Development of the Overlapping Oligonucleotide Database and its application to signal sequence search of the human genome

We have developed ODS (Overlapping Oligonucleotide Databasefor Signal Sequence Search)—the first relational databasethat integrates information on biological features into thesearch for signal sequences. In existing biological sequencedatabases, even relational ones, retrieving nucleotide sequencesbased on their biological features involves much labour andtime or even the development of a new program. GenBank sequencedata, including FEATURES records, are organized into three relationaltables in ODS. Nucleotide sequences are transformed into overlappingoligonucleotides in order to facilitate the signal sequencesearch rapidly without the need for specific alignment programs.This transformation leads to a one-to-one correspondence betweenthe nucleotide sequence and its biological feature. The signalsequence search by ODS is done in SQL queries and ODS obviatesthe need for molecular biologists to write computer programs.The application of ODS to searches of promoter regions revealedputative cis-acting elements and basic statistical analysesof occurrences of oligonucleotides showed interesting findingsconcerning the ‘cg’ dinucleotide.     

A deductive database system PACADE for analyzing 3-D and secondary structures of protein

We have developed a deductive database system PACADE for analyzing3-D and secondary structures of protein. The PA CADE systemconsists of a relational database created from Protein DataBank and a deductive engine DEE based on logic programming.It has the following features: (1) The system has an inferencemechanism. This means by which users can easily write and checkbiological hypotheses using logical and declarative rules insteadof procedural programs. (2) The relational database of the PACADE system stores data on bath 3-D and secondwy structuresof protein. The integration of this two level structure makesfeasible an abstract representation of the protein structure.We describe herein the design, functions, and implementationof this PACADE system.     

Impaired interleukin-3 (IL-3) response of the A/J mouse is caused by a branch point deletion in the IL-3 receptor alpha subunit gene.

Interleukin-3 (IL-3) alone does not support hematopoietic colony formation of bone marrow cells from the A/J mouse. To elucidate the molecular lesion in A/J mice, we examined expression of the alpha and beta subunits of the IL-3 receptor (IL-3R). While IL-3R beta was normally expressed, IL-3R alpha was not detectable on the surface of A/J-derived cells by antibody staining. Genetic linkage analysis using recombinant inbred mouse strains between A/J and IL-3-responsive C57BL/6 indicated that the IL-3R alpha gene locus was responsible for the impaired IL-3 response in A/J mice. Molecular cloning and characterization of A/J-derived IL-3R alpha cDNA revealed that it lacked the sequence corresponding to exon 8, which encodes 10 amino acid residues in the extracellular domain. The aberrant splicing was due to a 5 base pair deletion at the branch point in intron 7 and was reproduced in heterologous cells by transfecting with an IL-3R alpha minigene carrying the deleterious intron. The A/J-specific abnormal form of IL-3R alpha was localized inside the cells, but not on the cell surface, providing the molecular basis for the impaired IL-3 response in the A/J mouse.     

Characterization of a Dopamine-Releasing Action of 6R-l-erythro-Tetrahydrobiopterin: Comparison with a 6S-Form

Abstract: 6R-l -erythro-Tetrahydrobiopterin (6R-BH₄) is a cofactor for aromatic l -amino acid hydroxylases and nitric oxide synthase. Recently, we have reported that independently of its cofactor activities, 6R-BH₄ acts from the outside of neurons in the brain to enhance the release of monoamine neurotransmitters such as dopamine. To characterize the pharmacological properties of the action, we examined the effects of 6S-BH₄, a diastereoisomer of 6R-BH₄, on dopamine release in the rat striatum by using brain microdialysis and compared its effects with those of 6R-BH₄. Perfusion of 6S-BH₄ or 6R-BH₄ through the dialysis probe increased extracellular dopamine levels (an index of in vivo dopamine release) concentration dependently; the maximal increase by 6S-BH₄, was one-sixth of that by 6R-BH₄. 6S-BH₄ increased extracellular DOPA levels in the presence of NSD 1015, an inhibitor of aromatic l -amino acid decarboxylase (an index of in vivo tyrosine hydroxylase activity), to an extent similar to the increase induced by 6R-BH₄. The increase in the DOPA levels induced by either of the pteridines was abolished after pretreatment of rats with α-methyl-p-tyrosine (an inhibitor of tyrosine hydroxylase). Under the same conditions, the 6S-BH₄-induced dopamine release was abolished, but most of the 6R-BH₄-induced increase persisted. Coadministration of 6S-BH₄ with 6R-BH₄ inhibited the increase in dopamine release induced by 6R-BH₄ alone. These results show that 6R-BH₄ stimulates dopamine release by acting at the specific recognition site on the neuronal membrane, and that 6S-BH₄ acts as an antagonist of 6R-BH₄ at this site, although it has cofactor activities.     

