bluuebunny/crossref_metadata_2025 huggingface dataset:
Visualization of RNA tertiary structure by RNA-EDTA.Fe(II) autocleavage: analysis of tRNA(Phe) with uridine-EDTA.Fe(II) at position 47.
Authors: Han H , Dervan P B
Published: May 2006

To test whether intramolecular autocleavage of RNA labeled at a single nucleotide position with EDTA.Fe(II) is a useful approach for the investigation of tertiary structures of RNAs, yeast phenylalanine tRNA was synthesized with uridine-EDTA (*U) at position U47. Autocleavage of [*U47]tRNA(Phe) in the presence of Fe(NH4)2(SO4)2 and dithiothreitol produced a set of cleavage fragments which are in general agreement with the three-dimensional structure derived from x-ray analysis.
The human Ha-ras oncogene induces genomic instability in murine fibroblasts within one cell cycle.
Authors: Denko N C , Giaccia A J , Stringer J R , Stambrook P J
Published: May 2006

Many human tumors contain an activating mutation in one of the ras protooncogenes. Additionally, these tumor cells are often heteroploid and characterized by chromosome breaks and rearrangements that are consequences of the genomic instability that is thought to contribute to tumor progression. The concurrence of ras mutations and genomic instability in tumors prompted us to ask whether selective induction of an activated Ha-ras gene could render a genome unstable. The NIH 3T3 cells used in this study contained mutant p53 genes and carried a selectively inducible activated (EJ) Ha-ras transgene under the control of bacterial lactose regulatory elements. When stably transfected cells were induced to express activated Ha-ras by isopropyl beta-D-thiogalactoside administration, there was a marked increase in the number of gross chromosomal aberrations including acentric fragments, multicentric chromosomes, and double minutes, which occurred within the time frame of a single cell cycle from the time of induction. To confirm that these aberrations occurred within the first cell cycle after mutant Ha-ras induction, the cells were arrested in G1 phase by serum depletion and, subsequently, released by administration of isopropyl beta-D-thiogalactoside or serum. The mitoses from cells released with isopropyl beta-D-thiogalactoside contained a 3-fold elevation in the fraction of chromosomes containing aberrations compared to mitoses from parallel cell cultures that were released with serum. Thus, the induction of activated Ha-ras gene expression in these cells results in genomic instability that can be detected as aberrant chromosomes at the next mitosis.
Columbines: a geographically widespread species flock.
Authors: Hodges S A , Arnold M L
Published: May 2006

Species in the columbine genus, Aquilegia, are known for their broad variation in ecology and floral morphology. Aquilegia is also known for the large degree of intercompatibility among its species, which has led to the suggestion that the genus has arisen recently. However, intercompatibility does not always imply recent divergence and the widespread distribution pattern of the genus has suggested an older age. We constructed phylogenies for Aquilegia plus its close relatives by using nucleotide sequence data from both nuclear and chloroplast DNA. The sequence data averaged over 1250 bp per species. Among the 14 columbine species sampled from Europe, Asia, and North America only 16-bp changes and one insertion/deletion event were detected. In contrast, related genera had from 3 to 45 times this level of variation. The phylogenies derived from the chloroplast and nuclear DNA sequences were highly concordant and suggest that the columbines are the result of a recent, rapid radiation. In contrast to other examples of species flocks, Aquilegia has radiated on a widespread geographical scale. By comparison with their related taxa, we suggest that the evolution of the nectar spur in Aquilegia was a key innovation for this genus and allowed rapid speciation through specialization to specific pollinators.
Linker DNA accessibility in chromatin fibers of different conformations: a reevaluation.
Authors: Zlatanova J , Leuba S H , Yang G , Bustamante C , van Holde K
Published: May 2006

New studies on chromatin fiber morphology, using the technique of scanning force microscopy (SFM), have caused us to reexamine recent analysis of nuclease digestion of chromatin. Chicken erythrocyte chromatin fibers, glutaraldehyde-fixed at 0, 10, and 80 mM NaCl, were imaged with the help of SFM. The chromatin fibers possessed a loose three-dimensional 30-nm structure even in the absence of added salt. This structure slightly condensed upon addition of 10 mM NaCl, and highly compacted, irregularly segmented fibers were observed at 80 mM NaCl. This sheds new light upon our previously reported analysis of the kinetics of digestion by soluble and membrane-immobilized micrococcal nuclease [Leuba, S. H., Zlatanova, J. & van Holde, K. (1994) J. Mol. Biol. 235, 871-880]. While the low-ionic-strength fibers were readily digested, the highly compacted structure formed at 80 mM NaCl was refractory to nuclease attack, implying that the linkers were fully accessible in the low-ionic-strength conformation but not in the condensed fibers. We now find that cleavage of the linker DNA by a small molecule, methidiumpropyl-EDTA-Fe(II), proceeds for all types of conformations at similar rates. Thus, steric hindrance is responsible for the lack of accessibility to micrococcal nuclease in the condensed fiber. Taken in total the data suggest that reexamination of existing models of chromatin conformation is warranted.
BST-1, a surface molecule of bone marrow stromal cell lines that facilitates pre-B-cell growth.
Authors: Kaisho T , Ishikawa J , Oritani K , Inazawa J , Tomizawa H , Muraoka O , Ochi T , Hirano T
Published: May 2006

