Diversity of nonribosomal peptide synthetase genes in the microbial metagenomes of marine sponges

Genomic mining revealed one major nonribosomal peptide synthetase (NRPS) phylogenetic cluster in 12 marine sponge species, one ascidian, an actinobacterial isolate and seawater. Phylogenetic analysis predicts its taxonomic affiliation to the actinomycetes and hydroxy-phenyl-glycine as a likely substrate. Additionally, a phylogenetically distinct NRPS gene cluster was discovered in the microbial metagenome of the sponge Aplysina aerophoba, which shows highest similarities to NRPS genes that were previously assigned, by ways of single cell genomics, to a Chloroflexi sponge symbiont. Genomic mining studies such as the one presented here for NRPS genes, contribute to on-going efforts to characterize the genomic potential of sponge-associated microbiota for secondary metabolite biosynthesis.     

How relevant is recalcitrance for the stabilization of organic matter in soils?

Traditionally, the selective preservation of certain recalcitrant organic compounds and the formation of recalcitrant humic substances have been regarded as an important mechanism for soil organic matter (SOM) stabilization. Based on a critical overview of available methods and on results from a cooperative research program, this paper evaluates how relevant recalcitrance is for the long‐term stabilization of SOM or its fractions. Methodologically, recalcitrance is difficult to assess, since the persistence of certain SOM fractions or specific compounds may also be caused by other stabilization mechanisms, such as physical protection or chemical interactions with mineral surfaces. If only free particulate SOM obtained from density fractionation is considered, it rarely reaches ages exceeding 50 y. Older light particles have often been identified as charred plant residues or as fossil C. The degradability of the readily bioavailable dissolved or water‐extractable OM fraction is often negatively correlated with its content in aromatic compounds, which therefore has been associated with recalcitrance. But in subsoils, dissolved organic matter aromaticity and biodegradability both are very low, indicating that other factors or compounds limit its degradation. Among the investigated specific compounds, lignin, lipids, and their derivatives have mean turnover times faster or similar as that of bulk SOM. Only a small fraction of the lignin inputs seems to persist in soils and is mainly found in the fine textural size fraction (<20 µm), indicating physico‐chemical stabilization. Compound‐specific analysis of ¹³C : ¹²C ratios of SOM pyrolysis products in soils with C3‐C4 crop changes revealed no compounds with mean residence times of > 40–50 y, unless fossil C was present in substantial amounts, as at a site exposed to lignite inputs in the past. Here, turnover of pyrolysis products seemed to be much longer, even for those attributed to carbohydrates or proteins. Apparently, fossil C from lignite coal is also utilized by soil organisms, which is further evidenced by low ¹⁴C concentrations in microbial phospholipid fatty acids from this site. Also, black C from charred plant materials was susceptible to microbial degradation in a short‐term (60 d) and a long‐term (2 y) incubation experiment. This degradation was enhanced, when glucose was supplied as an easily available microbial substrate. Similarly, SOM mineralization in many soils generally increased after addition of carbohydrates, amino acids, or simple organic acids, thus indicating that stability may also be caused by substrate limitations. It is concluded that the presented results do not provide much evidence that the selective preservation of recalcitrant primary biogenic compounds is a major SOM‐stabilization mechanism. Old SOM fractions with slow turnover rates were generally only found in association with soil minerals. The only not mineral‐associated SOM components that may be persistent in soils appear to be black and fossil C.     

