bluuebunny/crossref_metadata_2025 huggingface dataset:
Genes encoding tumor necrosis factor alpha and granzyme A are expressed during development of autoimmune diabetes.
Authors: Held W , MacDonald H R , Weissman I L , Hess M W , Mueller C
Published: May 2006

Progressive destruction of the insulin-producing beta cells in nonobese diabetic mice is observed after infiltration of the pancreas with lymphocytes [Makino, S., Kunimoto, K., Muraoka, Y., Mizushima, Y., Katagiri, K. & Tochino, Y. (1980) Exp. Anim. (Tokyo) 29, 1-13]. We show that the genes for tumor necrosis factor alpha and granzyme A, a serine protease associated with cytoplasmic granules of cytotoxic cells, are expressed during the development of spontaneous diabetes mellitus in the nonobese diabetic mouse. Granzyme A-positive cells are found both in and surrounding the islets, implying induction prior to islet infiltration. Tumor necrosis factor alpha expression is exclusively observed in the intra-islet infiltrate, predominantly in lymphocytes adjacent to insulin-producing beta cells, the targets of the autoimmune destruction, implying that tumor necrosis factor alpha expression is induced locally--i.e., in the islet. A considerable portion of cells expressing tumor necrosis factor alpha appear to be CD4+ T cells. This T-cell subset was previously shown to be necessary for development of the disease. Thus, these findings may be important for understanding the pathogenesis of autoimmune diabetes mellitus and potentially also for that of other T-cell-mediated autoimmune diseases.
Correction of glucocerebrosidase deficiency after retroviral-mediated gene transfer into hematopoietic progenitor cells from patients with Gaucher disease.
Authors: Fink J K , Correll P H , Perry L K , Brady R O , Karlsson S
Published: May 2006

Retroviral gene transfer has been used successfully to correct the glucocerebrosidase (GCase) deficiency in primary hematopoietic cells from patients with Gaucher disease. For this model of somatic gene therapy, we developed a high-titer, amphotropic retroviral vector designated NTG in which the human GCase gene was driven by the mutant polyoma virus enhancer/herpesvirus thymidine kinase gene (tk) promoter (Py+/Htk). NTG normalized GCase activity in transduced Gaucher fibroblasts and efficiently infected human monocytic and erythroleukemic cell lines. RNA blot-hybridization (Northern blot) analysis of these hematopoietic cell lines showed unexpectedly high-level expression from the Moloney murine leukemia virus long terminal repeat (Mo-MLV LTR) and levels of Py+/Htk enhancer/promoter-initiated human GCase RNA that approximated endogenous GCase RNA levels. Furthermore, NTG efficiently infected human hematopoietic progenitor cells. Detection (by means of the polymerase chain reaction) of the provirus in approximately one-third of NTG-infected progenitor colonies that had not been selected in G418-containing medium indicates that relative resistance to G418 underestimated the actual gene transfer efficiency. Northern blot analysis of NTG-infected, progenitor-derived cells showed expression from both the Mo-MLV LTR and the Py+/Htk enhancer/promoter. NTG-transduced hematopoietic progenitor cells from patients with Gaucher disease generated progeny in which GCase activity had been normalized.
Hamster cell line suitable for transfection assay of transforming genes.
Authors: Higashi T , Sasai H , Suzuki F , Miyoshi J , Ohuchi T , Takai S , Mori T , Kakunaga T
Published: May 2006

We established a subclone, SHOK, from the GHE-L cell line, an immortal line derived from a primary culture of Syrian hamster embryo cells, as a recipient cell line useful for the detection of oncogenes by transfection. SHOK cells were almost as susceptible as NIH 3T3 cells to focus formation by many oncogenes, including v-raf, v-Ha-ras, v-Ki-ras, or activated c-Ha-ras. The susceptibility of SHOK to focus formation was higher than that of NIH 3T3 for v-mos but was lower for v-fps, v-fgr, v-src, v-sis, and v-abl. When DNAs extracted from 27 human and murine tumors were tested for focus formation, 5 DNAs were positive in NIH 3T3 cells, whereas 9 were positive in SHOK cells at the primary transfection. Using SHOK cells as recipients of tumor cellular DNA, we isolated another oncogene and a c-Ki-ras2 gene mutated at codon 146 that were difficult to detect in NIH 3T3 cells. SHOK cells have a low rate of spontaneous transformation, produce easily distinguishable foci, and maintain a stable karyotype in transformed cells. In addition to being useful for the screening of human tumor DNAs, SHOK cells will be useful for the isolation of oncogenes from murine tumors because of their hamster origin.
A simple genealogical structure of strongly balanced allelic lines and trans-species evolution of polymorphism.
Authors: Takahata N
Published: May 2006

Different alleles undergoing strong symmetric balancing selection show a simple genealogical structure (allelic genealogy), similar to the gene genealogy described by the coalescence process for a sample of neutral genes randomly drawn from a panmictic population at equilibrium. The only difference between the two genealogies lies in the different time scales. An approximate scaling factor for allelic genealogy relative to that of neutral gene genealogy is [square root of S/(2M)].[In[S/(16 pi M2)]]-3/2, where M = Nu and S = 2Ns (N, effective population size; u, mutation rate to selected alleles per locus per generation; s, selection coefficient). The larger the value of square root of S/M (greater than or equal to 100), the larger the scaling factor. These findings, supported by simulation results, allow one to apply the theoretical results of the coalescence process directly to the allelic genealogy. Combined with the trans-species evolution of the major histocompatibility complex polymorphism for which balancing selection is believed to be responsible, allelic genealogy predicts that the number of breeding individuals in the human population could not be as small as 50-100 at any time of its evolutionary history. The analysis appears to contradict the founder principle as being important in recent mammalian evolution.
The scurfy mouse mutant has previously unrecognized hematological abnormalities and resembles Wiskott-Aldrich syndrome.
Authors: Lyon M F , Peters J , Glenister P H , Ball S , Wright E
Published: May 2006

