Accelerated Evolution of Cytochrome b in Simian Primates: Adaptive Evolution in Concert with Other Mitochondrial Proteins?

We have sequenced the cytochrome b gene of Horsfield's tarsier, Tarsius bancanus, to complete a data set of sequences for this gene from representatives of each primate infraorder. These primate cytochrome b sequences were combined with those from representatives of three other mammalian orders (cat, whale, and rat) in an analysis of relative evolutionary rates. The nonsynonymous nucleotide substitution rate of the cytochrome b gene has increased approximately twofold along lineages leading to simian primates compared to that of the tarsier and other primate and nonprimate mammalian species. However, the rate of transversional substitutions at fourfold degenerate sites has remained uniform among all lineages. This increase in the evolutionary rate of cytochrome b is similar in character and magnitude to that described previously for the cytochrome c oxidase subunit II gene. We propose that the evolutionary rate increase observed for cytochrome b and cytochrome c oxidase subunit II may underlie an episode of coadaptive evolution of these two proteins in the mitochondria of simian primates. Received: 15 December 1997 / Accepted: 24 February 1998     

Prime region subsite specificity characterization of human cathepsin D: the dominant role of position 128.

In order to contribute to our understanding of cathepsin D (CatD) active site specificity, two series of chromogenic octapeptides with systematic substitutions in positions P2' and P3' were synthesized. This panel was characterized with native human liver cathepsin D (nHuCatD) and yielded information concerning specificity trends within the S2' and S3' subsites. The pepstatin inhibited crystal structure of nHuCatD (Baldwin et al., 1993) was then utilized in conjunction with these subsite preference data to identify residues suspected of contributing to "prime" side subsite specificity. These residues were targeted for site-directed mutagenesis using the re-engineered recombinant model, "short" pseudocathepsin D (Beyer & Dunn, 1996). As a result of these analyses it was determined that prime region subsites do contribute to the unique specificity of human CatD. Furthermore, it was ascertained that the poly-proline loop does not have an active role in S3' subsite specificity. Lastly, it appears that Ile128 has a dominant role on S2' subsite specificity whereas Val130 does not.     

Thermodynamics of the reconstitution of tuna cytochrome c from two peptide fragments

Two peptide fragments from tuna cytochrome c (cyt c), N-fragment (residues 1-44 containing the heme) and C-fragment (residues 45-103), combine to form a 1:1 fragment complex. This was clearly proved by ion-spray mass spectrometry. It was found from CD and NMR spectra that the structure of the fragment complex formed is similar to that of an intact cyt c, although each isolated fragment itself is unstructured. Binding constants and enthalpies upon the complex formation were directly observed by isothermal titration calorimetry. Thermodynamic parameters (deltaG(o)b, deltaHb, deltaS(o)b, and deltaC(b)p)) associated with the complex formation were determined at various pHs and temperatures. DeltaHb was found to be almost independent of pH values. The change in heat capacity accompanying the complex formation (deltaC(b)p) was directly determined from the temperature dependence of deltaHb. In addition, the change in heat capacity and enthalpy upon tuna cyt c unfolding were determined by differential scanning calorimetry. Thermodynamic parameters for the unfolding/dissociation process of the fragment complex were compared with those for cyt c unfolding at pH 3.9 and 303 K. In a comparison of two unfolding processes, the heat capacity change of each was very close to the other, while both the unfolding enthalpy and entropy of the fragment complex were larger than those of tuna cyt c. These thermodynamic data suggest that the internal interactions between polar groups (hydrogen bonding) and nonpolar groups (van der Waals interactions) are preserved in the fragment complex as well as in the native state of cyt c.     

Maximal T cell IL-13 production requires monocyte or monokine participation

The T cell-secreted lymphokine interleukin 13 (IL-13) exerts pleiotropic effects on monocytes (Mphi) and B cells. Since accessory cells, like Mphi and B cells, also act in antigen-presenting and lymphokine augmentation of T cells, Mphi and B cells may be able to effect T cell IL-13 production. Purified T cells produced slightly less IL-13 than the lower T cell numbers contained in peripheral blood mononuclear cell population, further suggesting accessory cell augmentation. Addition of 10% B cells [either unstimulated or pokeweed mitogen (PWM)-stimulated] to autologous T cells only moderately augmented T cell IL-13 levels. PWM-stimulated B cell culture supernates had even less augmenting effect on T cell IL-13 levels and unstimulated B cell culture supernates did not augment T cell IL-13 production. In contrast to the moderately augmenting effect of B cells or their stimulated culture supernates, addition of 10% Mphi, either unstimulated or muramyl dipeptide (MDP)+IFN-gamma stimulated, to autologous T cells produced a highly significant increase in T cell IL-13 production. Mphi culture supernates were equally effective in augmenting T cell IL-13 levels, suggesting both that cell-to-cell contact is not critical for Mphi augmentation of T cell IL-13 levels, and that Mphi secreted factors are pivotal. CD64(+) Mphi (or their culture supernates), which are known as poor antigen-presenting cells, also effectively augmented T cell IL-13 production, further supporting the involvement of Mphi secreted factors. Finally, experiments with exogenous addition of recombinant monokines, as well as neutralization experiments with different cytokine antibodies, suggested IL-1beta as a primary cytokine involved in the augmentation of T cell IL-13 levels by accessory cells. However, these experiments also indicated other unidentified Mphi factors as playing a significant role in producing maximal T cell IL-13 production.     

