Synthesis of geometrically realistic and watertight neuronal ultrastructure manifolds for in silico modeling.

Understanding the intracellular dynamics of brain cells entails performing three-dimensional molecular simulations incorporating ultrastructural models that can capture cellular membrane geometries at nanometer scales. While there is an abundance of neuronal morphologies available online, e.g. from NeuroMorpho.Org, converting those fairly abstract point-and-diameter representations into geometrically realistic and simulation-ready, i.e. watertight, manifolds is challenging. Many neuronal mesh reconstruction methods have been proposed; however, their resulting meshes are either biologically unplausible or non-watertight. We present an effective and unconditionally robust method capable of generating geometrically realistic and watertight surface manifolds of spiny cortical neurons from their morphological descriptions. The robustness of our method is assessed based on a mixed dataset of cortical neurons with a wide variety of morphological classes. The implementation is seamlessly extended and applied to synthetic astrocytic morphologies that are also plausibly biological in detail. Resulting meshes are ultimately used to create volumetric meshes with tetrahedral domains to perform scalable in silico reaction-diffusion simulations for revealing cellular structure-function relationships. Availability and implementation: Our method is implemented in NeuroMorphoVis, a neuroscience-specific open source Blender add-on, making it freely accessible for neuroscience researchers.

Ultraliser: a framework for creating multiscale, high-fidelity and geometrically realistic 3D models for in silico neuroscience.

Ultraliser is a neuroscience-specific software framework capable of creating accurate and biologically realistic 3D models of complex neuroscientific structures at intracellular (e.g. mitochondria and endoplasmic reticula), cellular (e.g. neurons and glia) and even multicellular scales of resolution (e.g. cerebral vasculature and minicolumns). Resulting models are exported as triangulated surface meshes and annotated volumes for multiple applications in in silico neuroscience, allowing scalable supercomputer simulations that can unravel intricate cellular structure-function relationships. Ultraliser implements a high-performance and unconditionally robust voxelization engine adapted to create optimized watertight surface meshes and annotated voxel grids from arbitrary non-watertight triangular soups, digitized morphological skeletons or binary volumetric masks. The framework represents a major leap forward in simulation-based neuroscience, making it possible to employ high-resolution 3D structural models for quantification of surface areas and volumes, which are of the utmost importance for cellular and system simulations. The power of Ultraliser is demonstrated with several use cases in which hundreds of models are created for potential application in diverse types of simulations. Ultraliser is publicly released under the GNU GPL3 license on GitHub (BlueBrain/Ultraliser). SIGNIFICANCE: There is crystal clear evidence on the impact of cell shape on its signaling mechanisms. Structural models can therefore be insightful to realize the function; the more realistic the structure can be, the further we get insights into the function. Creating realistic structural models from existing ones is challenging, particularly when needed for detailed subcellular simulations. We present Ultraliser, a neuroscience-dedicated framework capable of building these structural models with realistic and detailed cellular geometries that can be used for simulations.

Global taxonomic and phylogenetic assembly of AM fungi.

Arbuscular mycorrhizal (AM) fungi are a ubiquitous group of plant symbionts, yet processes underlying their global assembly - in particular the roles of dispersal limitation and historical drivers - remain poorly understood. Because earlier studies have reported niche conservatism in AM fungi, we hypothesized that variation in taxonomic community composition (i.e., unweighted by taxon relatedness) should resemble variation in phylogenetic community composition (i.e., weighted by taxon relatedness) which reflects ancestral adaptations to historical habitat gradients. Because of the presumed strong dispersal ability of AM fungi, we also anticipated that the large-scale structure of AM fungal communities would track environmental conditions without regional discontinuity. We used recently published AM fungal sequence data (small-subunit ribosomal RNA gene) from soil samples collected worldwide to reconstruct global patterns in taxonomic and phylogenetic community variation. The taxonomic structure of AM fungal communities was primarily driven by habitat conditions, with limited regional differentiation, and there were two well-supported clusters of communities - occurring in cold and warm conditions. Phylogenetic structure was driven by the same factors, though all relationships were markedly weaker. This suggests that niche conservatism with respect to habitat associations is weakly expressed in AM fungal communities. We conclude that the composition of AM fungal communities tracks major climatic and edaphic gradients, with the effects of dispersal limitation and historic factors considerably less apparent than those of climate and soil.