The X chromosome-linked scurfy (sf) mutant of the mouse is recognized by the scaliness of the skin from which the name is derived and results in death of affected males at about 3-4 weeks of age. Consideration of known man-mouse homologies of the X chromosome prompted hematological studies, which have shown that the blood is highly abnormal. The platelet and erythrocyte counts are both reduced and become progressively lower relative to normal as the disease progresses. There is gastrointestinal bleeding, and most animals appear to die of severe anemia. By contrast, the leukocyte count is consistently raised. Some animals showed signs of infection but it is not yet clear whether there is immunodeficiency. Other features include the scaly skin and apparently reduced lateral growth of the skin, conjunctivitis, and diarrhea in some animals. The mutant resembles Wiskott-Aldrich syndrome in man, which is characterized by thrombocytopenia, eczema, diarrhea, and immunodeficiency. The loci of the human and mouse genes lie in homologous segments of the X chromosome, although apparently in somewhat different positions relative to other gene loci. Scurfy differs from Wiskott-Aldrich syndrome in that scurfy males are consistently hypogonadal.
A method for difference cloning: gene amplification following subtractive hybridization.
Authors: Wieland I , Bolger G , Asouline G , Wigler M
Published: May 2006

We describe a procedure for genomic difference cloning, a method for isolating sequences present in one genomic DNA population ("tester") that is absent in another ("driver"). By subtractive hybridization, a large excess of driver is used to remove sequences common to a biotinylated tester, enriching the "target" sequences that are unique to the tester. After repeated subtractive hybridization cycles, tester is separated from driver by avidin/biotin affinity chromatography, and single-stranded target is amplified by the polymerase chain reaction, rendering it double-stranded and clonable. We model two situations: the gain of sequences that result from infection with a pathogen and the loss of sequences that result from a large hemizygous deletion. We obtain 100- to 700-fold enrichment of target sequences.
Frequent inactivation of the retinoblastoma anti-oncogene is restricted to a subset of human tumor cells.
Authors: Horowitz J M , Park S H , Bogenmann E , Cheng J C , Yandell D W , Kaye F J , Minna J D , Dryja T P , Weinberg R A
Published: May 2006

We have used polyclonal anti-synthetic peptide serum to study the role of retinoblastoma gene (RB) inactivation in a variety of human tumor cell lines. Our analysis indicates that inactivation of the RB protein, p105-Rb, is universal in retinoblastoma cells, vindicating the predictions of the Knudson "two-hit" hypothesis. In addition, our analysis has shown that inactivations of the RB gene are nearly as frequent in a more common human tumor, small cell lung carcinoma. One-third of bladder carcinomas surveyed also carry altered or absent p105-Rb. Other human tumors by contrast demonstrate only infrequent inactivation of the RB gene. These results suggest that inactivation of the RB gene is a critical step in the pathogenesis of a subset of human tumors.
Fibril in senile systemic amyloidosis is derived from normal transthyretin.
Authors: Westermark P , Sletten K , Johansson B , Cornwell G G
Published: May 2006

The amyloid fibril in senile systemic amyloidosis (SSA), like that of familial amyloidotic polyneuropathy, is derived from transthyretin (TTR). SSA, however, is a common disease, affecting to some degree 25% of the population greater than 80 years old. In familial amyloidotic polyneuropathy, the amyloidogenesis has been considered to depend on point mutations leading to TTR variants. We show that the TTR molecule in SSA, on the other hand, has a normal primary structure. Factors other than the primary structure of TTR must therefore be important in the pathogenesis of TTR-derived amyloid.
Calmodulin and calcium-dependent protease I coordinately regulate the interaction of fodrin with actin.
Authors: Harris A S , Morrow J S
Published: May 2006

The calcium-dependent proteolysis of fodrin has been implicated in the regulation of secretion, neutrophil and platelet activation, and long-term potentiation in neurons. In vitro studies indicate that calcium-dependent protease I (calpain I) cleaves fodrin in the middle of the alpha subunit and in the COOH-terminal third of the beta subunit. Cleavage at the beta site requires calmodulin, which binds with high affinity to a single site in the alpha subunit. In vitro binding assays, nondenaturing gel electrophoresis, and velocity sedimentation identify a linkage between calcium-dependent protease I proteolysis of fodrin and the ability of calmodulin to regulate the self-association of fodrin and its interaction with actin. Three functional states appear to exist: (i) intact fodrin, which constitutively forms tetramers and binds F-actin; (ii) alpha-cleaved fodrin, which loses its ability to self-associate and bind F-actin in the presence of calmodulin; and (iii) alpha,beta-cleaved fodrin, a form that is incompetent to establish tetramers or bind actin. Because actin binding and fodrin self-association occur at opposite ends of the molecule, whereas calmodulin binds at its center, these results indicate that long-range interactions exist within fodrin. They also offer an example of how two calcium-dependent regulatory processes may act synergistically to reversibly regulate a linkage between the membrane and the cytoskeleton.
Altered levels of amyloid protein precursor transcripts in the basal forebrain of behaviorally impaired aged rats.
Authors: Higgins G A , Oyler G A , Neve R L , Chen K S , Gage F H
Published: May 2006

