Application of in silico and in vitro methods in the development of adverse outcome pathway constructs in wildlife

There is a long history of using both in silico and in vitro methods to predict adverse effects in humans and environmental species where toxicity data are lacking. Currently, there is a great deal of interest in applying these methods to the development of so-called ‘adverse outcome pathway’ (AOP) constructs. The AOP approach provides a framework for organizing information at the chemical and biological level, allowing evidence from both in silico and in vitro studies to be rationally combined to fill gaps in knowledge concerning toxicological events. Fundamental to this new paradigm is a greater understanding of the mechanisms of toxicity and, in particular, where these mechanisms may be conserved across taxa, such as between model animals and related wild species. This presents an opportunity to make predictions across diverse species, where empirical data are unlikely to become available as is the case for most species of wildlife.     

Genetic risk score analysis indicates migraine with and without comorbid depression are genetically different disorders

Migraine and major depressive disorder (MDD) are comorbid, moderately heritable and to some extent influenced by the same genes. In a previous paper, we suggested the possibility of causality (one trait causing the other) underlying this comorbidity. We present a new application of polygenic (genetic risk) score analysis to investigate the mechanisms underlying the genetic overlap of migraine and MDD. Genetic risk scores were constructed based on data from two discovery samples in which genome-wide association analyses (GWA) were performed for migraine and MDD, respectively. The Australian Twin Migraine GWA study (N = 6,350) included 2,825 migraine cases and 3,525 controls, 805 of whom met the diagnostic criteria for MDD. The RADIANT GWA study (N = 3,230) included 1,636 MDD cases and 1,594 controls. Genetic risk scores for migraine and for MDD were used to predict pure and comorbid forms of migraine and MDD in an independent Dutch target sample (NTR–NESDA, N = 2,966), which included 1,476 MDD cases and 1,058 migraine cases (723 of these individuals had both disorders concurrently). The observed patterns of prediction suggest that the ‘pure’ forms of migraine and MDD are genetically distinct disorders. The subgroup of individuals with comorbid MDD and migraine were genetically most similar to MDD patients. These results indicate that in at least a subset of migraine patients with MDD, migraine may be a symptom or consequence of MDD.     

Environmental Predictors of Ice Seal Presence in the Bering Sea

Ice seals overwintering in the Bering Sea are challenged with foraging, finding mates, and maintaining breathing holes in a dark and ice covered environment. Due to the difficulty of studying these species in their natural environment, very little is known about how the seals navigate under ice. Here we identify specific environmental parameters, including components of the ambient background sound, that are predictive of ice seal presence in the Bering Sea. Multi-year mooring deployments provided synoptic time series of acoustic and oceanographic parameters from which environmental parameters predictive of species presence were identified through a series of mixed models. Ice cover and 10 kHz sound level were significant predictors of seal presence, with 40 kHz sound and prey presence (combined with ice cover) as potential predictors as well. Ice seal presence showed a strong positive correlation with ice cover and a negative association with 10 kHz environmental sound. On average, there was a 20–30 dB difference between sound levels during solid ice conditions compared to open water or melting conditions, providing a salient acoustic gradient between open water and solid ice conditions by which ice seals could orient. By constantly assessing the acoustic environment associated with the seasonal ice movement in the Bering Sea, it is possible that ice seals could utilize aspects of the soundscape to gauge their safe distance to open water or the ice edge by orienting in the direction of higher sound levels indicative of open water, especially in the frequency range above 1 kHz. In rapidly changing Arctic and sub-Arctic environments, the seasonal ice conditions and soundscapes are likely to change which may impact the ability of animals using ice presence and cues to successfully function during the winter breeding season.     

Sequence and Conformational Specificity in Substrate Recognition: SEVERAL HUMAN KUNITZ PROTEASE INHIBITOR DOMAINS ARE SPECIFIC SUBSTRATES OF MESOTRYPSIN*

Mesotrypsin is an isoform of trypsin that is uniquely resistant to polypeptide trypsin inhibitors and can cleave some inhibitors rapidly. Previous studies have shown that the amyloid precursor protein Kunitz protease inhibitor domain (APPI) is a specific substrate of mesotrypsin and that stabilization of the APPI cleavage site in a canonical conformation contributes to recognition by mesotrypsin. We hypothesized that other proteins possessing potential cleavage sites stabilized in a similar conformation might also be mesotrypsin substrates. Here we evaluated a series of candidate substrates, including human Kunitz protease inhibitor domains from amyloid precursor-like protein 2 (APLP2), bikunin, hepatocyte growth factor activator inhibitor type 2 (HAI2), tissue factor pathway inhibitor-1 (TFPI1), and tissue factor pathway inhibitor-2 (TFPI2), as well as E-selectin, an unrelated protein possessing a potential cleavage site displaying canonical conformation. We find that Kunitz domains within APLP2, bikunin, and HAI2 are cleaved by mesotrypsin with kinetic profiles of specific substrates. TFPI1 and TFPI2 Kunitz domains are cleaved less efficiently by mesotrypsin, and E-selectin is not cleaved at the anticipated site. Cocrystal structures of mesotrypsin with HAI2 and bikunin Kunitz domains reveal the mode of mesotrypsin interaction with its canonical substrates. Our data suggest that major determinants of mesotrypsin substrate specificity include sequence preferences at the P₁ and P′₂ positions along with conformational stabilization of the cleavage site in the canonical conformation. Mesotrypsin up-regulation has been implicated previously in cancer progression, and proteolytic clearance of Kunitz protease inhibitors offers potential mechanisms by which mesotrypsin may mediate pathological effects in cancer.     

