Stable isotopes as ecological tracers: an efficient method for assessing the contribution of multiple sources to mixtures

Stable isotopes are increasingly being used as tracers of ecological processes potentially providing relevant information to environmental management issues. An application of the methodology consists in relating the stable isotopic composition of a sample mixture to that of sources. The number of stable isotopes, however, is usually lower than that of potential sources existing in an ecosystem, which creates mathematical difficulties in correctly tracing sources. We discuss a linear programming model which efficiently derives information on the contribution of sources to mixtures for any number of stable isotopes and any number of sources by addressing multiple sources simultaneously. The model identifies which sources are present in all, present in a subset of the samples or absent from all samples simultaneously and calculates minimum and maximum values of each source in the mixtures. We illustrate the model using a data set consisting of the isotopic signatures of different plant sources ingested by primary consumers in tropical riverine habitat in Asia. The model discussed may contribute to extend the scope of stable isotopes methodology to a range of new problems dealing with multiple sources and multiple tracers. For instance, in food web studies, if particular organic matter sources disappear or decrease in availability (e.g. climate change scenarios) the model allows simulation of alternative diets of the consumers providing potentially relevant information for managers and decision makers

Structural representations of DNA regulatory substrates can enhance sequence-based algorithms by associating functional sequence variants

The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like representations are algorithmically very useful, here we fused over 60 currently available DNA physicochemical and conformational variables into compact structural representations that can encode single DNA binding sites to whole regulatory regions. We find that the main structural components reflect key properties of protein-DNA interactions and can be condensed to the amount of information found in a single nucleotide position. The most accurate structural representations compress functional DNA sequence variants by 30% to 50%, as each instance encodes from tens to thousands of sequences. We show that a structural distance function discriminates among groups of DNA substrates more accurately than nucleotide sequence-based metrics. As this opens up a variety of implementation possibilities, we develop and test a distance-based alignment algorithm, demonstrating the potential of using the structural representations to enhance sequence-based algorithms. Due to the bias of most current bioinformatic methods to nucleotide sequence representations, it is possible that considerable performance increases might still be achievable with such solutions.Comment: 20 pages, 8 figures, 3 tables, conferenc

Consistent Long-Term Therapeutic Efficacy of Human Umbilical Cord Matrix-Derived Mesenchymal Stromal Cells After Myocardial Infarction Despite Individual Differences and Transient Engraftment

Human mesenchymal stem cells gather special interest as a universal and feasible add-on therapy for myocardial infarction (MI). In particular, human umbilical cord matrix-derived mesenchymal stromal cells (UCM-MSC) are advantageous since can be easily obtained and display high expansion potential. Using isolation protocols compliant with cell therapy, we previously showed UCM-MSC preserved cardiac function and attenuated remodeling 2 weeks after MI. In this study, UCM-MSC from two umbilical cords, UC-A and UC-B, were transplanted in a murine MI model to investigate consistency and durability of the therapeutic benefits. Both cellular products improved cardiac function and limited adverse cardiac remodeling 12 weeks post-ischemic injury, supporting sustained and long-term beneficial therapeutic effect. Donor associated variability was found in the modulation of cardiac remodeling and activation of the Akt-mTOR-GSK3ß survival pathway. In vitro, the two cell products displayed similar ability to induce the formation of vessel-like structures and comparable transcriptome in normoxia and hypoxia, apart from UCM-MSCs proliferation and expression differences in a small subset of genes associated with MHC Class I. These findings support that UCM-MSC are strong candidates to assist the treatment of MI whilst calling for the discussion on methodologies to characterize and select best performing UCM-MSC before clinical application.This work was funded by European Structural and Investment Funds (ESIF), under Lisbon Portugal Regional Operational Programme and National Funds through Fundação para a Ciência e Tecnologia (FCT) ([POCI-01-0145-FEDER-030985], [POCI-01-0145-FEDER-016385]); by FCT/Ministério da Ciência, Tecnologia e Inovação in the framework of individual funding [CEECINST/00091/2018] to DN and by QREN funds through the project ClinUCX (QREN 30196) and individual fellowships: [PD/BD/127997/2016] to TL, [SFRH/BD/144490/2019] to RG and [SFRH/BD/111799/2015] to VS-P. The funding bodies other than ECBio had no role in design, in the collection, analysis, and interpretation of data; in the writing of the manuscript; or in the decision to submit the manuscript for publication

