bluuebunny/crossref_metadata_2025 huggingface dataset:
IgD receptors on murine T-helper cells bind to Fd and Fc regions of immunoglobulin D.
Authors: Tamma S M , Amin A R , Finkelman F D , Chen Y W , Thorbecke G J , Coico R F
Published: May 2006

Receptors for immunoglobulins on animal cells invariably show specificity for Fc regions of the protein and are hence called Fc receptors. The present study shows that immunoglobulin D receptors present an exception to this rule. Binding of IgD-coated erythrocytes to murine IgD-receptor-bearing T-helper cells is competitively inhibited by IgD, by its Fab delta fragments, and by deletion mutants of IgD lacking (i) the first constant domain of the delta heavy chain (KWD1), (ii) that region plus the delta heavy-chain-hinge region (KWD6), or (iii) the third constant domain of the delta heavy chain (Gen. 24). KWD1, Gen. 24, or KWD6 mutants bind to T-helper cells bearing receptors for IgD independently of each other. Furthermore, Gen. 24 and KWD6 mutants also competitively inhibit binding of each other in cross-blocking experiments. These results show that the IgD receptors binds to the Fd delta and the Fc delta and cannot readily be explained by sequence homology between the two parts of the IgD molecule.
Specificity of the murine IgD receptor on T cells is for N-linked glycans on IgD molecules.
Authors: Amin A R , Tamma S M , Oppenheim J D , Finkelman F D , Kieda C , Coico R F , Thorbecke G J
Published: May 2006

IgD receptors on murine T cells have been reported in this issue [Tamma, S. M. L., Amin, A. R., Finkelman, F. D., Chen, Y.-W., Thorbecke, G. J. & Coico, R. F. (1991) Proc. Natl. Acad. Sci. USA 88, 9233-9237] to bind either the first or third constant region of the heavy-chain of IgD molecules--findings that could not be satisfactorily explained by IgD amino acid sequences. We now find that boiled IgD molecules or low-Mr fragments from protease-digested IgD still inhibit binding of IgD-coated erythrocytes to IgD receptors. This inhibitory activity can be absorbed with the murine IgD-binding lectin from Griffonia simplicifolia 1 (GS-1) immobilized on Sepharose. N-linked glycans, obtained from N-glycanase-treated IgD and purified by binding to GS-1-Sepharose, also inhibit rosette formation of T-helper cells bearing receptors for IgD with IgD- or mutant IgD-coated erythrocytes. Deglycosylated IgD, produced by treatment with N-glycanase, no longer binds to the lectin and fails to inhibit IgD rosetting. Binding of intact IgD to T cells is also competitively inhibited by N-acetylgalactosamine, galactose, N-acetylglucosamine, and neoglycoproteins containing these sugars. These results clearly show that N-linked glycans, present in both the first and third constant regions of the delta heavy-chain domains, are prerequisites for binding of IgD to IgD receptors.
Inhibition of glutathione synthesis in the newborn rat: a model for endogenously produced oxidative stress.
Authors: Mårtensson J , Jain A , Stole E , Frayer W , Auld P A , Meister A
Published: May 2006

A model for oxidative stress is described in which glutathione (GSH) synthesis is selectively blocked in newborn rats by administration of L-buthionine-(S,R)-sulfoximine (BSO). In this model, the normal endogenous physiological formation of reactive oxygen species is largely unopposed, and therefore oxidative tissue damage occurs; because GSH is used for reduction of dehydroascorbate, tissue ascorbate levels decrease. In lung there are decreased numbers of lamellar bodies and decrease of intraalveolar surfactant. Proximal renal tubular, hepatic, and brain damage also occur. A diastereoisomer of BSO that does not inhibit GSH synthesis, L-buthionine-R-sulfoximine, does not produce toxicity; this control experiment renders it unlikely that the observed effects of BSO are produced by the sulfoximine moiety itself. There is correlation between the decrease of mitochondrial GSH levels and mitochondrial and cell damage. Oxidative stress as evaluated by mitochondrial damage and mortality can be prevented by treatment with GSH esters or ascorbate. There is apparent linkage between the antioxidant actions of GSH and ascorbate. This model, which may readily be applied to evaluation of the efficacy of other compounds in preventing oxidative stress, offers an approach to study of other effects of GSH deficiency (e.g., on lipid metabolism, hematopoiesis), and closely resembles oxidative stress that occurs in certain human newborns and in other clinical states.
Isolation of temperature-sensitive mutations of the tyrosine kinase receptor sevenless (sev) in Drosophila and their use in determining its time of action.
Authors: Mullins M C , Rubin G M
Published: May 2006

Loss-of-function mutations in the sevenless (sev) gene in Drosophila result in the failure to differentiate a specific photoreceptor cell type--namely, the R7 cell. The sev gene encodes a cell-surface receptor tyrosine kinase that functions in the presumptive R7 cell to transduce developmental cues from its neighbors, instructing it to differentiate along the R7 cell pathway. We have isolated temperature-sensitive alleles of sev and used them to show that Sev activity is required for several hours during the development of each R7 cell to specify R7 cell differentiation. Our data also suggest that the presumptive R7 cell remains for approximately 5 hr in an undetermined state in the absence of the Sev-mediated signal before committing to an alternative fate. We have determined the molecular lesions in four of the temperature-sensitive alleles. One of these mutations disrupts the Gly-Xaa-Gly-Xaa-Xaa-Gly consensus in the ATP-binding site of the kinase domain.
Mechanism of activation of sensory rhodopsin I: evidence for a steric trigger.
Authors: Yan B , Nakanishi K , Spudich J L
Published: May 2006

