eDNA in a bottleneck : obstacles to fish metabarcoding studies in megadiverse freshwater systems

The current capacity of environmental DNA (eDNA) to provide accurate insights into the biodiversity of megadiverse regions (e.g., the Neotropics) requires further evaluation to ensure its reliability for long‐term monitoring. In this study, we first evaluated the taxonomic resolution capabilities of a short fragment from the 12S rRNA gene widely used in fish eDNA metabarcoding studies, and then compared eDNA metabarcoding data from water samples with traditional sampling using nets. For the taxonomic discriminatory power analysis, we used a specifically curated reference dataset consisting of 373 sequences from 258 neotropical fish species (including 47 newly generated sequences) to perform a genetic distance‐based analysis of the amplicons targeted by the MiFish primer set. We obtained an optimum delimitation threshold value of 0.5% due to lowest cumulative errors. The barcoding gap analysis revealed only a 51.55% success rate in species recovery (133/258), highlighting a poor taxonomic resolution from the targeted amplicon. To evaluate the empirical performance of this amplicon for biomonitoring, we assessed fish biodiversity using eDNA metabarcoding from water samples collected from the Amazon (Adolpho Ducke Forest Reserve and two additional locations outside the Reserve). From a total of 84 identified Molecular Operational Taxonomic Units (MOTUs), only four could be assigned to species level using a fixed threshold. Measures of α‐diversity analyses within the Reserve showed similar patterns in each site between the number of MOTUs (eDNA dataset) and species (netting data) found. However, β‐diversity revealed contrasting patterns between the methods. We therefore suggest that a new approach is needed, underpinned by sound taxonomic knowledge, and a more thorough evaluation of better molecular identification procedures such as multi‐marker metabarcoding approaches and tailor‐made (i.e., order‐specific) taxonomic delimitation thresholds

Local variation of hashtag spike trains and popularity in Twitter

We draw a parallel between hashtag time series and neuron spike trains. In each case, the process presents complex dynamic patterns including temporal correlations, burstiness, and all other types of nonstationarity. We propose the adoption of the so-called local variation in order to uncover salient dynamics, while properly detrending for the time-dependent features of a signal. The methodology is tested on both real and randomized hashtag spike trains, and identifies that popular hashtags present regular and so less bursty behavior, suggesting its potential use for predicting online popularity in social media.Comment: 7 pages, 7 figure

The struggle for existence in the world market ecosystem

The global trade system can be viewed as a dynamic ecosystem in which exporters struggle for resources: the markets in which they export. We can think that the aim of an exporter is to gain the entirety of a market share (say, car imports from the United States). This is similar to the objective of an organism in its attempt to monopolize a given subset of resources in an ecosystem. In this paper, we adopt a multilayer network approach to describe this struggle. We use longitudinal, multiplex data on trade relations, spanning several decades. We connect two countries with a directed link if the source country's appearance in a market correlates with the target country's disappearing, where a market is defined as a country-product combination in a given decade. Each market is a layer in the network. We show that, by analyzing the countries' network roles in each layer, we are able to classify them as out-competing, transitioning or displaced. This classification is a meaningful one: when testing the future export patterns of these countries, we show that out-competing countries have distinctly stronger growth rates than the other two classes

Acidic microenvironment plays a key role in human melanoma progression through a sustained exosome mediated transfer of clinically relevant metastatic molecules

