Rearrangement patterns of the canine TCRγ locus in a distinct group of T cell lymphomas

The T cell antigen receptor chains are assembled through a rearrangement process that combines variable (V), diversity (D) and joining (J) region genes. Recently, the entire canine T cell receptor γ (TRG) locus was described. It is arranged in 8 cassettes with up to 3 V genes, 2 J genes and 1 C gene each. However, no data is available beyond the level of sequence analysis. The objective of this study was to identify rearranged genes of the canine TRG locus through experimental analysis and to assess gene usage and patterns of rearrangement in a series of canine T cell lymphomas. Rearranged genes were identified through computational analysis of recombination signal sequences (RSSs), a gene's potential to generate a polyclonal smear, and through sequencing of clonal rearrangements in a series of T cell lymphomas. Out of a total of 32 Vγ and Jγ genes, 21 genes were found to rearrange, 8 genes were considered not rearranged and 3 genes were suspected to rearrange but their status could not be determined definitely. Rearrangements of the canine TRG locus were assessed in a group of canine T cell lymphomas as well as 3 neoplastic T cell lines. An average of 4.6 rearrangements per lymphoma was found suggesting that canine T cells routinely rearrange multiple cassettes per allele. The most commonly rearranged Vγ genes belonged to subgroups Vγ2, Vγ3, and Vγ7. Genes in cassettes 2 and 3 preferentially rearranged within their respective cassettes, while Vγ genes in cassette 7 rearranged to a Jγ gene in cassette 8. There was a strong preference for Vγ2 genes to rearrange to a 3' Jγ gene and for Vγ3 and Vγ7 genes to rearrange to a 5' Jγ gene. This rearrangement pattern coincided with the conservation of the spacer sequence between V and J gene subgroups rather than the topologic location of genes. These data show that highly divergent spacer sequences allow for equally efficient recombination and suggest that spacer sequences can mediate compatibility between V and J genes.     

Water-mediated proton hopping on an iron oxide surface

The diffusion of hydrogen atoms across solid oxide surfaces is often assumed to be accelerated by the presence of water molecules. Here we present a high-resolution, high-speed scanning tunneling microscopy (STM) study of the diffusion of H atoms on an FeO thin film. STM movies directly reveal a water-mediated hydrogen diffusion mechanism on the oxide surface at temperatures between 100 and 300 kelvin. Density functional theory calculations and isotope-exchange experiments confirm the STM observations, and a proton-transfer mechanism that proceeds via an H(3)O(+)-like transition state is revealed. This mechanism differs from that observed previously for rutile TiO(2)(110), where water dissociation is a key step in proton diffusion.     

Bioindication and modelling of atmospheric deposition in forests enable exposure and effect monitoring at high spatial density across scales

Key message

Moss surveys provide spatially dense data on environmental concentrations of heavy metals and nitrogen which, together with other biomonitoring and modelling data, can be used for indicating deposition to terrestrial ecosystems and related effects across time and areas of different spatial extension.

Context

For enhancing the spatial resolution of measuring and mapping atmospheric deposition by technical devices and by modelling, moss is used complementarily as bio-monitor.

Aims

This paper investigated whether nitrogen and heavy metal concentrations derived by biomonitoring of atmospheric deposition are statistically meaningful in terms of compliance with minimum sample size across several spatial levels (objective 1), whether this is also true in terms of geostatistical criteria such as spatial auto-correlation and, by this, estimated values for unsampled locations (objective 2) and whether moss indicates atmospheric deposition in a similar way as modelled deposition, tree foliage and natural surface soil at the European and country level, and whether they indicate site-specific variance due to canopy drip (objective 3).

Methods

Data from modelling and biomonitoring atmospheric deposition were statistically analysed by means of minimum sample size calculation, by geostatistics as well as by bivariate correlation analyses and by multivariate correlation analyses using the Classification and Regression Tree approach and the Random Forests method.

