bluuebunny/crossref_metadata_2025 huggingface dataset:
Saturation mutagenesis of the octopine synthase enhancer: correlation of mutant phenotypes with binding of a nuclear protein factor.
Authors: Singh K , Tokuhisa J G , Dennis E S , Peacock W J
Published: May 2006

A 16-base-pair palindrome from the Agrobacterium tumefaciens octopine synthase gene functions as a constitutive enhancer in plant protoplasts. Degenerate oligonucleotide mutagenesis provided single base substitutions at every position in the element and a number of multiple base substitutions. The effects of these changes were determined in transient expression assays with tobacco and maize protoplasts. The majority of single and double base changes had little effect on the activity of the octopine synthase enhancer, but nearly all mutants with more than two base changes had low to essentially no activity. There were five positions where particular single base changes resulted in a 4- to 10-fold loss in enhancer activity. The distribution of these positions within the palindrome was asymmetric. Single base deletions had essentially no activity, demonstrating that the octopine synthase enhancer cannot tolerate internal changes in spacing. We find a strong correlation between mutant phenotype and reduced binding of a protein factor, suggesting that the DNA-protein complex is responsible for the transcriptional enhancement; the functionally active form of the DNA-protein complex probably involves more than a single protein molecule. The mutants exhibit similar phenotypes in protoplasts of both tobacco and maize, implying conservation of the DNA-protein interactions of the ocs enhancer sequence in monocotyledonous and dicotyledonous plants.
Model for clonal elimination in the thymus.
Authors: Kosaka H , Ogata M , Hikita I , Maruo S , Sugihara S , Matsubara H , Takai Y , Hamaoka T , Fujiwara H
Published: May 2006

A thymic stromal cell clone, MRL104.8a, expresses class I as well as class II H-2k antigens after exposure to gamma-interferon. This clone also produces thymic stroma-derived T-cell growth factor (TSTGF), which is distinct from other known interleukins and is capable of promoting the growth of various antigen-specific helper T cell (Th) clones without requiring a specific antigen or interleukin 2. When the keyhole limpet hemocyanin (KLH)-specific, I-Ek-restricted Th clone 9-16 was cultured on an Ia (I-Ak and I-Ek)-expressing MRL104.8a monolayer, potent proliferation of the 9-16 cells was induced by TSTGF produced by the monolayer. In contrast, the addition of KLH resulted in lethal growth inhibition of Th clone 9-16 cells. Another Th clone that is KLH-specific but I-Ab-restricted was capable of proliferating on the Iak-expressing MRL104.8a monolayer whether or not KLH was present. More importantly, death of Th clone 9-16 cells cultured on a MRL104.8a monolayer in the presence of KLH was almost completely prevented by the addition of anti-I-Ek or anti-CD3 monoclonal antibodies, which are capable of blocking antigen recognition by the T-cell receptor. However, when Th clone 9-16 cells were cultured in the presence of KLH but on a monolayer of MRL28.8a cells, another thymic stromal clone that expresses a comparable amount of I-Ek antigen but produces a marginal amount of TSTGF, cells did not die; a lethal effect was induced by adding TSTGF. These results indicate that the TSTGF-producing and Ia-expressing thymic stromal cells induce the continuous proliferation or selective elimination of each T-cell clone, depending on whether the T-cell receptor is stimulated by the relevant antigen associated with Ia molecules expressed on the stromal cell surface.
Idiotypic cascades in cancer patients treated with monoclonal antibody CO17-1A.
Authors: Wettendorff M , Iliopoulos D , Tempero M , Kay D , DeFreitas E , Koprowski H , Herlyn D
Published: May 2006

We have previously shown that gastrointestinal cancer patients treated with monoclonal antibody CO17-1A (Ab1) developed anti-idiotypic antibodies (Ab2) to the Ab1. We now demonstrate that patients produce anti-anti-idiotypic antibodies (Ab3) to their autologous Ab2. Ab3 were demonstrated in culture supernatants of peripheral blood mononuclear cells from five Ab1-treated patients after stimulation of the cells with heterologous Ab2 that functionally mimicked the tumor antigen (Ag) defined by Ab1 and immunologically cross reacted with the patients' Ab2. Ab3 shared idiotopes with Ab1 and were Ab1-like in their binding specificities to tumor cells, Ag, and Ab2. Such antibodies were also elicited by stimulating cells with Ag. However, they were not produced by stimulating posttreatment mononuclear cells with control proteins or by stimulating pretreatment cells with either Ag or Ab2. Our results demonstrate idiotypic cascades in cancer patients treated with monoclonal antibody. Ag-specific Ab3 responses may underlie delayed clinical responses often observed in cancer patients treated with monoclonal antibodies of various specificities.
Modeling sickle cell vasoocclusion in the rat leg: quantification of trapped sickle cells and correlation with 31P metabolic and 1H magnetic resonance imaging changes.
Authors: Fabry M E , Rajanayagam V , Fine E , Holland S , Gore J C , Nagel R L , Kaul D K
Published: May 2006

