Patterns of population structure at microsatellite and mitochondrial DNA markers in the franciscana dolphin (Pontoporia blainvillei)

The franciscana dolphin, Pontorporia blainvillei, is an endemic cetacean of the Atlantic coast of South America. Its coastal distribution and restricted movement patterns make this species vulnerable to anthropogenic factors, particularly to incidental bycatch. We used mitochondrial DNA control region sequences, 10 microsatellites, and sex data to investigate the population structure of the franciscana dolphin from a previously established management area, which includes the southern edge of its geographic range. F‐statistics and Bayesian cluster analyses revealed the existence of three genetically distinct populations. Based on the microsatellite loci, similar levels of genetic variability were found in the area; 13 private alleles were found in Monte Hermoso, but none in Claromecó. When considering the mitochondrial DNA control region sequences, lower levels of genetic diversity were found in Monte Hermoso, when compared to the other localities. Low levels of gene flow were found between most localities. Additionally, no evidence of isolation by distance nor sex‐biased dispersal was detected in the study area. In view of these results showing that populations from Necochea/Claromecó, Monte Hermoso, and Río Negro were found to be genetically distinct and the available genetic information for the species previously published, Argentina would comprise five distinct populations: Samborombón West/Samborombón South, Cabo San Antonio/Buenos Aires East, Necochea/Claromecó/Buenos Aires Southwest, Monte Hermoso, and Río Negro. In order to ensure the long‐term survival of the franciscana dolphin, management and conservation strategies should be developed considering each of these populations as different management units.     

Local and Landscape Factors Driving the Structure of Tropical Anuran Communities: Do Ephemeral Ponds have a Nested Pattern?

The sets of species in animal and plant communities often comprise nested subsets of the species in broader communities. Although most mechanisms causing nested patterns are known and have been demonstrated for different environments and taxa, how amphibian communities are structured in ephemeral ponds in tropical disturbed landscapes remains unknown. We investigated if pond size, duration, presence of trees (local factors), and the proportion of forest cover surrounding ponds (landscape factor) affect anuran species richness and composition, and if pond assemblages showed a nested pattern. We sampled 11 ephemeral ponds in a pasture matrix near a large Atlantic Forest remnant in Brazil and measured local and landscape variables inside two buffer zones around each pond (100 and 500 m). We marked 1514 individuals from 23 anuran species, and found that richness in ponds ranged from 3–14 species. Both local and landscape factors explained frog species richness in the sampled ponds, and seemed to affect community composition. Frog communities occurred in a non‐nested pattern, contrary to our expectations: species found in poor subsets were not found in larger, more complex ponds. Local and landscape characteristics create a variety of environments in ephemeral ponds, even in impoverished ones; these characteristics restrict pond occupancy for some species, and result in a non‐nested pattern.     

Stalk cell differentiation without polyketides in the cellular slime mold

Polyketides induce prestalk cell differentiation in Dictyostelium. In the double-knockout mutant of the SteelyA and B polyketide synthases, most of the pstA cells—the major part of the prestalk cells—are lost, and we show by whole mount in situ hybridization that expression of prestalk genes is also reduced. Treatment of the double-knockout mutant with the PKS inhibitor cerulenin gave a further reduction, but some pstA cells still remained in the tip region, suggesting the existence of a polyketide-independent subtype of pstA cells. The double-knockout mutant and cerulenin-treated parental Ax2 cells form fruiting bodies with fragile, single-cell layered stalks after cerulenin treatment. Our results indicate that most pstA cells are induced by polyketides, but the pstA cells at the very tip of the slug are induced in some other way. In addition, a fruiting body with a single-cell layered, vacuolated stalk can form without polyketides.     

