bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-dimensional structure of holo 3 alpha,20 beta-hydroxysteroid dehydrogenase: a member of a short-chain dehydrogenase family.
Authors: Ghosh D , Weeks C M , Grochulski P , Duax W L , Erman M , Rimsay R L , Orr J C
Published: May 2006

The x-ray structure of a short-chain dehydrogenase, the bacterial holo 3 alpha,20 beta-hydroxysteroid dehydrogenase (EC 1.1.1.53), is described at 2.6 A resolution. This enzyme is active as a tetramer and crystallizes with four identical subunits in the asymmetric unit. It has the alpha/beta fold characteristic of the dinucleotide binding region. The fold of the rest of the subunit, the quaternary structure, and the nature of the cofactor-enzyme interactions are, however, significantly different from those observed in the long-chain dehydrogenases. The architecture of the postulated active site is consistent with the observed stereospecificity of the enzyme and the fact that the tetramer is the active form. There is only one cofactor and one substrate-binding site per subunit; the specificity for both 3 alpha- and 20 beta-ends of the steroid results from the binding of the steroid in two orientations near the same cofactor at the same catalytic site.
A role for sunlight in skin cancer: UV-induced p53 mutations in squamous cell carcinoma.
Authors: Brash D E , Rudolph J A , Simon J A , Lin A , McKenna G J , Baden H P , Halperin A J , Pontén J
Published: May 2006

Sunlight is a carcinogen to which everyone is exposed. Its UV component is the major epidemiologic risk factor for squamous cell carcinoma of the skin. Of the multiple steps in tumor progression, those that are sunlight-related would be revealed if they contained mutations specific to UV. In a series of New England and Swedish patients, we find that 14/24 (58%) of invasive squamous cell carcinomas of the skin contain mutations in the p53 tumor suppressor gene, each altering the amino acid sequence. Involvement of UV light in these p53 mutations is indicated by the presence in three of the tumors of a CC----TT double-base change, which is only known to be induced by UV. UV is also implicated by a UV-like occurrence of mutations exclusively at dipyrimidine sites, including a high frequency of C----T substitutions. p53 mutations in internal malignancies do not show these UV-specific mutations. The dipyrimidine specificity also implicates dipyrimidine photoproducts containing cytosine as oncogenic photoproducts. We believe these results identify a carcinogen-related step in a gene involved in the subsequent human cancer.
A large array of human monoclonal antibodies to type 1 human immunodeficiency virus from combinatorial libraries of asymptomatic seropositive individuals.
Authors: Burton D R , Barbas C F , Persson M A , Koenig S , Chanock R M , Lerner R A
Published: May 2006

A panel of human monoclonal antibody Fab fragments has been generated against the surface glycoprotein gp120 of type 1 human immunodeficiency virus (HIV) by antigen selection from a random combinatorial library expressed on the surface of filamentous phage. The library was prepared from 5 ml of bone marrow from an asymptomatic individual who has been HIV-positive for 6 years. The antibodies have high affinity for antigen (mostly with affinity constants of greater than 10(8) M-1) and notable sequence diversity. Given appropriate donor selection, the methods described should allow the generation of antibodies for the evaluation of passive immunization as a therapy for AIDS.
Molecular cloning and characterization of a Ca2+/calmodulin-insensitive adenylyl cyclase from rat brain.
Authors: Feinstein P G , Schrader K A , Bakalyar H A , Tang W J , Krupinski J , Gilman A G , Reed R R
Published: May 2006

Biochemical, immunological, and molecular cloning studies have suggested the existence of multiple forms of adenylyl cyclase (EC 4.6.1.1). An adenylyl cyclase cDNA clone (type II) was isolated from a rat brain library and found to encode a protein of 1090 amino acids that was homologous to but distinct from the previously described Ca2+/calmodulin-stimulated adenylyl cyclase from bovine brain. Expression of the type II cDNA in an insect cell line resulted in an increased level of adenylyl cyclase activity that was insensitive to Ca2+/calmodulin. Addition of activated Gs alpha protein to type II-containing membranes increased enzyme activity. The mRNA encoding the type II protein was expressed at high levels in brain tissue and at low levels in olfactory epithelium and lung. The existence of multiple adenylyl cyclase enzymes may provide for complex and distinct modes of biochemical regulation of cAMP levels in the brain.
Early mutation of the neu (erbB-2) gene during ethylnitrosourea-induced oncogenesis in the rat Schwann cell lineage.
Authors: Nikitin AYu  , Ballering L A , Lyons J , Rajewsky M F
Published: May 2006

