Developmental Changes in the Molecular Weights of Polypeptides in the Human CNS That Carry the HNK-1 Epitope and Bind Phaseolus vulgaris Lectins

The binding patterns of electrophoresed polypeptides from homogenates of human frontal lobe, cerebellum, and spinal cord obtained at various stages of development were determined for several lectins with specificities for a wide range of oligosaccharides. A discrete developmental change in the molecular-weight pattern was seen only among polypeptides binding the two Phaseolus vulgaris agglutinins, E-phytohemagglutinin (E-PHA) and L-PHA. With increasing maturity, the apparent molecular weights of the major polypeptides binding these two lectins progressively decreased. Furthermore, at all stages of development, E-PHA and L-PHA bound to the same polypeptides as the monoclonal antibody HNK-1, which recognizes a carbohydrate epitope on polypeptides that may play roles in cell adhesion. Based on the carbohydrate specificities of the two PHAs, we conclude that it is likely that the HNK-1 epitope resides on a triantennary N-linked oligosaccharide bisected by N-acetylglucosamine.     

Compensatory substitutions and the evolution of the mitochondrial 12S rRNA gene in mammals

12S ribosomal RNA (rRNA) gene sequences from a suite of mammalian taxa (13 placentals, 4 marsupials, 1 monotreme), for which phylogenetic relationships are well established based on independent criteria, were employed to study the evolution of this gene. Phylogenetic analysis of 12S sequences produces a phylogeny that agrees with expectations. Base composition provides evidence for directional symmetrical substitution pressure in loops; in stems, base composition is much more even. Rates of nucleotide substitution are lower in stems than loops. Patterns of nucleotide substitution show an overall preference for transitions over transversions, with this difference more profound in stems than loops. Among different transversion pathways, there is a wide range of transformation frequencies. An analysis of compensatory substitutions shows that there is strong evidence for their occurrence and that a weighting factor of 0.61 should be applied in phylogenetic analyses to account for the dependence of mutations at stem positions relative to positions where changes are independent. Among stem variables (i.e., stem length, interaction distance, substitution rates, G+C content, and the percentage of bases that are paired), several significant correlations were discovered, but stem length and interaction distance are uncorrelated with other variables.      

A NEW PROCEDURE FOR THE MEASUREMENT OF ACID-SOLUBLE GLUTAMINE OF TISSUE WITH PARTICULAR REFERENCE TO THE BRAIN

—A simple method is described for the measurement of free brain glutamine by spectrophotometric means, without prior separation by either paper or column chromatography. Through the application of this method, it was also possible to obtain an approximate value for the combined concentrations of glutamic acid, y-aminobutyric acid and glutathione in brain.     

Comparative analysis of indices of central dopaminergic functions in man

Various postulated indices of central dopaminergic activity - cerebrospinal fluid (CSF) dopamine (DA), dihydroxy-phenylacetic acid (DOPAC), homovanillic acid (HVA), noradrenaline (NA), plasma NA, serum prolactin, serum dopamine-β-hydroxylase (DBH), and platelet monoamine oxidase (MAO) activity - were measured in 30 drug-free inpatients. The mean values and the ranges were similar to those described in the literature. Plasma NA showed significant positive correlation with age. Significant positive correlation was found between CSF DA and its metabolites DOPAC and HVA. Serum DBH activity showed a slight but significant inverse correlation with CSF DA and its two metabolites. CSF NA showed a significant positive correlation with CSF DOPAC, but only in females. Serum DBH activity had no significant correlation either with CSF or with plasma NA levels. These findings suggest that either CSF HVA or DOPAC and DA may be useful indicators of DA metabolism in humans. Serum DBH activity may be in relationship with the central dopaminergic functions.     

Implications and concepts of polyamine-nucleic acid interactions

Modeling, x-ray diffraction, and solution studies have contributed to the understanding of interactions between polyamines and nucleic acids. Polyamines stabilize a variety of unusual DNA structures and conformations in vitro, including both the left-handed Z and the right-handed A DNA. In addition, polyamines condense DNA and may be important in bending specific sequences. Investigations into the mechanisms of these effects provide support for both specific and nonspecific interactions between polyamines and DNA. Although exact relationships between the binding of polyamines and conformational changes in nucleic acids are still being clarified, polyamines remain important candidates for regulators of DNA conformation in vivo.     

A stopped-flow H-D exchange kinetic study of spermine-polynucleotide interactions.