Results

It was found that the compliance of measurements with the minimum sample size varies by spatial scale and element measured. For unsampled locations, estimation could be derived. Statistically significant correlations between concentrations of heavy metals and nitrogen in moss and modelled atmospheric deposition, and concentrations in leaves, needles and soil were found. Significant influence of canopy drip on nitrogen concentration in moss was proven.

Conclusion

Moss surveys should complement modelled atmospheric deposition data as well as other biomonitoring approaches and offer a great potential for various terrestrial monitoring programmes dealing with exposure and effects.

     

Impact of Waxy,Partial Waxy,and Wildtype Wheat Starch Fraction Properties on Hearth Bread Characteristics

Thirteen different wheat cultivars were selected to represent GBSS mutations: three each of wildtype, axnull, and bxnull, and two each of 2xnull and waxy. Starch and A‐ and B‐granules were purified from wheat flour. Hearth bread loaves were produced from the flours using a small‐scale baking method. A‐granules purified from wildtype and partial waxy (axnull, bxnull, and 2xnull) starches have significantly higher gelatinization enthalpy and peak viscosity compared with B‐granules. A‐ and B‐granules from waxy starch do not differ in gelatinization, pasting, and gelation properties. A‐ and B‐granules from waxy starch have the highest enthalpy, peak temperature, peak viscosity, breakdown, and lowest pasting peak time and pasting temperature compared with A‐ and B‐granules from partial waxy and wildtype starch. Waxy wheat flour has much higher water absorption compared with partial waxy and wildtype flour. No significant difference in hearth bread baking performance was observed between wildype and partial waxy wheat flour. Waxy wheat flour produced hearth bread with significantly lower form ratio, weight, a more open pore structure, and a bad overall appearance. Baking with waxy, partial waxy, and wildtype wheat flour had no significant effect on loaf volume.     

Short-term compatibility of furosemide with crystalloid solutions

Parenteral veterinary furosemide is a 50-mg/mL solution with a pH of 8.0-9.3. The purpose of this study was to determine whether a commonly used veterinary formulation of 50 mg/mL of furosemide solution could be diluted in vitro without precipitation. Furosemide 50 mg/mL was diluted to concentrations of 10 and 5 mg/mL with 5% dextrose in water (D5W), 0.9% saline, lactated Ringer solution (LRS), and sterile water. Acidic sterile water and basic sterile water solutions were made by the addition of hydrochloric acid and sodium hydroxide, respectively, for use as controls to assess the effect of pH extremes for each concentration. After furosemide dilution, the final pH of each sample was measured, and samples were grossly and microscopically examined for clarity and crystal formation immediately and 1, 3, 5, and 8 hours after dilution. Gross precipitation and microscopic crystals were immediately observed in the acidic controls. Solutions of 5 mg/mL in LRS and 0.9% saline became slightly cloudy immediately, but no crystals were observed microscopically for 8 hours. Solutions of 10 mg/mL in D5W, 0.9% saline, LRS, and sterile water and solutions of 5 mg/mL in D5W and sterile water and the basic control were grossly clear, and no microscopic crystals were observed for 8 hours. On the basis of the results obtained in this in vitro investigation, this veterinary formulation of furosemide 50 mg/mL can be diluted without precipitation to a concentration of 10 mg/mL with D5W, 0.9% saline, LRS, or sterile water and to 5 mg/mL with D5W or sterile water and held for 8 hours.     

