bluuebunny/crossref_metadata_2025 huggingface dataset:
Mechanism of promoter selection by RNA polymerase II: mammalian transcription factors alpha and beta gamma promote entry of polymerase into the preinitiation complex.
Authors: Conaway R C , Garrett K P , Hanley J P , Conaway J W
Published: May 2006

Productive binding of RNA polymerase II at the core region of TATA box-containing promoters is controlled by the action of the TATA factor and four additional transcription factors, designated alpha, beta gamma, delta, and epsilon, which have each been purified to near homogeneity from rat liver. This process is accomplished in three distinguishable stages. In the first stage (initial complex formation), the core promoter is packaged with the TATA factor into a binary complex that serves as the recognition site for RNA polymerase II. Here we show that, in the second stage (site selection), transcription factors alpha and beta gamma act in combination to promote selective binding of RNA polymerase II to the initial complex. Several lines of evidence argue that alpha and beta gamma function at this stage by a mechanism related to that utilized by bacterial sigma factors. In the third stage, transcription factors delta and epsilon promote assembly of the functional preinitiation complex. Our evidence supports the model that delta and epsilon enter the preinitiation complex and direct formation of stable protein-DNA contacts that anchor the transcription apparatus to the core promoter at sequences near the cap site.
Diverse point mutations in the human gene for polymorphic N-acetyltransferase.
Authors: Vatsis K P , Martell K J , Weber W W
Published: May 2006

Classification of humans as rapid or slow acetylators is based on hereditary differences in rates of N-acetylation of therapeutic and carcinogenic agents, but N-acetylation of certain arylamine drugs displays no genetic variations. Two highly homologous human genes for N-acetyltransferase (NAT; arylamine acetyltransferase, acetyl CoA:arylamine N-acetyltransferase, EC 2.3.1.5), NAT1 and NAT2, presumably code for the genetically invariant and variant NAT proteins, respectively. In the present investigation, 1.9-kilobase human genomic EcoRI fragments encoding NAT2 were generated by the polymerase chain reaction with liver and leukocyte DNA from seven subjects phenotyped as homozygous and heterozygous acetylators. Direct sequencing revealed multiple point mutations in the coding region of two distinct NAT2 variants. One of these was derived from leukocytes of a slow acetylator and was distinguished by a silent mutation (codon 94) and a separate G----A transition (position 590) leading to replacement of Arg-197 by Gln; the mutated guanine was part of a CpG dinucleotide and a Taq I site. The second NAT2 variant originated from liver with low N-acetylation activity. It was characterized by three nucleotide transitions giving rise to a silent mutation (codon 161), accompanied by obliteration of the sole Kpn I site, and two amino acid substitutions: Thr for Ile (codon 114) and Arg for Lys (codon 268). Heterozygosity was detected in three NAT2 samples: two were heterozygous for the rapid and one of the allelic variants, and the third was a compound heterozygote of both mutant alleles. The results show conclusively that the genetically variant NAT is encoded by NAT2.
Reversed siderophores act as antimalarial agents.
Authors: Shanzer A , Libman J , Lytton S D , Glickstein H , Cabantchik Z I
Published: May 2006

We describe here a family of biomimetic iron carriers that display high binding efficiency for ferric ions and favorable permeation properties across erythrocytic membranes. These carriers inhibit in vitro growth of Plasmodium falciparum by scavenging intracellular iron. The chemical features were realized by reproducing the iron-binding cavities of natural iron carriers (siderophores) and by systematic substitutions of their hydrophilic envelopes for more hydrophobic ones. In contrast to natural carriers, which participate in receptor-mediated iron uptake in cells and act as growth promoters, our synthetic carriers were designed to penetrate cellular membranes by diffusion, scavenge intracellular iron, and thereby act as growth inhibitors. Based on these properties we designate the compounds reversed siderophores and refer to the specific analogs of the natural ferrichrome as synthetic ferrichromes. The antimalarial activity of the synthetic ferrichromes correlated with their lipophilicity, and this antimalarial activity was averted when the chelators were applied as iron (III) complexes. The sites of synthetic ferrichrome action reside in the intraerythrocytic parasite and not in serum or on normal erythrocyte components. The agents were effective against all stages of parasite growth and against a variety of multidrug-resistant strains of P. falciparum. The most potent agent of this synthetic ferrichrome series, SF1-ileu, was not toxic to mammalian cells in culture and was 15-fold more potent and 20-fold faster acting than desferrioxamine. Taken in toto, these agents constitute a series of promising candidates for future use in malaria chemotherapy.
Mutations in 16S rRNA that affect UGA (stop codon)-directed translation termination.
Authors: Göringer H U , Hijazi K A , Murgola E J , Dahlberg A E
Published: May 2006

Site-directed mutagenesis was performed on a sequence motif within the 3' major domain of Escherichia coli 16S rRNA shown previously to be important for peptide chain termination. Analysis of stop codon suppression by the various mutants showed an exclusive response to UGA stop signals, which was correlated directly with the continuity of one or the other of two tandem complementary UCA sequences (bases 1199-1204). Since no other structural features of the mutated ribosomes were hampered and the translation initiation and elongation events functioned properly, we propose that a direct interaction occurs between the UGA stop codon on the mRNA and the 16S rRNA UCA motif as one of the initial events of UGA-dependent peptide chain termination. These results provide evidence that base pairing between rRNA and mRNA plays a direct role in termination, as it has already been shown to do for initiation and elongation.
Proximity measurements between H-2 antigens and the insulin receptor by fluorescence energy transfer: evidence that a close association does not influence insulin binding.
Authors: Liegler T , Szollosi J , Hyun W , Goodenow R S
Published: May 2006

