Vertical partitioning between sister species of Rhizopogon fungi on mesic and xeric sites in an interior Douglas‐fir forest

Understanding ectomycorrhizal fungal (EMF) community structure is limited by a lack of taxonomic resolution and autecological information. Rhizopogon vesiculosus and Rhizopogon vinicolor (Basidiomycota) are morphologically and genetically related species. They are dominant members of interior Douglas‐fir (Pseudotsuga menziesii var. glauca) EMF communities, but mechanisms leading to their coexistence are unknown. We investigated the microsite associations and foraging strategy of individual R. vesiculosus and R. vinicolor genets. Mycelia spatial patterns, pervasiveness and root colonization patterns of fungal genets were compared between Rhizopogon species and between xeric and mesic soil moisture regimes. Rhizopogon spp. mycelia were systematically excavated from the soil and identified using microsatellite DNA markers. Rhizopogon vesiculosus mycelia occurred at greater depth, were more spatially pervasive, and colonized more tree roots than R. vinicolor mycelia. Both species were frequently encountered in organic layers and between the interface of organic and mineral horizons. They were particularly abundant within microsites associated with soil moisture retention. The occurrence of R. vesiculosus shifted in the presence of R. vinicolor towards mineral soil horizons, where R. vinicolor was mostly absent. This suggests that competition and foraging strategy may contribute towards the vertical partitioning observed between these species. Rhizopogon vesiculosus and R. vinicolor mycelia systems occurred at greater mean depths and were more pervasive in mesic plots compared with xeric plots. The spatial continuity and number of trees colonized by genets of each species did not significantly differ between soil moisture regimes.     

A new method for evaluating defense of microalgae against protozoan grazing

Body-size spectrum has proved to be a highly informative indicator to summarize the functional structure of a community at taxon-free resolution. In this study, an approach based on body-size spectrum of protozoan communities was used to detect the defense of microalgae against protozoan grazing. The biofilm-dwelling protozoan communities were used as a test predator system, and two algal species, Chlorella sp. and Nannochloropsis oceanica, were employed as test microalgae. A nine-day bioassay test was carried out by exposing biofilm-dwelling protozoan communities to a gradient of concentrations 10⁰ (control), 10⁴, 10⁵, 10⁶, and 10⁷ cell ml⁻¹ of both microalgae, respectively. Results showed that both algal species represented strong defense effects on the test predator system at different levels of concentration. The body-size distinctness of the protozoan assemblages showed a sharp decrease at high concentration level more than 10⁶ cell ml⁻¹ in both algal treatments. Based on the paired body-size distinctness indices of the protozoa, ellipse tests demonstrated that the body-size spectrum showed an increasing trend of departure from the expected pattern with increasing concentrations of both test algae. Thus, it is suggested that the body-size spectrum of protozoa may be used as a useful indicator to identify the defense of microalgae against protozoan grazing.     

Identification of a four-gene metabolic signature predicting overall survival for hepatocellular carcinoma

While hundreds of consistently altered metabolic genes had been identified in hepatocellular carcinoma (HCC), the prognostic role of them remains to be further elucidated. Messenger RNA expression profiles and clinicopathological data were downloaded from The Cancer Genome Atlas—Liver Hepatocellular Carcinoma and GSE14520 data set from the Gene Expression Omnibus database. Univariate Cox regression analysis and lasso Cox regression model established a novel four-gene metabolic signature (including acetyl-CoA acetyltransferase 1, glutamic-oxaloacetic transaminase 2, phosphatidylserine synthase 2, and uridine-cytidine kinase 2) for HCC prognosis prediction. Patients in the high-risk group shown significantly poorer survival than patients in the low-risk group. The signature was significantly correlated with other negative prognostic factors such as higher α-fetoprotein. The signature was found to be an independent prognostic factor for HCC survival. Nomogram including the signature shown some clinical net benefit for overall survival prediction. Furthermore, gene set enrichment analyses revealed several significantly enriched pathways, which might help explain the underlying mechanisms. Our study identified a novel robust four-gene metabolic signature for HCC prognosis prediction. The signature might reflect the dysregulated metabolic microenvironment and provided potential biomarkers for metabolic therapy and treatment response prediction in HCC.     

