bluuebunny/crossref_metadata_2025 huggingface dataset:
CDR1 T-cell receptor beta-chain peptide induces major histocompatibility complex class II-restricted T-T cell interactions.
Authors: Broeren C P , Lucassen M A , van Stipdonk M J , van der Zee R , Boog C J , Kusters J G , van Eden W
Published: May 2006

T-T cell interactions have been proposed in postulated network theories of immunoregulation and autoimmunity. Despite previous reports of protection induced by T-cell receptor (TcR)-derived peptides in experimental autoimmunity, no evidence for T-T cell interactions by direct recognition of processed TcRs on native T cells was obtained. Here we report that immunization of rats with overlapping sets of peptides of the TcR alpha or beta chain allowed us to detect immunogenic TcR peptides. Remarkably enough, these TcR peptides appeared to cluster within the hypervariable complementarity-determining regions of the TcR. Immunization of rats with these TcR peptides induced CD4+ TcR peptide-specific T cells, which recognized both rDNA TcR proteins and the original, arthritogenic T cell in a major histocompatibility complex class II-restricted way. These findings indicate that activated T cells can process and present their own TcR in the context of major histocompatibility complex class II molecules and, furthermore, that such peptides can be recognized by TcR variable gene-specific T cells.
par-2, a gene required for blastomere asymmetry in Caenorhabditis elegans, encodes zinc-finger and ATP-binding motifs.
Authors: Levitan D J , Boyd L , Mello C C , Kemphues K J , Stinchcomb D T
Published: May 2006

The par-2 gene of Caenorhabditis elegans functions in early embryogenesis to ensure an asymmetric first cleavage and the segregation of cytoplasmic factors. Both processes appear to be required to generate daughter blastomeres with distinct developmental potential. We isolated an allele of par-2 by using a screen for maternal-effect lethal mutations in a strain known for its high frequency of transposition events. A transposable element was found to be linked to this allele. Sequences flanking the site of transposon insertion were cloned and found to rescue the par-2 mutant phenotype. DNA in the par-2 region hybridized to a 2.3-kb germ-line-enriched mRNA. The cDNA corresponding to this germ-line-enriched message was cloned, sequenced, and used to identify the molecular lesions associated with three par-2 alleles. Sequence analysis of the par-2 cDNA revealed that the predicted protein contained two distinct motifs found in other known proteins: an ATP-binding site and a cysteine-rich motif which identifies the par-2 gene product as a member of a growing class of putative zinc-binding proteins.
Life-spans of human T-cell responses to determinants from the circumsporozoite proteins of Plasmodium falciparum and Plasmodium vivax.
Authors: Zevering Y , Khamboonruang C , Rungruengthanakit K , Tungviboonchai L , Ruengpipattanapan J , Bathurst I , Barr P , Good M F
Published: May 2006

The longevity of specific human memory T-cell responses is largely unknown. However, a knowledge of the duration of memory is important for understanding immunity to an organism and for planning vaccine intervention. To address this, we have examined T-cell memory to malaria by determining T-cell responses by subjects recently exposed to peptides spanning the circumsporozoite (CS) proteins of two species of malaria-causing organisms, Plasmodium falciparum and Plasmodium vivax. Responses to vivax CS peptides by exposed Thai subjects were more frequent than responses by nonexposed individuals, permitting identification of determinants seen by vivax-induced responses. At the population level, there appears to be life-long memory, as the time since individuals were exposed did not diminish responsiveness to these determinants. In contrast, falciparum-exposed subjects were largely indistinguishable from nonexposed controls in responsiveness to falciparum CS determinants. However, a single peptide (F16: DNEKLRKPKHKKLKQPGDGN) was recognized significantly more frequently by P. falciparum-exposed than nonexposed Thai subjects. T cells responsive to this peptide were CD450+ and produced gamma-interferon. In contrast to the response to the vivax determinants and the other falciparum determinants, responsiveness to F16 was undetectable or minimal 2 years after exposure. Our data provide the average life-spans of certain malaria-specific T cells and are consistent with, but do not prove, the hypothesis that antigenic persistence (in the form of P. vivax hypnozoites) correlates with persistence of human T-cell memory.
In vivo phosphorylation of the Na,K-ATPase alpha subunit in sciatic nerves of control and diabetic rats: effects of protein kinase modulators.
Authors: Borghini I , Geering K , Gjinovci A , Wollheim C B , Pralong W F
Published: May 2006

The phosphorylation state of the Na,K-ATPase alpha subunit has been examined in 32P-labeled sciatic nerves of control and streptozotocin-treated diabetic rats. Intact nerves were challenged with protein kinase (PK) modulators and alpha-subunit 32P labeling was analyzed after immunoprecipitation. In control nerves, the PKC activator phorbol 12-myristate 13-acetate (PMA) had little effect on alpha-subunit 32P labeling. In contrast, staurosporine, a PKC inhibitor, and extracellular calcium omission decreased it. In Ca(2+)-free conditions, PMA restored the labeling to basal levels. The cAMP-raising agent forskolin reduced the 32P labeling of the alpha subunit. The results suggest that nerve Na,K-ATPase is tonically phosphorylated by PKC in a Ca(2+)-dependent manner and that PKA modulates the phosphorylation process. In nerves of diabetic rats, PMA increased 32P labeling of the alpha subunit. In contrast to staurosporine or extracellular calcium omission, the decreased state of phosphorylation seen with forskolin was no longer significant in diabetic nerves. No change in the level of alpha-subunit isoforms (alpha 1 or alpha 2) was detected by Western blot analysis in such nerves. In conclusion, the altered effect of PK activators on Na,K-ATPase phosphorylation state is consistent with the view that a defect in PKC activation exists in diabetic nerves.
High-affinity alpha-thrombin binding to platelet glycoprotein Ib alpha: identification of two binding domains.
Authors: Gralnick H R , Williams S , McKeown L P , Hansmann K , Fenton J W , Krutzsch H
Published: May 2006