The Influence of Polyvinylpyrrolidone on Freezing of Bovine IVF Blastocysts Following Biopsy

A study was conducted to develop a better freezing protocol for in vitro developed biopsied bovine blastocysts. Biopsied blastocysts were exposed to 1.8 M ethylene glycol (EG) + 0.05 M trehalose (T) and different concentration (5, 10, and 20%) of polyvinylpyrrolidone (PVP). Exposure to the solutions alone did not affect their in vitro development (Experiment 1). Experiments 2, 3, and 4 tested the viability of biopsied blastocysts cryopreserved in 1.8 M EG + different concentrations of T (0, 0.05, 0.1, and 0.3 M), 1.8 M EG + different concentrations of PVP (0, 5, 10, and 20%), and 1.8 M EG + 0.05 M T + different concentrations of PVP (0, 5, 10, and 20%), respectively. The proportion of biopsied blastocysts that reexpanded following cryopreservation in 1.8 M EG + 0.05 M T (38.5%) and 1.8 M EG + 0.1 M T (36.1%) was significantly (P < 0.05) higher than the proportion that reexpanded in 1.8 M EG + 0.3 M T (13.9%) (Experiment 2). The viability and the percentage of embryos that developed to >250 μm in diameter in the 5, 10, and 20% PVP groups (77.8 and 50.0%, 78.1 and 43.8%, 76.9 and 65.4%, respectively) were significantly higher than those that developed cryopreserved without PVP (55.1 and 20.7%) (Experiment 3). Optimum development of in vitro culture of frozen-thawed biopsied blastocysts was obtained using 1.8 M EG + 0.05 M T and 20% PVP. Analysis of blastocysts >250/μm in diameter showed that the number of ICM cells of biopsied blastocysts cryopreserved in 1.8 M EG + 0.05 M T with or without PVP was not different from the number of unfrozen biopsied blastocysts. These results indicate that PVP has some beneficial effect on freezing of biopsied bovine blastocysts.     

Differential Effects of Hypoxia on Ligand Binding Properties of Nicotinic and Muscarinic Acetylcholine Receptors on Cultured Bovine Adrenal Chromaffin Cells

Abstract: Hypoxia is known to disturb neuronal signal transmission at the synapse. Presynaptically, hypoxia is reported to suppress the release of neurotransmitters, but its postsynaptic effects, especially on the function of neurotransmitter receptors, have not yet been elucidated. To clarify the postsynaptic effects, we used cultured bovine adrenal chromaffin cells as a model of postsynaptic neurons and examined specific binding of l -[³H]nicotine (an agonist for nicotinic acetylcholine receptors: nAChRs) and ²²Na⁺ flux under control and hypoxic conditions. Experiments were performed in media preequilibrated with a gas mixture of either 21% O₂/79% N₂ (control) or 100% N₂ (hypoxia). Scatchard analysis of the specific binding to the cells revealed that the K_D under hypoxic conditions was twice as large as that under control conditions, whereas the B _max was unchanged. When the specific [³H]nicotine binding was kinetically analyzed, the association constant ( k ₁) but not the dissociation constant ( k ₋₁) was decreased to 40% of the control value by hypoxia. When the binding assay was performed using the membrane fraction, these changes were not observed. Nicotine-evoked ²²Na⁺ flux into the cells was suppressed by hypoxia. In contrast, specific [³H]quinuclidinyl benzilate binding to the intact cells was unaffected by hypoxia. These results demonstrate that hypoxia specifically suppresses the function of nAChRs (and hence, neuronal signal transmission through nAChRs), primarily by acting intracellularly.     

