PilZ domain is part of the bacterial c-di-GMP binding protein

Recent studies identified c-di-GMP as a universal bacterial secondary messenger regulating biofilm formation, motility, production of extracellular polysaccharide and multicellular behavior in diverse bacteria. However, except for cellulose synthase, no protein has been shown to bind c-di-GMP and the targets for c-di-GMP action remain unknown. Here we report identification of the PilZ ("pills") domain (Pfam domain PF07238) in the sequences of bacterial cellulose synthases, alginate biosynthesis protein Alg44, proteins of enterobacterial YcgR and firmicute YpfA families, and other proteins encoded in bacterial genomes and present evidence indicating that this domain is (part of) the long-sought c-di-GMP-binding protein. Association of the PilZ domain with a variety of other domains, including likely components of bacterial multidrug secretion system, could provide clues to multiple functions of the c-di-GMP in bacterial pathogenesis and cell development.     

A mechanism of leading-edge protrusion in the absence of Arp2/3 complex

Cells employ protrusive leading edges to navigate and promote their migration in diverse physiological environments. Classical models of leading-edge protrusion rely on a treadmilling dendritic actin network that undergoes continuous assembly nucleated by the Arp2/3 complex, forming ruffling lamellipodia. Recent work demonstrated, however, that, in the absence of the Arp2/3 complex, fibroblast cells adopt a leading edge with filopodia-like protrusions (FLPs) and maintain an ability to move, albeit with altered responses to different environmental signals. We show that formin-family actin nucleators are required for the extension of FLPs but are insufficient to produce a continuous leading edge in fibroblasts lacking Arp2/3 complex. Myosin II is concentrated in arc-like regions of the leading edge in between FLPs, and its activity is required for coordinated advancement of these regions with formin-generated FLPs. We propose that actomyosin contraction acting against membrane tension advances the web of arcs between FLPs. Predictions of this model are verified experimentally. The dependence of myosin II in leading-edge advancement helps explain the previously reported defect in directional movement in the Arpc3-null fibroblasts. We provide further evidence that this defect is cell autonomous during chemotaxis.     

Prostaglandin E2 stimulates cystogenesis through EP4 receptor in IMCD-3 cells

Previously, we demonstrated that prostaglandin E(2) (PGE(2)) induced cAMP and cyst formation through PGE(2) receptor-2 (EP2) activity in human autosomal-dominant polycystic kidney disease (ADPKD) epithelial cells. In this study, we determined the role of EP2 and EP4 receptors in mediating PGE(2) stimulation of cAMP signaling and cystogenesis in mouse renal epithelial cells using the inner medullary collecting duct-3 (IMCD-3) cell line. In contrast to human ADPKD cells, using novel EP2 and EP4 antagonists, we found that IMCD-3 cells expressed functional EP4 but not EP2, which stimulated cAMP formation and led to cyst formation in 3D culture system. The involvement of EP4 receptors in IMCD-3 cells was further supported by the specific effect of EP4 siRNA that inhibited PGE(2)-induced cystogenesis. We also observed different cellular localization of EP2 or EP4 receptors in IMCD-3 transfected cells. Collectively, our results suggest an important role of different expression of EP2 or EP4 receptors in the regulation of cystogenesis.     

Myrmecofauna of Ironstone Outcrops: Composition and Diversity

The Iron Quadrangle in the state of Minas Gerais, Brazil, harbors ironstone outcrops locally known as cangas, which are historically under great anthropic pressure. The functions performed by ants in environments with severe edapho-climatic conditions, such as cangas, are poorly known. Considering the lack of studies and the potential role of ants in cangas, this study aimed to identify the taxonomic composition of the myrmecofauna that occurs in the soil of two campo rupestre areas (rupestral plant communities) on cangas under different anthropic impacts and evaluate the influence of seasonality and degree of degradation on the diversity and composition of the myrmecofauna. This is the first study to systematically investigate ant fauna collected with baits on ironstone outcrops. Sardine and honey baits were used in dry and rainy periods. Fourteen species distributed among ten genera belonging to five subfamilies were found. The total number of baits visited in the dry season was lower than in the rainy season. Both habitats had a reasonable similarity in their composition (Jaccard similarity index?=?0.571). Multivariate analyses suggest a greater similarity between areas than seasons. The diversity of ants in the cangas is low compared to other Cerrado environments where more than 20 species are frequently collected in these types of study. This low richness may be related to the adverse conditions characteristic of ironstone outcrops. We hope our data will help to expand the actions to manage and preserve cangas in the Iron Quadrangle.     

