor for IgG (Fc gamma IR) to cytoskeletal actin microfilaments. Similar interaction between the thyrotropin (TSH) receptor and ABP in endocrine cells might explain the rapid and profound disruption of actin microfilaments induced by TSH in cultured thyroid follicular cells. By screening a thyroid lambda gt11 cDNA expression library with serum from a Graves disease patient, we identified a clone encoding a protein, designated truncated ABP (TABP), that shares extensive homology (approximately 70%) with ABP. TABP is a truncated ABP-like protein with an open reading frame of 195 aa that encodes a protein of approximately 21 kDa. TABP lacks an actin binding domain but contains two predicted beta-sheet repeats within which is a putative dimerization domain and between which lies a putative glycoprotein binding site containing a consensus site for phosphorylation by Ca(2+)-calmodulin kinase II. TABP contains a unique C-terminal insertion within which lies a hydrophobic predicted membrane-associated region, absent from ABP. Although TABP mRNA is expressed widely, immunoblot analysis demonstrated the presence of TABP antibodies specifically in the sera of a minority of subjects with autoimmune thyroid disease. A 24-residue sequence of similarity was identified between the TSH receptor and platelet glycoprotein GPIb alpha that may represent a transmembrane ABP binding site. We suggest, therefore, that signal transduction by TSH in the thyroid involves direct linkage of the TSH receptor to actin microfilaments by ABP and that TABP may interact with ABP to mediate TSH-induced actin microfilament disruption.
Six mRNAs with different 5' ends are encoded by a single gamma-glutamyltransferase gene in mouse.
Authors: Rajagopalan S , Wan D F , Habib G M , Sepulveda A R , McLeod M R , Lebovitz R M , Lieberman M W
Published: May 2006

The 5' region of the mouse gamma-glutamyltransferase (gamma GT; EC 2.3.2.2) gene has been cloned and analyzed. This analysis, combined with sequence information obtained from gamma GT cDNA clones, indicates that in mouse a single gamma GT gene codes for six different mRNAs that differ in their 5' sequences. Analysis of steady-state levels of gamma GT RNA reveals different expression patterns for these RNAs in different organs. The six different 5' sequences are widely separated within a 10-kb region and three of them show 75-86% identify with the three known rat gamma GT cDNAs. Although the heterogeneity of the 5' ends of gamma GT RNAs may be explained in part by alternative splicing, it is likely that multiple promoters are involved in their generation.
Functional reconstitution in Escherichia coli of the yeast mitochondrial matrix peptidase from its two inactive subunits.
Authors: Géli V
Published: May 2006

The matrix processing peptidase from yeast (Saccharomyces cerevisiae) mitochondria was expressed in Escherichia coli via a plasmid-borne operon encoding the mature forms of the alpha and beta subunits of the enzyme. The subunits assembled into a fully active, soluble enzyme. The mature subunits were also expressed individually. The alpha subunit accumulated in large amounts and was obtained at a purity of 80% after a single chromatographic step. The beta-subunit-producing strain expressed an intact and a degraded form of the beta subunit, both of them soluble in the cytoplasm. Extract from either the alpha- or the beta-subunit-producing strain (S-alpha or S-beta extract, respectively), as well as the purified alpha subunit, was enzymatically inactive. However, precursor cleavage activity was restored by mixing either the S-alpha extract or the purified alpha subunit with the S-beta extract. The reconstituted processing activity was indistinguishable from the authentic holopeptidase.
Molecular cloning and functional expression of the pituitary adenylate cyclase-activating polypeptide type I receptor.
Authors: Pisegna J R , Wank S A
Published: May 2006