alpha-Thrombin binding to and activation of platelets are of major importance in the initiation of physiologic thrombi and in the genesis of arterial thrombus formation. We have studied the site(s) and affinity of thrombin binding to human platelets. Our studies of the peptide inhibition of thrombin binding indicate that the glycoprotein Ib alpha binding site is of high affinity, Kd approximately 10(-10) M, while the seven-transmembrane-domain site is a moderate-affinity thrombin binding site, Kd approximately 10(-8) M. Further studies to modulate the high- or moderate-affinity thrombin binding can be directed to a specific class of sites. This would allow partial or total inhibition of specific thrombin-platelet interaction(s) in different clinical settings.
Axonal transport of herpes simplex virions to epidermal cells: evidence for a specialized mode of virus transport and assembly.
Authors: Penfold M E , Armati P , Cunningham A L
Published: May 2006

To examine the transmission of herpes simplex virus (HSV) from axon to epidermal cell, an in vitro model was constructed consisting of human fetal dorsal root ganglia cultured in the central chamber of a dual-chamber tissue culture system separated from autologous skin explants in an exterior chamber by concentric steel cylinders adhering to the substratum through silicon grease and agarose. Axons grew through the agarose viral diffusion barrier and terminated on epidermal cells in the exterior chamber. After inoculation of HSV onto dorsal root ganglia, anterograde axonal transport of glycoprotein and nucleocapsid antigen was observed by confocal microscopy to appear in exterior chamber axons within 12 h and in epidermal cells within 16 h, moving at 2-3 mm/h. Although both enveloped and unenveloped nucleocapsids were observed in the neuronal soma by transmission electron microscopy, only nucleocapsids were observed in the axons, closely associated with microtubules. Nodule formation at the surface of HSV-infected axons, becoming more dense at the axon terminus on epidermal cells, and patches of axolemmal HSV glycoprotein D expression were observed by scanning (immuno)electron microscopy, probably representing virus emerging from the axolemma. These findings strongly suggest a specialized mode of viral transport, assembly, and egress in sensory neurons: microtubule-associated intermediate-fast anterograde axonal transport of unenveloped nucleocapsids with separate transport of glycoproteins to the distal regions of the axon and assembly prior to virus emergence at the axon terminus.
Human immunodeficiency virus 1 (HIV-1)-specific reverse transcriptase (RT) inhibitors may suppress the replication of specific drug-resistant (E138K)RT HIV-1 mutants or select for highly resistant (Y181C-->C181I)RT HIV-1 mutants.
Authors: Balzarini J , Karlsson A , Sardana V V , Emini E A , Camarasa M J , De Clercq E
Published: May 2006

Mutant HIV-1 that expresses a Glu138-->Lys substitution in its RT [(E138K)RT] is resistant to the HIV-1-specific RT inhibitor 2',5'-bis-O-(tert-butyldimethylsilyl)-3'-spiro-5"-(4"-amino-1",2"- oxathiole-2",2"-dioxide)pyrimidine (TSAO). However, cell cultures infected with this mutant were completely protected against virus-mediated destruction by micromolar concentrations of the HIV-1-specific RT inhibitors tetrahydroimidazo[4,5,1-jk][1,4]benzodiazepin-2(1H)-one and -thione (TIBO), nevirapine, and bis(heteroaryl)piperazine (BHAP). In contrast, cells infected with a virus mutant that expresses a Tyr181-->Cys substitution in its RT [(Y181C)RT] were not protected by nevirapine and TIBO and were only temporarily protected by BHAP. HIV-1 mutant that emerged under the latter conditions contained a Cys181-->Ile substitution in their RT [(LC181I)RT]. This mutant proved highly resistant to all HIV-1-specific RT inhibitors tested, except for several 1-(2-hydroxyethoxymethyl)-6-(phenylthio)thymine (HEPT) derivatives. When recombinant (C181I)RT was evaluated for susceptibility to the HIV-1-specific RT inhibitors, it was resistant to all inhibitors except the HEPT compounds. Since a (Y181F)RT HIV mutant strain was isolated from cells infected with (Y181C)RT HIV-1 and treated with BHAP, we postulate that the Ile codon was derived from a Cys-->Phe transversion mutation (TGT-->TTT), followed by a Phe-->Ile transversion mutation (TTT-->ATT).
Two-photon scanning photochemical microscopy: mapping ligand-gated ion channel distributions.
Authors: Denk W
Published: May 2006

The locations and densities of ionotropic membrane receptors, which are responsible for receiving synaptic transmission throughout the nervous system, are of prime importance in understanding the function of neural circuits. It is shown that the highly localized liberation of "caged" neurotransmitters by two-photon absorption-mediated photoactivation can be used in conjunction with recording the induced whole-cell current to determine the distribution of ligand-gated ion channels. The technique is potentially sensitive enough to detect individual channels with diffraction-limited spatial resolution. Images of the distribution of nicotinic acetylcholine receptors on cultured BC3H1 cells were obtained using a photoactivatable precursor of the nicotinic agonist carbamoylcholine.
Drosophila mode of metamerization in the embryogenesis of the lepidopteran insect Manduca sexta.
Authors: Kraft R , Jäckle H
Published: May 2006