Dissolved and colloidal phosphorus fluxes in forest ecosystems—an almost blind spot in ecosystem research

Understanding and quantification of phosphorus (P) fluxes are key requirements for predictions of future forest ecosystems changes as well as for transferring lessons learned from natural ecosystems to croplands and plantations. This review summarizes and evaluates the recent knowledge on mechanisms, magnitude, and relevance by which dissolved and colloidal inorganic and organic P forms can be translocated within or exported from forest ecosystems. Attention is paid to hydrological pathways of P losses at the soil profile and landscape scales, and the subsequent influence of P on aquatic ecosystems. New (unpublished) data from the German Priority Program 1685 “Ecosystem Nutrition: Forest Strategies for limited Phosphorus Resources” were added to provide up‐to‐date flux‐based information. Nitrogen (N) additions increase the release of water‐transportable P forms. Most P found in percolates and pore waters belongs to the so‐called dissolved organic P (DOP) fractions, rich in orthophosphate‐monoesters and also containing some orthophosphate‐diesters. Total solution P concentrations range from ca. 1 to 400 µg P L^?1, with large variations among forest stands. Recent sophisticated analyses revealed that large portions of the DOP in forest stream water can comprise natural nanoparticles and fine colloids which under extreme conditions may account for 40–100% of the P losses. Their translocation within preferential flow passes may be rapid, mediated by storm events. The potential total P loss through leaching into subsoils and with streams was found to be less than 50 mg P m^?2 a^?1, suggesting effects on ecosystems at centennial to millennium scale. All current data are based on selected snapshots only. Quantitative measurements of P fluxes in temperate forest systems are nearly absent in the literature, probably due to main research focus on the C and N cycles. Therefore, we lack complete ecosystem‐based assessments of dissolved and colloidal P fluxes within and from temperate forest systems.     

Diurnal and seasonal variations in CH4 flux from termite mounds in tropical savannas of the Northern Territory, Australia

Termites are estimated to contribute between <5 and 19% of the global methane (CH₄) emissions. These estimates have large uncertainties because of the limited number of field-based studies and species studied, as well as issues of diurnal and seasonal variations. We measured CH₄ fluxes from four common mound-building termite species (Microcerotermes nervosus, M. serratus, Tumulitermes pastinator and Amitermes darwini) diurnally and seasonally in tropical savannas in the Northern Territory, Australia. Our results showed that there were significant diel and seasonal variations of CH₄ emissions from termite mounds and we observed large species specific differences. On a diurnal basis, CH₄ fluxes were least at the coolest time of the day (∼07.00 h) and greatest at the warmest (∼15.00 h) for all species for both wet and dry seasons. We observed a strong and significant positive correlation between CH₄ flux and mound temperature for all species. A mound excavation experiment demonstrated that the positive temperature effect on CH₄ emissions was not related to termite movement in and out of a mound but probably a direct effect of temperature on methanogenesis in the termite gut. Fluxes in the wet season were 5-26-fold greater than those in the dry season. A multiple stepwise regression model including mound temperature and mound water content described 70-99% of the seasonal variations in CH₄ fluxes for different species. CH₄ fluxes from M. nervosus, which was the most abundant mound-building termite species at our sites, had significantly lower fluxes than the other three species measured. Our data demonstrate that CH₄ flux estimates could result in large under- or over-estimation of CH₄ emissions from termites if the diurnal, seasonal and species specific variations are not accounted for, especially when flux data are extrapolated to landscape scales.     

Fossilized nuclei and germination structures identify Ediacaran "animal embryos" as encysting protists

Globular fossils showing palintomic cell cleavage in the Ediacaran Doushantuo Formation, China, are widely regarded as embryos of early metazoans, although metazoan synapomorphies, tissue differentiation, and associated juveniles or adults are lacking. We demonstrate using synchrotron-based x-ray tomographic microscopy that the fossils have features incompatible with multicellular metazoan embryos. The developmental pattern is comparable with nonmetazoan holozoans, including germination stages that preclude postcleavage embryology characteristic of metazoans. We conclude that these fossils are neither animals nor embryos. They belong outside crown-group Metazoa, within total-group Holozoa (the sister clade to Fungi that includes Metazoa, Choanoflagellata, and Mesomycetozoea) or perhaps on even more distant branches in the eukaryote tree. They represent an evolutionary grade in which palintomic cleavage served the function of producing propagules for dispersion.