We have developed an animal model to elucidate the acute effects of perfusion abnormalities on muscle metabolism induced by different density-defined classes of erythrocytes isolated from sickle cell anemia patients. Technetium-99m (99mTc)-labeled, saline-washed normal (AA), homozygous sickle (SS), or high-density SS (SS4) erythrocytes were injected into the femoral artery of the rat and quantitative 99mTc imaging, 31P magnetic resonance spectroscopy by surface coil at 2 teslas, and 1H magnetic resonance imaging at 0.15 tesla were performed. Between 5 and 25 microliters of SS4 cells was trapped in the microcirculation of the thigh (or 1-6 x 10(7) cells per cubic centimeter of tissue). In contrast, fewer SS discocytes (SS2) or AA cells were trapped (an equivalent packed cell volume of less than 6.7 microliters and 0.3 microliters, respectively). After injection of SS4 cells an initial increase in inorganic phosphate was observed in the region of the thigh served by the femoral artery, intracellular pH decreased, and subsequently the proton relaxation time T1 reached a broad maximum at 18-28 hr. When T1 obtained at this time was plotted against the volume of cells trapped, an increase of T1 over the control value of 411 +/- 48 msec was found that was proportional to the number of cells trapped. We conclude that the densest SS cells are most effective at producing vasoocclusion. The extent of the change detected by 1H magnetic resonance imaging is dependent on the amount of cells trapped in the microcirculation and the magnitude of the initial increase of inorganic phosphate.
Simian virus 40 (SV40) large tumor antigen causes stepwise changes in SV40 origin structure during initiation of DNA replication.
Authors: Roberts J M
Published: May 2006

We have studied structural changes in the simian virus 40 (SV40) replication origin induced by SV40 large tumor antigen (T antigen). T-antigen-induced changes in origin DNA conformation can be visualized as specific and discrete topologic changes in origin DNA minicircles. We discovered three origin-T-antigen complexes defined by changes in DNA linking number. These complexes probably reflected essential early steps in the initiation of DNA replication since their formation required DNA sequences that are necessary for DNA replication but do not affect T-antigen binding. There are striking parallels between the T antigen-origin interactions uncovered by this assay and the interactions between the DnaA, -B, and -C proteins and the Escherichia coli replication origin, suggesting a significant evolutionary conservation in the mechanisms that initiate DNA replication.
Activation of the T-DNA transfer process in
Agrobacterium
results in the generation of a T-strand—protein complex: Tight association of VirD2 with the 5′ ends of T-strands
Authors: Howard Elizabeth A. , Winsor Barbara A. , De Vos Guido , Zambryski Patricia
Published: May 2006

The T-DNA transfer process of
Agrobacterium
is activated following induction of expression of the Ti plasmid virulence (
vir
) genes. The
virD1
and
virD2
gene products are required for the production of nicks at the T-DNA borders and for the generation of free linear single-stranded copies of the T-DNA region, T-strands. T-strands are complexed with proteins in
vir
-induced bacteria, since T-strands partition to the aqueous/phenol interface in non-Pronasetreated total cell extracts. To determine whether the proteins are tightly associated with T-strands, DNA-protein complexes were purified away from bulk proteins by adsorption to glass beads. A 58-kDa protein was specifically released from
vir
-induced DNA-protein complexes after treatment with S1 nuclease to digest single-stranded DNA. The 58-kDa protein was identified as VirD2 by using VirD2-specific antibodies. The tight association of VirD2 with T-strands was shown directly by using VirD2-specific antibody to isolate T-strands. The 5′ side of the border nick sites on the Ti plasmid was also shown to be tightly associated with protein. The data suggest that after VirD1/VirD2-dependent nicking at the T-DNA borders, the VirD2 protein remains bound to the 5′ end of the nick, and the VirD2 protein continues to bind tightly to this 5′ end during unwinding (or displacement) of the T-strand from the Ti plasmid T-DNA region. The tight binding of VirD2 to T-strands suggests that this protein has additional functions in T-strand generation and potentially in the later steps of T-DNA transfer.
Specific binding of victorin to a 100-kDa protein from oats
Authors: Wolpert T. J. , Macko V.
Published: May 2006

Susceptibility of oats to victoria blight, caused by the fungus
Cochliobolus victoriae
, and sensitivity to the host-specific toxin victorin, produced by the fungus, are controlled by the dominant allele at the
Vb
locus. It has been postulated that the
Vb
locus encodes a toxin receptor, although direct evidence for such a receptor is not available. Our recent studies on structure—activity relationships of the toxin established a methodology for producing
125
I-labeled victorin. Electrophoretic analysis of proteins from isogenic susceptible and resistant oat genotypes following treatment of leaves with radiolabeled victorin showed that victorin binds in a covalent and a genotype-specific manner to a 100-kDa protein only in susceptible oat leaf slices. This
in vivo
binding was competitively displaced by reduced victorin, a nontoxic protective compound, and appeared to be correlated with biological activity.
In vitro
binding to the 100-kDa protein in leaf extracts showed several differences from
in vivo
binding. Binding was not genotype specific and required a reducing agent that was not required for
in vivo
binding. Differential centrifugation showed that the 100-kDa victorin binding protein was not a cytosolic protein but was enriched in a high-speed particulate fraction. The data support the hypothesis that the 100-kDa protein is the victorin receptor.
A sorting signal for the basolateral delivery of the vesicular stomatitis virus (VSV) G protein lies in its luminal domain: analysis of the targeting of VSV G-influenza hemagglutinin chimeras.
Authors: Compton T , Ivanov I E , Gottlieb T , Rindler M , Adesnik M , Sabatini D D
Published: May 2006