Reports based on coprecipitation experiments have suggested that major histocompatibility complex class I products are complexed with the insulin receptor on the cell surface. Using an independent method that avoids the creation of immunoprecipitation artifacts during membrane solubilization, we have studied insulin receptor-class I product associations by determining the proximity between these class I products and the insulin receptor on intact cells with the use of fluorescence energy transfer. Significant energy transfer was seen between the insulin receptor and both murine H-2K- as well as H-2D-end products, indicating close proximity (e.g., within 10 nm). This cell-surface association is not from the relatively high class I density in that no significant energy transfer was measured between H-2K- vs. H-2D-end proteins. To extend these observations, we also tested whether class I products influence insulin-receptor binding and postbinding events as a result of their physical association. Using related cell lines positive and negative for class I expression, we found no correlation between insulin-receptor density or binding affinity with H-2 product expression. The class I-null variant, however, demonstrated an increase in insulin-mediated insulin-receptor internalization to suggest that if major histocompatibility complex class I products directly affect insulin-receptor function through specific cell-surface interactions, they may do so after ligand binding.
Axon collaterals indicate broad intraspinal role for sacral preganglionic neurons.
Authors: Morgan C W , de Groat W C , Felkins L A , Zhang S J
Published: May 2006

The classic view of preganglionic neurons in spinal autonomic nuclei is that they convey information exclusively from the central nervous system to autonomic neurons in peripheral ganglia. The present morphological study in the cat sacral spinal cord demonstrates that these neurons may also make abundant synaptic connections within the spinal cord. Neurons labeled intracellularly with neurobiotin or horseradish peroxidase exhibited an expansive distribution of axon collaterals in spinal cord laminae I, V, VII, VIII, IX, X, and the ventrolateral funiculi. This broad-ranging axon-collateral system, which has the potential for multiple neuronal contacts, indicates widespread integrative functions for sacral preganglionic neurons within the spinal cord, in addition to functions currently known in the periphery.
Nonhuman primate model of alcohol abuse: effects of early experience, personality, and stress on alcohol consumption.
Authors: Higley J D , Hasert M F , Suomi S J , Linnoila M
Published: May 2006

Twenty-two 50-month-old rhesus monkeys were provided concurrent free access to an aspartame-sweetened 7% ethanol solution and an aspartame-sweetened vehicle before, during, and after social separation. Subjects had been reared for their first 6 months of life either without access to adults but with constant access to age mates (peer reared), a condition producing reduced exploration and increased fear-related behaviors, or as controls with their mothers; thereafter, all subjects received identical treatment. During home-cage periods, for 1 hr each day, 4 days a week, when the ethanol solution and vehicle were freely available, peer-reared subjects consumed significantly more alcohol than mother-reared subjects. When stress was increased via social separation, mother-reared animals increased their alcohol consumption to a level nearly as high as that of peer-reared monkeys. Average individual differences in alcohol consumption were markedly stable over time. In addition, there were strong positive correlations between alcohol consumption and distress behaviors. Biological indices of increased stress, such as plasma cortisol and corticotropin, were higher in peer-reared subjects. Within the peer- and mother-reared groups, these indices were positively correlated with alcohol consumption. The results suggest that early rearing experiences that predispose monkeys to increased fear-related behaviors produce excessive alcohol consumption under normal living conditions. Furthermore, a major challenge such as social separation increases alcohol consumption to levels producing intoxication even in monkeys not particularly vulnerable to stress.
Dualizing the Poisson summation formula.
Authors: Duffin R J , Weinberger H F
Published: May 2006

If f(x) and g(x) are a Fourier cosine transform pair, then the Poisson summation formula can be written as 2sumfrominfinityn = 1g(n) + g(0) = 2sumfrominfinityn = 1f(n) + f(0). The concepts of linear transformation theory lead to the following dual of this classical relation. Let phi(x) and gamma(x) = phi(1/x)/x have absolutely convergent integrals over the positive real line. Let F(x) = sumfrominfinityn = 1phi(n/x)/x - integralinfinity0phi(t)dt and G(x) = sumfrominfinityn = 1gamma (n/x)/x - integralinfinity0 gamma(t)dt. Then F(x) and G(x) are a Fourier cosine transform pair. We term F(x) the "discrepancy" of phi because it is the error in estimating the integral phi of by its Riemann sum with the constant mesh spacing 1/x.
Phosphorylation of insulin-like growth factor (IGF)-binding protein 1 in cell culture and in vivo: effects on affinity for IGF-I.
Authors: Jones J I , D'Ercole A J , Camacho-Hubner C , Clemmons D R
Published: May 2006

