Retinal ischemia induces α-SMA-mediated capillary pericyte contraction coincident with perivascular glycogen depletion

Increasing evidence indicates that pericytes are vulnerable cells, playing pathophysiological roles in various neurodegenerative processes. Microvascular pericytes contract during cerebral and coronary ischemia and do not relax after re-opening of the occluded artery, causing incomplete reperfusion. However, the cellular mechanisms underlying ischemia-induced pericyte contraction, its delayed emergence, and whether it is pharmacologically reversible are unclear. Here, we investigate i) whether ischemia-induced pericyte contractions are mediated by alpha-smooth muscle actin (α-SMA), ii) the sources of calcium rise in ischemic pericytes, and iii) if peri-microvascular glycogen can support pericyte metabolism during ischemia. Thus, we examined pericyte contractility in response to retinal ischemia both in vivo, using adaptive optics scanning light ophthalmoscopy and, ex vivo, using an unbiased stereological approach. We found that microvascular constrictions were associated with increased calcium in pericytes as detected by a genetically encoded calcium indicator (NG2-GCaMP6) or a fluoroprobe (Fluo-4). Knocking down α-SMA expression with RNA interference or fixing F-actin with phalloidin or calcium antagonist amlodipine prevented constrictions, suggesting that constrictions resulted from calcium- and α-SMA-mediated pericyte contractions. Carbenoxolone or a Cx43-selective peptide blocker also reduced calcium rise, consistent with involvement of gap junction-mediated mechanisms in addition to voltage-gated calcium channels. Pericyte calcium increase and capillary constrictions became significant after 1 h of ischemia and were coincident with depletion of peri-microvascular glycogen, suggesting that glucose derived from glycogen granules could support pericyte metabolism and delay ischemia-induced microvascular dysfunction. Indeed, capillary constrictions emerged earlier when glycogen breakdown was pharmacologically inhibited. Constrictions persisted despite recanalization but were reversible with pericyte-relaxant adenosine administered during recanalization. Our study demonstrates that retinal ischemia, a common cause of blindness, induces α-SMA- and calcium-mediated persistent pericyte contraction, which can be delayed by glucose driven from peri-microvascular glycogen. These findings clarify the contractile nature of capillary pericytes and identify a novel metabolic collaboration between peri-microvascular end-feet and pericytes.

Heck Diversification of Indole-Based Substrates under Aqueous Conditions: From Indoles to Unprotected Halo-tryptophans and Halo-tryptophans in Natural Product Derivatives

The blending of synthetic chemistry with biosynthetic processes provides a powerful approach to synthesis. Biosynthetic halogenation and synthetic cross-coupling have great potential to be used together, for small molecule generation, access to natural product analogues and as a tool for chemical biology. However, to enable enhanced generality of this approach, further synthetic tools are needed. Though considerable research has been invested in the diversification of phenylalanine and tyrosine, functionalisation of tryptophans thorough cross-coupling has been largely neglected. Tryptophan is a key residue in many biologically active natural products and peptides; in proteins it is key to fluorescence and dominates protein folding. To this end, we have explored the Heck cross-coupling of halo-indoles and halo-tryptophans in water, showing broad reaction scope. We have demonstrated the ability to use this methodology in the functionalisation of a brominated antibiotic (bromo-pacidamycin), as well as a marine sponge metabolite, barettin.

Identification of single nucleotide variants using position-specific error estimation in deep sequencing data

BACKGROUND

Targeted deep sequencing is a highly effective technology to identify known and novel single nucleotide variants (SNVs) with many applications in translational medicine, disease monitoring and cancer profiling. However, identification of SNVs using deep sequencing data is a challenging computational problem as different sequencing artifacts limit the analytical sensitivity of SNV detection, especially at low variant allele frequencies (VAFs).

METHODS

To address the problem of relatively high noise levels in amplicon-based deep sequencing data (e.g. with the Ion AmpliSeq technology) in the context of SNV calling, we have developed a new bioinformatics tool called AmpliSolve. AmpliSolve uses a set of normal samples to model position-specific, strand-specific and nucleotide-specific background artifacts (noise), and deploys a Poisson model-based statistical framework for SNV detection.

RESULTS

Our tests on both synthetic and real data indicate that AmpliSolve achieves a good trade-off between precision and sensitivity, even at VAF below 5% and as low as 1%. We further validate AmpliSolve by applying it to the detection of SNVs in 96 circulating tumor DNA samples at three clinically relevant genomic positions and compare the results to digital droplet PCR experiments.

CONCLUSIONS

AmpliSolve is a new tool for in-silico estimation of background noise and for detection of low frequency SNVs in targeted deep sequencing data. Although AmpliSolve has been specifically designed for and tested on amplicon-based libraries sequenced with the Ion Torrent platform it can, in principle, be applied to other sequencing platforms as well. AmpliSolve is freely available at https://github.com/dkleftogi/AmpliSolve .

Spatial and temporal influences on discrimination of vibrotactile stimuli on the arm

Body-machine interfaces (BMIs) provide a non-invasive way to control devices. Vibrotactile stimulation has been used by BMIs to provide performance feedback to the user, thereby reducing visual demands. To advance the goal of developing a compact, multivariate vibrotactile display for BMIs, we performed two psychophysical experiments to determine the acuity of vibrotactile perception across the arm. The first experiment assessed vibration intensity discrimination of sequentially presented stimuli within four dermatomes of the arm (C5, C7, C8, and T1) and on the ulnar head. The second experiment compared vibration intensity discrimination when pairs of vibrotactile stimuli were presented simultaneously vs. sequentially within and across dermatomes. The first experiment found a small but statistically significant difference between dermatomes C7 and T1, but discrimination thresholds at the other three locations did not differ. Thus, while all tested dermatomes of the arm and hand could serve as viable sites of vibrotactile stimulation for a practical BMI, ideal implementations should account for small differences in perceptual acuity across dermatomes. The second experiment found that sequential delivery of vibrotactile stimuli resulted in better intensity discrimination than simultaneous delivery, independent of whether the pairs were located within the same dermatome or across dermatomes. Taken together, our results suggest that the arm may be a viable site to transfer multivariate information via vibrotactile feedback for body-machine interfaces. However, user training may be needed to overcome the perceptual disadvantage of simultaneous vs. sequentially presented stimuli.

Outlook for coeliac disease patients: towards bread wheat with hypoimmunogenic gluten by gene editing of α- and γ-gliadin gene families

BACKGROUND

Wheat grains contain gluten proteins, which harbour immunogenic epitopes that trigger Coeliac disease in 1-2% of the human population. Wheat varieties or accessions containing only safe gluten have not been identified and conventional breeding alone struggles to achieve such a goal, as the epitopes occur in gluten proteins encoded by five multigene families, these genes are partly located in tandem arrays, and bread wheat is allohexaploid. Gluten immunogenicity can be reduced by modification or deletion of epitopes. Mutagenesis technologies, including CRISPR/Cas9, provide a route to obtain bread wheat containing gluten proteins with fewer immunogenic epitopes.

RESULTS

In this study, we analysed the genetic diversity of over 600 α- and γ-gliadin gene sequences to design six sgRNA sequences on relatively conserved domains that we identified near coeliac disease epitopes. They were combined in four CRISPR/Cas9 constructs to target the α- or γ-gliadins, or both simultaneously, in the hexaploid bread wheat cultivar Fielder. We compared the results with those obtained with random mutagenesis in cultivar Paragon by γ-irradiation. For this, Acid-PAGE was used to identify T1 grains with altered gliadin protein profiles compared to the wild-type endosperm. We first optimised the interpretation of Acid-PAGE gels using Chinese Spring deletion lines. We then analysed the changes generated in 360 Paragon γ-irradiated lines and in 117 Fielder CRISPR/Cas9 lines. Similar gliadin profile alterations, with missing protein bands, could be observed in grains produced by both methods.

CONCLUSIONS

The results demonstrate the feasibility and efficacy of using CRISPR/Cas9 to simultaneously edit multiple genes in the large α- and γ-gliadin gene families in polyploid bread wheat. Additional methods, generating genomics and proteomics data, will be necessary to determine the exact nature of the mutations generated with both methods.

