Toward molecular dissection of PrPC-PrPSc interactions

Direct interaction between endogenous cellular prion protein (PrP(C)) and misfolded, disease-associated (PrP(Sc)) conformers is a key event in prion propagation, which precedes templated conversion of PrP(C) into nascent PrP(Sc) and prion infectivity. Although almost none of the molecular details of this pivotal process are understood, the persistence of individual prion strains suggests that assembly of the prion replicative complex is mechanistically precise. To systematically map defined regions of PrP(C) sequence that bind tightly to PrP(Sc), we have generated a comprehensive panel of over 45 motif-grafted antibodies containing overlapping peptide grafts collectively spanning PrP residues 19-231. Grafted antibody binding experiments, performed under stringent conditions, clearly identified only three distinct and independent high affinity PrP(Sc) recognition motifs. The first of these binding motifs lies at the very N-terminal region of the mature PrP molecule within PrP-(23-33); the second motif lies within PrP-(98-110); and the third is contained within PrP-(136-158). Mutational analyses of these PrP(Sc)-binding regions revealed that reactivity of the 23-33 and 98-110 segments are largely dependent upon the presence of multiple positively charged amino acid residues. These studies yield new insight into critical peptidic components composing one side of the prion replicative interface.     

Identifying key factors using λ contribution analysis

1. Key factor analysis is widely used as the first step in analysing census data to identify factors responsible for population change, but is generally considered to be flawed. The conceptual problems can be overcome by assessing the effects of variation in the life-history parameters on population growth rate, λ. We refer to this as λ-contribution analysis. The difference from key factor analysis is that now each life history parameter is weighted by the sensitivity of λ to that parameter. The rationale for this modification is that population growth rate is the best available measure of population change.
2. The advantages of the new method are: that it correctly assesses the effects of life history parameters on population growth rate; that birth rates are included in the analysis in a natural way without making arbitrary assumptions about birth rate mortalities; that post-reproductive individuals who do not contribute to population growth rate are zero-weighted; and that the analysis can be applied to populations with overlapping generations.
3. It is proposed that λ-contribution analysis should replace conventional key-factor analysis as the first step in a wider analysis of population change and density dependence. λ-contribution analysis also links census studies of natural populations with the use of life-table response experiments.     

Identifying key cereal aphid predators by molecular gut analysis

We describe polymerase chain reaction (PCR) primers for gut analysis of aphid predators. The primers amplify aphid mitochondrial COII fragments ranging in size from 77 to 386 bp. Using these primers, we were able to distinguish six species of US Great Plains cereal aphids, including two congeners, Rhopalosiphum maidis (Fitch) and R. padi (L.), and to detect them in extracts of coccinellid and chrysopid predators. We devised a protocol for deriving half-lives of detectability for the DNA of a single aphid consumed by predators maintained under simulated field dietary and temperature conditions. Using this protocol and primers that amplify a 198-bp fragment, we determined statistically different half-lives of detectability for a single R. maidis of 3.95 h in Chrysoperla plorabunda (Fitch) and 8. 78 h in Hippodamia convergens Guerin. The detectability half-life for a 339-bp R. maidis fragment was statistically longer in C. plorabunda but not in H. convergens. The sensitivity of the assay for the 198-bp fragment is 10-7 aphid equivalents. For species-specific predator gut analysis, PCR is superior to monoclonal antibody technology, giving comparable detectability half-lives with lower expense, much shorter development times, and greater certainty of a successful outcome.     