The insulin-like growth factors (IGF-I and IGF-II) are present in extracellular fluids bound to specific IGF-binding proteins (IGFBPs). We and others have reported varying biologic activity of different preparations of IGFBP-1 that appeared to have identical amino acid sequences and molecular sizes. This observation prompted us to determine whether IGFBP-1 undergoes posttranslational modifications. Immunoprecipitation was used to show that Chinese hamster ovary cells (transfected with a human IGFBP-1 cDNA construct) and human hepatoma (HepG2) cells secrete 32P-labeled IGFBP-1 following incubation with [32P]orthophosphate. Phospho amino acid analysis of 32P-labeled IGFBP-1 revealed only phosphoserine residues. A method was developed that could separate nonphosphorylated IGFBP-1 from four or five phosphorylated isoforms. Using this technique we demonstrated that human amniotic fluid and human fetal serum contain a large proportion of nonphosphorylated IGFBP-1, as well as phosphorylated forms. In contrast, HepG2 cells and human decidual cells secrete predominantly the phosphorylated isoforms. These observations suggest that IGFBP-1 is secreted as a phosphoprotein and is subsequently dephosphorylated in vivo. Binding studies showed that the phosphorylated IGFBP-1 secreted by HepG2 cells has a 6-fold higher affinity for IGF-I than it does after dephosphorylation. We conclude that IGFBP-1 is phosphorylated and that this phosphorylation is a physiologically important posttranslational modification.
Enhanced GABAergic inhibition preserves hippocampal structure and function in a model of epilepsy.
Authors: Ylinen A M , Miettinen R , Pitkänen A , Gulyas A I , Freund T F , Riekkinen P J
Published: May 2006

Extensive electrical stimulation of the perforant pathway input to the hippocampus results in a characteristic pattern of neuronal death, which is accompanied by an impairment of cognitive functions similar to that seen in human temporal lobe epilepsy. The excitotoxic hypothesis of epileptic cell death [Olney, J. W. (1978) in Kainic Acid as a Tool in Neurobiology, eds. McGeer, E., Olney, J. W. & McGeer, P. (Raven, New York), pp. 95-121; Olney, J. W. (1983) in Excitotoxins, eds. Fuxe, K., Roberts, P. J. & Schwartch, R. (Wenner-Gren International Symposium Series, Macmillan, London), Vol. 39, pp. 82-96; and Rothman, S. M. & Olney, J. W. (1986) Ann. Neurol. 19, 105-111] predicts an imbalance between excitation and inhibition, which occurs probably as a result of hyperactivity in afferent pathways or impaired inhibition. In the present study, we investigated whether the enhancement of gamma-aminobutyric acid (GABA)-mediated (GABAergic) inhibition of neurotransmission by blocking the GABA-metabolizing enzyme, GABA transaminase, could influence the histopathological and/or the behavioral outcome in this epilepsy model. We demonstrate that the loss of pyramidal cells and hilar somatostatin-containing neurons can be abolished by enhancing the level of synaptically released GABA, and that the preservation of hippocampal structure is accompanied by a significant sparing of spatial memory as compared with placebo-treated controls. These results suggest that enhanced GABAergic inhibition can effectively block the pathophysiological processes that lead to excitotoxic cell death and, as a result, protect the brain from seizure-induced cognitive impairment.
Acetylcholine receptor-inducing activity stimulates expression of the epsilon-subunit gene of the muscle acetylcholine receptor.
Authors: Martinou J C , Falls D L , Fischbach G D , Merlie J P
Published: May 2006

Motor neurons regulate the transcription of acetylcholine receptor subunit genes in postsynaptic muscle fibers both through muscle electrical activity produced by motor neuron acetylcholine release and by mechanisms independent of such transmitter release. Factors secreted by the motor neuron may mediate activity-independent regulation, including the postnatal switch from alpha 2 beta gamma delta (embryonic type) to alpha 2 beta epsilon delta (adult type) receptors. We have investigated the effect of putative trophic factors, agents affecting second-messenger systems, and muscle activity on the levels of acetylcholine receptor subunit mRNAs in primary mouse muscle cultures. We found that ARIA (acetylcholine receptor-inducing activity), a 42-kDa glycoprotein purified on the basis of its ability to increase the synthesis of acetylcholine receptors in chick myotubes, increases epsilon-subunit mRNA levels up to 10-fold. In addition, ARIA stimulated alpha-, gamma-, and delta-subunit mRNA levels 2-fold but had no effect on the expression of the beta-subunit gene. These effects of ARIA were independent of muscle activity, and they were not mimicked by calcitonin gene-related peptide nor by thyroxine, forskolin, phorbol 12-myristate 13-acetate, the calcium ionophore A23187, basic fibroblast growth factor, or transforming growth factor beta. Based on these data, we suggest that ARIA may act at the mammalian neuromuscular junction to induce adult-type acetylcholine receptors.
Air-filled proteinaceous microbubbles: synthesis of an echo-contrast agent.
Authors: Grinstaff M W , Suslick K S
Published: May 2006

Air-filled microbubbles are in clinical use as echo-contrast agents for sonographic applications. The synthesis of aqueous suspensions of air-filled proteinaceous microbubbles involves the ultrasonic irradiation of aqueous protein solutions in the presence of O2. Yields and size distributions of human and bovine serum albumin microbubbles have been determined as a function of various experimental parameters. The chemical nature of these microbubbles and the origin of their remarkably long lifetimes have been explored. The microbubbles are held together primarily by interprotein cross-linking of cysteine residues. The principal cross-linking agent is superoxide created by the extremely high temperatures produced during acoustic cavitation.
Cold denaturation and 2H2O stabilization of a staphylococcal nuclease mutant.
Authors: Antonino L C , Kautz R A , Nakano T , Fox R O , Fink A L
Published: May 2006