Bone marrow stromal cells are essential for B-lymphocyte development. However, how stromal cells regulate B lymphopoiesis is not clear. In this paper, we report the molecular cloning of a stromal cell line-derived glycosyl-phosphatidylinositol-anchored molecule, BST-1, that facilitates pre-B-cell growth. The deduced amino acid sequence of BST-1 exhibited 33% identity with CD38. BST-1 was expressed in a wide range of tissues and in umbilical vein endothelial cells, whereas it was scarcely expressed in a variety of hematopoietic cell lines. The gene for BST-1 was assigned to chromosome 14q32.3, where immunoglobulin heavy-chain genes are clustered. BST-1 expression was enhanced in rheumatoid arthritis patient-derived bone marrow stromal cell lines that were previously shown to have an enhanced ability to support the growth of a pre-B-cell line as compared with stromal cell lines derived from healthy donors.
Glutamine repeats as polar zippers: their possible role in inherited neurodegenerative diseases.
Authors: Perutz M F , Johnson T , Suzuki M , Finch J T
Published: May 2006

Four inherited neurodegenerative diseases are linked to abnormally expanded repeats of glutamine residues in the affected proteins. Molecular modeling followed by optical, electron, and x-ray diffraction studies of a synthetic poly(L-glutamine) shows that it forms beta-sheets strongly held together by hydrogen bonds. Glutamine repeats may function as polar zippers, for example, by joining specific transcription factors bound to separate DNA segments. Their extension may cause disease either by increased, nonspecific affinity between such factors or by gradual precipitation of the affected proteins in neurons.
Resource edibility and trophic exploitation in an old-field food web.
Authors: Schmitz O J
Published: May 2006

I tested a food web model that predicts how environmental productivity (nutrient supply) and top carnivores should mediate interactions among herbivores, edible plants, and plants that are resistant to herbivory because they possess anti-herbivore defenses. Feeding trials with the dominant grasshopper herbivore at the study site confirmed that certain plant species were resistant to herbivory because of protection by pubescent leaves and stems. Experimental food webs with various numbers of trophic levels composed of edible and resistant plants, grasshoppers, and hunting spiders were assembled in enclosure cages. I randomly assigned half of the cages to a nutrient-enrichment treatment and half remained as a control. Nutrient supply directly enhanced primary productivity and plant and herbivore biomass. Experimentally changing spider abundance caused a classic "trophic cascade" in which herbivore biomass increased and edible plant biomass decreased. Resistant plant biomass increased. These results matched predictions of the model with one exception. A trophic cascade was not observed under enriched conditions. The study nevertheless shows that a simple model attempting to explain heterogeneous interactions in food webs may give considerable insight into the dynamics of natural systems.
Liberation of an interaction domain from the phosphotransfer region of CheA, a signaling kinase of Escherichia coli.
Authors: Morrison T B , Parkinson J S
Published: May 2006

The CheA protein of Escherichia coli is a histidine autokinase that donates its phosphate groups to two target proteins, CheY and CheB, to regulate flagellar rotation and sensory adaptation during chemotactic responses. The amino-terminal third of CheA contains the autophosphorylation site, determinants needed to interact with the catalytic center of the molecule, and determinants needed for specific recognition of its phosphorylation targets. To understand the structural basis for these activities, we examined the domain organization of the CheA phosphotransfer region by using DNA sequence analysis, limited proteolytic digestion, and a genetic technique called domain liberation. Comparison of the functionally interchangeable CheA proteins of E. coli and Salmonella typhimurium revealed two extensively mismatched segments within the phosphotransfer region, 22 and 25 aa long, with sequences characteristic of domain linkers. Both segments were readily susceptible to proteases, implying that they have an extended, flexible structure. In contrast, the intervening segments of the phosphotransfer region, designated P1 and P2 (roughly 140 and 65 aa, respectively), were relatively insensitive, suggesting they correspond to more compactly folded structural domains. Their functional properties were explored by identifying portions of the cheA coding region capable of interfering with chemotactic behavior when "liberated" and expressed as polypeptides. P1 fragments were not inhibitory, but P2 fragments blocked the interaction of CheY with the rotational switch at the flagellar motor, leading to incessant forward swimming. These results suggest that P2 contains CheY-binding determinants which are normally responsible for phosphotransfer specificity. Domain-liberation approaches should prove generally useful for analyzing multidomain proteins and their interaction targets.
Role of abnormally phosphorylated tau in the breakdown of microtubules in Alzheimer disease.
Authors: Alonso A C , Zaidi T , Grundke-Iqbal I , Iqbal K
Published: May 2006

The microtubule assembly-promoting activity of different pools of tau protein isolated from Alzheimer disease (AD) and control brains and the effect of dephosphorylation on this activity were studied. Tau isolated from a 2.5% perchloric extract of AD brain had almost the same activity as that obtained from control brain, and this activity did not change significantly on dephosphorylation. Abnormally phosphorylated tau (AD P-tau) isolated from brain homogenate of AD patients had little activity, and upon dephosphorylation with alkaline phosphatase, its activity increased to approximately the same level as the acid-soluble tau. Addition of AD P-tau to a mixture of normal tau and tubulin inhibited microtubule assembly. AD P-tau bound to normal tau but not to tubulin. These studies suggest that the abnormal phosphorylation of tau might be responsible for the breakdown of microtubules in affected neurons in AD not only because the altered protein has little microtubule-promoting activity but also because it interacts with normal tau, making the latter unavailable for promoting the assembly of tubulin into microtubules.
Neurally expressed Drosophila genes encoding homologs of the NSF and SNAP secretory proteins.
Authors: Ordway R W , Pallanck L , Ganetzky B
Published: May 2006

