Diversity of lacewing assemblages (Neuropterida:Neuroptera) in different forest habitats and agricultural areas in the East Mediterranean area of Turkey

The objectives of this study were to understand lacewing diversity patterns and the role of environmental factors in determining lacewing diversity in four habitat types: agricultural area (crops and orchards), pine forest (Pinus nigra Arnold and, Pinus brutia Ten), natural forest (cedar and willow‐oak), and mixed forest (beech and oak). Several diversity patterns were evaluated, including evenness and dominance, in the East Mediterranean area of Turkey by analyzing the abundance and species composition of lacewing assemblages using the Simpson and Shannon Diversity Indices. It was questioned whether these communities are structured according to environmental conditions such as altitude, temperature, rainfall, wind and humidity. This question was explored using generalized linear models (GLMs) and principal component analysis (PCA) to detect the effect of ecological parameters on the species composition of the lacewing assemblages. The data suggest that the species abundance, composition, and diversity of lacewings are affected by different forest and agricultural habitat types. Based on the results of the present study, it is recommended that the area of farmland under cultivation is decreased and the area of sustainably managed forest and agricultural land is increased in order to better protect lacewing diversity in the East Mediterranean area of Turkey.     

Degradation of cultivated bench terraces in the Three Gorges Area: Field mapping and data mining

Due to resettlements, construction of new infrastructure, and new land reclamation the rapid agricultural changes in the Three Georges Area (TGA) in Central China are expected to force the degradation of the cultivated terraced landscape. Consequently, increased soil erosion can hamper a sustainable land management in the mountainous TGA. This paper presents the model framework TerraCE (Terrace Condition Erosion) for determining the causes for different terrace conditions and terrace degradation based on field surveys and spatial data mining. For a total of 987 bench terrace plots in the Xiangxi catchment we collected data on their state of maintenance and terrace design to account for terrace stability and thus capability of soil conservation. Assessing the driving factors of terrace degradation was done by embedding terrain-based predictors and distance-transforms of remote-sensing data as indicators of environmental and anthropogenic influences. Random forests classification and regression models were applied for data mining. Terrace degradation in the Xiangxi catchment is obvious. The sequence of degradation ranges from ‘well maintained’ (21%), ‘fairly maintained’ (44%), and ‘partially collapsed’ (23%) to ‘completely collapsed’ (11%) terraces. The cross-validation error of the supervised TerraCE model is below 8%, allowing for reasonable and valid interpretations of the causes of terrace degradation. Data mining reveals indicators for anthropogenic effects such as the distance to settlements or to roads as major drivers for the spatial distribution of terrace conditions. The effect of relief, which can be regarded as the major natural driver for terrace degradation by erosive action is tributary but altered and overlaid by land use dynamics associated with the Three Gorges Dam. An important indicator representing a combined effect of terrain and human activity is the distance to stream channels of different orders. Applying TerraCE we reveal mechanisms of terrace degradation in disturbed environments and present a framework for standardized mapping and analysis of terrace degradation under cultivation. The approach might also be used to develop guidelines for terrace planning in mountainous terraced landscapes of limited carrying capacity, with respect to socio-economic as well as environmental conditions.     

ECOLOGICAL CAUSES OF DECELERATING DIVERSIFICATION IN CARNIVORAN MAMMALS

Clade diversification is a central topic in macroevolutionary studies. Recently, it has been shown that diversification rates appear to decelerate over time in many clades. What causes this deceleration remains unclear, but it has been proposed that competition for limited resources between sympatric, ecologically similar species slows diversification. Employing carnivoran mammals as a model system, we test this hypothesis using a comprehensive time‐calibrated phylogeny. We also explore several conceptually related explanations including limited geographic area and limited rates of niche evolution. We find that diversification slowdowns are strong in carnivorans. Surprisingly, these slowdowns are independent of geographic range overlap between related species and are also decoupled from rates of niche evolution, suggesting that slowdowns are unrelated to competition and niche filling. When controlling for the effects of clade diversity, diversification slowdowns appear independent of geographic area. There is a significant effect of clade diversity on diversification slowdowns, but simulations show that this relationship may arise as a statistical artifact (i.e., greater clade diversity increases the ability of the gamma statistic to refute constant diversification). Overall, our results emphasize the need to test hypotheses about the causes of diversification slowdowns with ecological data, rather than assuming ecological processes from phylogenies alone.     

Mechanisms for the inclusion of cumulative impacts in conservation decision-making are sensitive to vulnerability and irreplaceability in a stochastically simulated landscape

It is commonly understood that the cumulative impact of increased habitat destruction on biological systems does not scale linearly. Despite this, current environmental decision-making strategies often fail to incorporate these non-linearities because impact assessments are regularly performed independently without considering contributions to future cumulative impacts, which are, instead, externalised to the environment. Here we used a stochastic modelling framework to examine the effect of three decision-making strategies – externalised, individually-borne and shared cumulative costs – on the number of species driven to extinction by the development of a region. We also tested how different levels of vulnerability (quantified as the correlation between development benefits and species richness) and irreplaceability (expressed as the average area of occupancy of an assemblage) influence the outcomes of development. Overall, the inclusion of cumulative impacts in our simulations resulted in the destruction of fewer patches and, as a consequence, more modest benefits obtained from developments. Moreover, these patterns were strongest when cumulative costs were shared by all developers. The most striking finding was that the distinction between decision-making strategies was highest in landscapes of high vulnerability and irreplaceability. Environmental decision-makers are recommended to commit to a strategy for incorporating the cumulative costs of development because, as this study suggests, this affects the endpoints of conservation and development considerably; especially in the most vulnerable and irreplaceable landscapes.     