When synthesized in polarized epithelial cells, the envelope glycoproteins hemagglutinin of influenza and G of vesicular stomatitis virus are targeted to the apical and basolateral plasma membranes, respectively. To determine which portions of these transmembrane proteins contain information necessary for their sorting, the behavior of two different G-hemagglutinin chimeric polypeptides, consisting of all or nearly all the luminal portion of the vesicular stomatitis virus G protein linked to C-terminal segments of influenza hemagglutinin that included its transmembrane and cytoplasmic domains, was studied in MDCK cells transformed with the corresponding cDNAs. Both chimeras were transported from the endoplasmic reticulum to the Golgi apparatus and from there to the cell surface with the same rapid kinetics as the intact G protein. By using a cell surface immunoprecipitation assay with monolayers cultured on permeable filters that allows the recovery of labeled protein molecules present in each cell surface domain, it was found that both chimeric proteins as well as the intact G protein were delivered almost exclusively to the basolateral surface. This polarized distribution of the polypeptides did not change during a subsequent 90-min chase period, although during this time a large fraction of the glycoprotein molecules underwent degradation. In addition, a small fraction of the cell surface-associated glycoprotein molecules shed their ectoplasmic segments into the basolateral compartment, apparently as a result of a proteolytic cleavage. Immunofluorescence on transverse frozen sections and immunoelectron microscopy revealed a prominent accumulation of the chimeric polypeptides in the lateral cell membranes, with lesser amounts on the basal and apical surfaces. These results indicate that information specifying the basolateral transport of the G glycoprotein is located within the first 426 N-terminal amino acids of its ectoplasmic portion.
Influence of steroids on the hypothalamic corticotropin-releasing factor and preproenkephalin mRNA responses to stress.
Authors: Lightman S L , Young W S
Published: May 2006

We have used in situ hybridization histochemistry to investigate the influence of both circulating corticosteroids and the stress paradigm of i.p. hypertonic saline on the levels of mRNAs encoding corticotropin-releasing factor (CRF) and preproenkephalin in parvocellular neurons of the rat hypothalamus. Stress increased both CRF and preproenkephalin mRNAs, whereas adrenalectomy increased only CRF mRNA. After adrenalectomy, even when CRF mRNA had reached peak levels, stress still further increased CRF mRNA and caused an exaggerated rise in preproenkephalin mRNA. Dexamethasone administration in the fast or intermediate-feedback time domains had no effect on CRF or preproenkephalin mRNA responses to stress; however, when administered over a longer period of time in the slow-feedback time domain dexamethasone reduced basal CRF mRNA levels and the stress-stimulated levels of CRF and preproenkephalin mRNA. These results show that different stimuli to the parvocellular paraventricular hypothalamus differentially regulate CRF transcript levels. Furthermore, in spite of the lack of any detectable effect of changes in circulating glucocorticoid levels on basal levels of preproenkephalin mRNA, glucocorticoids markedly alter the preproenkephalin mRNA response to stress.
Dual affinity fusion approach and its use to express recombinant human insulin-like growth factor II.
Authors: Hammarberg B , Nygren P A , Holmgren E , Elmblad A , Tally M , Hellman U , Moks T , Uhlén M
Published: May 2006

A dual affinity fusion concept has been developed in which the gene encoding the desired product is fused between two flanking heterologous genes encoding IgG- and albumin-binding domains. Using sequential IgG and serum albumin affinity chromatography, a full-length tripartite fusion protein is obtained. This approach was used to recover a full-length fusion product in Escherichia coli containing the human insulin-like growth factor II (IGF-II). Surprisingly, the recombinant IGF-II showed increased stability against proteolytic degradation in E. coli when produced as a dual affinity fusion protein, as compared to an N-terminal fusion protein. After site-specific cleavage of the tripartite fusion protein, IGF-II molecules with immunological and receptor binding activity were obtained without renaturation steps. The results demonstrate that proteins can fold into biologically active structures, even if provided with large flanking heterologous protein domains. The concept was further used to characterize the specific degradation of recombinant IGF-II in this heterologous host.
Centrally truncated and stabilized porcine neuropeptide Y analogs: design, synthesis, and mouse brain receptor binding.
Authors: Krstenansky J L , Owen T J , Buck S H , Hagaman K A , McLean L R
Published: May 2006

Porcine neuropeptide Y (pNPY) has been proposed to form an intramolecularly stabilized structure characterized by N- and C-terminal helical regions arranged antiparallel due to a central turn region. Analogs based on this structural model that have the central turn region and various amounts of the helical regions removed, yet retain the N and C termini in a similar spatial orientation were designed. The gap formed by removal of the central residues (residues 8-17 or 7-20) was spanned with a single 8-aminooctanoic acid residue (Aoc) and the structure was further stabilized by the introduction of a disulfide bridge. [D-Cys7,Aoc8-17,Cys20]pNPY and [Cys5,Aoc7-20,D-Cys24]pNPY were synthesized and found to have receptor binding affinities of 2.3 nM and 150 nM, respectively, in mouse brain membranes (pNPY affinity is 3.6 nM in this assay). It is proposed that the central region (residues 7-17) of pNPY serves a structural role in the peptide and is not involved in direct receptor interaction.
X-ray analysis of D-xylose isomerase at 1.9 A: native enzyme in complex with substrate and with a mechanism-designed inactivator.
Authors: Carrell H L , Glusker J P , Burger V , Manfre F , Tritsch D , Biellmann J F
Published: May 2006

