A One-Bead One-Peptide Combinatorial Library Method for B-Cell Epitope Mapping

The one-bead one-peptide combinatorial library method represents a powerful approach to the discovery of binding peptides for various macromolecular targets. It involves the synthesis of millions of peptides on beads such that each bead displays only one peptide entity. The peptide–beads that interact with a specific macromolecular target are then isolated for structure determination. We have applied this method to discovering peptide ligands for several murine monoclonal antibodies: (i) anti-β-endorphin (continuous epitope), (ii) anti-vmos peptide, (iii) anti-human insulin (discontinuous epitope), and (iv) surface immunoglobulins (μκ) of two murine B-cell lymphoma cell lines (antigen unknown).     

Biological electron transfer

Many oxidoreductases are constructed from (a) local sites of strongly coupled substrate-redox cofactor partners participating in exchange of electron pairs, (b) electron pair/single electron transducing redox centers, and (c) nonadiabatic, long-distance, single-electron tunneling between weakly coupled redox centers. The latter is the subject of an expanding experimental program that seeks to manipulate, test, and apply the parameters of theory. New results from the photosynthetic reaction center protein confirm that the electronic-tunneling medium appears relatively homogeneous, with any variances evident having no impact on function, and that control of intraprotein rates and directional specificity rests on a combination of distance, free energy, and reorganization energy. Interprotein electron transfer between cytochromec and the reaction center and in lactate dehydrogenase, a typical oxidoreductase from yeast, are examined. Rates of interprotein electron transfer appear to follow intraprotein guidelines with the added essential provision of binding forces to bring the cofactors of the reacting proteins into proximity.     

A guaianolide from Magnolia grandiflora

The leaves of Magnolia grandiflora afforded in addition to costunolide diepoxide and parthenolide a guaianolide named magnograndiolide.     

Isolation of Adenylate Cyclase Gene-Specific Sequences from Ophiostoma novo-ulmi, Candida albicans, and Agaricus bisporus by PCR

Degenerate primers corresponding to consensus sequences in the catalytic domains of known fungal adenylate cyclases were used to isolate gene-specific homologs from the Dutch elm disease pathogen Ophiostoma novo-ulmi, the dimorphic human pathogen Candida albicans, and the commercial mushroom Agaricus bisporus. All three fungi gave the expected PCR product of about 390 bp. Computer searches of the databases revealed that the products generated from O. novo-ulmi and C. albicans were highly similar to the adenylate cyclase gene of Magnaporthe grisea, the rice blast fungus (91% and 79%, respectively). The PCR product from the homobasidiomycete A. bisporus, on the other hand, showed 78% similarity to the uac1 gene of the heterobasidiomycete smut fungus, Ustilago maydis. Southern hybridization indicated that all three fungi contain a single adenylate cyclase gene. Our data suggest that PCR will be highly successful for the isolation of adenylate cyclase sequences from other fungi. Received: 13 April 1998 / Accepted: 27 May 1998     

The Diffuse Interstellar Bands: A Tracer For Organics In The Diffuse Interstellar Medium?

The diffuse interstellar bands (DIBs) are absorption bands seen in the spectra of stars obscured by interstellar dust. DIBs are recognized as a tracer for free, organic molecules in the diffuse interstellar medium (ISM). The potential molecular carriers for the DIBs are discussed with an emphasis on neutral and ionized polycyclic aromatic hydrocarbons (PAHs) for which the most focused effort has been made to date. From the combined astronomical, laboratory and theoretical study, it is concluded that a distribution of free neutral and ionized complex organics (PAHs, fullerenes, unsaturated hydrocarbons) represents the most promising class of candidates to account for the DIBs. The case for aromatic hydrocarbons appears particularly strong. The implied widespread distribution of complex organics in the diffuse ISM bears profound implications for our understanding of the chemical complexity of the ISM, the evolution of prebiotic molecules and its impact on the origin and the evolution of life on early Earth through the exogenous delivery (cometary encounters and metoritic bombardments) of prebiotic organics.     

Tetra-n-propylammonium tetra-oxoruthenate(VII): a reagent of choice for the oxidation of diversely protected glycopyranoses and glycofuranoses to lactones

2,3,4,6-Tetra-O-benzyl- -glucopyranose, 2,3,5-tri-O-allyl- -ribofuranose, 2,3,5-tri-O-allyl- and -tri-O-benzyl- -arabinofuranose, and 2-deoxy-3,5-di-O-allyl- -erythro-pentofuranose were oxidized to their corresponding lactones 6–10 by dimethyl sulfoxide activated by oxalyl chloride, pyridinium dichromate in the presence of molecular sieves and acetic acid, and tetra-n-propylammonium tetra-oxoruthenate(VII) using 4-methylmorpholine N-oxide as cooxidant. With the latter reagent, analytically pure lactones were obtained in 83–98% yield. A multistep preparation of 3,4,6-tri-O-benzyl-2-deoxy- -arabino-hexono-1,5-lactone (14) from 3,4,6-tri-O-benzyl-1,5-anhydro-2-deoxy- -arabino-hex-1 enitol (65% overall yield) is described.     

Production of oxytetracycline by immobilized Streptomyces rimosus cells in calcium alginate gels

Streptomyces rimosus Pfizer 18234–2 cells were immobilized in calcium alginate and used for the production of oxytetracycline. The influence of the incubation period, alginate concentration and storage in CaCl₂ were investigated. From the results of the repeated batch fermentations of the shake flasks, a good level of antibiotic was maintained for a period of about 28 days using 4% calcium alginate. The cell leakage and cell concentration inside the beads were affected by the alginate concentration and storage in CaCl₂ solution.     

iProtGly‐SS: Identifying protein glycation sites using sequence and structure based features

Glycation is chemical reaction by which sugar molecule bonds with a protein without the help of enzymes. This is often cause to many diseases and therefore the knowledge about glycation is very important. In this paper, we present iProtGly‐SS, a protein lysine glycation site identification method based on features extracted from sequence and secondary structural information. In the experiments, we found the best feature groups combination: Amino Acid Composition, Secondary Structure Motifs, and Polarity. We used support vector machine classifier to train our model and used an optimal set of features using a group based forward feature selection technique. On standard benchmark datasets, our method is able to significantly outperform existing methods for glycation prediction. A web server for iProtGly‐SS is implemented and publicly available to use: http://brl.uiu.ac.bd/iprotgly-ss/ .     

Optimization of the composition of the nutrient medium for cellulase and protein biosynthesis by thermophilic Aspergillus fumigatus NRC 272

An active strain of Aspergillus spp. has been selected for the production of cellulolytic enzymes and proteins when grown on peracetic acid-treated wheat straw. This strain produced a considerable amount of cellulase [see 1,4-(1,3;1,4)-β-d-glucan 4-glucanohydrolase, EC 3.2.1.4] in the extracellular supernatant and exhibited good overall cellulolytic activity, as measured using filter paper and Avicel as substrates. Also, under the same conditions the strain showed high activities of β-d-glucosidase (β-d-glucoside glucohydrolase, EC 3.2.1.21) and β-d-xylosidase (1,4-β-d-xylan xylohydrolase, EC 3.2.1.37). The maximum enzyme yields (carboxymethylcellulose activity 26.4 units ml^?1, filter paper activity 2.26 units ml^?1 and Avicel activity 16.82 units ml^?1; β-d-glucosidase 9.09 units ml^?1 and β-d-xylosidase 1.92 units ml^?1) were obtained after 96 h incubation at 45°C.