An unsupervised neuromorphic clustering algorithm

Brains perform complex tasks using a fraction of the power that would be required to do the same on a conventional computer. New neuromorphic hardware systems are now becoming widely available that are intended to emulate the more power efficient, highly parallel operation of brains. However, to use these systems in applications, we need "neuromorphic algorithms" that can run on them. Here we develop a spiking neural network model for neuromorphic hardware that uses spike timing-dependent plasticity and lateral inhibition to perform unsupervised clustering. With this model, time-invariant, rate-coded datasets can be mapped into a feature space with a specified resolution, i.e., number of clusters, using exclusively neuromorphic hardware. We developed and tested implementations on the SpiNNaker neuromorphic system and on GPUs using the GeNN framework. We show that our neuromorphic clustering algorithm achieves results comparable to those of conventional clustering algorithms such as self-organizing maps, neural gas or k-means clustering. We then combine it with a previously reported supervised neuromorphic classifier network to demonstrate its practical use as a neuromorphic preprocessing module.

Deposition of a cutin apoplastic barrier separating seed maternal and zygotic tissues

BACKGROUND

In flowering plants, proper seed development is achieved through the constant interplay of fertilization products, embryo and endosperm, and maternal tissues. Communication between these compartments is supposed to be tightly regulated at their interfaces. Here, we characterize the deposition pattern of an apoplastic lipid barrier between the maternal inner integument and fertilization products in Arabidopsis thaliana seeds.

RESULTS

We demonstrate that an apoplastic lipid barrier is first deposited by the ovule inner integument and undergoes de novo cutin deposition following central cell fertilization and relief of the FERTILIZATION INDEPENDENT SEED Polycomb group repressive mechanism. In addition, we show that the WIP zinc-finger TRANSPARENT TESTA 1 and the MADS-Box TRANSPARENT TESTA 16 transcription factors act maternally to promote its deposition by regulating cuticle biosynthetic pathways. Finally, mutant analyses indicate that this apoplastic barrier allows correct embryo sliding along the seed coat.

CONCLUSIONS

Our results revealed that the deposition of a cutin apoplastic barrier between seed maternal and zygotic tissues is part of the seed coat developmental program.

Active mode of excretion across digestive tissues predates the origin of excretory organs

Most bilaterian animals excrete toxic metabolites through specialized organs, such as nephridia and kidneys, which share morphological and functional correspondences. In contrast, excretion in non-nephrozoans is largely unknown, and therefore the reconstruction of ancestral excretory mechanisms is problematic. Here, we investigated the excretory mode of members of the Xenacoelomorpha, the sister group to Nephrozoa, and Cnidaria, the sister group to Bilateria. By combining gene expression, inhibitor experiments, and exposure to varying environmental ammonia conditions, we show that both Xenacoelomorpha and Cnidaria are able to excrete across digestive-associated tissues. However, although the cnidarian Nematostella vectensis seems to use diffusion as its main excretory mode, the two xenacoelomorphs use both active transport and diffusion mechanisms. Based on these results, we propose that digestive-associated tissues functioned as excretory sites before the evolution of specialized organs in nephrozoans. We conclude that the emergence of a compact, multiple-layered bilaterian body plan necessitated the evolution of active transport mechanisms, which were later recruited into the specialized excretory organs.

Using nutritional geometry to define the fundamental macronutrient niche of the widespread invasive ant Monomorium pharaonis

The emerging field of nutritional geometry (NG) provides powerful new approaches to test whether and how organisms prioritize specific nutritional blends when consuming chemically complex foods. NG approaches can thus help move beyond food-level estimates of diet breadth to predict invasive success, for instance by revealing narrow nutritional niches if broad diets are actually composed of nutritionally similar foods. We used two NG paradigms to provide different, but complementary insights into nutrient regulation strategies and test a hypothesis of extreme nutritional generalism in colony propagules of the globally distributed invasive ant Monomorium pharaonis. First, in two dimensions (protein:carbohydrates; P:C), M. pharaonis colonies consistently defended a slightly carbohydrate-biased intake target, while using a generalist equal-distance strategy of collectively overharvesting both protein and carbohydrates to reach this target when confined to imbalanced P:C diets. Second, a recently developed right-angled mixture triangle method enabled us to define the fundamental niche breadth in three dimensions (protein:carbohydrates:lipid, P:C:L). We found that colonies navigated the P:C:L landscape, in part, to mediate a tradeoff between worker survival (maximized on high-carbohydrate diets) and brood production (maximized on high-protein diets). Colonies further appeared unable to avoid this tradeoff by consuming extra lipids when the other nutrients were limiting. Colonies also did not rely on nutrient regulation inside their nests, as they did not hoard or scatter fractions of harvested diets to adjust the nutritional blends they consumed. These complementary NG approaches highlight that even the most successful invasive species with broad fundamental macronutrient niches must navigate complex multidimensional nutritional landscapes to acquire limiting macronutrients and overcome developmental constraints as small propagules.

Single Crystal FLIM Characterization of Clofazimine Loaded in Silica-Based Mesoporous Materials and Zeolites

Clofazimine (CLZ) is an effective antibiotic used against a wide spectrum of Gram-positive bacteria and leprosy. One of its main drawbacks is its poor solubility in water. Silica based materials are used as drug delivery carriers that can increase the solubility of different hydrophobic drugs. Here, we studied how the properties of the silica framework of the mesoporous materials SBA-15, MCM-41, Al-MCM-41, and zeolites NaX, NaY, and HY affect the loading, stability, and distribution of encapsulated CLZ. Time-correlated single-photon counting (TCSPC) and fluorescence lifetime imaging microscopy (FLIM) experiments show the presence of neutral and protonated CLZ (1.3-3.8 ns) and weakly interacting aggregates (0.4-0.9 ns), along with H- and J-type aggregates (<0.1 ns). For the mesoporous and HY zeolite composites, the relative contribution to the overall emission spectra from H-type aggregates is low (<10%), while for the J-type aggregates it becomes higher (~30%). For NaX and NaY the former increased whereas the latter decreased. Although the CLZ@mesoporous composites show higher loading compared to the CLZ@zeolites ones, the behavior of CLZ is not uniform and its dynamics are more heterogeneous across different single mesoporous particles. These results may have implication in the design of silica-based drug carriers for better loading and release mechanisms of hydrophobic drugs.

Vapour sensing properties of graphene-covered gold nanoparticles

We investigated the vapour sensing properties of different graphene-gold hybrid nanostructures. We observed the shifts in the optical spectra near the local surface plasmon resonance of the gold nanoparticles by changing the concentration and nature of the analytes (ethanol, 2-propanol, and toluene). The smaller, dome-like gold nanoparticles proved to be more sensitive to these vapours compared to slightly larger, flat nanoparticles. We investigated how the optical response of the gold nanoparticles can be tuned with a corrugated graphene overlayer. We showed that the presence of graphene increased the sensitivity to ethanol and 2-propanol, while it decreased it towards toluene exposure (at concentrations ≥ 30%). The slope changes observed on the optical response curves were discussed in the framework of capillary condensation. These results can have potential impact on the development of new sensors based on graphene-gold hybrids.

Dynamical analysis of bacteria in microscopy movies

Recent advances in microscopy, computing power and image processing have enabled the analysis of ever larger datasets of movies of microorganisms to study their behaviour. However, techniques for analysing the dynamics of individual cells from such datasets are not yet widely available in the public domain. We recently demonstrated significant phenotypic heterogeneity in the adhesion of Escherichia coli bacteria to glass surfaces using a new method for the high-throughput analysis of video microscopy data. Here, we present an in-depth analysis of this method and its limitations, and make public our algorithms for following the positions and orientations of individual rod-shaped bacteria from time-series of 2D images to reconstruct their trajectories and characterise their dynamics. We demonstrate in detail how to use these algorithms to identify different types of adhesive dynamics within a clonal population of bacteria sedimenting onto a surface. The effects of measurement errors in cell positions and of limited trajectory durations on our results are discussed.

When a leader job resource can be ambivalent or even destructive: Independence at work as a double-edged sword

Independence at work is commonly considered a job resource which fosters motivation and employee well-being. Somewhat paradoxically, it is embedded in a relationship, and employees’ independence also hinges on their leaders’ willingness to grant it. Analyzing this resource as part of the leader-follower relationship can be useful in exploring its beneficial, ambivalent, or detrimental reciprocal effects. We present two Actor-Partner Interdependence Models (APIM) which analyze leaders’ and followers’ independence as antecedents, and work engagement and emotional exhaustion as outcomes. We test our models on 112 pairs of UK workers, finding a significant partner effect between leaders’ independence and followers’ exhaustion. Our findings confirm the utility of a dyadic perspective for investigating leadership and well-being at work, and suggest improvements for leadership training and measures fostering job well-being.