Sensory rhodopsin I (SR-I) and bacteriorhodopsin (BR) from Halobacterium halobium show broad structural and spectroscopic similarities and yet perform distinct functions: photosensory reception and proton pumping, respectively. Probing the photoactive sites of SR-I and BR with 24 retinal analogs reveals differences in the protein environments near the retinal 13-methyl group and near the beta-ionone ring. 13-cis-Retinal does not form a retinylidene pigment with the SR-I apoprotein, although this isomer binds to the BR apoprotein even more rapidly than all-trans-retinal, the functional isomer of both pigments. The activation of both SR-I and BR requires all-trans/13-cis isomerization of retinal;however, a steric interaction between the retinal 13-methyl group and the protein is required for SR-I activation but not for that of BR. These results reveal a key difference between SR-I and BR that is likely to be the initial diverging point in their photoactivation pathways. We propose the 13-methyl group-protein interaction functions as a trigger for SR-I activation--i.e., converts photon absorption by the chromophore into protein conformational changes. A similar steric trigger is essential for activation of mammalian rhodopsin, indicating a common mechanism for receptor activation in archaebacterial and vertebrate retinylidene photosensors.
Geonium "K" experiment using spin dependency of cyclotron frequency supports g data of earlier geonium "S" work.
Authors: Mittleman R , Palmer F , Gabrielse G , Dehmelt H
Published: May 2006

By substituting the relativistic spin state dependence of the cyclotron frequency for the continuous Stern-Gerlach effect and running the geonium atom as a microsynchrocyclotron accelerator we have detected spin flips of the individual trapped electron. In our initial efforts we have been able to obtain a simple symmetric spin resonance about 4-fold narrower instead of a complex asymmetric one and also to support but not as yet seriously test the result of the earlier geonium "S" work, g/2 = 1. 001 159 652 185 5(40).
Invertebrate cytokines: tunicate cell proliferation stimulated by an interleukin 1-like molecule.
Authors: Raftos D A , Cooper E L , Habicht G S , Beck G
Published: May 2006

Tunicate pharyngeal cells include lymphocyte-like cells and granular amoebocytes. They are involved in the specific allogeneic and phagocytic reactions of tunicates. Little is known about their regulation or control. A tunicate interleukin 1 (IL-1)-like fraction is shown to stimulate the proliferation of these cells in vitro. This fraction, designated tunicate IL-1 beta, was isolated from tunicate hemolymph by gel filtration and chromatofocusing chromatography. Mitogenic responses to tunicate IL-1 beta were dose dependent and could be eliminated rapidly by removing tunicate IL-1 beta from culture medium. A second tunicate hemolymph fraction had no effect on tunicate cell proliferation even though it exhibited IL-1-like activity in a mouse thymocyte proliferation assay. Phytohemagglutin did not act synergistically with either fraction. These data are discussed in terms of the function and evolution of IL-1-like molecules in invertebrates.
The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding.
Authors: Yuan H S , Finkel S E , Feng J A , Kaczor-Grzeskowiak M , Johnson R C , Dickerson R E
Published: May 2006

The 98-amino acid Fis protein from Escherichia coli functions in a variety of reactions, including promotion of Hin-mediated site-specific DNA inversion when bound to an enhancer sequence. It is unique among site-specific DNA-binding proteins in that it binds to a large number of different DNA sequences, for which a consensus sequence is difficult to establish. X-ray crystal structure analyses have been carried out at 2.3 A resolution for wild-type Fis and for an Arg-89----Cys mutant that does not stimulate DNA inversion. Each monomer of the Fis dimer has four alpha-helices, A-D; the first 19 residues are disordered in the crystal. The end of each C helix is hydrogen bonded to the beginning of helix B' from the opposite subunit in what effectively is one long continuous, although bent, helix. The four helices, C, B', C', and B, together define a platform through the center of the Fis molecule: helices A and A' are believed to be involved with Hin recombinase on one side, and helices D and D' interact with DNA lying on the other side of the platform. Helices C and D of each subunit comprise a helix-turn-helix (HTH) DNA-binding element. The spacing of these two HTH elements in the dimer, 25 A, is too short to allow insertion into adjacent major grooves of a straight B-DNA helix. However, bending the DNA at discrete points, to an overall radius of curvature of 62 A, allows efficient docking of a B-DNA helix with the Fis molecule. The proposed complex explains the experimentally observed patterns of methylation protection and DNase I cleavage hypersensitivity. The x-ray structure accounts for the effects of mutations in the Fis sequence. Those that affect DNA inversion but not DNA binding are located within the N-terminal disordered region and helix A. This inversion activation domain is physically separated in the Fis molecule from the HTH elements and may specify a region of contact with the Hin recombinase. In contrast, mutations that affect HTH helices C and D, or interactions of these with helix B, have the additional effect of decreasing or eliminating binding to DNA.
Acetylaminofluorene and aminofluorene adducts inhibit in vitro transcription of a Xenopus 5S RNA gene only when located on the coding strand.
Authors: Chen Y H , Matsumoto Y , Shibutani S , Bogenhagen D F
Published: May 2006

Unique N-acetyl-2-aminofluorene (AAF) or 2-aminofluorene (AF) adducts were introduced into the Xenopus borealis somatic 5S RNA gene between the intragenic control region and the transcription termination site. The effects of these bulky adducts on transcription were studied in a cell-free extract derived from Xenopus laevis oocytes. AAF and AF adducts inhibit transcription only when they are on the template strand, whereas transcription passes through these adducts when they are placed on the nontemplate strand. In the presence of the AAF or AF adduct on the template strand, transcription usually terminates one nucleotide before the altered guanine residue. Premature termination at these bulky adducts does not block reinitiation of transcription, since several transcripts are produced per gene per hour on these damaged templates.
Direct binding of a synthetic multichain polypeptide to class II major histocompatibility complex molecules on antigen-presenting cells and stimulation of a specific T-cell line require processing of the polypeptide.
Authors: Zisman E , Sela M , Mozes E
Published: May 2006