Antimicrobial peptides: key components of the innate immune system

Life-threatening infectious diseases are on their way to cause a worldwide crisis, as treating them effectively is becoming increasingly difficult due to the emergence of antibiotic resistant strains. Antimicrobial peptides (AMPs) form an ancient type of innate immunity found universally in all living organisms, providing a principal first-line of defense against the invading pathogens. The unique diverse function and architecture of AMPs has attracted considerable attention by scientists, both in terms of understanding the basic biology of the innate immune system, and as a tool in the design of molecular templates for new anti-infective drugs. AMPs are gene-encoded short (<100 amino acids), amphipathic molecules with hydrophobic and cationic amino acids arranged spatially, which exhibit broad spectrum antimicrobial activity. AMPs have been the subject of natural evolution, as have the microbes, for hundreds of millions of years. Despite this long history of co-evolution, AMPs have not lost their ability to kill or inhibit the microbes totally, nor have the microbes learnt to avoid the lethal punch of AMPs. AMPs therefore have potential to provide an important breakthrough and form the basis for a new class of antibiotics. In this review, we would like to give an overview of cationic antimicrobial peptides, origin, structure, functions, and mode of action of AMPs, which are highly expressed and found in humans, as well as a brief discussion about widely abundant, well characterized AMPs in mammals, in addition to pharmaceutical aspects and the additional functions of AMPs.     

Antimicrobial peptides: key components of the innate immune system

Life-threatening infectious diseases are on their way to cause a worldwide crisis, as treating them effectively is becoming increasingly difficult due to the emergence of antibiotic resistant strains. Antimicrobial peptides (AMPs) form an ancient type of innate immunity found universally in all living organisms, providing a principal first-line of defense against the invading pathogens. The unique diverse function and architecture of AMPs has attracted considerable attention by scientists, both in terms of understanding the basic biology of the innate immune system, and as a tool in the design of molecular templates for new anti-infective drugs. AMPs are gene-encoded short (<100 amino acids), amphipathic molecules with hydrophobic and cationic amino acids arranged spatially, which exhibit broad spectrum antimicrobial activity. AMPs have been the subject of natural evolution, as have the microbes, for hundreds of millions of years. Despite this long history of co-evolution, AMPs have not lost their ability to kill or inhibit the microbes totally, nor have the microbes learnt to avoid the lethal punch of AMPs. AMPs therefore have potential to provide an important breakthrough and form the basis for a new class of antibiotics. In this review, we would like to give an overview of cationic antimicrobial peptides, origin, structure, functions, and mode of action of AMPs, which are highly expressed and found in humans, as well as a brief discussion about widely abundant, well characterized AMPs in mammals, in addition to pharmaceutical aspects and the additional functions of AMPs.     

Long-term nano-mechanical properties of biomodified dentin-resin interface components

Failures of dental composite restorative procedures are largely attributed to the degradation of dentin-resin interface components. Biomodification of dentin using bioactive agents may improve the quality and durability of the dentin-resin bonds. The aim of this study was to nanomechanically assess the reduced modulus of elasticity (Er) and nano-hardness (H) of major components of the dentin-resin interface (hybrid layer, adhesive layer and underlying dentin) biomodified by collagen cross-linkers at 24h, 3 and 6 months following restorative procedure. Demineralized dentin surfaces were biomodified with 5% glutaraldehyde (GD) or 6.5% grape seed extract (GSE) prior to placement of adhesive systems and composite resin. Nano-measurements of the interface components in a fluid cell showed that both agents increased the Er and H of underlying dentin after 3 and 6 months when compared to a control. The mechanical properties of the adhesive and hybrid layers decreased over time. Biomodification of the dentin-resin interface structures using GD and GSE can increase the mechanical properties of the interface over time and may contribute to the long-term quality of adhesive restorations.     

Identifying key biodiversity areas as marine conservation priorities in the greater Caribbean

Increasing rates of Anthropocene biodiversity extinctions suggest a possible sixth mass extinction event. Conservation planners are seeking effective ways to protect species, hotspots of biodiversity, and dynamic ecosystems to reduce and eventually eliminate the degradation and loss of diversity at the scale of genes, species, and ecosystems. While well-established, adequately enforced protected areas (PAs) increase the likelihood of preserving species and habitats, traditional placement methods are frequently inadequate in protecting biodiversity most at risk. Consequently, the Key Biodiversity Area (KBA) Partnership developed a set of science-based criteria and thresholds that iteratively identify sites where biodiversity is most in need of protection. KBA methodology has been rarely applied in the marine realm, where data are often extremely limited. We tested the feasibility of KBA population metrics in the Greater Caribbean marine region using occurrence and population data and threat statuses for 1669 marine vertebrates. These data identified areas where site-specific conservation measures can effectively protect biodiversity. Using KBA criteria pertaining to threatened and irreplaceable biodiversity, we identified 90 geographically unique potential KBAs, 34 outside and 56 within existing PAs. These provide starting points for local conservation managers to verify that KBA thresholds are met and to delineate site boundaries. Significant data gaps, such as population sizes, life history characteristics, and extent of habitats, prevent the full application of the KBA criteria to data-poor marine species. Increasing the rate and scope of marine sampling programs and digital availability of occurrence datasets will improve identification and delineation of KBAs in the marine environment.