A gradient‐forming MipZ protein mediating the control of cell division in the magnetotactic bacterium Magnetospirillum gryphiswaldense

Cell division needs to be tightly regulated and closely coordinated with other cellular processes to ensure the generation of fully viable offspring. Here, we investigate division site placement by the cell division regulator MipZ in the alphaproteobacterium Magnetospirillum gryphiswaldense, a species that forms linear chains of magnetosomes to navigate within the geomagnetic field. We show that M. gryphiswaldense contains two MipZ homologs, termed MipZ1 and MipZ2. MipZ2 localizes to the division site, but its absence does not cause any obvious phenotype. MipZ1, by contrast, forms a dynamic bipolar gradient, and its deletion or overproduction cause cell filamentation, suggesting an important role in cell division. The monomeric form of MipZ1 interacts with the chromosome partitioning protein ParB, whereas its ATP‐dependent dimeric form shows non‐specific DNA‐binding activity. Notably, both the dimeric and, to a lesser extent, the monomeric form inhibit FtsZ polymerization in vitro. MipZ1 thus represents a canonical gradient‐forming MipZ homolog that critically contributes to the spatiotemporal control of FtsZ ring formation. Collectively, our findings add to the view that the regulatory role of MipZ proteins in cell division is conserved among many alphaproteobacteria. However, their number and biochemical properties may have adapted to the specific needs of the host organism.     

Integrating alpha,beta, and phylogenetic diversity to understand anuran fauna along environmental gradients of tropical forests in western Ecuador

The study of current distribution patterns of amphibian species in South America is of particular interest in areas such as evolutionary ecology and conservation biology. These patterns could be playing an important role in biological interactions, population size, and connectivity, and potential extinction risk in amphibians. Here, we tested the effects of spatial and environmental factors on the variation, turnover, and phylogenetic diversity of anuran amphibian species in tropical forests of western Ecuador. Data for presence/absence of 101 species of 34 genera and 10 families registered in 12 sites (nested in four biogeographic units) were obtained through fieldwork, museum collections, and literature records. We examined the influence of geographical, altitudinal, temperature, and precipitation distances on differences in anuran composition between sites. We found significant positive correlations among all of these variables with anuran distribution. The greatest alpha diversity (species richness) was found in the Equatorial Chocó biogeographic unit. Equatorial Pacific biogeographic unit could act as a transition zone between the Equatorial Chocó and Equatorial Tumbes. The western Andes (Western Cordillera biogeographic unit) was the most dissimilar and exhibited a higher species turnover rate than the other biogeographic units. Our results suggest that precipitation and elevation play a key role in maintaining the diversity of amphibian species in western Ecuador.     

Radical sites in Mycobacterium tuberculosis KatG identified using electron paramagnetic resonance spectroscopy, the three-dimensional crystal structure, and electron transfer couplings

Catalase-peroxidase (KatG) from Mycobacterium tuberculosis, a Class I peroxidase, exhibits high catalase activity and peroxidase activity with various substrates and is responsible for activation of the commonly used antitubercular drug, isoniazid (INH). KatG readily forms amino acid-based radicals during turnover with alkyl peroxides, and this work focuses on extending the identification and characterization of radicals forming on the millisecond to second time scale. Rapid freeze-quench electron paramagnetic resonance spectroscopy (RFQ-EPR) reveals a change in the structure of the initially formed radical in the presence of INH. Heme pocket binding of the drug and knowledge that KatG[Y229F] lacks this signal provides evidence for radical formation on residue Tyr(229). High field RFQ-EPR spectroscopy confirmed a tryptophanyl radical signal, and new analyses of X-band RFQ-EPR spectra also established its presence. High field EPR spectroscopy also confirmed that the majority radical species is a tyrosyl radical. Site-directed mutagenesis, along with simulations of EPR spectra based on x-ray structural data for particular tyrosine and tryptophan residues, enabled assignments based on predicted hyperfine coupling parameters. KatG mutants W107F, Y229F, and the double mutant W107F/Y229F showed alteration in type and yield of radical species. Results are consistent with formation of a tyrosyl radical reasonably assigned to residue Tyr(229) within the first few milliseconds of turnover. This is followed by a mixture of tyrosyl and tryptophanyl radical species and finally to only a tyrosyl radical on residue Tyr(353), which lies more distant from the heme. The radical processing of enzyme lacking the Trp(107)-Tyr(229)-Met(255) adduct (found as a unique structural feature of catalase-peroxidases) is suggested to be a reasonable assignment of the phenomena.