Insect embryos have been classified as intermediate- and short-germ embryos, in which posterior segments are thought to be generated sequentially from an uncommitted growth zone, or as long-term embryos, such as Drosophila melanogaster, which develop primordia for all segments simultaneously. In Drosophila the coordinated activities among a three-tiered cascade of zygotic segmentation genes subdivide the embryo into progressively smaller units along the anterior-posterior axis. The mode of pattern specification in lepidopteran embryos has not been determined, although on morphological grounds they have been characterized as intermediate-germ insects. We have cloned orthologues of Drosophila segmentation genes from the tobacco hawkmoth Manduca sexta and have found that the blastoderm expression patterns of these genes show a molecular prepatterning typical of Drosophila. Thus, successive segment formation in Manduca embryos may not be due to sequential addition but rather may be the consequence of a lateral compression of the embryo proceeding in an anterior-to-posterior progression. These data challenge the view that the classification of insect development according to morphological criteria can serve as a reliable indicator of the molecular mechanisms underlying segmentation.
A fluorescence-based assay for monitoring helicase activity.
Authors: Raney K D , Sowers L C , Millar D P , Benkovic S J
Published: May 2006

A continuous fluorescence-based assay is described for measuring helicase-mediated unwinding of duplex DNA. The assay utilizes an oligonucleotide substrate containing the fluorescent adenine analog, 2-aminopurine, at regular intervals. 2-Aminopurine forms a Watson-Crick-type base pair with thymine and does not distort normal B-form DNA. Fluorescence of the 2-aminopurines within this oligonucleotide is quenched 2-fold upon its hybridization to a complementary strand. Unwinding of this substrate by the T4 dda helicase restores the fluorescence of the 2-aminopurines and is easily followed using stopped-flow or steady-state fluorescence spectroscopy. The flourescence-based assay provides rate data comparable to that obtained from conventional discontinuous assays using labeled substrates and additionally furnishes a means for following a single turnover. This assay should prove useful for defining the mechanism by which helicases unwind duplex DNA.
High-level expression and deletion mutagenesis of human tryptophan hydroxylase.
Authors: Yang X J , Kaufman S
Published: May 2006

Human tryptophan hydroxylase has been expressed as a soluble and active form in Escherichia coli by fusion with an affinity tag, maltose-binding protein. The fusion protein has been purified to near homogeneity by affinity chromatography on crosslinked amylose resin. The purified fusion protein has a specific activity of 86 nmol of 5-hydroxytryptophan per min per mg of fusion protein. A series of truncation mutants have also been made to explore the domain organization of tryptophan hydroxylase. All deletion mutants were subject to affinity purification and kinetic characterization. While removal of the N-terminal 164 amino acids completely inactivates the enzyme, deletion of the first 91 residues results in a 7-fold reduction in specific activity. From the C terminus, deletion of 36, 55, or 112 amino acids abolishes the activity, whereas deletion of 19 residues decreases the specific activity by approximately 11-fold. These results are consistent with a model for tryptophan hydroxylase in which the enzyme consists of an N-terminal regulatory domain, a catalytic core, and a small C-terminal region of uncertain but important function.
The Fanconi anemia polypeptide FACC is localized to the cytoplasm.
Authors: Yamashita T , Barber D L , Zhu Y , Wu N , D'Andrea A D
Published: May 2006

Fanconi anemia (FA) is an autosomal recessive disease characterized by congenital anomalies, aplastic anemia, and chromosomal instability. A cDNA encoding the FA complementation group C (FACC) polypeptide was recently cloned [Strathdee, C. A., Gavish, H., Shannon, W. R. & Buchwald, M. (1992) Nature (London) 356, 763-767]. To further characterize this polypeptide, we generated a rabbit polyclonal antiserum against its carboxyl terminus. We used this antiserum to analyze the FACC polypeptide from normal or mutant (FA) lymphoblast cell lines. By immunoprecipitation, the wild-type FACC was a 60-kDa protein, consistent with its predicted molecular mass. FA group C cell lines expressed full-length FACC, truncated FACC, or no detectable FACC polypeptide. In addition, the antiserum specifically immunoprecipitated a 50-kDa and a 150-kDa FACC-related protein (FRP-50 and FRP-150). Unexpectedly, cell fractionation and immunofluorescence studies demonstrated that the FACC polypeptide localizes to the cytoplasm. In conclusion, we have generated an antiserum specific for the human FACC polypeptide. The antiserum should be useful for screening FA cells for mutant FACC polypeptides and for identifying and cloning FACC-related proteins.
Tempo, mode, the progenote, and the universal root.
Authors: Doolittle W F , Brown J R
Published: May 2006

Early cellular evolution differed in both mode and tempo from the contemporary process. If modern lineages first began to diverge when the phenotype-genotype coupling was still poorly articulated, then we might be able to learn something about the evolution of that coupling through comparing the molecular biologies of living organisms. The issue is whether the last common ancestor of all life, the cenancestor, was a primitive entity, a progenote, with a more rudimentary genetic information-transfer system. Thinking on this issue is still unsettled. Much depends on the placement of the root of the universal tree and on whether or not lateral transfer renders such rooting meaningless.
The role of extinction in evolution.
Authors: Raup D M
Published: May 2006