Temperature and pH define the realised niche space of arbuscular mycorrhizal fungi.

The arbuscular mycorrhizal (AM) fungi are a globally distributed group of soil organisms that play critical roles in ecosystem function. However, the ecological niches of individual AM fungal taxa are poorly understood. We collected > 300 soil samples from natural ecosystems worldwide and modelled the realised niches of AM fungal virtual taxa (VT; approximately species-level phylogroups). We found that environmental and spatial variables jointly explained VT distribution worldwide, with temperature and pH being the most important abiotic drivers, and spatial effects generally occurring at local to regional scales. While dispersal limitation could explain some variation in VT distribution, VT relative abundance was almost exclusively driven by environmental variables. Several environmental and spatial effects on VT distribution and relative abundance were correlated with phylogeny, indicating that closely related VT exhibit similar niche optima and widths. Major clades within the Glomeraceae exhibited distinct niche optima, Acaulosporaceae generally had niche optima in low pH and low temperature conditions, and Gigasporaceae generally had niche optima in high precipitation conditions. Identification of the realised niche space occupied by individual and phylogenetic groups of soil microbial taxa provides a basis for building detailed hypotheses about how soil communities respond to gradients and manipulation in ecosystems worldwide.

Solanaceae diversity in South America and its distribution in Argentina.

Solanaceae is one of the most diverse families in the Americas, particularly in Argentina where it represents the fourth family in terms of species number. Although checklists for most South American countries have been published, some are outdated and there has been no analysis of Solanaceae diversity at country level. We present an updated summary of Solanaceae diversity in South America, an analysis of its distribution in Argentina, and preliminary conservation assessments for all species endemic to Argentina. Regression analyses were used for evaluating the ratio between taxa/area and endemic/total species, multivariate ordering methods were used to analyze the relationships between Argentine ecoregions, and the IUCN criteria were applied for conservation assessments. Results show that Solanaceae comprises 1611 species in South America. The highest diversity is in Peru, which, together with Ecuador, possesses more diversity than expected for the area; Chile and Brazil have the greatest percentage of endemic species. In Argentina, the Chaco ecoregion hosts the highest number of taxa, but largest number of endemic species is found in the Monte ecoregion. According to the IUCN criteria, 28 endemic species from Argentina are considered threatened. We discuss South American countries and Argentine ecoregions in terms of conservation priorities.

Global diversity and distribution of nitrogen-fixing bacteria in the soil.

Our knowledge of microbial biogeography has advanced in recent years, yet we lack knowledge of the global diversity of some important functional groups. Here, we used environmental DNA from 327 globally collected soil samples to investigate the biodiversity patterns of nitrogen-fixing bacteria by focusing on the nifH gene but also amplifying the general prokaryotic 16S SSU region. Globally, N-fixing prokaryotic communities are driven mainly by climatic conditions, with most groups being positively correlated with stable hot or seasonally humid climates. Among soil parameters, pH, but also soil N content were most often shown to correlate with the diversity of N-fixer groups. However, specific groups of N-fixing prokaryotes show contrasting responses to the same variables, notably in Cyanobacteria that were negatively correlated with stable hot climates, and showed a U-shaped correlation with soil pH, contrary to other N-fixers. Also, the non-N-fixing prokaryotic community composition was differentially correlated with the diversity and abundance of N-fixer groups, showing the often-neglected impact of biotic interactions among bacteria.

Metabarcoding of soil environmental DNA to estimate plant diversity globally.

Introduction: Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. Methods: We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Results: Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. Discussion: eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.