Several lines of investigation have now converged to indicate that the neurotransmitter release apparatus is formed by assembly of cytosolic proteins with proteins of the synaptic vesicle and presynaptic terminal membranes. We are undertaking a genetic approach in Drosophila melanogaster to investigate the functions of two types of cytosolic proteins thought to function in this complex: N-ethylmaleimide-sensitive fusion protein (NSF) and the soluble NSF attachment proteins (SNAPs). We have identified Drosophila homologs of the vertebrate and yeast NSF and SNAP genes. Both Drosophila genes encode polypeptides that closely resemble their vertebrate counterparts and are expressed in the nervous system; neither appears to be in a family of closely related Drosophila genes. These results indicate that the Drosophila NSF and SNAP genes are excellent candidates for mutational analysis of neurotransmitter release.
Mechanism of inositol monophosphatase, the putative target of lithium therapy.
Authors: Pollack S J , Atack J R , Knowles M R , McAllister G , Ragan C I , Baker R , Fletcher S R , Iversen L L , Broughton H B
Published: May 2006

myo-Inositol monophosphatase (myo-inositol-1-phosphate phosphohydrolase, EC 3.1.3.25) is an attractive target for mechanistic investigation due to its critical role in the phosphatidylinositol signaling pathway and the possible relevance of its inhibition by Li+ to manic depression therapy. The x-ray crystallographic structure of human inositol monophosphatase in the presence of the inhibitory metal Gd3+ showed only one metal bound per active site, whereas in the presence of Mn2+, three ions were present with one being displaced upon phosphate binding. We report here modeling, kinetic, and mutagenesis studies on the enzyme, which reveal the requirement for two metal ions in the catalytic mechanism. Activity titration curves with Zn2+ or Mn2+ in the presence or absence of Mg2+ are consistent with a two-metal mechanism. Modeling studies based on the various x-ray crystallographic structures (including those with Gd3+ and substrate bound) further support a two-metal mechanism and define the positions of the two metal ions relative to substrate. While the first metal ion may activate water for nucleophilic attack, a second metal ion, coordinated by three aspartate residues, appears to act as a Lewis acid, stabilizing the leaving inositol oxyanion. In this model, the 6-OH group of substrate acts as a ligand for this second metal ion, consistent with the reduced catalytic activity observed with substrate analogues lacking the 6-OH. Evidence from Tb3+ fluorescence quenching and the two-metal kinetic titration curves suggests that Li+ binds at the site of this second metal ion.
Adeno-associated virus (AAV) Rep proteins mediate complex formation between AAV DNA and its integration site in human DNA.
Authors: Weitzman M D , Kyöstiö S R , Kotin R M , Owens R A
Published: May 2006

AAV is unique among eukaryotic viruses in the ability of its DNA to integrate preferentially into a specific region of the human genome. Understanding AAV integration may aid in developing gene therapy systems with predictable integration sites. Using a gel mobility-shift assay, we have identified a DNA sequence within the AAV integration locus on human chromosome 19 which is specifically bound by the AAV Rep78 and Rep68 proteins. This Rep recognition sequence is a GCTC repeating motif very similar to sequences within the inverted terminal repeats of the AAV genome which are also bound by Rep78 and Rep68. Cloned oligonucleotides containing the recognition sequence can direct specific binding by Rep proteins. Binding assays with mutant Rep proteins show that the amino-terminal portion of Rep78 and Rep68 can direct binding to either the AAV terminal repeat hairpin DNA or chromosome 19. This human genomic DNA can be complexed with AAV DNA by Rep proteins as demonstrated by a dual-label (32P/biotin) assay. These results suggest a role for Rep in targeting viral integration.
Positive and negative transcriptional control by the TAL1 helix-loop-helix protein.
Authors: Hsu H L , Wadman I , Tsan J T , Baer R
Published: May 2006

Tumor-specific activation of the TAL1 gene is the most common genetic defect associated with T-cell acute lymphoblastic leukemia. The TAL1 gene products possess a basic helix-loop-helix (bHLH) motif, a protein-dimerization and DNA-binding domain found in several transcription factors. TAL1 polypeptides interact, in vitro and in vivo, with class A bHLH proteins (e.g., E47) to form heterodimers with sequence-specific DNA-binding activity. In this study, we show that TAL1 can regulate the transcription of an artificial reporter gene that contains binding sites for bHLH heterodimers involving TAL1. Transcription of the reporter is strongly induced by E47-E47 homodimers and moderately induced by TAL1-E47 heterodimers. Thus, in a cellular environment that allows formation of E47-E47 homodimers (e.g., in the absence of Id regulatory proteins) TAL1 can repress transcription by recruiting E47 into bHLH complexes with less transcriptional activity (i.e., TAL1-E47 heterodimers). However, in other settings TAL1 can activate transcription because TAL1-E47 heterodimers are more resistant to negative regulation by Id proteins. Hence, TAL1 can potentially regulate transcription in either a positive or negative fashion.
Efficient manipulation of the human adenovirus genome as an infectious yeast artificial chromosome clone.
Authors: Ketner G , Spencer F , Tugendreich S , Connelly C , Hieter P
Published: May 2006

