Key challenges for the creation and maintenance of specialist protein resources

As the volume of data relating to proteins increases, researchers rely more and more on the analysis of published data, thus increasing the importance of good access to these data that vary from the supplemental material of individual articles, all the way to major reference databases with professional staff and long‐term funding. Specialist protein resources fill an important middle ground, providing interactive web interfaces to their databases for a focused topic or family of proteins, using specialized approaches that are not feasible in the major reference databases. Many are labors of love, run by a single lab with little or no dedicated funding and there are many challenges to building and maintaining them. This perspective arose from a meeting of several specialist protein resources and major reference databases held at the Wellcome Trust Genome Campus (Cambridge, UK) on August 11 and 12, 2014. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. In laying out these challenges, we aim to inform users about how these issues impact our resources and illustrate ways in which our working together could enhance their accuracy, currency, and overall value. Proteins 2015; 83:1005–1013. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

BREEDING SYSTEMS OF CENTRAL AMERICAN APHELANDRA (ACANTHACEAE)

Controlled pollinations, followed by germination studies of seeds resulting from self- and cross-pollination, were carried out using plants from 12 populations of nine species of Aphelandra (Acanthaceae), a genus of neotropical shrubs and herbs. These results are combined with data from field studies of flower morphology, phenology, and pollinator relationships to estimate breeding system of each species. All species have floral morphological traits that prevent autogamy. Plants from five populations of five species experience low levels of geitonogamous pollen transfer; they produce few flowers daily and are pollinated by traplining hummingbirds. Excepting A. storkii, these plants are fully self-compatible (SC), and seeds from selfing are as viable as crossed seeds. Aphelandra storkii is partially self-incompatible (SI) and produces seeds from selfing that tend to germinate less successfully than crossed seeds. Plants from the remaining populations are profusely flowering shrubs, and even those pollinated by traplining hummingbirds should experience higher levels of geitonogamy. Aphelandra deppeana is pollinated by territorial hummingbirds, which should further increase the incidence of geitonogamy. All shrub species are partially SI, and two species (A. leonardii and A. sinclairiana) show significant reduced germination of selfed vs. crossed seeds. The breeding system of these species is thus modified by postpollination factors that favor the formation and maturation of outcrossed seeds. It is suggested that Aphelandra species, like other herbs and shrubs of tropical forest understory, possess a combination of breeding system traits that promote outcrossing but do not exclude geitonogamy.     

The dynamics of coupled populations subject to control

The dynamics of coupled populations have mostly been studied in the context of metapopulation viability with application to, for example, species at risk. However, when considering pests and pathogens, eradication, not persistence, is often the end goal. Humans may intervene to control nuisance populations, resulting in reciprocal interactions between the human and natural systems that can lead to unexpected dynamics. The incidence of these human-natural couplings has been increasing, hastening the need to better understand the emergent properties of such systems in order to predict and manage outbreaks of pests and pathogens. For example, the success of the growing aquaculture industry depends on our ability to manage pathogens and maintain a healthy environment for farmed and wild fish. We developed a model for the dynamics of connected populations subject to control, motivated by sea louse parasites that can disperse among salmon farms. The model includes exponential population growth with a forced decline when populations reach a threshold, representing control interventions. Coupling two populations with equal growth rates resulted in phase locking or synchrony in their dynamics. Populations with different growth rates had different periods of oscillation, leading to quasiperiodic dynamics when coupled. Adding small amounts of stochasticity destabilized quasiperiodic cycles to chaos, while stochasticity was damped for periodic or stable dynamics. Our analysis suggests that strict treatment thresholds, although well intended, can complicate parasite dynamics and hinder control efforts. Synchronizing populations via coordinated management among farms leads to more effective control that is required less frequently. Our model is simple and generally applicable to other systems where dispersal affects the management of pests and pathogens.     

Crystal Structures of α-Crystallin Domain Dimers of αB-Crystallin and Hsp20

Small heat shock proteins (sHsps) are a family of large and dynamic oligomers highly expressed in long-lived cells of muscle, lens and brain. Several family members are upregulated during stress, and some are strongly cytoprotective. Their polydispersity has hindered high-resolution structure analyses, particularly for vertebrate sHsps. Here, crystal structures of excised α-crystallin domain from rat Hsp20 and that from human αB-crystallin show that they form homodimers with a shared groove at the interface by extending a β sheet. However, the two dimers differ in the register of their interfaces. The dimers have empty pockets that in large assemblies will likely be filled by hydrophobic sequence motifs from partner chains. In the Hsp20 dimer, the shared groove is partially filled by peptide in polyproline II conformation. Structural homology with other sHsp crystal structures indicates that in full-length chains the groove is likely filled by an N-terminal extension. Inside the groove is a symmetry-related functionally important arginine that is mutated, or its equivalent, in family members in a range of neuromuscular diseases and cataract. Analyses of residues within the groove of the αB-crystallin interface show that it has a high density of positive charges. The disease mutant R120G α-crystallin domain dimer was found to be more stable at acidic pH, suggesting that the mutation affects the normal dynamics of sHsp assembly. The structures provide a starting point for modelling higher assembly by defining the spatial locations of grooves and pockets in a basic dimeric assembly unit. The structures provide a high-resolution view of a candidate functional state of an sHsp that could bind non-native client proteins or specific components from cytoprotective pathways. The empty pockets and groove provide a starting model for designing drugs to inhibit those sHsps that have a negative effect on cancer treatment.     

Effects of chemical and botanical insecticides used for locust control on Metarhizium anisopliae var. acridum conidia after short- to medium-term storage at 30°C

The short- to medium-term viability and growth of Metarhizium anisopliae var. acridum conidia were investigated when combined with six insecticides, at three different concentrations. All of the insecticides used in this study were suitable for immediate spraying with M. anisopliae var. acridum conidia except for fenitrothion. Fipronil, teflubenzuron, and fenitrothion formulations significantly reduced conidial viability over time. The 10% teflubenzuron treatment caused loss of viability relatively quickly with 9.9% germination after 28 days. Mycelial growth was affected by all the treatments except fenitrothion.     

Scat DNA provides important data for effective monitoring of mammal and bird biodiversity

Despite the roles they play in ecosystem function, animals have have long been neglected in the monitoring of ecological restoration. Vertebrate surveys can be time consuming and costly, often requiring multiple methodologies and taxonomic expertise, making comprehensive monitoring cost prohibitive. Here, we evaluate a new method of assessing mammal and bird diversity through the genetic identification of scat collections. Using DNA metabarcoding of scat collections from three bioregions, we generated bird and mammalian assemblage data and distinguished between sites with different restoration histories. However, scat detectability was affected by environmental conditions (e.g. rainfall and vegetative cover), suggesting that our approach is most applicable at certain times of year or in arid (or semi-arid) environments with rocky soils, where conditions are favourable for scat preservation. Taken together these data provide a pathway to: plan, monitor and establish best-practice when restoring landscapes and add to the growing body of literature on the value of DNA metabarcoding in biomonitoring applications.