Microbial community drivers of PK/NRP gene diversity in selected global soils

BACKGROUND

The emergence of antibiotic-resistant pathogens has created an urgent need for novel antimicrobial treatments. Advances in next-generation sequencing have opened new frontiers for discovery programmes for natural products allowing the exploitation of a larger fraction of the microbial community. Polyketide (PK) and non-ribosomal pepetide (NRP) natural products have been reported to be related to compounds with antimicrobial and anticancer activities. We report here a new culture-independent approach to explore bacterial biosynthetic diversity and determine bacterial phyla in the microbial community associated with PK and NRP diversity in selected soils.

RESULTS

Through amplicon sequencing, we explored the microbial diversity (16S rRNA gene) of 13 soils from Antarctica, Africa, Europe and a Caribbean island and correlated this with the amplicon diversity of the adenylation (A) and ketosynthase (KS) domains within functional genes coding for non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), which are involved in the production of NRP and PK, respectively. Mantel and Procrustes correlation analyses with microbial taxonomic data identified not only the well-studied phyla Actinobacteria and Proteobacteria, but also, interestingly, the less biotechnologically exploited phyla Verrucomicrobia and Bacteroidetes, as potential sources harbouring diverse A and KS domains. Some soils, notably that from Antarctica, provided evidence of endemic diversity, whilst others, such as those from Europe, clustered together. In particular, the majority of the domain reads from Antarctica remained unmatched to known sequences suggesting they could encode enzymes for potentially novel PK and NRP.

CONCLUSIONS

The approach presented here highlights potential sources of metabolic novelty in the environment which will be a useful precursor to metagenomic biosynthetic gene cluster mining for PKs and NRPs which could provide leads for new antimicrobial metabolites.

Molecular Design of Microcapsule Shells for Visible Light-Triggered Release

The development of photo-responsive capsules to tune and control the sustained-release of encapsulated actives is a fascinating and challenging route to improve the performances and effectiveness of a wide range of delivery applications. In this work, we report the preparation of visible light-responsive capsules obtained via oil-in-water interfacial polycondensation between modified diacyl-chloride azobenzene moiety and diamine flexible spacer in the presence of cross-linkers with different structures and functionalities. The effect on the release profile of the encapsulated perfume oil was investigated using three flexible spacers with different lengths (1,8-diaminooctane; 1,6-diaminohexane and 1,4-diaminobutane) and two types of cross-linkers (1,3,5-benzenetricarbonyl trichloride and melamine). We analyzed how the properties of microcapsules can be tailored changing the design of the shell structure. Fine tuning of the perfume release profiles was obtained. The changes in capsules size and morphology due to visible light irradiation were monitored via light scattering, optical microscopy and atomic force microscopy. Perfume release was 50% faster in the systems prepared with melamine as the cross-linker. Modelling studies were carried out to support the discussion of the experimental results.

Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process

Fossil information is essential for estimating species divergence times, and can be integrated into Bayesian phylogenetic inference using the fossilized birth-death (FBD) process. An important aspect of palaeontological data is the uncertainty surrounding specimen ages, which can be handled in different ways during inference. The most common approach is to fix fossil ages to a point estimate within the known age interval. Alternatively, age uncertainty can be incorporated by using priors, and fossil ages are then directly sampled as part of the inference. This study presents a comparison of alternative approaches for handling fossil age uncertainty in analysis using the FBD process. Based on simulations, we find that fixing fossil ages to the midpoint or a random point drawn from within the stratigraphic age range leads to biases in divergence time estimates, while sampling fossil ages leads to estimates that are similar to inferences that employ the correct ages of fossils. Second, we show a comparison using an empirical dataset of extant and fossil cetaceans, which confirms that different methods of handling fossil age uncertainty lead to large differences in estimated node ages. Stratigraphic age uncertainty should thus not be ignored in divergence time estimation and instead should be incorporated explicitly.

Terrestrial Microorganisms: Cell Factories of Bioactive Molecules with Skin Protecting Applications

It is well known that terrestrial environments host an immense microbial biodiversity. Exposed to different types of stress, such as UV radiation, temperature fluctuations, water availability and the inter- / intra-specific competition for resources, terrestrial microorganisms have been evolved to produce a large spectrum of bioactive molecules. Bacteria, archaea, protists, fungi and algae have shown a high potential of producing biomolecules for pharmaceutical or other industrial purposes as they combine a sustainable, relatively low-cost and fast-production process. Herein, we provide an overview of the different bioactive molecules produced by terrestrial microorganisms with skin protecting applications. The high content in polyphenolic and carotenoid compounds produced by several strains, as well as the presence of exopolysaccharides, melanins, indole and pyrrole derivatives, mycosporines, carboxylic acids and other molecules, are discussed in the context of their antioxidant, photo-protective and skin-whitening activity. Relevant biotechnological tools developed for the enhanced production of high added value natural products, as well as the protecting effect of some antioxidant, hydrolytic and degrading enzymes are also discussed. Furthermore, we describe classes of microbial compounds that are used or have the potential to be used as antimicrobials, moisturizers, biosurfactants, pigments, flavorings and fragrances.

Multi-omics characterization of the necrotrophic mycoparasite Saccharomycopsis schoenii

Pathogenic yeasts and fungi are an increasing global healthcare burden, but discovery of novel antifungal agents is slow. The mycoparasitic yeast Saccharomycopsis schoenii was recently demonstrated to be able to kill the emerging multi-drug resistant yeast pathogen Candida auris. However, the molecular mechanisms involved in the predatory activity of S. schoenii have not been explored. To this end, we de novo sequenced, assembled and annotated a draft genome of S. schoenii. Using proteomics, we confirmed that Saccharomycopsis yeasts have reassigned the CTG codon and translate CTG into serine instead of leucine. Further, we confirmed an absence of all genes from the sulfate assimilation pathway in the genome of S. schoenii, and detected the expansion of several gene families, including aspartic proteases. Using Saccharomyces cerevisiae as a model prey cell, we honed in on the timing and nutritional conditions under which S. schoenii kills prey cells. We found that a general nutrition limitation, not a specific methionine deficiency, triggered predatory activity. Nevertheless, by means of genome-wide transcriptome analysis we observed dramatic responses to methionine deprivation, which were alleviated when S. cerevisiae was available as prey, and therefore postulate that S. schoenii acquired methionine from its prey cells. During predation, both proteomic and transcriptomic analyses revealed that S. schoenii highly upregulated and translated aspartic protease genes, probably used to break down prey cell walls. With these fundamental insights into the predatory behavior of S. schoenii, we open up for further exploitation of this yeast as a biocontrol yeast and/or source for novel antifungal agents.

Drug discovery for psychiatric disorders using high-content single-cell screening of signaling network responses ex vivo

There is a paucity of efficacious new compounds to treat neuropsychiatric disorders. We present a novel approach to neuropsychiatric drug discovery based on high-content characterization of druggable signaling network responses at the single-cell level in patient-derived lymphocytes ex vivo. Primary T lymphocytes showed functional responses encompassing neuropsychiatric medications and central nervous system ligands at established (e.g., GSK-3β) and emerging (e.g., CrkL) drug targets. Clinical application of the platform to schizophrenia patients over the course of antipsychotic treatment revealed therapeutic targets within the phospholipase Cγ1-calcium signaling pathway. Compound library screening against the target phenotype identified subsets of L-type calcium channel blockers and corticosteroids as novel therapeutically relevant drug classes with corresponding activity in neuronal cells. The screening results were validated by predicting in vivo efficacy in an independent schizophrenia cohort. The approach has the potential to discern new drug targets and accelerate drug discovery and personalized medicine for neuropsychiatric conditions.