The structures of crystalline D-xylose isomerase (D-xylose ketol-isomerase; EC 5.3.1.5) from Streptomyces rubiginosus and of its complexes with substrate and with an active-site-directed inhibitor have been determined by x-ray diffraction techniques and refined to 1.9-A resolution. This study identifies the active site, as well as two metal-binding sites. The metal ions are important in maintaining the structure of the active-site region and one of them binds C3-O and C5-O of the substrate forming a six-membered ring. This study has revealed a very close contact between histidine and C1 of a substrate, suggesting that this is the active-site base that abstracts a proton from substrate. The mechanism-based inhibitor is a substrate analog and is turned over by the enzyme to give a product that alkylates this same histidine, reinforcing our interpretation. The changes in structure of the native enzyme, the enzyme with bound substrate, and the alkylated enzyme indicate that the mechanism involves an "open-chain" conformation of substrate and that the intermediate in the isomerization reaction is probably a cis-ene diol because the active-site histidine is correctly placed to abstract a proton from C1 or C2 of the substrate. A water molecule binds to C1O and C2O of the substrate and so may act as a proton donor or acceptor in the enolization of a ring-opened substrate.
Effect of cell spreading on cytoplasmic pH in normal and transformed fibroblasts.
Authors: Schwartz M A , Both G , Lechene C
Published: May 2006

Growth of normal fibroblasts requires an adhesive substratum on which to spread, whereas transformed cells can grow in suspension. Since an alkaline cytoplasm has been shown to be required for growth, we measured cytoplasmic pH in individual cells as a function of spreading. The degree of spreading was controlled by coating tissue culture plastic with varying amounts of the nonadhesive polymer polyHEMA. Completely round BALB/c 3T3 cells were 0.15 pH unit more acidic than spread cells. In short-term experiments, cells were treated with the peptide Gly-Arg-Gly-Asp-Ser-Pro to induce rounding or by plating on fibronectin to induce spreading. When cells were induced to change shape, pH changed rapidly and reversibly. All of the anchorage-dependent cell lines tested behaved similarly, but 3T3 cells transformed by the plasma membrane oncogene src or ras were able to maintain a relatively alkaline pH even when completely round. Cells transformed by the nuclear oncogene myc behaved like normal cells. Our results suggest that the requirement for spreading may in part be mediated by cytoplasmic pH. Anchorage-independent growth due to oncogenes that localize to the plasma membrane is associated with loss of this control mechanism.
A gene encoding the tryptophan synthase beta subunit of Arabidopsis thaliana.
Authors: Berlyn M B , Last R L , Fink G R
Published: May 2006

The DNA sequence of a tryptophan synthase gene and the flanking 5' and 3' regions has been determined for Arabidopsis thaliana. The sequence encodes only the beta subunit domain, indicating that alpha and beta subunits are specified by separate genes. The gene contains four introns and encodes 470 amino acid residues. The plant amino acid sequence is highly conserved with respect to corresponding microbial sequences. The NH2-terminal amino acid sequence is characteristic of chloroplast transit peptides. Identity of the sequences of the genomic exons and a cDNA clone and the presence of cellular RNA corresponding in size and 5' sequence to the gene indicate that the gene is expressed. Analysis of Arabidopsis genomic DNA suggests the presence of a second gene for the beta subunit.
Quantifying the infectivity of human immunodeficiency virus.
Authors: Layne S P , Spouge J L , Dembo M
Published: May 2006

We have developed a mathematical model that quantifies lymphocyte infection by human immunodeficiency virus (HIV) and lymphocyte protection by blocking agents such as soluble CD4. We use this model to suggest standardized parameters for quantifying viral infectivity and to suggest techniques for calculating these parameters from well-mixed infectivity assays. We discuss the implications of the model for our understanding of the infectious process and virulence of HIV in vivo.
Small nuclear RNA-associated proteins are immunologically related as revealed by mapping of autoimmune reactive B-cell epitopes.
Authors: Habets W J , Sillekens P T , Hoet M H , McAllister G , Lerner M R , van Venrooij W J
Published: May 2006

Autoantibodies from a patient with systemic lupus erythematosus, which recognize U1 and U2 small nuclear ribonucleoprotein particles (snRNPs), were used to map B-cell autoepitopes on the U1 snRNP-specific A protein. This protein contains two regions that are highly similar to regions in the U2 snRNP-specific B" protein. A site termed epitope 2 maps in one such region and was found to react with antibodies cross-reactive between A and B". A second site, epitope 1, is situated in a proline-rich region that shows no homology with B". This epitope can bind three different autoantibodies with distinct specificities. Epitope 1-affinity-purified antibodies from different patients react with either (i) the A protein exclusively; (ii) proteins A, B'/B, a synthetic peptide for part of the N polypeptide, and an unidentified protein with a molecular mass of 50 kDa; or (iii) proteins A, B'/B, C, and the N-derived peptide. Comparison of the primary structures of proteins B'/B, N, and C reveals multiple epitope 1-like sequences in all of them. The possibility that these repeating regions act as immunogens in patients with autoimmune disease is discussed.
Blood-brain barrier transport of cationized immunoglobulin G: enhanced delivery compared to native protein.
Authors: Triguero D , Buciak J B , Yang J , Pardridge W M
Published: May 2006

