Top‐down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model

Gut microbiome–host metabolic interactions affect human health and can be modified by probiotic and prebiotic supplementation. Here, we have assessed the effects of consumption of a combination of probiotics (Lactobacillus paracasei or L. rhamnosus) and two galactosyl‐oligosaccharide prebiotics on the symbiotic microbiome–mammalian supersystem using integrative metabolic profiling and modeling of multiple compartments in germ‐free mice inoculated with a model of human baby microbiota. We have shown specific impacts of two prebiotics on the microbial populations of HBM mice when co‐administered with two probiotics. We observed an increase in the populations of Bifidobacterium longum and B. breve, and a reduction in Clostridium perfringens, which were more marked when combining prebiotics with L. rhamnosus. In turn, these microbial effects were associated with modulation of a range of host metabolic pathways observed via changes in lipid profiles, gluconeogenesis, and amino‐acid and methylamine metabolism associated to fermentation of carbohydrates by different bacterial strains. These results provide evidence for the potential use of prebiotics for beneficially modifying the gut microbial balance as well as host energy and lipid homeostasis.     

South Patagonian ombrotrophic bog vegetation reflects biogeochemical gradients at the landscape level

Question: Which environmental variables affect the floristic composition of south Patagonian bog vegetation along a gradient of climate and biogeochemical changes with increasing distance from the Pacific ocean? Location: Trans‐Andean transect (53° S), southern Patagonia Material and Methods: Floristic composition, peat characteristics (water level, decomposition, pH, total nitrogen, total carbon, ash content and plant available P, K, Na, Ca, Mg, Fe, Mn, Zn, and Al) and climatic constraints of ombrotrophic peat‐lands were measured at 82 plots along a gradient of increasing distance from the Pacific Ocean. Results: Climatic constraints and biogeochemical peat characteristics significantly change with increasing distance from the Pacific. Peatland vegetation shifted from hyperoceanic blanket bogs dominated by cushion forming vascular plants to the west to Sphagnum bogs to the east. Climatic and biogeochemical variables explained a large proportion of the floristic variation along the first DCA axis. The second axis represented a water level gradient. When ‘distance to the Pacific’ was defined as a covariable in partial CCA, the proportion of variance explained declined for most other variables, especially in the case of annual precipitation and exchangeable base cations and related traits. The differences in biogeochemical characteristics related to peat were mainly attributed to the input of sea‐borne cations. Conclusions: While variation in vegetation composition along a longitudinal gradient crossing the southern Andes was attributed to climatic constraints as expected, vegetation composition was also strongly affected by the biogeochemical characteristics of peat. Sea spray was of high ecological importance to peat chemistry and, consequently, to floristic composition. Presumably, south Patagonian peat bogs represent a glimpse of pre‐industrial environments, so that these peat bogs may act as reference systems with respect to atmospheric inputs in mire ecology research.     

Regulation and characterization of two inducible amino-acid transport systems in Chlorella vulgaris

Glucose or non-metabolizable glucose analogues induce two amino-acid transport systems in Chlorella vulgaris: an arginine system (arginine and lysine) and a proline system (proline, glycine, alanine and serine). the same amino-acid transport systems are induced in the absence of glucose, when the cells are depleted of their nitrogen source as judged by a comparison of K_m values and the lack of additive induction by the two treatments Changes in the concentration of neither internal free amino acids nor of soluble carbohydrate pools correlate prefectly with the induction of amino-acid transport. Also exogenous cAMP had no effect on the induction of transport. Both aminoacid transport systems are able to accumulate free amino acids more than 1000-fold. The accumulation plateau is not due to a steady state of influx and efflux, but rather arises by a shut-off of influx. No significant effux is observed. The biological importance of this frequently observed behaviour in amino-acid transport is discussed.     