The extinction of species is not normally considered an important element of neodarwinian theory, in contrast to the opposite phenomenon, speciation. This is surprising in view of the special importance Darwin attached to extinction, and because the number of species extinctions in the history of life is almost the same as the number of originations; present-day biodiversity is the result of a trivial surplus of originations, cumulated over millions of years. For an evolutionary biologist to ignore extinction is probably as foolhardy as for a demographer to ignore mortality. The past decade has seen a resurgence of interest in extinction, yet research on the topic is still at a reconnaissance level, and our present understanding of its role in evolution is weak. Despite uncertainties, extinction probably contains three important elements. (i) For geographically widespread species, extinction is likely only if the killing stress is one so rare as to be beyond the experience of the species, and thus outside the reach of natural selection. (ii) The largest mass extinctions produce major restructuring of the biosphere wherein some successful groups are eliminated, allowing previously minor groups to expand and diversify. (iii) Except for a few cases, there is little evidence that extinction is selective in the positive sense argued by Darwin. It has generally been impossible to predict, before the fact, which species will be victims of an extinction event.
How can the low levels of DNA sequence variation in regions of the drosophila genome with low recombination rates be explained?
Authors: Hudson R R
Published: May 2006

Different regions of the Drosophila genome have very different rates of recombination. For example, near centromeres and near the tips of chromosomes, the rates of recombination are much lower than in other regions. Several surveys of polymorphisms in Drosophila have now documented that levels of DNA polymorphism are positively correlated with rates of recombination; i.e., regions with low rates of recombination tend to have low levels of DNA polymorphism within populations of Drosophila. Three hypotheses are reviewed that might account for these observations. The first hypothesis is that regions of low recombination have low neutral mutation rates. Under this hypothesis between-species divergences should also be low in regions of low recombination. In fact, regions of low recombination have diverged at the same rate as other regions of the genome. On this basis, this strictly neutral hypothesis is rejected. The second hypothesis is that the process of fixation of favorable mutations leads to the observed correlation between polymorphism and recombination. This occurs via genetic hitchhiking, in which linked regions of the genome are swept along with the selectively favored mutant as it increases in frequency and eventually fixes in the population. This hitchhiking model with fixation of favorable mutations is compatible with major features of the data. By assuming this model is correct, one can estimate the rate of fixation of favorable mutations. The third hypothesis is that selection against continually arising deleterious mutations results in reduced levels of polymorphism at linked loci. Analysis of this background selection model shows that it can produce some reduction in levels of polymorphism but cannot explain some extreme cases that have been observed. Thus, it appears that hitchhiking of favorable mutations and background selection against deleterious mutations must be considered together to correctly account for the patterns of polymorphism that are observed in Drosophila.
Isolation of the bile canalicular actin-myosin II motor.
Authors: Tsukada N , Azuma T , Phillips M J
Published: May 2006

Cytoskeleton-rich canalicular membranes (CCMs) with preserved cytoskeleton and demembranated CCMs, consisting only of cytoskeletal elements, were used to examine the relationship of pericanalicular microfilaments, myosin II phosphorylation, and canalicular contraction. The components of CCMs were visualized by fluorescence microscopy using the filamentous actin probe rhodamine-phalloidin and by electron microscopy, before and after incubation in 1 microM Ca2+/1 mM ATP (contraction solution). Canalicular contraction (luminal closure) was evaluated by morphometric analysis. Myosin II was extracted from CCMs, purified by immunoprecipitation, and analyzed on Western blots. In sequential experiments, autoradiographs of gels from [gamma-32P]-ATP-treated CCMs in the presence or absence of Ca2+ were examined after 0.25, 0.50, 1, 2, 3, 5, and 10 min, and the effects of W7 (a calmodulin antagonist) and ML9 (a myosin light chain kinase inhibitor) were evaluated. The results showed that phosphorylation of the 20-kDa protein was low in controls but enhanced beginning 0.25-0.50 min after addition of contraction solution. Both W7 and ML9 significantly inhibited this reaction and inhibited canalicular contraction. The results indicate that phosphorylation of the regulatory 20-kDa myosin light chain of canaliculus-associated myosin II coincides with or precedes contraction of the canaliculus. We conclude that the canalicular contractile apparatus is composed of actin filaments and a myosin II motor.
Cloning and sequencing of thiol-specific antioxidant from mammalian brain: alkyl hydroperoxide reductase and thiol-specific antioxidant define a large family of antioxidant enzymes.
Authors: Chae H Z , Robison K , Poole L B , Church G , Storz G , Rhee S G
Published: May 2006

A cDNA corresponding to a thiol-specific antioxidant enzyme (TSA) was isolated from a rat brain cDNA library with the use of antibodies to bovine TSA. The cDNA clone encoded an open reading frame capable of encoding a 198-residue polypeptide. The rat and yeast TSA proteins show significant sequence homology to the 21-kDa component (AhpC) of Salmonella typhimurium alkyl hydroperoxide reductase, and we have found that AhpC exhibits TSA activity. AhpC and TSA define a family of > 25 different proteins present in organisms from all kingdoms. The similarity among the family members extends over the entire sequence and ranges between 23% and 98% identity. A majority of the members of the AhpC/TSA family contain two conserved cysteines. At least eight of the genes encoding AhpC/TSA-like polypeptides are found in proximity to genes encoding other oxidoreductase activities, and the expression of several of the homologs has been correlated with pathogenicity. We suggest that the AhpC/TSA family represents a widely distributed class of antioxidant enzymes. We also report that a second family of proteins, defined by the 57-kDa component (AhpF) of alkyl hydroperoxide reductase and by thioredoxin reductase, has expanded to include six additional members.
Central location of the Mu strong gyrase binding site is obligatory for optimal rates of replicative transposition.
Authors: Pato M L
Published: May 2006