Cold denaturation is now recognized as a general property of proteins but has been observed only under destabilizing conditions, such as moderate denaturant concentration or low pH. By destabilizing the protein using site-directed mutagenesis, we have observed cold denaturation at pH 7.0 in the absence of denaturants in a mutant of staphylococcal nuclease, which we call NCA S28G for a hybrid protein between staphylococcal nuclease and concanavalin A in which there is the point mutation Ser-28----Gly. The temperature of maximum stability (tmax) as determined by circular dichroism (CD) was 18.1 degrees C, and the midpoints of the thermal unfolding transitions (tm) were 0.6 degrees C and 30.0 degrees C. These values may be compared with the tm of 52.5 degrees C for wild-type staphylococcal nuclease, for which no cold denaturation was observed under these conditions. When the stability of the mutant was examined in 2H2O by NMR, CD, or fluorescence, a substantial increase in the amount of folded protein at the tmax was noted as well as a decrease in tmax, reflecting increased stability.
A close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria.
Authors: Diffley J F , Stillman B
Published: May 2006

ABF2 (ARS-binding factor 2), a small, basic DNA-binding protein that binds specifically to the autonomously replicating sequence ARS1, is located primarily in the mitochondria of the yeast Saccharomyces cerevisiae. The abundance of ABF2 and the phenotype of abf2- null mutants argue that this protein plays a key role in the structure, maintenance, and expression of the yeast mitochondrial genome. The predicted amino acid sequence of ABF2 is closely related to the high-mobility group proteins HMG1 and HMG2 from vertebrate cell nuclei and to several other DNA-binding proteins. Additionally, ABF2 and the other HMG-related proteins are related to a globular domain from the heat shock protein hsp70 family. ABF2 interacts with DNA both nonspecifically and in a specific manner within regulatory regions, suggesting a mechanism whereby it may aid in compacting the mitochondrial genome without interfering with expression.
The initiator directs the assembly of a transcription factor IID-dependent transcription complex.
Authors: Carcamo J , Buckbinder L , Reinberg D
Published: May 2006

Highly purified RNA polymerase II was found to be able to weakly recognize the initiator (Inr) present in the adenovirus IVa2 and major late promoters. The association of RNA polymerase II with the Inr was enhanced by the general transcription factors. The Inr was capable of directing the formation of a DNA-protein complex. Transcription competent complexes on the adenovirus major late and IVa2 promoters appear to be formed by alternative pathways mediated through the Inr and/or "TATA" motif. The presence of both motifs, however, is required for efficient transcription utilizing a discrete start site. Complexes formed at either site required transcription factor TFIID, the TATA binding protein. Consistent with this observation, a TFIID requirement was demonstrated for transcription from a mutant adenovirus major late promoter construct lacking a functional TATA motif.
Dynamics, structure, and function are coupled in the mitochondrial matrix.
Authors: Scalettar B A , Abney J R , Hackenbrock C R
Published: May 2006

The coupling between molecular diffusion and the structure and function of the rat liver mitochondrial matrix was explored using fluorescence anisotropy techniques and electron microscopy. The results confirm that matrix ultrastructure and the concentration of matrix protein are influenced by the respiratory state of mitochondria and the osmolarity of the external medium. At physiological osmolarity, a fluorescent metabolite-sized probe was found to diffuse slowly in the mitochondrial matrix but not to be completely immobile. In addition, significant differences in diffusion rates were found to exist between different mitochondrial respiratory states, with the slowest diffusion occurring in states with the highest matrix protein concentration. These data support the concept of a matrix structure in which diffusion is considerably hindered due to limited probe-accessible water and further suggest that volume-dependent regulation of matrix protein packing may modulate metabolite diffusion and, in turn, mitochondrial metabolism.
Tat-dependent adenosine-to-inosine modification of wild-type transactivation response RNA.
Authors: Sharmeen L , Bass B , Sonenberg N , Weintraub H , Groudine M
Published: May 2006

Tat is a potent activator of gene expression in human immunodeficiency virus type 1 (HIV-1). Activation by Tat requires a cis-acting element, the transactivation response (TAR) site, located in the viral long terminal repeat and the 5' end of all viral mRNAs. Sequences in TAR RNA can fold into a specific stem-loop structure, and certain features of the stem-loop are essential for Tat-mediated transactivation. In Xenopus oocytes, TAR sequences can inhibit the translation of 3' cis-linked mRNAs. However, coinjection of Tat and the TAR-containing RNA into oocyte nuclei relieves this translational inhibition [Braddock, M., Chambers, A., Wilson, W., Esnout, M. A., Adams, S.E. & Kingsman, S.M. (1989) Cell 58, 269-279]. We report here that the intramolecular TAR stem-loop structure is a substrate for the double-stranded RNA (dsRNA)-modifying activity, which converts adenosines to inosines. This activity is located in the nuclei of Xenopus oocytes. The specificity and extent of modification of adenosines in TAR is dependent on Tat. We propose that the dsRNA-modifying activity may be one of the cellular proteins that interacts with TAR in the nucleus. The possible role of TAR RNA modification in the expression of HIV-1 is discussed.
Assembly of the Escherichia coli 30S ribosomal subunit reveals protein-dependent folding of the 16S rRNA domains.
Authors: Mandiyan V , Tumminia S J , Wall J S , Hainfeld J F , Boublik M
Published: May 2006