IgG molecules are potential neuropharmaceuticals that may be used for therapeutic or diagnostic purposes. However, IgG molecules are excluded from entering brain, owing to a lack of transport of these plasma proteins through the brain capillary wall, or blood-brain barrier (BBB). The possibility of enhanced IgG delivery through the BBB by cationization of the proteins was explored in the present studies. Native bovine IgG molecules were cationized by covalent coupling of hexamethylenediamine and the isoelectric point was raised to greater than 10.7 based on isoelectric focusing studies. Native and cationized IgG molecules were radiolabeled with 125I and chloramine T. Cationized IgG, but not native IgG, was rapidly taken up by isolated bovine brain microvessels, which were used as an in vitro model system of the BBB. Cationized IgG binding was time and temperature dependent and was saturated by increasing concentrations of unlabeled cationized IgG (dissociation constant of the high-affinity binding site, 0.90 +/- 0.37 microM; Bmax, 1.4 +/- 0.4 nmol per mg of protein). In vivo studies documented enhanced brain uptake of 125I-labeled cationized IgG relative to [3H]albumin, and complete transcytosis of the 125I-labeled cationized IgG molecule through the BBB and into brain parenchyma was demonstrated by thaw-mount autoradiography of frozen sections of rat brain obtained after carotid arterial infusions of 125I-labeled cationized IgG. These studies demonstrate that cationization of IgG molecules greatly facilitates the transport of these plasma proteins through the BBB in vivo, and this process may provide a new strategy for IgG delivery through the BBB.
Norepinephrine induces pathway-specific long-lasting potentiation and depression in the hippocampal dentate gyrus.
Authors: Dahl D , Sarvey J M
Published: May 2006

The study presented here indicates that norepinephrine (NE) selectively induces long-lasting modifications of synaptically mediated responses in the dentate gyrus of the rat hippocampal slice. A low concentration of NE (1.0 microM; in the presence of 50 microM phentolamine, an alpha-adrenergic antagonist) or a 1.0 microM concentration of the specific beta-adrenergic agonist isoproterenol induced long-lasting pathway-specific alterations of granule cell electrophysiological responses. Excitatory postsynaptic potentials and population spikes evoked by stimulation of the medial perforant pathway (PP) were potentiated for more than 45 min. In contrast, responses to lateral PP stimulation were depressed for the same period. Both potentiation and depression were blocked by the beta-adrenergic antagonist propranolol (1.0 microM). These results indicate that NE can act differentially on projections to the dentate gyrus arising in the entorhinal cortex. Such selective persistent modifications of cortical circuits may be involved in processes in the mammalian brain underlying attention, learning, and memory.
F-actin affinity chromatography: technique for isolating previously unidentified actin-binding proteins.
Authors: Miller K G , Alberts B M
Published: May 2006

We have developed stable and easy to use filamentous actin (F-actin) affinity-chromatography columns that selectively purify proteins that bind to actin filaments from cell extracts. Most traditional assays for actin-associated proteins screen for their effects on actin polymerization or actin filament crosslinking. Because our technique requires only actin-filament binding, it can identify additional types of proteins involved in the function of the actin cytoskeleton. By chromatographing extracts of several types of cells on these columns, we show that known actin-binding proteins are selectively retained as a subset of a larger group of actin-binding proteins that have not been identified previously.
Transient state kinetic evidence for an oligomer in the mechanism of Na+-H+ exchange.
Authors: Otsu K , Kinsella J , Sacktor B , Froehlich J P
Published: May 2006

Pre-steady-state kinetic measurements of 22Na+ uptake by the amiloride-sensitive Na+-H+ exchanger in renal brush border membrane vesicles (BBMV) were performed at 0 degrees C to characterize the intermediate reactions of the exchange cycle. At 1 mM Na+, the initial time course of Na+ uptake was resolved into three separate components: (i) a lag phase, (ii) an exponential or "burst" phase, and (iii) a constant velocity or steady-state phase. Pulse-chase experiments using partially loaded BBMV showed no evidence for 22Na+ back-flux, suggesting that the decline in the rate of Na+ uptake rate following the burst represents completion of the first turnover of the exchanger. Gramicidin completely abolished Na+ uptake, indicating that the burst phase results from the translocation of Na+ rather than from residual Na+ binding to external sites. Raising the [Na+] from 1 to 10 mM at constant pH (internal pH 5.7; external pH 7.7) produced a sigmoidal increase in the amplitude of the burst phase without affecting the lag duration or the apparent burst rate. In contrast, Na+ uptake in the steady state obeyed Michaelis-Menten kinetics. These results suggest that a minimum of two Na+ transport sites must be occupied to activate Na+ uptake in the pre-steady state. The transition to Michaelis-Menten kinetics in the steady state can be explained by a "flip-flop" or alternating site mechanism in which the functional transport unit is an oligomer and only one promoter per cycle is allowed to form a translocation complex with Na+ after the first turnover.
Specific binding of a HeLa cell nuclear protein to RNA sequences in the human immunodeficiency virus transactivating region.
Authors: Gaynor R , Soultanakis E , Kuwabara M , Garcia J , Sigman D S
Published: May 2006

The transactivator protein, tat, encoded by the human immunodeficiency virus is a key regulator of viral transcription. Activation by the tat protein requires sequences downstream of the transcription initiation site called the transactivating region (TAR). RNA derived from the TAR is capable of forming a stable stem-loop structure and the maintenance of both the stem structure and the loop sequences located between +19 and +44 is required for complete in vivo activation by tat. Gel retardation assays with RNA from both wild-type and mutant TAR constructs generated in vitro with SP6 polymerase indicated specific binding of HeLa nuclear proteins to the TAR. To characterize this RNA-protein interaction, a method of chemical "imprinting" has been developed using photoactivated uranyl acetate as the nucleolytic agent. This reagent nicks RNA under physiological conditions at all four nucleotides in a reaction that is independent of sequence and secondary structure. Specific interaction of cellular proteins with TAR RNA could be detected by enhanced cleavages or imprints surrounding the loop region. Mutations that either disrupted stem base-pairing or extensively changed the primary sequence resulted in alterations in the cleavage pattern of the TAR RNA. Structural features of the TAR RNA stem-loop essential for tat activation are also required for specific binding of the HeLa cell nuclear protein.
Expression of the chicken vimentin gene in transgenic mice: efficient assembly of the avian protein into the cytoskeleton.
Authors: Capetanaki Y , Starnes S , Smith S
Published: May 2006