A yeast artificial chromosome (YAC) containing a complete human adenovirus type 2 genome was constructed, and viral DNA derived from the YAC was shown to be infectious upon introduction into mammalian cells. The adenovirus YAC could be manipulated efficiently using homologous recombination-based methods in the yeast host, and mutant viruses, including a variant that expresses the human analog of the Saccharomyces cerevisiae CDC27 gene, were readily recovered from modified derivatives of the YAC. The application of powerful yeast genetic techniques to an infectious adenovirus clone promises to significantly enhance the genetic analysis of adenovirus and to simplify the construction of adenovirus-based vectors for vaccines or for gene transfer to mammalian cells or whole animals. The adenovirus YAC was produced by homologous recombination in vivo between adenovirus 2 virion DNA and YAC vector plasmids carrying segments of the viral left and right genomic termini. This recombinational cloning strategy is generally applicable to the construction of YACs containing other DNA segments, such as the genomes of other viruses. Further, it is very efficient and may permit the targeted cloning of segments of the genomes of higher organisms directly from genomic DNA.
Chronic cardiac rejection: identification of five upregulated genes in transplanted hearts by differential mRNA display.
Authors: Utans U , Liang P , Wyner L R , Karnovsky M J , Russell M E
Published: May 2006

Transplant arteriosclerosis, the major manifestation of chronic rejection, develops after allogeneic (Lewis to F344) but not syngeneic (Lewis to Lewis) rat cardiac transplantation. To identify transcriptionally regulated mediators associated with chronic cardiac rejection, we adapted the differential mRNA display technique for in vivo transplant specimens. Gene transcript patterns in four allogeneic hearts showing early signs of chronic rejection were compared with those in two syngeneic hearts exposed to the same surgical procedure but histologically normal. Twelve differentially expressed cDNA bands were identified. We improved the probability of isolating one or more allograft-specific cDNAs from a single display band by first using recovered and reamplified PCR products as probes in RNA blot analysis. cDNA fragments cloned from individual bands were then used in a second RNA blot analysis, which allowed for the correlation of specific mRNA transcripts with cDNA clones. Five cDNA clones produced time-dependent, allograft-specific hybridization. Sequence analysis demonstrated that two of these cDNAs corresponded to unknown genes, whereas the other three represented known genes not previously associated with chronic rejection. The latter group included the macrophage lectin specific for galactose/N-acetylgalactosamine (a cell-surface receptor), the nuclear P1 gene (a homologue of a yeast replication protein), and a ubiquitin-like gene. Our application of the differential display technique allowed the direct identification of potential mediators under in vivo conditions that preserve the environment of the disease process--including infiltrating cell populations critical to the inflammatory response.
Casimir light: field pressure.
Authors: Schwinger J
Published: May 2006

The electromagnetic field is assigned a self-consistent role in which abrupt slowing of the collapse produces radiation and the pressure of the radiation produces abrupt slowing. A simple expression is introduced for the photon spectrum. Conditions for light emission are proposed that imply a high degree of spatial localization. Some numerical checks are satisfied. A study of the mechanical equations of motion suggests an explanation of the very short time scale in terms of oppositely directed field pressures and the speed of light.
Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes.
Authors: Nekludova L , Pabo C O
Published: May 2006

We have analyzed DNA conformations in a series of protein-DNA complexes, and we find that a distinctive conformation--with an enlarged major groove--occurs in a number of different complexes. During this analysis, we also developed a simplified model of DNA structure that illustrates the relative position of (i) the base pairs, (ii) the phosphate backbone, and (iii) the double-helical axis. This model highlights the key structural features of each duplex, facilitating the analysis and comparison of structures that are distinct from canonical A-DNA or B-DNA. Comparing DNA conformations in this way revealed that an otherwise unrelated set of protein-DNA complexes have interesting structural similarities, including an enlarged major groove. We refer to this class of structures as Beg-DNA (where eg means enlarged groove). Since related features occur in such a diverse set of protein-DNA complexes, we suggest that this conformation may have a significant role in protein-DNA recognition.
RNA template-directed RNA synthesis by T7 RNA polymerase.
Authors: Cazenave C , Uhlenbeck O C
Published: May 2006

In an attempt to synthesize an oligoribonucleotide by run-off transcription by bacteriophage T7 RNA polymerase, a major transcript was produced that was much longer than expected. Analysis of the reaction indicated that the product resulted from initial DNA-directed run-off transcription followed by RNA template-directed RNA synthesis. This reaction occurred because the RNA made from the DNA template displayed self-complementarity at its 3' end and therefore could form an intra- or intermolecular primed template. In reactions containing only an RNA template, the rate of incorporation of NTPs was quite comparable to DNA-dependent transcription. RNA template-directed RNA synthesis has been found to occur with a great number of oligoribonucleotides, even with primed templates that are only marginally stable. In one instance, we observed a multistep extension reaction converting the oligonucleotide into a final product longer than twice its original length. Presumably, such a process could have generated some of the RNAs found to be efficiently replicated by T7 RNA polymerase.
Cytochrome P-450 mediates tissue-damaging hydroxyl radical formation during reoxygenation of the kidney.
Authors: Paller M S , Jacob H S
Published: May 2006