Protein-nucleic acid interactions involved in the assembly process of the Escherichia coli 30S ribosomal subunit were quantitatively analyzed by high-resolution scanning transmission electron microscopy. The in vitro reconstituted ribonucleoprotein (core) particles were characterized by their morphology, mass, and radii of gyration. During the assembly of the 30S subunit, the 16S rRNA underwent significant conformational changes that were governed by the cooperative interactions of the ribosomal proteins. The sequential association of the first 12 proteins with the 16S rRNA resulted in the formation of core particles containing up to three mass centers at distinct stages of the assembly process. These globular mass centers may correspond to the three major domains (5', central, and 3') of the 16S rRNA. Through the subsequent interactions of the late assembly proteins with the 16S rRNA, two of the three domains merge, yielding the basic structural traits of the native 30S subunit. The fine morphological features of the native 30S subunit became distinctly resolved only after the addition of the full complement of proteins. The fully reconstituted 30S subunits are active in polyphenylalanine synthesis assays. Visualization of the assembly mechanism of the E. coli 30S ribosomal subunit revealed domain-specific folding of the 16S rRNA through the formation of distinct intermediate core particles hitherto not observed.
Rapid renaturation of complementary DNA strands mediated by cationic detergents: a role for high-probability binding domains in enhancing the kinetics of molecular assembly processes.
Authors: Pontius B W , Berg P
Published: May 2006

The rate of renaturation for complementary DNA strands can be enhanced greater than 10(4)-fold by the addition of simple cationic detergents, and the reaction is qualitatively and quantitatively very similar to that found with purified heterogeneous nuclear ribonucleoprotein A1 protein. Under optimal conditions, renaturation rates are greater than 2000-fold faster than reactions run in 1 M NaCl at 68 degrees C. The reaction is second-order with respect to DNA concentration, and reaction rates approach or equal the rate with which complementary strands are expected to encounter each other in solution. Renaturation can even be observed well above the expected melting temperature of the duplex DNA, demonstrating that some cationic detergents have DNA double-helix-stabilizing properties. The reaction is also extremely rapid in the presence of up to a 10(6)-fold excess of noncomplementary sequences, establishing that renaturation is specific and relatively independent of heterologous DNA. This finding also implies that up to several thousand potential target sequences can be sampled per strand per second. Such reagents may be useful for procedures that require rapid nucleic acid renaturation, and these results suggest ways to identify and design other compounds that increase the kinetics of association reactions. Moreover, this work provides further support for a model relating the existence of flexible, weakly interacting, repeating domains to their function in rapid molecular assembly processes in vitro and in vivo.
Physical map of human Xq27-qter: localizing the region of the fragile X mutation.
Authors: Poustka A , Dietrich A , Langenstein G , Toniolo D , Warren S T , Lehrach H
Published: May 2006

We describe a physical map of the end of the long arm of the human X chromosome encompassing the region from Xq27.2 to the q telomere, inclusive of the chromosomal band Xq28. This region is of particular interest, since it contains the highest density of genes associated with genetic diseases. The map covers a total of 12 megabases (Mb) of DNA and extends from the telomere to 3 Mb beyond the most likely position of the fragile X mutation, defined by a cluster of translocation breakpoints in somatic cell hybrids. The map determines order and position of loci throughout the Xq28 region and localizes cell line breakpoints marking the fragile X region to an interval of 300-700 kilobases between 8 and 8.7 Mb proximal of the Xq telomere.
Expression of proteins encoded by Epstein-Barr virus trans-activator genes depends on the differentiation of epithelial cells in oral hairy leukoplakia.
Authors: Becker J , Leser U , Marschall M , Langford A , Jilg W , Gelderblom H , Reichart P , Wolf H
Published: May 2006

The Epstein-Barr virus (EBV) immediate early gene product BZLF1 was localized by indirect immunofluorescence to the cytoplasm of the basal epithelial layer at the lateral border and dorsum of tongue in human immunodeficiency virus-infected and -seronegative patients. Two biopsies of oral hairy leukoplakia revealed a sporadic cytoplasmic staining of the BHRF1 and BRLF1 gene products in the basal epithelial layer. The widespread presence of BZLF1 in the basal epithelial layer indicated that this cell layer contained EBV DNA and was probably directly infected by EBV. Nuclear localization of the immediate early and early gene products BZLF1, BHRF1, BRLF1, and BMLF1 was limited to oral hairy leukoplakia in human immunodeficiency virus-seropositive patients and revealed a codistribution with the virus capsid antigen. Our results indicate that the epithelium of the tongue is a potential reservoir for EBV and that in heavily immunocompromised patients EBV may move from the cytoplasm to the nucleus with increasing differentiation and be coactivated there during the terminal differentiation of epithelial cells at the lateral border and dorsum of tongue.
Evolution of aminoacyl-tRNA synthetase quaternary structure and activity: Saccharomyces cerevisiae mitochondrial phenylalanyl-tRNA synthetase.
Authors: Sanni A , Walter P , Boulanger Y , Ebel J P , Fasiolo F
Published: May 2006

Phenylalanyl-tRNA synthetases [L-phenylalanine:tRNAPhe ligase (AMP-forming), EC 6.1.1.20] from Escherichia coli, yeast cytoplasm, and mammalian cytoplasm have an unusual conserved alpha 2 beta 2 quaternary structure that is shared by only one other aminoacyl-tRNA synthetase. Both subunits are required for activity. We show here that a single mitochondrial polypeptide from Saccharomyces cerevisiae is an active phenylalanyl-tRNA synthetase. This protein (the MSF1 gene product) is active as a monomer. It has all three characteristic sequence motifs of the class II aminoacyl-tRNA synthetases, and its activity may result from the recruitment of additional sequences into an alpha-subunit-like structure.
A PCR procedure to determine the sequence of large polypeptides by rapid walking through a cDNA library.
Authors: Gibbons I R , Asai D J , Ching N S , Dolecki G J , Mocz G , Phillipson C A , Ren H , Tang W J , Gibbons B H
Published: May 2006