ESR Studies of a Series of Phthalocyanines. Mechanism of Phototoxicity. Comparative Quantitation of O2-using ESR Spin-Trapping and Cytochrome c Reduction Techniques

ESR experiments with 2,2,6,6-tetramethyl-4-piperi-done (4-oxo-TEMP) and the spin-trap 5,5-dimethyl pyrroline-N-oxide (DMPO) have been performed on a series of new phthalocyanines: the bis(tri-n-hexyl-siloxy) silicon phthalocyanine ([(nhex)₃SiO]₂SiPc), the hexadecachloro zinc phthalocyanine (ZnPcCl₁₆), the hexadecachloro aluminum phthalocyanine (AlPcCl₁₆), the hexadecachloro aluminum phthalocyanine sulfate (HSO₄A1PcCl₁₆), whose photocytotoxicity has been studied against various leukemic and melanotic cell lines. Type I and Type II pathways occur simultaneously in DMF although the Type II seems to be prevalent. These results are not changed when the bis(tri-n-hexylsiloxy) silicon phthalocyanine is entrapped into liposomes. By contrast, the Type I process is favored in membrane models for all the perchlori-nated phthalocyanines. This modified behavior may be accounted on a possible stacking of phthalocyanines in membranes and a preventing effect of axial ligands against aggregation in the case of the bis(tri-n-hexyl-siloxy) silicon phthalocyanine. The photodynamic action of zinc perchlorinated phthalocyanine is not dependent on singlet oxygen, phototoxicity of this molecule being essentially mediated by oxygen free radicals. Quantitation of the superoxide radical was accomplished, with good agreement, by two techniques: the cytochrome c reduction and the ESR quantitation based on the double integration of the first derivative of the ESR signal. The disproportionation of the superoxide radical or degradation of the spin-trap seem to be avoided in aprotic solvents such as DMF.     

Molecular Modeling of Calixarenes with Group I Metal Ions

Molecular mechanics calculations have been used to model the geometries of the complexes of Group I metal ions with calix[n]arenes (n = 4,5). A simple procedure in which the calixarene atoms are assigned partial charges on the basis of AM1 calculations and the metal ions are allowed to bind electrostatically to the calixarenes produces surprising good results when the resulting structures are compared to known crystallographic data on the complexes. Encapsulated solvent molecules and/or counterions can be included in the calculations and, indeed, are necessary to reproduce the X-ray data. Electronic Supplementary Material available.     

Glacial oceanographic contrasts explain phylogeography of Australian bull kelp

The evolutionary effects of Southern Hemisphere Pleistocene oceanographic conditions — marked by fluctuations in sea levels and water temperatures, and redirected currents — are poorly understood. The southeastern tip of Australia presents an intriguing model system for studying the biological impacts of palaeoceanography. In particular, contrasting oceanographic conditions that existed on eastern vs. western sides of the Bassian Isthmus during Pleistocene glacial periods allow for natural comparisons between putative refugial vs. re-invading populations. Whereas many western Tasmanian marine taxa were likely eliminated by cold subantarctic water during the last glacial period, eastern Tasmanian populations would have persisted in relatively warm temperatures mediated by the ongoing influence of the East Australian Current (EAC). Here we test for the effects of contrasting palaeoceanographic conditions on endemic bull kelp, Durvillaea potatorum , using DNA sequence analysis (COI; rbc L) of more than 100 individuals from 14 localities in southeastern Australia. Phylogenetic reconstructions reveal a deep (maximum divergence 4.7%) genetic split within D. potatorum , corresponding to the 'eastern' and 'western' geographical regions delimited by the Bassian Isthmus, a vicariant barrier during low Pleistocene sea levels. Concordant with the western region's cold glacial conditions, samples from western Tasmania and western Victoria are genetically monomorphic, suggesting postglacial expansion from a mainland refugium. Eastern samples, in contrast, comprise distinct regional haplogroups, suggesting the species persisted in eastern Tasmania throughout recent glacial periods. The deep east–west divergence seems consistent with earlier reports of morphological differences between 'western' and 'eastern' D. potatorum , and it seems likely that these forms represent reproductively isolated species.     

Molecular diversity of Germany's freshwater fishes and lampreys assessed by DNA barcoding

This study represents the first comprehensive molecular assessment of freshwater fishes and lampreys from Germany. We analysed COI sequences for almost 80% of the species mentioned in the current German Red List. In total, 1056 DNA barcodes belonging to 92 species from all major drainages were used to (i) build a reliable DNA barcode reference library, (ii) test for phylogeographic patterns, (iii) check for the presence of barcode gaps between species and (iv) evaluate the performance of the barcode index number (BIN) system, available on the Barcode of Life Data Systems. For over 78% of all analysed species, DNA barcodes are a reliable means for identification, indicated by the presence of barcode gaps. An overlap between intra‐ and interspecific genetic distances was present in 19 species, six of which belong to the genus Coregonus. The Neighbour‐Joining phenogram showed 60 nonoverlapping species clusters and three singleton species, which were related to 63 separate BIN numbers. Furthermore, Barbatula barbatula, Leucaspius delineatus, Phoxinus phoxinus and Squalius cephalus exhibited remarkable levels of cryptic diversity. In contrast, 11 clusters showed haplotype sharing, or low levels of divergence between species, hindering reliable identification. The analysis of our barcode library together with public data resulted in 89 BINs, of which 56% showed taxonomic conflicts. Most of these conflicts were caused by the use of synonymies, inadequate taxonomy or misidentifications. Moreover, our study increased the number of potential alien species in Germany from 14 to 21 and is therefore a valuable groundwork for further faunistic investigations.