Analysis of p53 "latency" and "activation" by fluorescence correlation spectroscopy. Evidence for different modes of high affinity DNA binding

The concept that the tumor suppressor p53 is a latent DNA-binding protein that must become activated for sequence-specific DNA binding recently has been challenged, although the "activation" phenomenon has been well established in in vitro DNA binding assays. Using electrophoretic mobility shift assays and fluorescence correlation spectroscopy, we analyzed the binding of "latent" and "activated" p53 to double-stranded DNA oligonucleotides containing or not containing a p53 consensus binding site (DNAspec or DNAunspec, respectively). In the absence of competitor DNA, latent p53 bound DNAspec and DNAunspec with high affinity in a sequence-independent manner. Activation of p53 by the addition of the C-terminal antibody PAb421 significantly decreased the binding affinity for DNAunspec and concomitantly increased the binding affinity for DNAspec. The net result of this dual effect is a significant difference in the affinity of activated p53 for DNAspec and DNAunspec, which explains the activation of p53. High affinity nonspecific DNA binding of latent p53 required both the p53 core domain and the p53 C terminus, whereas high affinity sequence-specific DNA binding of activated p53 was mediated by the p53 core domain alone. The data suggest that high affinity nonspecific DNA binding of latent and high affinity sequence-specific binding of activated p53 to double-stranded DNA differ in their requirement for the C terminus and involve different structural features of the core domain. Because high affinity nonspecific DNA binding of latent p53 is restricted to wild type p53, we propose that it relates to its tumor suppressor functions.     

Energy,Water and Fish: Biodiversity Impacts of Energy-Sector Water Demand in the United States Depend on Efficiency and Policy Measures

Rising energy consumption in coming decades, combined with a changing energy mix, have the potential to increase the impact of energy sector water use on freshwater biodiversity. We forecast changes in future water use based on various energy scenarios and examine implications for freshwater ecosystems. Annual water withdrawn/manipulated would increase by 18–24%, going from 1,993,000–2,628,000 Mm³ in 2010 to 2,359,000–3,271,000 Mm³ in 2035 under the Reference Case of the Energy Information Administration (EIA). Water consumption would more rapidly increase by 26% due to increased biofuel production, going from 16,700–46,400 Mm³ consumption in 2010 to 21,000–58,400 Mm³ consumption in 2035. Regionally, water use in the Southwest and Southeast may increase, with anticipated decreases in water use in some areas of the Midwest and Northeast. Policies that promote energy efficiency or conservation in the electric sector would reduce water withdrawn/manipulated by 27–36 m³GJ⁻¹ (0.1–0.5 m³GJ⁻¹ consumption), while such policies in the liquid fuel sector would reduce withdrawal/manipulation by 0.4–0.7 m³GJ⁻¹ (0.2–0.3 m³GJ⁻¹ consumption). The greatest energy sector withdrawal/manipulation are for hydropower and thermoelectric cooling, although potential new EPA rules that would require recirculating cooling for thermoelectric plants would reduce withdrawal/manipulation by 441,000 Mm³ (20,300 Mm³ consumption). The greatest consumptive energy sector use is evaporation from hydroelectric reservoirs, followed by irrigation water for biofuel feedstocks and water used for electricity generation from coal. Historical water use by the energy sector is related to patterns of fish species endangerment, where water resource regions with a greater fraction of available surface water withdrawn by hydropower or consumed by the energy sector correlated with higher probabilities of imperilment. Since future increases in energy-sector surface water use will occur in areas of high fish endemism (e.g., Southeast), additional management and policy actions will be needed to minimize further species imperilment.     

Intraspecific variation in reproductive physiology and egg quality in the European Starling Sturnus vulgaris

Egg mass shows large intraspecific variation in birds and is repeatable within individuals. The mechanisms underlying this variation are unknown. We hypothesized that measures of egg quality (the mass of yolk protein, yolk lipid, and albumen protein) would be positively correlated with the plasma pools of the yolk precursor vitellogenin, and the masses of the oviduct, metabolic machinery (liver, heart, lungs, kidneys, gizzard, small intestine and pancreas), and endogenous stores of protein and lipid. We tested these predictions in European Starlings Sturnus vulgaris collected at the peak of egg production effort. In contrast to our predictions, both yolk protein and yolk lipid were negatively correlated with plasma vitellogenin levels. Albumen protein was positively related to oviduct mass, but other aspects of body composition failed to explain variation in egg quality. Hence, while we observed correlations between egg composition and peripheral systems (circulating precursor pools and the oviduct), we found no evidence that egg quality is determined by more general processes, i.e., the supply and processing of nutrients.     