The beta/A4 protein is a constituent of plaque and vascular amyloid deposits in Alzheimer disease. Previous studies have shown increased levels of amyloid protein precursor (APP) mRNA in basal forebrain neurons in the disease. Morphological and neurochemical changes occur within the forebrain in Alzheimer disease and are also correlated with behavioral impairments in aged rats. Recent studies suggest that decreased nerve growth factor responsiveness of basal forebrain neurons is a feature of normal aging and of Alzheimer disease. We have used in situ hybridization to show that the abundance of specific forms of APP mRNA, which contain an inserted Kunitz-type serine protease inhibitor motif (APP-751, APP-770, and APP-related 563), are increased relative to the noninserted form (APP-695) of APP mRNA in the basal forebrain of aged rats. This increase appears to be specific to animals who exhibit spatial memory deficits but not aged rats without behavioral impairments.
Immortalization of bipotential and plastic glio-neuronal precursor cells.
Authors: Evrard C , Borde I , Marin P , Galiana E , Prémont J , Gros F , Rouget P
Published: May 2006

Permanent clonal cell lines from newborn mouse striatum have been established after transfer of the simian virus 40 large tumor oncogene by means of a retroviral vector. Some of the lines obtained displayed properties of bipotential and plastic glio-neuronal precursors. Depending on the culture conditions, these cells express either the glial fibrillary acidic protein or neurofilaments. In addition, the cells can display adrenergic, D1 and D2 dopaminergic, muscarinic, and 5-hydroxytryptamine type 2 serotoninergic receptors, which are coupled either to the adenylate cyclase or to the phosphatidylinositol signaling pathways. The panel of receptors for neurotransmitters exhibited by these lines closely resembles that of primary striatal neurons. Results suggest that plastic common precursors of astrocytes and neurons persist in the striatum at a late developmental stage. As these permanent cell lines constitute an unlimited source of homogenous cell material, we suggest that they should be useful for molecular and pharmacological studies on the mechanisms and regulation of signal transduction as well as the commitment, plasticity, and differentiation of neural cells.
Identification of two types of tumor necrosis factor receptors on human cell lines by monoclonal antibodies.
Authors: Brockhaus M , Schoenfeld H J , Schlaeger E J , Hunziker W , Lesslauer W , Loetscher H
Published: May 2006

The pleiotropic cyto/lymphokine tumor necrosis factor (TNF) exerts its functions by binding to specific cell-surface receptors. We have prepared two sets of monoclonal antibodies (mAbs) against TNF-binding proteins from the HL-60 (htr-mAb series) and U-937 (utr-mAb series) cell lines. The htr antibodies inhibit the binding of 125I-labeled TNF-alpha to HL-60 cells only partially, whereas they block the TNF-alpha binding to several adenocarcinoma cell lines (HEp-2, HeLa, and MCF7) almost completely. In contrast, the utr antibodies have no effect on TNF-alpha binding to the adenocarcinoma cell lines but partially inhibit TNF-alpha binding to HL-60 and U-937 cells. However, htr-9 and utr-1 antibodies in combination fully inhibit the TNF-alpha binding to HL-60 and U-937 cells. The binding of TNF-beta to HEp-2 and U-937 cells is also inhibited by htr and utr antibodies. Neither htr nor utr mAb has an effect on the TNF-sensitive murine cell lines L929 and WEHI 164. Flow cytometry studies show that mAbs htr-9 and utr-1 detect two distinct TNF-binding sites on human cell lines. Immunologic blot and immunoprecipitation analyses indicate that mAbs htr-9 and utr-1 recognize proteins of approximately 55 kDa and 75 kDa, respectively. These data provide evidence for the existence of two distinct TNF receptor molecules that contribute to varying extent to the TNF binding by different human cells.
Human epidermal growth factor receptor residue covalently cross-linked to epidermal growth factor.
Authors: Wu D G , Wang L H , Chi Y , Sato G H , Sato J D
Published: May 2006

An epidermal growth factor (EGF) receptor monoclonal antibody (mAb), mAb LA22, was used to analyze the covalent coupling of human EGF receptors to mouse EGF by the amine-reactive cross-linking agent disuccinimidyl suberate. A soluble Mr 105,000 truncated form of the receptor secreted by A-431 epidermoid carcinoma cells and consisting of the ligand-binding extracellular domain was cross-linked to 125I-labeled EGF. Digestion of this complex with an endoproteinase that specifically cleaves at the COOH side of glutamyl residue released a single radiolabeled glycosylated fragment of Mr 18,000 that reacted with mAb LA22. As the epitope for mAb LA22 resided between Ala-351 and Asp-364 of the mature receptor, this result localized the cross-linked receptor residue(s) to the 47-amino acid interval from Phe-321 to Glu-367. The receptor residue(s) involved in the covalent coupling of rat 125I-labeled transforming growth factor alpha was similarly localized to this region of the receptor. This receptor interval, which included two glycosylated asparaginyl residues at positions 328 and 337, contained but three amino acid residues that were potentially reactive with disuccinimidyl suberate: Lys-332, Lys-333, and Lys-336. Characterization of mAb LA22-reactive 125I-EGF-labeled receptor fragments generated by an endoproteinase specific for the COOH side of lysyl residue placed the NH2 termini of the two smallest fragments between the glycosylated residues Asn-328 and Asn-337. These results indicated that disuccinimidyl suberate cross-linked the NH2 group of EGF residue Asn-1 to the human EGF receptor residue Lys-336. Our results further suggest that EGF and transforming growth factor alpha, two members of the EGF family of peptide growth factors, interact with closely apposed or identical features of the receptor.
Monoclonal antibodies to individual tyrosine-phosphorylated protein substrates of oncogene-encoded tyrosine kinases.
Authors: Kanner S B , Reynolds A B , Vines R R , Parsons J T
Published: May 2006

