Computational basis of knowledge-based conformational probabilities derived from local- and long-range interactions in proteins

The probabilities of the various basins in Ramachandran maps are examined critically. The theoretical basis of probability calculations both from molecular computations and from protein libraries are discussed. The well-defined basins of the Ramachandran maps are treated as rotational isomeric states. Statistical independence and dependence of the states of different residues along the peptide chain are discussed. The Flory isolated pair hypothesis, near neighbor correlations, context effects, and long-range correlations are examined critically. A method of evaluating long-range correlations in helical and extended sequences is introduced in analogy with earlier polymer theory. Three different protein libraries are constructed where data is considered from residues in the (i) coiled regions, (ii) all regions, and (iii) only the helical and extended regions of proteins. Singlet and pairwise dependent probabilities calculated from these libraries are used to predict whether a given sequence is helical or extended. Predictions using pairwise dependence were not better than those using singlet probabilities. Modeling of long-range correlations improved the predictions significantly. Removal of the Chameleon sequences from the data set also improved the predictions, but to a lesser extent.     

Influence of upwelling on the sedimentation and biota of the segmented margin of the western Neotethys: a case study from the Middle Triassic of the Balaton Highland (Hungary)

In the Middle Anisian, extensional tectonic movements led to the development of a small isolated carbonate platform in the middle part of the Balaton Highland, Transdanubian Range, Hungary. In the Late Illyrian, a condensed pelagic carbonate succession with phosphorite horizons was formed on the top of the already drowned platform. These strata contain an extraordinarily diverse ammonite fauna. This unit is overlain by radiolarian-rich carbonates, locally with radiolarite interbeds. We suggest that the drowning process and the post-drowning sediment deposition were controlled partly by regional factors, i.e., the onset of opening of the Neotethys Ocean, and partly by local factors such as the bottom topography and related current activity, which may also be connected with the opening of the ocean. The predominance of the radiolarian-rich sediments suggests eutrophic surface water, which may be explained by a monsoon-driven upwelling model. The segmented sea-floor topography together with the high-fertility surface water conditions may have provided favorable habitats for the ammonites, which may have adapted to various ecological conditions, leading to extreme diversification of this group. Since similar Middle to Late Anisian evolution was reported from many other units of the western Neotethys margin, regional factors such as the establishment of an extensional tectonic regime and related marginal basin formation, monsoon-driven upwelling, and related high surface water productivity seem to be of critical importance in controlling the depositional conditions.     

The AAA+ ATPase TRIP13 remodels HORMA domains through N‐terminal engagement and unfolding

Proteins of the conserved HORMA domain family, including the spindle assembly checkpoint protein MAD2 and the meiotic HORMADs, assemble into signaling complexes by binding short peptides termed “closure motifs”. The AAA+ ATPase TRIP13 regulates both MAD2 and meiotic HORMADs by disassembling these HORMA domain–closure motif complexes, but its mechanisms of substrate recognition and remodeling are unknown. Here, we combine X‐ray crystallography and crosslinking mass spectrometry to outline how TRIP13 recognizes MAD2 with the help of the adapter protein p31^comet. We show that p31^comet binding to the TRIP13 N‐terminal domain positions the disordered MAD2 N‐terminus for engagement by the TRIP13 “pore loops”, which then unfold MAD2 in the presence of ATP. N‐terminal truncation of MAD2 renders it refractory to TRIP13 action in vitro, and in cells causes spindle assembly checkpoint defects consistent with loss of TRIP13 function. Similar truncation of HORMAD1 in mouse spermatocytes compromises its TRIP13‐mediated removal from meiotic chromosomes, highlighting a conserved mechanism for recognition and disassembly of HORMA domain–closure motif complexes by TRIP13.     

Holocene mammal extinctions in the Carpathian Basin: a review

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Metacommunity dynamics of amphibians in years with differing rainfall

Many studies investigated the habitat preference and behaviour ecology of individual amphibian species while we know less about how their community assembly reflects changes in environmental factors, including the role of climatic extremes. Community-level studies also allow us to apply trait-based analyses that are crucial for a better understanding of the functioning of amphibian communities and metacommunities. In two years with contrasting rainfall (2012 and 2013), we found amphibian species in 85 different waterbodies of a heterogeneous landscape in Central Europe (Hungary). Within the metacommunity framework, the contributions of local, landscape and spatial variables to community assembly were assessed. We also measured the local extinction–colonisation rates in the ponds for all species between the two years. To investigate the role of dispersal traits in explaining the spatial distribution of species, we studied the relationship between body size and the pure spatial fraction of variation. According to our results, the main drivers were the same in both the dry and wet year, but their relative contribution changed. Local variables played a predominant role in the assembly of the amphibian metacommunity. Spatial signals were more evident in the dry year. This implies not only the adverse effect of decreased connectivity due to the drying out of several habitats but also a loss of breeding sites for the studied amphibians. Local colonisation rates were higher in primarily terrestrial species (Hyla arborea, Pelobates fuscus, Bufo bufo) which only visit ponds during breeding. We found a negative relationship between the pure spatial effect and body size, suggesting an increased level of dispersal limitation in small-bodied species. Our results showed that while the strength and relative role of local and spatial processes changed between years, the role of dispersal traits in explaining the spatial distribution of species was similar. Specialisation to different habitats seems to be a major process in determining vertebrate metacommunities in landscapes. Dispersal traits of different species should be taken more into consideration in the practical conservation of amphibian habitats.     

