Novel hopanoid cyclases from the environment

Hopanoids are ubiquitous isoprenoid lipids found in modern biota, in recent sediments and in low-maturity sedimentary rocks. Because these lipids primarily are derived from bacteria, they are used as proxies to help decipher geobiological communities. To date, much of the information about sources of hopanoids has come from surveys of culture collections, an approach that does not address the vast fraction of prokaryotic communities that remains uncharacterized. Here we investigated the phylogeny of hopanoid producers using culture-independent methods. We obtained 79 new sequences of squalene-hopene cyclase genes (sqhC) from marine and lacustrine bacterioplankton and analysed them along with all 31 sqhC fragments available from existing metagenomics libraries. The environmental sqhCs average only 60% translated amino acid identity to their closest relatives in public databases. The data imply that the sources of these important geologic biomarkers remain largely unknown. In particular, genes affiliated with known cyanobacterial sequences were not detected in the contemporary environments analysed here, yet the geologic record contains abundant hopanoids apparently of cyanobacterial origin. The data also suggest that hopanoid biosynthesis is uncommon: < 10% of bacterial species may be capable of producing hopanoids. A better understanding of the contemporary distribution of hopanoid biosynthesis may reveal fundamental insight about the function of these compounds, the organisms in which they are found, and the environmental signals preserved in the sedimentary record.     

Social dominance does not increase oxidative stress in a female dominance hierarchy of an African cichlid fish

In many group living animal species, individuals use aggression to gain and maintain social dominance to secure access to ecological resources and potential mates. While social dominance has many fitness benefits, there are also potential costs associated with frequent agonistic interactions and status display. One potential cost of social dominance is oxidative stress, the imbalance of reactive oxygen species and antioxidant capacity. In the cichlid species Astatotilapia burtoni, dominant males are aggressive, hold a breeding territory, and have an activated reproductive system resulting in larger gonads. Subordinate males are submissive, school with females, and are nonreproductive. Females are submissive under natural conditions, but in a female-only group, a dominance hierarchy will form with dominant females taking on male-typical behaviours including aggression, territory defence, and increased androgen levels. However, in contrast to males, social dominance is not linked to increased activation of the reproductive system in females, allowing us to test whether social dominance alone exposes individuals to increased oxidative stress. We compared dominant and subordinate females in female-only groups in five markers of oxidative stress. Dominant females did not have higher levels of oxidative damage compared to same-sex subordinates. This result contrasted to the trend in males in which dominant males had higher oxidative damage than their subordinate counterparts. Our findings suggest that the oxidative cost of social dominance is limited and support the notion that previously reported associations between high rank and increased oxidative stress is most likely driven by increased investment in reproduction.     

Phylogenetic topology mapped onto dietary ecospace reveals multiple pathways in the evolution of the herbivorous niche in African Bovidae

Understanding the evolutionary history of the herbivore niche within African bovids has traditionally relied on examining anatomical adaptations to diet, particularly those related to digestive strategy. More recently, mesowear and stable isotope analyses have been used to great effect to reconstruct dietary preferences. We use these dietary proxies to construct a morphology‐free dietary ecospace and examine the topology of the phylogenetic relationships of African bovids mapped onto this ecospace. The reconstructed dietary ecospace provides evidence for four distinct dietary classes: species with C3‐ or C4‐dominated diets that produce low or high occlusal relief, likely related to diets high or low in abrasives, respectively. We detected no evidence for a discrete mixed feeder category; the species often categorized as such represent the end members of groups of species with either C3‐ or C4‐ dominated diets. Our analysis reveals high variability within the C4 grazing ecospace, and phylogenetic evidence indicates at least two pathways to grazing, likely related to the abrasive qualities of ingested food, which may be determined by the moisture content or the height of consumed grasses. These different pathways probably contribute to the high diversity of African grazers, both today and in the fossil record. C3 browsers (non‐frugivores) also display a high degree of variation, but there are no species associated with highly abrasive diets and there is evidence for only a single evolutionary pathway. We find evidence for only one evolutionary route towards frugivory, which includes species with diets that produce both high and low occlusal reliefs. The cause of abrasive wear in frugivores may be related to grit and/or the hard parts of fruits, but this requires further examination.     

