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

A probabilistic model to recover individual genomes from metagenomes

Dröge J, Schönhuth A, McHardy AC. A probabilistic model to recover individual genomes from metagenomes. PeerJ Computer Science. 2017;3: e117.Shotgun metagenomics of microbial communities reveal information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial but very challenging step due to the complexity of the underlying biological system and technical factors. Microbial communities are heterogeneous, with oftentimes hundreds of present genomes deriving from different species or strains, all at varying abundances and with different degrees of similarity to each other and reference data. We present a versatile probabilistic model for genome recovery and analysis, which aggregates three types of information that are commonly used for genome recovery from metagenomes. As potential applications we showcase metagenome contig classification, genome sample enrichment and genome bin comparisons. The open source implementation MGLEX is available via the Python Package Index and on GitHub and can be embedded into metagenome analysis workflows and programs.</jats:p

Bioboxes: standardised containers for interchangeable bioinformatics software

Belmann P, Dröge J, Bremges A, McHardy AC, Sczyrba A, Barton MD. Bioboxes: standardised containers for interchangeable bioinformatics software. GigaScience. 2015;4(1): 47.Software is now both central and essential to modern biology, yet lack of availability, difficult installations, and complex user interfaces make software hard to obtain and use. Containerisation, as exemplified by the Docker platform, has the potential to solve the problems associated with sharing software. We propose bioboxes: containers with standardised interfaces to make bioinformatics software interchangeable

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

The band structure of BeTe - a combined experimental and theoretical study

Using angle-resolved synchrotron-radiation photoemission spectroscopy we have determined the dispersion of the valence bands of BeTe(100) along $\Gamma X$, i.e. the [100] direction. The measurements are analyzed with the aid of a first-principles calculation of the BeTe bulk band structure as well as of the photoemission peaks as given by the momentum conserving bulk transitions. Taking the calculated unoccupied bands as final states of the photoemission process, we obtain an excellent agreement between experimental and calculated spectra and a clear interpretation of almost all measured bands. In contrast, the free electron approximation for the final states fails to describe the BeTe bulk band structure along $\Gamma X$ properly.Comment: 21 pages plus 4 figure

A dinuclear ruthenium(II) phototherapeutic that targets duplex and quadruplex DNA

With the aim of developing a sensitizer for photodynamic therapy, a previously reported luminescent dinuclear complex that functions as a DNA probe in live cells was modified to produce a new isostructural derivative containing RuII(TAP)2 fragments (TAP = 1,4,5,8- tetraazaphenanthrene). The structure of the new complex has been confirmed by a variety of techniques including single crystal X-ray analysis. Unlike its parent, the new complex displays RuL-based 3MLCT emission in both MeCN and water. Results from electrochemical studies and emission quenching experiments involving guanosine monophosphate are consistent with an excited state located on a TAP moiety. This hypothesis is further supported by detailed DFT calculations, which take into account solvent effects on excited state dynamics. Cell-free steady-state and time-resolved optical studies on the interaction of the new complex with duplex and quadruplex DNA show that the complex binds with high affinity to both structures and indicate that its photoexcited state is also quenched by DNA, a process that is accompanied by the generation of the guanine radical cation sites as photo-oxidization products. Like the parent complex, this new compound is taken up by live cells where it primarily localizes within the nucleus and displays low cytotoxicity in the absence of light. However, in complete contrast to [{RuII(phen)2}2(tpphz)]4+, the new complex is therapeutically activated by light to become highly phototoxic toward malignant human melanoma cell line showing that it is a promising lead for the treatment of this recalcitrant cancer.EPSRC grant EP/M015572/1 Unviersity of Sheffield/EPSRC Doctoral Fellowship Prize EPSRC Capital Equipment Award ERASMUS

From Sun to Interplanetary Space: What is the Pathlength of Solar Energetic Particles?

Solar energetic particles (SEPs), accelerated during solar eruptions, propagate in turbulent solar wind before being observed with in situ instruments. In order to interpret their origin through comparison with remote sensing observations of the solar eruption, we thus must deconvolve the transport effects due to the turbulent magnetic fields from the SEP observations. Recent research suggests that the SEP propagation is guided by the turbulent meandering of the magnetic fieldlines across the mean magnetic field. However, the lengthening of the distance the SEPs travel, due to the fieldline meandering, has so far not been included in SEP event analysis. This omission can cause significant errors in estimation of the release times of SEPs at the Sun. We investigate the distance traveled by the SEPs by considering them to propagate along fieldlines that meander around closed magnetic islands that are inherent in turbulent plasma. We introduce a fieldline random walk model which takes into account the physical scales associated to the magnetic islands. Our method remedies the problem of the diffusion equation resulting in unrealistically short pathlengths, and the fractal dependence of the pathlength of random walk on the length of the random-walk step. We find that the pathlength from the Sun to 1au can be below the nominal Parker spiral length for SEP events taking place at solar longitudes 45E to 60W, whereas the western and behind-the-limb particles can experience pathlengths longer than 2au due to fieldline meandering

Solar interacting protons versus interplanetary protons in the core plus halo model of diffusive shock acceleration and stochastic re-acceleration

With the first observations of solar γ-rays from the decay of pions, the relationship of protons producing ground level enhancements (GLEs) on the Earth to those of similar energies producing the γ-rays on the Sun has been debated. These two populations may be either independent and simply coincident in large flares, or they may be, in fact, the same population stemming from a single accelerating agent and jointly distributed at the Sun and also in space. Assuming the latter, we model a scenario in which particles are accelerated near the Sun in a shock wave with a fraction transported back to the solar surface to radiate, while the remainder is detected at Earth in the form of a GLE. Interplanetary ions versus ions interacting at the Sun are studied for a spherical shock wave propagating in a radial magnetic field through a highly turbulent radial ray (the acceleration core) and surrounding weakly turbulent sector in which the accelerated particles can propagate toward or away from the Sun. The model presented here accounts for both the first-order Fermi acceleration at the shock front and the second-order, stochastic re-acceleration by the turbulence enhanced behind the shock. We find that the re-acceleration is important in generating the γ-radiation and we also find that up to 10% of the particle population can find its way to the Sun as compared to particles escaping to the interplanetary space

Observations of Electrons from the Decay of Solar Flare Neutrons

We have found evidence for fluxes of energetic electrons in interplanetary space on board the ISEE-3 spacecraft which we interpret as the decay products of neutrons generated in a solar flare on 1980 June 21. The decay electrons arrived at the s/c shortly before the electrons from the flare and can be distinguished from the latter by their distinctive energy spectrum. The time profile of the decay electrons is in good agreement with the results from a simulation based on a scattering mean free path derived from a fit to the flare electron data. The comparison with simultaneously observed decay protons and a published direct measurement of high-energy neutrons places important constraints on the parent neutron spectrum.Comment: 4 pages (postscript), accepted by Astrophysical Journal Letter