Evaluation of diagnostic tests in the absence of a gold standard using an Anaplasma marginale field data set

The evaluation of newly developed diagnostic tests (tests) commonly involves the comparison of the test outcomes (pos/neg.) of a sample of animals to those of a reference test (gold standard) in order to derive sensitivity and specificity estimates. Often, however, new tests have to be evaluated against an imperfect reference test since a true gold standard test is either too expensive or too costly to apply. This results in bias in the test characteristic estimates. To solve this problem, latent class and Bayesian models can be used to estimate sensitivity and specificity when evaluating a diagnostic test in the absence of a gold standard. They require at least two imperfect reference tests applied to all individuals in the study. In our approach we used a two-test two-population scenario. Both the gold standard and these modelling approaches rely on various assumptions. When violated, biased results will be obtained. The analysis of field data from an Anaplasma marginale outbreak in cattle in Switzerland with four diagnostic procedures (detection of the agent, serology, PCR and hematocrit measurements) was used as a practical example to demonstrate and critically discuss the approaches taken. In this relatively small data set (n = 275) the estimates for the test characteristics obtained by the different methods were quite similar. Overall, the bias in the point estimates depended mainly on the chosen estimation approach. All tests showed a non-negligible correlation mainly in the test sensitivities. This emphasizes the importance of taking into account test dependence even if it seems not biologically plausible at first thought.     

Intracellular survival of Salmonella strains in Caco-2 cells

In the in vitro model using Caco-2 cells at different stages of differentiation the invasion and intracellular survival of virulent (predominant infection strains) and less virulent (predominant attenuated mutant strains) Salmonella strains were studied. The statistical evaluation of experimental data has shown that the logarithmized colony forming unit after 18 hours of incubation in differentiated cells (14 days old) is a suitable parameter for the determination of intracellular survival. Using this parameter a relationship between intracellular survival and Salmonella virulence (LD50 mouse) was demonstrated and quantified. The model presented could be suitable for the replacement of animal experiments after further investigations.     

Morphological and immunohistochemical studies in testes of normal and cryptorchid boars

Scrotal (n = 66), inguinal (n = 7) and abdominal (n = 36) testes from pigs differing in age (from 1 day to 4 years) were collected after slaughtering or by castration, fixed in 4% formalin and examined by light microscopy. The expression of vimentin, desmin, alpha-actin and PCNA was detected by immunohistochemical technique. Histologically no differences between scrotal and cryptorchid testes are obvious during the prepubertal period, until the age of 10-12 weeks, but with the onset of puberty degenerative alterations (Sertoli-cell-only morphology, giant cells) in dystopic testes occur. Additionally the differentiation of the interstitial cells is disturbed in abdominal testes resulting in a deviating expression pattern of alpha-actin. The Sertoli cells show different distribution patterns (basal, perinuclear, apical) of vimentin depending on the position of the testis and the age of the animal.     

Endothelial–platelet interactions in influenza-induced pneumonia: A potential therapeutic target

Every year, influenza viruses spread around the world, infecting the respiratory systems of countless humans and animals, causing illness and even death. Severe influenza infection is associated with pulmonary epithelial damage and endothelial dysfunction leading to acute lung injury (ALI). There is evidence that an aggressive cytokine storm and cell damage in lung capillaries as well as endothelial/platelet interactions contribute to vascular leakage, pro-thrombotic milieu and infiltration of immune effector cells. To date, treatments for ALI caused by influenza are limited to antiviral drugs, active ventilation or further symptomatic treatments. In this review, we summarize the mechanisms of influenza-mediated pathogenesis, permissive animal models and histopathological changes of lung tissue in both mice and men and compare it with histological and electron microscopic data from our own group. We highlight the molecular and cellular interactions between pulmonary endothelium and platelets in homeostasis and influenza-induced pathogenesis. Finally, we discuss novel therapeutic targets on platelets/endothelial interaction to reduce or resolve ALI.     

Can nitrogen input mapping from aerial imagery improve nitrous oxide emissions estimates from grazed grassland?

Precision Agriculture - Most nitrogen (N) lost to the environment from grazed grassland is produced as a result of N excreted by livestock, released in the form of nitrous oxide (N2O) emissions,...     

Endopeptidase EP-1 as a Marker for the Eyespot Resistance Gene Pch-1 from Aegilops ventricosa in Wheat Line 'H-93-70'

Biochemical marker endopeptidase EP-1 was used to determine that an eyespot resistance gene, transferred from Aegilops ventricosa to the hexaploid wheat line ‘H-93-70’ is located on the long arm of the chromosome 7D.