Pituitary adenylate cyclase-activating polypeptide (PACAP), a neuropeptide belonging to the vasoactive intestinal peptide (VIP)/secretion/glucagon family of peptides, interacts with a distinct high-affinity receptor (type I receptor) on a number of tissues. These PACAP type I receptors have a high affinity for PACAP and a low affinity for VIP and are present in the hypothalamus and anterior pituitary, where they regulate the release of adrenocorticotropin, luteinizing hormone, growth hormone, and prolactin, and in the adrenal medulla, where they regulate the release of epinephrine. Type I PACAP receptors are also present in high concentrations in testicular germ cells, where they may regulate spermatogenesis, and some transformed cell lines, such as the rat pancreatic acinar carcinoma cell AR4-2J. Here we report the molecular cloning and functional expression of the PACAP type I receptor isolated from an AR4-2J cell cDNA library by cross-hybridization screening with a rat VIP receptor cDNA. The cDNA sequence encodes a unique 495-amino acid protein with seven transmembrane domains characteristic of guanine nucleotide-binding regulatory protein-coupled receptors. A high degree of sequence homology with the VIP, secretin, glucagon-like peptide 1, parathyroid, and calcitonin receptors suggests its membership in this subfamily of Gs-coupled receptors. Results of binding studies and stimulation of cellular cAMP accumulation in COS-7 cells transfected with this cDNA are characteristic of a PACAP type I receptor. Cloning of the PACAP type I receptor will enhance our understanding of its distribution, structure, and functional properties and ultimately increase our understanding of its physiological role.
Kinematics and thermodynamics of a folding heteropolymer.
Authors: Fukugita M , Lancaster D , Mitchard M G
Published: May 2006

In order to elucidate the folding dynamics of protein, we have carried out numerical simulations of a heteropolymer model of self-interacting random chains. We find that folding propensity depends strongly on sequence and that both folding and nonfolding sequences exist. Furthermore we show that folding is a two-step process: the transition from coil state to unique folded state takes place through a globule phase. In addition to the continuous coil-globule transition, there exists an abrupt transition that separates the unique folded state from the globule state and ensures the stability of the native state.
Cell cycle regulation of nuclear localization of hepatitis B virus core protein.
Authors: Yeh C T , Wong S W , Fung Y K , Ou J H
Published: May 2006

The hepatitis B virus (HBV) core protein has been found in the nucleus, the cytoplasm, or both of HBV-infected hepatocytes. However, the mechanism that regulates the subcellular localization of the HBV core protein is still unclear. In this report, we demonstrate that nuclear localization of the HBV core protein is cell cycle-regulated in two different cell lines. The amount of the core protein in the nucleus was increased during the G1 phase, reduced to an undetectable level during the S phase, and increased again when the cells were confluent and ceased to grow. Thus, the nuclear localization of the core protein during HBV infection can be at least partially attributed to liver injury and regeneration, which cause the hepatocytes to enter cell cycles. Based on the observation that the cytoplasmic core protein was phosphorylated and the nuclear core protein was not, we speculate that nuclear localization of the HBV core protein is negatively regulated by phosphorylation during the cell cycle.
A mouse homolog of the Escherichia coli recA and Saccharomyces cerevisiae RAD51 genes.
Authors: Morita T , Yoshimura Y , Yamamoto A , Murata K , Mori M , Yamamoto H , Matsushiro A
Published: May 2006

Analysis of mitotic and meiotic recombination in mammalian cells has been hampered by the complexity of the reactions involved as well as lack of mutants. Furthermore, none of the genes involved in the process has yet been identified. In budding yeast, Saccharomyces cerevisiae, the RAD51 gene is essential along with other genes of the RAD52 epistasis group for mitotic and meiotic recombination and DNA repair. The Rad51 protein is structurally similar to Escherichia coli RecA protein, which is required in homologous recombination and SOS responses in bacteria. Here we report the isolation of a mouse homolog of the yeast RAD51 gene. The amino acid sequence predicted from the gene shows 83% and 55% homology with those of the yeast RAD51 and the E. coli recA product, respectively. The mouse gene complemented a rad51 mutation of S. cerevisiae with sensitivity to methyl-methanesulfonate, which produces double-strand breaks of DNA. This gene is expressed in the thymus, testis, ovary, spleen, and intestine, suggesting that its product is involved in mitotic and meiotic recombination in addition to DNA repair.
Generation of nitric oxide and induction of major histocompatibility complex class II antigen in macrophages from mice lacking the interferon gamma receptor.
Authors: Kamijo R , Shapiro D , Le J , Huang S , Aguet M , Vilcek J
Published: May 2006