The rates of H-D exchange for imino and amino protons in adenosine, calf thymus DNA, poly (dA-dT), poly(dG-dC), and poly (dG-me5dC) were determined using stopped flow kinetic methods in the presence of various concentrations of Tris, imidazole, Mg2+, and spermine in citrate buffer (pH 7, 25 degrees C). CD spectroscopic studies showed that all polynucleotides always remain in the B-form under these conditions. An increase in the concentration of Tris and imidazole from 5 mu M to 20 mM caused an increase in the rates of exchange of both fast-exchanging imino and slow-exchanging amino protons. The limiting rates of exchange at infinite concentrations of catalysts were found to be different for fast (31-57 sec-1) and slow (1-2 sec-1) exchanging protons. These results indicate that imino and amino protons of B-DNA exchange asymmetrically from two different open states as observed for Z-DNA. An increase in the concentration of spermine from a ratio of 1:50 to 1:2 of positive charge/phosphate decreased the rate of exchange of imino protons of calf-thymus DNA, poly(dG-dC), and poly(dG-me5dC), but increased the rate of exchange of the imino protons of poly(dA-dT) without affecting the exchange rate of the amino protons of any of the polynucleotides. These results are interpreted in terms of possible spermine-induced change of conformations of oligonucleotides of specific sequence that has been suggested by theoretical model building studies.     

Delivery of antibodies to the cytosol: Debunking the myths

The use of antibodies to target their antigens in living cells is a powerful analytical tool for cell biology research. Not only can molecules be localized and visualized in living cells, but interference with cellular processes by antibodies may allow functional analysis down to the level of individual post-translational modifications and splice variants, which is not possible with genetic or RNA-based methods. To utilize the vast resource of available antibodies, an efficient system to deliver them into the cytosol from the outside is needed. Numerous strategies have been proposed, but the most robust and widely applicable procedure still remains to be identified, since a quantitative ranking of the efficiencies has not yet been done. To achieve this, we developed a novel efficiency evaluation method for antibody delivery based on a fusion protein consisting of a human IgG₁ Fc and the recombination enzyme Cre (Fc-Cre). Applied to suitable GFP reporter cells, it allows the important distinction between proteins trapped in endosomes and those delivered to the cytosol. Further, it ensures viability of positive cells and is unsusceptible to fixation artifacts and misinterpretation of cellular localization in microscopy and flow cytometry. Very low cytoplasmic delivery efficiencies were found for various profection reagents and membrane penetrating peptides, leaving electroporation as the only practically useful delivery method for antibodies. This was further verified by the successful application of this method to bind antibodies to cytosolic components in living cells.     

Cell Proliferation in the Adult Rat Rostral Migratory Stream Following Exposure to Gamma Irradiation

Summary One of the few areas of the adult CNS, that are known to be competent for neuronal proliferation, is the subventricular zone (SVZ) lining the brain lateral ventricles. Cells proliferating in the SVZ migrate along a defined pathway, the rostral migratory stream (RMS), where their proliferation continues until reaching the olfactory bulb.1. In relation to the fact that brain is, in general, regarded as a radioresistant organ composed from non dividing cells, the aim of the present study was to investigate effect of ionizing radiation on proliferating cell numbers in the RMS of adult rats.2. Male Wistar rats were investigated 25 and 80 days after whole body gamma irradiation with the dose of 3 Gy. Dividing cells were labeled by bromodeoxyuridine (BrdU). BrdU-positive cells were counted by Disector program. The mean number of BrdU⁺ cells in the whole RMS and in its individual parts (vertical arm, elbow, and horizontal arm) was evaluated.3. Temporary increase in proliferating cell number (by 30%) was seen in the whole RMS at the 25th day after irradiation.4. The most expressive increase occurred in the vertical arm (by 60%) and elbow (about 37%). The values reduced till the 80th day after exposure.Our results show that ionizing irradiation significantly influences the extent of cell proliferation and migration in the adult rat RMS.     

Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values

The aim of this paper was to compare the effect of haplotype definition on the precision of QTL-mapping and on the accuracy of predicted genomic breeding values. In a multiple QTL model using identity-by-descent (IBD) probabilities between haplotypes, various haplotype definitions were tested i.e. including 2, 6, 12 or 20 marker alleles and clustering base haplotypes related with an IBD probability of > 0.55, 0.75 or 0.95. Simulated data contained 1100 animals with known genotypes and phenotypes and 1000 animals with known genotypes and unknown phenotypes. Genomes comprising 3 Morgan were simulated and contained 74 polymorphic QTL and 383 polymorphic SNP markers with an average r² value of 0.14 between adjacent markers. The total number of haplotypes decreased up to 50% when the window size was increased from two to 20 markers and decreased by at least 50% when haplotypes related with an IBD probability of > 0.55 instead of > 0.95 were clustered. An intermediate window size led to more precise QTL mapping. Window size and clustering had a limited effect on the accuracy of predicted total breeding values, ranging from 0.79 to 0.81. Our conclusion is that different optimal window sizes should be used in QTL-mapping versus genome-wide breeding value prediction.