The development of malignant tumors of the peripheral nervous system (schwannomas) within a defined intracranial section of the rat trigeminal nerve ("trigeminal box") was used as a model to identify genetic alterations typically associated with the process of cell-lineage-specific oncogenesis induced by exposure to N-ethyl-N-nitrosourea on postnatal day 1. All 47 trigeminal schwannomas (and 12 extracranial neurinomas) investigated carried a T.A----A.T transversion mutation at nucleotide 2012 of the neu (erbB-2) gene sequence encoding the transmembrane domain of pg185neu. This mutation was absent in all 18 tumors in the brain and spinal cord (central nervous system) isolated from the same animals. Identical observations were made in cell lines derived from N-ethyl-N-nitrosourea-induced rat schwannomas vs. brain tumors. By asymmetric PCR and mutant-specific Mnl I restriction fragment length analyses, cells carrying the mutant neu allele became detectable and could be localized within the trigeminal box as early as 7 days after the carcinogen pulse. The proliferation rate of the mutant cells strongly exceeded that of the wild-type cells up to the time of maturation of the trigeminal nerve around postnatal day 30 and thereafter to a lesser extent until the appearance of schwannomas. A specific mutation of the neu gene thus represents a very early, probably the first, step in the malignant conversion of immature rat Schwann cells exposed to N-ethyl-N-nitrosourea in vivo and is diagnostic for a subset of proliferative cells at high risk of progressing toward the expression of fully malignant phenotypes. Loss of heterozygosity for the mutant neu allele is a candidate event for a critical second step in the process.
Purification and characterization of particulate endothelium-derived relaxing factor synthase from cultured and native bovine aortic endothelial cells.
Authors: Pollock J S , Förstermann U , Mitchell J A , Warner T D , Schmidt H H , Nakane M , Murad F
Published: May 2006

The particulate enzyme responsible for the synthesis of endothelium-derived relaxing factor has been purified from cultured and native (noncultured) bovine aortic endothelial cells. Purification of the solubilized particulate enzyme preparation by affinity chromatography on adenosine 2',5'-bisphosphate coupled to Sepharose followed by Superose 6 gel filtration chromatography resulted in a single protein band after denaturing polyacrylamide gel electrophoresis that corresponded to approximately 135 kDa. The enzyme activity in the various fractions was assayed by its stimulatory effect on soluble guanylyl cyclase of rat fetal lung fibroblasts (RFL-6 cells), by the formation of L-citrulline from L-arginine, by measuring nitrite/nitrate formation, and by bioassay on endothelium-denuded vascular strips. Endothelium-derived relaxing factor synthase was purified 3419-fold from the crude particulate fraction of cultured bovine aortic endothelial cells with a 12% recovery (RFL-6 assay). Purified endothelium-derived relaxing factor synthase required L-arginine, NADPH, Ca2+, calmodulin, and 5,6,7,8-tetrahydrobiopterin for full activity.
A contingent replication assay for the detection of protein-protein interactions in animal cells.
Authors: Vasavada H A , Ganguly S , Germino F J , Wang Z X , Weissman S M
Published: May 2006

We have developed a sensitive and rapid assay system termed the contingent replication assay (CRA) for selecting cDNAs with desired functional properties from a cDNA library. The system functions in animal cells and permits enrichment of the desired cDNA in small-scale and convenient experiments. The assay can be used for the enrichment of proteins that activate transcription from conditional enhancers, bind to specific DNA sequences, or interact with target proteins of interest. In this communication we report the application of this assay to study protein-protein interactions in animal cells.
Immunological identification and characterization of a delayed rectifier K+ channel polypeptide in rat brain.
Authors: Trimmer J S
Published: May 2006

Antibodies specific for the drk1 polypeptide were used to characterize the corresponding protein in rat brain. Recombinant and synthetic immunogens containing fragments of the drk1 polypeptide were produced. Antibodies raised to these immunogens display monospecific reactions with the same 130-kDa polypeptide on immunoblots of adult rat brain membranes. Immunoprecipitation of 125I-labeled brain membranes identifies a 38-kDa peptide in tight association with the drk1 polypeptide. Immunohistochemical staining of sections of adult rat cortex shows that drk1 protein is restricted to neurons, where staining is present on dendrites and cell bodies but not on axons. These studies point to the value of such immunological reagents to the further characterization of the components of this delayed rectifier K+ channel in the mammalian central nervous system.
Abnormal expression of two microtubule-associated proteins (MAP2 and MAP5) in specific subfields of the hippocampal formation in schizophrenia.
Authors: Arnold S E , Lee V M , Gur R E , Trojanowski J Q
Published: May 2006

A variety of cytoarchitectural disturbances have been described in limbic regions in postmortem studies of schizophrenia, many of which suggest a developmental disturbance of normal neuronal geometry. This geometry is established and maintained by elements of the neuronal cytoskeleton. Immunohistochemistry with a panel of 15 monoclonal antibodies was used to monitor the presence of neuronal cytoskeletal proteins in the hippocampal formations of six patients with schizophrenia, six normal controls, and six with neurodegenerative disorders. In five of the six subjects with schizophrenia, prominent and specific alterations were found in the distribution of two microtubule-associated proteins, MAP2 and MAP5, which were anatomically selective for the subiculum and entorhinal cortex. In contrast, the immunoreactivity of other cytoskeletal proteins (i.e., tau, tubulins, and selected neurofilament protein phosphoisoforms) was similar for all subjects. Defects in the expression of MAP2 and MAP5, two proteins that contribute to the establishment and maintenance of neuronal polarity, could underlie some of the cytoarchitectural abnormalities described in schizophrenia and impair signal transduction in the affected dendrites. The subiculum and entorhinal cortex interconnect the hippocampal formation with widespread cortices and subcortical nuclei and play important roles in higher cognitive functions. Hence, pathologic lesions that distort the polarized geometry of neurons could play a role in the emergence of aberrant behavior in schizophrenia.
Allelic variation in the effects of the nef gene on replication of human immunodeficiency virus type 1.
Authors: Terwilliger E F , Langhoff E , Gabuzda D , Zazopoulos E , Haseltine W A
Published: May 2006