T-cell activation involves the recognition of foreign antigens as a complex with self-major histocompatibility complex (MHC) proteins on the surface of antigen-presenting cells (APC). Protein antigens usually require uptake by the APC and processing that results in the generation of peptide fragments. The branched synthetic polypeptide (Tyr, Glu)-Ala--Lys was chosen as a model antigen to follow the processing requirements, leading to T-cell activation. It has been demonstrated, by using fixed APC and various inhibitors of proteases, that (Tyr, Glu)-Ala--Lys has to be processed to stimulate a (Tyr, Glu)-Ala--Lys-specific T-cell line of C3H.SW (H-2b) origin to proliferate. To determine whether processing of (Tyr,Glu)-Ala--Lys is required to allow its association with the MHC class II molecules, biotin was covalently attached to it. Binding of the biotinylated (Tyr,Glu)-Ala--Lys to MHC class II gene products on the surface of intact normal APC was directly detected by phycoerythrin-streptavidin. The specificity of the binding was confirmed by its inhibition with anti-I-Ab antibodies as well as with excess of nonlabeled (Tyr,Glu)-Ala--Lys. Furthermore, introducing several inhibitors of proteases to the binding assay, we could substantiate that the proteolysis of (Tyr,Glu)-Ala--Lys is required to allow association of the resulting peptidyl T-cell epitopes with the MHC class II molecules themselves. The presence of the biotin moiety in the resulting peptides suggests that the T-cell epitopes of (Tyr,Glu)-Ala--Lys contain the N-terminal portion of the side chains of the branched polypeptide. An apparent Kd of 8.05 x 10(-8) M was determined, and optimal binding was detected after 10 hr of incubation with the antigen. The latter phenomenon is not due to slow uptake, since uptake of (Tyr,Glu)-Ala--Lys occurs mainly during the first 30 min of incubation, but rather reflects the events of processing that precede MHC interaction.
DS28-6, a temperature-sensitive mutant of Chinese hamster ovary cells, expresses key phenotypic changes associated with brefeldin A treatment.
Authors: Zuber C , Roth J , Misteli T , Nakano A , Moremen K
Published: May 2006

The temperature-sensitive Chinese hamster ovary (CHO) cell mutant DS28-6 has been previously shown to be pleiotropically defective in protein secretion. We have examined the mutant cells to determine the intracellular site of the block in secretion. By transmission electron microscopy a time-dependent disassembly of the Golgi apparatus was found under nonpermissive temperature, which resulted in the loss of the cisternal stack. Complete reorganization of the Golgi apparatus occurred after shift to permissive temperature. Under nonpermissive temperature, a microtubule- and energy-dependent redistribution of Golgi mannosidase II and galactosyltransferase into a pattern characteristic of the endoplasmic reticulum (ER) was observed. Inhibition of protein synthesis by cycloheximide had no influence on Golgi mannosidase II redistribution. Evidence for Golgi apparatus-associated processing of oligosaccharides in the ER was obtained by lectin-gold cytochemistry revealing the presence of the galactose (beta 1----4)N-acetylglucosamine sequence and sialic acid residues. Furthermore, 7-nitrobenz-2-oxa-1,3-diazol-4-yl-tagged ceramide, a lipidic trans-Golgi apparatus marker in CHO cells, exhibited an energy-dependent redistribution into the ER. These effects were fully reversible upon shift to permissive temperature. Thus, mutant DS28-6 cells exhibit key features of the brefeldin A phenotype, which suggests that the observed brefeldin A effects result from interference with a normally occurring cellular process.
Chimeric human immunodeficiency virus type 1/type 2 reverse transcriptases display reversed sensitivity to nonnucleoside analog inhibitors.
Authors: Shih C K , Rose J M , Hansen G L , Wu J C , Bacolla A , Griffin J A
Published: May 2006

Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), an important therapeutic target in the treatment of AIDS, is effectively inhibited by a class of nonnucleoside analog compounds that includes nevirapine (BI-RG-587) and tetrahydroimidazo[4,5,1-jk]-[1,4]benzodiazepin-2(1H)-one and -thione. We show that both tyrosine residues at positions 181 and 188 flanking the putative catalytic site of HIV-1 RT are required for sensitivity of the enzyme to these compounds. HIV-2 RT, which does not have tyrosines at these positions, is resistant to these nonnucleoside analog inhibitors. Substitution of the HIV-2 RT amino acid residues at position 181 or 188 into HIV-1 RT results in an enzyme that is resistant to these compounds while retaining sensitivity to 3'-azido-2',3'-dideoxythymidine triphosphate. HIV-2 RT substituted with amino acids 176-190 from HIV-1 RT acquires sensitivity to these nonnucleoside analog inhibitors.
Identification of a limited T-cell receptor beta chain variable region repertoire associated with diabetes in the BB rat.
Authors: Gold D P , Bellgrau D
Published: May 2006