Characterization of a gene cluster for glycogen biosynthesis and a heterotetrameric ADP-glucose pyrophosphorylase from Bacillus stearothermophilus.

A chromosomal region of Bacillus stearothermophilus TRBE14 which contains genes for glycogen synthesis was cloned and sequenced. This region includes five open reading frames (glgBCDAP). It has already been demonstrated that glgB encodes branching enzyme (EC 2.4.1.18 [H. Takata et al., Appl. Environ. Microbiol. 60:3096-3104, 1994]). The putative GlgC (387 amino acids [aa]) and GlgD (343 aa) proteins are homologous to bacterial ADP-glucose pyrophosphorylase (AGP [EC 2.7.7.27]): the sequences share 42 to 70% and 20 to 30% identities with AGP, respectively. Purification of GlgC and GlgD indicated that AGP is an alpha2beta2-type heterotetrameric enzyme consisting of these two proteins. AGP did not seem to be an allosteric enzyme, although the activities of most bacterial AGPs are known to be allosterically controlled. GlgC protein had AGP activity without GlgD protein, but its activity was lower than that of the heterotetrameric enzyme. The GlgA (485 aa) and GlgP (798 aa) proteins were shown to be glycogen synthase (EC 2.4.1.21) and glycogen phosphorylase (EC 2.4.1.1), respectively. We constructed plasmids harboring these five genes (glgBCDAP) and assayed glycogen production by a strain carrying each of the derivative plasmids on which the genes were mutated one by one. Glycogen metabolism in B. stearothermophilus is discussed on the basis of these results.     

Transient Ischemia Differentially Increases Tyrosine Phosphorylation of NMDA Receptor Subunits 2A and 2B

Abstract: Activation of the N -methyl- d -aspartate (NMDA) receptor has been implicated in the events leading to ischemia-induced neuronal cell death. Recent studies have indicated that the properties of the NMDA receptor channel may be regulated by tyrosine phosphorylation. We have therefore examined the effects of transient cerebral ischemia on the tyrosine phosphorylation of NMDA receptor subunits NR2A and NR2B in different regions of the rat brain. Transient (15 min) global ischemia was produced by the four-vessel occlusion procedure. The tyrosine phosphorylation of NR2A and NR2B subunits was examined by immunoprecipitation with anti-tyrosine phosphate antibodies followed by immunoblotting with antibodies specific for NR2A or NR2B, and by immunoprecipitation with subunit-specific antibodies followed by immunoblotting with anti-phosphotyrosine antibodies. Transient ischemia followed by reperfusion induced large (23–29-fold relative to sham-operated controls), rapid (within 15 min of reperfusion), and sustained (for at least 24 h) increases in the tyrosine phosphorylation of NR2A and smaller increases in that of NR2B in the hippocampus. Ischemia-induced tyrosine phosphorylation of NR2 subunits in the hippocampus was higher than that of cortical and striatal NR2 subunits. The enhanced tyrosine phosphorylation of NR2A or NR2B may contribute to alterations in NMDA receptor function or in signaling pathways in the postischemic brain and may be related to pathogenic events leading to neuronal death.     

Optimization of a medium for the production of 1,2-epoxytetradecane by Nocardia corallina B-276

Summary A medium for the production of 1,2-epoxytetradecane from 1-tetradecene by Nocardia corallina B-276 was optimized. The activity of cells producing 1,2-epoxytetradecane increased when cell growth was suppressed by limiting nitrogen or potassium ion in the medium. Mg²⁺ was found to be essential for the production of 1,2-epoxide. Cell mass was increased, without reducing production of 1,2-epoxide, by increasing the concentration of yeast extract and limiting the concentration of potassium ion. The concentration of 1,2-epoxytetradecane reached 80 g/l in 6 days after optimization and the yield of 1,2-epoxytetradecane was 65 mol% based on consumed 1-tetradecene. Long chain 1,2-epoxyalkanes containing 13–17 carbon atoms also were produced under these conditions.