Ecological and methodological drivers of species' distribution and phenology responses to climate change

Climate change is shifting species' distribution and phenology. Ecological traits, such as mobility or reproductive mode, explain variation in observed rates of shift for some taxa. However, estimates of relationships between traits and climate responses could be influenced by how responses are measured. We compiled a global data set of 651 published marine species' responses to climate change, from 47 papers on distribution shifts and 32 papers on phenology change. We assessed the relative importance of two classes of predictors of the rate of change, ecological traits of the responding taxa and methodological approaches for quantifying biological responses. Methodological differences explained 22% of the variation in range shifts, more than the 7.8% of the variation explained by ecological traits. For phenology change, methodological approaches accounted for 4% of the variation in measurements, whereas 8% of the variation was explained by ecological traits. Our ability to predict responses from traits was hindered by poor representation of species from the tropics, where temperature isotherms are moving most rapidly. Thus, the mean rate of distribution change may be underestimated by this and other global syntheses. Our analyses indicate that methodological approaches should be explicitly considered when designing, analysing and comparing results among studies. To improve climate impact studies, we recommend that (1) reanalyses of existing time series state how the existing data sets may limit the inferences about possible climate responses; (2) qualitative comparisons of species' responses across different studies be limited to studies with similar methodological approaches; (3) meta-analyses of climate responses include methodological attributes as covariates; and (4) that new time series be designed to include the detection of early warnings of change or ecologically relevant change. Greater consideration of methodological attributes will improve the accuracy of analyses that seek to quantify the role of climate change in species' distribution and phenology changes.

Shortfalls in the global protected area network at representing marine biodiversity

The first international goal for establishing marine protected areas (MPAs) to conserve the ocean's biodiversity was set in 2002. Since 2006, the Convention on Biological Diversity (CBD) has driven MPA establishment, with 193 parties committed to protecting >10% of marine environments globally by 2020, especially 'areas of particular importance for biodiversity' (Aichi target 11). This has resulted in nearly 10 million km(2) of new MPAs, a growth of ~360% in a decade. Unlike on land, it is not known how well protected areas capture marine biodiversity, leaving a significant gap in our understanding of existing MPAs and future protection requirements. We assess the overlap of global MPAs with the ranges of 17,348 marine species (fishes, mammals, invertebrates), and find that 97.4% of species have <10% of their ranges represented in stricter conservation classes. Almost all (99.8%) of the very poorly represented species (<2% coverage) are found within exclusive economic zones, suggesting an important role for particular nations to better protect biodiversity. Our results offer strategic guidance on where MPAs should be placed to support the CBD's overall goal to avert biodiversity loss. Achieving this goal is imperative for nature and humanity, as people depend on biodiversity for important and valuable services.

Abstract 1231: Live cell and in vitro analysis of p53 interactions

Dysregulation of protein-protein interactions between the tumor suppressor p53 and its binding partners is implicated in the pathogenesis of various cancers. Here we describe several novel assays for analysis of p53 interactions and their inhibitors both in live mammalian cells and in vitro.

To evaluate putative inhibitors of protein-protein interactions between p53 and its negative regulators Mdm2 and Mdm4, we recently developed two comparative live-cell Fluorescent-Two Hybrid (F2H) assays. The F2H principle is based on a tethering strategy: the GFP-tagged protein (here p53) is enriched at the protein interaction platform of the engineered F2H-BHK cells and serves as bait, whereas the RFP-tagged protein serves as a prey (here Mdm2 or Mdm4). By performing p53:Mdm2 and p53:Mdm4 F2H assays side-by-side, we could evaluate the dual inhibitory activity of the previously published stapled peptides. Furthermore, since F2H allows visualization of the dynamics of protein-protein interactions, we could compare the compound's kinetics with real-time imaging. We performed a mutant analysis with F2H and showed that several Nutlin-resistant mutants of Mdm2 are sensitive to inhibition with stapled peptides sMTide-02 and sMTide-02a.