To study expression and function of the vimentin gene, transgenic mice were generated by microinjecting the entire chicken gene plus 2.4 kilobases of 5' and 2.6 kilobases of 3' flanking sequences. All the transgenic mice obtained had incorporated multiple copies of the gene. RNA analyses demonstrated that the chicken vimentin gene was efficiently expressed in an appropriate tissue-specific pattern and that the transcripts were properly processed, as in chicken, giving rise to two RNAs. The vimentin transgene was predominantly expressed in lens at levels of up to 10-fold the endogenous level in every transgenic line studied. The chicken vimentin transcripts were efficiently translated into polypeptides that were modified posttranslationally and could assemble into the mouse cytoskeleton. Overexpression of the chicken vimentin gene did not obviously affect the expression of the endogenous gene at the RNA or the protein level. Immunofluorescence microscopy further demonstrated that the chicken protein was properly expressed spatially in lens. However, the levels were much higher in the transgenic animals.
Identification of des-(Gly-Ile)-endozepine as an effector of corticotropin-dependent adrenal steroidogenesis: stimulation of cholesterol delivery is mediated by the peripheral benzodiazepine receptor.
Authors: Besman M J , Yanagibashi K , Lee T D , Kawamura M , Hall P F , Shively J E
Published: May 2006

Delivery of cholesterol to inner mitochondrial membranes is rate-limiting for steroidogenesis in the zona fasciculata of adrenal cortex. A protein that stimulates this process was isolated to homogeneity from bovine adrenal tissue. This protein's primary structure has been determined in its entirety by a combination of automated Edman microsequencing, fast-atom bombardment mass spectrometry (FAB-MS). The sequence was identical to that previously reported for bovine brain endozepine, except that it lacks the last two residues, -Gly-Ile, at the C terminus. To our knowledge, isolation of an endozepine-related protein from a tissue other than brain has not been reported previously. Endozepine competes with benzodiazepines for saturable binding sites in synaptosomes and in mitochondria of specific peripheral tissues. Previous reports have localized the adrenal benzodiazepine receptor to the outer mitochondrial membrane. In this report, we show that the prototypic benzodiazepine, diazepam, effects a stimulation of adrenal mitochondrial cholesterol delivery similar to that observed for endozepine. The effective diazepam concentration was consistent with that previously shown to displace a high-affinity ligand of the mitochondrial benzodiazepine receptor. The action of diazepam in adrenal mitochondria suggests that the mediation of corticotropin-induced steroidogenesis may be the physiological function of the peripheral-type benzodiazepine receptor. These studies provide new insights into the previously unknown function of peripheral benzodiazepine receptors and should allow new investigations into the stimulation of steroidogenesis by endozepines and benzodiazepines in the brain and in certain peripheral tissues.
In vitro methylation of Escherichia coli 16S ribosomal RNA and 30S ribosomes.
Authors: Nègre D , Weitzmann C , Ofengand J
Published: May 2006

Treatment of synthetic 30S particles lacking all of the normally methylated nucleotides with S-adenosyl-[3H]methionine and either an S100 or ribosomal high salt wash extract resulted in ribosome-dependent incorporation of [3H]methyl groups into trichloroacetic acid-insoluble material. No incorporation was observed when naturally methylated isolated 30S particles were used, showing that methylation at unnatural sites did not occur. Enzymatic hydrolysis of the labeled RNA to nucleosides followed by HPLC analysis identified the [3H]methylated residues. Activities for the formation of N6-methyladenosine, N6-dimethyladenosine, 5-methylcytidine (m5C), 3-methyluridine, and N2-methylguanosine were found. Fractionation by ammonium sulfate partially resolved the different activities. All of the fractions with m5C activity were 6-8 times more active on synthetic unmethylated 16S RNA than on synthetic 30S ribosomes, whereas the N2-methylguanosine activity preferred 30S ribosomes to 16S RNA by a factor of more than 10. The N6-methyladenosine and N6-dimethyladenosine activities were 30S ribosome-specific. The m5C activity present in the 55-85% ammonium sulfate fraction of the high salt wash yielded a maximum of 1.0 mol of m5C per mol of 16S RNA, although two m5C residues, positions 967 and 1407, are found in vivo. RNase protection by hybridization with the appropriate oligodeoxynucleotide identified the methylated residue as C-967. Methylation of m5C-967 did not require prior methylation of G-966, and methylation of A-1518 and A-1519 was not dependent on prior methylation of G-1516.
Iron-sulfur clusters of hydrogenase I and hydrogenase II of Clostridium pasteurianum.
Authors: Adams M W , Eccleston E , Howard J B
Published: May 2006