The bacteriophage Mu genome contains a strong DNA gyrase binding site (SGS) near its center, and disruption of the SGS by deletion or by insertion results in long delays in replication following induction of the appropriate lysogen. To determine if the central location of the SGS is obligatory for its function in Mu replication, we pursued two lines of investigation. First, fragments of Mu DNA containing the SGS were inserted into various locations in a Mu prophage lacking the central SGS. Replication following induction was restored in all of the lysogens constructed, but the observed rate of replication for different prophages decreased with increasing distance between the new location of the SGS and the center of the genome. We also deleted different lengths of DNA from within the right half of a wild-type prophage, retaining the SGS and displacing it from a central location. Replication rates of the deleted prophages were reduced, with larger deletions resulting in larger reductions. Pairing deletions in the right half of the prophage with a deletion in the left half resulted in substantially higher rates of replication than observed with the right half deletions alone. We conclude that the SGS must be located centrally between the Mu termini for optimal rates of Mu replication. These results are discussed in terms of a model that proposes that the SGS is involved in organizing the topology of supercoiled prophage DNA to assist in synapsis of the Mu termini.
Identification of a melanosomal matrix protein encoded by the murine si (silver) locus using "organelle scanning".
Authors: Zhou B K , Kobayashi T , Donatien P D , Bennett D C , Hearing V J , Orlow S J
Published: May 2006

To identify a broad spectrum of melanosomal proteins, antisera were raised in rabbits against melanosomal protein fractions separated on the basis of their solubility in the nonionic detergent Triton X-114. Antisera against the different fractions each recognized a distinct set of bands when used for immunoblotting analysis with extracts of melanocytes cultured from wild-type black mice. Immunoblotting with antisera to whole melanosomes or to Triton X-114-soluble melanosomal proteins that segregated with the detergent phase gave identical patterns with protein extracts from melanocytes from wild-type mice and from mice homozygous for the si (silver) coat color mutation. By contrast, an antiserum against Triton X-114 soluble melanosomal proteins that segregated in the aqueous phase recognized an 85-kDa protein that was present in extracts from wild-type melanocytes but was absent from si melanocytes. This suggested that the protein was encoded at the si (silver) locus. This was confirmed by employing an antiserum directed against the carboxyl terminus of the predicted murine silver protein sequence. The detergent solubility, biochemical characteristics, and immunologic properties of the 85-kDa protein and of the authentic si gene product were identical. Further analysis demonstrated that this protein corresponds to a melanosomal matrix glycoprotein that we recently described. Our results suggest that employing polyclonal antisera to fractionated organelles such as melanosomes, to screen tissues from mutant mice, a technique that we call "organelle scanning", can serve as a powerful means of identifying new organellar proteins and their respective genes.
Spermatophore size as determinant of paternity in an arctiid moth (Utetheisa ornatrix).
Authors: LaMunyon C W , Eisner T
Published: May 2006

Female Utetheisa ornatrix exercise postcopulatory mate selection, favoring sperm of larger males. Larger males also produce larger spermatophores, raising the question whether males are selected on the basis of body size or the size of their spermatophore. We here present evidence, based on matings in which males were induced to deliver spermatophores disproportionate in size to body mass, that the determinant is spermatophore mass.
Transfection and transient expression of chloramphenicol acetyltransferase gene in the protozoan parasite Entamoeba histolytica.
Authors: Nickel R , Tannich E
Published: May 2006

Hybrid plasmids were constructed and used for successful transfection and transient expression of the chloramphenicol acetyltransferase (CAT) gene in the protozoan parasite Entamoeba histolytica. Transfection was performed by electroporation of the amebae in a potassium phosphate-based buffer under conditions of 3000 V/cm and 25 microF, resulting in a time constant of 0.4 ms. Expression of CAT activity was achieved with constructs in which the CAT coding region was flanked by untranslated upstream and downstream sequences of E. histolytica genes. Highest activity was detected after culturing transfected cells for 48 hr. Activity was found to be proportional to the amount of DNA transfected.
A fully active catalytic domain of bovine aspartyl (asparaginyl) beta-hydroxylase expressed in Escherichia coli: characterization and evidence for the identification of an active-site region in vertebrate alpha-ketoglutarate-dependent dioxygenases.
Authors: Jia S , McGinnis K , VanDusen W J , Burke C J , Kuo A , Griffin P R , Sardana M K , Elliston K O , Stern A M , Friedman P A
Published: May 2006