Establishing a novel biosynthetic pathway for the production of 3,4-dihydroxybutyric acid from xylose in Escherichia coli

3-Hydroxy-γ-butyrolactone (3HBL) is an attractive building block owing to its broad applications in pharmaceutical industry. Currently, 3HBL is commercially produced by chemical routes using petro-derived carbohydrates, which involves hazardous materials and harsh processing conditions. Only one biosynthetic pathway has been reported for synthesis of 3HBL and its hydrolyzed form 3,4-dihydroxybutyric acid (3,4-DHBA) using glucose and glycolic acid as the substrates and coenzyme A as the activator, which involves multiple steps (>10 steps) and suffers from low productivity and yield. Here we established a novel five-step biosynthetic pathway for 3,4-DHBA generation from D-xylose based on the non-phosphorylative D-xylose metabolism, which led to efficient production of 3,4-DHBA in Escherichia coli. Pathway optimization by incorporation of efficient enzymes for each step and host strain engineering by knocking out competing pathways enabled 1.27 g/L 3,4-DHBA produced in shake flasks, which is the highest titer reported so far. The novel pathway established in engineered E. coli strain demonstrates a new route for 3,4-DHBA biosynthesis from xylose, and this engineered pathway has great potential for industrial biomanufacturing of 3,4-DHBA and 3HBL.     

The action of excessive,inorganic silicon (Si) on the mineral metabolism of calcium (Ca) and magnesium (Mg)

The influence of silicon treatment on the levels of calcium and magnesium in blood serum and tissues was studied in rats. The concentrations of both elements were estimated in samples of sera and tissues of rats receiving per os a soluble, inorganic silicon compound—sodium metasilicate nonahydrate (Na₂SiO₃·9H₂O (REACHIM, USSR)), dissolved in the animals' drinking water. A decrease of magnesium concentration in serum was observed with accompanying elevation of registered calcemia. Moreover, a reduction of tissue calcium levels was found with a simultaneous increase of magnesium tissue pool. The results provide evidence for silicon involvement in mineral metabolism. It could result in a modification of pathological processes concerning bone tissue.     

Concurrent quantitative HPLC–mass spectrometry profiling of small selenium species in human serum and urine after ingestion of selenium supplements

Selenium metabolic patterns in the human body originating from five distinct selenium dietary sources, selenate, selenite, selenomethionine (SeMet), methylselenocysteine (MeSeCys) and selenized yeast, were investigated by performing concurrent HPLC–mass spectrometric analysis of human serum and urine. Total selenium and selenium species time profiles were generated by sampling and analyzing serum and urine from volunteers treated with selenium supplements, up to 5 and 24 h following ingestion, respectively. We found that an increase in total serum selenium levels, accompanied by elevated selenium urinary excretion, was the common pattern for all treatments, except for that of selenite supplementation. Selenosugar 1 was a universal serum metabolite in all treatments, indicating that ingested selenium is favorably metabolized to the sugar. Except for selenite and selenized yeast ingestion, these patterns were reflected in the urine time series of the different treatments. Selenosugar 1 was the major selenium species present in urine in all treatments except for the selenate treatment, accounting for about 80% of the identified excreted species within 24 h of ingestion. Furthermore, the urinary metabolite trimethylselenonium ion (TMSe) was detected for the first time in human background serum by using HPLC coupled to elemental and molecular mass spectrometry. The concurrent monitoring of non-protein selenium species in both body fluids provides the relation between bioavailability and excretion of the individual ingested species and of their metabolic products, while the combined use of elemental and molecular mass spectrometry enables the accurate quantitation of structurally confirmed species. This successfully applied approach is anticipated to be a useful tool for more extensive future studies into human selenium metabolism.     

Biogeography of salt marsh plant zonation on the Pacific coast of South America

Aim

The aim of this study was to investigate the biogeography of plant zonation in salt marshes on the Pacific coast of South America; to examine whether salt marsh plant zonation varies with latitude; and to explore the relative importance of climatic, tidal, edaphic and disturbance factors in explaining large‐scale variation in salt marsh plant community structure.

Location

A 2,000‐km latitudinal gradient on the Pacific coast in Chile, with a climate shift from hyper‐arid at low to hyper‐humid at high latitudes.

Methods

Plant zonation was quantified in field surveys of ten marshes. Climate, tidal regimes, edaphic factors and disturbances (tsunami and rainfall floods) were determined. We used multivariate analyses to explore their relative importance in explaining large‐scale variation in salt marsh plant community structure.

Results

Across latitude, marshes were dominated by distinct plant communities in different climate regions, especially at the extreme dry and wet latitudes. Intertidal plant species zonation was present in hyper‐arid and semi‐arid climates, but not in arid, humid and hyper‐humid climates. Latitudinal variation in low‐marsh plant communities (regularly flooded at high tide) was largely a function of precipitation, while at high marshes (never flooded at high tide) latitudinal variation was explained with precipitation, temperature, tidal cycles, soil salinity and disturbances.

Main conclusions

Salt marshes on the Pacific coast of South America belong to Dry Coast and Temperate biogeographic types. Salt marsh plant zonation varies across latitude, and is explained by climatic, tidal, edaphic and disturbance factors. These patterns appear to be mechanistically explained by extrapolating experimentally generated community assembly models and have implications for predicting responses to climate change.