The iron and acid-labile sulfide contents and the electron paramagnetic resonance (EPR) properties of hydrogenase I (bidirectional) and hydrogenase II (uptake) of Clostridium pasteurianum (strain W5) have been determined on the basis of quantitative amino acid analyses. The iron and acid-labile sulfide values are approximately 20 and 18 atoms per molecule of hydrogenase I and 14 and 11 atoms per molecule of hydrogenase II, respectively. These amounts are substantially greater than previously reported values, which relied on protein concentration determined by colorimetric assay. The oxidized hydrogenases exhibit unusual EPR signals that originate from a novel type of iron-sulfur center, termed the hydrogenase or H cluster, which covalently binds the inhibitor CO. This EPR signal represents approximately one unpaired electron per molecule in each enzyme with and without bound CO, which is consistent with the presence of one oxidized H cluster (S = 1/2) per enzyme molecule. The two enzymes also contain ferredoxin-type four-iron centers or F clusters. The EPR signals from the F clusters observed in the reduced forms of hydrogenase I and hydrogenase II account for approximately four and one unpaired electron per molecule, respectively. We conclude from the iron determinations and the EPR results, together with a reevaluation of previous spectroscopic data, that in both hydrogenases the H cluster probably comprises six iron atoms. Mechanistic models of the two hydrogenases are presented that account for their cluster compositions and the dramatic differences in their catalytic activities.
Physical mapping of complex genomes by cosmid multiplex analysis.
Authors: Evans G A , Lewis K A
Published: May 2006

A rapid and powerful approach for linking individual clones of a cosmid library and the assembly of a large physical map is presented, which depends on the simultaneous analysis of many cosmid clones for overlapping regions. This method uses cosmid vectors that contain endogenous bacteriophage T3 and T7 promoters to allow for the identification of overlapping clones through the synthesis of end-specific RNA probes. A genomic library is constructed and organized as an ordered matrix such that each clone is assigned an identifying coordinate. DNA from mixtures of cosmid clones is pooled such that each pool contains only one common member with any other pool, RNA probes are prepared from mixtures of cosmid clones, and groups of clones overlapping with the constituents of the mixtures are determined by hybridization. Pooled probes are most simply prepared by grouping clones according to the rows and columns of the library matrix. The pairwise comparison of data generated by the hybridization of mixed probes can be decoded by using simple algorithms that predict the order and linkage of all clones in the collection and organize them into predicted contigs. To demonstrate the feasibility of multiplexed analysis of cosmids, a genomic library was prepared from a mouse-human somatic cell hybrid that contains a portion of the long arm of human chromosome 11. Preparation, arrangement on a matrix, and analysis of pooled cosmid clones from this collection resulted in the detection of 1099 linked pairs of cosmids, which could be assembled into 315 contigs. Thus, with a minimal amount of effort, a substantial portion of this genomic region has been linked in multiple overlapping contigs. This method may have practical applications in the large-scale mapping and sequencing of mammalian genomes.
Double-negative (CD4-CD8-) lymphocytes bearing T-cell receptor alpha and beta chains in normal human skin.
Authors: Groh V , Fabbi M , Hochstenbach F , Maziarz R T , Strominger J L
Published: May 2006

Double-negative (CD4-CD8-) T-cell receptor alpha- and beta-chain (TCR alpha beta)-expressing lymphocytes have been identified in human skin. Two skin-derived lymphocyte cell lines (II-1 and II-2) expressing this phenotype were obtained. They each expressed full-length TCR alpha- and beta-chain transcripts and lacked TCR gamma- and delta-chain as well as CD4 and CD8 mRNAs. These polyclonal cell lines shared one predominant TCR beta-chain gene rearrangement. The CD3/TCR alpha beta complexes were functionally competent as evidenced by their capacity to transduce activation signals resulting in cell proliferation, lymphokine secretion, and cytolytic activity. The demonstration of CD4-CD8-TCR alpha beta lymphocytes as a subpopulation of the skin-associated immune system should contribute to understanding the biologic potential of this cell population as well as of this organ-specific immune system.
Essential features of the P-glycoprotein pharmacophore as defined by a series of reserpine analogs that modulate multidrug resistance.
Authors: Pearce H L , Safa A R , Bach N J , Winter M A , Cirtain M C , Beck W T
Published: May 2006

We have shown previously that reserpine is an effective "modulator" of P-glycoprotein-associated multidrug resistance (MDR). In addition to enhancing drug cytotoxicity in our multidrug-resistant human leukemia cell line, CEM/VLB100, reserpine strongly competes with a photoactivatible analog of vinblastine, N-(p-azido-3-[125I]iodosalicyl)-N'-(beta-aminoethyl)vindesine, for binding to P-glycoprotein. We also demonstrated previously that there are three substructural domains present in many compounds that modulate P-glycoprotein-associated MDR: a basic nitrogen atom and two planar aromatic rings. In the present study, we wished to test more rigorously the hypothesis that not only are these domains necessary for modulators of MDR but also they must exist in an appropriate conformation. Reserpine is a modulator of MDR in which these domains are present in a well-defined conformation. Accordingly, we prepared eight compounds that vary the spatial orientation of these domains, using either naturally occurring reserpine or yohimbine as chemical templates. When tested for their ability to enhance the cytotoxic activity of natural product antitumor drugs in CEM/VLB100 cells, five compounds that retained the pendant benzoyl function in an appropriate spatial orientation all modulated MDR. By contrast, compounds lacking this moiety failed to do so. These active modulators competed strongly with the 125I-labeled vinblastine analog for binding to P-glycoprotein in plasma membrane vesicles prepared from these cells. Conformational analysis using molecular mechanics revealed the structural similarities of the active modulators. Our results support the hypothesis that the relative disposition of aromatic rings and basic nitrogen atom is important for modulators of P-glycoprotein-associated MDR, and they suggest a ligand-receptor relationship for these agents. These results also provide direction for the definition of an MDR "pharmacophore."
Hepatitis B virus X gene activates kappa B-like enhancer sequences in the long terminal repeat of human immunodeficiency virus 1.
Authors: Twu J S , Chu K , Robinson W S
Published: May 2006