For in vitro validation of p53 interactions, we developed novel p53 immunoprecipitation reagents. We employed the single-domain antibody technology in conjunction with phage display to isolate two specific anti-p53 VHHs (also termed nanobodies) from immunized alpacas. When conjugated to agarose beads, these VHHs serve as highly efficient pull-down reagents (p53-Traps), specific exclusively against N- and C-terminus of p53 respectively. Using both p53-Traps, we could confirm our F2H results in immunoprecipitation followed by Western blotting. Furthermore, p53-Traps enabled us to extend our analysis of the p53 interaction network and evaluate interactions between the p53 isoforms.

Taken together, we developed a toolbox for analysis of p53 interactions both biochemically and by fluorescence microscopy. Our fully reversible live-cell F2H assays can be applied for side-by-side profiling of new inhibitors of p53:Mdm2 and p53:Mdm4 interactions with respect to their intracellular activity, cell penetration and kinetics. Our N- and C-terminal p53-Traps complement p53 interaction analysis and enable highly efficient biochemical investigation of the p53 network and discovery of new interaction partners of p53.

Citation Format: Larisa Yurlova, Andrea Buchfellner, Benjamin Ruf, Sebastien Gabriel Michel Jo, Jean-Christophe Bourdon, Farid J. Ghadessy, Christopher J. Brown, David P. Lane, Tina Romer. Live cell and in vitro analysis of p53 interactions. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1231. doi:10.1158/1538-7445.AM2015-1231

Assessing the Efficacy of Mdm2/Mdm4-Inhibiting Stapled Peptides Using Cellular Thermal Shift Assays

Previous publications on stapled peptide inhibitors against Mdm2/Mdm4-p53 interactions have established that this new class of drugs have the potential to be easily optimised to attain high binding affinity and specificity, but the mechanisms controlling their cellular uptake and target engagement remain elusive and controversial. To aid in understanding the rules of peptide and staple design, and to enable rapid optimisation, we employed the newly-developed cellular thermal shift assay (CETSA). CETSA was able to validate stapled peptide binding to Mdm2 and Mdm4, and the method was also used to determine the extent of cellular uptake, cellular availability, and intracellular binding of the endogenous target proteins in its native environment. Our data suggest that while the stapled peptides engage their targets intracellularly, more work is needed to improve their cellular entry and target engagement efficiency in vivo. CETSA now provides a valuable tool to optimize such in vivo properties of stapled peptides.

Randomized double-blind trial comparing the cosmetic outcome of cutting diathermy versus scalpel for skin incisions

Background

Controversy exists about whether cutting diathermy for skin incisions leads to a cosmetically inferior scar. Cosmetic outcomes were compared between skin incisions created with cutting diathermy versus scalpel. Wound infection rates and postoperative incisional pain were also compared.

Methods

This was a randomized double-blind trial comparing cutting diathermy and scalpel in patients undergoing bowel resection. Scar cosmesis was assessed at 6 months after surgery by a plastic surgeon and a research associate using the Vancouver Scar Scale (VSS) and the Patient and Observer Scar Assessment Scale (POSAS). Patients also used POSAS to self-evaluate their scars. Wound infections within 30 days were recorded, and incision pain scores were measured on the first 5 days after operation.

Results

A total of 66 patients were randomized to cutting diathermy (31) or scalpel (35). At 6 months, there was no significant difference between the diathermy and scalpel groups in mean(s.d.) VSS scores (4·9(2·6) versus 5·0(1·9); P = 0·837), mean POSAS total scores (19·2(8·0) versus 20·0(7·4); P = 0·684) or subjective POSAS total scores (20·2(12·1) versus 21·3(10·4); P = 0·725). Neither were there significant differences in wound infection rates between the groups (5 of 30 versus 5 of 32; P = 1·000). Pain scores on day 1 after operation were significantly lower in the diathermy group (mean 1·68 versus 3·13; P = 0·018), but were not significantly different on days 2–5.

Conclusion

Cutting diathermy is a cosmetically acceptable technique for abdominal skin incisions. There is no increased risk of wound infection, and diathermy may convey benefit in terms of early postoperative wound pain. Registration number: NCT01496404 (http://www.clinicaltrials.gov).