Pollination Biology of the Exotic Rattleweed Crotalaria retusa L. (Fabaceae) in NE Brazil1

The rattleweed Crotalaria retusa was introduced in Brazil from Africa, and combines a series of characters that have ensured its establishment in NE Brazil. We focused on its reproductive biology and pollinator behavior to explain its reproductive success. We performed manual pollination and germination experiments, and monitored the behavior of C. retusa's main pollinators in monospecific plots, and in mixed plots where C. retusa occurred together with two congeners, Crotalaria pallida and Crotalaria lanceolata. Crotalaria retusa is self‐compatible and capable of automatic selfing. Inbreeding depression was expressed at the level of percent seed germination, but not seed set. Few insects visited the inflorescences. Legitimate pollinators were two large carpenter bees, Xylocopa frontalis and Xylocopa grisescens which, together, accounted for more than 90 percent of the visits. The former foraged on C. retusa exclusively and has low pollen spread potential. The latter flew longer distances between plants and visited fewer flowers per inflorescence, potentially increasing the extent of pollen carryover, but at the risk of increasing heterospecific pollen transfer, because it visits other Crotalaria species during the same foraging bout. The different foraging strategies, allied to morphological disadvantages represented by pollen overlap on X. grisescens' body, may partially explain the much lower seed germination observed in C. pallida and C. lanceolata. These results are consistent with the hypothesis that a reduction in flower constancy may significantly depress viable seed set by increasing the chances of self‐pollination.     

Acquisition of novel catalytic activity by the M1 RNA ribozyme: the cost of molecular adaptation.

The ribonucleoprotein RNase P is a critical component of metabolism in all known organisms. In Escherichia coli, RNase P processes a vast array of substrates, including precursor-tRNAs and precursor 4. 5S RNA. In order to understand how such catalytic versatility is achieved and how novel catalytic activity can be acquired, we evolve the M1 RNA ribozyme (the catalytic component of E. coli RNase P) in vitro for cleavage of a DNA substrate. In so doing, we probe the consequences of enhancing catalytic activity on a novel substrate and investigate the cost this versatile enzyme pays for molecular adaptation. A total of 25 generations of in vitro evolution yield a population showing more than a 1000-fold increase in DNA substrate cleavage efficiency (kcat/KM) relative to wild-type M1 RNA. This enhancement is accompanied by a significant reduction in the ability of evolved ribozymes to process the ptRNA class of substrates but also a contrasting increase in activity on the p4.5S RNA class of substrates. This change in the catalytic versatility of the evolved ribozymes suggests that the acquired activity comes at the cost of substrate versatility, and indicates that E. coli RNase P catalytic flexibility is maintained in vivo by selection for the processing of multiple substrates. M1 RNA derivatives enhance cleavage of the DNA substrate by accelerating the catalytic step (kcat) of DNA cleavage, although overall processing efficiency is offset by reduced substrate binding. The enhanced ability to cleave a DNA substrate cannot be readily traced to any of the predominant mutations found in the evolved population, and must instead be due to multiple sequence changes dispersed throughout the molecule. This conclusion underscores the difficulty of correlating observed mutations with changes in catalytic behavior, even in simple biological catalysts for which three-dimensional models are available.     

Feeding of Arapaima sp.: integrating stomach contents and local ecological knowledge