The effects of released pheasants on invertebrate populations in and around woodland release sites

The release of gamebirds for recreational shooting exerts a series of effects on the ecosystems into which they are placed. Pheasants (Phasianus colchicus) are omnivorous and eat invertebrates, especially when young or, if females, when breeding. Consequently, the release of large numbers of pheasants into woodland release pens may affect local invertebrate populations. Previous studies have reported mixed evidence. We conducted pitfall trapping at 13 sites (49 pens) in central England over 2 years (totaling 65 pen measures), comprising three surveys annually, immediately prior to releases in mid‐summer, 4 weeks later when most birds were still in the pens, and another 5 weeks later when most birds had dispersed. We compared traps inside and 25 m outside pens in the same wood. We considered release densities and whether the birds had prior experience of eating invertebrates. While accounting for overall seasonal declines in invertebrates trapped, we detected changes for total invertebrate biomass and total counts indicative of released pheasants causing local decreases inside pens, either directly by predation or indirectly by modifying vegetation. There were also relative decreases outside pens when the pheasants start to disperse, suggesting that the released pheasants may be affecting invertebrates in those nearby areas or that their earlier effects inside the pen, modifying vegetation or increasing invertebrate activity, increased the relative susceptibility of invertebrates there to trapping. However, these effects were not seen for specific invertebrate groups believed to be especially susceptible to pheasants. For slugs and detritivores, we detected small population increases inside pens. Across the study period, decreases for most measures were greater outside pens than inside them. We conclude that any effects pheasants have on invertebrate communities at release sites in woodlands are complex and that long‐term and taxon‐specific studies should be considered to understand the local net ecological effects of gamebird releases on invertebrates.     

Accuracy in the prediction of disease epidemics when ensembling simple but highly correlated models

Ensembling combines the predictions made by individual component base models with the goal of achieving a predictive accuracy that is better than that of any one of the constituent member models. Diversity among the base models in terms of predictions is a crucial criterion in ensembling. However, there are practical instances when the available base models produce highly correlated predictions, because they may have been developed within the same research group or may have been built from the same underlying algorithm. We investigated, via a case study on Fusarium head blight (FHB) on wheat in the U.S., whether ensembles of simple yet highly correlated models for predicting the risk of FHB epidemics, all generated from logistic regression, provided any benefit to predictive performance, despite relatively low levels of base model diversity. Three ensembling methods were explored: soft voting, weighted averaging of smaller subsets of the base models, and penalized regression as a stacking algorithm. Soft voting and weighted model averages were generally better at classification than the base models, though not universally so. The performances of stacked regressions were superior to those of the other two ensembling methods we analyzed in this study. Ensembling simple yet correlated models is computationally feasible and is therefore worth pursuing for models of epidemic risk.     

Controlled destabilization of a liposomal drug delivery system enhances mitoxantrone antitumor activity.

Programmable fusogenic vesicles (PFVs) are lipid-based drug-delivery systems that exhibit time-dependent destabilization. The rate at which this destabilization occurs is determined by the exchange rate of a bilayer-stabilizing component, polyethylene glycol-phosphatidylethanolamine (PEG-PE) from the vesicle surface. This exchange rate is controlled, in turn, by the acyl chain composition of the PEG-PE. We describe in vitro and in vivo studies using PFVs as delivery vehicles for the anticancer drug mitoxantrone. We demonstrate that the PEG-PE acyl composition determined the rate at which PFVs are eliminated from plasma after intravenous administration, and the rate of mitoxantrone leakage from PFV. The nature of the PEG-PE component also determined the antitumor efficacy of mitoxantrone-loaded PFV in murine and human in murine and human xenograft tumor models. Increased circulation time and improved activity were obtained for PFV containing PEG-PE with an 18-carbon acyl chain length, as a result of slower vesicle destabilization.     

The ubiquitous nature of the progesterone receptor binding factor-1 (RBF-1) in avian tissues

The avian oviduct receptor binding factor-1 (RBF-1) is a 10 kDa nuclear matrix protein that was originally identified through its ability to effect high affinity interaction of activated progesterone receptor (PR) with chromatin. In the present study, the RBF-1 is shown to not be restricted to reproductive tissues (e.g., oviduct) but present in all avian tissues examined by Western blot analysis with a monoclonal antibody prepared against purified RBF-1. The heart and pancreas had the highest and lowest RBF-1 levels, respectively; the concentration ranging by ～ 50-fold in these tissues. The 10 kDa size of the RBF-1 detected in all tissues suggests no significant tissue-specific differences in the protein. This was consistent with the finding that purified hepatic and oviductal RBF-1 have identical amino-terminal sequence. Using a recently isolated cDNA to RBF-1, the levels of RBF-1 mRNA were found to correlate well with the ubiquitous presence of the protein as well as tissue-specific differences in concentration. The presence of RBF-1 in non-progesterone responsive tissues suggests the possibility that RBF-1 may not be specifically involved in PR-DNA interactions but may play a more diverse role, possibly involving other steroid receptors such as the glucocorticoid receptor. © 1994 Wiley-Liss, Inc.