A thioesterase bypasses the requirement for exogenous fatty acids in the plsX deletion of Streptococcus pneumoniae

PlsX is an acyl‐acyl carrier protein (ACP):phosphate transacylase that interconverts the two acyl donors in Gram‐positive bacterial phospholipid synthesis. The deletion of plsX in Staphylococcus aureus results in a requirement for both exogenous fatty acids and de novo type II fatty acid biosynthesis. Deletion of plsX (SP0037) in Streptococcus pneumoniae did not result in an auxotrophic phenotype. The ΔplsX S. pneumoniae strain was refractory to myristic acid‐dependent growth arrest, and unlike the wild‐type strain, was susceptible to fatty acid synthesis inhibitors in the presence of exogenous oleate. The ΔplsX strain contained longer chain saturated fatty acids imparting a distinctly altered phospholipid molecular species profile. An elevated pool of 18‐ and 20‐carbon saturated fatty acids was detected in the ΔplsX strain. A S. pneumoniae thioesterase (TesS, SP1408) hydrolyzed acyl‐ACP in vitro, and the ΔtesS ΔplsX double knockout strain was a fatty acid auxotroph. Thus, the TesS thioesterase hydrolyzed the accumulating acyl‐ACP in the ΔplsX strain to liberate fatty acids that were activated by fatty acid kinase to bypass a requirement for extracellular fatty acid. This work identifies tesS as the gene responsible for the difference in exogenous fatty acid growth requirement of the ΔplsX strains of S. aureus and S. pneumoniae.     

The Role of Conformational Dynamics and Allostery in the Disease Development of Human Ferritin

Determining the three-dimensional structure of myoglobin, the first solved structure of a protein, fundamentally changed the way protein function was understood. Even more revolutionary was the information that came afterward: protein dynamics play a critical role in biological functions. Therefore, understanding conformational dynamics is crucial to obtaining a more complete picture of protein evolution. We recently analyzed the evolution of different protein families including green fluorescent proteins (GFPs), β-lactamase inhibitors, and nuclear receptors, and we observed that the alteration of conformational dynamics through allosteric regulation leads to functional changes. Moreover, proteome-wide conformational dynamics analysis of more than 100 human proteins showed that mutations occurring at rigid residue positions are more susceptible to disease than flexible residue positions. These studies suggest that disease-associated mutations may impair dynamic allosteric regulations, leading to loss of function. Thus, in this study, we analyzed the conformational dynamics of the wild-type light chain subunit of human ferritin protein along with the neutral and disease forms. We first performed replica exchange molecular dynamics simulations of wild-type and mutants to obtain equilibrated dynamics and then used perturbation response scanning (PRS), where we introduced a random Brownian kick to a position and computed the fluctuation response of the chain using linear response theory. Using this approach, we computed the dynamic flexibility index (DFI) for each position in the chain for the wild-type and the mutants. DFI quantifies the resilience of a position to a perturbation and provides a flexibility/rigidity measurement for a given position in the chain. The DFI analysis reveals that neutral variants and the wild-type exhibit similar flexibility profiles in which experimentally determined functionally critical sites act as hinges in controlling the overall motion. However, disease mutations alter the conformational dynamic profile, making hinges more loose (i.e., softening the hinges), thus impairing the allosterically regulated dynamics.     

Oil Spill Response Risk Judgments,Decisions, and Mental Models: Findings from Surveying U.S. Stakeholders and Coastal Residents

This study applies a mental models survey approach to assess public thinking about oil spills and oil spill response. Based on prior interdisciplinary oil spill response research, the study first applies qualitative interview results and a response risk decision model to the design of a survey instrument. The decision model considers controlled burning, public health, and seafood safety. Surveying U.S. coastal residents (36,978 pairs of responses) through Google Insights identifies beliefs and gaps in understanding as well as related values and preferences about oil spills, and oil spill responses. A majority of respondents are concerned about economic impacts of major oil spills, and tend to see ocean ecosystems as fragile. They tend to see information about chemical dispersants as more important than ecological baseline information, and dispersants as toxic, persistent, and less effective than other response options. Although respondents regard laboratory studies as predictive of the effects of oil and of controlled burning, they are less confident that scientists agree on the toxicity and effectiveness of dispersants. The results illustrate opportunities to reframe discussions of oil spill response in terms of tradeoffs between response options, and new possibilities for assessing public opinions and beliefs during events.