Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes

Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrophoretic distances. They were applied to data for the human, chimpanzee, gorilla, orangutan, and gibbon species. Among the four different sets of data used, DNA sequences for an 895-nucleotide segment of mitochondrial DNA (Brown et al. 1982) gave the most reliable tree, whereas electrophoretic data (Bruce and Ayala 1979) gave the least reliable one. The DNA sequence data suggested that the chimpanzee is the closest and that the gorilla is the next closest to the human species. The orangutan and gibbon are more distantly related to man than is the gorilla. This topology of the tree is in agreement with that for the tree obtained from chromosomal studies and DNA-hybridization experiments. However, the difference between the branching point for the human and the chimpanzee species and that for the gorilla species and the human-chimpanzee group is not statistically significant. In addition to this analysis, various factors that affect the accuracy of an estimated tree are discussed.      

Amplification of lymph node cell tube leukocyte adherence inhibition (LAI) reactivity by leukocyte adherence inhibition factor (LAIF)

This investigation examines the immunologic basis for specific antigen-induced tube leukocyte adherence inhibition (LAI) reactivity of draining lymph node cells (LNC) from dogs with canine transmissible venereal sarcoma (CTVS). CTVS regressor LNC, macrophage-depleted LNC, and enriched T lymphocyte fractions, but not enriched B lymphocyte fractions, were specifically reactive to CTVS antigen extract in direct tube LAI. In addition, regressor LNC amplified tube LAI responses by generating supernatants with leukocyte adherence inhibition factor (LAIF) activity for normal dog indicator LNC and enriched peripheral blood mononuclear cells (PBMC) in an indirect tube LAI assay. However, macrophage-depleted LNC and enriched T lymphocyte fractions failed to generate supernatants with LAIF activity, suggesting that macrophage accessory cells play a central role in the amplification of tube LAI. Interestingly, CTVS regressor peripheral blood leukocytes (PBL) and PBMC, which were specifically reactive in direct tube LAI, also failed to generate supernatants with LAIF activity. These findings demonstrate a distinction between LAIF-mediated amplification and direct tube LAI reactivity, and suggest that leukocyte populations with differing cellular proportions and from different immunologic compartments may participate in tube LAI via different mechanisms.     

Conformation of sequential polypeptides of (Lysi-Leuj), (Lysi-Serj), and (Lys-Gly) in sodium dodecyl sulfate solution

A series of sequential polypeptides (Lys_iR_j)_n (R is Leu, Ser, or Gly) and random copolypeptides, (Lys^x, Leu^y)_n, were synthesized. Their conformation in NaDodSO₄ solution was determined by CD. Only (Lys-Leu)_n, (Lys-Ser)_n, and (Lys₃-Ser)_n adopt a stable β-form in the surfactant solution; (Lys-Ser₂)_n, (Lys-Ser₃)_n, (Lys₂-Ser₂)_n, and (Lys₂-Ser)_n have an unstable β-form, which reverts to an unordered form in high NaDodSO₄ concentrations, even though both Ser and DodSO-bound Lys⁺ are β-formers. In contrast, (Lys-Gly)_n remains unordered in NaDodSO₄ solution. On the other hand, Lys-rich (Lys₂-Leu)_n forms an unstable helix and (Lys₂-Leu₂)_n a stable helix in NaDodSO₄ solution. In 25 mM NaDodSO₄ (Lys^x, Leu^y)_n also forms a helix up to x = 75 and reverts to the β-form at x = 90. This compares with the helical conformation of (Lys^x, Ala^y)_n up to x = 65 and its β-form at x = 90, suggesting that Leu is an even stronger helix-former than Ala. Our results may provide a plausible explanation for the increase in helicity and disruption of the β-form for many proteins in NaDodSO₄ solution, that is, the polypeptide chain of a protein usually favors a helical conformation over a β-form in the presence of excess surfactant.     

Effect of chain length and concentration of anionic surfactants on the conformational transitions of poly(L-ornithine) and poly(L-lysine) in aqueous solution

The conformation of poly(L-ornithine) (PLO) and poly(L-lysine) (PLL) in solutions of sodium alkyl sulfates, CH₃(CH₂)_nSO₄Na with n = 7, 9, 11, 13 and 15 was studied by circular dichroism. PLO adopts a helical conformation in all 5 homologs and PLL a β-form in only 4 of the homologs. With octyl sulfate PLL has a helical conformation instead. These conformations were observed in solution of surfactants both below and above the critical micelle concentration.     

Gas-liquid chromatographic analysis of cyasin in cycad flour

A method for the quantitative determination of cycasin from cycad flour by gas-liquid chromatography is described. The flour is extracted with 70% ethanol and the residue from the dried extract is directly trimethylsilylated. Androsterone was found to be an excellent internal standard. The average content of cycasin from ten separate analyses of one lot of flour was $\text{0.429 gm}\text{100 gm}$. The method is rapid, sensitive, and not hindered by contaminating compounds.     

Combined in-beam electron impact-B/E-linked scan mass spectrometry of oxazoline derivatives for the structure determination of long-chain unsaturated fatty acids

Long-chain unsaturated fatty acids (UFA) having up to six double bonds are derivatized to 2-substituted 4,4-dimethyloxazolines (DMOX) and then analyzed by combined in-beam electron impact (IBEI)-B/E-linked scan mass spectrometry. This technique provides highly characteristic mass spectra and may serve as an auxiliary means for direct structure determination of individual UFA in mixtures.