Identification of consensus patterns in unaligned DNA sequences known to be functionally related

We have developed a method for identifying consensus patternsin a set of unaligned DNA sequences known to bind a common proteinor to have some other common biochemical function. The methodis based on a tnatrix representation of binding site patterns.Each row of the matrix represents one of the four possible bases,each column represents one of the positions of the binding siteand each element is determined by the frequency the indicatedbase occurs at the indicated position. The goal of the methodis to find the most significant matrix-i.e. the one with thelowest probability of occurring by chance-out of all the matricesthat can be formed from the set of related sequences. The reliabilityof the method improves with the number of sequences, while thetime required increases only linearly with the number of sequences.To test this method, we analysed 11 DNA sequences containingpromoters regulated by the Escherichia coli LexA protein. Thematrices we' found were consistent with the known consensussequence, and could distinguish the generally accepted LexAbinding sites from other DNA sequences. Received on November 6, 1989; accepted on December 20, 1989     

Purification of the hepatic vasopressin receptor using a novel affinity column

A vasopressin receptor was purified, using a novel affinity column, from rat liver plasma membranes treated with guanosine 5'-(3-O-thio)triphosphate and solubilized with 0.8% cholate. Incubation of the membranes with the GTP analogue resulted in a dissociation of the receptor-guanine nucleotide regulatory protein complex. This manipulation, although resulting in a low-affinity state of the receptor, facilitated purification. The solubilized receptor was assayed using a new reconstitution procedure in which the soluble extracts were inserted into lipid vesicles composed of phosphatidylcholine and phosphatidylinositol. The receptor was purified by sequential chromatography on Q-Sepharose and hydroxyapatite. The use of a novel affinity column, a V1-vasopressin antagonist-agarose, resulted in a near-homogeneous preparation of a protein which exhibited an Mr = 58,000 on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Autoradiography of purified receptor, as well as crude membrane preparations cross-linked to [125I]arginine vasopressin, also revealed a protein band with an approximate Mr = 58,000. These findings indicate that V1-antagonist affinity chromatography should be useful for purifying adequate amounts of the receptor for studies of structure and function.     

Serum ferritin, iron and transferrin in women with thyrotoxic Graves' disease before and after methimazole treatment

We investigated iron metabolism in 47 women with thyrotoxic Graves' disease. Serum iron, ferritin, transferrin, triiodothyronine and thyroxine concentrations were RIA measured before and after methimazole treatment when patients became euthyroid. The control group consisted of 52 healthy women. We noted that serum ferritin levels and the ferritin to transferrin ration were significantly lower while the iron to ferritin ratio was higher in patients before and after methimazole therapy. Iron concentration as well as the iron to transferrin and the iron to thyroid hormone ratios were decreased only before treatment.     

Three month treatment with budesonide in patients with corticoid dependent bronchial asthma--personal experience

The experiment aimed at evaluating a three-month therapy of asthmatic patients with budesonide inhalations. The study involved 32 patients with long-lasting bronchial asthma depended on steroids. Therapy with budesonide (Pulmicort Astra) in a mean daily dose 1.6 mg enabled withdrawal of depot steroids and inhalation treatment only. In patients receiving prednisone in a mean daily dose 5.0 +/- 4.8 mg, budesonide therapy enabled a reduction of the oral dose by 50 percent. A significant improvement in the psychophysical status of patients has been noted despite a lack of significant differences in the results of lung functioning tests. Adverse reactions such as relaxation, insufficiency of the vocal cords at phonation and hoarseness were seen in 20 percent of patients, and in one of them required cessation of the drug. An increase in the number of Candida albicans colonies in throat swabs (over 20 colonies per plate) was seen in 7 treated patients but clinical symptoms which required an additional treatment were noted only in 1 patient.     