Availability of mice with a targeted disruption of the interferon gamma (IFN-gamma) receptor gene (IFN-gamma R0/0 mice) made it possible to examine parameters of macrophage activation in the absence of a functional IFN-gamma receptor. We asked to what extent other cytokines could replace IFN-gamma in the induction of nitric oxide or major histocompatibility complex class II antigen (Ia) expression in peritoneal macrophages. In thioglycollate-elicited macrophages from wild-type mice, tumor necrosis factor (TNF) alone was virtually ineffective in inducing release of NO2- (the endproduct of nitric oxide generation), but TNF enhanced NO2- release in the presence of IFN-gamma. In macrophages from IFN-gamma R0/0 mice, which were unresponsive to IFN-gamma, TNF completely failed to stimulate NO2- release. The stimulatory actions of IFN-alpha/beta on NO2- release were indistinguishable in wild-type and IFN-gamma R0/0 macrophages: IFN-alpha/beta was ineffective on its own, showed marginal stimulation of NO2- release in combination with TNF, and was moderately effective in the presence of lipopolysaccharide. The level of constitutive Ia antigen expression was not significantly different in peritoneal macrophages from wild-type and IFN-gamma R0/0 mice. An increased Ia expression was induced by IL-4 and granulocyte-macrophage colony-stimulating factor in both wild-type and IFN-gamma R0/0 macrophages, but the magnitude of this induction was less than with optimal concentrations of IFN-gamma in macrophages from wild-type mice. IFN-alpha/beta showed only a minor stimulatory effect on Ia expression in both wild-type and IFN-gamma R0/0 macrophages. Simultaneous treatment of wild-type macrophages with IFN-alpha/beta and IFN-gamma reduced the IFN-gamma-induced Ia expression in wild-type macrophages, but IFN-alpha/beta did not show an inhibitory effect on IL-4- or granulocyte-macrophage-colony-stimulating factor-induced Ia expression in either wild-type or IFN-gamma R0/0 macrophages. The important role of IFN-gamma in the regulation of the induced expression of major histocompatibility complex class II antigen was confirmed by showing that after systemic infection with the BCG strain of Mycobacterium bovis resident peritoneal macrophages from IFN-gamma R0/0 mice had a lower level of Ia expression than macrophages from wild-type mice. The inability of other cytokines to substitute fully for IFN-gamma in macrophage activation helps to explain the earlier observed decreased resistance of IFN-gamma R0/0 mice to some infections.
Phytochrome-regulated expression of the genes encoding the small GTP-binding proteins in peas.
Authors: Yoshida K , Nagano Y , Murai N , Sasaki Y
Published: May 2006

We examined the effect of light on the mRNA levels of 11 genes (pra1-pra9A, pra9B, and pra9C) encoding the small GTP-binding proteins that belong to the ras superfamily in Pisum sativum. When the dark-grown seedlings were exposed to continuous white light for 24 hr, the levels of several pra mRNAs in the pea buds decreased: pra2 and pra3 mRNAs decreased markedly; pra4, pra6, and pra9A mRNAs decreased slightly; the other 6 pra mRNAs did not decrease. We studied the kinetics of mRNA accumulation for pra2, pra3, and pra9B in detail during white light illumination and compared them with those of the phytochrome gene and the small subunit gene of ribulose bisphosphate carboxylase: mRNA levels of pra2 and pra3 decreased in a manner similar to that of phytochrome while that of the small subunit increased as was expected. The decreases were triggered by a 2-min monochromatic red light (660 nm) irradiation. The effect of red light was reversed by subsequent exposure to far-red light, indicating an involvement of phytochrome as a photoreceptor in this light-regulated event. This work reports negative regulation of mRNA levels of small GTP-binding proteins by light, mediated by phytochrome.
Differential organ-specific expression of three poly(A)-binding-protein genes from Arabidopsis thaliana.
Authors: Belostotsky D A , Meagher R B
Published: May 2006