The effects of the viral gene nef on human immunodeficiency virus type 1 (HIV-1) replication in culture were investigated using nef alleles of the HIV-1 IIIB and ELI strains. The results demonstrate significant allelic variation in the effect of nef on virus replication in both an established human CD4+ T-cell line and primary human lymphocytes. In the context of the HXB2 virus, the ELI nef allele but not the IIIB nef allele permits initiation of efficient low-multiplicity infection in primary peripheral blood mononuclear cells, including unfractionated peripheral blood lymphocytes, T cells, and monocyte/macrophages. Within the same genetic context, the IIIB nef allele slightly retards replication of the virus in a T-cell line, whereas the ELI nef allele accelerates replication of the virus. Sequences in the IIIB and ELI genomes outside of nef also moderate the effects of nef on HIV-1 replication. nef did not appear to determine the host-cell preference of the virus. These studies may help to reconcile apparently conflicting reports on the role of nef in HIV-1 replication and suggest that HIV-1 nef may play an important role in viral pathogenesis.
Ascorbic acid protects against endogenous oxidative DNA damage in human sperm.
Authors: Fraga C G , Motchnik P A , Shigenaga M K , Helbock H J , Jacob R A , Ames B N
Published: May 2006

Damage to the DNA of germ cells can lead to mutation, which may result in birth defects, genetic diseases, and cancer. The very high endogenous rate of oxidative DNA damage and the importance of dietary ascorbic acid (AA) in preventing this damage has prompted an examination of these factors in human sperm DNA. The oxidized nucleoside 8-hydroxy-2'-deoxyguanosine (8-oxo-7,8-dihydro-2'-deoxyguanosine; oxo8dG), 1 of approximately 20 major products of oxidative damage to DNA, was measured in DNA isolated from human sperm provided by healthy subjects and compared to the seminal fluid AA levels. This relationship was studied in two groups. In a group of 24 free-living individuals 20-50 years old high levels of oxo8dG were correlated with low seminal plasma AA. The endogenous level of oxo8dG in this group was 13 fmol per microgram of DNA or approximately 25,000 adducts per sperm cell. The second group of individuals was maintained on a controlled diet that varied only in AA content. When dietary AA was decreased from 250 to 5 mg/day, the seminal fluid AA decreased by half and the level of oxo8dG in sperm DNA increased 91%. Repletion of dietary AA for 28 days (from 5 mg/day to 250 or 60 mg/day) caused a doubling in seminal fluid AA and reduced oxo8dG by 36%. These results indicate that dietary AA protects human sperm from endogenous oxidative DNA damage that could affect sperm quality and increase risk of genetic defects, particularly in populations with low AA such as smokers.
The structure of the antigen-binding groove of major histocompatibility complex class I molecules determines specific selection of self-peptides.
Authors: van Bleek G M , Nathenson S G
Published: May 2006

We have examined the effect of diversity in the antigen-binding groove of the Kb, Db, Kbm1, and Kbm8 major histocompatibility complex (MHC) class I molecules on the set of self-peptides they present on the cell surface, by using a procedure we recently developed in our laboratory to isolate endogenously processed peptides bound to MHC class I molecules. We found that such naturally processed peptides are 7-10 amino acids long. A major motif of tyrosine and phenylalanine residues at positions three and five was found for peptides binding to Kb. The availability of Kb mutant molecules Kbm1 and Kbm8, each with localized clustered changes in the antigen-binding cleft, allowed us to probe the effect of such small alterations on peptide selection. We found that such changes in different regions in the antigen-binding groove exert an absolute effect by changing subsets of self-peptides bound to these MHC molecules. In the Kbm1 mutant, the binding of the characteristic major set of Kb-associated peptides with tyrosine at position three or both positions three and five is abrogated, although this MHC molecule still binds peptides with tyrosine at position seven; the latter peptides also bind to Kb. Kbm8 shares the major Tyr-3, Tyr-5 peptide set that binds to Kb but does not bind the peptides with tyrosine at position seven. Thus differences in binding selectivity in Kbm1 and Kbm8 appear to be the major determinant for the observed alterations in in vivo immune responses.
The C-terminal region of the Vibrio fischeri LuxR protein contains an inducer-independent lux gene activating domain.
Authors: Choi S H , Greenberg E P
Published: May 2006

The Vibrio fischeri luminescence genes are activated by an autoinducer and the 250-amino acid residue LuxR protein. To develop a general view of LuxR structure and function, a set of luxR 5'-deletion mutations was generated. Ten luxR mutant plasmids encoding active LuxR proteins with deletions ranging from residues 2-5 (delta 2-5) to residues 2-182 (delta 2-182) were studied. The degree of transcriptional activation of luminescence genes by the truncated LuxR proteins ranged from 0.01% to greater than 200% of the wild-type level. LuxR proteins with small deletions (up to delta 2-20) were active and remained autoinducer-dependent, LuxR proteins with deletions between residues 2-58 and 2-138 showed low activity and were not affected by autoinducer, and LuxR proteins with large deletions such as the delta 2-162 protein were highly active and autoinducer-independent. However, proteins with deletions equal to or greater than delta 2-20 were unable to autoregulate luxR. Our data indicate there is a C-terminal LuxR domain capable of functioning as a transcriptional activator. We suggest that an N-terminal region of LuxR starting between residues 20 and 58 and extending to the region of residues 138-162 masks the activator function of the C-terminal domain. Residues prior to position 20 are needed for autoregulatory function. Experiments showing that wild-type luxR is dominant over luxR genes coding the delta 2-58 through delta 2-138 proteins indicate the N-terminal arm masks lux DNA binding.
Ectopic dendrites occur only on cortical pyramidal cells containing elevated GM2 ganglioside in alpha-mannosidosis.
Authors: Goodman L A , Livingston P O , Walkley S U
Published: May 2006