Dominance, diversity, and niche breadth in arbuscular mycorrhizal fungal communities.

Classical theory identifies resource competition as the major structuring force of biotic communities and predicts that (i) levels of dominance and richness in communities are inversely related, (ii) narrow niches allow dense "packing" in niche space and thus promote diversity, and (iii) dominants are generalists with wide niches, such that locally abundant taxa also exhibit wide distributions. Current empirical support, however, is mixed. We tested these expectations using published data on arbuscular mycorrhizal (AM) fungal community composition worldwide. We recorded the expected negative relationship between dominance and richness and, to a degree, the positive association between local and global dominance. However, contrary to expectations, dominance was pronounced in communities where more specialists were present and, conversely, richness was higher in communities with more generalists. Thus, resource competition and niche packing appear to be of limited importance in AM fungal community assembly; rather, patterns of dominance and diversity seem more consistent with habitat filtering and stochastic processes.

Living in extreme environments: distribution of Lyciumhumile (Solanaceae), an endemic halophyte from the Altiplano-Puna region, South America.

Very few Solanaceae species are able to grow in saline soils; one of them is Lyciumhumile. This species is endemic to the Altiplano-Puna region (Central Andes, South America) where there are multiple extreme environmental conditions such as hypersaline soils. Here we present an updated description and distribution of L.humile including its new record for Bolivia at the edges of "Salar de Uyuni", the largest salt flat in the world; we discuss its ecological role in saline environments by analyzing soil salinity and cover-abundance values ​​of the studied sites. According to IUCN criteria, we recommend a category of Least Concern for L.humile, but the growing development of lithium mining in saline environments of the Altiplano-Puna region may potentially threaten exclusive communities.

New insights into the salt tolerance of the extreme halophytic species Lycium humile (Lycieae, Solanaceae).

Knowledge about Solanaceae species naturally adapted to salinity is scarce, despite the fact that a considerable number of Solanaceae has been reported growing in saline environments. Lycium humile Phil. inhabits extreme saline soils in the Altiplano-Puna region (Central Andes, South America) and represents a promising experimental model to study salt tolerance in Solanaceae plants. Seeds, leaves and roots were collected from a saline environment (Salar del Diablo, Argentina). Seeds were scarified and 30 days after germination salt treatments were applied by adding NaCl salt pulses (up to 750 or 1000 mM). Different growth parameters were evaluated, and leaf spectral reflectance, endogenous phytohormone levels, antioxidant capacity, proline and elemental content, and morpho-anatomical characteristics in L. humile under salinity were analyzed both in controlled and natural conditions. The multiple salt tolerance mechanisms found in this species are mainly the accumulation of the phytohormone abscisic acid, the increase of the antioxidant capacity and proline content, together with the development of a large leaf water-storage parenchyma that allows Na+ accumulation and an efficient osmotic adjustment. Lycium humile is probably one of the most salt-tolerant Solanaceae species in the world, and, in controlled conditions, can effectively grow at high NaCl concentrations (at least, up to 750 mM NaCl) but also, in the absence of salts in the medium. Therefore, we propose that natural distribution of L. humile is more related to water availability, as a limiting factor of growth in Altiplano-Puna saline habitats, than to high salt concentrations in the soils.

Impact of alien pines on local arbuscular mycorrhizal fungal communities-evidence from two continents.

The introduction of alien plants can influence biodiversity and ecosystems. However, its consequences for soil microbial communities remain poorly understood. We addressed the impact of alien ectomycorrhizal (EcM) pines on local arbuscular mycorrhizal (AM) fungal communities in two regions with contrasting biogeographic histories: in South Africa, where no native EcM plant species are present; and in Argentina, where EcM trees occur naturally. The effect of alien pines on AM fungal communities differed between these regions. In South Africa, plantations of alien EcM pines exhibited lower AM fungal richness and significantly altered community composition, compared with native fynbos. In Argentina, the richness and composition of local AM fungal communities were similar in plantations of alien EcM pines and native forest. However, the presence of alien pines resulted in slight changes to the phylogenetic structure of root AM fungal communities in both regions. In pine clearcut areas in South Africa, the richness and composition of AM fungal communities were intermediate between the native fynbos and the alien pine plantation, which is consistent with natural regeneration of former AM fungal communities following pine removal. We conclude that the response of local AM fungal communities to alien EcM pines differs between biogeographic regions with different histories of species coexistence.