Renal reperfusion injury results from oxygen radical generation. During reoxygenation of hypoxic kidney cells, xanthine oxidase produces superoxide radical, which eventuates in hydroxyl radical formation by the Fenton reaction. This reaction, catalyzed by transition metals such as iron, is particularly important because hydroxyl radical is highly reactive with a wide variety of biomolecules. We tested the hypothesis that this catalytic function is fostered by iron released from the heme moiety of cytochrome P-450. Primary cultures of rat proximal tubule epithelial cells studied in a subconfluent stage were subjected to 60 min of hypoxia and 30 min of reoxygenation. When cells were pretreated with one of three cytochrome P-450 inhibitors (piperonyl butoxide, cimetidine, or ketoconazole), lethal cell injury was attenuated. There was the expected increase in O2-. production during hypoxia/reoxygenation that cytochrome P-450 inhibitors did not prevent; on the other hand, inhibitors did prevent reoxygenation-induced hydroxyl radical formation. Analogously, the increase in catalytic iron (bleomycin-detectable iron) that accompanies hypoxia/reoxygenation did not occur in the presence of cytochrome P-450 inhibitors. In vivo studies confirmed a protective effect of cytochrome P-450 inhibition because glomerular filtration rate was better preserved in rats pretreated with cimetidine and then subjected to renal artery occlusion. In summary, several chemically distinct cytochrome P-450 inhibitors reduced iron release, and thereby, hydroxyl radical formation and reoxygenation-induced lethal cell injury, without inhibiting superoxide radical formation. We conclude that highly labile P-450 may act as an Fe-donating catalyst for Fenton reaction production of HO.-mediated reperfusion injury.
Primary structure and expression of the dihydropteroate synthetase gene of Plasmodium falciparum.
Authors: Triglia T , Cowman A F
Published: May 2006

The enzyme dihydropteroate synthetase (DHPS) from Plasmodium falciparum is involved in the mechanism of action of the sulfone/sulfonamide group of drugs. We describe the cloning and sequencing of the gene encoding the P. falciparum DHPS enzyme and show that it is a bifunctional enzyme that includes dihydro-6-hydroxymethylpterin pyrophosphokinase (PPPK) at the N terminus of DHPS. The gene encodes a putative protein of 83 kDa that contains two domains that are homologous with the DHPS and PPPK enzymes of other organisms. The PPPK-DHPS gene is encoded on chromosome 8 and has two introns. An antibody raised to the PPPK region of the protein was found to recognize a 68-kDa protein that is expressed throughout the asexual life cycle of the parasite. We have determined the sequence of the DHPS portion of the gene from sulfadoxine-sensitive and -resistant P. falciparum clones and identified sequence differences that may have a role in sulfone/sulfonamide resistance.
Controlled expression of plastid transgenes in plants based on a nuclear DNA-encoded and plastid-targeted T7 RNA polymerase.
Authors: McBride K E , Schaaf D J , Daley M , Stalker D M
Published: May 2006

Phage T7 RNA polymerase has been used extensively in Escherichia coli for high-level expression of selected genes placed under the control of the phage T7 gene 10 promoter. We have constructed an analogous system for use in plastids of higher plants. A T7 RNA polymerase chimeric gene containing a cauliflower mosaic virus 35S promoter and a tobacco ribulose-bisphosphate carboxylase/oxygenase small-subunit chloroplast transit-peptide sequence was introduced into tobacco by nuclear transformation. Stable plastid transformation of tobacco expressing the T7 RNA polymerase activity with a T7 promoter/beta-glucuronidase (GUS) reporter gene construct resulted in expression of GUS mRNA and enzyme activity in all tissues examined. Expression of GUS activity was extremely high in mature leaves, moderate in young leaves and petals, and low in stems, roots, and developing seeds. Plastid transformation of wild-type tobacco with the same chimeric GUS gene resulted in undetectable levels of GUS mRNA and enzyme activity. Genetic crosses demonstrated that a silent T7/GUS reporter gene could be activated in the F1 generation by transmission of an active nuclear T7 RNA polymerase gene from the male parent.
Selectin ligands.
Authors: Varki A
Published: May 2006

The selectins initiate many critical interactions among blood cells. The volume of information and diversity of opinions on the nature of the biologically relevant ligands for selectins is remarkable. This review analyzes the matter and suggests the hypothesis that at least some of the specificity may involve recognition of "clustered saccharide patches."
An unusual type of mitochondrial DNA inheritance in the blue mussel Mytilus.
Authors: Zouros E , Oberhauser Ball A , Saavedra C , Freeman K R
Published: May 2006

In animals, mitochondrial DNA (mtDNA) inheritance is predominantly maternal. In a few cases incidental transmission of paternal mtDNA was observed and estimated to account for only 10(-4)-10(-3) of an individual's mtDNA content. In contrast, biparental inheritance is common in mussels of the genus Mytilus. Here we present direct evidence that sex and mtDNA inheritance are coupled in Mytilus. Females inherit mtDNA only from their mother, but they transmit it to both daughters and sons. Males inherit mtDNA from both parents, but they transmit to sons only the mtDNA they inherited from their father. In pair matings, this mtDNA inheritance pattern is associated with a strong sex-ratio bias. These findings establish a newly discovered type of cytoplasmic DNA transmission. We also present evidence that the phenomenon breaks down in interspecific hybrids.
Expression cloning of a CMP-NeuAc:NeuAc alpha 2-3Gal beta 1-4Glc beta 1-1'Cer alpha 2,8-sialyltransferase (GD3 synthase) from human melanoma cells.
Authors: Nara K , Watanabe Y , Maruyama K , Kasahara K , Nagai Y , Sanai Y
Published: May 2006