In a variety of neuronal storage diseases, cortical pyramidal cells elaborate ectopic dendrites at the axon hillock. A feature common to all the diseases characterized by ectopic dendrites is an elevated level of GM2 ganglioside in cerebral cortex. In cats with one such disease, alpha-mannosidosis, the number of pyramidal cells bearing ectopic dendrites is small; the present study shows that GM2 ganglioside is stored only in those pyramidal neurons exhibiting ectopic dendrites. Using a Golgi-electron microscopy method with periodic acid-Schiff (PAS) staining, we first established that pyramidal cells bearing ectopic dendrites contained PAS+ membranous inclusions, consistent with storage of glycolipids. In contrast, those with smooth axon hillocks accumulated PAS- floccular inclusions, consistent with storage of oligosaccharides. Next, application of a monoclonal antibody against GM2 ganglioside revealed that subsets of both pyramidal and intrinsic neurons contained GM2-like immunoreactivity. Every GM2+ cell contained PAS+ membranous inclusions, indicating that pyramidal cells bearing ectopic dendrites stored GM2 ganglioside. In cats with alpha-mannosidosis induced by swainsonine, some pyramidal neurons showed GM2-like immunoreactivity after 4 weeks of treatment, whereas ectopic dendrites only became evident after 7 weeks of treatment. Thus, GM2 ganglioside accumulated in pyramidal neurons before ectopic dendrites emerged from the axon hillock. We propose that the reinitiation of dendrite growth on mature pyramidal cells is brought about by accumulated GM2 ganglioside.
Cloning and expression of a cDNA encoding the alpha subunit of rat p21ras protein farnesyltransferase.
Authors: Chen W J , Andres D A , Goldstein J L , Brown M S
Published: May 2006

The complete amino acid sequence of the alpha subunit of heterodimeric p21ras protein farnesyltransferase from rat has been deduced from the sequence of a cloned cDNA. The cDNA encodes a 377-amino acid protein that migrates on NaDodSO4/polyacrylamide gels identically to the alpha subunit purified from rat brain. When introduced into mammalian cells by transfection, the cDNA for the alpha subunit produced no immunodetectable protein or farnesyltransferase activity unless the cells were simultaneously transfected with a cDNA encoding beta subunit. In light of previous evidence that alpha subunit forms a heterodimer with at least two different beta subunits, current data suggest a mechanism for coordinating amounts of alpha and beta subunits. If an alpha subunit were stable only as a complex with a beta subunit, the number of alpha subunits would be automatically maintained at a level just sufficient to balance all beta subunits, thereby avoiding the potentially toxic overaccumulation of free alpha subunits.
Mutants of Escherichia coli initiator tRNA that suppress amber codons in Saccharomyces cerevisiae and are aminoacylated with tyrosine by yeast extracts.
Authors: Lee C P , RajBhandary U L
Published: May 2006

We recently described mutants of Escherichia coli initiator tRNA that suppress amber termination codons (UAG) in E. coli. These mutants have changes in the anticodon sequence (CAU----CUA) that allow them to read the amber codon and changes in the acceptor stem that allow them to bind to the ribosomal aminoacyl (A) site. We show here that a subset of these mutants suppress amber codons in Saccharomyces cerevisiae and that they are aminoacylated with tyrosine by yeast extracts. Analysis of a number of mutants as substrates for yeast tyrosyl-tRNA synthetase has led to identification of the C1.G72 base pair and the discriminator base A73, conserved in all eukaryotic cytoplasmic and archaebacterial tyrosine tRNAs, as being important for recognition. Our results suggest that the C1.G72 base pair and the discriminator base, in addition to the anticodon nucleotides previously identified [Bare, L.A. & Uhlenbeck, O.C. (1986) Biochemistry 25, 5825-5830] as important in yeast tyrosyl-tRNA synthetase recognition, may comprise the critical identity determinants in yeast tyrosine tRNA.
Cytotactin binding: inhibition of stimulated proliferation and intracellular alkalinization in fibroblasts.
Authors: Crossin K L
Published: May 2006

Cytotactin is an extracellular matrix protein that is dynamically and transiently expressed in a place-dependent fashion during development by glial cells, fibroblasts, and several other cell types. In the present study, the effects of cytotactin on cell proliferation were examined in fibroblastic cells in culture. NIH 3T3 mouse cells plated on tissue culture substrata in the presence of soluble cytotactin remained rounded for longer periods than untreated control cells, similar to their response to cytotactin-coated substrates. These rounding effects could be prevented by pretreatment of the cells with nocodazole, a microtubule-disrupting agent. Cytotactin inhibited the proliferation of fibroblasts in culture in a dose- and time-dependent manner, and this inhibition occurred even after nocodazole treatment. In addition, the presence of cytotactin inhibited proliferation stimulated by growth factors or tumor promoter. These effects on cell growth were accompanied by an early inhibition of the intracellular alkalinization that normally occurs upon mitogenic stimulation by a number of growth-promoting agents. Together these observations suggest that cytotactin is an endogenous cell surface modulatory protein and provide a possible mechanism whereby cytotactin may contribute to pattern formation during development, regeneration, tumorigenesis, and wound healing.
Neural networks as a tool for utilizing laboratory information: comparison with linear discriminant analysis and with classification and regression trees.
Authors: Reibnegger G , Weiss G , Werner-Felmayer G , Judmaier G , Wachter H
Published: May 2006