Phagocytic glioblastoma-associated microglia and macrophages populate invading pseudopalisades

Altres ajuts: This project was supported by grants from the Spanish Ministry of Economy and Competitiveness, and the European Regional Development Fund (Fondo Europeo de Desarrollo Regional, FEDER;), Generalitat de Catalunya, Spanish Ministry of Science, Innovation and Universities and by the Asociación Española Contra el Cancer (AECC).Hypoxic pseudopalisades are a pathological hallmark of human glioblastoma, which is linked to tumour malignancy and aggressiveness. Yet, their function and role in the tumour development have scarcely been explored. It is thought that pseudopalisades are formed by malignant cells escaping from the hypoxic environment, although evidence of the immune component of pseudopalisades has been elusive. In the present work, we analyse the immunological constituent of hypoxic pseudopalisades using high-resolution three-dimensional confocal imaging in tissue blocks from excised tumours of glioblastoma patients and mimic the hypoxic gradient in microfluidic platforms in vitro to understand the cellular motility. We visualize that glioblastoma-associated microglia and macrophages abundantly populate pseudopalisades, displaying an elongated kinetic morphology across the pseudopalisades, and are oriented towards the necrotic focus. In vitro experiments demonstrate that under hypoxic gradient, microglia show a particular motile behaviour characterized by the increase of cellular persistence in contrast with glioma cells. Importantly, we show that glioblastoma-associated microglia and macrophages utilize fibres of glioma cells as a haptotactic cue to navigate along the anisotropic structure of the pseudopalisades and display a high phagocytic activity at the necrotic border of the pseudopalisades. In this study, we demonstrate that glioblastoma-associated microglia and macrophages are the main immune cells of pseudopalisades in glioblastoma, travelling to necrotic areas to clear the resulting components of the prothrombotic milieu, suggesting that the scavenging features of glioblastoma-associated microglia and macrophages at the pseudopalisades serve as an essential counterpart for glioma cell invasion. In this article, Saavedra-Lopez and colleagues described that glioblastoma-associated microglia and macrophages infiltrate hypoxic pseudopalisades, a well-known invading niche of extremely aggressive brain tumours. They show these highly motile immune cells with great phagocytic capacity as a counterpart of the glioma cell invasion

Identifying and preventing burnout in young oncologists, an overwhelming challenge in the COVID-19 era: a study of the Spanish Society of Medical Oncology (SEOM)

COVID-19; Esgotament professional; Oncòlegs jovesCOVID-19; Agotamiento profesional; Oncólogos jóvenesCOVID-19; Professional burnout; Young oncologistsBackground Young oncologists are at particular risk of professional burnout, and this could have a significant impact on their health and care of their patients. The coronavirus disease 2019 (COVID-19) pandemic has forced rapid changes in professionals' jobs and training, with the consequent physical and psychological effects. We aimed to characterize burnout levels and determinants in young oncologists, and the effects of the pandemic on their training and health. Methods Two online surveys were conducted among oncology residents and young oncology specialists in Spain. The first addressed professional burnout and its determinants before the COVID-19 pandemic, while the second analyzed the impact of the pandemic on health care organization, training, and physical and psychological health in the same population. Results In total, 243 respondents completed the first survey, and 263 the second; 25.1% reported significant levels of professional burnout. Burnout was more common among medical oncology residents (28.2%), mainly in their second year of training. It was significantly associated with a poor work–life balance, inadequate vacation time, and the burnout score. Nearly three-quarters of respondents (72%) were reassigned to COVID-19 care and 84.3% of residents missed part of their training rotations. Overall, 17.2% of this population reported that they had contracted COVID-19, 37.3% had scores indicating anxiety, and 30.4% moderate to severe depression. Almost a quarter of young oncologists (23.3%) had doubts about their medical vocation. Conclusions Burnout affects a considerable number of young oncologists. The COVID-19 pandemic has had a profound impact on causes of burnout, making it even more necessary to periodically monitor it to define appropriate detection and prevention strategies.This project received funding from the Spanish Society of Medical Oncology (SEOM)