Development and validation of an exome-based SNP marker set for identification of the St, Jr and Jvs genomes of Thinopyrym intermedium in a wheat background

KEY MESSAGE

Cytogenetic analysis and array-based SNP genotyping of wheat- Th. intermedium introgression lines allowed identification of 634 chromosome-specific SNP markers across all twenty-one chromosomes of Th. intermedium (StJ r J vs , 2 n  = 6 x  = 42). Thinopyrum intermedium (2n = 6x = 42, StJrJvs) is one of the most promising reservoirs of useful genes including tolerance to abiotic stresses, perenniality and disease resistance not available in the cultivated bread wheat. The transfer of genetic diversity from wild species to wheat offers valuable responses to the effects of climate change. The new array-based single-nucleotide polymorphism (SNP) marker technology provides cheap and easy-to-use molecular markers for marker-assisted selection (MAS) in wheat breeding programmes. Here, we focus on the generation of a new chromosome-specific SNP marker set that can be used to characterize and identify the Th. intermedium chromosomes or chromosome segments transferred into wheat. A progressive investigation of marker development was conducted using 187 various newly developed wheat-Th. intermedium introgression lines and the Axiom® Wheat-Relative Genotyping array. We employed molecular cytogenetic techniques to clarify the genome constitution of the Th. intermedium parental lines and validated 634 chromosome-specific SNPs. Our data confirmed the allohexaploid nature of Th. intermedium and demonstrated that the St genome-specific GISH signal and markers are present at the centromeric regions of chromosomes 1Jvs, 2Jvs, 3Jvs and 7Jvs. The SNP markers presented here will be introduced into current wheat improvement programmes, offering a significant speed-up in wheat breeding and making it possible to deal with the transfer of the full genetic potential of Th. intermedium into wheat.

Spatial segregation of the biological soil crust microbiome around its foundational cyanobacterium, Microcoleus vaginatus, and the formation of a nitrogen-fixing cyanosphere

BACKGROUND

Biological soil crusts (biocrusts) are a key component of arid land ecosystems, where they render critical services such as soil surface stabilization and nutrient fertilization. The bundle-forming, filamentous, non-nitrogen-fixing cyanobacterium Microcoleus vaginatus is a pioneer primary producer, often the dominant member of the biocrust microbiome, and the main source of leaked organic carbon. We hypothesized that, by analogy to the rhizosphere of plant roots, M. vaginatus may shape the microbial populations of heterotrophs around it, forming a specialized cyanosphere.

RESULTS

By physically isolating bundles of M. vaginatus from biocrusts, we were able to study the composition of the microbial populations attached to it, in comparison to the bulk soil crust microbiome by means of high-throughput 16S rRNA sequencing. We did this in two M. vaginatus-dominated biocrust from distinct desert biomes. We found that a small, selected subset of OTUs was significantly enriched in close proximity to M. vaginatus. Furthermore, we also found that a majority of bacteria (corresponding to some two thirds of the reads) were significantly more abundant away from this cyanobacterium. Phylogenetic placements suggest that all typical members of the cyanosphere were copiotrophs and that many were diazotrophs (Additional file 1: Tables S2 and S3). Nitrogen fixation genes were in fact orders of magnitude more abundant in this cyanosphere than in the bulk biocrust soil as assessed by qPCR. By contrary, competition for light, CO2, and low organic carbon concentrations defined at least a part of the OTUs segregating from the cyanobacterium.

CONCLUSIONS

We showed that M. vaginatus acts as a significant spatial organizer of the biocrust microbiome. On the one hand, it possesses a compositionally differentiated cyanosphere that concentrates the nitrogen-fixing function. We propose that a mutualism based on C for N exchange between M. vaginatus and copiotrophic diazotrophs helps sustains this cyanosphere and that this consortium constitutes the true pioneer community enabling the colonization of nitrogen-poor soils. On the other hand, a large number of biocrust community members segregate away from the vicinity of M. vaginatus, potentially through competition for light or CO2, or because of a preference for oligotrophy.

Macroevolutionary dynamics of nectar spurs, a key evolutionary innovation

Floral nectar spurs are widely considered a key innovation promoting diversification in angiosperms by means of pollinator shifts. We investigated the macroevolutionary dynamics of nectar spurs in the tribe Antirrhineae (Plantaginaceae), which contains 29 genera and 300-400 species (70-80% spurred). The effect of nectar spurs on diversification was tested, with special focus on Linaria, the genus with the highest number of species. We generated the most comprehensive phylogeny of Antirrhineae to date and reconstructed the evolution of nectar spurs. Diversification rate heterogeneity was investigated using trait-dependent and trait-independent methods, and accounting for taxonomic uncertainty. The association between changes in spur length and speciation was examined within Linaria using model testing and ancestral state reconstructions. We inferred four independent acquisitions of nectar spurs. Diversification analyses revealed that nectar spurs are loosely associated with increased diversification rates. Detected rate shifts were delayed by 5-15 Myr with respect to the acquisition of the trait. Active evolution of spur length, fitting a speciational model, was inferred in Linaria, which is consistent with a scenario of pollinator shifts driving diversification. Nectar spurs played a role in diversification of the Antirrhineae, but diversification dynamics can only be fully explained by the complex interaction of multiple biotic and abiotic factors.

Microstimulation in a spiking neural network model of the midbrain superior colliculus

The midbrain superior colliculus (SC) generates a rapid saccadic eye movement to a sensory stimulus by recruiting a population of cells in its topographically organized motor map. Supra-threshold electrical microstimulation in the SC reveals that the site of stimulation produces a normometric saccade vector with little effect of the stimulation parameters. Moreover, electrically evoked saccades (E-saccades) have kinematic properties that strongly resemble natural, visual-evoked saccades (V-saccades). These findings support models in which the saccade vector is determined by a center-of-gravity computation of activated neurons, while its trajectory and kinematics arise from downstream feedback circuits in the brainstem. Recent single-unit recordings, however, have indicated that the SC population also specifies instantaneous kinematics. These results support an alternative model, in which the desired saccade trajectory, including its kinematics, follows from instantaneous summation of movement effects of all SC spike trains. But how to reconcile this model with microstimulation results? Although it is thought that microstimulation activates a large population of SC neurons, the mechanism through which it arises is unknown. We developed a spiking neural network model of the SC, in which microstimulation directly activates a relatively small set of neurons around the electrode tip, which subsequently sets up a large population response through lateral synaptic interactions. We show that through this mechanism the population drives an E-saccade with near-normal kinematics that are largely independent of the stimulation parameters. Only at very low stimulus intensities the network recruits a population with low firing rates, resulting in abnormally slow saccades.

Two conformationally distinct α-synuclein oligomers share common epitopes and the ability to impair long-term potentiation

Parkinson’s Disease (PD) is a neurodegenerative disease for which there currently is no cure. Aggregation of the pre-synaptic protein α-synuclein (aSN) into oligomers (αSOs) is believed to play a key role in PD pathology, but little is known about αSO formation in vivo and how they induce neurodegeneration. Both the naturally occurring polyunsaturated fatty acid docosahexaenoic acid (DHA) and the lipid peroxidation product 4-hydroxynonenal (HNE), strongly upregulated during ROS conditions, stimulate the formation of αSOs, highlighting a potential role in PD. Yet, insight into αSOs structure and biological effects is still limited as most oligomer preparations studied to date are heterogeneous in composition. Here we have aggregated aSN in the presence of HNE and DHA and purified the αSOs using size exclusion chromatography. Both compounds stimulate formation of spherical αSOs containing anti-parallel β-sheet structure which have the same shape as unmodified αSOs though ca. 2-fold larger. Furthermore, the yield and stabilities of these oligomers are significantly higher than for unmodified aSN. Both modified and unmodified αSOs permeabilize synthetic vesicles, show high co-localisation with glutamatergic synapses and decrease Long Term Potentiation (LTP), in line with the reported synaptotoxic effects of αSOs. We conclude that DHA- and HNE-αSOs are convenient models for pathogenic disease-associated αSOs in PD.