Using an expression cloning approach, we have isolated a cDNA encoding GD3 synthase (CMP-NeuAc:NeuAc alpha 2-3Gal beta 1-4Glc beta 1-1'Cer alpha 2,8-sialyltransferase, EC 2.4.99.8), which is a key regulatory enzyme determining the prominence of the ganglioside biosynthesis pathway. The cloned cDNA encodes a 341-amino acid protein containing a single transmembrane domain at its N-terminal region, suggesting that the protein has a type II transmembrane topology. The sequence of alpha 2,8-sialyltransferase showed a high level of similarity with other sialyltransferases at two conserved regions typical in the sialyltransferase family. Transfected cells containing the cloned cDNA expressed GD3 ganglioside on the cell surface, which was detectable with specific anti-GD3 antibody by immunofluorescence and immunostaining after separation of isolated glycolipids on thin-layer chromatography. The cDNA hybridized to a single mRNA species of 2.4 kb in melanoma cells. This sialyltransferase is distinctive in catalyzing the formation of the alpha 2-8 linkage of sialic acids.
Impulse flow dependency of galanin release in vivo in the rat ventral hippocampus.
Authors: Consolo S , Baldi G , Russi G , Civenni G , Bartfai T , Vezzani A
Published: May 2006

Using microdialysis and a sensitive RIA, we have studied the in vivo release of the neuropeptide galanin (GAL) from the ventral hippocampus of freely moving rats. The spontaneous outflow of GAL-like immunoreactivity (GAL-LI) (1.8 +/- 0.3 fmol per ml per 20 min) was dependent on the presence of extracellular Ca2+ and was inhibited by tetrodotoxin. Evoked release induced by infusion of KCl (60 mM) or veratridine (148 microM) was also Ca(2+)-dependent and sensitive to tetrodotoxin. Electrical stimulation of the ventral limb of the diagonal band nuclei induced a frequency-dependent (50-200 Hz) and tetrodotoxin-sensitive overflow of GAL-LI in the hippocampus. In vitro GAL-LI release (1.0 +/- 0.02 fmol per ml per 5 min), studied in slices of rat ventral hippocampus, was also Ca(2+)-dependent and was increased in a concentration-dependent manner by KCl depolarization. This study demonstrates the release of the neuropeptide GAL in the rat central nervous system. The in vivo release is related to the activity of the cholinergic GAL-LI-containing cells in the septal diagonal band nuclei. The results are discussed in relation to the coexistence of GAL and acetylcholine within the septal/diagonal band complex.
A 92-kDa human immunostimulatory protein.
Authors: Fontan E , Briend E , Saklani-Jusforgues H , d'Alayer J , Vandekerckhove J , Fauve R M
Published: May 2006

We purified to apparent homogeneity a human urinary glycoprotein of 92 kDa (HGP.92) that, administered intravenously at 250 micrograms/kg, fully protected mice against a lethal inoculum of Listeria monocytogenes. Since HGP.92 protected scid mice, which lack B and T lymphocytes, this increased resistance to Listeria did not appear to be lymphocyte mediated. Furthermore, inflammatory macrophages incubated with 6 nM HGP.92 inhibited the growth of Lewis carcinoma cells in vitro. These two activities appeared to depend on an oligosaccharide moiety, as they were lost after N-Glycanase treatment of HGP.92. Thus, the biological activity of HGP.92 was in some way related to a glycan moiety.
Expression cloning of a gibberellin 20-oxidase, a multifunctional enzyme involved in gibberellin biosynthesis.
Authors: Lange T , Hedden P , Graebe J E
Published: May 2006

In the biosynthetic pathway to the gibberellins (GAs), carbon-20 is removed by oxidation to give the C19-GAs, which include the biologically active plant hormones. We report the isolation of a cDNA clone encoding a GA 20-oxidase [gibberellin, 2-oxoglutarate:oxygen oxidoreductase (20-hydroxylating, oxidizing) EC 1.14.11.-] by screening a cDNA library from developing cotyledons of pumpkin (Cucurbita maxima L.) for expression of this enzyme. When mRNA from either the cotyledons or the endosperm was translated in vitro using rabbit reticulocyte lysates, the products contained GA12 20-oxidase activity. A polyclonal antiserum was raised against the amino acid sequence of a peptide released by tryptic digestion of purified GA 20-oxidase from the endosperm. A cDNA expression library in lambda gt11 was prepared from cotyledon mRNA and screened with the antiserum. The identity of positive clones was confirmed by the demonstration of GA12 20-oxidase activity in single bacteriophage plaques. Recombinant protein from a selected clone catalyzed the three-step conversions of GA12 to GA25 and of GA53 to GA17, as well as the formation of the C19-GAs, GA1, GA9, and GA20, from their respective aldehyde precursors, GA23, GA24, and GA19. The nucleotide sequence of the cDNA insert contains an open reading frame of 1158 nt encoding a protein of 386 amino acid residues. The predicted M(r) (43,321) and pI (5.3) are similar to those determined experimentally for the native GA 20-oxidase. Furthermore, the derived amino acid sequence includes sequences obtained from the N terminus and two tryptic peptides from the native enzyme. It also contains regions that are highly conserved in a group of non-heme Fe-containing dioxygenases.
Divergent T-cell cytokine patterns in inflammatory arthritis.
Authors: Simon A K , Seipelt E , Sieper J
Published: May 2006

