Streptococcal dTDP‐L‐rhamnose biosynthesis enzymes: functional characterization and lead compound identification

Biosynthesis of the nucleotide sugar precursor dTDP‐L‐rhamnose is critical for the viability and virulence of many human pathogenic bacteria, including Streptococcus pyogenes (Group A Streptococcus; GAS), Streptococcus mutans and Mycobacterium tuberculosis. Streptococcal pathogens require dTDP‐L‐rhamnose for the production of structurally similar rhamnose polysaccharides in their cell wall. Via heterologous expression in S. mutans, we confirmed that GAS RmlB and RmlC are critical for dTDP‐L‐rhamnose biosynthesis through their action as dTDP‐glucose‐4,6‐dehydratase and dTDP‐4‐keto‐6‐deoxyglucose‐3,5‐epimerase enzymes respectively. Complementation with GAS RmlB and RmlC containing specific point mutations corroborated the conservation of previous identified catalytic residues. Bio‐layer interferometry was used to identify and confirm inhibitory lead compounds that bind to GAS dTDP‐rhamnose biosynthesis enzymes RmlB, RmlC and GacA. One of the identified compounds, Ri03, inhibited growth of GAS, other rhamnose‐dependent streptococcal pathogens as well as M. tuberculosis with an IC₅₀ of 120–410 µM. Importantly, we confirmed that Ri03 inhibited dTDP‐L‐rhamnose formation in a concentration‐dependent manner through a biochemical assay with recombinant rhamnose biosynthesis enzymes. We therefore conclude that inhibitors of dTDP‐L‐rhamnose biosynthesis, such as Ri03, affect streptococcal and mycobacterial viability and can serve as lead compounds for the development of a new class of antibiotics that targets dTDP‐rhamnose biosynthesis in pathogenic bacteria.     

Protist Biodiversity and Biogeography in Lakes From Four Brazilian River–Floodplain Systems

The biodiversity and biogeography of protists inhabiting many ecosystems have been intensely studied using different sequencing approaches, but tropical ecosystems are relatively under‐studied. Here, we sampled planktonic waters from 32 lakes associated with four different river–floodplains systems in Brazil, and sequenced the DNA using a metabarcoding approach with general eukaryotic primers. The lakes were dominated by the largely free‐living Discoba (mostly the Euglenida), Ciliophora, and Ochrophyta. There was low community similarity between lakes even within the same river–floodplain. The protists inhabiting these floodplain systems comprise part of the large and relatively undiscovered diversity in the tropics.     

Diversity and distribution of hidden cultivable fungi associated with marine animals of Antarctica

In the present study, we surveyed the distribution and diversity of fungal assemblages associated with 10 species of marine animals from Antarctica. The collections yielded 83 taxa from 27 distinct genera, which were identified using molecular biology methods. The most abundant taxa were Cladosporium sp. 1, Debaryomyces hansenii, Glaciozyma martinii, Metschnikowia australis, Pseudogymnoascus destructans, Thelebolus cf. globosus, Pseudogymnoascus pannorum, Tolypocladium tundrense, Metschnikowia australis, and different Penicillium species. The diversity, richness, and dominance of fungal assemblages ranged among the host; however, in general, the fungal community, which was composed of endemic and cold-adapted cosmopolitan taxa distributed across the different sites of Antarctic Peninsula, displayed high diversity, richness, and dominance indices. Our results contribute to knowledge about fungal diversity in the marine environment across the Antarctic Peninsula and their phylogenetic relationships with species that occur in other cold, temperate, and tropical regions of the World. Additionally, despite their extreme habitats, marine Antarctic animals shelter cryptic and complex fungal assemblages represented by endemic and cosmopolitan cold-adapted taxa, which may represent interesting models to study different symbiotic associations between fungi and their animal hosts in the extreme conditions of Antarctica.     

Symplocos saxatilis (Symplocaceae), a new dioecious species from Serra do Cipó, Minas Gerais, Brazil

Symplocos saxatilis from Serra do Cipó, Minas Gerais State, Brazil, is newly described and illustrated on the basis of field and herbarium studies. It appears to be restricted to “campo rupestre” (rocky field) habitats. This new species is characterized by its 1- to 3-flowered pedunculate inflorescence, 11 to 14 staminodes of the pistillate flowers, and 0.7–1.5 mm thick endocarp.     

Habitat fragmentation, variable edge effects, and the landscape-divergence hypothesis

Edge effects are major drivers of change in many fragmented landscapes, but are often highly variable in space and time. Here we assess variability in edge effects altering Amazon forest dynamics, plant community composition, invading species, and carbon storage, in the world's largest and longest-running experimental study of habitat fragmentation. Despite detailed knowledge of local landscape conditions, spatial variability in edge effects was only partially foreseeable: relatively predictable effects were caused by the differing proximity of plots to forest edge and varying matrix vegetation, but windstorms generated much random variability. Temporal variability in edge phenomena was also only partially predictable: forest dynamics varied somewhat with fragment age, but also fluctuated markedly over time, evidently because of sporadic droughts and windstorms. Given the acute sensitivity of habitat fragments to local landscape and weather dynamics, we predict that fragments within the same landscape will tend to converge in species composition, whereas those in different landscapes will diverge in composition. This 'landscape-divergence hypothesis', if generally valid, will have key implications for biodiversity-conservation strategies and for understanding the dynamics of fragmented ecosystems.     

