Errors between sites in restriction site mapping

Restriction site mapping programs construct maps by generatingpermutations of fragments and checking for consistency. Unfortunatelymany consistent maps often are obtained within the experimentalerror bounds, even though there is only one actual map. A particularlyefficient algorithm is presented that aims to minimize errorbounds between restriction sites. The method is generalizedfor linear and circular maps. The time complexity is derivedand execution times are given for multiple enzymes and a rangeof error bounds. Received on July 17, 1987; accepted on November 3, 1987     

Ultrastructure of acapsular mutant Cryptococcus neoformans cap 67 and monosaccharide composition of cell extracts

Acapsular mutant Cryptococcus neoformans cap 67 was grown in Pine's citrate broth medium for 3 days and the cells then transferred to a nitrogen-free medium for 6 days. The cells were subjected to a four stage extraction with buffered Triton-X1OO, cold dilute alkaline borohydride, hot dilute acetic acid, and a second alkaline extraction. Galactoxylomannan antigens were recovered from the culture supernates of both 3 day old and 9 day-old yeast cells. The alkaline extracts contained water-soluble galactoxylomannan and a water-insoluble glucan. Dilute acid treatment released a minor amount of carbohydrate from the cells. The second alkaline extraction yielded increased amounts of glucan and galactoxylomannan from the 9 day-old cells. Soluble non-dialyzable cell extracts were antigenically identical in immunodiffusion with the culture supernate antigens. After the extraction sequence, all of the galactose, xylose, and mannose were removed from the cells. The walls retained their shape after extraction but their layers were loosened. Cells resuspended in nitrogen-free medium for six days developed thickened walls with alternating electron-dense and electronlucent layers. The major constituent of the thickened 9 day-old cell walls was glucose, only 5% glucosamine was detected.     

Transgenic tobacco (Nicotiana tabacum L. cv. Samsun-NN) plants over-expressing a synthetic HRP-C gene are altered in growth, development and susceptibility to abiotic stress

The physiological role of class III peroxidases (EC 1.11.1.7) in controlling plant growth and development has been investigated by over-expression of both native and heterologous peroxidases. However, it has remained an enigma as to why the phenotypes of different peroxidase over-expressing transgenics vary. In order to resolve the conflicting information about the consequences of peroxidase over-expression, we have explored the role of the subcellular targeting of HRP-C in controlling stem growth, root development, axillary branching and abiotic stress tolerance in tobacco (Nicotiana tabacum L.). Altering the sub-cellular targeting of vacuolar HRP-C, such that over-expressed peroxidase accumulates in the cytoplasm and cell wall, induced phenotypic changes that are typically associated with altered auxin homeostasis, and over-expression of cell wall located peroxidases. We conclude that sub-cellular targeting is a determinant of the phenotype of peroxidase over-expressing plants.     

A GTPase reaction accompanying the rejection of Leu-tRNA2 by UUU-programmed ribosomes. Proofreading of the codon-anticodon interaction by ribosomes

The characteristics of a GTPase reaction between poly(U)-programmed ribosomes, EFTu . GTP, and the near-cognate aminoacyl (aa)-tRNA, Leu-tRNA Leu 2, have been studied to assess the role of this reaction in proofreading of the codon-anticodon interaction. The reaction resembles the GTPase reaction with cognate aa-tRNAs and EFTu . GTP in its substrate requirements, in its involving EFTu . GTP . aa-tRNA ternary complexes, and in its requiring a free ribosomal A-site. The noncognate reaction differs from the cognate one in that aa-tRNA becomes stably bound to the ribosomes only 5% of the time; it therefore seems best characterized as an abortive enzymatic binding reaction. The rate of reaction is a significant fraction (4%) of that of the cognate aa-tRNA, indicating that recognition of ternary complexes by ribosomes involves a level of error greater than that of translation as a whole. The rejection of the noncognate aa-tRNA following GTP hydrolysis is therefore a vital step in the translation process and fulfills the criteria set for a proofreading reaction. Leu-tRNA Leu 2 which escapes rejection through proofreading, forms a stable complex with the ribosomal A-site, so it appears that the Leu-tRNA2 which was rejected never reached the A-site and that proofreading precedes full A-site binding.     

The incidence of hematologic tumours: A cellular model for the age dependence

Most hematologic tumors (acute and chronic myelogenous leukemia, chronic lymphatic leukemia, polycythemia vera, and multiple myeloma) exhibit an exponential increase in incidence with advancing age of the host. This age-incidence pattern resembles that for carcinomas and can be explained by the accumulation of harmful mutations in the stem cells of the tissues of tumor origin during the course of normal aging. The age-incidence pattern for acute lymphatic leukemia is unique and complex with a linear increase in incidence from birth to age 3, an exponential decline in incidence form age 3 to 34, a low and constant rate of incidence from age 34 to 60, and a slight increase in incidence at ages greater than 60. We conclude that variation in tumor incidence with host age is determined by the pattern of cell proliferation in the tissue of tumor origin. We suggest that cell proliferation in the tissue of origin of acute lymphatic leukemia occurs in stages: (1) rapid stem cell proliferation from before birth to age 3, (2) random stem cell differentiation from age 3 to 34, and (3) a constant rate of stem cell proliferation and differentiation after age 34.     

Double staining technique for rat foetus skeletons in teratological studies.

Cartilage and bone were differentiated using alcian blue and alizarin red S respectively. Anomalies of both cartilaginous and bony parts of the skeleton could be examined.     

Design rationale, synthesis, and characterization of non-natural analogs of the cationic amino acids arginine and lysine.

A series of non-natural isosteric analogs of the cationic, ion-pairing, natural amino acids arginine and lysine have been synthesized, characterized with regard to relevant physical parameters, and protected for routine inclusion in Merrifield solid-phase synthesis. The design of these molecules is based on the concept of steric inhibition of solvation, in that judicious placement of alkyl groups can destabilize aqueous ion solvation and favor ion-pairing [see Beeson & Dix (1993) J. Am. Chem. Soc. 115, 10275]. When the residues are substituted for the natural amino acids in biologically active peptides, enhanced ion-pairing of the peptides to their receptors to increase the peptides' biological activities can result. The increased lipophilicity of the non-natural residues can also improve pharmacokinetic parameters and agonist/antagonist behaviors of peptides. While the synthesis of the L-series is described, the D-isomers were also prepared using identical chemistry.