Small RNAs from plants, bacteria and fungi within the order Hypocreales are ubiquitous in human plasma

Background

The human microbiome plays a significant role in maintaining normal physiology. Changes in its composition have been associated with bowel disease, metabolic disorders and atherosclerosis. Sequences of microbial origin have been observed within small RNA sequencing data obtained from blood samples. The aim of this study was to characterise the microbiome from which these sequences are derived.

Abundant non-human small RNA sequences were identified in plasma and plasma exosomal samples. Assembly of these short sequences into longer contigs was the pivotal novel step in ascertaining their origin by BLAST searches. Most reads mapped to rRNA sequences. The taxonomic profiles of the microbes detected were very consistent between individuals but distinct from microbiomes reported at other sites. The majority of bacterial reads were from the phylum Proteobacteria, whilst for 5 of 6 individuals over 90% of the more abundant fungal reads were from the phylum Ascomycota; of these over 90% were from the order Hypocreales. Many contigs were from plants, presumably of dietary origin.  In addition, extremely abundant small RNAs derived from human Y RNAs were detected.

A characteristic profile of a subset of the human microbiome can be obtained by sequencing small RNAs present in the blood. The source and functions of these molecules remain to be determined, but the specific profiles are likely to reflect health status. The potential to provide biomarkers of diet and for the diagnosis and prognosis of human disease is immense.

COD and NH4-N Estimation in the Inflow of Wastewater Treatment Plants using Machine Learning Techniques

The in-line measurement of COD and NH4-N in the WWTP inflow is crucial for the timely monitoring of biological wastewater treatment processes and for the development of advanced control strategies for optimized WWTP operation. As a direct measurement of COD and NH4-N requires expensive and high maintenance in-line probes or analyzers, an approach estimating COD and NH4-N based on standard and spectroscopic in-line inflow measurement systems using Machine Learning Techniques is presented in this paper. The results show that COD estimation using Radom Forest Regression with a normalized MSE of 0.3, which is sufficiently accurate for practical applications, can be achieved using only standard in-line measurements. In the case of NH4-N, a good estimation using Partial Least Squares Regression with a normalized MSE of 0.16 is only possible based on a combination of standard and spectroscopic in-line measurements. Furthermore, the comparison of regression and classification methods shows that both methods perform equally well in most cases.

Effects of Elodea nuttallii on temperate freshwater plants, microalgae and invertebrates: small differences between invaded and uninvaded areas

The invasive aquatic plant species Elodea nuttallii could pose a considerable risk to European freshwater ecosystems based on its current distribution, rate of spread and potential for high biomass. However, little research has been conducted on the impacts of this species on native biota. This study takes an ecosystem-wide approach and examines the impact of E. nuttallii on selected physicochemical parameters (dissolved oxygen and pH), algae, invertebrate and macrophyte communities. Elodea nuttallii had small but significant impacts on plant, invertebrate and algal species. The richness of algal periphyton was lower on E. nuttallii than on native macrophytes. The taxonomic composition of invertebrate communities associated with E. nuttallii differed from that associated with similar native plant species, but did not differ in terms of total biomass or species richness. Macrophyte species richness and total cover were positively correlated with percentage cover of E. nuttallii. Not all macrophyte species responded in the same way to E. nuttallii invasion; cover of the low-growing species, Elodea canadensis and charophytes were negatively correlated with E. nuttallii cover, whilst floating-rooted plants were positively correlated with E. nuttallii cover. All observed differences in the macrophyte community were small relative to other factors such as nutrient levels, inter-annual variation and differences between sites. Despite this, the observed negative association between E. nuttallii and charophytes is a key concern due to the rarity and endangered status of many charophyte species.

Plants Fagonia cretica L. and Hedera nepalensis K. Koch contain natural compounds with potent dipeptidyl peptidase-4 (DPP-4) inhibitory activity

Ethnopharmacological relevance
The two plants investigated here (Fagonia cretica L. and Hedera nepalensis K. Koch) have been previously reported as natural folk medicines for the treatment of diabetes but until now no scientific investigation of potential anti-diabetic effects has been reported. 

Materials and methods
In vitro inhibitory effect of the two tested plants and their five isolated compounds on the dipeptidyl peptidase 4 (DPP-4) was studied for the assessment of anti-diabetic activity. 