Structure⁻Activity Study, Characterization, and Mechanism of Action of an Antimicrobial Peptoid D2 and Its d- and l-Peptide Analogues

Methicillin-resistant Staphylococcus pseudintermedius (MRSP) constitutes an emerging health problem for companion animals in veterinary medicine. Therefore, discovery of novel antimicrobial agents for treatment of Staphylococcus-associated canine infections is urgently needed to reduce use of human antibiotics in veterinary medicine. In the present work, we characterized the antimicrobial activity of the peptoid D2 against S. pseudintermedius and Pseudomonas aeruginosa, which is another common integumentary pathogen in dogs. Furthermore, we performed a structure⁻activity relationship study of D2, which included 19 peptide/peptoid analogs. Our best compound D2D, an all d-peptide analogue, showed potent minimum inhibitory concentrations (MICs) against canine S. pseudintermedius (2⁻4 µg/mL) and P. aeruginosa (4 µg/mL) isolates as well as other selected dog pathogens (2⁻16 µg/mL). Time⁻kill assays demonstrated that D2D was able to inhibit MRSP in 30 min at 1× MIC, significantly faster than D2. Our results suggest that at high concentrations D2D is rapidly lysing the bacterial membrane while D2 is inhibiting macromolecular synthesis. We probed the mechanism of action at sub-MIC concentrations of D2, D2D, the l-peptide analog and its retro analog by a macromolecular biosynthesis assay and fluorescence spectroscopy. Our data suggest that at sub-MIC concentrations D2D is membrane inactive and primarily works by cell wall inhibition, while the other compounds mainly act on the bacterial membrane.

Unraveling the Homologation Reaction Sequence of the Zeolite-Catalyzed Ethanol-to-Hydrocarbons Process

Although industrialized, the mechanism for catalytic upgrading of bioethanol over solid-acid catalysts (that is, the ethanol-to-hydrocarbons (ETH) reaction) has not yet been fully resolved. Moreover, mechanistic understanding of the ETH reaction relies heavily on its well-known "sister-reaction" the methanol-to-hydrocarbons (MTH) process. However, the MTH process possesses a C1 -entity reactant and cannot, therefore, shed any light on the homologation reaction sequence. The reaction and deactivation mechanism of the zeolite H-ZSM-5-catalyzed ETH process was elucidated using a combination of complementary solid-state NMR and operando UV/Vis diffuse reflectance spectroscopy, coupled with on-line mass spectrometry. This approach establishes the existence of a homologation reaction sequence through analysis of the pattern of the identified reactive and deactivated species. Furthermore, and in contrast to the MTH process, the deficiency of any olefinic-hydrocarbon pool species (that is, the olefin cycle) during the ETH process is also noted.

Natural enemies of armored scales (Hemiptera: Diaspididae) and soft scales (Hemiptera: Coccidae) in Chile: Molecular and morphological identification

Scale insects (Hemiptera: Sternorrhyncha: Coccomorpha) are key pests of agricultural crops and ornamental plants worldwide. Their populations are difficult to control, even with insecticides, due to their cryptic habits. Moreover, there is growing concern over the use of synthetic pesticides for their control, due to deleterious environmental effects and the emergence of resistant populations of target pests. In this context, biological control may be an effective and sustainable approach. Hymenoptera Chalcidoidea includes natural enemies of scale insects that have been successfully used in many biological control programs. However, the correct identification of pest scale species and their natural enemies is particularly challenging because these insects are very small and highly specialized. Integrative taxonomy, coupling DNA barcoding and morphological analysis, has been successfully used to characterize pests and natural enemy species. In this study, we performed a survey of parasitoids and predators of armored and soft scales in Chile, based on 28S and COI barcodes. Fifty-three populations of Diaspididae and 79 populations of Coccidae were sampled over the entire length of the country, from Arica (18°S) to Frutillar (41°S), between January 2015 and February 2016. The phylogenetic relationships obtained by Bayesian inference from multilocus haplotypes revealed 41 putative species of Chalcidoidea, five Coccinellidae and three Neuroptera. Species delimitation was confirmed using ABGD, GMYC and PTP model. In Chalcidoidea, 23 species were identified morphologically, resulting in new COI barcodes for 12 species and new 28S barcodes for 14 species. Two predator species (Rhyzobius lophantae and Coccidophilus transandinus) were identified morphologically, and two parasitoid species, Chartocerus niger and Signiphora bifasciata, were recorded for the first time in Chile.

Ball milling: a green technology for the preparation and functionalisation of nanocellulose derivatives

Ball milling is a simple, fast, cost-effective green technology with enormous potential. One of the most interesting applications of this technology in the field of cellulose is the preparation and the chemical modification of cellulose nanocrystals and nanofibers. Although a number of studies have been reported in the literature, the potential of this technique in the field of cellulose nanoparticles has not been fully exploited. This minireview aims at putting existing work into perspective, highlighting the significance and the potential of this green, sustainable technique to facilitate the identification of areas of future development.

Cubosomes: The Next Generation of Smart Lipid Nanoparticles?

Cubosomes are highly stable nanoparticles formed from the lipid cubic phase and stabilized by a polymer based outer corona. Bicontinuous lipid cubic phases consist of a single lipid bilayer that forms a continuous periodic membrane lattice structure with pores formed by two interwoven water channels. Cubosome composition can be tuned to engineer pore sizes or include bioactive lipids, the polymer outer corona can be used for targeting and they are highly stable under physiological conditions. Compared to liposomes, the structure provides a significantly higher membrane surface area for loading of membrane proteins and small drug molecules. Owing to recent advances, they can be engineered in vitro in both bulk and nanoparticle formats with applications including drug delivery, membrane bioreactors, artificial cells, and biosensors. This review outlines recent advances in cubosome technology enabling their application and provides guidelines for the rational design of new systems for biomedical applications.

Genetic algorithm as an optimization tool for the development of sponge cell culture media

Sponges are rich sources of novel natural products. Production in cell cultures may be an option for supply of these compounds but there are currently no sponge cell lines. Because there is a lack of understanding about the precise conditions and nutritional requirements that are necessary to sustain sponge cells in vitro, there has yet to be a defined, sponge-specific nutrient medium. This study utilized a genetic algorithm approach to optimize the amino acid composition of a commercially available basal cell culture medium in order to increase the metabolic activity of cells of the marine sponge Dysidea etheria. Four generations of the algorithm were carried out in vitro in wet lab conditions and an optimal medium combination was selected for further evaluation. When compared to the basal medium control, there was a twofold increase in metabolic activity. The genetic algorithm approach can be used to optimize other components of culture media to efficiently optimize chosen parameters without the need for detailed knowledge on all possible interactions.

Propofol-induced deep sedation reduces emotional episodic memory reconsolidation in humans

The adjustment of maladaptive thoughts and behaviors associated with emotional memories is central to treating psychiatric disorders. Recent research, predominantly with laboratory animals, indicates that memories can become temporarily sensitive to modification following reactivation, before undergoing reconsolidation. A method to selectively impair reconsolidation of specific emotional or traumatic memories in humans could translate to an effective treatment for conditions such as posttraumatic stress disorder. We tested whether deep sedation could impair emotional memory reconsolidation in 50 human participants. Administering the intravenous anesthetic propofol following memory reactivation disrupted memory for the reactivated, but not for a non-reactivated, slideshow story. Propofol impaired memory for the reactivated story after 24 hours, but not immediately after propofol recovery. Critically, memory impairment occurred selectively for the emotionally negative phase of the reactivated story. One dose of propofol following memory reactivation selectively impaired subsequent emotional episodic memory retrieval in a time-dependent manner, consistent with reconsolidation impairment.

Hydrogen-Bond-Enabled Dynamic Kinetic Resolution of Axially Chiral Amides Mediated by a Chiral Counterion

Non-biaryl atropisomers are valuable in medicine, materials, and catalysis, but their enantioselective synthesis remains a challenge. Herein, a counterion-mediated O-alkylation method for the generation of atropisomeric amides with an er up to 99:1 is outlined. This dynamic kinetic resolution is enabled by the observation that the rate of racemization of atropisomeric naphthamides is significantly increased by the presence of an intramolecular O-H⋅⋅⋅NCO hydrogen bond. Upon O-alkylation of the H-bond donor, the barrier to rotation is significantly increased. Quantum calculations demonstrate that the intramolecular H-bond reduces the rotational barrier about the aryl-amide bond, stabilizing the planar transition state for racemization by approximately 40 kJ mol-1 , thereby facilitating the observed dynamic kinetic resolution.