The role of the hepatitis B virus (HBV) X gene during virus infection has not been defined. We previously showed that expression of the HBV X gene in the human hepatocellular carcinoma cell line HepG2 trans-activates chloramphenicol acetyltransferase gene expression under control of the human immunodeficiency virus 1 (HIV-1) long terminal repeat and we have now identified a specific sequence in the HIV-1 long terminal repeat that is responsive to the HBV X gene. Plasmid constructs with the chloramphenicol acetyltransferase gene regulated by an isolated and twice-repeated 12-base-pair HIV-1 enhancer sequence homologous to the nucleotide sequence that binds the nuclear transcription factor NF-kappa B (the HIV-1 kappa B-like sequence) were trans-activated by the HBV X gene in HepG2 cells, indicating that the kappa B-like enhancer sequence in the HIV-1 long terminal repeat is responsive to the X gene. When eight copies of the HIV-1 kappa B-like sequence were used to regulate beta-globin gene expression, transcription of this gene was activated by the HBV X gene in HepG2 cells and no beta-globin gene transcription was detected in the absence of the HBV X gene. beta-globin gene expression regulated by the activator protein 2 (AP-2) binding sequence was not activated by the HBV X gene. Treatment of HepG2 cells with phorbol ester resulted in modest activation of the HIV-1 kappa B-like enhancer sequence suggesting that an NF-kappa B-like factor was induced in these cells as it is in T lymphocytes by phorbol ester; however, phorbol ester did not demonstrably enhance the activation of the HIV-1 enhancer observed with the HBV X gene. These experiments indicate that the HIV-1 kappa B-like transcriptional enhancer sequence is activated by the HBV X gene and suggest that the HBV X gene might play a role in regulating transcription of a gene under control of a kappa B-like enhancer during HBV infection. Since such a sequence has not been found in the HBV genome and HBV gene expression appears not to be regulated by the HBV X gene, a cellular gene that plays a role in HBV replication could be the target of the X gene during HBV infection.
The (A)BC excinuclease of Escherichia coli has only the UvrB and UvrC subunits in the incision complex.
Authors: Orren D K , Sancar A
Published: May 2006

The uvrA, uvrB, and uvrC genes control excision repair in Escherichia coli. Cells with mutations in any of these three genes cannot repair DNA by nucleotide excision. When the purified gene products--the UvrA, UvrB, and UvrC proteins--are mixed together, an excision nuclease is formed that incises on both sides of the damaged nucleotide in an ATP-dependent reaction; it has been presumed that the excision nuclease was an ABC complex containing all three Uvr proteins. To determine the stoichiometry of the subunits in the enzyme, we conducted hydrodynamic studies with mixtures of the subunits with or without DNA substrate. We found that without DNA the UvrA subunit is a dimer and that when UvrB protein is also present, a (UvrA)2(UvrB)1 complex forms. Without DNA no detectable interaction of either the UvrA or UvrB subunits or the (UvrA)2(UvrB)1 complex with the UvrC subunit occurs. Unexpectedly, with UV-irradiated DNA, the UvrA/UvrB ratio in isolated DNA-protein complexes is variable, and the ratio becomes infinitesimally low as the UvrA concentration in the reaction mixture decreases. Under conditions of saturating UvrB protein approximately one UvrB molecule binds to DNA per damaged site in a reaction that requires catalytic amounts of UvrA subunit. Addition of UvrC protein to purified UvrB-DNA complexes results in rapid incision of the DNA, presumably catalyzed by an excision nuclease containing only UvrB and UvrC subunits.
Glutathione metabolism in the lung: inhibition of its synthesis leads to lamellar body and mitochondrial defects.
Authors: Mårtensson J , Jain A , Frayer W , Meister A
Published: May 2006

Mice treated with buthionine sulfoximine, an inhibitor of glutathione synthesis, showed striking alterations of morphology of lung type 2 cell lamellar bodies (swelling and disintegration) and mitochondria (degeneration) and of lung capillary endothelial cells (mitochondrial swelling). These effects probably may be ascribed to glutathione deficiency; administration of glutathione monoester protects against them. Measurements of arteriovenous plasma glutathione levels across the lung indicate that the net uptake of glutathione by this organ is substantial. Thus, glutathione exported from the liver to the blood plasma is utilized by the lung which, like the liver, kidney, and lymphocytes (and unlike skeletal muscle), exhibits a high overall rate of glutathione turnover. Intraperitoneal injection of glutathione into buthionine sulfoximine-treated mice leads to very high levels of plasma glutathione without significant increase in the glutathione levels of liver, lung, and lymphocytes; on the other hand, administration of glutathione monoester leads to markedly increased tissue and mitochondrial levels of glutathione. Administration of glutathione monoester (in contrast to glutathione) to control mice also increases mitochondrial glutathione levels. The findings indicate that glutathione is required for mitochondrial integrity and that it probably also functions in the processing and storage of surfactant in lamellar bodies. The morphological changes observed after treatment with buthionine sulfoximine and their prevention by glutathione monoester as well as findings on glutathione metabolism indicate that this tripeptide plays an important role in the lung. The previously observed failure of buthionine sulfoximine-treated mice to gain weight is mainly due to glutathione deficiency in the intestinal mucosa.