Poly(A)-binding protein (PABP) is considered an essential component of a eukaryotic cell; deletion of the PABP-coding gene in yeast leads to a lethal phenotype. PABP is implicated in numerous aspects of posttranscriptional regulation, including mRNA turnover and translational initiation. A nested set of degenerate PCR primers designed from regions conserved among yeast, Xenopus, and human PABP sequences was used to amplify genomic DNA fragments from Arabidopsis thaliana. Hybridization screening of genomic and cDNA libraries with a genomic PCR probe led to the isolation of three diverse Arabidopsis genes encoding PABPs, PAB1, PAB3, and PAB5. All three sequences contain the expected four RNA-recognition motifs. Sequence diversity between these genes equals or exceeds the diversity among animal and fungal sequences. One of the genes, PAB5, and its cDNA were completely sequenced. Its open reading frame encodes a 73.2-kDa protein containing a number of amino acid motifs characteristic of PABPs from different species. Moreover, in vitro synthesized PAB5 protein bound to poly(A)-Sepharose with high specificity. All three genes isolated showed organ-specific patterns of expression. PAB5 and PAB3 RNAs were detected only in floral organs, with the highest level of expression in immature flowers. PAB1 RNA was observed predominantly in roots, was less abundant in immature flowers, and was not detected in any other organ examined (stems, leaves, mature flowers, siliques). This suggests a potentially unique role for PABPs in organ-specific posttranscriptional regulation in plants.
Processing of the herpes simplex virus regulatory protein alpha 22 mediated by the UL13 protein kinase determines the accumulation of a subset of alpha and gamma mRNAs and proteins in infected cells.
Authors: Purves F C , Ogle W O , Roizman B
Published: May 2006

We reported previously that the posttranslational processing associated with phosphorylation of the herpes simplex virus 1 infected-cell protein 22 (ICP22), a regulatory protein, is encoded by UL13, a gene encoding a structural protein of the virion. We now report the following. (i) In cells infected with a mutant lacking UL13 (delta UL13), restricted infected cells accumulate reduced levels of the regulatory protein ICP0 and several late viral proteins. Identical reductions have been observed in the same cell lines infected with a mutant from which the alpha 22 gene, encoding ICP22, had been deleted (delta alpha 22). We conclude that the UL13-mediated processing of ICP22 is essential for its gene-regulatory function. (ii) The reduced accumulations of specific viral protein in cells infected with either delta UL13 or delta alpha 22 viruses correlate with reduced levels of specific mRNAs for both ICP0 and the affected late genes. (iii) ICP22 is not modified by the UL13 protein introduced into cells during infection. (iv) ICP22 is also modified by the protein kinase encoded by US3, but this modification is different from that of the UL13 protein kinase. These results predict that UL13 encodes a protein kinase or phosphotransferase which is expressed late in the replicative life cycle and which directly or indirectly phosphorylates ICP22. This modification is essential for stabilization or increased transcription of a specific subset of viral RNAs and, ultimately, for the accumulation of corresponding viral proteins.
Circumvention of prey defense by a predator: ant lion vs. ant.
Authors: Eisner T , Baldwin I T , Conner J
Published: May 2006

The pit-dwelling ant lion Myrmeleon carolinus, although topically sensitive to formic acid, is able to prey on formic acid-spraying ants (Camponotus floridanus). It kills the ants without inducing them to spray, and it sucks out the ant's body contents without puncturing the acid sac. Ordinarily, when Camponotus is attacked it retaliates by simultaneously biting and spraying, but it usually refrains from spraying until it has secured a grip with the mandibles. When Myrmeleon pulls Camponotus into the sand at the bottom of the pit, the ant is seemingly unable to grasp the ant lion and it is killed without being induced to spray. When feeding on the ant, the ant lion sucks up the contents of the nutrient-laden crop. How the ant lion differentiates between crop and acid sac, managing to spare the latter while rupturing the former, remains unknown.
The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates.
Authors: Xu F , Lin-Chao S , Cohen S N
Published: May 2006

Previous work has shown that RNase E-mediated cleavage of RNAI, an antisense repressor of the replication of ColE1-type plasmids, relieves repression in vivo by endonucleolytically converting RNAI to a rapidly decaying product. We report that mutations in the Escherichia coli pcnB gene result in a 10-fold prolongation of the half-life of RNAI decay intermediates and also of truncated RNAI primary transcripts lacking sites attacked by RNase E. Using Northern blotting, primer extension analysis, [32P]GTP capping of 5'-triphosphate termini, and PCR amplification methods, we show that pcnB-mediated acceleration of RNAI degradation is associated with posttranscriptional 3' addition of adenosine residues in vivo to native and processed forms of RNAI. Accumulation of antisense RNAI decay products in pcnB mutants potentially explains the reduced copy number of ColE1-type plasmids seen in the mutated bacteria.
Alzheimer disease A68 proteins injected into rat brain induce codeposits of beta-amyloid, ubiquitin, and alpha 1-antichymotrypsin.
Authors: Shin R W , Bramblett G T , Lee V M , Trojanowski J Q
Published: May 2006