Developmental profiles of SUMOylation pathway proteins in rat cerebrum and cerebellum

Protein SUMOylation regulates multiple processes involved in the differentiation and maturation of cells and tissues during development. Despite this, relatively little is known about the spatial and temporal regulation of proteins that mediate SUMOylation and deSUMOylation in the CNS. Here we monitor the expression of key SUMO pathway proteins and levels of substrate protein SUMOylation in the forebrain and cerebellum of Wistar rats during development. Overall, the SUMOylation machinery is more highly-expressed at E18 and decreases thereafter, as previously described. All of the proteins investigated are less abundant in adult than in embryonic brain. Furthermore, we show for first time that the profiles differ between cerebellum and cerebrum, indicating differential regional regulation of some of the proteins analysed. These data provide further basic observation that may open a new perspective of research about the role of SUMOylation in the development of different brain regions.

The use of tail-anchored protein chimeras to enhance liposomal cargo delivery

Background

Liposomes are employed as drug delivery vehicles offering a beneficial pharmacokinetic/distribution mechanism for in vivo therapeutics. Therapeutic liposomes can be designed to target specific cell types through the display of epitope-specific targeting peptides on their surface. The majority of peptides are currently attached by chemical modification of lipid constituents. Here we investigate an alternative and novel method of decorating liposomes with targeting ligand, using remotely and spontaneously inserting chimeric tail-anchored membrane (TA) proteins to drug loaded liposomes.

Methods and results

An artificial TA protein chimera containing the transmembrane domain from the spontaneously inserting TA protein cytochrome b5 (Cytb5) provided a robust membrane tether for the incorporation of three different targeting moieties into preformed liposomes. The moieties investigated were the transactivator of transcription (TAT) peptide, the EGF-receptor binding sequence GE11 and the placental and tumour homing ligand CCGKRK. In all cases, TA protein insertion neither significantly altered the size of the liposomes nor reduced drug loading. The efficacy of this novel targeted delivery system was investigated using two human cell lines, HeLa M and BeWo. Short term incubation with one ligand-modified TA chimera, incorporating the TAT peptide, significantly enhanced liposomal delivery of the encapsulated carboxyfluorescein reporter.

Conclusion

The Cytb5 TA was successfully employed as a membrane anchor for the incorporation of the desired peptide ligands into a liposomal drug delivery system, with minimal loss of cargo during insertion. This approach therefore provides a viable alternative to chemical conjugation and its potential to accommodate a wider range of targeting ligands may provide an opportunity for enhancing drug delivery.

Enhancing X-ray Attenuation of 3D Printed Gelatin Methacrylate (GelMA) Hydrogels Utilizing Gold Nanoparticles for Bone Tissue Engineering Applications

Bone tissue engineering is a rapidly growing field which is currently progressing toward clinical applications. Effective imaging methods for longitudinal studies are critical to evaluating the new bone formation and the fate of the scaffolds. Computed tomography (CT) is a prevailing technique employed to investigate hard tissue scaffolds; however, the CT signal becomes weak in mainly-water containing materials, which hinders the use of CT for hydrogels-based materials. Nevertheless, hydrogels such as gelatin methacrylate (GelMA) are widely used for tissue regeneration due to their optimal biological properties and their ability to induce extracellular matrix formation. To date, gold nanoparticles (AuNPs) have been suggested as promising contrast agents, due to their high X-ray attenuation, biocompatibility, and low toxicity. In this study, the effects of different sizes and concentrations of AuNPs on the mechanical properties and the cytocompatibility of the bulk GelMA-AuNPs scaffolds were evaluated. Furthermore, the enhancement of CT contrast with the cytocompatible size and concentration of AuNPs were investigated. 3D printed GelMA and GelMA-AuNPs scaffolds were obtained and assessed for the osteogenic differentiation of mesenchymal stem cells (MSC). Lastly, 3D printed GelMA and GelMA-AuNPs scaffolds were scanned in a bone defect utilizing µCT as the proof of concept that the GelMA-AuNPs are good candidates for bone tissue engineering with enhanced visibility for µCT imaging.

An efficient method for markerless mutant generation by allelic exchange in Clostridium acetobutylicum and Clostridium saccharobutylicum using suicide vectors

BACKGROUND

Clostridium acetobutylicum and Clostridium saccharobutylicum are Gram-positive, spore-forming, anaerobic bacterium capable of converting various sugars and polysaccharides into solvents (acetone, butanol, and ethanol). The sequencing of their genomes has prompted new approaches to genetic analysis, functional genomics, and metabolic engineering to develop industrial strains for the production of biofuels and bulk chemicals.

RESULTS

The method used in this paper to knock-out, knock-in, or edit genes in C. acetobutylicum and C. saccharobutylicum combines an improved electroporation method with the use of (i) restrictionless Δupp (which encodes uracil phosphoribosyl-transferase) strains and (ii) very small suicide vectors containing a markerless deletion/insertion cassette, an antibiotic resistance gene (for the selection of the first crossing-over) and upp (from C. acetobutylicum) for subsequent use as a counterselectable marker with the aid of 5-fluorouracil (5-FU) to promote the second crossing-over. This method was successfully used to both delete genes and edit genes in both C. acetobutylicum and C. saccharobutylicum. Among the edited genes, a mutation in the spo0A gene that abolished solvent formation in C. acetobutylicum was introduced in C. saccharobutylicum and shown to produce the same effect.

CONCLUSIONS

The method described in this study will be useful for functional genomic studies and for the development of industrial strains for the production of biofuels and bulk chemicals.

Transcriptional profiling at the DLK1/MEG3 domain explains clinical overlap between imprinting disorders

Imprinting disorders (IDs) often affect growth in humans, leading to diseases with overlapping features, regardless of the genomic region affected. IDs related to hypomethylation of the human 14q32.2 region and its DLK1/MEG3 domain are associated with Temple syndrome (TS14). TS14 is a rare type of growth retardation, the clinical signs of which overlap considerably with those of Silver-Russell syndrome (SRS), another ID related to IGF2 down-regulation at 11p15.5 region. We show that 14q32.2 hypomethylation affects expression, not only for genes at this locus but also for other imprinted genes, and especially lowers IGF2 levels at 11p15.5. Furthermore, expression of nonimprinted genes is also affected, some of which are also deregulated in SRS patients. These findings highlight the epigenetic regulation of gene expression at the DLK1/MEG3 domain. Expression profiling of TS14 and SRS patients highlights common signatures, which may account for the clinical overlap observed between TS14 and SRS.

Mitochondrial proline catabolism activates Ras1/cAMP/PKA-induced filamentation in Candida albicans

Amino acids are among the earliest identified inducers of yeast-to-hyphal transitions in Candida albicans, an opportunistic fungal pathogen of humans. Here, we show that the morphogenic amino acids arginine, ornithine and proline are internalized and metabolized in mitochondria via a PUT1- and PUT2-dependent pathway that results in enhanced ATP production. Elevated ATP levels correlate with Ras1/cAMP/PKA pathway activation and Efg1-induced gene expression. The magnitude of amino acid-induced filamentation is linked to glucose availability; high levels of glucose repress mitochondrial function thereby dampening filamentation. Furthermore, arginine-induced morphogenesis occurs more rapidly and independently of Dur1,2-catalyzed urea degradation, indicating that mitochondrial-generated ATP, not CO2, is the primary morphogenic signal derived from arginine metabolism. The important role of the SPS-sensor of extracellular amino acids in morphogenesis is the consequence of induced amino acid permease gene expression, i.e., SPS-sensor activation enhances the capacity of cells to take up morphogenic amino acids, a requisite for their catabolism. C. albicans cells engulfed by murine macrophages filament, resulting in macrophage lysis. Phagocytosed put1-/- and put2-/- cells do not filament and exhibit reduced viability, consistent with a critical role of mitochondrial proline metabolism in virulence.