Background: Microenvironment cues involved in melanoma progression are largely unknown. Melanoma is highly influenced in its aggressive phenotype by the changes it determinates in its microenvironment, such as pH decrease, in turn influencing cancer cell invasiveness, progression and tissue remodelling through an abundant secretion of exosomes, dictating cancer strategy to the whole host. A role of exosomes in driving melanoma progression under microenvironmental acidity was never described. Methods: We studied four differently staged human melanoma lines, reflecting melanoma progression, under microenvironmental acidic pHs pressure ranging between pH 6.0-6.7. To estimate exosome secretion as a function of tumor stage and environmental pH, we applied a technique to generate native fluorescent exosomes characterized by vesicles integrity, size, density, markers expression, and quantifiable by direct FACS analysis. Functional roles of exosomes were tested in migration and invasion tests. Then we performed a comparative proteomic analysis of acid versus control exosomes to elucidate a specific signature involved in melanoma progression. Results: We found that metastatic melanoma secretes a higher exosome amount than primary melanoma, and that acidic pH increases exosome secretion when melanoma is in an intermediate stage, i.e. metastatic non-invasive. We were thus able to show that acidic pH influences the intercellular cross-talk mediated by exosomes. In fact when exposed to exosomes produced in an acidic medium, pH naïve melanoma cells acquire migratory and invasive capacities likely due to transfer of metastatic exosomal proteins, favoring cell motility and angiogenesis. A Prognoscan-based meta-analysis study of proteins enriched in acidic exosomes, identified 11 genes (HRAS, GANAB, CFL2, HSP90B1, HSP90AB1, GSN, HSPA1L, NRAS, HSPA5, TIMP3, HYOU1), significantly correlating with poor prognosis, whose high expression was in part confirmed in bioptic samples of lymph node metastases. Conclusions: A crucial step of melanoma progression does occur at melanoma intermediate -stage, when extracellular acidic pH induces an abundant release and intra-tumoral uptake of exosomes. Such exosomes are endowed with pro-invasive molecules of clinical relevance, which may provide a signature of melanoma advancement

Zoledronic acid renders human M1 and M2 macrophages susceptible to Vδ2(+) γδ T cell cytotoxicity in a perforin-dependent manner.

Vδ2(+) T cells are a subpopulation of γδ T cells in humans that are cytotoxic towards cells which accumulate isopentenyl pyrophosphate. The nitrogen-containing bisphosphonate, zoledronic acid (ZA), can induce tumour cell lines to accumulate isopentenyl pyrophosphate, thus rendering them more susceptible to Vδ2(+) T cell cytotoxicity. However, little is known about whether ZA renders other, non-malignant cell types susceptible. In this study we focussed on macrophages (Mϕs), as these cells have been shown to take up ZA. We differentiated peripheral blood monocytes from healthy donors into Mϕs and then treated them with IFN-γ or IL-4 to generate M1 and M2 Mϕs, respectively. We characterised these Mϕs based on their phenotype and cytokine production and then tested whether ZA rendered them susceptible to Vδ2(+) T cell cytotoxicity. Consistent with the literature, IFN-γ-treated Mϕs expressed higher levels of the M1 markers CD64 and IL-12p70, whereas IL-4-treated Mϕs expressed higher levels of the M2 markers CD206 and chemokine (C-C motif) ligand 18. When treated with ZA, both M1 and M2 Mϕs became susceptible to Vδ2(+) T cell cytotoxicity. Vδ2(+) T cells expressed perforin and degranulated in response to ZA-treated Mϕs as shown by mobilisation of CD107a and CD107b to the cell surface. Furthermore, cytotoxicity towards ZA-treated Mϕs was sensitive-at least in part-to the perforin inhibitor concanamycin A. These findings suggest that ZA can render M1 and M2 Mϕs susceptible to Vδ2(+) T cell cytotoxicity in a perforin-dependent manner, which has important implications regarding the use of ZA in cancer immunotherapy