Anticipative management for coral reef ecosystem services in the 21st century

Under projections of global climate change and other stressors, significant changes in the ecology, structure and function of coral reefs are predicted. Current management strategies tend to look to the past to set goals, focusing on halting declines and restoring baseline conditions. Here, we explore a complementary approach to decision making that is based on the anticipation of future changes in ecosystem state, function and services. Reviewing the existing literature and utilizing a scenario planning approach, we explore how the structure of coral reef communities might change in the future in response to global climate change and overfishing. We incorporate uncertainties in our predictions by considering heterogeneity in reef types in relation to structural complexity and primary productivity. We examine 14 ecosystem services provided by reefs, and rate their sensitivity to a range of future scenarios and management options. Our predictions suggest that the efficacy of management is highly dependent on biophysical characteristics and reef state. Reserves are currently widely used and are predicted to remain effective for reefs with high structural complexity. However, when complexity is lost, maximizing service provision requires a broader portfolio of management approaches, including the provision of artificial complexity, coral restoration, fish aggregation devices and herbivore management. Increased use of such management tools will require capacity building and technique refinement and we therefore conclude that diversification of our management toolbox should be considered urgently to prepare for the challenges of managing reefs into the 21st century.

Development of a series of aryl pyrimidine kynurenine monooxygenase inhibitors as potential therapeutic agents for the treatment of Huntington's disease

We report on the development of a series of pyrimidine carboxylic acids that are potent and selective inhibitors of kynurenine monooxygenase and competitive for kynurenine. We describe the SAR for this novel series and report on their inhibition of KMO activity in biochemical and cellular assays and their selectivity against other kynurenine pathway enzymes. We describe the optimization process that led to the identification of a program lead compound with a suitable ADME/PK profile for therapeutic development. We demonstrate that systemic inhibition of KMO in vivo with this lead compound provides pharmacodynamic evidence for modulation of kynurenine pathway metabolites both in the periphery and in the central nervous system.

Electronic cigarettes: product characterisation and design considerations

Objective

To review the available evidence regarding electronic cigarette (e-cigarette) product characterisation and design features in order to understand their potential impact on individual users and on public health.

Methods

Systematic literature searches in 10 reference databases were conducted through October 2013. A total of 14 articles and documents and 16 patents were included in this analysis.

Results

Numerous disposable and reusable e-cigarette product options exist, representing wide variation in product configuration and component functionality. Common e-cigarette components include an aerosol generator, a flow sensor, a battery and a nicotine-containing solution storage area. e-cigarettes currently include many interchangeable parts, enabling users to modify the character of the delivered aerosol and, therefore, the product's ‘effectiveness’ as a nicotine delivery product. Materials in e-cigarettes may include metals, rubber and ceramics. Some materials may be aerosolised and have adverse health effects. Several studies have described significant performance variability across and within e-cigarette brands. Patent applications include novel product features designed to influence aerosol properties and e-cigarette efficiency at delivering nicotine.

Conclusions

Although e-cigarettes share a basic design, engineering variations and user modifications result in differences in nicotine delivery and potential product risks. e-cigarette aerosols may include harmful and potentially harmful constituents. Battery explosions and the risks of exposure to the e-liquid (especially for children) are also concerns. Additional research will enhance the current understanding of basic e-cigarette design and operation, aerosol production and processing, and functionality. A standardised e-cigarette testing regime should be developed to allow product comparisons.

Abstract 5386: Disrupting p53:Mdm2 and p53:Mdm4 - Comparative cell-based assays for drug screening

The important interconnected protein-protein interactions between the tumor suppressor p53 and its regulatory binding partners Mdm2 and Mdm4 (= MdmX/ HdmX) are implicated in pathogenesis of various cancers. However, until now there is a lack of reversible cell-based assays for concurrent analysis for both PPIs: p53/Mdm2 and p53/Mdm4. Our aim was to develop two comparative assays based on the Fluorescent 2-Hybrid (F2H) assay principle, which enable side-by-side analysis of antagonistic compounds.

The F2H assay is a fully reversible microscopy-assisted assay for the direct intracellular analysis of PPIs. It offers a fast and straight-forward readout: an interaction-dependent co-localization of two fluorescent signals at a defined spot in the nucleus of mammalian cells.