Effects of simulated acid rain on the physiology of carmine spider mite, Tetranychus cinnabarinus (Boisduvals) (Acari: Tetranychidae)

Abstract:  The physiological effect of simulated acid rain sprayed on carmine spider mite Tetranychus cinnabarinus (Boisduvals) and host plant, were measured in a series of laboratory trials. We examined potential changes in three kinds of protective enzymes [peroxidase (POD), superoxide dismutase (SOD) and catalase (CAT)] and three hydrolases [acid phosphatase (ACP), alkaline phosphatase (ALP) and carboxylesterase (CarE)] in response to changes in pH values of simulated acid rain at different time of exposure. POD, SOD and CAT activities increased significantly with the increase in the acidity of the acid rain, reaching the highest levels at pH 4.0 or 3.0, and then declined. Changes in ACP activity were similar to those observed in the protective enzymes. The increasing extent of the activities of these four enzymes after 30 and 45 days treatment became smaller than that after 15 days treatment . ALP activities decreased as pH value declined. There were no significant changes in CarE activities after 15 and 45 days, but that in pH 4.0 and 3.0 decreased after 30 days. The enhanced anti-oxidation enzyme levels (POD, SOD and CAT) and ACP activities in pH 4.0 and 3.0 reduced the effects of these toxic products on mites, resulting in the strengthening of the defensive power, and increase in survival and reproductive power of the mites, thus leading to an increase in the density of mites on host plant. From these results, we inferred that POD, SOD, CAT and ACP might be relevant to population changes of mites under acid rain pressure.     

3H]prostaglandin uptake in vivo by rabbit uterine tissues and blastocysts

Day-6 pregnant rabbits were anesthetized and subjected to a mid-ventral laparotomy. [3H] Prostaglandin F2alpha) (PGF2alpha) [3H]PGE2, [14C]Urea or [14C]Sucrose were instilled into the uterine lumen via the uterotubal junction. The amounts instilled/uterine horn were respectively 3.7 +/- 0.3, 3.5 +/- 0.3, 5.7 +/- 1.3 and 2.7 +/- 1.6 muCi in 20mul of buffer. Animals were killed at 1, 2, 9, 19 or 21 h after radioactive instillation, and the amounts of radioactivity in blastocysts, uterine tissue, peritoneal cavity washings and urine evaluated by liquid scintillation spectrometry. A gradient of radioactivity was observed from the uterotubal junction to the cervical end of the uterus. Large amounts of [3H]PG were found in the injected horn and associated blastocysts with a considerable crossover to the non-injected horn, but little in the associated blastocysts. Much of the blastocysts associated- [3H]PG remained unmetabolized. Large amounts of metabolized [3 H] were found in urine. [14C]Urea was taken up by uterine tissue in the injected horn, but there was little cross over to the non-injected horn. Urea was also found in urine. Much of the [14C]Sucrose remained in the injected horn, and little was recovered from the urine. It was found that at 9 h, but not at 19 h, after [3 H]PG instillation, the PG was localized at the site of the blastocysts in the injected but not in the contralateral horn. Significantly more [3H]PGF2alpha than [3H]PGE2 was localized in this situation. [14C]Urea was not localized at the site of the blastocysts in urea injected horns. (ABSTRACT TRUNCATED AT 250 WORDS)     

Effects of fructose on human fibroblast metabolism: the application of DNA measurements as a basis for interpretation

Summary A fluorometric procedure for measuring DNA was used to study growth and metabolic responses of eight cell strains of human foreskin fibroblasts. In preliminary studies this procedure gave more precise specific activity changes inN-acetyl-β-d-glucosaminidase (NAG) than did a protein activity basis, when changes in this enzyme's specific activity were investigated as a function of experimental cell manipulation. When fibroblast growth in eight cell strains was compared in 134 mM d-fructose vs. 13.4 mM glucose-supplemented minimum essential media, a significant increase in cellular DNA (50%) and protein (45%) occurred over an 11-d period. No significant differences in media pH change, lactate production, or carbohydrate uptake occurred on a DNA basis when cell metabolism was compared over the last 24 h of culture in the two media. Cells grown in fructose-containing media tended to show a reduction in NAG specific activity when compared with those grown in glucose-containing media.     