Aberrantly phosphorylated tau proteins (i.e., A68 or PHF-tau) and beta-amyloid or A4 (beta A4) peptides are major components of pathologic lesions in Alzheimer disease (AD). Although A68 and beta A4 colocalize in AD neurofibrillary tangles (NFTs) and amyloid-rich senile plaques (SPs), the mechanisms leading to the convergence of A68, beta A4, and other proteins in the same AD lesions are unknown. To probe the biological properties of A68 in vivo, and to assess interactions of A68 with endogenous proteins in the rodent brain, we injected A68, dephosphorylated A68 (DEP-A68), and normal adult human tau protein into the hippocampus and neocortex of rats. In marked contrast to DEP-A68 and tau, A68 resisted rapid proteolysis and induced codeposits of three rodent proteins--i.e., beta A4, ubiquitin, and alpha 1-antichymotrypsin (ACT)--that accumulate in AD NFTs and SPs together with A68. These findings suggest that A68 may interact with beta A4, ubiquitin, and ACT in neuronal perikarya as well as in the extracellular space after release of A68 from degenerating neurons. The model system described here will facilitate efforts to elucidate mechanisms leading to the convergence of A68, beta A4, ubiquitin, and ACT in hallmark lesions of AD.
The linker of des-Glu84-calmodulin is bent.
Authors: Raghunathan S , Chandross R J , Cheng B P , Persechini A , Sobottka S E , Kretsinger R H
Published: May 2006

The crystal structure of a mutant calmodulin (CaM) lacking Glu-84 has been refined to R = 0.23 using data measured to 2.9-A resolution. In native CaM the central helix is fully extended, and the molecule is dumbbell shaped. In contrast, the deletion of Glu-84 causes a bend of 95 degrees in the linker region of the central helix at Ile-85. However, EF-hand domains 1 and 2 (lobe 1,2) do not touch lobe 3,4. The length, by alpha-carbon separation, of des-Glu84-CaM is 56 A; that of native CaM is 64 A. The shape of des-Glu84-CaM is similar to that of native CaM, as it is bound to the target peptide of myosin light-chain kinase. This result supports the proposal that the linker region of the central helix of CaM functions as a flexible tether.
Are there ecological limits to population?
Authors: Keyfitz N
Published: May 2006

Policy on population and environment in the United States and abroad has been vacillating, unsure of its course; it would be more decisive if the several disciplines could agree on the nature of the problems and their urgency. The two disciplines principally concerned are biology and economics, and the contribution of this paper is to identify eight of the many axes or directions on which the methods and traditions of the two are different. For example, the first of the axes runs between contingency and orderly progress, with biology tending to seek out the former and economics the latter; thus biologists can more easily comprehend catastrophes, such as the demise of the dinosaurs or widespread desertification. The third axis concerns indefinite market-driven substitutability, seen by economists as resulting from scientific discovery; natural scientists, including biologists, whose discoveries make possible the substitutions, are skeptical. Axis 7 results from the fact that economics concentrates on goods that are on the market, and so deals with a truncated part of the commodity cycle, while ecology aims at the whole; because goods disappear from economic statistics once they pass into the hands of consumers many of their ecological effects are invisible. I believe that from similar further study of the two disciplines a common set of policy recommendations will ultimately emerge.
Genetic fusion of subunits of a dimeric protein substantially enhances its stability and rate of folding.
Authors: Liang H , Sandberg W S , Terwilliger T C
Published: May 2006

The gene V protein of bacteriophage f1 is a single-stranded DNA and RNA-binding protein composed of two identical subunits. We have constructed single-chain variants of the protein using short peptide linkers of five or six amino acids to connect the carboxyl terminus of one monomer to the amino terminus of the second monomer. The resulting subunit-fusion gene V proteins were found to bind single-stranded DNA nearly as tightly as the wild-type protein. Denaturation measurements show that the subunit-fusion gene V proteins are 5 kcal/mol (1 kcal = 4.18 kJ) more stable than the wild-type protein at a protein concentration of 10 microM. The rate of unfolding of the protein is essentially unaffected by the fusion of monomeric subunits, whereas the rate of folding is greatly enhanced. Our results suggest a simple way of obtaining a substantial thermodynamic stabilization for some oligomeric proteins.
Regional cerebral glucose metabolism in late-life depression and Alzheimer disease: a preliminary positron emission tomography study.
Authors: Kumar A , Newberg A , Alavi A , Berlin J , Smith R , Reivich M
Published: May 2006