Chemoautotrophic growth of Rhodopseudomonas species with hydrogen and chemotrophic utilization of methanol and formate

A chemolithoautotrophic type of metabolism, which was hitherto unknown for purple nonsulfur bacteria, was demonstrated by growth experiments using Rhodopseudomonas capsulata Kb1 and Rhodopseudomonas acidophila 10050. These strains were able to grow in a mineral medium in the dark at the expense of H₂, O₂, and CO₂. A minimum doubling time of 9 h was obtained for R. capsulata under an atmosphere containing less than 15% oxygen; higher oxygen concentrations suppressed autotrophic but not chemoorganotrophic growth. Oxygen sensitivity of chemoautotrophically growing cells of R. acidophila was even more pronounced, whereas cells growing chemotrophically on methanol almost tolerated the oxygen concentration of air. Highest oxygen sensitivity of growth of R. acidophila was observed with formate as substrate. The growth yield of cultures grown semiaerobically in the dark on methanol was 0.23 g dry cell material per g methanol consumed.     

Selective synthesis of depsipeptides by the immobilized multienzyme enniatin synthetase

Summary The multifunctional enzyme enniatin synthetase was immobilized by adsorption to propyl agarose. The immobilized multienzyme retained 45% of the activity of the free enzyme; an operational half-life of about 15 h was estimated. Selective synthesis of several different enniatin homologues was achieved with propyl agarose-bound enniatin synthetase. In addition to enniatin A, B, and C formation, a selective synthesis of non-naturally occurring depsipeptides, containing norvaline, norleucine, or -aminobutyric acid as sole amino acid moieties, was observed.     

High-affinity uptake of γ-[3H]aminobutyric acid by isolated mouse oligodendrocytes in culture

Oligodendrocytes were isolated from mixed glial cultures of neonatal mouse forebrain and further grown in serum-free hormone supplemented culture medium. Cell populations were identified by indirect immunofluorescence using a range of specific antibodies, revealing a predominantly immature population of oligodendrocytes, the majority expressing the myelin glycolipids galactocerebroside and sulfatide on their plasma membrane. Astroglial contamination was found to be minimal. Simultaneous autoradiography and immunofluorescence demonstrated the presence of a transport system for the major inhibitory neurotransmitter GABA in the oligodendrocytes. The transport system was found to be energy, sodium and temperature dependent. Kinetic analysis revealed a high affinity system, with aK _m of 6.27 M and aV _max of 0.714 nmol/min/mg protein, which is comparable to that found previously for CNS neurons and astrocytes.Special Issue dedicated to Dr. E. M. Shooter and Dr. S. Varon.     

Acetylene inhibition technique underestimates in situ denitrification rates in intact cores of freshwater sediment

Abstract Denitrification in intact sediment cores was measured by the acetylene inhibition technique and compared with the nitrate flux between water and sediment. Less than half of the nitrate-N consumed by the sediment could be recovered as nitrous oxide-N. The low recovery rate of nitrous oxide from intact sediment cores indicated losses of nitrous oxide by diffusion down to nitrate-free sediment layers, where reduction of nitrous oxide may take place. In sediment slurries 100% of nitrate-N could be recovered as nitrous oxide-N as long as the nitrate concentration in the liquid phase was above 10 μM. Nitrous oxide added to nitrate-free sediment slurries was reduced regardless of whether acetylene was present or not. Therefore denitrification may be significantly underestimated by this method.     

Labeling and enrichment of Arabidopsis thaliana matrix metalloproteases using an active-site directed, marimastat-based photoreactive probe

Matrix metalloproteases (MMPs) are secreted or membrane-bound zinc-containing proteases that play diverse roles in development and immunity in plants and in tissue remodeling in animals. We developed a photoreactive probe based on the MMP inhibitor marimastat, conjugated to a 4-azidotetrafluorobenzoyl moiety as photoreactive group and biotin as detection or sorting function. The probe labels At2-MMP, At4-MMP, At5-MMP, and likely other plant MMPs in leaf extracts, as shown by transient At-MMP expression in Nicotiana benthamiana, protein blot, and LC-MS/MS analysis. This MMP probe is a valuable tool to study the post-translational status of MMPs during plant immunity and other MMP-regulated processes.     

Iron Regulatory Proteins Control a Mucosal Block to Intestinal Iron Absorption

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Highlights? Disruption of intestinal IRP function constrains iron absorption in adult mice ? IRPs must limit mucosal ferritin for efficient iron absorption ? IRPs control ferroportin directly and DMT1 directly or through HIF2α ? IRPs define a set point for hepcidin-mediated regulation of iron absorption