Remains of Late Pleistocene reindeer from Chmielewo,northeast Poland

Reindeer (Rangifer tarandus L.) remains in Europe are well represented in Late Pleistocene sites in France, Germany, Ukraine, Poland and other countries. In a chalk mine at Chmielewo (near niardwy Lake, NE Poland) four antlers were recovered. Radiocarbon assays date the fossils to the end of the Pleistocene. All antlers belong to male reindeer. One of the discovered specimens is an uncast antler of the tundra reindeer form, while the others are of the woodland reindeer form. The uncast antler has distinctly visible parieto-frontal fixation of the beam to the skull that confirms its parallel position in relation to the ground.     

NMR solution structure of Cn12, a novel peptide from the Mexican scorpion Centruroides noxius with a typical beta-toxin sequence but with alpha-like physiological activity.

Cn12 isolated from the venom of the scorpion Centruroides noxius has 67 amino-acid residues, closely packed with four disulfide bridges. Its primary structure and disulfide bridges were determined. Cn12 is not lethal to mammals and arthropods in vivo at doses up to 100 microg per animal. Its 3D structure was determined by proton NMR using 850 distance constraints, 36 phi angles derived from 36 coupling constants obtained by two different methods, and 22 hydrogen bonds. The overall structure has a two and half turn alpha-helix (residues 24-32), three strands of antiparallel beta-sheet (residues 2-4, 37-40 and 45-48), and a type II turn (residues 41-44). The amino-acid sequence of Cn12 resembles the beta scorpion toxin class, although patch-clamp experiments showed the induction of supplementary slow inactivation of Na(+) channels in F-11 cells (mouse neuroblastoma N18TG-2 x rat DRG2), which means that it behaves more like an alpha scorpion toxin. This behaviour prompted us to analyse Na(+) channel binding sites using information from 112 Na(+) channel gene clones available in the literature, focusing on the extracytoplasmic loops of the S5-S6 transmembrane segments of domain I and the S3-S4 segments of domain IV, sites considered to be responsible for binding alpha scorpion toxins.     

Mutation of Gluconobacter oxydans and Bacillus megaterium in a two-step process of l-ascorbic acid manufacture by ion beam

AIM: To increase the transformation rate of l-sorbose to 2-keto-l-gulonic (2-KLG) acid in a two-step process of l-ascrobic acid manufacture by ion beam. METHODS AND RESULTS: Gluconobacter oxydans (GO29) and Bacillus megaterium (BM80) were used in the present study. Ion implantation was carried out with the heavy ion implantation facility at the institute of Plasma Physics in China. 2-KLG in whole culture broth was determined by iodometry. Mutants were screened by single-colony isolation and 2-KLG accumulation in broth. GO29 and BM80 were implanted by either hydrogen ions (H(+)) or nitrogen ions (N(+)) with various doses, respectively. The average transformation rate of GM112-302 bred by ion beam in Gram-molecule was increased from 79.3 to 94.5% after eight passages in shaking flasks. Furthermore, in 180-ton fermentors in Jiangsu Jiangshan Pharmaceutical Co. Ltd, the transformation rate was stable at 92.0%, indicating a producer could get 0.99 kg of gulonic acid from 1.0 kg of sorbose. CONCLUSION: Ion beam as a new mutation source had potential advantages in breeding. Comparing with original mixture GO29 and BM80, GM112-302 is more efficient in accumulating 2-KLG, especially at the later phase. SIGNIFICANCE AND IMPACT OF THE STUDY: GM112-302 bred by ion beam implantation dramatically increased the transformation rate by 19.2%, which greatly increased efficiency and reduced the cost of l-ascorbic acid manufacture in a two-step process.