Eight subjects with late-life depression, eight subjects with probable Alzheimer disease, and eight healthy age-matched controls were studied using 2-[18F]fluoro-2-deoxy-D-glucose positron emission tomography in the resting state with their eyes open and ears unoccluded. The depressed subjects showed widespread reductions in the regional cerebral metabolic rate for glucose in most major neocortical, subcortical, and paralimbic regions that were significantly different from control values (P < 0.01). The metabolic decrements in the depressed group were comparable in magnitude to those seen in the Alzheimer disease group. These data demonstrate widespread nonfocal decline in glucose metabolism in late-life depression that is comparable to the hypometabolism seen in Alzheimer disease. These findings have pathophysiological implications in major depressive disorder in the elderly.
Integrin alpha IIb beta 3 mediates binding of the Lyme disease agent Borrelia burgdorferi to human platelets.
Authors: Coburn J , Leong J M , Erban J K
Published: May 2006

Lyme disease is a chronic, multisystemic infection caused by the tick-borne spirochete Borrelia burgdorferi. Attachment of the spirochete to host cells via specific receptors is likely to be important in the establishment of infection. B. burgdorferi have previously been shown to bind to a variety of mammalian cells in vitro. Here we demonstrate that binding of B. burgdorferi to human platelets is mediated by the integrin alpha IIb beta 3 (glycoprotein IIb-IIIa), a critical receptor in thrombosis and hemostasis. Functional expression of this receptor requires platelet activation, and binding of the spirochete was observed only to activated platelets. Binding was inhibited by a synthetic Arg-Gly-Asp peptide that blocks ligand interaction with many integrins and by a synthetic peptide based on the gamma chain of fibrinogen that blocks binding to alpha IIb beta 3. In addition, attachment of the spirochete to platelets was inhibited by monoclonal antibodies directed against alpha IIb beta 3 that are known to block ligand-receptor interaction. No inhibition was seen with control peptides or with antibodies directed against other platelet receptors. B. burgdorferi bound efficiently to purified alpha IIb beta 3 but did not bind to platelets deficient in this integrin. Efficient platelet binding was displayed by a cloned, infectious B. burgdorferi strain, whereas a cloned noninfectious strain did not bind to platelets. Binding to integrins may be important for the ability of B. burgdorferi to establish infection in the diverse tissues affected by Lyme disease.
Target-derived influences on axon growth modes in cultures of trigeminal neurons.
Authors: Erzurumlu R S , Jhaveri S , Takahashi H , McKay R D
Published: May 2006

Cellular and molecular signals involved in axon elongation versus collateral and arbor formation may be intrinsic to developing neurons, or they may derive from targets. To identify signals regulating axon growth modes, we have developed a culture system in which trigeminal ganglion cells are challenged by various target tissues. Embryonic day 15 (E15) rat trigeminal ganglion explants were placed between peripheral (vibrissa pad) and central nervous system targets. Normally, bipolar trigeminal ganglion cells extend one process to the vibrissa pad and another to the brainstem trigeminal complex. Under coculture conditions, the peripheral processes invade the vibrissa pad explants and form a characteristic circumfollicular pattern. Central processes of E15 ganglion cells invade many, but not all, central nervous system tissues. In isochronic (E15) central nervous system explants such as brainstem, olfactory bulb, or neocortex, these central processes elongate and form a "tract" but have virtually no arbors. However, in more mature targets (e.g., a section from postnatal brainstem or neocortex), they form arbors instead of a tract. We conclude from these observations that whether trigeminal axons elongate to form a tract, or whether they begin to arborize, is dictated by the target tissue and not by an intrinsic developmental program of the ganglion cell body. The explant coculture system is an excellent model for analysis of the molecular basis of neuron-target interactions.