Is metagenomics resolving identification of functions in microbial communities?

We are coming up on the tenth anniversary of the broad use of the method involving whole metagenome shotgun sequencing, referred to as metagenomics. The application of this approach has definitely revolutionized microbiology and the related fields, including the realization of the importance of the human microbiome. As such, metagenomics has already provided a novel outlook on the complexity and dynamics of microbial communities that are an important part of the biosphere of the planet. Accumulation of massive amounts of sequence data also caused a surge in the development of bioinformatics tools specially designed to provide pipelines for data analysis and visualization. However, a critical outlook into the field is required to appreciate what could be and what has currently been gained from the massive sequence databases that are being generated with ever‐increasing speed.     

Irradiance-driven 20-hydroxyecdysone production and morphophysiological changes in Pfaffia glomerata plants grown in vitro

Pfaffia glomerata possesses potential pharmacological and medicinal properties, mainly owing to the secondary metabolite 20-hydroxyecdysone (20E). Increasing production of biomass and 20E is important for industrial purposes. This study aimed to evaluate the influence of irradiance on plant morphology and production of 20E in P. glomerata grown in vitro. Nodal segments of accessions 22 and 43 (Ac22 and Ac43) were inoculated in culture medium containing MS salts and vitamins. Cultures were maintained at 25 ± 2 °C under a 16-h photoperiod and subjected to irradiance treatments of 65, 130, and 200 μmol m⁻² s⁻¹ by fluorescent lamps. After 30 days, growth parameters, pigment content, stomatal density, in vitro photosynthesis, metabolites content, and morphoanatomy were assessed. Notably, Ac22 plants exhibited 10-fold higher 20E production when cultivated at 200 μmol m⁻² s⁻¹ than at 65 μmol m⁻² s⁻¹, evidencing the importance of light quantity for the accumulation of this metabolite. 20E production was twice as high in Ac22 as in Ac43 plants although both accessions responded positively to higher irradiance. Growth under 200 μmol m⁻² s⁻¹ stimulated photosynthesis and consequent biomass accumulation, but lowered carotenoids and anthocyanins. Furthermore, increasing irradiance enhanced the number of palisade and spongy parenchyma cells, enhancing the overall growth of P. glomerata.

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Peculiar salivary glands in a silk‐producing mite Bakericheyla chanayi (Cheyletidae)

This is the first ultrastructural investigation of salivary glands in the family Cheyletidae. In both sexes of Bakericheyla chanayi, paired acinous salivary glands and tubular coxal glands were shown to be united into the common podocephalic system. The secretory portion of the salivary gland includes medial and lateral lobes composed of the five and two cells, respectively, with clearly distinct ultrastructure. The cytoplasm of the cells is occupied by the secretory granules containing fine fibrous material. The fine structure of both cell types suggest a proteinaceous nature of their secretions. A single central process extending from the apical face of each secretory cell passes through the common acinar cavity to enter the conducting duct. A pair of intercalary cells at the base of the conducting duct links it with the secretory portion of the gland. Extending towards the acinar cavity, protrusions of intercalary cells alternate the apical regions of the secretory cells and form with them highly‐specialized contacts characterized by the apical network of microtubules and microfilaments. Two possible ways of secretion are suggested: 1) exocytosis into the acinar cavity and 2) direct passage via the central processes. The detection of axon profiles in the gland body suggests a neural control for the glandular cell function. In tritonymphs, neither secretion nor large lateral lobe cells were observed up to the pharate stage when the lateral lobe undergoes rapid differentiation. The arrangement of the acinous gland is compared to that of other arthropods. Its composition appears to be close to the class three of insect glands. The involvement of the lateral lobe cells in silk production is discussed. J. Morphol. 276:772–786, 2015. © 2015 Wiley Periodicals, Inc.     

Nitrile- and Amide-converting Microbial Enzymes: Stereo-, Regio- and Chemoselectivity

Biotransformations using microbial nitrile- and amide-converting enzymes have developed considerably in the recent years. Most processes profited from the stereo-, regio- and chemoselectivity of nitrile hydratases, nitrilases and amidases specific for primary or secondary amides. The aim of this review is to discuss the developments in this branch of biotransformations in the last ca. 5 years by taking highlights from research journals, patents and industrial applications.     

The effect of the colostral cells on gene expression of cytokines in cord blood cells

Beneficial effect of maternal milk is acknowledged, but there is still question whether maternal milk from allergic mother is as good as from healthy one. In our study, we have assayed the effect of cells from colostrum of healthy and allergic mothers on gene expression of cytokines in cord blood cells of newborns of healthy and allergic mothers. Cytokines typical for Th1 (IL-2, IFN-gamma), Th2 (IL-4, IL-13), Tregs (IL-10, TGF-beta), and IL-8 were followed. We were not able to detect significant influence of colostral cells on gene expression of cytokines in cord blood after 2-day coculture using Transwell system. There was no difference in gene expression of cytokines in nonstimulated cord blood cells of newborns of healthy and allergic mothers, but generally increased gene expression of cytokines except IL-10 and TGF-beta after polyclonal stimulation was detected in cord blood cells of children of allergic mothers. There was no difference in IL-10 expression in stimulated cord blood cells of children of healthy and allergic mothers. Gene expression of TGF-beta was even decreased in stimulated cord blood cells of children of allergic mothers in comparison to healthy ones. We have not observed difference in the capacity of colostral cells of healthy and allergic mothers to influence gene expression of cytokines in cord blood cells, but we have described difference in the reactivity of cord blood cells between children of allergic and healthy mothers.     

Mild hydrolysis of nitriles by the immobilized nitrilase from Aspergillus niger K10

The cell free extract from the nitrile-hydrolyzing strain Aspergillus niger K10 (0.25 mg of protein) was adsorped onto a 1 mL HiTrap Butyl Sepharose column. The benzonitrile-hydrolyzing activity of the immobilized enzyme (about 1.6 U/mg of protein) was stable at pH 8 and 35 °C within the examined period (4 h). The enzyme load on the above column was increased 18 times in order to achieve high nitrile conversion. This enzyme preparation was used for the conversion of 3-cyanopyridine and 4-cyanopyridine under the above conditions. The initial substrate conversion was nearly quantitative. The activity was fairly stable; the conversion of 3-cyanopyridine decreased to 70% after 15 h, while the conversion of 4-cyanopyridine was 60% of the initial value after 39 h. The former substrate was converted into nicotinic acid and nicotinamide (molar ratio approximately 16:1) and the latter one into isonicotinic acid and isonicotinamide (molar ratio approximately 3:1).