Capacity of different cell types to stimulate cytotoxic T lymphocyte precursor cells in the presence of interleukin 2

Plastic-adherent cells enriched for dendritic cells (AC) were found to be among the most potent stimulator cells for the activation of cytotoxic T lymphocytes (CTL) in vitro in the presence of interleukin 2 (IL 2) and a constant second set of allogeneic stimulator cells. Concanavalin A-activated nylon wool-nonadherent spleen cells ( CNWT ), concanavalin A-activated unfractionated spleen cells ( Cspl ), and some variants of the ESb T lymphoma line were equally effective as stimulator cells, however, and provoked a substantial cytotoxic response at concentrations of 10(4) cells per culture or less. In contrast, nonactivated nylon wool-nonadherent spleen cells ( NWT ) or unfractionated spleen cells (Spl) and cells of the P815 mastocytoma, the Meth A fibrosarcoma, and the T cell lymphomas Ly 5178 Eb and ESb did not stimulate cytotoxic responses at these cell concentrations. The strong stimulatory potential of the Cspl preparation was reduced by treatment with anti-Thy-1 antibody plus complement, whereas the stimulatory activity of the AC preparation was resistant to this treatment. All cell types tested expressed class I major histocompatibility antigens. Nonactivated NWT cells, in contrast to the CNWT preparation, showed no detectable staining with anti-I-E or anti-I-A antibodies and also a slightly weaker staining with class I antisera. Experiments with the tumor cell lines revealed, however, that there was no strict correlation between stimulatory potential and density of class I alloantigens or the expression of I-E determinants. Experiments on primary cytotoxic responses in vivo gave similar results. Experiments in cultures with a single set of stimulator cells and I region-compatible responder cells indicated that AC and Cspl or CNWT also have a markedly stronger capacity than NWT to induce IL 2-dependent DNA synthesis

Drift induced perpendicular transport of solar energetic particles

Drifts are known to play a role in galactic cosmic ray transport within the heliosphere and are a standard component of cosmic ray propagation models. However, the current paradigm of solar energetic particle (SEP) propagation holds the effects of drifts to be negligible, and they are not accounted for in most current SEP modeling efforts. We present full-orbit test particle simulations of SEP propagation in a Parker spiral interplanetary magnetic field (IMF), which demonstrate that high-energy particle drifts cause significant asymmetric propagation perpendicular to the IMF. Thus in many cases the assumption of field-aligned propagation of SEPs may not be valid. We show that SEP drifts have dependencies on energy, heliographic latitude, and charge-to-mass ratio that are capable of transporting energetic particles perpendicular to the field over significant distances within interplanetary space, e.g., protons of initial energy 100 MeV propagate distances across the field on the order of 1 AU, over timescales typical of a gradual SEP event. Our results demonstrate the need for current models of SEP events to include the effects of particle drift. We show that the drift is considerably stronger for heavy ion SEPs due to their larger mass-to-charge ratio. This paradigm shift has important consequences for the modeling of SEP events and is crucial to the understanding and interpretation of in situ observations. © 2013. The American Astronomical Society. All rights reserved.

The large longitudinal spread of solar energetic particles during the January 17, 2010 solar event

We investigate multi-spacecraft observations of the January 17, 2010 solar energetic particle event. Energetic electrons and protons have been observed over a remarkable large longitudinal range at the two STEREO spacecraft and SOHO suggesting a longitudinal spread of nearly 360 degrees at 1AU. The flaring active region, which was on the backside of the Sun as seen from Earth, was separated by more than 100 degrees in longitude from the magnetic footpoints of each of the three spacecraft. The event is characterized by strongly delayed energetic particle onsets with respect to the flare and only small or no anisotropies in the intensity measurements at all three locations. The presence of a coronal shock is evidenced by the observation of a type II radio burst from the Earth and STEREO B. In order to describe the observations in terms of particle transport in the interplanetary medium, including perpendicular diffusion, a 1D model describing the propagation along a magnetic field line (model 1) (Dr\"oge, 2003) and the 3D propagation model (model 2) by (Dr\"oge et al., 2010) including perpendicular diffusion in the interplanetary medium have been applied, respectively. While both models are capable of reproducing the observations, model 1 requires injection functions at the Sun of several hours. Model 2, which includes lateral transport in the solar wind, reveals high values for the ratio of perpendicular to parallel diffusion. Because we do not find evidence for unusual long injection functions at the Sun we favor a scenario with strong perpendicular transport in the interplanetary medium as explanation for the observations.Comment: The final publication is available at http://www.springerlink.co

Drift-induced deceleration of Solar Energetic Particles

We investigate the deceleration of Solar Energetic Particles (SEPs) during their propagation from the Sun through interplanetary space, in the presence of weak to strong scattering in a Parker spiral configuration, using relativistic full orbit test particle simulations. The calculations retain all three spatial variables describing particles’ trajectories, allowing to model any transport across the magnetic field. Large energy change is shown to occur for protons, due to the combined effect of standard adiabatic deceleration and a significant contribution from particle drift in the direction opposite to that of the solar wind electric field. The latter drift-induced deceleration is found to have a stronger effect for SEP energies than for galactic cosmic rays. The kinetic energy of protons injected at 1 MeV is found to be reduced by between 35 and 90% after four days, and for protons injected at 100 MeV by between 20 and 55%. The overall degree of deceleration is a weak function of the scattering mean free path, showing that, although adiabatic deceleration plays a role, a large contribution is due to particle drift. Current SEP transport models are found to account for drift-induced deceleration in an approximate way and their accuracy will need to be assessed in future work

Solar energetic particle access to distant longitudes through turbulent field-line meandering