Potent inhibition of Western Equine Encephalitis virus by a fraction rich in flavonoids and phenolic acids obtained from Achyrocline satureioides

ABSTRACT Achyrocline satureioides (Lam.) DC. Asteraceae, ‘marcela del campo', possess several pharmacological properties. Previously we reported antiviral activity of an aqueous extract of A. satureioides against an alphavirus, Western Equine Encephalitis virus. Alphaviruses are highly virulent pathogens which cause encephalitis in humans and equines. There are no effective antiviral to treat its infections. The aim of this study was to evaluate in vitro cytotoxic and antiviral activities against Western Equine Encephalitis virus of five water extract chromatographic fractions from A. satureioides and identify the main compounds of the bioactive fraction. Also, it was to assess in vivo cytogenotoxic ability of the active fraction. Cytotoxicity studies revealed low toxicity of the most of fractions in Vero and in equine peripheral blood mononuclear cells. Antiviral studies showed that the water crude extract – Sephadex LH 20 – fraction 3 MeOH–H2O (Fraction 3) was active against Western Equine Encephalitis virus with Effective Concentration 50% = 5 µg/ml. Selectivity Indices were 126.0 on Vero and 133.6 on peripheral blood mononuclear cells, four times higher than aqueous extract selectivity index. Regarding the mechanism of action we demonstrated that F3 exerted its action in intracellular replication stages. Further, fraction 3 showed important virucidal action. Fraction 3 contains, in order of highest to lowest: chlorogenic acid, luteolin, 5,7,8-trimethoxyflavone, 3-O-methylquercetin and caffeic acid. Fraction 3 did not induce in vivo toxic nor mutagenic effect. Therefore, it is safe its application as antiviral potential. Further studies of antiviral activity in vivo will be developed using a murine model.

In vitro propagation of "jarilla" (Larrea divaricata CAV.) and secondary metabolite production.

An efficient protocol for the in vitro germination and propagation of Larrea divaricata CAV. (Jarilla) was established. To determine the effect of different growth regulators on the growth rates and phenol production, apical-node microshoots from in vitro germinated plantlets were incubated on the following media: 1) full-strength MS (Murashige and Skoog) salt medium with different ratios of alpha-naphthaleneacetic acid (NAA) and N(6)-benzyladenine (BA); 2) after pre-treatment with indolebutyric acid (IBA), transfer to MS medium of different inorganic salt strengths; and 3) full-strength MS salt medium with different ratios of sucrose and IBA. Successful microshoot rooting percentages were achieved by the second and third strategies, the highest being 87.5-100%. The maximum principal shoot length and node number obtained by the second strategy corresponded to the plantlets previously induced with 50 microM IBA, and grown on half- or full-strength MS salt media (7.03+/-0.93 and 9.86+/-1.07 cm, respectively) while in the third strategy the most efficient micropropagation medium was full-strength MS salt medium supplemented with 7.5 microM IBA: 3% (w/v) sucrose (7.05+/-1.08 and 7.0+/-1.51 cm, respectively). The phenol concentration was determined by analytical HPLC. The highest content of nordihydroguiaretic acid (NDGA) accumulated in microplants of L. divaricata cultivated on half-strength MS salt medium (35.90+/-3.82 mg/g DW). Reducing the MS medium salt concentration by half, in the absence of IBA, it resulted in a higher NDGA production. NDGA production was not sensitive to the variation of IBA concentration. The medium supplemented with 5% (w/v) sucrose and 2.5 microM IBA induced not only a higher NDGA production but also a higher quercetin production.