Motivations for Sexual Behavior and Intentions to Use Condoms: Development of the Regulatory Focus in Sexuality Scale

Despite recurrent efforts to prevent sexually transmitted diseases through the use of condoms, HIV infections are still prevalent across Europe. Recent research framed by the regulatory focus theory has shown that prevention (vs. promotion)-focused individuals are more likely to adopt strategies to protect their health. Therefore, these individuals should also be more motivated to use condoms, because they are more likely to perceive greater health threats. In two cross-sectional preregistered studies (combined N = 520 Portuguese participants; databases available at https://doi.org/10.17605/osf.io/zzkc2 ), we developed the new Regulatory Focus in Sexuality scale (Study 1), and tested if the association between prevention focus and intentions to use condoms was mediated by the perception of health threat (Study 2). Results from Study 1 suggested that the scale is reliable and valid. Results from Study 2 showed, as expected, that a predominant focus on prevention was associated with more condom use intentions with casual and regular sexual partners, because individuals perceived greater threat to their health. Additional exploratory analyses further showed that this mediation occurred only for individuals without a romantic relationship and was independent of how salient the condom use norm was. In contrast, for romantically involved individuals, there was no evidence for the mediation by perceived health threat. Instead, a predominant focus on prevention was positively associated with condom use intentions with the regular partner, but only when the condom use norm was more salient. Taken together, these results emphasize the importance of examining individual motivations for safe sex practices.

Self-Assembling Hybrid Linear-Dendritic Block Copolymers: The Design of Nano-Carriers for Lipophilic Antitumoral Drugs

Two series of amphiphilic block copolymers with a hybrid linear-dendritic structure are presented. The compounds consisted of a hydrophilic poly (ethylene glycol) (PEG) block and a 2,2'-bis(hydroxymethyl)propionic acid (bis-MPA) dendron functionalized with stearic acid chains that impart a hydrophobic nature to the block. Different self-assembled nanostructures with a hydrophobic interior and a hydrophilic external part were obtained depending on the length of the PEG chain (Mn = 2000 and Mn = 5000) and the generation of the bis-MPA dendron. The materials were characterized by transmission electron microscopy (TEM). The shapes of the aggregates ranged from spherical or cylindrical micelles to flexible bilayers. The hydrophobic core enabled these nanostructures to encapsulate the water-insoluble drug plitidepsin. The efficacy of these new plitidepsin-containing carriers was evaluated in four cancer cell-lines and they showed similar anticancer activity to the current standard drug formulation.

Triple oral beta-lactam containing therapy for Buruli ulcer treatment shortening

The potential use of clinically approved beta-lactams for Buruli ulcer (BU) treatment was investigated with representative classes analyzed in vitro for activity against Mycobacterium ulcerans. Beta-lactams tested were effective alone and displayed a strong synergistic profile in combination with antibiotics currently used to treat BU, i.e. rifampicin and clarithromycin; this activity was further potentiated in the presence of the beta-lactamase inhibitor clavulanate. In addition, quadruple combinations of rifampicin, clarithromycin, clavulanate and beta-lactams resulted in multiplicative reductions in their minimal inhibitory concentration (MIC) values. The MIC of amoxicillin against a panel of clinical isolates decreased more than 200-fold within this quadruple combination. Amoxicillin/clavulanate formulations are readily available with clinical pedigree, low toxicity, and orally and pediatric available; thus, supporting its potential inclusion as a new anti-BU drug in current combination therapies.

Buruli ulcer (BU) is a chronic debilitating disease of the skin and soft tissue, mainly affecting children and young adults in tropical regions. Before 2004, the only treatment option was surgery; a major breakthrough was the discovery that BU could be cured in most cases with a standard treatment that involved 8 weeks of combination therapy with rifampicin and streptomycin. However, the use of streptomycin is often associated with severe side effects such as ototoxicity, or nephrotoxicity. More recently, a clinical trial demonstrated equipotency of replacing the injectable streptomycin by the clarithromycin, which is orally available and associated with fewer side effects. BU treatment is now moving toward a full orally available treatment of clarithromycin-rifampicin. Although effective and mostly well tolerated, this new treatment is still associated with side effects and only moxifloxacin is additionally recommended by WHO for BU therapy. New drugs are thus needed to increase the number of available treatments, reduce side effects, and improve efficacy with treatments shorter than 8 weeks. In this work, we describe for the first time the potential inclusion of beta-lactams in BU therapy. More specifically, we propose the use of amoxicillin/clavulanate since it is oral, suitable for the treatment of children, and readily available with a long track record of clinical pedigree. Its inclusion in a triple oral therapy complementing current combinatorial rifampicin-clarithromycin treatment has the potential to counteract resistance development and to reduce length of treatment and time to cure.

Introducing and evaluating a knowledge transfer approach to support problem solving in and around protected areas

Protected areas (PAs) can generate many benefits inside and outside their borders, and achieving objectives for diverse stakeholders raises many challenges. There are many examples of successful PA management around the globe, although a systematic and comprehensive approach to developing and sharing these solutions has been lacking. We present "solutioning" as a structured process of peer-learning, which can inform management strategies in and around protected areas. We explain how the PANORAMA-Solutions for a Healthy Planet initiative has put solutioning into practice through an interactive community and web portal to learn about protected area solutions around the globe. Unlike other web platforms and initiatives reviewed, PANORAMA facilitates adaptation of solution elements (i.e., building blocks) for novel implementation. Supported by theories of resilience and peer-learning, PANORAMA appears to have potential to promote efficiency and equitable benefits for PAs and associated stakeholders focused on nature conservation and sustainable development, although further research is needed to assess whether this learning leads to better solutions or more effective PA management.

Subjective ratings and emotional recognition of children's facial expressions from the CAFE set

Access to validated stimuli depicting children's facial expressions is useful for different research domains (e.g., developmental, cognitive or social psychology). Yet, such databases are scarce in comparison to others portraying adult models, and validation procedures are typically restricted to emotional recognition accuracy. This work presents subjective ratings for a sub-set of 283 photographs selected from the Child Affective Facial Expression set (CAFE [1]). Extending beyond the original emotion recognition accuracy norms [2], our main goal was to validate this database across eight subjective dimensions related to the model (e.g., attractiveness, familiarity) or the specific facial expression (e.g., intensity, genuineness), using a sample from a different nationality (N = 450 Portuguese participants). We also assessed emotion recognition (forced-choice task with seven options: anger, disgust, fear, happiness, sadness, surprise and neutral). Overall results show that most photographs were rated as highly clear, genuine and intense facial expressions. The models were rated as both moderately familiar and likely to belong to the in-group, obtaining high attractiveness and arousal ratings. Results also showed that, similarly to the original study, the facial expressions were accurately recognized. Normative and raw data are available as supplementary material at https://osf.io/mjqfx/.

Long-term soil metal exposure impaired temporal variation in microbial metatranscriptomes and enriched active phages

BACKGROUND

It remains unclear whether adaptation and changes in diversity associated to a long-term perturbation are sufficient to ensure functional resilience of soil microbial communities. We used RNA-based approaches (16S rRNA gene transcript amplicon coupled to shotgun mRNA sequencing) to study the legacy effects of a century-long soil copper (Cu) pollution on microbial activity and composition, as well as its effect on the capacity of the microbial community to react to temporal fluctuations.

RESULTS

Despite evidence of microbial adaptation (e.g., iron homeostasis and avoidance/resistance strategies), increased heterogeneity and richness loss in transcribed gene pools were observed with increasing soil Cu, together with an unexpected predominance of phage mRNA signatures. Apparently, phage activation was either triggered directly by Cu, or indirectly via enhanced expression of DNA repair/SOS response systems in Cu-exposed bacteria. Even though total soil carbon and nitrogen had accumulated with increasing Cu, a reduction in temporally induced mRNA functions was observed. Microbial temporal response groups (TRGs, groups of microbes with a specific temporal response) were heavily affected by Cu, both in abundance and phylogenetic composition.

CONCLUSION

Altogether, results point toward a Cu-mediated "decoupling" between environmental fluctuations and microbial activity, where Cu-exposed microbes stopped fulfilling their expected contributions to soil functioning relative to the control. Nevertheless, some functions remained active in February despite Cu, concomitant with an increase in phage mRNA signatures, highlighting that somehow, microbial activity is still happening under these adverse conditions.

SugarSketcher: Quick and Intuitive Online Glycan Drawing

SugarSketcher is an intuitive and fast JavaScript interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences (e.g., GlycoCT) or quality images (e.g., svg). It does not require a backend server or any specific browser plugins and can be integrated in any web glycoinformatics project. SugarSketcher allows drawing glycans both for glycobiologists and non-expert users. The "quick mode" allows a newcomer to build up a glycan structure having only a limited knowledge in carbohydrate chemistry. The "normal mode" integrates advanced options which enable glycobiologists to tailor complex carbohydrate structures. The source code is freely available on GitHub and glycoinformaticians are encouraged to participate in the development process while users are invited to test a prototype available on the ExPASY web-site and send feedback.