     

Identifying key conservation sites for the reptiles of the Tandilia mountains in Pampas highlands

Reptile populations are facing a global decline as a consequence of anthropic disturbs. For its conservation, it is necessary to know its geographical distribution and the main factors influencing it. Tandilia Mountains are located in the centre of Buenos Aires province, Argentina. These mountains contain high biodiversity and several endemic species, but the current Natural Protected Areas network covers a low area of ​​0.12 %. In this work, we modelled the geographic distribution of reptiles in the Tandilia Mountains to: a) explore the environmental factors affecting the distribution of reptiles on the highland grasslands of the Tandilia Mountain System and (b) identify the key biodiversity areas. We used ten environmental variables and several sources of records (fieldwork, scientific literature, museum collections, and an online database) to model the distribution of each reptile species. The best sites to propose natural reserves were determined in Zonation software. We determined the representativeness of the current system of Natural Protected Areas in the Tandilia Mountain range by overlapping the sites with the Zonation results. We obtained 20 species distribution models with two general patterns: continuous and patched. In most species, the two most informative variables were growing degree-days below 0 °C and precipitation of the wettest quarter. The current system of Natural Protected Areas of the Tandilia Mountains covers 0.35 % of the conservation priority sites (4341 km²) and therefore is insufficient in protecting reptile biodiversity.     

Identifying key habitats for the conservation of Bonelli's Eagle Aquila fasciata using radiotracking

Identifying the priority habitats of endangered species is crucial to implementing effective conservation actions. We characterize the key habitats used by Bonelli's Eagle Aquila fasciata, an umbrella and flagship species that is endangered in Mediterranean countries. We radiotracked 17 breeding individuals (10 males and seven females) in Catalonia (NE Iberian Peninsula) and used compositional analysis to determine the key habitats in home‐ranges of both sexes. The main habitats identified within the home‐range area were scrubland, coniferous forests, cropland, sclerophyllous forests, rock outcrops and urban areas, with little difference in habitat use between the sexes. Bonelli's Eagles preferred rocky habitats as breeding areas and scrubland as foraging areas, as these hold the highest abundance of their main prey, Rabbits Oryctolagus cuniculus and Red‐legged Partridges Alectoris rufa. Habitat selection varied seasonally in foraging areas: scrubland was the most preferred habitat type during the breeding season, whereas rocky areas were preferred during the non‐breeding season (although scrubland was also highly selected). Urban areas were avoided both as breeding and as foraging areas. Home‐range size was inversely correlated with the proportion of scrubland, suggesting that this is a key habitat for Bonelli's Eagle. To conserve this species effectively, policies that ensure the preservation of the cliffs used as breeding sites, as well as suitable management of the scrubland used for foraging, should be implemented in the areas inhabited by this species. The promotion of traditional land uses and management techniques that will enhance open areas in Mediterranean landscapes should in the future play an essential role in the conservation of Bonelli's Eagle in Mediterranean habitats.     