Successful applications of neural network architecture have been described in various fields of science and technology. We have applied one such technique, error back-propagation, to a medical classification problem stemming from clinical chemistry, and we have compared the performance of two different neural networks with results obtained by conventional linear discriminant analysis or by the technique of classification and regression trees. The results obtained by the various models were tested for robustness by jackknife validation ("leave n out" method). Compared with the two other techniques, neural networks show a unique ability to detect features hidden in the input data which are not explicitly formulated as input. Thus, neural network techniques appear promising in the field of clinical chemistry, and their application, particularly in situations with complex data structures, should be investigated with more emphasis.
A developmental switch in B lymphopoiesis.
Authors: Hardy R R , Hayakawa K
Published: May 2006

B and T lymphocytes are generated from hematopoietic stem cells during both fetal and adult life. A critical unresolved issue is whether the differentiation pathways in lymphopoiesis are the same in fetal and adult animals or whether they differ, similar to the hemoglobin switch in erythropoiesis. We report here that a developmental switch occurs in B lymphopoiesis. We isolated "pro-B" cells (i.e., cells that have initiated, but not completed, heavy-chain gene rearrangement) from fetal and adult sources and investigated their B-cell progeny generated both in vitro and in vivo. Most of the cells from fetal liver, but few from adult bone marrow, expressed CD5. Further, fetal pro-B cells failed to generate cells expressing high levels of IgD in severe combined immunodeficiency mice, whereas adult pro-B cells gave rise to CD5-B cells bearing IgD at levels comparable to the bulk of cells in the spleen of adult mice. Thus, all committed B progenitors in fetal liver of day 16 gestation mice give rise to phenotypically distinct progeny when compared to cells at a comparable differentiation stage in the bone marrow of adult animals. We conclude that the cohort of B-lineage progenitors in early fetal development is committed to a differentiation pathway distinct from that seen in the adult.
Depletion of extrinsic pathway inhibitor (EPI) sensitizes rabbits to disseminated intravascular coagulation induced with tissue factor: evidence supporting a physiologic role for EPI as a natural anticoagulant.
Authors: Sandset P M , Warn-Cramer B J , Rao L V , Maki S L , Rapaport S I
Published: May 2006

Although in vitro experiments have established that extrinsic pathway inhibitor (EPI) is the only known plasma inhibitor of factor VIIa-tissue factor (TF) catalytic activity of potential physiologic significance, evidence of its function in vivo has been lacking. TF-induced intravascular coagulation may occur in patients despite normal plasma levels of EPI and, in our earlier studies, normal plasma EPI levels did not protect rabbits from intravascular coagulation induced by an infusion of purified TF (1 microgram/kg). Studies have now been carried out in which plasma EPI levels were reduced in rabbits to below 20% of the initial level by injection of anti-rabbit EPI IgG. Infusion into such animals of purified rabbit TF apoprotein (0.25 microgram/kg) reconstituted into phospholipid vesicles induced substantial disseminated intravascular coagulation. Infusion of control saline or phospholipid vesicles not containing TF was without significant effect as was infusion of TF (0.25 microgram/kg) into animals injected with nonimmune goat IgG. These data establish that EPI can dampen TF-induced intravascular coagulation in rabbits. They support the hypothesis that EPI plays a significant role in regulating coagulation resulting from the exposure of blood to trace concentrations of TF during the illnesses and minor injuries of normal existence.
Negative supercoiling of DNA facilitates an interaction between transcription factor IID and the fibroin gene promoter.
Authors: Mizutani M , Ohta T , Watanabe H , Handa H , Hirose S
Published: May 2006

Transcription of the fibroin gene can be reconstituted with partially purified components from HeLa cells. Transcription factors IIB, IID, and IIE and RNA polymerase II are required for accurate initiation of transcription. Linear and relaxed closed circular DNA show a similar level of template activity. However, transcription of closed circular DNA is stimulated when negative supercoils are introduced by the addition of DNA topoisomerase II and supercoiling factor purified from the posterior silk gland of Bombyx mori. Dissection of transcription into pre- and postinitiation steps by the use of Sarkosyl reveals that DNA supercoiling promotes formation of a preinitiation complex. Furthermore, order of addition experiments suggest that DNA supercoiling facilitates a functional binding of transcription factor IID to the promoter.
Cord factor (alpha,alpha-trehalose 6,6'-dimycolate) inhibits fusion between phospholipid vesicles.
Authors: Spargo B J , Crowe L M , Ioneda T , Beaman B L , Crowe J H
Published: May 2006