On the relative stabilities of the alkali cations 222 cryptates in the gas phase and in water-methanol solution

The relative stabilities of the alkali [M ⊂ 222]⁺ cryptates (M = Na, K, Rb and Cs) in the gas phase and in solution (80:20 v/v methanol:water mixture) at 298 K, are computed using a combination of ab initio quantum-chemical calculations (HF/6-31G and MP2/6-31+G*//HF/6-31+G*) and explicit-solvent Monte Carlo free-energy simulations. The results suggest that the relative stabilities of the cryptates in solution are due to a combination of steric effects (compression of large ions within the cryptand cavity), electronic effects (delocalization of the ionic charge onto the cryptand atoms) and solvent effects (dominantly the ionic dessolvation penalty). Thus, the relative stabilities in solution cannot be rationalized solely on the basis of a simple match or mismatch between the ionic radius and the cryptand cavity size as has been suggested previously. For example, although the [K ⊂ 222]⁺ cryptate is found to be the most stable in solution, in agreement with experimental data, it is the [Na ⊂ 222]⁺ cryptate that is the most stable in the gas phase. The present results provide further support to the notion that the solvent in which supramolecules are dissolved plays a key role in modulating molecular recognition processes. Figure Alkali cryptates [M ⊂ 222]+ (M = Na, K, Rb and Cs) relative stabilities in gas and methanol:water solution: solvent effects and molecular recognition

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Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Analysis of the Paracoccidioides brasiliensis triosephosphate isomerase suggests the potential for adhesin function

Paracoccidioides brasiliensis is an important fungal pathogen. The disease it causes, paracoccidioidomycosis (PCM), ranges from localized pulmonary infection to systemic processes that endanger the life of the patient. Paracoccidioides brasiliensis adhesion to host tissues contributes to its virulence, but we know relatively little about molecules and the molecular mechanisms governing fungal adhesion to mammalian cells. Triosephosphate isomerase (TPI: EC 5.3.1.1) of P. brasiliensis (PbTPI) is a fungal antigen characterized by microsequencing of peptides. The protein, which is predominantly expressed in the yeast parasitic phase, localizes at the cell wall and in the cytoplasmic compartment. TPI and the respective polyclonal antibody produced against this protein inhibited the interaction of P. brasiliensis to in vitro cultured epithelial cells. TPI binds preferentially to laminin, as determined by peptide inhibition assays. Collectively, these results suggest that TPI is required for interactions between P. brasiliensis and extracellular matrix molecules such as laminin and that this interaction may play an important role in the fungal adherence and invasion of host cells.     

Global patterns in anuran–prey networks: structure mediated by latitude

Life on Earth is supported by an infinite number of interactions among organisms. Species interactions in these networks are influenced by latitude, evolutionary history and species traits. We performed a global‐scale literature analysis to build up a database of interactions between anuran communities and their preys, from a wide range of geographical areas, using a network approach. For this purpose, we compiled a total of 55 weighted anuran–prey interaction networks, 39 located in the tropics and 16 in temperate areas. We tested the influence of latitude, as well as anuran taxonomic, functional and phylogenetic richness on network metrics. We found that anuran–prey networks are not nested, exhibit low complementary specialization and modularity and high connectance when compared to other types of networks. The main effects on network metrics were related to latitude, followed by anuran taxonomic, functional and phylogenetic richness, a pattern similar to the emerging in mutualistic networks. Our study is the first integrated analysis of the structural patterns in anuran–prey antagonistic interaction networks in different parts of the world. We suggest that different processes, mediated mainly by latitude, are modeling the architecture of anuran–prey networks across the globe.     

Atlantic Forest topsoil nutrients can be resistant to disturbance and forest clearing

Human impacts can affect the soil properties through erosion and leaching, the ecosystem functions and, consequently, the capacity of a forest to regenerate. Here, we determine the effects of forest disturbance and succession on selected soil chemical properties using two different approaches, before‐after‐control‐impact (BACI) and space‐for‐time (SFT) substitution, and the threatened Atlantic Forest biome as model. We assessed with BACI the long‐term (37‐year) effects of clear cutting on soil properties by comparing data from two topsoil surveys (1978–2017) divided into two treatments: a preserved old growth forest (control) and an adjacent forest that was experimentally cleared with full tree removal (clear‐cut). We examined with SFT the relationship between stand age and soil properties using soil data from three old growth and 13 s growth forests ranging from 7 to 33 years. We found no significant differences between treatments for any soil property or significant changes in phosphorus, potassium, and calcium + magnesium over time. In contrast, pH increased and aluminum decreased in both areas. No relation was found between forest age and most of soil properties, with the exception of potassium which returned to old growth forest levels after 20 years of natural succession, and pH. BACI indicated that deforestation of old growth forest caused no significant effects on soil chemical properties after 37 years of regeneration. SFT demonstrated that soil properties did not change significantly during forest regeneration on formerly disturbed lands. Our findings indicate that natural nutrient‐depleted lowland forests were overall resistant to deforestation followed by passive regeneration at landscape scale. Abstract in Portuguese is available with online material.