The alpha-ketoglutarate-dependent dioxygenase aspartyl (asparaginyl) beta-hydroxylase (EC 1.14.11.16) specifically hydroxylates one aspartic or asparagine residue in certain epidermal growth factor-like domains of a number of proteins. The expression in Escherichia coli, purification, characterization of a fully active catalytic domain, and evidence for the identification of an active-site region of this enzyme are described. Sequence alignment analyses among the vertebrate alpha-ketoglutarate-dependent dioxygenases and chemical modification studies were undertaken aimed at locating specific regions of 52-kDa recombinant aspartyl (asparaginyl) beta-hydroxylase involved in substrate binding and/or catalysis. Based upon these studies, an alignment of the C-terminal regions of prolyl and lysyl hydroxylase and of aspartyl (asparaginyl) beta-hydroxylase is proposed. When histidine-675, an invariant residue located in a region of homology within this alignment, was mutated to an alanine residue in aspartyl (asparaginyl) beta-hydroxylase (H675A), no enzymatic activity was detected. Chemical modification studies show that the wild-type protein is protected from iodo[14C]acetamide labeling by Fe2+/alpha-ketoglutarate whereas the H675A mutant protein is not, suggesting that this mutant does not bind Fe2+/alpha-ketoglutarate.
Physical association of JAK1 and JAK2 tyrosine kinases with the interleukin 2 receptor beta and gamma chains.
Authors: Tanaka N , Asao H , Ohbo K , Ishii N , Takeshita T , Nakamura M , Sasaki H , Sugamura K
Published: May 2006

The functional interleukin 2 (IL-2) receptors contain the beta and gamma chains which are necessary for the transduction of cell growth signals. Monoclonal antibodies specific for the beta chain and gamma chain coimmunoprecipitated JAK1 and 114-kDa JAK2 tyrosine kinases, respectively. Tyrosine phosphorylation of JAK1 and JAK2 was induced upon IL-2 stimulation, and IL-2 activated the JAK2 kinase. These results demonstrate that the JAK1 and JAK2 tyrosine kinases are physically associated with the beta chain and gamma chain, respectively, and suggest that regulation of the kinases may be linked to IL-2-induced signal transduction.
Retinoic acid is necessary for development of the ventral retina in zebrafish.
Authors: Marsh-Armstrong N , McCaffery P , Gilbert W , Dowling J E , Dräger U C
Published: May 2006

In the embryonic zebrafish retina, as in other vertebrates, retinoic acid is synthesized from retinaldehyde by two different dehydrogenases, one localized dorsally, the other primarily ventrally. Early in eye development only the ventral enzyme is present. Citral competitively inhibits the ventral enzyme in vitro and decreases the production of retinoic acid in the ventral retina in vivo. Treatment of neurula-stage zebrafish embryos with citral during the formation of the eye primordia results in eyes lacking a ventral retina. This defect can be partially rescued by retinoic acid. The results demonstrate that synthesis of retinoic acid can be selectively inhibited in vivo and suggest that retinoic acid is necessary for the proper development of the ventral retina.
Effects of monovalent cations and divalent metal ions on Escherichia coli selenophosphate synthetase.
Authors: Kim I Y , Stadtman T C
Published: May 2006

A labile selenium donor compound, selenophosphate, is formed from selenide and ATP by selenophosphate synthetase. A divalent metal ion, Mg2+, and a monovalent cation, K+, NH4+, or Rb+, are required for selenophosphate synthetase activity [Veres, Z., Kim, I. Y., Scholz, T. D. & Stadtman, T. C. (1994) J. Biol. Chem. 269, 10597-10603]. Na+ and Li+ are ineffective as activators and in the presence of K+ are inhibitory. Mn-ATP, although not able to replace Mg-ATP for catalytic activity, binds to the enzyme provided an active monovalent cation is present. No Mn-ATP is bound when K+ is replaced with Na+. The requirement for K+, both for Mn-ATP binding and for catalytic activity of the synthetase, indicates a specific monovalent cation-induced conformational state of the enzyme. Previously we reported that activity of the enzyme is markedly inhibited by micromolar levels of Zn2+ in the presence of millimolar levels of Mg2+ [Kim, I. Y., Veres, Z. & Stadtman, T. C. (1993) J. Biol. Chem. 268, 27020-27025]. Binding of Mn-ATP also is decreased upon addition of Zn2+, indicating that the inhibitory effect of Zn2+ is exerted at the substrate-binding step of the overall selenophosphate synthetase reaction. When a cysteine residue at position 17 or 19 is replaced with serine, Mn-ATP binding to these mutant enzymes is unaffected by Zn2+ addition. Direct involvement of these cysteine residues in the zinc binding site was shown by use of 65ZnCl2. Radioactive Zn2+ bound to wild-type enzyme and was retained after gel filtration, but under the same conditions the catalytically inactive Cys-17 mutant protein and the catalytically active Cys-19 mutant enzyme were unlabeled.
A structural model for fidelity in transcription.
Authors: Eichhorn G L , Chuknyisky P P , Butzow J J , Beal R B , Garland C , Janzen C P , Clark P , Tarien E
Published: May 2006

Distances between the metal ions bound to the product terminus i site and the substrate i + 1 site of Escherichia coli RNA polymerase range from 5.0 to 5.6 A when the substrate is complementary to a template base and from 6.5 to 7.0 A for a noncomplementary relationship. The metal bound to the substrate at the i + 1 site exhibits a constant distance to the three phosphates on the substrate regardless of complementarity, but the distance to base and ribose protons changes. The differences in these geometric parameters are explained by the ability of the enzyme to assume two conformations, one to place correct nucleotide substrates in optimal position for bond formation and the other to prevent incorrect nucleotides from assuming such a position. In this scheme a metal-triphosphate complex can move toward or away from the terminal 3' OH group of the growing RNA chain, to assure fidelity of transcription.
Local rule-based theory of virus shell assembly.
Authors: Berger B , Shor P W , Tucker-Kellogg L , King J
Published: May 2006