Context. Current solar energetic particle (SEP) propagation models describe the effects of interplanetary plasma turbulence on SEPs as diffusion, using a Fokker-Planck (FP) equation. However, FP models cannot explain the observed fast access of SEPs across the average magnetic field to regions that are widely separated in longitude within the heliosphere without using unrealistically strong cross-field diffusion. Aims. We study whether the recently suggested early non-diffusive phase of SEP propagation can explain the wide SEP events with realistic particle transport parameters. Methods. We used a novel model that accounts for the SEP propagation along field lines that meander as a result of plasma turbulence. Such a non-diffusive propagation mode has been shown to dominate the SEP cross-field propagation early in the SEP event history. We compare the new model to the traditional approach, and to SEP observations. Results. Using the new model, we reproduce the observed longitudinal extent of SEP peak fluxes that are characterised by a Gaussian profile with σ = 30 − 50◦ , while current diffusion theory can only explain extents of 11◦ with realistic diffusion coefficients. Our model also reproduces the timing of SEP arrival at distant longitudes, which cannot be explained using the diffusion model. Conclusions. The early onset of SEPs over a wide range of longitudes can be understood as a result of the effects of magnetic fieldline random walk in the interplanetary medium and requires an SEP transport model that properly describes the non-diffusive early phase of SEP cross-field propagation

Developing fencing policies in dryland ecosystems

The daily energy requirements of animals are determined by a combination of physical and physiological factors, but food availability may challenge the capacity to meet nutritional needs. Western gorillas (Gorilla gorilla) are an interesting model for investigating this topic because they are folivore-frugivores that adjust their diet and activities to seasonal variation in fruit availability. Observations of one habituated group of western gorillas in Bai-Hokou, Central African Republic (December 2004-December 2005) were used to examine seasonal variation in diet quality and nutritional intake. We tested if during the high fruit season the food consumed by western gorillas was higher in quality (higher in energy, sugar, fat but lower in fibre and antifeedants) than during the low fruit season. Food consumed during the high fruit season was higher in digestible energy, but not any other macronutrients. Second, we investigated whether the gorillas increased their daily intake of carbohydrates, metabolizable energy (KCal/g OM), or other nutrients during the high fruit season. Intake of dry matter, fibers, fat, protein and the majority of minerals and phenols decreased with increased frugivory and there was some indication of seasonal variation in intake of energy (KCal/g OM), tannins, protein/fiber ratio, and iron. Intake of non-structural carbohydrates and sugars was not influenced by fruit availability. Gorillas are probably able to extract large quantities of energy via fermentation since they rely on proteinaceous leaves during the low fruit season. Macronutrients and micronutrients, but not digestible energy, may be limited for them during times of low fruit availability because they are hind-gut fermenters. We discuss the advantages of seasonal frugivores having large dietary breath and flexibility, significant characteristics to consider in the conservation strategies of endangered species

CAMISIM: Simulating metagenomes and microbial communities

© 2019 The Author(s). Background: Shotgun metagenome data sets of microbial communities are highly diverse, not only due to the natural variation of the underlying biological systems, but also due to differences in laboratory protocols, replicate numbers, and sequencing technologies. Accordingly, to effectively assess the performance of metagenomic analysis software, a wide range of benchmark data sets are required. Results: We describe the CAMISIM microbial community and metagenome simulator. The software can model different microbial abundance profiles, multi-sample time series, and differential abundance studies, includes real and simulated strain-level diversity, and generates second- and third-generation sequencing data from taxonomic profiles or de novo. Gold standards are created for sequence assembly, genome binning, taxonomic binning, and taxonomic profiling. CAMSIM generated the benchmark data sets of the first CAMI challenge. For two simulated multi-sample data sets of the human and mouse gut microbiomes, we observed high functional congruence to the real data. As further applications, we investigated the effect of varying evolutionary genome divergence, sequencing depth, and read error profiles on two popular metagenome assemblers, MEGAHIT, and metaSPAdes, on several thousand small data sets generated with CAMISIM. Conclusions: CAMISIM can simulate a wide variety of microbial communities and metagenome data sets together with standards of truth for method evaluation

Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)

The workshop-hackathon was convened by the Global Biodiversity Information Facility (GBIF) at its secretariat in Copenhagen over 22-24 May 2013 with additional support from several projects (RCN4GSC, EAGER, VertNet, BiSciCol, GGBN, and Micro B3). It assembled a team of experts to address the challenge of adapting the Darwin Core standard for a wide variety of sample data. Topics addressed in the workshop included 1) a review of outstanding issues in the Darwin Core standard, 2) issues relating to publishing of biodiversity data through Darwin Core Archives, 3) use of Darwin Core Archives for publishing sample and monitoring data, 4) the case for modifying the Darwin Core Text Guide specification to support many-to-many relations, and 5) the generalization of the Darwin Core Archive to a "Biodiversity Data Archive". A wide variety of use cases were assembled and discussed in order to inform further developments

Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)

The workshop-hackathon was convened by the Global Biodiversity Information Facility (GBIF) at its secretariat in Copenhagen over 22-24 May 2013 with additional support from several projects (RCN4GSC, EAGER, VertNet, BiSciCol, GGBN, and Micro B3). It assembled a team of experts to address the challenge of adapting the Darwin Core standard for a wide variety of sample data. Topics addressed in the workshop included 1) a review of outstanding issues in the Darwin Core standard, 2) issues relating to publishing of biodiversity data through Darwin Core Archives, 3) use of Darwin Core Archives for publishing sample and monitoring data, 4) the case for modifying the Darwin Core Text Guide specification to support many-to-many relations, and 5) the generalization of the Darwin Core Archive to a "Biodiversity Data Archive". A wide variety of use cases were assembled and discussed in order to inform further developments