Cellular transformation by oncogenic retroviruses encoding protein tyrosine kinases coincides with the tyrosine-specific phosphorylation of multiple protein substrates. Previous studies have shown that tyrosine phosphorylation of a protein of 120 kDa, p120, correlated with src transformation in chicken embryo fibroblasts. Additionally, we previously identified two phosphotyrosine-containing cellular proteins, p130 and p110, that formed stable complexes with activated variants of pp60src, the src-encoded tyrosine kinase. To study transformation-relevant tyrosine kinase substrates, we have generated monoclonal antibodies to individual tyrosine phosphoproteins, including p130, p120, p110, and five additional phosphoproteins (p210, p125, p118, p85, and p185/p64). These antibodies detected several of the same tyrosine phosphoproteins in chicken embryo fibroblasts transformed by avian retroviruses Y73 and CT10, encoding the yes and crk oncogenes, respectively. Protein substrates in mouse, rat, hamster, and human cells overexpressing activated variants of chicken pp60src were also detected by several of the monoclonal antibodies.
Inhibition of IgE synthesis by anti-IgE: role in long-term inhibition of IgE synthesis by neonatally administered soluble IgE.
Authors: Haba S , Nisonoff A
Published: May 2006

Inoculation of syngeneic IgE into 2- to 12-day-old mice results in prolonged synthesis of anti-IgE antibodies without further challenge. These anti-IgE antibodies may be largely responsible for the long-term inhibition of synthesis of IgE that is known to result from a perinatal challenge with IgE. This conclusion is supported by the effect of passive inoculation of syngeneic polyclonal anti-IgE antibodies into young mice, which similarly results in selective inhibition of IgE synthesis. Further evidence is the close relationship between the age dependency of IgE-induced inhibition of subsequent IgE synthesis and the ability of IgE to induce anti-IgE antibodies. IgE synthesis was monitored at the level of secretion by B cells as well as serum IgE levels and IgE antibody responses.
Mechanism of the selective functionalization of saturated hydrocarbons by Gif systems: relationship with methane monooxygenase.
Authors: Barton D H , Csuhai E , Doller D , Ozbalik N , Balavoine G
Published: May 2006

Two intermediates, A and B, have been identified in the selective oxidation of saturated hydrocarbons to ketones by Gif-type systems. Intermediate A has been characterized as an Fev species with a secondary iron sigma-bond to carbon; it is captured by four different reagents or transformed into the second intermediate, B, which hydrolyzes to form a secondary alcohol. A mu-oxo Fe2III dimer is proposed as a basis for Gif-type reactivity. If the first iron is involved in the synthesis of intermediate A, the second is used to oxidize intermediate B intramolecularly to a ketal, which on hydrolysis yields a ketone. The enzyme methane monooxygenase shows a remarkable similarity to Gif-type systems in its selective hydrocarbon oxidation, particularly in the case of adamantane.
HLA-B37 and HLA-A2.1 molecules bind largely nonoverlapping sets of peptides.
Authors: Carreno B M , Anderson R W , Coligan J E , Biddison W E
Published: May 2006

T-cell recognition of peptides that are bound and presented by class I major histocompatibility complex molecules is highly specific. At present it is unclear what role class I peptide binding plays relative to T-cell receptor specificity in determination of immune recognition. A previous study from our group demonstrated that the HLA-A2.1 molecule could bind to 25% of the members of a panel of unrelated synthetic peptides as assessed by a functional peptide competition assay. To determine the peptide-binding specificity of another HLA class I molecule, we have examined the capacity of this panel of peptides to compete for the presentation of influenza virus nucleoprotein peptide NP-(335-350) by HLA-B37 to NP-peptide-specific HLA-B37-restricted cytotoxic T-lymphocyte lines. Forty-two percent of peptides tested were capable of inhibiting NP-(335-350) presentation by HLA-B37. Remarkably, none of these HLA-B37-binding peptides belong to the subset that was previously shown to bind to the HLA-A2.1 molecule. Only the NP-(335-350) peptide was capable of binding to both HLA-A2.1 and HLA-B37. These findings demonstrate that the peptide-binding specificities of HLA-B37 and HLA-A2.1 are largely nonoverlapping and suggest that, from the universe of peptides, individual HLA class I molecules can bind to clearly distinct subsets of these peptides.
Mitogenic activity from trout embryos.
Authors: Collodi P , Barnes D W
Published: May 2006

An extract of 21-day rainbow trout embryos stimulated growth of several piscine cell lines in the absence of added serum. Established lines from trout (RTG-2 and STE-137), salmon (CHSE-214), carp (EPC), and goldfish (CAR) and early-passage cells initiated from trout embryos grew in serum-free medium containing the embryo extract. In addition the extract was sufficient for maintaining long-term cultures of CHSE-214 cells for several months through a minimum of 20 passages (approximately 50 population doublings) in the absence of serum. Optimal response was achieved with 100 micrograms of extract protein per ml, but a significant growth-promoting effect was observed with as little as 2.5 micrograms/ml. The activity was nondialyzable, protease-sensitive, and stable in 200 mM acetic acid. The level of mitogenic response induced by the extract could not be duplicated with purified mammalian growth factors added individually or in combination, and the extract did not stimulate DNA synthesis in quiescent mouse fibroblasts. These results suggest that trout embryo extract may contain a novel growth-promoting activity for fish cells.
Structure of the anti-human immunodeficiency virus agent 3'-fluoro-3'-deoxythymidine and electronic charge calculations for 3'-deoxythymidines.
Authors: Camerman N , Mastropaolo D , Camerman A
Published: May 2006