Elucidation of critical pH-dependent structural changes in Botulinum Neurotoxin E

Botulinum Neurotoxins (BoNT) are the most potent toxins currently known. However, they also have therapeutic applications for an increasing number of motor related conditions due to their specificity, and low diffusion into the system. Although the start- and end- points for the BoNT mechanism of action are well-studied, a critical step remains poorly understood. It is theorised that BoNTs undergo a pH-triggered conformational shift, activating the neurotoxin by priming it to form a transmembrane (TM) channel. To test this hypothesis, we combined molecular dynamics (MD) simulations and small-angle x-ray scattering (SAXS), revealing a new conformation of serotype E (BoNT/E). This conformation was exclusively observed in simulations below pH 5.5, as determined by principal component analysis (PCA), and its theoretical SAXS profile matched an experimental SAXS profile obtained at pH 4. Additionally, a localised secondary structural change was observed in MD simulations below pH 5.5, in a region previously identified as instrumental for membrane insertion for serotype A (BoNT/A). These changes were found at a critical pH value for BoNTs in vivo, and may be relevant for their therapeutic use.     

The Wallacean Shortfall and the role of historical distribution records in the conservation assessment of an elusive Neotropical snake in a threatened landscape

Documenting species distribution is essential to extinction risk asessments and subsequent conservation actions. Historical records are thus essential to understand how species are distributed and how their range has changed over time. However, using historical records might contribute to overestimating the species current range and misrepresent their conservation status. Here, we illustrate the pitfalls of this approach using a widespread but elusive Neotropical snake species, Philodryas livida (Dipsadidae Bonaparte, 1838). We mapped occurrences of this species over time and calculated its Extent of Occurrence and Area of Habitat. Our results show that due to the intense, widespread anthropic land-use transformation since the discovery of P. livida in 1920, most historical localities are now likely unsuitable for its occurrence and both its current Extent of Occurrence and Area of Habitat become remarkably smaller (5.7% and 19.1% remaining, respectively) if only localities from the last 30 years are considered. Apart from the natural elusiveness of the species, intense habitat loss and fragmentation may also explain the low number of recent records of P. livida, all concentrated within or near protected areas, indicating a putative decline in range relevant to its conservation status. We thus highlight how failing to consider the date of records and the associated land-use change over time might underestimate species range reduction and thus threat status. We strongly encourage the inclusion of the date of each occurrence record in conservation assessments, as suggested by the IUCN’s mapping standards, such that historical records are carefully considered, especially in highly dynamic and threatened biomes such as the Cerrado savannas in Brazil.     

The species-area relation II. A second model for continuous sampling

A second mathematical model describing the species-area relation was proposed for continuous expanding of sample area. This model is expressed as S=λ ln(1+x/E) where S is the number of species occurring in an area x, and λ and E are the constants termed specific diversity and elemental area respectively. As a result of testing the validity of the model for several sets of data, it was shown that the above equation would provide an adequate fit to a group of species belonging to a single synusia which exists in an open habitat. The ecological implications of parameters involved were discussed and the characteristic area presented previously (Kobayashi , 1974) was defined in terms of E. The relation between results obtained by discrete sampling and continuous sampling was examined and the possibility of converting one to another was suggested.     

Molecular dynamics and simulation analysis against superoxide dismutase (SOD) target of Micrococcus luteus with secondary metabolites from Bacillus licheniformis recognized by genome mining approach

Micrococcus luteus, also known as M. luteus, is a bacterium that inhabits mucous membranes, human skin, and various environmental sources. It is commonly linked to infections, especially among individuals who have compromised immune systems. M. luteus is capable of synthesizing the enzyme superoxide dismutase (SOD) as a component of its protective response to reactive oxygen species (ROS). This enzyme serves as a promising target for drug development in various diseases. The current study utilized a subtractive genomics approach to identify potential therapeutic targets from M. luteus. Additionally, genome mining was employed to identify and characterize the biosynthetic gene clusters (BGCs) responsible for the production of secondary metabolites in Bacillus licheniformis (B. licheniformis), a bacterium known for its production of therapeutically relevant secondary metabolites. Subtractive genomics resulted in identification of important extracellular protein SOD as a drug target that plays a crucial role in shielding cells from damage caused by ROS. Genome mining resulted in identification of five potential ligands (secondary metabolites) from B. licheniformis such as, Bacillibactin (BAC), Paenibactin (PAE), Fengycin (FEN), Surfactin (SUR) and Lichenysin (LIC). Molecular docking was used to predict and analyze the binding interactions between these five ligands and target protein SOD. The resulting protein–ligand complexes were further analyzed for their motions and interactions of atoms and molecules over 250 ns using molecular dynamics (MD) simulation analysis. The analysis of MD simulations suggests, Bacillibactin as the probable candidate to arrest the activities of SOD. All the five compounds reported in this study were found to act by directly/indirectly interacting with ROS molecules, such as superoxide radicals (O₂–) and hydrogen peroxide (H₂O₂), and transforming them into less reactive species. This antioxidant activity contributes to its protective effects against oxidative stress-induced damage in cells making them likely candidate for various applications, including in the development of antioxidant-based therapies, nutraceuticals, and functional foods.