A major immunoregulatory mechanism in inflammatory infections and allergic diseases is the control of the balance of cytokines secreted by Th1/Th2 subsets of T helper (Th) cells. This might also be true in autoimmune diseases; a Th2 pattern that prevents an effective immune response in infections with intracellular bacteria may favor immunosuppression in autoimmune disease. The pattern of cytokine expression was compared in the synovial tissue from patients with a typical autoimmune disease, rheumatoid arthritis, and with a disorder with similar synovial pathology but driven by persisting exogenous antigen, reactive arthritis. We screened 12 rheumatoid and 9 reactive arthritis synovial tissues by PCR and in situ hybridization for their expression of T-cell cytokines. The cytokine pattern differs significantly between the two diseases; rheumatoid arthritis samples express a Th1-like pattern whereas in reactive arthritis interferon gamma expression is accompanied by that of interleukin 4. Studying the expression of cytokines by in situ hybridization confirmed the results found by PCR; they also show an extremely low frequency of cytokine-transcribing cells. In a double-staining experiment, it was demonstrated that interleukin 4 is made by CD4 cells. These experiments favor the possibility of therapeutic intervention in inflammatory rheumatic disease by means of inhibitory cytokines.
Monocyte deactivation by interleukin 10 via inhibition of tyrosine kinase activity and the Ras signaling pathway.
Authors: Geng Y , Gulbins E , Altman A , Lotz M
Published: May 2006

Activation of monocytes by bacterial lipopolysaccharides (LPSs) is a central component in the pathogenesis of septic shock syndrome. Interleukin 10 (IL-10) is a potent monocyte-deactivating factor and transcriptionally inhibits LPS-induced expression of proinflammatory mediators. The intracellular signaling pathways of LPS have been only partially characterized and mechanisms of IL-10 signaling remain unknown. We show that LPS activates the protein tyrosine kinase (PTK) p56lyn and that this is associated with tyrosine phosphorylation of the protooncogene product Vav. These events are completely blocked by the tyrosine kinase inhibitor herbimycin A. LPS also increases Ras activation in monocytes. LPS-triggered phosphorylation of mitogen-activated protein kinase is a downstream activation event that is also reduced by herbimycin A. Analysis of the IL-10 effects shows that it completely inhibits the p56lyn tyrosine kinase activation and all other subsequent events in this pathway including Ras activation. The IL-10 effects are selective since it reduced PTK-dependent cytokine mRNA expression but not the PTK independent induction of c-jun and c-fos mRNA in LPS-activated monocytes. These results identify the Ras signaling pathway as a component of intracellular signaling in LPS-stimulated monocytes and define early events in this response as targets of monocyte deactivation by IL-10.
Activated Ki-Ras complements erythropoietin signaling in CTLL-2 cells, inducing tyrosine phosphorylation of a 160-kDa protein.
Authors: Yamamura Y , Noda M , Ikawa Y
Published: May 2006

We have previously shown that expression of erythropoietin (EPO) receptor (EPOR) alone failed to confer EPO responsiveness on the interleukin 2-dependent T-cell line CTLL-2, whereas the introduction of the EPOR into interleukin 3-dependent pro-B-cell lines, such as BAF-B03, allowed the cells to proliferate in response to EPO. Here, we report that additional expression of v-Ki-Ras conferred EPO-dependent growth on CTLL-2 cells expressing the EPOR, with additional formation of a high-affinity EPOR. To investigate possible mechanisms of EPOR downstream signaling induced by v-Ki-Ras expression in these CTLL-2-derived cells, we carried out anti-phosphotyrosine immunoblot analysis of the EPOR complex immunoprecipitated with anti-EPOR antibody from lysates of cells with and without cytokine stimulation, revealing two 160-kDa and 130-kDa phosphotyrosyl proteins. An anti-JAK2 antibody did not react with these proteins, suggesting that they may represent cellular components involved in an EPO-EPOR signaling pathway induced by v-Ki-Ras. Similar phosphotyrosyl proteins were present among Friend erythroleukemia cell lines, in which the Friend virus gp55/EPOR complex on the cell surface constitutively sends signals for cell growth.
The cellular retinoic acid binding protein I is dispensable.
Authors: Gorry P , Lufkin T , Dierich A , Rochette-Egly C , Décimo D , Dollé P , Mark M , Durand B , Chambon P
Published: May 2006

The cellular retinoic acid binding proteins I and II (CRABPI and CRABPII) bind retinoic acid with high affinity, exhibit distinct patterns of expression during embryonic development, and are thought to play important roles in the RA signaling pathway. We have generated a targeted mutation of the CRABPI gene using the "hit-and-run" strategy and shown that it prevents the production of a functional CRABPI protein. Homozygous mutant mice were normal, indicating that CRABPI does not play a crucial role in the RA signaling pathway.
Peptide-induced T-cell tolerance to prevent autoimmune diabetes in a transgenic mouse model.
Authors: Aichele P , Kyburz D , Ohashi P S , Odermatt B , Zinkernagel R M , Hengartner H , Pircher H
Published: May 2006

A synthetic peptide corresponding to an immunodominant epitope of lymphocytic choriomeningitis virus glycoprotein (LCMV GP) was used to prime or to tolerize CD8+ T cells in vivo, dependent on mode of immunization. Peptide-specific tolerance was then examined in transgenic mice expressing LCMV GP in the beta islet cells of the pancreas; these mice develop CD8+ T-cell-mediated diabetes within 8-14 days after LCMV infection. Specific peptide-induced tolerance prevented autoimmune destruction of beta islet cells and diabetes in this transgenic mouse model.
Ribosomal gene promoter domains can function as artificial enhancers of RNA polymerase I transcription, supporting a promoter origin for natural enhancers in Xenopus.
Authors: Pikaard C S
Published: May 2006