Diabetes-prone BB rats spontaneously develop type 1 diabetes due to a T-cell-dependent destruction of insulin-producing beta-islet cells. A number of T-cell abnormalities including lymphopenia, poor cell-mediated responsiveness to alloantigen, and an absence of an RT6+ T-cell subset are associated with disease susceptibility. Our previous studies have implicated the thymic antigen-presenting cell in influencing disease potential and responsiveness to alloantigen. Since this cell type is also known to influence T-cell receptor expression in developing thymocytes, we examined the thymic and peripheral T-cell receptor beta chain variable region repertoire in diabetes-prone and diabetes-resistant rats. Our findings indicate that animals susceptible to diabetes induction have a characteristic and limited peripheral beta chain variable region repertoire that differs markedly from that expressed in the thymus.
Pharmacological properties of a potent and selective nonpeptide substance P antagonist.
Authors: Garret C , Carruette A , Fardin V , Moussaoui S , Peyronel J F , Blanchard J C , Laduron P M
Published: May 2006

We describe here the pharmacological properties of RP 67580 [(3aR,7aR)-7,7-diphenyl-2-[1-imino-2-(2-methoxyphenyl)ethyl] perhydroisoindol-4-one], a nonpeptide antagonist of substance P (SP). In vitro, the compound was found to inhibit in a competitive manner (Ki = 4.16 +/- 0.59 nM) [3H]SP binding to neurokinin receptors type 1 (NK1 receptors) in rat brain membranes. Contractions induced by SP and septide (a selective NK1 agonist) in guinea pig ileum were competitively inhibited by RP 67580 (pA2 = 7.16 and 7.59, respectively). Moreover, RP 67580 displayed the profile of a specific antagonist of NK1 receptors: it was not active on NK2 and NK3 receptors as seen in binding assays and in isolated preparations of rabbit pulmonary artery and rat portal vein. In the rat, low intravenous doses of RP 67580 totally inhibited the plasma extravasation induced by SP in the urinary bladder (ED50 = 0.04 mg/kg i.v.) and by antidromic electrical stimulation of the saphenous nerve in the hind paw skin (ED50 = 0.15 mg/kg i.v.). This compound was also active in two classical analgesic tests in mice: phenylbenzoquinone-induced writhing (ED50 = 0.07 mg/kg s.c.) and the formalin test (ED50 = 3.7 mg/kg s.c.). Its potency was of the same order as that of morphine. Thus we conclude that RP 67580, a SP antagonist, belongs to a class of drugs that may be useful in the management of various clinical pathologies where pain and neurogenic inflammation are involved.
Rapid activation of hippocampal casein kinase II during long-term potentiation.
Authors: Charriaut-Marlangue C , Otani S , Creuzet C , Ben-Ari Y , Loeb J
Published: May 2006

Several studies suggest that protein kinase C and type II Ca2+/calmodulin-dependent protein kinase are activated during induction of long-term potentiation (LTP). We now report that casein kinase II (CK-II), which is present in high concentration in the hippocampus, is also activated in the CA1 region during LTP. CK-II activity increased within 2 min after a train of high-frequency electrical stimulations and reached a maximum (2-fold increase) 5 min later before returning to baseline value. The stimulated protein kinase activity, which was blocked by a selective antagonist of N-methyl-D-aspartate receptors, exhibited specific properties of CK-II, including phosphorylation of the specific substrates of CK-II, marked inhibition by a low heparin concentration, and the use of GTP as a phosphate donor. CK-II activity was also selectively and rapidly augmented in another form of LTP produced by bath application of tetraethylammonium; this LTP (called LTPk) is Ca2+ dependent but N-methyl-D-aspartate independent. Phosphorylation of casein that was not inhibited by heparin (i.e., casein kinase I) remained unchanged. We suggest that an increase in CK-II activity is important in LTP induction.
Post's program and incomplete recursively enumerable sets.
Authors: Harrington L , Soare R I
Published: May 2006

A set A of nonnegative integers is recursively enumerable (r.e.) if A can be computably listed. It is shown that there is a first-order property, Q(X), definable in E, the lattice of r.e. sets under inclusion, such that (i) if A is any r.e. set satisfying Q(A) then A is nonrecursive and Turing incomplete and (ii) there exists an r.e. set A satisfying Q(A). This resolves a long open question stemming from Post's program of 1944, and it sheds light on the fundamental problem of the relationship between the algebraic structure of an r.e. set A and the (Turing) degree of information that A encodes.
Suppression of diabetes in nonobese diabetic mice by oral administration of porcine insulin.
Authors: Zhang Z J , Davidson L , Eisenbarth G , Weiner H L
Published: May 2006

Nonobese diabetic (NOD) mice spontaneously develop an autoimmune form of diabetes associated with insulitis. A number of immunomodulatory therapies have been investigated as a treatment for the disease process. Oral administration of the autoantigens myelin basic protein and collagen type II suppresses experimental models of encephalomyelitis and arthritis. We have now found that oral administration of insulin delays the onset and reduces the incidence of diabetes in NOD mice over a 1-year period in animals administered 1 mg of porcine insulin orally twice a week for 5 weeks and then weekly until 1 year of age. As expected, orally administered insulin had no metabolic effect on blood glucose levels. The severity of lymphocytic infiltration of pancreatic islets was also reduced by oral administration of insulin. Furthermore, splenic T cells from animals orally treated with insulin adoptively transfer protection against diabetes, demonstrating that oral insulin administration generates active cellular mechanisms that suppress disease. These results show that oral insulin affects diabetes and the pancreatic cellular inflammatory process in the NOD mouse and raise the possibility that oral administration of insulin or other pancreatic autoantigens may provide a new approach for the treatment of autoimmune diabetes.
Expression of active secreted forms of human amyloid beta-protein precursor by recombinant baculovirus-infected insect cells.
Authors: Bhasin R , Van Nostrand W E , Saitoh T , Donets M A , Barnes E A , Quitschke W W , Goldgaber D
Published: May 2006