A procedure that uses the PCR to make rapid successive steps through a random-primed cDNA library has been developed to provide a method for sequencing very long genes that are difficult to obtain as a single clone. In each successive step, the portions of partial clones that extend out from the region of known DNA sequence are amplified by two stages of PCR with nested, outward-directed primers designed approximately 50 bases in from the end of the known sequence, together with a general primer based on the sequence of the vector. This procedure has been used to determine the coding sequence of the cDNA for the beta heavy chain of axonemal dynein from embryos of the sea urchin Tripneustes gratilla. By starting from a single parent clone, whose translated amino acid sequence overlapped the microsequence of a tryptic peptide of the beta heavy chain, and making 3 such walk steps downstream and 14 walk steps upstream, we obtained a sequence of 13,799 base pairs that had an open reading frame of 13,398 base pairs. This sequence encodes a polypeptide with 4466 residues of Mr 511,804 that is believed to correspond to the complete beta heavy chain of ciliary outer arm dynein.
Locations of Arg-82, Asp-85, and Asp-96 in helix C of bacteriorhodopsin relative to the aqueous boundaries.
Authors: Greenhalgh D A , Altenbach C , Hubbell W L , Khorana H G
Published: May 2006

The amino acids Asp-96, Asp-85, and Arg-82, which are important for proton transport by bacteriorhodopsin, are located in helix C. Site-directed spin labeling has been used to map their positions relative to the aqueous boundaries of the membrane. Selected amino acids in helix C, in the B-C loop on the extracellular side, and in the C-D loop on the intracellular side of the membrane were replaced by cysteine residues and derivatized with a sulfhydryl-specific spin label. The topographical locations of the nitroxide groups were determined by electron paramagnetic resonance spectroscopy in terms of both motional restriction and collision frequencies with dissolved molecular oxygen and membrane-impermeable chromium oxalate. The results show that in dark-adapted bacteriorhodopsin, Tyr-79 is at the aqueous-protein interface on the extracellular side of helix C whereas Val-101 is close to the aqueous boundary on the intracellular side of the protein. Further, Asp-96 is estimated to be within 7 A of the aqueous medium on the intracellular side of the membrane, whereas Arg-82 and Asp-85 are within 5 A and 9 A, respectively, of the aqueous boundary on the extracellular side of the membrane.
Direct amplification of a single dissected chromosomal segment by polymerase chain reaction: a human brain sodium channel gene is on chromosome 2q22-q23.
Authors: Han J A , Lu C M , Brown G B , Rado T A
Published: May 2006

We have devised a general strategy for gene mapping based upon the direct amplification of a target sequence within a single microdissected Giemsa-banded chromosomal segment using the polymerase chain reaction. The usefulness of this approach was demonstrated by mapping a cloned human brain sodium channel (alpha subunit) gene sequence to chromosome 2q22-q23. When DNA from single, dissected chromosome segments 2q21-qter and 2q24-pter were used as templates, a sodium channel-specific 172-base-pair polymerase chain reaction product was obtained. This product was not synthesized when segments 2q21-pter and 2q24-qter were used. Chromosome microdissection-polymerase chain reaction is not only a simple, fast, and accurate method for gene mapping but also may offer significant advantages for other applications, such as cancer cytogenetics and linkage analysis.
Amplification of major histocompatibility complex class II gene diversity by intraexonic recombination.
Authors: She J X , Boehme S A , Wang T W , Bonhomme F , Wakeland E K
Published: May 2006

The roles of mutational and recombinational processes in the diversification of the exon encoding the antigen binding site in the murine major histocompatibility complex class II gene Ab were assessed by phylogenetic analysis of allelic nucleotide sequences. A total of 46 alleles of Ab exon 2 from 12 Mus species or subspecies and 2 Rattus species were sequenced after amplification by the polymerase chain reaction. Reliable allelic genealogies could not be determined by phylogenetic analyses, due to extensive homoplasy in the data set. This homoplasy results from the shuffling of polymorphisms between alleles by recombinational processes, indicating that polymorphisms in the antigen binding site encoded by Ab are generated by a combination of two processes. First, the accumulation of point mutations has produced highly divergent polymorphic sequence motifs in five regions of Ab exon 2, each encoding a portion of the binding site. Some of these motifs have persisted as polymorphisms in rodents since before the divergence of mouse and rat (greater than 10 million years ago). The second process mediating Ab diversification involves the shuffling of these polymorphic sequence motifs into numerous allelic combinations by repeated intraexonic recombination. Site-specific hyperrecombinational mechanisms are not involved in this process within the exon. We postulate that these mechanisms continuously generate new Ab alleles with highly divergent binding sites from which alleles with advantageous antigen-binding properties are selectively maintained by some form of balancing selection.
Stable configurations of confined cold ionic systems.
Authors: Rafac R , Schiffer J P , Hangst J S , Dubin D H , Wales D J
Published: May 2006