Anti-tumour activity of bisphosphonates in preclinical models of breast cancer

There is increasing evidence of anti-tumour effects of bisphosphonates from pre-clinical studies, supporting a role for these drugs beyond their traditional use in treatment of cancer-induced bone disease. A range of model systems have been used to investigate the effects of different bisphosphonates on tumour growth, both in bone and at peripheral sites. Most of these studies conclude that bisphosphonates cause a reduction in tumour burden, but that early intervention and the use of high and/or repeated dosing is required. Successful eradication of cancer may only be achievable by targeting the tumour cells directly whilst also modifying the tumour microenvironment. In line with this, bisphosphonates are demonstrated to be particularly effective at reducing breast tumour growth when used in combination with agents that directly target cancer cells. Recent studies have shown that the effects of bisphosphonates on breast tumours are not limited to bone, and that prolonged anti-tumour effects may be achieved following their inclusion in combination therapy. This has opened the field to a new strand of bisphosphonate research, focussed on elucidating their effects on cells and components of the local, regional and distal tumour microenvironment. This review highlights the recent developments in relation to proposed anti-tumour effects of bisphosphonates reported from in vitro and in vivo models, and summarises the data from key breast cancer studies. Evidence for effects on different processes and cell types involved in cancer development and progression is discussed, and the main outstanding issues identified

Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine species

Background As global change and anthropogenic pressures continue to increase, conservation and management increasingly needs to consider species’ potential to adapt to novel environmental conditions. Therefore, it is imperative to characterise the main selective forces acting on ecosystems, and how these may influence the evolutionary potential of populations and species. Using a multi-model seascape genomics approach, we compare putative environmental drivers of selection in three sympatric southern African marine invertebrates with contrasting ecology and life histories: Cape urchin (Parechinus angulosus), Common shore crab (Cyclograpsus punctatus), and Granular limpet (Scutellastra granularis). Results Using pooled (Pool-seq), restriction-site associated DNA sequencing (RAD-seq), and seven outlier detection methods, we characterise genomic variation between populations along a strong biogeographical gradient. Of the three species, only S. granularis showed significant isolation-by-distance, and isolation-by-environment driven by sea surface temperatures (SST). In contrast, sea surface salinity (SSS) and range in air temperature correlated more strongly with genomic variation in C. punctatus and P. angulosus. Differences were also found in genomic structuring between the three species, with outlier loci contributing to two clusters in the East and West Coasts for S. granularis and P. angulosus, but not for C. punctatus. Conclusion The findings illustrate distinct evolutionary potential across species, suggesting that species-specific habitat requirements and responses to environmental stresses may be better predictors of evolutionary patterns than the strong environmental gradients within the region. We also found large discrepancies between outlier detection methodologies, and thus offer a novel multi-model approach to identifying the principal environmental selection forces acting on species. Overall, this work highlights how adding a comparative approach to seascape genomics (both with multiple models and species) can elucidate the intricate evolutionary responses of ecosystems to global change

Establishment of a coastal fish in the Azores : recent colonisation or suddenexpansion of an ancient relict population?

The processes and time scales associated with ocean-wide changes in the distribution of marinespecies have intrigued biologists since Darwin’s earliest insights into biogeography. The Azores, amid-Atlantic volcanic archipelago located more than 1000 km off the European continental shelf,offers ideal opportunities to investigate phylogeographic colonization scenarios. The benthopelagicsparid fish known as the common two-banded seabream (Diplodus vulgaris) is now relativelycommon along the coastline of the Azores archipelago, but was virtually absent prior to the 1990s.We employed a multiple genetic marker approach to test whether the successful establishment of theAzorean population derives from a recent colonization from western continental/island populationsor from the demographic explosion of an ancient relict population.Results from nuclear and mtDNA sequences show that all Atlantic and Mediterranean populationsbelong to the same phylogroup, though microsatellite data indicate significant genetic divergencebetween the Azorean sample and all other locations, as well as among Macaronesian, westernIberian and Mediterranean regions. The results from Approximate Bayesian Computation indicatethat D. vulgaris has likely inhabited the Azores for approximately 40 (95% C.I.: 5.5─83.6) to 52(95% C.I.; 6.32─89.0) generations, corresponding to roughly 80-150 years, which suggests nearcontemporary colonisation, followed by a more recent demographic expansion which could havebeen facilitated by changing climate conditions. Moreover, the lack of previous records of thisspecies over the past century, together with the absence of lineage separation and the presence ofrelatively few private alleles, do not exclude the possibility of an even more recent colonisationevent