The persistence of numerous pathogenic bacteria important in disease states, such as tuberculosis, in humans and domestic animals has been ascribed to an inhibition of fusion between the phagosomal vesicles containing the bacteria and lysosomes in the host cells [Elsbach, P. & Weiss, J. (1988) Biochim. Biophys. Acta 974, 29-52; Thoen, C. O. (1988) J. Am. Vet. Med. Assoc. 193, 1045-1048]. In tuberculosis this effect has been indirectly attributed to the production of cord factor (alpha,alpha-trehalose 6,6'-dimycolate). We show here that cord factor is extraordinarily effective at inhibiting Ca2(+)-induced fusion between phospholipid vesicles and suggest a mechanism by which cord factor confers this effect. These findings are likely to be important in our understanding of the pathogenesis and treatment of many diseases of bacterial etiology.
Splice-mediated insertion of an Alu sequence inactivates ornithine delta-aminotransferase: a role for Alu elements in human mutation.
Authors: Mitchell G A , Labuda D , Fontaine G , Saudubray J M , Bonnefont J P , Lyonnet S , Brody L C , Steel G , Obie C , Valle D
Published: May 2006

In studies of mutations causing deficiency of ornithine delta-aminotransferase (EC 2.6.1.13), we found an allele whose mature mRNA has a 142-nucleotide insertion at the junction of sequences from exons 3 and 4. The insert derives from an Alu element in ornithine delta-aminotransferase intron 3 oriented in the direction opposite to transcription (an "antisense Alu"). A guanine----cytosine transversion creates a donor splice site in this Alu, activating a cryptic acceptor splice site at its 5' end and causing splice-mediated insertion of an Alu fragment into the mature ornithine-delta-aminotransferase mRNA. We note that the complement of the Alu consensus sequence has at least two cryptic acceptor sites and several potential donor sequences and predict that similar mutations will be found in other genes.
Sequence determination and modeling of structural motifs for the smallest monomeric aminoacyl-tRNA synthetase.
Authors: Hou Y M , Shiba K , Mottes C , Schimmel P
Published: May 2006

Polypeptide chains of 19 previously studied Escherichia coli aminoacyl-tRNA synthetases are as large as 951 amino acids and, depending on the enzyme, have quaternary structures of alpha, alpha 2, alpha 2 beta 2, and alpha 4. These enzymes have been organized into two classes which are defined by sequence motifs that are associated with specific three-dimensional structures. We isolated, cloned, and sequenced the previously uncharacterized gene for E. coli cysteine-tRNA synthetase (EC 6.1.1.16) and showed that it encodes a protein of 461 amino acids. Biochemical analysis established that the protein is a monomer, thus establishing this enzyme as the smallest known monomeric synthetase. The sequence shows that cysteine-tRNA synthetase is a class I enzyme that is most closely related to a subgroup that includes the much larger methionine-, isoleucine-, leucine-, and valine-tRNA synthetases, which range in size from 677 to 951 amino acids. The amino-terminal 293 amino acids of the cysteine enzyme can be modeled as a nucleotide-binding fold that is more compact than that of its closest relatives by virtue of truncations of two insertions that split the fold. This smaller nucleotide-binding fold accounts for much of the reduced size of the cysteine enzyme and establishes the limit to which the structure of this domain is contracted in the five members of this subgroup of class I enzymes.
Positive transcriptional regulation of an iron-regulated virulence gene in Vibrio cholerae.
Authors: Goldberg M B , Boyko S A , Calderwood S B
Published: May 2006

We have previously described a virulence gene in Vibrio cholerae (irgA) that is more than 850-fold regulated in response to iron. Negative regulation of irgA by iron occurred at the transcriptional level, and there was a dyad symmetric nucleotide sequence in the vicinity of the irgA promoter homologous to the Fur binding site in Escherichia coli. When irgA was cloned into E. coli, we showed that transcription of irgA required 900 base pairs of DNA upstream of the irgA promoter that contained an open reading frame in inverse orientation to irgA. In the present study, we show that this upstream region of DNA encodes a gene in inverse orientation to irgA (named irgB) that is also negatively regulated by iron. Insertional inactivation of irgB on the V. cholerae chromosome leads to loss of expression of a chromosomal irgA'-'phoA fusion (in which the primes indicate truncated genes), which is restored to normal by provision of irgB on a plasmid in trans. DNA sequencing of irgB shows that the protein product (IrgB) is homologous to the LysR family of positive transcriptional activators, and secondary structure analysis of IrgB predicts a helix-turn-helix DNA binding motif. The promoters of irgB and irgA are divergent but overlap each other and the previously defined Fur-binding site. We propose a model for iron regulation of irgA expression in V. cholerae. In the presence of sufficient iron, transcription of both irgA and irgB is negatively regulated by a Fur-like protein. In low iron conditions, negative regulation of transcription is removed, and production of IrgB leads to positive transcriptional activation of irgA. It seems likely that the high induction ratio of irgA expression under low- and high-iron conditions (850-fold) relates to the fact that its cognate positive transcriptional activator (irgB) is itself negatively regulated by iron.
Cotranslational autoproteolysis involved in gene expression from a double-stranded RNA genetic element associated with hypovirulence of the chestnut blight fungus.
Authors: Choi G H , Shapira R , Nuss D L
Published: May 2006