The simple structures formed by charged particles confined in a harmonic potential have been investigated and the configurations of minimum potential energy were identified. For fewer than 12 particles these form polyhedrons centered on the origin. For structures with 13-22 particles one sits in the middle, for 23-26 particles two are in the interior, etc., until a third shell starts forming at 60. When the isotropy of the trap is changed, distortions and discrete phase changes are seen. These structures should correspond to ones formed in ion traps at very low temperatures
Formation of DNA triplexes accounts for arrests of DNA synthesis at d(TC)n and d(GA)n tracts.
Authors: Baran N , Lapidot A , Manor H
Published: May 2006

To study the mechanism of arrest of DNA synthesis at d(TC)n and d(GA)n sequences, single-stranded DNA molecules including d(TC)27 or d(TC)31 tracts or a d(GA)27 tract were used as templates for in vitro assays of complementary DNA synthesis performed by extension of a primer with the Klenow polymerase or the Taq polymerase (Thermus aquaticus DNA polymerase). Electrophoresis of the products revealed that arrests occurred around the middle of these tracts. The arrests in the d(TC)n sequences were eliminated when dATP or dGTP was replaced with the analogue 7-deaza dATP or 7-deaza dGTP, respectively, or when the templates were preincubated with the Escherichia coli single-strand binding protein (SSB). Preincubation of the template including a d(GA)27 tract with SSB has also eliminated the arrests at this sequence. Furthermore, arrests did not occur at d[G(7-deaza A)]27 or d[(7-deaza G)A]27 tracts when molecules including such tracts were used as templates. These results are compatible with the notion that the arrests were caused by formation of d(TC)i.d(GA)i.d(TC)i and d(GA)i.d(GA)i.d(TC)i triplexes, in which the bases in the uncopied portions of the d(TC)n tracts, or of the d(GA)27 tract, and the purine bases in the newly synthesized d(TC)i.d(GA)i duplexes were bound by hydrogen bonds. In the assays performed with the Taq polymerase, the pH dependence (in the range of 6.0-9.0) and the temperature dependence of the arrests were determined. As the pH was lowered, the arrests in the d(TC)27 tract were enhanced, in line with the expected properties of d(TC)i.d(GA)i.d(TC)i triplexes. The arrests in the d(GA)27 tract were enhanced by an increase in the pH. At pH 7.2 the arrests in the d(GA)27 tract persisted up to 80 degrees C, whereas the arrests in the d(TC)27 tract were eliminated at 50 degrees C; these results presumably reflect the relative stabilities of the two triplexes mentioned above at this physiological pH value and could be biologically significant.
Yeast signal peptidase contains a glycoprotein and the Sec11 gene product.
Authors: YaDeau J T , Klein C , Blobel G
Published: May 2006

Partially purified yeast microsomal signal peptidase appears to be a complex of four polypeptides of 13, 18, 20, and 25 kDa. The 18-kDa chain is the product of the Sec11 gene, which is necessary for signal peptidase activity. The 25-kDa subunit is a glycoprotein that binds Con A. Two related methods for purification of the enzyme are presented; the first includes removal of peripheral membrane proteins from microsomes by alkali extraction, solubilization of the enzyme by nonionic detergent and high salt, and four different chromatographic procedures. An alternative method was developed based on lectin-affinity chromatography.
Progression of human papillomavirus type 18-immortalized human keratinocytes to a malignant phenotype.
Authors: Hurlin P J , Kaur P , Smith P P , Perez-Reyes N , Blanton R A , McDougall J K
Published: May 2006

We have developed a model system for progression of human epithelial cells to malignancy, using a human papillomavirus type 18 (HPV-18)-immortalized human keratinocyte cell line. Cells of cell line FEP-1811 were nontumorigenic in athymic mice through at least 12 passages in culture, but after 32 passages were weakly tumorigenic, producing tumors that regressed. After 62 passages they produced invasive squamous cell carcinomas that grew progressively. The progression to malignancy was associated with an increase in the efficiency of forming colonies in soft agar and with altered differentiation properties. In an organotypic culture system, FEP-1811 cells at passages 12 and 32 exhibited features typical of premalignant intraepithelial neoplasia in vivo, and cells at passage 68 exhibited features consistent with squamous cell carcinomas. No change in copy number of the transfected HPV-18 genome or in the level of expression of the viral transforming gene products E6 and E7 was detected between tumorigenic and nontumorigenic cells. Cytogenetic analysis of cells at early, middle, and late passage levels and cells cultured from tumors revealed that several chromosomal abnormalities segregated with the tumorigenic cell populations.
Cellular activation of latent transforming growth factor beta requires binding to the cation-independent mannose 6-phosphate/insulin-like growth factor type II receptor.
Authors: Dennis P A , Rifkin D B
Published: May 2006

The activation of latent transforming growth factor beta (LTGF-beta) normally seen in cocultures of bovine aortic endothelial and bovine smooth muscle cells can be inhibited by coculturing the cells with either mannose 6-phosphate (Man-6-P) or antibodies directed against the cation-independent Man-6-P/insulin-like growth factor type II receptor (anti-Man-6-PR). This result was established by measuring the ability of coculture conditioned medium (formed with or without Man-6-P or anti-Man-6-PR) to suppress bovine aortic endothelial cell migration and protease production, activities previously shown to be related to transforming growth factor beta activity. The inhibition by Man-6-P is dose dependent, with maximal inhibition seen at 100 microM and is specific because mannose 1-phosphate and glucose 6-phosphate do not interfere with activation of LTGF-beta. The inhibitory effect of anti-Man-6-PR is also specific and dose dependent; maximal inhibition of activation occurs at 400 micrograms/ml. Control experiments indicate that Man-6-P and anti-Man-6-PR do not interfere with the basal level of migration of bovine aortic endothelial cells, the migration observed when exogenous transforming growth factor beta is added, the activation of transforming growth factor beta by plasmin or transient acidification, and the release of LTGF-beta. Thus, binding to the cation-independent Man-6-P/insulin-like growth factor type II receptor appears to be a requirement for activation of LTGF-beta.
Inhibitors of DNA topoisomerase II prevent chromatid separation in mammalian cells but do not prevent exit from mitosis.
Authors: Downes C S , Mullinger A M , Johnson R T
Published: May 2006