A local rule-based theory is developed which shows that the self-assembly of icosahedral virus shells may depend on only the lower-level interactions of a protein subunit with its neighbors--i.e., on local rules rather than on larger structural building blocks. The local rule theory provides a framework for understanding the assembly of icosahedral viruses. These include both viruses that fall in the quasiequivalence theory of Caspar and Klug and the polyoma virus structure, which violates quasi-equivalence and has puzzled researchers since it was first observed. Local rules are essentially templates for energetically favorable arrangements. The tolerance margins for these rules are investigated through computer simulations. When these tolerance margins are exceeded in a particular way, the result is a "spiraling" malformation that has been observed in nature.
Complexes between STE5 and components of the pheromone-responsive mitogen-activated protein kinase module.
Authors: Marcus S , Polverino A , Barr M , Wigler M
Published: May 2006

We present genetic evidence for complex formation of STE5 and the STE11, STE7, and FUS3 protein kinases, the pheromone-responsive mitogen-activated protein kinase module of Saccharomyces cerevisiae. Interaction between STE5 and STE11 is not dependent on STE7, and interaction between STE5 and STE7 does not require STE11. The N-terminal regulatory domain of STE11 is both necessary and sufficient for interaction with STE5. Interaction between STE7 and STE11 is bridged by STE5, suggesting the formation of a multiprotein complex. We also demonstrate biochemical interaction between STE5 and STE11 by using a combination of bacterially expressed fusion proteins and extracts prepared from yeast. Our results suggest that STE5 is a scaffolding protein that facilitates interactions between components of the pheromone-responsive mitogen-activated protein kinase module. We further propose that such scaffolding proteins serve to inhibit cross-talk between functionally unrelated mitogen-activated protein kinase modules within the same cell.
Antisense oligonucleotide inhibition of acetylcholinesterase gene expression induces progenitor cell expansion and suppresses hematopoietic apoptosis ex vivo.
Authors: Soreq H , Patinkin D , Lev-Lehman E , Grifman M , Ginzberg D , Eckstein F , Zakut H
Published: May 2006

To examine the role of acetylcholinesterase (EC 3.1.1.7) in hematopoietic cell proliferation and differentiation, we administered a 15-mer phosphorothioate oligonucleotide, antisense to the corresponding ACHE gene (AS-ACHE), to primary mouse bone marrow cultures. Within 2 hr of AS-ACHE addition to the culture, ACHE mRNA levels dropped by approximately 90%, as compared with those in cells treated with the "sense" oligomer, S-ACHE. Four days after AS-ACHE treatment, ACHE mRNA increased to levels 10-fold higher than in S-ACHE cultures or in fresh bone marrow. At this later time point, differential PCR display revealed significant differences between cellular mRNA transcripts in bone marrow and those in AS-ACHE- or S-ACHE-treated cultures. These oligonucleotide-triggered effects underlay considerable alterations at the cellular level: AS-ACHE but not S-ACHE increased cell counts, reflecting enhanced proliferation. In the presence of erythropoietin it also enhanced colony counts, reflecting expansion of progenitors. AS-ACHE further suppressed apoptosis-related fragmentation of cellular DNA in the progeny cells, and it diverted hematopoiesis toward production of primitive blasts and macrophages in a dose-dependent manner promoted by erythropoietin. These findings suggest that the hematopoietic role of acetylcholinesterase, anticipated to be inverse to the observed antisense effects, is to reduce proliferation of the multipotent stem cells committed to erythropoiesis and megakaryocytopoiesis and macrophage production and to promote apoptosis in their progeny. Moreover, these findings may explain the tumorigenic association of perturbations in ACHE gene expression with leukemia.
Antisense oligodeoxynucleotide phosphorothioate complementary to Gag mRNA blocks replication of human immunodeficiency virus type 1 in human peripheral blood cells.
Authors: Lisziewicz J , Sun D , Weichold F F , Thierry A R , Lusso P , Tang J , Gallo R C , Agrawal S
Published: May 2006

Gene-expression modulator 91 (GEM91) is a 25-nt antisense oligodeoxynucleotide phosphorothioate complementary to the Gag mRNA of human immunodeficiency virus type 1 (HIV-1). Cellular uptake and intracellular distribution of GEM91 within cells suggest that this oligomer is readily available for antisense activity. GEM91 inhibited HIV-1 replication in a dose-dependent and sequence-specific manner. In a comparative study, 2 microM GEM91 was as effective as 5 microM 3'-azido-3'-deoxythymidine in blocking virus replication during the 28-day treatment of an HIV-1-infected T-cell line. GEM91 also completely inhibited (> 99%) the growth of three different HIV-1 isolates in primary lymphocytes and prevented the cytopathic effect of the virus in primary CD4+ T cells. Similarly, treatment with GEM91 for 3 weeks of HIV-1/BaL-infected primary macrophages blocked virus replication. Based on GEM91 anti-HIV-activity, safety, and pharmacokinetic profile in animals, a clinical trial was started using this compound as an antisense oligonucleotide drug for the treatment of the acquired immunodeficiency syndrome.
Cleavage of the nascent transcript induced by TFIIS is insufficient to promote read-through of intrinsic blocks to elongation by RNA polymerase II.
Authors: Cipres-Palacin G , Kane C M
Published: May 2006