With these assays we analyzed a set of newly developed stapled peptides as potent p53:Mdm2 and/ or p53:Mdm4 inhibitors. Live cell data generated by the F2H assays enabled us to discriminate and describe the peptides according to their ability to penetrate into the cells, their efficacy on the PPIs and their cytotoxic side effects in one single assay.

In parallel we performed a pilot F2H screen with a sub-set or 20 small molecule compounds (including Nutlin-3) that exhibited activity against one or both interactions at various potencies in ELISAs before. We could identify 5 potent compounds, which were dramatically reducing the number of p53:Mdm2 interactions. However, none of the small molecules, but only the stapled peptides exhibited an intracellular activity on p53:Mdm4. Furthermore, we were able to expand these assays and to identify mutants of Mdm2 resistant to Nutlin inhibition.

In summary, we show that the p53:Mdm2 and p53:Mdm4 F2H assays described here,

- enable side-by-side analysis of substances' dual Mdm2-Mdm4 activity

- are suitable for screening and testing various types of compounds, such as peptidic inhibitors or small molecules

- concurrently provide initial data on compound cell-permeability and cytotoxicity

- allow real-time visualization of PPI dynamics in living cells.

Citation Format: Larisa Yurlova, Christopher J. Brown, Maarten Derks, Farid John Ghadessy, Ian Hickson, David P. Lane, Eberhard Krausz, Kourosh Zolghadr. Disrupting p53:Mdm2 and p53:Mdm4 - Comparative cell-based assays for drug screening. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5386. doi:10.1158/1538-7445.AM2014-5386

Structure of a stapled peptide antagonist bound to nutlin-resistant Mdm2

As key negative regulator of the p53 tumour suppressor, Mdm2 is an attractive therapeutic target. Small molecules such as Nutlin have been developed to antagonise Mdm2, resulting in p53-dependent death of tumour cells. We have recently described a mutation in Mdm2 (M62A), which precludes binding of Nutlin, but not p53. This Nutlin-resistant variant is not, however, refractory to binding and inhibition by stapled peptide antagonists targeting the same region of Mdm2. A detailed understanding of how stapled peptides are recalcitrant to Mdm2 mutations conferring Nutlin-resistance will aid in the further development of potent Mdm2 antagonists. Here, we report the 2.00 Å crystal structure of a stapled peptide antagonist bound to Nutlin resistant Mdm2. The stapled peptide relies on an extended network of interactions along the hydrophobic binding cleft of Mdm2 for high affinity binding. Additionally, as seen in other stapled peptide structures, the hydrocarbon staple itself contributes to binding through favourable interactions with Mdm2. The structure highlights the intrinsic plasticity present in both Mdm2 and the hydrocarbon staple moiety, and can be used to guide future iterations of both small molecules and stapled peptides for improved antagonists of Mdm2.

Unintended cultivation, shifting baselines, and conflict between objectives for fisheries and conservation

The effects of fisheries on marine ecosystems, and their capacity to drive shifts in ecosystem states, have been widely documented. Less well appreciated is that some commercially valuable species respond positively to fishing-induced ecosystem change and can become important fisheries resources in modified ecosystems. Thus, the ecological effects of one fishery can unintentionally increase the abundance and productivity of other fished species (i.e., cultivate). We reviewed examples of this effect in the peer-reviewed literature. We found 2 underlying ecosystem drivers of the effect: trophic release of prey species when predators are overfished and habitat change. Key ecological, social, and economic conditions required for one fishery to unintentionally cultivate another include strong top-down control of prey by predators, the value of the new fishery, and the capacity of fishers to adapt to a new fishery. These unintended cultivation effects imply strong trade-offs between short-term fishery success and conservation efforts to restore ecosystems toward baseline conditions because goals for fisheries and conservation may be incompatible. Conflicts are likely to be exacerbated if fisheries baselines shift relative to conservation baselines and there is investment in the new fishery. However, in the long-term, restoration toward ecosystem baselines may often benefit both fishery and conservation goals. Unintended cultivation can be identified and predicted using a combination of time-series data, dietary studies, models of food webs, and socioeconomic data. Identifying unintended cultivation is necessary for management to set compatible goals for fisheries and conservation.

