Simulatie van veranderingen in concentraties van voedingselementen rond plantewortels

Simulation of changes in nutrient concentrations around plant roots.Factors determining nutrient uptake by plant roots can be divided into those influencing root geometry and root growth and those influencing the transport of nutrients to the roots. Experiments were carried out with maize on a nutrient solution in coarse sand and on mixtures of synthetic ion-exchangers onto which nutritive ions were adsorbed. The exchangers were used as a growth medium with characteristics between those of nutrient solution and soil.The results from these experiments and especially from those with nutrient solution were used for computer simulation models (written in CSMP), describing the changes in ion concentration around roots caused by the uptake of nutrients and water by the roots as a function of time over long periods and more in detail over short periods.<p/

Metagenomic evidence for a polymicrobial signature of sepsis

Our understanding of the host component of sepsis has made significant progress. However, detailed study of the microorganisms causing sepsis, either as single pathogens or microbial assemblages, has received far less attention. Metagenomic data offer opportunities to characterize the microbial communities found in septic and healthy individuals. In this study we apply gradient-boosted tree classifiers and a novel computational decontamination technique built upon SHapley Additive exPlanations (SHAP) to identify microbial hallmarks which discriminate blood metagenomic samples of septic patients from that of healthy individuals. Classifiers had high performance when using the read assignments to microbial genera [area under the receiver operating characteristic (AUROC=0.995)], including after removal of species ‘culture-confirmed’ as the cause of sepsis through clinical testing (AUROC=0.915). Models trained on single genera were inferior to those employing a polymicrobial model and we identified multiple co-occurring bacterial genera absent from healthy controls. While prevailing diagnostic paradigms seek to identify single pathogens, our results point to the involvement of a polymicrobial community in sepsis. We demonstrate the importance of the microbial component in characterising sepsis, which may offer new biological insights into the aetiology of sepsis, and ultimately support the development of clinical diagnostic or even prognostic tools

Large-scale network analysis captures biological features of bacterial plasmids

Many bacteria can exchange genetic material through horizontal gene transfer (HGT) mediated by plasmids and plasmid-borne transposable elements. Here, we study the population structure and dynamics of over 10,000 bacterial plasmids, by quantifying their genetic similarities and reconstructing a network based on their shared k-mer content. We use a community detection algorithm to assign plasmids into cliques, which correlate with plasmid gene content, bacterial host range, GC content, and existing classifications based on replicon and mobility (MOB) types. Further analysis of plasmid population structure allows us to uncover candidates for yet undescribed replicon genes, and to identify transposable elements as the main drivers of HGT at broad phylogenetic scales. Our work illustrates the potential of network-based analyses of the bacterial ‘mobilome’ and opens up the prospect of a natural, exhaustive classification framework for bacterial plasmids

Molecule-by-Molecule Writing Using a Focused Electron Beam

The resolution of lithography techniques needs to be extended beyond their current limits to continue the trend of miniaturization and enable new applications. But what is the ultimate spatial resolution? It is known that single atoms can be imaged with a highly focused electron beam. Can single atoms also be written with an electron beam? We verify this with focused electron-beam-induced deposition (FEBID), a direct-write technique that has the current record for the smallest feature written by (electron) optical lithography. We show that the deposition of an organometallic precursor on graphene can be followed molecule-by-molecule with FEBID. The results show that mechanisms that are inherent to the process inhibit a further increase in control over the process. Hence, our results present the resolution limit of (electron) optical lithography techniques. The writing of isolated, subnanometer features with nanometer precision can be used, for instance, for the local modification of graphene and for catalysis.</p

Pre-existing T cell-mediated cross-reactivity to SARS-CoV-2 cannot solely be explained by prior exposure to endemic human coronaviruses

T-cell-mediated immunity to SARS-CoV-2-derived peptides in individuals unexposed to SARS-CoV-2 has been previously reported. This pre-existing immunity was suggested to largely derive from prior exposure to ‘common cold’ endemic human coronaviruses (HCoVs). To test this, we characterised the sequence homology of SARS-CoV-2-derived T-cell epitopes reported in the literature across the full proteome of the Coronaviridae family. 54.8% of these epitopes had no homology to any of the HCoVs. Further, the proportion of SARS-CoV-2-derived epitopes with any level of sequence homology to the proteins encoded by any of the coronaviruses tested is well-predicted by their alignment-free phylogenetic distance to SARS-CoV-2 (Pearson's r = −0.958). No coronavirus in our dataset showed a significant excess of T-cell epitope homology relative to the proportion of expected random matches, given their genetic similarity to SARS-CoV-2. Our findings suggest that prior exposure to human or animal-associated coronaviruses cannot completely explain the T-cell repertoire in unexposed individuals that recognise SARS-CoV-2 cross-reactive epitopes

Graphene growth from photo-polymerized bi-phenylthiol self-assembled monolayers

We present an enhanced methodology for the synthesis of graphene, from photo-polymerized self-assembled monolayers (SAMs) of 1,1ʹ-biphenyl-4-thiol on both electropolished and oxidized copper substrates. The SAMs were subjected to a two-step process involving light-induced polymerization followed by annealing in a vacuum furnace to yield the two-dimensional solid. Comprehensive characterization using contact angle measurements, X-ray photoelectron spectroscopy, and Raman spectroscopy, as well as scanning electron and transmission electron microscopy, provided conclusive evidence of growth of single-layer graphene. Notably, our findings revealed superior quality graphene on oxidized copper substrates compared to their electropolished counterparts, highlighting the impact of substrate choice on the quality of the resultant material

Estimating entropies from molecular dynamics simulations

The methods to compute the excess entropy and the entropy of solvation using liquid water as a test system were studied. The accuracy and convergence behavior of five methods based on thermodynamic integration and perturbation techniques was evaluated. Through the thermodynamic integration accurate entropy differences were obtained in which many copies of a solute were desolvated. Only two methods yield useful results, the calculation of solute-solvent entropy through thermodynamic integration and the calculation of solvation entropy through the temperature derivative of the corresponding free-energy difference, when one solute molecule is involved

Anti-thymocyte globulin with CsA and MMF as GVHD prophylaxis in nonmyeloablative HLA-mismatched allogeneic HCT

Nonmyeloablative regimens are used for allogeneic hematopoietic cell transplantation (HCT) of older or medically unfit patients, but successful outcome is still hindered by graft-versus-host disease (GVHD), especially in the setting of HLA-mismatched HCT. New GVHD prophylaxis strategies are emerging, including the triple drug strategy, that improve the GVHD-free and relapse-free survival (GRFS). Because the impact of ATG in HLA-mismatched Flu-TBI-based nonmyeloablative HCT has not been investigated, we did a retrospective analysis in three Dutch centers. 67 patients were evaluable, with a median age of 56 years. Overall survival, relapse-free survival and GRFS at 4 years were 52%, 43%, and 38%, respectively. NRM findings and cumulative incidence of relapse at 4 years were 26% and 31%, respectively. At 1-year grade II-IV had occurred in 40% of the patients, and the incidence of moderate-severe chronic GVHD incidence was 16%. Acknowledging the limitations of retrospective analyses, we conclude that the use of ATG for HLA-mismatched truly nonmyeloablative Flu-TBI HCT is feasible and results in acceptable long term outcomes, especially with regards to GRFS. We consider ATG in combination with cyclosporin and mycophenolate mofetil as an alternative for the triple drug strategy that uses sirolimus for GVHD prophylaxis in this particular setting