Three alternatively spliced forms of the amyloid precursor protein (APP), APP-695, APP-751, and APP-770, were expressed in the baculovirus expression vector system. The recombinant proteins were secreted into the culture medium by infected insect cells, and APP molecules were detected in insect cells and medium 2 days after infection with the recombinant APP-baculoviruses. A partial sequence of the NH2 terminus of the secreted protein revealed identity with the native secreted protein and showed that the signal peptide was recognized and properly cleaved in insect cells. Purified secreted recombinant APP-751 comigrated with protease nexin 2 purified from platelets and fibroblasts. A 15-kDa COOH-terminal fragment of APP was also detected in cells infected with recombinant baculoviruses, suggesting that recombinant APP proteins were cleaved at the COOH-terminal end like native APP protein. Recombinant APP-751 and APP-770 formed complexes with epidermal growth factor-binding protein, whereas APP-695 did not. In addition, recombinant APP-751 and APP-770 inhibited trypsin and chymotrypsin activity, whereas APP-695 did not. Growth of a human fibroblast cell line, A-1, that required APP for complete growth, was restored upon addition of secreted recombinant APP-695 or APP-751. Thus, the appropriately sized, secreted recombinant APP proteins produced in this expression system are biologically active.
Recognition of beta 2-microglobulin-negative (beta 2m-) T-cell blasts by natural killer cells from normal but not from beta 2m- mice: nonresponsiveness controlled by beta 2m- bone marrow in chimeric mice.
Authors: Höglund P , Ohlén C , Carbone E , Franksson L , Ljunggren H G , Latour A , Koller B , Kärre K
Published: May 2006

The role of major histocompatibility complex (MHC) class I expression in control of the sensitivity of normal cells to natural killer (NK) cells was studied by the use of mutant mice made deficient for expression of beta 2-microglobulin (beta 2m) through homologous recombination in embryonal stem cells. T-cell blasts from beta 2m-deficient (beta 2m -/-) mice were killed by NK cells from normal mice in vitro, while beta 2m +/- blasts were resistant. The beta 2m defect also affected the NK effector cell repertoire: NK cells from beta 2m -/- mice failed to kill beta 2m -/- blasts, while they retained the ability to kill the prototype NK cell target lymphoma YAC-1, although at reduced levels. The inability to recognize beta 2m -/- blasts could be transferred with beta 2m -/- bone marrow to irradiated beta 2m-expressing mice. In contrast, the development of CD8+ T cells (deficient in beta 2m -/- mice) was restored in such chimera. These results indicate that loss of MHC class I/beta 2m expression is sufficient to render normal cells sensitive to NK cells, and that the same defect in the hemopoietic system of a mouse renders its NK cells tolerant to beta 2m-deficient but otherwise normal cells. In the beta 2m -/- mice, NK cells may be selected or educated by other bone marrow cells to tolerate the MHC class I deficiency. Alternatively, the specificity may be controlled directly by the class I molecules on the NK cells themselves.
The small subunit of transcription factor IIF recruits RNA polymerase II into the preinitiation complex.
Authors: Flores O , Lu H , Killeen M , Greenblatt J , Burton Z F , Reinberg D
Published: May 2006

We found that transcription factor IIF mediates the association of RNA polymerase II with promoter sequences containing transcription factors IID, IIB, and IIA (DAB complex). The resulting DNA-protein complex contained RNA polymerase II and the two subunits of transcription factor IIF (RAP 30 and RAP 74). Cloned human RAP 30 was sufficient for the recruitment of RNA polymerase II to the DAB complex. This ability of RAP 30 to recruit RNA polymerase to a promoter is also a characteristic of sigma factors in prokaryotes.
Proteolysis patterns of epitopically labeled yeast DNA topoisomerase II suggest an allosteric transition in the enzyme induced by ATP binding.
Authors: Lindsley J E , Wang J C
Published: May 2006

A cloned yeast TOP2 gene was modified to produce yeast DNA topoisomerase II (EC 5.99.1.3) epitopically labeled at its amino or carboxyl terminus. Limited digestion with SV8 endoprotease shows three distinct protease-sensitive sites in each polypeptide of the dimeric enzyme. These sites were mapped by immunostaining of the end-labeled proteolytic fragments resolved by SDS/polyacrylamide gel electrophoresis; two of the mapped locations were confirmed by sequencing the amino ends of two unlabeled peptic fragments. Proteolytic cleavage by SV8 endoprotease at a pair of sites corresponding to the carboxyl sides of Glu-411 and Glu-680 is modulated by the binding of the nonhydrolyzable ATP analogs adenosine 5'-[beta, gamma-imido]triphosphate (5'-adenylyl imidodiphosphate) and adenosine 5'-[gamma-thio]triphosphate: in their absence cleavage occurs predominantly at Glu-411; in the presence of either analog, cleavage occurs predominantly at Glu-680. These results are interpreted in terms of allosteric interdomainal movements in the type II DNA topoisomerase following the binding of ATP.
The promoter of the CD11b gene directs myeloid-specific and developmentally regulated expression.
Authors: Shelley C S , Arnaout M A
Published: May 2006