Risk prediction for estrogen receptor-specific breast cancers in two large prospective cohorts

BACKGROUND

Few published breast cancer (BC) risk prediction models consider the heterogeneity of predictor variables between estrogen-receptor positive (ER+) and negative (ER-) tumors. Using data from two large cohorts, we examined whether modeling this heterogeneity could improve prediction.

METHODS

We built two models, for ER+ (ModelER+) and ER- tumors (ModelER-), respectively, in 281,330 women (51% postmenopausal at recruitment) from the European Prospective Investigation into Cancer and Nutrition cohort. Discrimination (C-statistic) and calibration (the agreement between predicted and observed tumor risks) were assessed both internally and externally in 82,319 postmenopausal women from the Women's Health Initiative study. We performed decision curve analysis to compare ModelER+ and the Gail model (ModelGail) regarding their applicability in risk assessment for chemoprevention.

RESULTS

Parity, number of full-term pregnancies, age at first full-term pregnancy and body height were only associated with ER+ tumors. Menopausal status, age at menarche and at menopause, hormone replacement therapy, postmenopausal body mass index, and alcohol intake were homogeneously associated with ER+ and ER- tumors. Internal validation yielded a C-statistic of 0.64 for ModelER+ and 0.59 for ModelER-. External validation reduced the C-statistic of ModelER+ (0.59) and ModelGail (0.57). In external evaluation of calibration, ModelER+ outperformed the ModelGail: the former led to a 9% overestimation of the risk of ER+ tumors, while the latter yielded a 22% underestimation of the overall BC risk. Compared with the treat-all strategy, ModelER+ produced equal or higher net benefits irrespective of the benefit-to-harm ratio of chemoprevention, while ModelGail did not produce higher net benefits unless the benefit-to-harm ratio was below 50. The clinical applicability, i.e. the area defined by the net benefit curve and the treat-all and treat-none strategies, was 12.7 × 10- 6 for ModelER+ and 3.0 × 10- 6 for ModelGail.

CONCLUSIONS

Modeling heterogeneous epidemiological risk factors might yield little improvement in BC risk prediction. Nevertheless, a model specifically predictive of ER+ tumor risk could be more applicable than an omnibus model in risk assessment for chemoprevention.

Research trends and geographical distribution of mammalian carnivores in Portugal (SW Europe)

Information regarding species’ status at a regional scale is instrumental for effective conservation planning. Some regions of southwestern Europe, such as Portugal, albeit included in the Mediterranean biodiversity hotspot, lack a detailed assessment of the distribution patterns of several taxonomic groups, such as carnivores. Moreover, information is scattered, often unreliable and biased towards some species or regions. This study aimed at reviewing the existing knowledge on mammalian terrestrial carnivores in Portugal, to analyse research trends, update the species checklist and assess their historical and current distribution patterns. We conducted a comprehensive review of 755 scientific studies to analyse several publication metrics and compiled 20,189 presence records of all mammalian terrestrial carnivores occurring in Portugal since historical times to evaluate their distribution patterns. Carnivore research in Portugal began in the 18th century, with a recent boost in the mid-1990s, and has been biased towards certain research topics and regionally threatened species. There are 15 extant species in Portugal, with nine occurring across the country, six showing a more limited range, as well as one additional species currently locally extinct (Ursus arctos). Over the last decades, the distribution ranges of seven species apparently remained stable, two expanded, two contracted, and three showed unclear trends. The presence of a new invasive carnivore, the raccoon (Procyon lotor), is also documented here. This study illustrates the relevance of a comprehensive analysis of non-systematic data to assess the historic and current status of mammalian terrestrial carnivores at a national level, and to identify knowledge gaps and research priorities.

Lectins at Interfaces-An Atomic Force Microscopy and Multi-Parameter-Surface Plasmon Resonance Study

Lectins are a diverse class of carbohydrate binding proteins with pivotal roles in cell communication and signaling in many (patho)physiologic processes in the human body, making them promising targets in drug development, for instance, in cancer or infectious diseases. Other applications of lectins employ their ability to recognize specific glycan epitopes in biosensors and glycan microarrays. While a lot of research has focused on lectin interaction with specific carbohydrates, the interaction potential of lectins with different types of surfaces has not been addressed extensively. Here, we screen the interaction of two specific plant lectins, Concanavalin A and Ulex Europaeus Agglutinin-I with different nanoscopic thin films. As a control, the same experiments were performed with Bovine Serum Albumin, a widely used marker for non-specific protein adsorption. In order to test the preferred type of interaction during adsorption, hydrophobic, hydrophilic and charged polymer films were explored, such as polystyrene, cellulose, N,-N,-N-trimethylchitosan chloride and gold, and characterized in terms of wettability, surface free energy, zeta potential and morphology. Atomic force microscopy images of surfaces after protein adsorption correlated very well with the observed mass of adsorbed protein. Surface plasmon resonance spectroscopy studies revealed low adsorbed amounts and slow kinetics for all of the investigated proteins for hydrophilic surfaces, making those resistant to non-specific interactions. As a consequence, they may serve as favorable supports for biosensors, since the use of blocking agents is not necessary.

Associations between ambient air temperature, low birth weight and small for gestational age in term neonates in southern Israel

BACKGROUND

The increase in ambient temperatures (Ta) and emissions of greenhouse gases over the last century has focused attention on the effects of ambient temperatures on health outcomes. We aimed to investigate the association between Ta and the clinical measures of term low birth weight (tLBW) and small for gestational age (SGA) in singleton term infants using a decade of regional hospital data in southern Israel.

METHODS

We linked all births in Soroka University Medical Center in the southern district of Israel insured by Clalit Health Services with pregnancy Ta estimated by our novel hybrid spatio-temporally resolved prediction model. Logistic regression generalized additive models and general linear models were used, with either tLBW or SGA as the dependent variable, modeling entire pregnancy and trimester-specific Ta adjusting for seasonality, time trend, particulate matter, maternal age, gravidity, parity, ethnicity, sex, poverty index and population density.

RESULTS

The study population included 56,141 singleton term newborns, with 1716 (3.1%) cases of tLBW and 8634 (15.4%) cases of SGA. The average and the median Ta across the entire pregnancy were 19.9 (SD: 1.77, range: 14.6-24.9) degrees centigrade. The lowest Ta quartile (Ta = < 18.5) was associated with higher risk of tLBW (odds ratio = 1.33, 95%CI 1.11-1.58) while the highest Ta quartile (Ta > =21.3) was not significantly associated with tLBW (odds ratio = 1.17, 95%CI 0.99-1.38), in comparison to the two intermediate quartiles. When analyzing SGA as the dependent variable, the lowest Ta quartile was associated with significantly higher risk of SGA (odds ratio = 1.18, 95%CI 1.09-1.29) while the highest quartile was associated with significantly lower risk of SGA (odds ratio = 0.91, 95%CI 0.84-0.99) in comparison to the two intermediate quartiles.

CONCLUSIONS

Our findings suggest that lower pregnancy Ta may increase the risk of tLBW and SGA, and higher pregnancy Ta may decrease the risk of SGA in singleton term infants in southern Israel.

Whole-head recording of chemosensory activity in the marine annelid Platynereis dumerilii

Chemical detection is key to various behaviours in both marine and terrestrial animals. Marine species, though highly diverse, have been underrepresented so far in studies on chemosensory systems, and our knowledge mostly concerns the detection of airborne cues. A broader comparative approach is therefore desirable. Marine annelid worms with their rich behavioural repertoire represent attractive models for chemosensation. Here, we study the marine worm Platynereis dumerilii to provide the first comprehensive investigation of head chemosensory organ physiology in an annelid. By combining microfluidics and calcium imaging, we record neuronal activity in the entire head of early juveniles upon chemical stimulation. We find that Platynereis uses four types of organs to detect stimuli such as alcohols, esters, amino acids and sugars. Antennae are the main chemosensory organs, compared to the more differentially responding nuchal organs or palps. We report chemically evoked activity in possible downstream brain regions including the mushroom bodies (MBs), which are anatomically and molecularly similar to insect MBs. We conclude that chemosensation is a major sensory modality for marine annelids and propose early Platynereis juveniles as a model to study annelid chemosensory systems.