Energy Landscapes of Protein Aggregation and Conformation Switching in Intrinsically Disordered Proteins

The protein folding problem was apparently solved recently by the advent of a deep learning method for protein structure prediction called AlphaFold. However, this program is not able to make predictions about the protein folding pathways. Moreover, it only treats about half of the human proteome, as the remaining proteins are intrinsically disordered or contain disordered regions. By definition these proteins differ from natively folded proteins and do not adopt a properly folded structure in solution. However these intrinsically disordered proteins (IDPs) also systematically differ in amino acid composition and uniquely often become folded upon binding to an interaction partner. These factors preclude solving IDP structures by current machine-learning methods like AlphaFold, which also cannot solve the protein aggregation problem, since this meta-folding process can give rise to different aggregate sizes and structures. An alternative computational method is provided by molecular dynamics simulations that already successfully explored the energy landscapes of IDP conformational switching and protein aggregation in multiple cases. These energy landscapes are very different from those of ‘simple’ protein folding, where one energy funnel leads to a unique protein structure. Instead, the energy landscapes of IDP conformational switching and protein aggregation feature a number of minima for different competing low-energy structures. In this review, I discuss the characteristics of these multifunneled energy landscapes in detail, illustrated by molecular dynamics simulations that elucidated the underlying conformational transitions and aggregation processes.     

The nutritional value of feeding on crops: Diets of vervet monkeys in a humanized landscape

Anthropogenic influences have dramatically altered the environments with which primates interact. In particular, the introduction of anthropogenic food sources to primate groups has implications for feeding behaviour, social behaviour, activity budgets, demography and life history. While the incorporation of anthropogenic foods can be beneficial to primates in a variety of nutritional ways including increased energetic return, they also carry risks associated with proximity to humans, such as risk of being hunted, disease risk and risk of conflict. Given such risks, we initiated a 3‐year study where we sought to understand the underlying nutritional motivations for anthropogenic food resource use by vervet monkeys (Cercopithecus aethiops) in the humanized matrix surrounding the Nabugabo Field Station in central Uganda. Feeding effort, defined as proportion of feeding scans spent on anthropogenic food, was not associated with ripe fruit availability nor with crop availability as determined by phenological monitoring. Likewise, there was no difference in the protein, fibre, or lipid composition of crop food items compared to wild food items. Individuals spent less time feeding overall in months over the 3 years with a higher proportion of time spent feeding on crop foods, suggesting a potential benefit in terms of accessibility (reduction in the proportion of activity budget devoted to feeding).     

Fragrep： An Efficient Search Tool for Fragmented Patterns in Genomic Sequences

Many classes of non-coding RNAs （ncRNAs; including Y RNAs, vault RNAs, RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum） can be characterized by a pattern of short but well-conserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detecting the pattern fragments that occur in a given order. For each pattern fragment, the mismatch tolerance and bounds on the length of the intervening sequences can be specified separately. Furthermore, matches can be ranked by a statistically well-motivated scoring scheme.     

Speciation and the neutral theory of biodiversity

The neutral theory of biodiversity purports that patterns in the distribution and abundance of species do not depend on adaptive differences between species (i.e. niche differentiation) but solely on random fluctuations in population size (“ecological drift”), along with dispersal and speciation. In this framework, the ultimate driver of biodiversity is speciation. However, the original neutral theory made strongly simplifying assumptions about the mechanisms of speciation, which has led to some clearly unrealistic predictions. In response, several recent studies have combined neutral community models with more elaborate speciation models. These efforts have alleviated some of the problems of the earlier approaches, while confirming the general ability of neutral theory to predict empirical patterns of biodiversity. However, the models also show that the mode of speciation can have a strong impact on relative species abundances. Future work should compare these results to diversity patterns arising from non‐neutral modes of speciation, such as adaptive radiations.     

Insights into wolf presence in human‐dominated landscapes: the relative role of food availability,humans and landscape attributes

Aim Understanding which human or environmental factors interact to enable or to limit the occurrence and persistence of large carnivores in human‐dominated landscapes is an important issue for their effective conservation, especially under the current scenario of global change where most of their former habitat is being transformed by humans. Location NW Iberian Peninsula. Methods We combine data on the distribution of Iberian wolves (Canis lupus signatus) living in a human‐dominated landscape in NW Spain and variation and partitioning methods to investigate the relative importance of three groups of predictors: food availability, humans and landscape attributes – each group expected to have unequal effects on wolf reproduction and survival – and their interactions on the occurrence of this species. Results We found that the group of predictors related with landscape attributes (altitude, roughness and refuge) strongly determined wolf occurrence, followed by humans and food availability. Variance partitioning analysis revealed that the three most important components determining wolf occurrence were related with landscape attributes: (1) the joint effects of the three predictor groups, (2) the joint effect of humans and landscape attributes and (3) the pure effect of landscape attributes. Altitude had the main independent contribution to explain the probability of wolf occurrence. Main conclusions In human‐dominated landscapes, the occurrence of wolves is the result of a complex interaction among several environmental and human factors. Our results suggest that the characteristics of the landscape (spatial context) – factors associated with the security of wolves facilitating that animals go unnoticed by humans, wolf movements, dispersal events and short‐time colonization – become more important in human‐dominated landscapes and may have played a key role in the occurrence and persistence of this species throughout decades modulating the relationship between humans and wolf distribution.     