The crystal and molecular structures of the anti-human immunodeficiency virus agent 3'-fluoro-3'-deoxythymidine have been determined by x-ray diffraction and stereochemical comparisons with thymidine have been made. Atomic charge distributions have been calculated by the complete neglect of differential overlap method for thymidine and antiretrovirally active and inactive C3'-substituted analogues. The structural and electronic results suggest that antiviral activity in these analogues may be correlated with the presence of an electronegative atom attached to C3'.
Differential effects of the cytoplasmic domains of cell adhesion molecules on cell aggregation and sorting-out.
Authors: Jaffe S H , Friedlander D R , Matsuzaki F , Crossin K L , Cunningham B A , Edelman G M
Published: May 2006

Cell adhesion molecules (CAMs) are cell surface glycoproteins that play important roles in morphogenesis and histogenesis, particularly in defining discrete borders between cell populations. Previous studies have suggested that the cytoplasmic domains of CAMs play a significant role in their adhesion properties. These domains may also be involved in regulating other cellular interactions, such as those involved in the sorting-out of cells to form tissues. In the present studies, we have compared the effects of replacing the cytoplasmic domain of one CAM with that of another CAM of different homophilic binding specificity on cell adhesion and cell sorting-out. The molecules studied were liver CAM (L-CAM) and the neural CAM (N-CAM) sd polypeptide. One cDNA was constructed that encodes a chimeric molecule composed of the extracellular domain of L-CAM and the cytoplasmic plus transmembrane domains of the sd polypeptide of chicken N-CAM (called L/N-CAM). Another was constructed encoding a truncated L-CAM missing the last 50 residues of the cytoplasmic domain. Permanently transfected lines of mouse L cells were obtained expressing the truncated L-CAM ("L-L-50 cells") or the chimeric L/N-CAM ("L-L/N cells") and were compared with cells expressing intact L-CAM ("L-L cells"). Immunoblotting and ELISA analyses demonstrated that these various cell lines expressed similar amounts of CAMs at the cell surface. Aggregation of L-L and L-L/N cells occurred at similar rates in short-term aggregation assays and was inhibited by antibodies to the extracellular L-CAM binding domain. In contrast, L-L-50 cells did not aggregate. Incubation of transfected cells with cytochalasin D, which disrupts microfilaments, markedly inhibited aggregation of L-L cells but had no effect on L-L/N cell aggregation. Mixed L-L and L-L/N cells co-aggregated in short-term assays; in the longer-term sorting-out assays, however, they behaved differently: L-L cells sorted out from both L-L/N and untransfected cells, whereas L-L/N cells did not sort out from untransfected cells. These studies not only suggest that interactions of cytoplasmic domains of different CAMs with the cytoskeleton can modulate cell adhesion but also suggest that specific interactions with certain cytoskeletal components are required for events such as cell sorting and cell patterning.
Identification and characterization of a HeLa nuclear protein that specifically binds to the trans-activation-response (TAR) element of human immunodeficiency virus.
Authors: Marciniak R A , Garcia-Blanco M A , Sharp P A
Published: May 2006

Human immunodeficiency virus type 1 RNAs contain a sequence, trans-activation-response (TAR) element, which is required for tat protein-mediated trans-activation of viral gene expression. We have identified a nuclear protein from extracts of HeLa cells that binds to the TAR element RNA in a sequence-specific manner. The binding of this 68-kDa polypeptide was detected by UV cross-linking proteins to TAR element RNA transcribed in vitro. Competition experiments were performed by using a partially purified preparation of the protein to quantify the relative binding affinities of TAR element RNA mutants. The binding affinity of the TAR mutants paralleled the reported ability of those mutants to support tat trans-activation in vivo. We propose that this cellular protein moderates TAR activity in vivo.
Modulation of the general anesthetic sensitivity of a protein: a transition between two forms of firefly luciferase.
Authors: Moss G W , Franks N P , Lieb W R
Published: May 2006

The activities of most proteins are relatively insensitive to general anesthetics. A notable exception is firefly luciferase, whose sensitivity to a wide range of anesthetic agents closely parallels that of whole animals. We have now found that this sensitivity can be controlled by ATP. The enzyme is insensitive at low (microM) concentrations of ATP and very sensitive at high (mM) concentrations. The differential sensitivity varies from anesthetic to anesthetic, being greatest (about a 100-fold difference) for molecules with large apolar segments. This suggests that anesthetic sensitivity is modulated by changes in the hydrophobicity of the anesthetic-binding pocket. Parallel changes in the binding of the substrate firefly luciferin, for which anesthetics compete, indicate that anesthetics bind at the same site as the luciferin substrate. These changes in the nature of the binding pocket modify not only the sensitivity to anesthetics but also the position of the "cutoff" in the homologous series of primary alcohol anesthetics; the cutoff position can vary from octanol to pentadecanol, depending upon the concentration of ATP. Our results suggest that particularly sensitive anesthetic target sites in the central nervous system may possess anesthetic-binding pockets whose polarities are regulated by neuromodulatory agents.
Reconstitution of a group I intron self-splicing reaction with an activator RNA.
Authors: van der Horst G , Christian A , Inoue T
Published: May 2006