The genetic information responsible for reduced virulence (hypovirulence) of the chestnut blight fungus Cryphonectria parasitica is thought to reside on cytoplasmically replicating double-stranded RNA (dsRNA) molecules. Cell-free translation of synthetic transcripts corresponding to the 5'-terminal 2640 nucleotides of the sense strand of the large dsRNA present in C. parasitica hypovirulent strain EP713 yielded two polypeptides with apparent molecular masses of 29 and 40 kDa. Nucleotide sequence analysis indicated that p29 and p40 were encoded by a single large open reading frame. The coding regions for p29 and p40 were mapped to nonoverlapping portions of the 5'- and 3'-terminal domains of the open reading frame, respectively. Kinetic analysis and in vitro translation studies with chimeric transcripts indicated that p29 is autocatalytically released from a nascent polyprotein during translation. Microsequence analysis of the amino terminus of radiolabeled p40 indicated that cleavage occurred between Gly-248 and Gly-249, consistent with translational mapping analysis. Examination of the p29 amino acid sequence revealed similarity to the Potyvirus-encoded cysteine-type proteinase HC-Pro. These results indicate the types of mechanism that operate during gene expression by hypovirulence-associated dsRNA genetic elements.
Tyrosine phosphate hydrolysis of host proteins by an essential Yersinia virulence determinant.
Authors: Bliska J B , Guan K L , Dixon J E , Falkow S
Published: May 2006

The plasmid-encoded YopH protein is a protein-tyrosine phosphatase (PTPase; EC 3.1.3.48) that is essential for Yersinia virulence. We have investigated the molecular basis for the role of PTPase activity in Yersinia pathogenesis. Allelic recombination was employed to introduce a defined mutation into the yopH plasmid gene. Conversion of the essential Cys-403 to Ala in the catalytic domain of the protein abolished YopH PTPase activity and significantly reduced the virulence of Yersinia pseudotuberculosis in a murine infection model. 32P-labeled phosphotyrosine-containing proteins were immunoprecipitated from extracts of Y. pseudotuberculosis-infected cell monolayers and analyzed by SDS/PAGE to assess the impact of YopH on host protein phosphorylation. Major proteins of 200, 120, and 60 kDa were dephosphorylated in macrophages associated with wild-type Y. pseudotuberculosis. Selective removal of phosphate from the 120- and 60-kDa proteins was shown to be specific to the YopH PTPase activity. Phagocytosis of the bacteria was not required for this dephosphorylation activity, suggesting that YopH is functionally expressed by extracellular bacteria. These observations indicate that the essential function of YopH in Yersinia pathogenesis is host-protein dephosphorylation.
Genetically modified skin fibroblasts persist long after transplantation but gradually inactivate introduced genes.
Authors: Palmer T D , Rosman G J , Osborne W R , Miller A D
Published: May 2006

Genetically engineered fibroblasts have been successfully used to produce therapeutic proteins in animals, but sustained production of the proteins has not been achieved. This limits the potential of fibroblast-mediated gene therapy in humans. We have studied the phenomenon of decreased production in rats by using retroviral vectors carrying genes encoding human adenosine deaminase and neomycin phosphotransferase. While transplanted skin fibroblasts containing vector sequences persisted at constant levels for at least 8.5 mo, vector expression decreased by greater than 1500-fold after 1 mo. Cellular or antibody-mediated immune responses were not detected in transplanted animals, and expression could not be restored in fibroblasts recultivated from the grafts. This phenomenon is reminiscent of sequence-specific gene inactivation observed in other cell types. Because genetic manipulation and expression of foreign proteins did not affect survival of the transplanted cells, effective long-term therapy may be possible with the use of alternative gene regulatory elements.
Early phenotype expression of cortical neurons: evidence that a subclass of migrating neurons have callosal axons.
Authors: Schwartz M L , Rakic P , Goldman-Rakic P S
Published: May 2006

The use of [3H]thymidine labeling in combination with various axonal transport tracers has revealed that a subset of migrating neurons in the fetal monkey cerebrum issue axons to the opposite cerebral hemisphere while still migrating to their final positions in the cortical plate. Other cortical neurons with the same "birthdate" (i.e., that underwent their last round of DNA synthesis on the same day) are not retrogradely labeled by tracer injections of the opposite hemisphere. These findings suggest that the cardinal distinction between projection and local circuit neurons may be specified in postmitotic neurons before they acquire their final positions in the cortex.
Search for cellular phosphorylation products of D-allose.
Authors: Ullrey D B , Kalckar H M
Published: May 2006

The all-cis hexose D-allose, fed to hamster fibroblast cultures over 14-20 hr, brings about a striking down-regulation of hexose transport. This down-regulation by allose is inhibited by 2,4-dinitrophenol. By using D-[14C]allose and thin-layer chromatography, two types of products accumulated that have been identified as allose and allose phosphate. We suspect that allose phosphate might be the down-regulator.
Inducer-dependent conditional-lethal mutant animal viruses.
Authors: Zhang Y F , Moss B
Published: May 2006

Regulatory elements of the Escherichia coli lac operon were used to construct an inducer-dependent conditional-lethal mutant animal virus. The gene encoding the repressor protein of the lac operon was integrated into the vaccinia virus genome so that it was expressed constitutively, and the lac operator was inserted next to the promoter of a gene that encodes an 11-kDa virion-associated protein of unknown function. The addition of inducer to the cell culture medium provided permissive conditions for isolation of a conditional-lethal mutant virus. Under nonpermissive conditions, the isolated virus did not form plaques, and the yield was decreased by at least 1000-fold under one-step growth conditions. Transcription of the operator-controlled gene was inducer-dependent and necessary for synthesis of the 11-kDa protein. Application of this mutagenesis strategy to other viruses is discussed.
Cloning and expression of human deoxycytidine kinase cDNA.
Authors: Chottiner E G , Shewach D S , Datta N S , Ashcraft E , Gribbin D , Ginsburg D , Fox I H , Mitchell B S
Published: May 2006