Enhancers of RNA polymerase I transcription in higher eukaryotes are repetitive elements within the intergenic spacers of rRNA genes. In Xenopus and mouse, enhancers and the gene promoter bind the activator protein, upstream binding factor, and in Xenopus, enhancers also share sequence similarity with an upstream domain of the promoter. This upstream promoter domain can act as an efficient enhancer when polymerized and cloned adjacent to a ribosomal gene promoter injected into oocytes. A core promoter domain lacking similarity with spacer sequences in Xenopus laevis but analogous to a repeated sequence in Xenopus borealis can also function as an enhancer. These data demonstrate functional relatedness between the promoter and enhancers, supporting the hypothesis that enhancers could have evolved from duplicated promoter domains that bind essential transcription factors. The ability of upstream binding factor to bind enhancers inactivated by mutation suggests that upstream binding factor binding alone cannot explain enhancer function.
Targeted disruption of metallothionein I and II genes increases sensitivity to cadmium.
Authors: Masters B A , Kelly E J , Quaife C J , Brinster R L , Palmiter R D
Published: May 2006

We inactivated the mouse metallothionein (MT)-I and MT-II genes in embryonic stem cells and generated mice homozygous for these mutant alleles. These mice were viable and reproduced normally when reared under normal laboratory conditions. They were, however, more susceptible to hepatic poisoning by cadmium. This proves that these widely expressed MTs are not essential for development but that they do protect against cadmium toxicity. These mice provide a means for testing other proposed functions of MT in vivo.
Light-harvesting chlorophyll c-like pigment in Prochloron.
Authors: Larkum A W , Scaramuzzi C , Cox G C , Hiller R G , Turner A G
Published: May 2006

A chlorophyll c-like pigment, similar to magnesium-3,8-divinyl pheoporphyrin a5 monomethyl ester, has been isolated from Prochloron sp. obtained from five species of didemnid ascidians from the Great Barrier Reef, Australia, and from Palau, Micronesia. The pigment represents 4-15% of the total chlorophyll content and is shown to function in a light-harvesting pigment protein complex of Prochloron. The observation that all of the major chlorophylls (a+b+c) function in a light-harvesting role in Prochloron and possibly in other prochlorophytes is discussed in terms of the phylogeny of the prochlorophytes.
Peptidase activities of proteasomes are differentially regulated by the major histocompatibility complex-encoded genes for LMP2 and LMP7.
Authors: Gaczynska M , Rock K L , Spies T , Goldberg A L
Published: May 2006

Recent studies have implicated proteasomes in the generation of the antigenic peptides that are presented on major histocompatibility complex class I molecules to T lymphocytes. Interferon gamma modifies the subunit composition of proteasomes and causes changes in their peptidase activities that should favor the production of peptides with hydrophobic or basic carboxyl termini (i.e., the types found on major histocompatibility complex class I molecules). It has been proposed that these changes in peptidase activity are due to incorporation into proteasomes of the major histocompatibility complex-encoded subunits LMP2 and -7, which are induced by interferon gamma. Here we show by gene transfection into lymphoblasts or HeLa cells that LMP7 increases the capacity (Vmax) of 20S and 26S proteasomes to cleave peptides after hydrophobic and basic residues without affecting hydrolysis after acidic residues. These changes depended on the amount of LMP7 subunits incorporated into proteasomes. Transfection of LMP2 reduced cleavage of peptides after acidic residues, increased hydrolysis after basic residues, and did not affect the hydrophobic activity. Since the activity of the total proteasome population changed after incorporation of only small amounts of LMP2 or -7, these subunits must cause major alterations in peptidase activity. Thus, their expression can account for the changes in proteasome activity induced by inteferon gamma, and these findings lend further support to the proposed roles of LMPs in altering the nature of the peptides generated for antigen presentation.
ATP-dependent transport of organic anions in secretory vesicles of Saccharomyces cerevisiae.
Authors: St-Pierre M V , Ruetz S , Epstein L F , Gros P , Arias I M
Published: May 2006

Secretory mutants (sec1, sec6) of Saccharomyces cerevisiae accumulate large pools of secretory vesicles at the restrictive temperature (37 degrees C) because of a block in the delivery of vesicles to the cell surface. We report that secretory vesicles isolated from sec mutants exhibit ATP-dependent uptake of two classes of organic anions that are substrates for the canalicular carriers of mammalian liver. Transport of the bile acid taurocholate (TC) and the glutathione conjugate of 1-chloro-2,4-dinitrobenzene (GS-DNP) into vesicles was temperature dependent and saturable and required ATP and Mg2+. Estimates of Km and Vmax were 177 microM and 1.2 nmol.min-1.mg-1 and 262 microM and 0.53 nmol.min-1.mg-1 for TC and GS-DNP, respectively. TC and GS-DNP did not complete for transport. TC transport was sensitive to vanadate and 4,4'-diisothiocyanostilbene-2,2'-disulfonate, inhibited by glycocholate, and retained partial activity when UTP and GTP, but not nonhydrolyzable ATP analogues, replaced ATP. Dissipation of the electrochemical potential with a nitrate buffer and ionophores partially decreased (30-40%) the transport of both anions. Direct testing of the influence of membrane potential was performed in sec6-4 mutants, in which the expression of electrogenic [H+]ATPase activity is reduced by > 85% in glucose-containing medium. Vesicles from sec6-4 retained full activity for ATP-dependent TC and GS-DNP transport. These results indicate that the transporters operate independently of the membrane potential and that ATP is required. These findings reveal that yeast possess separate ATP-dependent transport mechanisms for elimination of bile acids and glutathione conjugates. The mechanisms are functionally similar to those present in mammalian systems.