The self-splicing rRNA intron of Tetrahymena thermophila belongs to a subgroup of group I introns that contain a conserved extra stem-loop structure termed P5abc. A Tetrahymena mutant precursor RNA lacking this P5abc is splicing-defective under standard conditions (5 mM MgCl2/200 mM NH4Cl, pH 7.5) in vitro. However, the mutant precursor RNA by itself is capable of performing the self-splicing reaction without P5abc under different conditions (15 mM MgCl2/2 mM spermidine, pH 7.5). We have investigated the functional role of the P5abc in the mechanism of the self-splicing reaction. When an RNA consisting of the P5abc but lacking the rest of the Tetrahymena intron is incubated with the mutant precursor, the self-splicing reaction proceeds highly efficiently under standard conditions (5 mM MgCl2/200 mM NH4Cl, pH 7.5). Two steps of the bimolecular self-splicing reaction can be performed accurately by a shortened precursor RNA containing all essential components required in the self-splicing reaction and an activator RNA consisting of the P5abc. Gel-mobility-shift assays suggest that two molecules associate by a direct RNA-RNA interaction during the splicing reaction. The results imply that there might exist other small RNAs whose role is to activate ribozymes.
Genetic disease detection and DNA amplification using cloned thermostable ligase.
Authors: Barany F
Published: May 2006

Polymerase chain reaction, using thermostable DNA polymerase, has revolutionized DNA diagnostics. Another thermostable enzyme, DNA ligase, is harnessed in the assay reported here that both amplifies DNA and discriminates a single-base substitution. This cloned enzyme specifically links two adjacent oligonucleotides when hybridized at 65 degrees C to a complementary target only when the nucleotides are perfectly base-paired at the junction. Oligonucleotide products are exponentially amplified by thermal cycling of the ligation reaction in the presence of a second set of adjacent oligonucleotides, complementary to the first set and the target. A single-base mismatch prevents ligation/amplification and is thus distinguished. This method was exploited to detect 200 target molecules as well as to discriminate between normal beta A- and sickle beta S- globin genotypes from 10-microliters blood samples.
Nonhomologous chromatid exchange in hereditary and sporadic renal cell carcinomas.
Authors: Kovacs G , Kung H F
Published: May 2006

For the development of renal cell carcinomas, it has been suggested that a germ-line or somatic mutation occurs on one of the homologous chromosomes 3p, and subsequently the other 3p segment is lost. We have examined the karyotype and/or the allelic combination on chromosomes 3 and 5 by restriction fragment length polymorphism analysis in normal kidney and tumor samples from 28 renal cell carcinomas that developed in two patients with von Hippel-Lindau disease; we then compared the results to those of sporadic tumors. An unbalanced translocation between chromosome 3p and 5q or other chromosomes was found to be the most common aberration. We developed a model of nonhomologous chromatid exchange involving breakpoint clusters at chromosomes 3p13, 3p11.2, 5q22, and 8q11.2. Subsequent chromatid segregation may result in net loss of the 3p segment either (i) in one step or (ii) after a nondisjunctional loss of the derivative chromosome carrying the 3p segment. This general mechanism could also be implicated to explain genetic changes occurring in other types of solid tumors.
Reassociation with beta 2-microglobulin is necessary for Db class I major histocompatibility complex binding of an exogenous influenza peptide.
Authors: Rock K L , Gamble S , Rothstein L , Benacerraf B
Published: May 2006

A synthetic peptide corresponding to residues 365-380 of the influenza nucleoprotein (NP365-380) has been previously shown to associate with class I major histocompatibility complex-encoded molecules and to stimulate cytotoxic T lymphocytes [Townsend, A. R. M., Rothbard, J., Gotch, F. M., Bahadur, G., Wraith, D. & McMichael, A. J. (1986) Cell 44, 959-968]. We find that intact Db class I heterodimers on the cell surface are unreceptive to binding this antigen. However, NP365-380 readily associates with Db molecules on the plasma membrane in the presence of exogenous beta 2-microglobulin. In addition, there is a second pathway through which this peptide associates with class I molecules that requires energy and de novo protein synthesis. These findings have implications for maintaining the immunological identity of cells and for the use of peptides as vaccines for priming cytolytic T-cell immunity.
Scanning tunneling microscopy of a wheat seed storage protein reveals details of an unusual supersecondary structure.
Authors: Miles M J , Carr H J , McMaster T C , I'Anson K J , Belton P S , Morris V J , Field J M , Shewry P R , Tatham A S
Published: May 2006

Scanning tunneling microscopy has been used to demonstrate that a spiral structure based on beta-reverse turns is adopted by the repeat sequences present in a group of wheat gluten proteins. This structure is similar to the beta-spiral formed by a synthetic polypentapeptide based on a repeat sequence present in elastin. Wheat gluten and elastin are both elastomeric and it is possible that the spiral structure contributes to this property.
Differential expression of three glutamate receptor genes in developing rat brain: an in situ hybridization study.
Authors: Pellegrini-Giampietro D E , Bennett M V , Zukin R S
Published: May 2006