Human CD11b/CD18 (complement receptor type 3) is a member of the beta 2 integrin subfamily which also includes the heterodimers CD11a/CD18 and CD11c/CD18. The CD11 molecules and the common CD18 are the products of different genes that exhibit distinct though overlapping patterns of tissue- and developmental-specific expression. Whereas expression of CD11b and CD11c is almost exclusively restricted to cells of the myeloid lineage, that of CD11a and CD18 is panleukocytic. To begin to understand the mechanisms by which expression of these gene products is restricted to leukocytes and leukocyte subpopulations and to elucidate the mechanisms by which their expression is coordinated, we have cloned and characterized the promoter region of the CD11b gene. A single transcription initiation site has been identified and the region extending 242 base pairs upstream and 71 base pairs downstream of this site has been shown to be sufficient to direct tissue-, cell-, and development-specific expression in vitro, which mimics that of the CD11b gene in vivo. Within this region there are potential binding sites for transcription factors known to be involved in hematopoietic-specific and phorbol ester-inducible gene expression. Further analysis of this region of the CD11b gene and comparison with the promoters of the CD11a, CD11c, and CD18 genes should lead to significant insights into the molecular mechanisms by which these genes are regulated during hematopoietic development and upon activation.
Identification of the second common Jewish Gaucher disease mutation makes possible population-based screening for the heterozygous state.
Authors: Beutler E , Gelbart T , Kuhl W , Sorge J , West C
Published: May 2006

Gaucher disease is an autosomal recessive glycolipid storage disease characterized by a deficiency of glucocerebrosidase. The disease is most common in persons of Ashkenazi Jewish ancestry and the most common mutation, accounting for about 75% of the mutant alleles in this population, is known to be an A----G substitution at cDNA nucleotide (nt) 1226. Screening for this disease has not been possible because nearly 25% of the mutant alleles had not been identified, but linkage analysis led to the suggestion that most of these could be accounted for by a single mutation. We now report the discovery of this mutation. The insertion of a single nucleotide, a second guanine at cDNA nt 84 (the 84GG mutation), has been detected in the 5' coding region of the glucocerebrosidase gene. The amount of mRNA produced is shown to be normal but since the frameshift produced early termination, no translation product is seen. This finding is consistent with the virtual absence of antigen found in patients carrying this mutation. The 84GG mutation accounts for most of the previously unidentified Gaucher disease mutations in Jewish patients. The common Jewish mutation at nt 1226, the 84GG mutation, and the less-common mutation at nt 1448 accounted for 95% of all of the Gaucher disease-producing alleles in 71 Jewish patients. This now makes it possible to screen for heterozygotes on a DNA level with a relatively low risk of missing couples at risk for producing infants with Gaucher disease.
Gene transfer with subsequent removal of the selection gene from the host genome.
Authors: Dale E C , Ow D W
Published: May 2006

A general method of gene transfer that does not leave behind a selectable marker in the host genome is described. A luciferase gene was introduced into the tobacco genome by using the hygromycin phosphotransferase gene (hpt) as a linked selectable marker. Flanked by recombination sites from the bacteriophage P1 Cre/lox recombination system, the hpt gene was subsequently excised from the plant genome by the Cre recombinase. The Cre-catalyzed excision event in the plant genome was precise and conservative--i.e., without loss or alteration of nucleotides in the recombinant site. After removal of the Cre-encoding locus by genetic segregation, plants were obtained that had incorporated only the desired transgene. Gene transfer without the incorporation of antibiotic-resistance markers in the host genome should ease public concerns over the field release of transgenic organisms expressing such traits. Moreover, it would obviate the need for different selectable markers in subsequent rounds of gene transfer into the same host.
Intramolecular crosslinking of monomeric fibrinogen by tissue transglutaminase.
Authors: Murthy S N , Wilson J , Guy S L , Lorand L
Published: May 2006

In addition to generating polymeric products from human fibrinogen, human erythrocyte transglutaminase (protein-glutamine:amine gamma-glutamyltransferase, EC 2.3.2.13) was shown to catalyze the intramolecular reaction of crosslinking two of the constituent chains within monomeric fibrinogen itself. This internally fused protein derivative contains appreciable amounts of the N epsilon-(gamma-glutamyl)lysine bridge peptide and displays the A alpha.gamma hybrid chain pattern of crosslinking, characteristic for the actions of tissue transglutaminases on fibrinogen. Diagnostic analysis in pathological situations, where such enzymes might have escaped from cells into the plasma environment, should include a search for the internally crosslinked soluble fibrinogen monomer.
URF13, a maize mitochondrial pore-forming protein, is oligomeric and has a mixed orientation in Escherichia coli plasma membranes.
Authors: Korth K L , Kaspi C I , Siedow J N , Levings C S
Published: May 2006

URF13, an inner mitochondrial membrane protein of the maize Texas male-sterile cytoplasm (cms-T), has one orientation in the inner membrane of maize mitochondria but two topological orientations in the plasma membrane when expressed in Escherichia coli. Antibodies specific for the carboxyl terminus of URF13 and for an amino-terminal tag fused to URF13 in E. coli were used to determine the location of each end of the protein following protease treatments of right-side-out and inside-out vesicles derived from cms-T mitochondria and the E. coli plasma membrane. Cross-linking studies indicate that a portion of the URF13 population in mitochondria and E. coli exists in membranes in an oligomeric state and, in combination with proteolysis studies, show that individual subunits within a given multimer have the same orientation. A three-membrane-spanning helical model for URF13 topology is presented.
Identification of a cold shock transcriptional enhancer of the Escherichia coli gene encoding nucleoid protein H-NS.
Authors: La Teana A , Brandi A , Falconi M , Spurio R , Pon C L , Gualerzi C O
Published: May 2006