Identifying signatures of sexual selection using genomewide selection components analysis

Sexual selection must affect the genome for it to have an evolutionary impact, yet signatures of selection remain elusive. Here we use an individual‐based model to investigate the utility of genome‐wide selection components analysis, which compares allele frequencies of individuals at different life history stages within a single population to detect selection without requiring a priori knowledge of traits under selection. We modeled a diploid, sexually reproducing population and introduced strong mate choice on a quantitative trait to simulate sexual selection. Genome‐wide allele frequencies in adults and offspring were compared using weighted F_ST values. The average number of outlier peaks (i.e., those with significantly large F_ST values) with a quantitative trait locus in close proximity (“real” peaks) represented correct diagnoses of loci under selection, whereas peaks above the F_ST significance threshold without a quantitative trait locus reflected spurious peaks. We found that, even with moderate sample sizes, signatures of strong sexual selection were detectable, but larger sample sizes improved detection rates. The model was better able to detect selection with more neutral markers, and when quantitative trait loci and neutral markers were distributed across multiple chromosomes. Although environmental variation decreased detection rates, the identification of real peaks nevertheless remained feasible. We also found that detection rates can be improved by sampling multiple populations experiencing similar selection regimes. In short, genome‐wide selection components analysis is a challenging but feasible approach for the identification of regions of the genome under selection.     

The effect of the interface on the bone stresses beneath tibial components

It was proposed that the stresses in the layer of bone immediately beneath a tibial component are an important determinant of fixation durability. Using finite element analysis, (ANSYS), the stresses were determined as a function of the amount of bone resection, the localization or completeness of implant-bone contact, and the interface material. The model was of two-dimensional sagittal slices consisting of quadrilateral elements (1 mm) with a range of seventeen material properties determined by CT scans. Typical prosthesis designs shifted the center of pressure more centrally rather than posteriorly, and thus increased anterior bone stresses. Resection up to 10 mm could actually decrease bone stresses due to an increase in bone surface area as long as complete coverage was obtained. A cement interface or direct metal on bone produced identical stresses. However a 1 mm complian: interface significantly reduced stresses in regions of high elastic modulus gradient. For rigid interfaces, the contact can be irregular, which leads to areas of over and understressing of bone. These conclusions have implications related to implant design.     

Identifying ontogenetic, environmental and individual components of forest tree growth

Background and Aims

This study aimed to identify and characterize the ontogenetic, environmental and individual components of forest tree growth. In the proposed approach, the tree growth data typically correspond to the retrospective measurement of annual shoot characteristics (e.g. length) along the trunk.

Methods

Dedicated statistical models (semi-Markov switching linear mixed models) were applied to data sets of Corsican pine and sessile oak. In the semi-Markov switching linear mixed models estimated from these data sets, the underlying semi-Markov chain represents both the succession of growth phases and their lengths, while the linear mixed models represent both the influence of climatic factors and the inter-individual heterogeneity within each growth phase.

Key Results

On the basis of these integrative statistical models, it is shown that growth phases are not only defined by average growth level but also by growth fluctuation amplitudes in response to climatic factors and inter-individual heterogeneity and that the individual tree status within the population may change between phases. Species plasticity affected the response to climatic factors while tree origin, sampling strategy and silvicultural interventions impacted inter-individual heterogeneity.

Conclusions

The transposition of the proposed integrative statistical modelling approach to cambial growth in relation to climatic factors and the study of the relationship between apical growth and cambial growth constitute the next steps in this research.     

Decidual NK cells regulate key developmental processes at the human fetal-maternal interface

Human CD56(bright) NK cells accumulate in the maternal decidua during pregnancy and are found in direct contact with fetal trophoblasts. Several mechanisms have been proposed to explain the inability of NK cells to kill the semiallogeneic fetal cells. However, the actual functions of decidual NK (dNK) cells during pregnancy are mostly unknown. Here we show that dNK cells, but not peripheral blood-derived NK subsets, regulate trophoblast invasion both in vitro and in vivo by production of the interleukin-8 and interferon-inducible protein-10 chemokines. Furthermore, dNK cells are potent secretors of an array of angiogenic factors and induce vascular growth in the decidua. Notably, such functions are regulated by specific interactions between dNK-activating and dNK-inhibitory receptors and their ligands, uniquely expressed at the fetal-maternal interface. The overall results support a 'peaceful' model for reproductive immunology, in which elements of innate immunity have been incorporated in a constructive manner to support reproductive tissue development.