Non-N-methyl-D-aspartate glutamate receptors (GluRs) are encoded by a gene family, known members of which are designated GluR-1, -2, -3, -4, and -5. The present study examined the developmental pattern of GluR-1, -2, and -3 gene expression in rat brain. In situ hybridization revealed different spatial patterns throughout the brain for the cognate mRNAs at all ages examined, as well as different temporal patterns during development. In the adult all three mRNAs were expressed prominently in the pyramidal and granule layers of the hippocampus and in the Purkinje cell layer of the cerebellum, where detailed differences were apparent at the cellular level. In neocortex, GluR-2 mRNA exhibited prominent lamination and regional differences, which were less marked for GluR-1 and -3 mRNAs. In caudate-putamen GluR-2 mRNA was at high levels, but GluR-1 and -3 mRNAs were not. At early ages transcripts were transiently elevated relative to adult levels. GluR-1 mRNA reached peak expression in cortex at postnatal day 14 (P14) (225% of adult), in striatum at P4 (255% of adult), in hippocampus at P14 (195% of adult), and in cerebellum at P21 (150% of adult). GluR-3 exhibited more modest peaks in neocortex and hippocampus. In contrast, GluR-2 mRNA was at near adult levels throughout the first days of postnatal life and exhibited a peak only in cerebellum at P14 (168% of adult). The finding of differential developmental regulation of the GluR-1, -2, and -3 genes indicates that the receptors they encode may have different influences on synaptic plasticity, neuronal survival, and susceptibility to excitatory amino acid toxicity.
Human dermal mast cells contain and release tumor necrosis factor alpha, which induces endothelial leukocyte adhesion molecule 1.
Authors: Walsh L J , Trinchieri G , Waldorf H A , Whitaker D , Murphy G F
Published: May 2006

Tumor necrosis factor alpha (TNF-alpha) is a proinflammatory cytokine that mediates endothelial leukocyte interactions by inducing expression of adhesion molecules. In this report, we demonstrate that human dermal mast cells contain sizeable stores of immunoreactive and biologically active TNF-alpha within granules, which can be released rapidly into the extracellular space upon degranulation. Among normal human dermal cells, mast cells are the predominant cell type that expresses both TNF-alpha protein and TNF-alpha mRNA. Moreover, induction of endothelial leukocyte adhesion molecule 1 expression is a direct consequence of release of mast cell-derived TNF-alpha. These findings establish a role for human mast cells as "gatekeepers" of the dermal microvasculature and indicate that mast cell products other than vasoactive amines influence endothelium in a proinflammatory fashion.
Isolation and properties of a nitrile hydratase from the soil fungus Myrothecium verrucaria that is highly specific for the fertilizer cyanamide and cloning of its gene.
Authors: Maier-Greiner U H , Obermaier-Skrobranek B M , Estermaier L M , Kammerloher W , Freund C , Wülfing C , Burkert U I , Matern D H , Breuer M , Eulitz M
Published: May 2006

A protein was purified from crude extracts of the soil fungus Myrothecium verrucaria by gel filtration and hydrophobic chromatography to homogeneity; this protein catalyzed the stoichiometric hydration of the fertilizer cyanamide to urea with high substrate specificity. This cyanamide hydratase (urea hydro-lyase; EC 4.2.1.69) contained zinc and consisted of six identical subunits with Mr = 27,700. It was partially sequenced. The protein was detectable only when the fungus was grown on cyanamide as the sole nitrogen source. Genomic DNA from the fungus was cloned, and the gene encoding the enzyme was mapped with an oligonucleotide probe derived from the amino acid sequence within a 25,800-base-pair DNA region. The subunit of the enzyme is encoded by a 795-base-pair DNA sequence containing a 63-base-pair intron. A cDNA clone containing the intronless gene with an open reading frame encoding a sequence of 244 amino acids expressed the enzyme in active form in Escherichia coli with excellent yield.
Resolution of the electronic transitions of cytochrome c oxidase: evidence for two conformational states of ferrous cytochrome alpha.
Authors: Sherman D , Kotake S , Ishibe N , Copeland R A
Published: May 2006

Second-derivative absorption spectra are reported for a variety of oxidation and ligation states of bovine cytochrome c oxidase (ferrocytochrome-c:oxygen oxidoreductase, EC 1.9.3.1). The high resolving power of the second-derivative method allows us to assign the individual electronic transitions of cytochrome alpha and cytochrome alpha 3 in many of these states. In the fully reduced enzyme, one observes a single electronic transition at 444 nm, corresponding to the Soret transition for both ferrous cytochrome alpha and ferrous cytochrome alpha 3. When the cytochrome alpha 3 site is occupied by an exogenous ligand (CN or CO), one observes two absorption bands assignable to the ferrous cytochrome alpha chromophore, one at ca, 443 nm and the other at ca, 450 nm. The appearance of the 450-nm band is dependent only on ligand occupancy at the cytochrome alpha 3 site and not on the oxidation state of the cytochrome alpha 3 iron. These results can be interpreted either in terms of a heterogeneous mixture of two ferrous cytochrome alpha conformers in the cytochrome alpha 3-ligated enzyme or in terms of a reduction in the effective molecular symmetry of the ferrous cytochrome alpha site that results in a lifting of the degeneracy of the lowest unoccupied molecular orbital associated with the Soret pi,pi* transition of cytochrome alpha. In either case, the present data indicate that ferrous cytochrome alpha can adopt two distinct conformations. One possible structural difference between these two states could be related to differences in the strength of hydrogen bonding between the ferrous cytochrome alpha formyl oxygen and a proton donor from an unidentified amino acid side chain of the enzyme. The implications of such modulation of hydrogen-bond strength are discussed in terms of possible mechanisms of proton translocation and electron transfer in the enzyme.
Serodiagnosis of hepatitis C virus (HCV) infection with an HCV core protein molecularly expressed by a recombinant baculovirus.
Authors: Chiba J , Ohba H , Matsuura Y , Watanabe Y , Katayama T , Kikuchi S , Saito I , Miyamura T
Published: May 2006