The hns (27 min) gene encoding the 15.4-kDa nucleoid protein H-NS was shown to belong to the cold shock regulon of Escherichia coli, its expression being enhanced 3- to 4-fold during the growth lag that follows a shift from 37 degrees C to 10 degrees C. A 110-base-pair (bp) DNA fragment containing the promoter of hns fused to a promoterless cat gene (hns-cat fusion) conferred a similar cold shock response to the expression of chloramphenicol acetyltransferase (CAT) activity in vivo and in coupled transcription-translation systems prepared with extracts of cold-shocked cells. Extracts of the same cells produce a specific gel shift of the 110-bp DNA fragment and this fragment, immobilized on a solid support, specifically retains a single 7-kDa protein present only in cold-shocked cells that was found to be identical to F10.6 (CS7.4), the product of cspA. This purified protein, which is homologous to human DNA-binding protein YB-1, recognizes some feature of the 110-bp promoter region of hns and acts as a cold shock transcriptional activator of this gene since it stimulates the expression of CAT activity and of cat transcription in in vitro systems programmed with plasmid DNA carrying the hns-cat fusion.
Identification of the most common mutation within the porphobilinogen deaminase gene in Swedish patients with acute intermittent porphyria.
Authors: Lee J S , Anvret M
Published: May 2006

Acute intermittent porphyria (AIP) is a metabolic disorder characterized by a partial deficiency of the porphobilinogen deaminase (PBGD, EC 4.3.1.8) activity. Previous haplotype analysis combined with genealogical data suggested a common origin of the PBGD gene mutation in the AIP families originating from northern Sweden (Lappland), where the highest prevalence of the disease (1 in 1500) is observed. An AIP family from Lappland consisting of two patients and two unaffected subjects was investigated. The genomic DNA fragments of the PBGD gene were amplified by polymerase chain reaction (PCR) and directly sequenced, and the sequence of the coding region was compared with the normal sequence to identify the mutation. A base substitution, G to A, in exon 10 of the PBGD gene was identified. The mutation changes the codon for Trp198 to a stop codon (nonsense mutation) and creates a recognition site for the restriction enzyme Nhe I. Screening of 33 Swedish AIP families showed that 15 had this mutation. Genealogical data revealed that 12 of the 15 families were related to the northern family. This finding supports the hypothesis of a "founder effect" of the mutation in the families originating from Lappland. In addition, a method is described for detection of specific sequences in the genome by one-sided PCR using Taq polymerase. This method is simple, fast, and economical and can be substituted for hybridization analysis using allele-specific oligonucleotides.
Transmissible familial Creutzfeldt-Jakob disease associated with five, seven, and eight extra octapeptide coding repeats in the PRNP gene.
Authors: Goldfarb L G , Brown P , McCombie W R , Goldgaber D , Swergold G D , Wills P R , Cervenakova L , Baron H , Gibbs C J , Gajdusek D C
Published: May 2006

The PRNP gene, encoding the amyloid precursor protein that is centrally involved in Creutzfeldt-Jakob disease (CJD), has an unstable region of five variant tandem octapeptide coding repeats between codons 51 and 91. We screened a total of 535 individuals for the presence of extra repeats in this region, including patients with sporadic and familial forms of spongiform encephalopathy, members of their families, other neurological and non-neurological patients, and normal controls. We identified three CJD families (in each of which the proband's disease was neuropathologically confirmed and experimentally transmitted to primates) that were heterozygous for alleles with 10, 12, or 13 repeats, some of which had "wobble" nucleotide substitutions. We also found one individual with 9 repeats and no nucleotide substitutions who had no evidence of neurological disease. These observations, together with data on published British patients with 11 and 14 repeats, strongly suggest that the occurrence of 10 or more octapeptide repeats in the encoded amyloid precursor protein predisposes to CJD.
Two distinct alpha beta T-cell lineages can be distinguished by the differential usage of T-cell receptor V beta gene segments.
Authors: Lahti J M , Chen C L , Tjoelker L W , Pickel J M , Schat K A , Calnek B W , Thompson C B , Cooper M D
Published: May 2006

Avian T cells can be divided into three subpopulations based on their expression of distinct T-cell receptors (TCR1, TCR2, and TCR3), ontogeny, and tissue distribution. The TCR1 cells appear to be the equivalent of mammalian gamma delta cells, but the derivation of cells expressing TCR2 and TCR3 has been unclear. Here we report that chickens contain two families of TCR beta variable (V) gene segments, V beta 1 and V beta 2. Furthermore, TCR2 and TCR3 represent subsets of alpha beta cells that are defined by mutually exclusive usage of these two families of V beta gene segments. Sequence comparisons of V beta 1 and V beta 2 with mammalian TCR beta V segments reveal that V beta 1 gene segments encode the conserved amino acids used to define the mammalian V beta consensus subgroup I, while V beta 2 encodes the amino acids used to define the mammalian V beta subgroup II. Although the beta chains of TCR2 and TCR3 cells are encoded by the same diversity (D), joining (J), and constant (C) region segments, V beta 1 gene segments undergo rearrangement before V beta 2 gene segments during T-cell development. This may result from the fact that TCR2 cells undergo V-DJ joining by deletional rearrangement, whereas TCR3 cells undergo V-DJ joining by inversional rearrangement. These data suggest that the TCR alpha beta cells can be divided into two distinct and evolutionarily conserved lineages based on V beta gene segment usage. The clear-cut separation of these lineages in the chicken may help to define their immunologic role.
Chemical implementation of neural networks and Turing machines.
Authors: Hjelmfelt A , Weinberger E D , Ross J
Published: May 2006