The enigmatic meiotic dense body and its newly discovered component,SCML1, are dispensable for fertility and gametogenesis in mice

Meiosis is a critical phase in the life cycle of sexually reproducing organisms. Chromosome numbers are halved during meiosis, which requires meiosis-specific modification of chromosome behaviour. Furthermore, suppression of transposons is particularly important during meiosis to allow the transmission of undamaged genomic information between generations. Correspondingly, specialized genome defence mechanisms and nuclear structures characterize the germ line during meiosis. Survival of mammalian spermatocytes requires that the sex chromosomes form a distinct silenced chromatin domain, called the sex body. An enigmatic spherical DNA-negative structure, called the meiotic dense body, forms in association with the sex body. The dense body contains small non-coding RNAs including microRNAs and PIWI-associated RNAs. These observations gave rise to speculations that the dense body may be involved in sex body formation and or small non-coding RNA functions, e.g. the silencing of transposons. Nevertheless, the function of the dense body has remained mysterious because no protein essential for dense body formation has been reported yet. We discovered that the polycomb-related sex comb on midleg-like 1 (SCML1) is a meiosis-specific protein and is an essential component of the meiotic dense body. Despite abolished dense body formation, Scml1-deficient mice are fertile and proficient in sex body formation, transposon silencing and in timely progression through meiosis and gametogenesis. Thus, we conclude that dense body formation is not an essential component of the gametogenetic program in the mammalian germ line.     

Differential signal sensitivities can contribute to the stability of multispecies bacterial communities

Background

Bacterial species present in multispecies microbial communities often react to the same chemical signal but at vastly different concentrations. The existence of different response thresholds with respect to the same signal molecule has been well documented in quorum sensing which is one of the best studied inter-cellular signalling mechanisms in bacteria. The biological significance of this phenomenon is still poorly understood, and cannot be easily studied in nature or in laboratory models. The aim of this study is to establish the role of differential signal response thresholds in stabilizing microbial communities.

Results

We tested binary competition scenarios using an agent-based model in which competing bacteria had different response levels with respect to signals, cooperation factors or both, respectively. While in previous scenarios fitter species outcompete slower growing competitors, we found that stable equilibria could form if the fitter species responded to a higher chemical concentration level than the slower growing competitor. We also found that species secreting antibiotic could form a stable community with other competing species if antibiotic production started at higher response thresholds.

Conclusions

Microbial communities in nature rely on the stable coexistence of species that necessarily differ in their fitness. We found that differential response thresholds provide a simple and elegant way for keeping slower growing species within the community. High response thresholds can be considered as self-restraint of the fitter species that allows metabolically useful but slower growing species to remain within a community, and thereby the metabolic repertoire of the community will be maintained.

Reviewers

This article was reviewed by Michael Gromiha, Sebastian Maurer-Stroh, István Simon and L. Aravind.

     

Comparative studies of H2O2 detoxifying enzymes in green and greening barley seedlings under cadmium stress

Cadmium(Cd) stress induced alterations in the activities of several representatives of the enzymatic antioxidant defense system such as guiacol peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) were comparatively studied in green and greening barley seedlings that represent two different stages of plant development. Although roots were the main site of Cd accumulation, 1.5–3% of Cd was translocated into leaves and it induced oxidative damage which was indicated by the reduced chlorophyll and increased malondialdehyde content of the leaves. In roots of both types of seedlings exposed to various Cd concentrations, the APX activity was enhanced without any increase in the activity of POD. In leaves, however, elevated activities of both POD and APX could be observed. In roots of green seedlings at high concentration of Cd, the APX activity was reduced on the fourth day of culture but no inhibition was found in the POD activity. Leaf CAT which mainly represented the peroxisomal enzyme activity did not display any changes under Cd stress. Our results show that at both developmental stages barley seedlings exhibit a well-defined activity of the enzymatic antioxidant system, which operates differentially in roots and shoots subjected to Cd stress.     

Growth‐form and spatiality driving the functional difference of native and alien aquatic plants in Europe

Trait‐based approaches are widely used in community ecology and invasion biology to unravel underlying mechanisms of vegetation dynamics. Although fundamental trade‐offs between specific traits and invasibility are well described among terrestrial plants, little is known about their role and function in aquatic plant species. In this study, we examine the functional differences of aquatic alien and native plants stating that alien and native species differ in selected leaf traits. Our investigation is based on 60 taxa (21 alien and 39 native) collected from 22 freshwater units of Hungarian and Italian lowlands and highlands. Linear mixed models were used to investigate the effects of nativeness on four fundamental traits (leaf area, leaf dry matter content, specific leaf area, and leaf nitrogen content), while the influence of growth‐form, altitude, and site were employed simultaneously. We found significantly higher values of leaf areas and significantly lower values of specific leaf areas for alien species if growth‐form was included in the model as an additional predictor.We showed that the trait‐based approach of autochthony can apply to aquatic environments similar to terrestrial ones, and leaf traits have relevance in explaining aquatic plant ecology whether traits are combined with growth‐forms as a fixed factor. Our results confirm the importance of traits related to competitive ability in the process of aquatic plant invasions. Alien aquatic plants can be characterized as species producing soft leaves faster. We argue that the functional traits of alien aquatic plants are strongly growth‐form dependent. Using the trait‐based approach, we found reliable characteristics of aquatic plants related to species invasions, which might be used, for example, in conservation management.