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

Conjugation of DNA through a type IV secretion system (T4SS) drives horizontal gene transfer. Yet little is known on the diversity of these nanomachines. We previously found that T4SS can be divided in eight classes based on the phylogeny of the only ubiquitous protein of T4SS (VirB4). Here, we use an ab initio approach to identify protein families systematically and specifically associated with VirB4 in each class. We built profiles for these proteins and used them to scan 2262 genomes for the presence of T4SS. Our analysis led to the identification of thousands of occurrences of 116 protein families for a total of 1623 T4SS. Importantly, we could identify almost always in our profiles the essential genes of well-studied T4SS. This allowed us to build a database with the largest number of T4SS described to date. Using profile-profile alignments, we reveal many new cases of homology between components of distant classes of T4SS. We mapped these similarities on the T4SS phylogenetic tree and thus obtained the patterns of acquisition and loss of these protein families in the history of T4SS. The identification of the key VirB4-associated proteins paves the way toward experimental analysis of poorly characterized T4SS classes.Funding. Spanish Ministry of Economy [BFU2011-26608]; European Seventh Framework Program [282004/FP7-HEALTH.2011, 612146/FP7-ICT-2013]; European Research Council Grant [EVOMOBILOME no. 281605]. Source of open access funding: European Research Council grant to the PI

Dynamic risk control by human nucleus accumbens

Real-world decisions about reward often involve a complex counterbalance of risk and value. Although the nucleus accumbens has been implicated in the underlying neural substrate, its criticality to human behaviour remains an open question, best addressed with interventional methodology that probes the behavioural consequences of focal neural modulation. Combining a psychometric index of risky decision-making with transient electrical modulation of the nucleus accumbens, here we reveal profound, highly dynamic alteration of the relation between probability of reward and choice during therapeutic deep brain stimulation in four patients with treatment-resistant psychiatric disease. Short-lived phasic electrical stimulation of the region of the nucleus accumbens dynamically altered risk behaviour, transiently shifting the psychometric function towards more risky decisions only for the duration of stimulation. A critical, on-line role of human nucleus accumbens in dynamic risk control is thereby established

Revisiting the reactivity between HCO and CH3_3 on interstellar grain surfaces

Formation of interstellar complex organic molecules is currently thought to be dominated by the barrierless coupling between radicals on the interstellar icy grain surfaces. Previous standard DFT results on the reactivity between CH$_3$ and HCO on amorphous water surfaces, showed that formation of CH$_4$ + CO by H transfer from HCO to CH$_3$ assisted by water molecules of the ice was the dominant channel. However, the adopted description of the electronic structure of the biradical (i.e., CH$_3$/HCO) system was inadequate (without the broken-symmetry (BS) approach). In this work, we revisit the original results by means of BS-DFT both in gas phase and with one water molecule simulating the role of the ice. Results indicate that adoption of BS-DFT is mandatory to describe properly biradical systems. In the presence of the single water molecule, the water-assisted H transfer exhibits a high energy barrier. In contrast, CH$_3$CHO formation is found to be barrierless. However, direct H transfer from HCO to CH$_3$ to give CO and CH$_4$ presents a very low energy barrier, hence being a potential competitive channel to the radical coupling and indicating, moreover, that the physical insights ofthe original work remain valid.Comment: Submitted to MNRAS main journal. For associated supporting material refer to the publication in MNRAS. Accepted 2020 February 14. Received 2020 February 1