The fluorescent two-hybrid assay to screen for protein-protein interaction inhibitors in live cells: targeting the interaction of p53 with Mdm2 and Mdm4

Protein-protein interactions (PPIs) are attractive but challenging targets for drug discovery. To overcome numerous limitations of the currently available cell-based PPI assays, we have recently established a fully reversible microscopy-assisted fluorescent two-hybrid (F2H) assay. The F2H assay offers a fast and straightforward readout: an interaction-dependent co-localization of two distinguishable fluorescent signals at a defined spot in the nucleus of mammalian cells. We developed two reversible F2H assays for the interactions between the tumor suppressor p53 and its negative regulators, Mdm2 and Mdm4. We then performed a pilot F2H screen with a subset of compounds, including small molecules (such as Nutlin-3) and stapled peptides. We identified five cell-penetrating compounds as potent p53-Mdm2 inhibitors. However, none exhibited intracellular activity on p53-Mdm4. Live cell data generated by the F2H assays enable the characterization of stapled peptides based on their ability to penetrate cells and disrupt p53-Mdm2 interaction as well as p53-Mdm4 interaction. Here, we show that the F2H assays enable side-by-side analysis of substances' dual Mdm2-Mdm4 activity. In addition, they are suitable for testing various types of compounds (e.g., small molecules and peptidic inhibitors) and concurrently provide initial data on cellular toxicity. Furthermore, F2H assays readily allow real-time visualization of PPI dynamics in living cells.

Functionalised staple linkages for modulating the cellular activity of stapled peptides

A divergent synthetic strategy for generating helical p53 peptides bearing functionalised staple linkages, allowing for efficient optimisation of cellular activity.

Rational optimization of conformational effects induced by hydrocarbon staples in peptides and their binding interfaces

eIF4E is frequently over-expressed in different cancers and causes increased translation of oncogenic proteins via deregulated cap-dependent translation. Inhibitors of the eIF4E:eIF4G interactions represent an approach that would normalize cap-dependent translation. Stapled peptides represent an emerging class of therapeutics that can target protein: protein interactions. We present here molecular dynamics simulations for a set of rationally designed stapled peptides in solution and in complex with eIF4E, supported with biophysical and crystallographic data. Clustering of the simulated structures revealed the favoured conformational states of the stapled peptides in their bound or free forms in solution. Identifying these populations has allowed us to design peptides with improved affinities by introducing mutations into the peptide sequence to alter their conformational distributions. These studies emphasise the effects that engineered mutations have on the conformations of free and bound peptides, and illustrate that both states must be considered in efforts to attain high affinity binding.

EYA4 is inactivated biallelically at a high frequency in sporadic lung cancer and is associated with familial lung cancer risk

In an effort to identify novel biallelically inactivated tumor suppressor genes (TSG) in sporadic invasive and pre-invasive non-small cell lung cancer (NSCLC) genomes, we applied a comprehensive integrated multi-‘omics approach to investigate patient matched, paired NSCLC tumor and non-malignant parenchymal tissues. By surveying lung tumor genomes for genes concomitantly inactivated within individual tumors by multiple mechanisms, and by the frequency of disruption in tumors across multiple cohorts, we have identified a putative lung cancer TSG, Eyes Absent 4 (EYA4). EYA4 is frequently and concomitantly deleted, hypermethylated and underexpressed in multiple independent lung tumor data sets, in both major NSCLC subtypes, and in the earliest stages of lung cancer. We find not only that decreased EYA4 expression is associated with poor survival in sporadic lung cancers, but EYA4 SNPs are associated with increased familial cancer risk, consistent with EYA4’s proximity to the previously reported lung cancer susceptibility locus on 6q. Functionally, we find that EYA4 displays TSG-like properties with a role in modulating apoptosis and DNA repair. Cross examination of EYA4 expression across multiple tumor types suggests a cell type-specific tumorigenic role for EYA4, consistent with a tumor suppressor function in cancers of epithelial origin. This work shows a clear role for EYA4 as a putative TSG in NSCLC.