RNA polymerases encounter a variety of types of blocks to elongation during transcription in eukaryotic cells. At least one protein, TFIIS, can promote read-through of many types of blocks to elongation by RNA polymerase II, and this protein stimulates cleavage of the nascent transcript in stalled elongation complexes as a prelude to read-through. The C-terminal half of the TFIIS protein is sufficient for stimulating the cleavage and read-through reactions in vitro. To study how TFIIS changes the response of RNA polymerase II elongation complexes to such blocks, targeted amino acids in the C terminus of HeLa TFIIS were mutated to alanines. Two mutant TFIIS proteins as well as the unmutated C-terminal half of the TFIIS protein were purified following overexpression in Escherichia coli. Each protein was examined for read-through activity and ability to stimulate transcript cleavage in ternary elongation complexes. Mutant TFIIS5 (E174A, E175A) was reduced in read-through and cleavage activities relative to the unmutated, truncated TFIIS (delta TFIIS). Mutant TFIIS7 (K187A, K189A) was able to stimulate cleavage nearly at the rate and to the extent of the TFIIS5 mutant. In contrast to what was observed with TFIIS5, no detectable read-through was observed in the presence of the TFIIS7 mutant during the course of the reaction. Thus, there is no simple, direct correlation between the ability of TFIIS to promote cleavage and its ability to promote read-through by RNA polymerase II. These results suggest that although TFIIS is necessary to mediate the cleavage reaction that precedes the read-through event, the cleavage event itself is not sufficient to allow read-through by RNA polymerase II.
A purified selenophosphate-dependent enzyme from Salmonella typhimurium catalyzes the replacement of sulfur in 2-thiouridine residues in tRNAs with selenium.
Authors: Veres Z , Stadtman T C
Published: May 2006

A tRNA-modifying enzyme tentatively termed tRNA 2-selenouridine synthase was purified by a five-step procedure that resulted in 50-60% pure preparations. This enzyme catalyzes the conversion of a 5-methylaminomethyl-2-thiouridine residue in the tRNA substrate to 5-methylaminomethyl-2-selenouridine. The selenium donor substrate for this reaction is shown to be selenophosphate which is formed from ATP and selenide by selenophosphate synthetase. Replacement of sulfur with selenium in tRNAs catalyzed by tRNA 2-selenouridine synthase occurs in the absence of ATP. The dependence of reaction velocity on selenophosphate concentration obeys Michaelis-Menten kinetics indicating an apparent Km value of 17.1 microM. Bulk thio-tRNA preparations from Escherichia coli and Salmonella typhimurium are equally effective as substrates for the selenium incorporation reaction. An intact 3' end of the tRNA molecule does not seem to be essential for selenium incorporation. Identity of the product of the reaction was confirmed by HPLC analysis of digests of [75Se]seleno-tRNAs labeled by incubation with the purified enzyme. A labeled compound in the nucleoside mixture was coeluted with authentic 5-methylaminomethyl-2-selenouridine.
Electrophysiological analysis of Na+/Pi cotransport mediated by a transporter cloned from rat kidney and expressed in Xenopus oocytes.
Authors: Busch A , Waldegger S , Herzer T , Biber J , Markovich D , Hayes G , Murer H , Lang F
Published: May 2006

Phosphate (Pi) reabsorption in renal proximal tubules involves Na+/Pi cotransport across the brush border membrane; its transport rate is influenced by the Na(+)-coupled transport of other solutes as well as by pH. In the present study, we have expressed a cloned rat renal brush border membrane Na+/Pi cotransporter (NaPi-2) in Xenopus laevis oocytes and have analyzed its electrophysiologic properties in voltage- and current-clamp studies. Addition of Pi to Na(+)-containing superfusates resulted in a depolarization of the membrane potential and, in voltage-clamped oocytes, in an inward current (IP). An analysis of the Na+ and/or Pi concentration dependence of IP suggested a Na+/Pi stoichiometry of 3:1. IP was increased by increasing the pH of the superfusate; this phenomenon seems to be mainly related to a lowering of the affinity for Na+ interaction by increasing H+ concentration. The present data suggest that known properties of Pi handling at the tubular/membrane level are "directly" related to specific characteristics of the transport molecule (NaPi-2) involved.
Feedback regulation of cell-substratum adhesion by integrin-mediated intracellular Ca2+ signaling.
Authors: Sjaastad M D , Angres B , Lewis R S , Nelson W J
Published: May 2006

Integrin binding to extracellular matrix (ECM) regulates cell migration and gene expression in embryogenesis, metastasis, would healing, and the inflammatory response. In many cases, binding of integrins to ECM triggers intracellular signaling pathways. The regulatory roles of intracellular signaling mechanisms in these events are poorly understood. Using single-cell analysis, we demonstrate that beads coated with peptide containing Arg-Gly-Asp (RGD), an integrin recognition motif found in many ECM proteins, elicit a rapid transient increase in intracellular calcium in Madin-Darby canine kidney (MDCK) epithelial cells. Also, significantly more beads bind to responding cells than to nonresponders. Several independent methods that inhibit RGD-induced Ca2+ signaling decrease both the number of beads bound and the strength of adhesion to an RGD-coated substratum. These results indicate that intracellular Ca2+ signaling participates in a positive feedback loop that enhances integrin-mediated cell adhesion.