DNA topoisomerase II (EC 5.99.1.3) is necessary for chromosome condensation and disjunction in yeast but not for other functions. In mammalian cells, it has been reported to be necessary for progression toward mitosis but not for transit through mitosis. We have found, on the contrary, that specific inhibition of topoisomerase II (but not of topoisomerase I) interferes with mammalian mitotic progression. Metaphase is prolonged, and anaphase separation of chromatids is completely inhibited, in cells given high concentrations of topoisomerase II inhibitors; nevertheless these cells attempt cleavage, sometimes generating nucleate and anucleate daughters. Lower concentrations of inhibitors interfere with anaphase and produce abnormalities of segregation. DNA topoisomerase II activity is therefore necessary for mammalian chromatid separation, but it is not tightly coupled to the control of other mitotic events.
Heterologous in vivo processing of human preproendothelin 1 into bioactive peptides.
Authors: Fabbrini M S , Vitale A , Patrono C , Zamai M , Vaghi F , Caiolfa V , Monaco L , Benatti L
Published: May 2006

Endothelin (ET) is an extremely potent vasoconstrictor peptide of 21 amino acids, originally found in the supernatant of cultured vascular endothelial cells. To gain insights into its biosynthetic pathway, we expressed a synthetic RNA coding for the 212-amino acid precursor of human ET-1 (preproET-1) in Xenopus oocytes. Cell homogenates and oocyte incubation medium were tested by RIA using an anti-ET-1 serum. ET-1-like immunoreactivity was detected in oocytes injected with preproET-1 synthetic RNA but not in control oocytes and was much higher in medium than in cell homogenates. When preproET-1 was expressed in oocytes treated with monensin, a dramatic decrease in secretion of immunoreactive material was observed, indicating that secretion is mediated by the Golgi complex. ET-1-like immunoreactive material present in oocyte incubation medium was fractionated by reverse-phase HPLC into two main peaks, corresponding to the retention times of human big ET-1 and ET-1. Incubation medium of oocytes expressing the synthetic preproET-1 RNA elicited a characteristic vasoconstrictor response on rabbit vena cava, consistent with the biological activity that would be predicted from the amount of ET-1-like immunoreactivity measured. These results suggest that common pathways of ET maturation exist in widely different cells and that Xenopus oocytes may represent a useful tool in studying the cell biology of ET-1 synthesis.
Cloning of a human cDNA encoding a CDC2-related kinase by complementation of a budding yeast cdc28 mutation.
Authors: Ninomiya-Tsuji J , Nomoto S , Yasuda H , Reed S I , Matsumoto K
Published: May 2006

We have cloned two different human cDNAs that can complement cdc28 mutations of budding yeast Saccharomyces cerevisiae. One corresponds to a gene encoding human p34CDC2 kinase, and the other to a gene (CDK2; cell division kinase) that has not been characterized previously. The CDK2 protein is highly homologous to p34CDC2 kinase (65% identical) and more significantly is homologous to Xenopus Eg1 kinase (89% identical), suggesting that CDK2 is the human homolog of Eg1. The human CDC2 and CDK2 genes were both able to complement the inviability of a null allele of S. cerevisiae CDC28. This result indicates that the CDK2 protein has a biological activity closely related to the CDC28 and p34CDC2 kinases. However, CDK2 was unable to complement cdc2 mutants in fission yeast Schizosaccharomyces pombe under the condition where the human CDC2 gene could complement them. CDK2 mRNA appeared late in G1 or in early S phase, slightly before CDC2 mRNA, after growth stimulation in normal human fibroblast cells. These results suggest that in human cells, two different CDC2-like kinases may regulate the cell cycle at distinct stages.
Antiparallel plasmid-plasmid pairing may control P1 plasmid replication.
Authors: Abeles A L , Austin S J
Published: May 2006

The copy number of the P1 plasmid replicon is stringently controlled, giving only one or two copies per newborn cell. Control is achieved by the action of the copy-control locus incA, which contains nine repeats of the 19-basepair binding site for the plasmid-encoded initiator protein RepA. A set of five similar repeats are present in the replication origin where RepA acts to trigger initiation. Using an in vitro replication system consisting of an Escherichia coli extract, the P1 origin as a template, and purified RepA protein, we show that supercoiled DNA circles containing the incA locus block origin function in trans. Shutdown becomes complete at a 1:1 ratio of origin to incA sequences. This is not due to titration of the RepA protein, as an excess of RepA can be added without restoring activity. Rather, the incA sequences appear to block the origin by direct contact in a plasmid-plasmid pairing event. When both the origin and the incA locus are present on one plasmid, trans contacts with daughter molecules appear to predominate over cis looping. The results are consistent with a model for replication control where daughter plasmids block their own replication by a pairing in which each origin is in contact with the incA locus of its partner.