Results
A crude extract of Fagonia cretica possessed good inhibitory activity (IC₅₀value: 38.1 μg/ml) which was also present in its n-hexane (FCN), ethyl acetate (FCE) or aqueous (FCA) fractions. A crude extract of Hedera nepalensis (HNC) possessed even higher inhibitory activity (IC₅₀value: 17.2 μg/ml) and this activity was largely retained when further fractionated in either ethyl acetate (HNE; IC₅₀: 34.4 μg/ml) or n-hexane (HNN; 34.2 μg/ml). Bioactivity guided isolation led to the identification of four known compounds (isolated for the first time) from Fagonia cretica: quinovic acid (1), quinovic acid-3β-O-β-d-glycopyranoside (2), quinovic acid-3β-O-β-d-glucopyranosyl-(28→1)-β-d-glucopyranosyl ester (3), and stigmasterol (4) all of which inhibited DPP-4 activity (IC₅₀: 30.7, 57.9, 23.5 and >100 μM, respectively). The fifth DPP-4 inhibitor, the triterpenoid lupeol (5) was identified in Hedera nepalensis (IC₅₀: 31.6 μM). 

Conclusion
The experimental study revealed that Fagonia cretica and Hedera nepalensis contain compounds with significant DPP-4 inhibitory activity which should be further investigated for their anti-diabetic potential.

Burkholderia cenocepacia Lipopolysaccharide Modification and Flagellin Glycosylation Affect Virulence but Not Innate Immune Recognition in Plants

Burkholderia cenocepacia causes opportunistic infections in plants, insects, animals, and humans, suggesting that “virulence” depends on the host and its innate susceptibility to infection. We hypothesized that modifications in key bacterial molecules recognized by the innate immune system modulate host responses to B. cenocepacia. Indeed, modification of lipo- polysaccharide (LPS) with 4-amino-4-deoxy-L-arabinose and flagellin glycosylation attenuates B. cenocepacia infection in Arabi- dopsis thaliana and Galleria mellonella insect larvae. However, B. cenocepacia LPS and flagellin triggered rapid bursts of nitric oxide and reactive oxygen species in A. thaliana leading to activation of the PR-1 defense gene. These responses were drastically reduced in plants with fls2 (flagellin FLS2 host receptor kinase), Atnoa1 (nitric oxide-associated protein 1), and dnd1-1 (reduced production of nitric oxide) null mutations. Together, our results indicate that LPS modification and flagellin glycosylation do not affect recognition by plant receptors but are required for bacteria to establish overt infection.

A comparison of carbon flow from pre-labelled and pulse-labelled plants

Perennial rye-grass was subjected to two different¹⁴C labelling regimes to enable a partitioning of the carbon sources contributing to rhizosphere carbon-flow. Plant/soil microcosms were designed which enabled rye-grass plants to either receive a single pulse of¹⁴C-CO₂ or to be pre-labelled using a series of¹⁴C-CO₂ pulses, allowing the fate of newly photoassimilated carbon and carbon lost by root decomposition to be followed into the soil. For young rye-grass plants grown over a short period, rhizosphere carbon flow was found to be dominated by newly photoassimilated carbon. Evidence for this came from the observed percentage of the total¹⁴C budget (i.e. total¹⁴C-CO₂ fixed by the plants) lost from the root/soil system, which was 30 times greater for the pulse labelled compared to pre-labelled plants. Root decomposition was found to be less at 10°C compared to 20-25°C, though input of¹⁴C into the soil was the same at both temperatures. © 1988 Kluwer Academic Publishers.

Do leaves of plants on phosphorus-impoverished soils contain high concentrations of phenolic defence compounds?

Prominent theories of plant defence have predicted that plants growing on nutrient-poor soils produce more phenolic defence compounds than those on richer soils. Only recently has the Protein Competition Model (PCM) of phenolic allocation suggested that N and P limitation could have different effects because the nutrients are involved in different cellular metabolic processes. 2. We extend the prediction of the PCM and hypothesize that N will have a greater influence on the production of phenolic defensive compounds than P availability, because N limitation reduces protein production and thus competition for phenylalanine, a precursor of many phenolic compounds. In contrast, P acts as a recyclable cofactor in these reactions, allowing protein and hence phenolic production to continue under low P conditions. 3. We test this hypothesis by comparing the foliar concentrations of phenolic compounds in (i) phenotypes of 21 species growing on P-rich alluvial terraces and P-depleted marine terraces in southern New Zealand, and (ii) 87 species growing under similar climates on comparatively P-rich soils in New Zealand vs. P-depleted soils in Tasmania. 4. Foliar P concentrations of plants from the marine terraces were about half those of plants from alluvial soils, and much lower in Tasmania than in New Zealand. However, foliar concentrations of N and phenolic compounds were similar across sites in both comparisons, supporting the hypothesis that N availability is a more important determinant of plant investment in phenolic defensive compounds than P availability. We found no indication that reduced soil P levels influenced plant concentrations of phenolic compounds. There was wide variation in the foliar N and P concentrations among species, and those with low foliar nutrient concentrations produced more phenolics (including condensed tannins). 5. Our study is the first trait comparison extending beyond standard leaf economics to include secondary metabolites related to defence in forest plants, and emphasizes that N and P have different influences on the production of phenolic defence compounds. © 2009 British Ecological Society.