Environmental influences on and antimicrobial activity of the skin microbiota of Proceratophrys boiei (Amphibia,Anura) across forest fragments

The composition of the skin microbiota of amphibians is related to the biology of host species and environmental microbial communities. In this system, the environment serves as a microbial source and can modulate the hosted community. When habitats are fragmented and the environment disturbed, changes in the structure of this microbial community are expected. One important potential consequence of fragmentation is a compromised protective function of the microbiota against pathogenic microorganisms. In this study, the skin microbiota of the amphibian Proceratophrys boiei was characterized, evaluated for relationships with environmental variables and environmental sources of microbial communities, and its diversity evaluated for frog populations from fragmented and continuous forests. In addition, the antimicrobial activity of this skin community was studied in frogs from both forest types. Culture methods and 16S rRNA high‐throughput gene sequencing were used to characterize the microbial community and demonstrated that the skin microbiota of P. boiei is more closely related to the soil microbial communities than those inhabiting water bodies or fragment matrix, the unforested area around the forested fragment. The microbial diversity and abundance of P. boiei skin microbiota are different between continuous forests and fragments. This community is correlated with environmental variables, especially with temperature of microhabitat and distance to human dwelling. All individuals of P. boiei harbored bacteria capable of inhibiting the growth of pathogenic bacteria and different strains of the pathogenic fungus Batrachochytrium dendrobatidis, and a total of 27 bacterial genera were detected. The results of this study indicate that the persistence of populations of this species will need balanced and sustained interactions among host, microorganisms, and environment.     

The late Holocene palaeoecological sequence of Serranía de las Villuercas (southern Meseta,western Spain)

New pollen results and radiocarbon dating from a valley mire in south-western Spain are presented. This is a region where few palaeoecological records have been preserved and the sequence yields important new palaeobotanical evidence for the late Holocene. The landscape is shown as having been largely open woodland, but more wooded than at present. The vegetation history of the last four millennia in these montane territories of south-western Iberia is discussed in the light of anthropogenic indicators, archaeological and documentary archives; fire incidence and climate change. Alnus is the predominant pollen type, although a decline is noted during the last couple of centuries. Its presence is connected with local topography behaving as a phreatophyte, that is, a plant which obtains a significant amount of water from the zone of saturated soil. A framework is also provided for the age and ecological dynamics of some major woodland taxa—Betula, Corylus, Ilex, evergreen and deciduous oaks, Ericaceae and Pinus. In addition, the natural status of several pollen taxa and local trends in biodiversity are discussed. We consider that the results of our work will have important implications for the understanding of the vegetation history in a floristically very rich area, with a noticeable diversity of woody taxa, and a relatively well preserved ecosystem structure.     

Canopy Openness Enhances Diversity of Ant–Plant Interactions in the Brazilian Amazon Rain Forest

In closed‐canopy tropical forest understory, light availability is a significant determinant of habitat diversity because canopy structure is highly variable in most tropical forests. Consequently, variation in canopy cover affects the composition and distribution of plant species via creating variable light environments. Nevertheless, little is known about how variation in canopy openness structures patterns of plant–animal interactions. Because of the great diversity and dominance of ants in tropical environments, we used ant–plant interactions as a focal network to evaluate how variation in canopy cover influences patterns of plant–insect interactions in the Brazilian Amazon rain forest. We observed that small increases in canopy openness are associated with increased diversity of ant–plant interactions in our study area, and this change is independent of plant or ant species richness. Additionally, we found smaller niche overlap for both ants and plants associated with greater canopy openness. We hypothesize that enhanced light availability increases the breadth of ant foraging sources because variation in light availability gives rise to plant resources of different quality and amounts. Moreover, greater light availability promotes vegetative growth in plants, creating ant foraging ‘bridges’ between plants. In sum, our results highlight the importance of environmental heterogeneity as a determinant of ant–plant interaction diversity in tropical environments.     

Genetic variation and hybridization in SwedishSchoenus (Cyperaceae)

Schoenus ferrugineus andS. nigricans have restricted distributions in Sweden and are almost exclusively confined to calcareous fen habitats. AtS. nigricans sites,S. ferrugineus is usually also present, and hybrids are frequently found. In this report, I used allozymes to estimate the amount of gene flow between the two species, and to compare the partitioning of genetic diversity in each of them. Thirteen loci were analysed at eight different enzyme systems. Seven loci were variable between or within the species. The two species had completely different alleles at two of the seven variable loci, whereas there was overlap at five loci. In all, 22 different alleles were found. Six of these alleles were confined toS. nigricans, and five alleles were confined toS. ferrugineus. Nei's genetic identity was 0.55.—InS. ferrugineus, three loci (23%) were polymorphic, and the average number of alleles per polymorphic locus was 2.0 (each polymorphic locus had two alleles). InS. nigricans, three loci (23%) were polymorphic, and the average number of alleles per polymorphic locus was 2.3.—The proportion of genetic diversity due to variation among sites (G _ST) was fairly similar in the two species, mean over loci = 0.12 inS. ferrugineus and 0.15 inS. nigricans. However, the proportion of genetic diversity due to variation among individuals within sites (G _IS) differed markedly between the two species, mean over loci = 0.54 inS. ferrugineus and 0.17 inS. nigricans. Accordingly, there was a much higher individual heterozygosity inS. nigricans than inS. ferrugineus. — Most hybrids were interpreted as F₁ hybrids. However, a small proportion, 0.5–1.6 %, were F_n hybrids or back-crosses.—On the Swedish mainland, all former occurrences ofS. nigricans are extinct, but viable hybrids are still present at a few sites in southernmost Sweden.