Deoxycytidine (dCyd) kinase is required for the phosphorylation of several deoxyribonucleosides and certain nucleoside analogs widely employed as antiviral and chemotherapeutic agents. Detailed analysis of this enzyme has been limited, however, by its low abundance and instability. Using oligonucleotides based on primary amino acid sequence derived from purified dCyd kinase, we have screened T-lymphoblast cDNA libraries and identified a cDNA sequence that encodes a 30.5-kDa protein corresponding to the subunit molecular mass of the purified protein. Expression of the cDNA in Escherichia coli results in a 40-fold increase in dCyd kinase activity over control levels. In dCyd kinase-deficient murine L cells, transfection with dCyd kinase cDNA in a mammalian expression vector produces a 400-fold increase over control in dCyd phosphorylating activity. The expressed enzyme has an apparent Km of 1.0 microM for dCyd and is also capable of phosphorylating dAdo and dGuo. Northern blot analysis reveals a single 2.8-kilobase mRNA expressed in T lymphoblasts at 5- to 10-fold higher levels than in B lymphoblasts, and decreased dCyd kinase mRNA levels are present in T-lymphoblast cell lines resistant to arabinofuranosylcytosine and dideoxycytidine. These findings document that this cDNA encodes the T-lymphoblast dCyd kinase responsible for the phosphorylation of dAdo and dGuo as well as dCyd and arabinofuranosylcytosine.
AIDS epidemiology: inconsistencies with human immunodeficiency virus and with infectious disease.
Authors: Duesberg P H
Published: May 2006

The newly defined syndrome AIDS includes 25 unrelated parasitic, neoplastic, and noninfectious indicator diseases. Based on epidemiological correlations, the syndrome is thought to be due to a new, sexually or parenterally transmitted retrovirus termed human immunodeficiency virus (HIV). The following epidemiological data conflict with this hypothesis. (i) Noncorrelations exist between HIV and AIDS; for example, the AIDS risks of infected subjects vary greater than 10-fold with their gender or country. Abnormal health risks that are never controlled as independent AIDS causes by AIDS statistics, such as drug addiction and hemophilia, correlate directly with an abnormal incidence of AIDS diseases. Above all, the AIDS diseases occur in all risk groups in the absence of HIV. (ii) American AIDS is incompatible with infectious disease, because it is almost exclusively restricted to males (91%), because if it occurs, then only on average 10 years after transfusion of HIV, because specific AIDS diseases are not transmissible among different risk groups, and because unlike a new infectious disease, AIDS has not spread exponentially since the AIDS test was established and AIDS received its current definition in 1987. (iii) Epidemiological evidence indicates that HIV is a long-established, perinatally transmitted retrovirus. HIV acts as a marker for American AIDS risks, because it is rare and not transmissible by horizontal contacts other than frequent transfusions, intravenous drugs, and repeated or promiscuous sex. It is concluded that American AIDS is not infectious, and suggested that unidentified, mostly noninfectious pathogens cause AIDS.
Lymphocyte activation induces rapid changes in nuclear and cytoplasmic glycoproteins.
Authors: Kearse K P , Hart G W
Published: May 2006

A unique form of nucleoplasmic and cytoplasmic protein glycosylation, O-linked GlcNAc, (O-GlcNAc) is present on proteins ranging from those of yeast to man, including many chromatin proteins, transcription factors, nuclear pore proteins, and certain types of cytoskeletal proteins. In this report we have studied the effects of cellular activation on O-GlcNAc-modified proteins, using T lymphocytes as a model system. Results indicate that the apparent levels of O-GlcNAc on many nuclear proteins increases rapidly after lymphocyte activation, returning to control levels after a few hours. In contrast, the apparent levels of O-GlcNAc on a distinct population of cytosolic proteins decreases rapidly after cellular activation and also returns to control levels after a few hours. These data are consistent with the hypothesis that O-GlcNAc is a regulatory modification and suggest that O-GlcNAc modification may play an important role in the early stages of T-lymphocyte activation.
Expression of the amyloid precursor protein gene in mouse oocytes and embryos.
Authors: Fisher S , Gearhart J D , Oster-Granite M L
Published: May 2006

The amyloid precursor protein (APP) is thought to be processed aberrantly to yield the major constituent of the amyloid plaques observed in the brains of patients with Alzheimer disease and Down syndrome. However, the gene encoding APP is expressed widely in normal human tissues and in adult and fetal mouse tissues and is alternatively spliced in a tissue-specific pattern in the adult. There is evidence that APP may function as a growth factor and as a mediator of cell adhesion and in these roles could be important in morphogenesis. As a step toward determining the role of APP in development and in determining how the adult pattern of tissue-specific splicing is established, we have used reverse transcription and the polymerase chain reaction to demonstrate APP expression in mouse oocytes, preimplantation embryos, and postimplantation embryonic stages to the late embryonic period. All three splicing forms described in mouse were present at each stage, although there were changes in the ratios of the splicing forms at different stages. Screens for APP clones in embryonic cDNA libraries from the egg cylinder stage and the early somite stage were used to confirm the results of the polymerase chain reaction, and APP clone abundance was found to increase 10-fold between the two stages.