An enzyme-linked immunosorbent assay (ELISA) was developed for serological diagnosis of hepatitis C virus (HCV) infection, using HCV core protein (p22) synthesized by a recombinant baculovirus. Among 58 clinically well-defined chronic non-A, non-B hepatitis (NANBH) patients, 49 (84.5%) were positive for p22 antibody (anti-p22), whereas 42 (72.4%) were positive for C100-3 antibody (anti-C100-3), as measured by the present assay using the HCV nonstructural protein as antigen. Thirty-nine patients (67.2%) had both antibodies. No significant level of anti-p22 was detected in sera of chronic hepatitis B patients or normal blood donors. In typical post-transfusion NANBH patients, anti-p22 could be detected at, or even before, the first alanine aminotransferase peak. Anti-p22 was also detected in blood donors who were previously shown to be involved in transmitting HCV but in whose serum anti-C100-3 was not detectable. The ELISA detecting antibody to the HCV core protein expressed and properly processed in animal cells will be useful for mass screening of donor blood as well as for early diagnosis of hepatitis C.
Characterization of posttranslational modifications in neuron-specific class III beta-tubulin by mass spectrometry.
Authors: Alexander J E , Hunt D F , Lee M K , Shabanowitz J , Michel H , Berlin S C , MacDonald T L , Sundberg R J , Rebhun L I , Frankfurter A
Published: May 2006

Class III beta-tubulin, isolated from adult bovine brain, is resolved into at least seven charge variants on isoelectric focusing gels. To identify the posttranslational modifications responsible for this heterogeneity, a mixture of brain tubulins was treated with cyanogen bromide and the C-terminal fragments from the class III beta-tubulin isoforms were then isolated by binding them to the monoclonal antibody TuJ1. Combined use of tandem mass spectrometry and both subtractive and automated Edman degradation chemistry on the isolated peptides indicates that many of the isoforms differ by phosphorylation at Ser-444 plus attachment of one to six glutamic acid molecules to the side chain of the first glutamate residue, Glu-438, in the C-terminal sequence Tyr-Glu-Asp-Asp-Glu-Glu-Glu-Ser-glu-Ala-Gln-Gly-Pro-Lys.
Altered expression of insulin receptor types A and B in the skeletal muscle of non-insulin-dependent diabetes mellitus patients.
Authors: Mosthaf L , Vogt B , Häring H U , Ullrich A
Published: May 2006

The human insulin receptor exists in two isoforms, HIR-A and HIR-B, which are generated by alternative splicing of a primary gene transcript and differ by a 12-amino acid insertion sequence in the alpha-subunit. The two receptor isoforms bind insulin with different affinities and are differentially expressed in human tissues. We report here a tissue-specific alteration of the insulin receptor RNA splice pattern in non-insulin-dependent diabetes mellitus (NIDDM) patients. Whereas skeletal muscle of healthy individuals contains exclusively high-affinity HIR-A-encoding RNA, we consistently find low-affinity HIR-B RNA expression in NIDDM muscle tissue at levels similar to HIR-A.
Deletion of sequences upstream of the proteinase improves the proteolytic processing of human immunodeficiency virus type 1.
Authors: Partin K , Zybarth G , Ehrlich L , DeCrombrugghe M , Wimmer E , Carter C
Published: May 2006

Human immunodeficiency virus type 1 expresses structural proteins and replicative enzymes within gag and gag-pol precursor polyproteins. Specific proteolytic processing of the precursors by the viral proteinase is essential for maturation of infectious viral particles. We have studied the activity of proteinase in its immature form, as part of a gag-pol fusion protein, in an in vitro expression system. We found that deletion of p6*, the region in pol upstream of proteinase, resulted in improved processing of the precursor. A modified proteinase is released, but it functions less efficiently than wild type. Improved autoprocessing correlates with increased accessibility of the active site region in the polyprotein carrying the p6* deletion. Our results suggest that p6* is involved in the regulation of proteinase activation, perhaps as a region limiting the interaction of the active site and substrate binding domain with the remainder of the polyprotein. Release of p6* inhibition may be an activation step necessary for infectious particle maturation.
Desmosomal glycoprotein DGI, a component of intercellular desmosome junctions, is related to the cadherin family of cell adhesion molecules.
Authors: Wheeler G N , Parker A E , Thomas C L , Ataliotis P , Poynter D , Arnemann J , Rutman A J , Pidsley S C , Watt F M , Rees D A
Published: May 2006

Among the variety of specialized intercellular junctions, those of the adherens type have the most obvious association with cytoskeletal elements. This may be with the actin microfilament system as in the zonula adherens or with intermediate filaments as in the macula adherens, or desmosome. In the former case, it is clear that transmembrane glycoproteins of the cadherin family are important adhesive components of the molecular assembly. We now show for desmosomes that a major glycoprotein component (desmosomal glycoprotein DGI) has extensive homology with the cadherins, defining an extended family, but also has unique features in its cytoplasmic domain that are likely to be relevant to the association with intermediate rather than actin filaments. A novel 282-residue extension contains repeats of approximately 29 amino acid residues predicted to have an antiparallel beta-sheet structure, followed by a glycine-rich sequence. As in the cadherins, the extracellular domain contains possible Ca2(+)-binding sequences and a potential protease processing site. The cell adhesion recognition region (His-Ala-Val) of the cadherins is modified to Arg-Ala-Leu.