Direct Comparisons of 2D and 3D Dental Microwear Proxies in Extant Herbivorous and Carnivorous Mammals

The analysis of dental microwear is commonly used by paleontologists and anthropologists to clarify the diets of extinct species, including herbivorous and carnivorous mammals. Currently, there are numerous methods employed to quantify dental microwear, varying in the types of microscopes used, magnifications, and the characterization of wear in both two dimensions and three dimensions. Results from dental microwear studies utilizing different methods are not directly comparable and human quantification of wear features (e.g., pits and scratches) introduces interobserver error, with higher error being produced by less experienced individuals. Dental microwear texture analysis (DMTA), which analyzes microwear features in three dimensions, alleviates some of the problems surrounding two-dimensional microwear methods by reducing observer bias. Here, we assess the accuracy and comparability within and between 2D and 3D dental microwear analyses in herbivorous and carnivorous mammals at the same magnification. Specifically, we compare observer-generated 2D microwear data from photosimulations of the identical scanned areas of DMTA in extant African bovids and carnivorans using a scanning white light confocal microscope at 100x magnification. Using this magnification, dental microwear features quantified in 2D were able to separate grazing and frugivorous bovids using scratch frequency; however, DMTA variables were better able to discriminate between disparate dietary niches in both carnivorous and herbivorous mammals. Further, results demonstrate significant interobserver differences in 2D microwear data, with the microwear index remaining the least variable between experienced observers, consistent with prior research. Overall, our results highlight the importance of reducing observer error and analyzing dental microwear in three dimensions in order to consistently interpret diets accurately.     

Interconversion of active and inactive 30 S ribosomal subunits is accompanied by a conformational change in the decoding region of 16 S rRNA

Zamir, Elson and their co-workers have shown that 30 S ribosomal subunits are reversibly inactivated by depletion of monovalent or divalent cations. We have re-investigated the conformation of 16 S rRNA in the active and inactive forms of the 30 S subunit, using a strategy that is designed to eliminate reversible ion-dependent conformational effects that are unrelated to the heat-dependent Zamir-Elson transition. A combination of structure-specific chemical probes enables us to monitor the accessibility of pyrimidines at N-3 and purines at N-1 and N-7. Chemically modified bases are identified by end-labeling followed by analine-induced strand scission (in some cases preceded by hybrid selection), or by primer extension using synthetic DNA oligomers. These studies show the following: The transition from the active to the inactive state cannot be described as a simple loosening or unfolding of native structure, such as that which is observed under conditions of more severe ion depletion. Instead, it has the appearance of a reciprocal interconversion between two differently structured states; some bases become more reactive toward the probes, whilst others become less reactive as a result of inactivation. Changes in reactivity are almost exclusively confined to the "decoding site" centered at positions 1400 and 1500, but significant differences are also detected at U723 and G791 in the central domain. This may reflect possible structural and functional interactions between the central and 3' regions of 16 S rRNA. The inactive form also shows significantly decreased reactivity at positions 1533 to 1538 (the Shine-Dalgarno region), in agreement with earlier findings. The principal changes in reactivity involve the universally conserved nucleotides G926, C1395, A1398 and G1401. The three purines show reciprocal behavior at their N-1 versus N-7 positions. G926 loses its reactivity at N-1, but becomes highly reactive at N-7 as a result of the transition of the inactive state. In contrast, A1398 and G1401 become reactive at N-1, but lose their hyper-reactivity at N-7. The possible structural and functional implications of these findings are discussed.     

The effect of pH and lysosomal extract on rat liver metallothionein (Cd-thionein)

Was studied in vitro. The¹⁰⁹Cd-labeled protein was isolated by gel filtration and incubated with a lysosomal extract from the same source. No degradation was seen when the pH of the incubation medium was 5 or higher, whereas the degradation of Cd-thionein was completed in 2 h at a pH of 4.5. Dissociation of Cd²⁺ from thionein, which takes place to a fair extent at a pH below 5, appears necessary before the enzymatic breakdown of the thionein moiety can take place.     

Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans

Recent studies of mitochondrial DNA (mtDNA) variation in mammals and Drosophila have shown an excess of amino acid variation within species (replacement polymorphism) relative to the number of silent and replacement differences fixed between species. To examine further this pattern of nonneutral mtDNA evolution, we present sequence data for the ND3 and ND5 genes from 59 lines of Drosophila melanogaster and 29 lines of D. simulans. Of interest are the frequency spectra of silent and replacement polymorphisms, and potential variation among genes and taxa in the departures from neutral expectations. The Drosophila ND3 and ND5 data show no significant excess of replacement polymorphism using the McDonald-Kreitman test. These data are in contrast to significant departures from neutrality for the ND3 gene in mammals and other genes in Drosophila mtDNA (cytochrome b and ATPase 6). Pooled across genes, however, both Drosophila and human mtDNA show very significant excesses of amino acid polymorphism. Silent polymorphisms at ND5 show a significantly higher variance in frequency than replacement polymorphisms, and the latter show a significant skew toward low frequencies (Tajima's D = -1.954). These patterns are interpreted in light of the nearly neutral theory where mildly deleterious amino acid haplotypes are observed as ephemeral variants within species but do not contribute to divergence. The patterns of polymorphism and divergence at charge-altering amino acid sites are presented for the Drosophila ND5 gene to examine the evolution of functionally distinct mutations. Excess charge-altering polymorphism is observed at the carboxyl terminal and excess charge-altering divergence is detected at the amino terminal. While the mildly deleterious model fits as a net effect in the evolution of nonrecombining mitochondrial genomes, these data suggest that opposing evolutionary pressures may act on different regions of mitochondrial genes and genomes.      

Chemotaxonomy of the genus Talaromyces

Species of the ascomycetous genus Talaromyces have been examined for profiles of secondary metabolites on TLC. The greatest number of specific metabolites were produced on oatmeal-, malt extract- and yeast-extract sucrose agars. Profiles of intracellular secondary metabolites produced on oatmeal agar were specific for each species and provided a means of simple differentiation of the taxa. Examination of the most important species using high performence liquid chromatography (HPLC) allowed to solve some taxonomic problems. Known mycotoxins are produced by T. stipitatus (duclauxin, talaromycins, botryodiploidin), T. stipitatus chemotype II (emodin), T. panasenkoi (spiculisporic acid), T. trachyspermus (spiculisporic acid), T. trac macrosporus (duclauxin) and T. wortmannii (rugulosin). Wortmannin is produced by an atypical strain of T. flavus but not T. wortmannii. Several other secondary metabolites were discovered for the first time in the following species: Glauconic acid is produced by T. panasenkoi, T. ohiensis and T. trachyspermus; vermiculine by T. ohiensis; duclauxin by T. flavus var. macrosporus and the mitorubrins by T. flavus and T. udagawae. The profiles of secondary metabolites support the established taxonomy of the species based on morphology, showing the genetic stability of profiles of secondary metabolites in Talaromyces. Two new taxa are proposed: T. macrosporus comb. nov. (stat. anam. Penicillium macrosporum stat. nov.), and Penicillium vonarxii, sp. nov. for the anamorph of T. luteus.     

Elimination of African Onchocerciasis: Modeling the Impact of Increasing the Frequency of Ivermectin Mass Treatment

The African Programme for Onchocerciasis Control (APOC) is currently shifting its focus from morbidity control to elimination of infection. To enhance the likelihood of elimination and speed up its achievement, programs may consider to increase the frequency of ivermectin mass treatment from annual to 6-monthly or even higher. In a computer simulation study, we examined the potential impact of increasing the mass treatment frequency for different settings. With the ONCHOSIM model, we simulated 92,610 scenarios pertaining to different assumptions about transmission conditions, history of mass treatment, the future mass treatment strategy, and ivermectin efficacy. Simulation results were used to determine the minimum remaining program duration and number of treatment rounds required to achieve 99% probability of elimination. Doubling the frequency of treatment from yearly to 6-monthly or 3-monthly was predicted to reduce remaining program duration by about 40% or 60%, respectively. These reductions come at a cost of additional treatment rounds, especially in case of 3-monthly mass treatment. Also, aforementioned reductions are highly dependent on maintained coverage, and could be completely nullified if coverage of mass treatment were to fall in the future. In low coverage settings, increasing treatment coverage is almost just as effective as increasing treatment frequency. We conclude that 6-monthly mass treatment may only be worth the effort in situations where annual treatment is expected to take a long time to achieve elimination in spite of good treatment coverage, e.g. because of unfavorable transmission conditions or because mass treatment started recently.