We propose a reversible reaction mechanism with a single stationary state in which certain concentrations assume either high or low values dependent on the concentration of a catalyst. The properties of this mechanism are those of a McCulloch-Pitts neuron. We suggest a mechanism of interneuronal connections in which the stationary state of a chemical neuron is determined by the state of other neurons in a homogeneous chemical system and is thus a "hardware" chemical implementation of neural networks. Specific connections are determined for the construction of logic gates: AND, NOR, etc. Neural networks may be constructed in which the flow of time is continuous and computations are achieved by the attainment of a stationary state of the entire chemical reaction system, or in which the flow of time is discretized by an oscillatory reaction. In another article, we will give a chemical implementation of finite state machines and stack memories, with which in principle the construction of a universal Turing machine is possible.
In vitro selection of lymphocytic choriomeningitis virus escape mutants by cytotoxic T lymphocytes.
Authors: Aebischer T , Moskophidis D , Rohrer U H , Zinkernagel R M , Hengartner H
Published: May 2006

Cytotoxic T lymphocyte (CTL)-mediated cytolysis is induced via the interaction of the specific T-cell antigen receptor and the peptidic viral antigen associated with the major histocompatibility complex class I antigen. Here we demonstrate in vitro that lymphocytic choriomeningitis virus (LCMV) can escape the cytotoxic activity of LCMV-specific cloned CTLs by single amino acid changes within the recognized T-cell epitope defined by residues 275-289 of the LCMV glycoprotein [LCMV-GP-(275-289)]. LCMV-infected fibroblasts at a multiplicity of infection of 10(-3) exposed to virus-specific CTL at an effector-to-target cell ratio of 4:1 4 hr after infection was optimal for virus mutant selection. The selections were carried out with three LCMV-GP-(275-289)-specific CTL clones expressing T-cell antigen receptors containing the identical variable gene segments V alpha 4 and V beta 10 but different junctional regions; selection was also possible with LCMV-GP-(275-289)-specific cytotoxic polyclonal T cells. The most common escape mutation was an amino acid change of asparagine (AAT) to aspartic acid (GAT) at position 280; an additional mutation was glycine (GGT) to aspartic acid (GAT) at position 282. The results presented show that relevant point mutations within the T-cell epitope of LCMV-GP-(275-289) occur frequently and that they are selectable in vitro by CTLs.
Isolation of the cDNA for erythrocyte integral membrane protein of 28 kilodaltons: member of an ancient channel family.
Authors: Preston G M , Agre P
Published: May 2006

CHIP28 is a 28-kDa integral membrane protein with similarities to membrane channels and is found in erythrocytes and renal tubules. A cDNA for CHIP28 was isolated from human fetal liver cDNA template by a three-step polymerase chain reaction (PCR) cloning strategy, starting with degenerate oligonucleotide primers corresponding to the N-terminal amino acid sequence determined from purified CHIP28 protein. Using the third-step PCR product as a probe, we isolated a recombinant from a human bone marrow cDNA library. The combined sequence of the PCR products and bone marrow cDNA contains 38 base pairs of 5' untranslated nucleotide sequence, an 807-bp open reading frame, and approximately 2 kilobases of 3' untranslated sequence containing a polyadenylation signal. This corresponds to the 3.1-kilobase transcript identified by RNA blot-hybridization analysis. Authenticity of the deduced amino acid sequence of the CHIP28 protein C terminus was confirmed by expression and immunoblotting. Analysis of the deduced amino acid sequence suggests that CHIP28 protein contains six bilayer-spanning domains, two exofacial potential N-glycosylation sites, and intracellular N and C termini. Search of the DNA sequence data base revealed a strong homology with the major intrinsic protein of bovine lens, which is the prototype of an ancient but recently recognized family of membrane channels. These proteins are believed to form channels permeable to water and possibly other small molecules. CHIP28 shares homology with all known members of this channel family, and it is speculated that CHIP28 has a similar function.
Nitric oxide and another potent vasodilator are formed from NG-hydroxy-L-arginine by cultured endothelial cells.
Authors: Zembowicz A , Hecker M , Macarthur H , Sessa W C , Vane J R
Published: May 2006

The hypothesis was investigated that NG-hydroxy-L-arginine (L-HOArg) is an intermediate in the biosynthesis of nitric oxide (.NO) from L-arginine (L-Arg) by the constitutive .NO synthase (NOS) present in endothelial cells (ECs). When infused through a column of bovine aortic ECs on beads, either L-HOArg or D-HOArg (1-10 microM) substantially potentiated relaxations of the bioassay tissues to .NO released from the cells by ADP or bradykinin, and this effect was abolished by coinfusions of NG-nitro-L-arginine (L-NO2Arg) methyl ester (10 microM) or NG-monomethyl-L-arginine (L-MeArg; 30 microM). Both L-HOArg and D-HOArg, irrespective of the presence of ECs, also potentiated relaxations induced by authentic .NO, but not glyceryl trinitrate. This was due to a rapid chemical reaction of either isomer with .NO, resulting in the formation of a potent and more stable vasodilator. When infusions of L-HOArg (3 microM) were consequently made in the presence of D-HOArg (10 microM), the L-isomer no longer had any effect on relaxations induced by authentic .NO, but significantly increased the stimulated release of .NO from the column of ECs. The conclusion that L-HOArg is a substrate for the constitutive NOS in cultured ECs was strongly supported by the L-NO2Arg-sensitive conversion of L-HOArg, but not D-HOArg, to .NO by NOS preparations from these cells. Interestingly, cultured ECs produced from L-HOArg (greater than or equal to 3 microM), but not D-HOArg, a stable vasodilator, the effects of which were inhibited by oxyhemoglobin (0.3-3 microM). However, the formation of this substance was not prevented by L-NO2Arg methyl ester (10 microM) or L-MeArg (10-100 microM), suggesting an enzymatic pathway different from NOS.