The giant arapaima (Arapaima sp.) has been described as a fish of change in Amazonia because of its important role in the conservation of floodplains, food security and income generation for rural communities. Nonetheless, despite the cultural, ecological and economic importance of arapaima, data on diet are scarce. Aiming to expand knowledge about arapaima diet in western Amazonia, scientific knowledge was integrated with the knowledge of local dwellers. During the low-water period (September 2018) and the falling-water period (June 2019), arapaima stomachs were collected from 11 floodplain lakes in the middle Juruá River. All fishes were measured [TL (total length)] and sexed. Food items from each stomach were categorized as fishes, invertebrates, plants and bone remains and weighed. Also, in the latter period, experienced local fishers were interviewed about arapaima feeding. This integrated approach revealed that young arapaima eat fish and invertebrates but adult arapaima eat fish of a wide range of species, which were mainly of low and intermediate trophic positions. This study reports the first case of cannibalism for arapaima and also shows that during the low-water period, many individuals had empty stomachs or only some small fish-bone remains and/or plant material. Arapaima sex and TL had no influence on the absence of prey in stomach contents. Overall, it can be concluded that local people had consistent ethnobiological knowledge of arapaima feeding ecology that could be useful within management projects in the region.     

Enhanced Erythrocyte Adhesiveness/Aggregation in Obesity Corresponds to Low‐Grade Inflammation

Objective: Previous studies have suggested that obesity enhances the inflammatory response, producing macromolecules involved in the induction and/or maintenance of increased erythrocyte aggregation. The objectives of this study were to evaluate the correlation between inflammation markers, erythrocyte adhesiveness/aggregation, and the degree of obesity and to assess phosphatidylserine expression on erythrocyte surface membrane of obese vs. nonobese individuals. Research Methods and Procedures: Erythrocyte adhesiveness/aggregation in the peripheral venous blood was evaluated by using a new biomarker, phosphatidylserine expression was assessed by means of flow cytometry, and markers of inflammation were measured in 65 subjects: 30 obese [body mass index (BMI) = 41 ± 7.7 kg/m²] and 35 nonobese (BMI = 24 ± 2.7 kg/m²) individuals. Pearson correlations and Student's t test were performed. Results: A highly significant difference was noted in the degree of erythrocyte adhesiveness/aggregation and markers of inflammation between the study groups. BMI correlated with erythrocyte adhesiveness/aggregation (r = 0.42, p = 0.001), erythrocyte sedimentation rate (r = 0.42, p = 0.001), high‐sensitive C‐reactive protein (r = 0.55, p < 10^?4), fibrinogen (r = 0.37, p = 0.004), and white blood cell count (r = 0.45, p < 10^?4). The degree of erythrocyte adhesiveness/aggregation correlated with erythrocyte sedimentation rate (r = 0.5, p < 10^?4), high‐sensitive C‐reactive protein (r = 0.56, p < 10^?4), fibrinogen (r = 0.54, p < 10^?4), and white blood cell count (r = 0.32, p = 0.01). Discussion: Our results suggest that obesity‐related erythrocyte adhesiveness/aggregation is probably mediated through increased concentrations of adhesive macromolecules in the circulation and not necessarily through hyperlipidemia or phosphatidylserine exposure on erythrocyte's membrane.     

Extending networks of protected areas to optimize connectivity and population growth rate

Protected areas (PAs) are recognized as the flagship tool to offset biodiversity loss on Earth. Spatial conservation planning seeks optimal designs of PAs that meet multiple targets such as biodiversity representation and population persistence. Since connectivity between PAs is a fundamental requirement for population persistence, several methods have been developed to include connectivity into PA design algorithms. Among these, the eigenvalue decomposition of the connectivity matrix allows for identifying clusters of strongly connected sites and selecting the sites contributing the most to population persistence. So far, this method was only suited to optimize an entire network of PAs without considering existing PAs in the new design. However, a more cost‐effective and realistic approach is to optimize the design of an extended network to improve its connectivity and thus population persistence. Here, we develop a flexible algorithm based on eigenvalue decomposition of connectivity matrices to extend existing networks of PAs while optimizing connectivity and population growth rate. We also include a splitting algorithm to improve cluster identification. The new algorithm accounts for the change in connectivity due to the increased biological productivity often observed in existing PAs. We illustrate the potential of our algorithm by proposing an extension of the network of ～100 Mediterranean marine PAs to reach the targeted 10% surface area protection from the current 1.8%. We identify differences between the clean slate scenario, where all sites are available for protection, irrespective of their current protection status, and the scenario where existing PAs are forced to be included into the optimized solution. By integrating this algorithm to existing multi‐objective and multi‐specific algorithms of PA selection, the demographic effects of connectivity can be explicitly included into conservation planning.