Abundance and Survival Rates of the Hawai’i Island Associated Spinner Dolphin (Stenella longirostris) Stock

Reliable population estimates are critical to implement effective management strategies. The Hawai’i Island spinner dolphin (Stenella longirostris) is a genetically distinct stock that displays a rigid daily behavioural pattern, foraging offshore at night and resting in sheltered bays during the day. Consequently, they are exposed to frequent human interactions and disturbance. We estimated population parameters of this spinner dolphin stock using a systematic sampling design and capture–recapture models. From September 2010 to August 2011, boat-based photo-identification surveys were undertaken monthly over 132 days (>1,150 hours of effort; >100,000 dorsal fin images) in the four main resting bays along the Kona Coast, Hawai’i Island. All images were graded according to photographic quality and distinctiveness. Over 32,000 images were included in the analyses, from which 607 distinctive individuals were catalogued and 214 were highly distinctive. Two independent estimates of the proportion of highly distinctive individuals in the population were not significantly different (p = 0.68). Individual heterogeneity and time variation in capture probabilities were strongly indicated for these data; therefore capture–recapture models allowing for these variations were used. The estimated annual apparent survival rate (product of true survival and permanent emigration) was 0.97 SE±0.05. Open and closed capture–recapture models for the highly distinctive individuals photographed at least once each month produced similar abundance estimates. An estimate of 221±4.3 SE highly distinctive spinner dolphins, resulted in a total abundance of 631±60.1 SE, (95% CI 524–761) spinner dolphins in the Hawai’i Island stock, which is lower than previous estimates. When this abundance estimate is considered alongside the rigid daily behavioural pattern, genetic distinctiveness, and the ease of human access to spinner dolphins in their preferred resting habitats, this Hawai’i Island stock is likely more vulnerable to negative impacts from human disturbance than previously believed.     

The c‐ring ion binding site of the ATP synthase from Bacillus pseudofirmus OF4 is adapted to alkaliphilic lifestyle

In the c‐ring rotor of ATP synthases ions are shuttled across the membrane during ATP synthesis by a unique rotary mechanism. We investigated characteristics of the c‐ring from the alkaliphile Bacillus pseudofirmus OF4 with respect to evolutionary adaptations to operate with protons at high environmental pH. The X‐ray structures of the wild‐type c₁₃ ring at pH 9.0 and a ‘neutralophile‐like’ mutant (P51A) at pH 4.4, at 2.4 and 2.8 Å resolution, respectively, reveal a dependency of the conformation and protonation state of the proton‐binding glutamate (E⁵⁴) on environmental hydrophobicity. Faster labelling kinetics with the inhibitor dicyclohexylcarbodiimide (DCCD) demonstrate a greater flexibility of E⁵⁴ in the mutant due to reduced water occupancy within the H⁺ binding site. A second ‘neutralophile‐like’ mutant (V21N) shows reduced growth at high pH, which is explained by restricted conformational freedom of the mutant's E⁵⁴ carboxylate. The study directly connects subtle structural adaptations of the c‐ring ion binding site to in vivo effects of alkaliphile cell physiology.     

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill

The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ∼4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using ¹⁴C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of ¹⁴C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)''s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem.     

Honest signals and sexual conflict: Female lizards carry undesirable indicators of quality

Sex differences in animal coloration often result from sex‐dependent regulatory mechanisms. Still, some species exhibit incomplete sexual dimorphism as females carry a rudimentary version of a costly male trait, leading to intralocus sexual conflict. The underlying physiology and condition dependence of these traits can inform why such conflicts remain unresolved. In eastern fence lizards (Sceloporus undulatus), blue iridophore badges are found in males and females, but melanin pigmentation underneath and surrounding badges is male‐exclusive. We track color saturation and area of badges across sexual maturity, and their relationship to individual quality (body condition and immunocompetence) and relevant hormones (testosterone and corticosterone). Saturation and testosterone were positively correlated in both sexes, but hormone and trait had little overlap between males and females. Saturation was correlated with body condition and immunocompetence in males but not in females. Co‐regulation by androgens may have released females from resource allocation costs of color saturation, even when in high condition. Badge area was independent of testosterone, but associated with low corticosterone in females, indicating that a nonsex hormone underlies incomplete sexual dimorphism. Given the evidence in this species for female reproductive costs associated with ornamentation, this sex‐nonspecific regulation of an honest signal may underlie intralocus sexual conflict.     

Community dynamics of nematodes after Larsen ice‐shelf collapse in the eastern Antarctic Peninsula

Free‐living marine nematode communities of the Larsen B embayment at the eastern Antarctic Peninsula were investigated to provide insights on their response and colonization rate after large‐scale ice‐shelf collapse. This study compares published data on the post‐collapse situation from 2007 with new material from 2011, focusing on two locations in the embayment that showed highly divergent communities in 2007 and that are characterized by a difference in timing of ice‐shelf breakup. Data from 2007 exposed a more diverse community at outer station B.South, dominated by the genus Microlaimus. On the contrary, station B.West in the inner part of Larsen B was poor in both numbers of individuals and genera, with dominance of a single Halomonhystera species. Re‐assessment of the situation in 2011 showed that communities at both stations diverged even more, due to a drastic increase in Halomonhystera at B.West compared to relatively little change at B.South. On a broader geographical scale, it seems that B.South gradually starts resembling other Antarctic shelf communities, although the absence of the genus Sabatieria and the high abundance of Microlaimus still set it apart nine years after the main Larsen B collapse. In contrast, thriving of Halomonhystera at B.West further separates its community from other Antarctic shelf areas.