Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli

Rhizobiaceas are bacteria that fix nitrogen during symbiosis with plants. This symbiotic relationship is crucial for the nitrogen cycle, and understanding symbiotic mechanisms is a scientific challenge with direct applications in agronomy and plant development. Rhizobium etli is a bacteria which provides legumes with ammonia (among other chemical compounds), thereby stimulating plant growth. A genome-scale approach, integrating the biochemical information available for R. etli, constitutes an important step toward understanding the symbiotic relationship and its possible improvement. In this work we present a genome-scale metabolic reconstruction (iOR363) for R. etli CFN42, which includes 387 metabolic and transport reactions across 26 metabolic pathways. This model was used to analyze the physiological capabilities of R. etli during stages of nitrogen fixation. To study the physiological capacities in silico, an objective function was formulated to simulate symbiotic nitrogen fixation. Flux balance analysis (FBA) was performed, and the predicted active metabolic pathways agreed qualitatively with experimental observations. In addition, predictions for the effects of gene deletions during nitrogen fixation in Rhizobia in silico also agreed with reported experimental data. Overall, we present some evidence supporting that FBA of the reconstructed metabolic network for R. etli provides results that are in agreement with physiological observations. Thus, as for other organisms, the reconstructed genome-scale metabolic network provides an important framework which allows us to compare model predictions with experimental measurements and eventually generate hypotheses on ways to improve nitrogen fixation.     

A century of conservation: The ongoing recovery of Svalbard reindeer

Several caribou and reindeer (Rangifer tarandus) populations have experienced recent population declines, often attributed to anthropogenic stressors such as harvesting, landscape fragmentation, and climate change. Svalbard reindeer (R. t. platyrhynchus), the wild reindeer subspecies endemic to the high-Arctic Svalbard archipelago, was protected in 1925, after most subpopulations had been eradicated by harvest. Although direct pressure from harvest has ceased, indirect anthropogenic stressors from environmental changes have increased in this climate change hot spot. An assessment of the current distribution and abundance is therefore urgently needed. We combined distance sampling (300 km transects, n = 489 reindeer groups) and total counts (1,350 km², n = 1,349 groups) to estimate the Svalbard reindeer distribution and abundance across its entire range, which we compared with historical data from the literature and radiocarbon-dated bones. Reindeer have now recolonized nearly all non-glaciated land (i.e., areas occupied prior to human presence), and their spatial variation in abundance reflects vegetation productivity. Independent of vegetation productivity, however, recently recolonized areas have lower reindeer densities than areas not subject to past extirpation. This suggests that recovery from past overharvesting is still in progress. These incompletely recovered areas are potential targets for increased monitoring frequency and maintaining strict conservation to follow the Svalbard management goal (i.e., virtually untouched wilderness areas). Because of such ongoing recolonization, possibly combined with vegetation greening effects of recent warming, our status estimate of Svalbard reindeer abundance (22,435 [95% CI = 21,452–23,425]) is more than twice a previous estimate based on opportunistic counts. Thus, although our study demonstrates the successful outcome of strict harvesting control implemented a century ago, current and future population trajectories are likely shaped by climate change. © 2019 The Authors. Journal of Wildlife Management Published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.     

Prognostic molecular markers in pediatric liver disease – Are there any?

Pediatric liver disease (PLD) is a major cause of severe morbidity and prolonged hospitalizations in children. Stratifying patients in terms of prognosis remains challenging. The limited knowledge about molecular mechanisms causing and accompanying PLD remains the main obstacle in a search for reliable prognostic biomarkers. A systematic search of MEDLINE via PubMed and Embase via OVID was conducted on studies published between August 2007 and August 2017. Molecular markers with a prognostic potential in terms of survival, need for liver transplantation or disease progression/regression were selected. In general, identified studies were single center smaller case-control studies or case series with a low level of evidence and a high risk of bias. Only 23 studies comprising 898 patients could be included, mostly focusing on biliary atresia, non-alcoholic fatty liver disease, viral hepatitis, and LT; and markers related to morphogenesis and fibrosis. Furthermore, molecular markers in metabolic pathways and inflammation shown to be relevant, however requiring further validation. Hence, further biological and clinical studies are needed to gain greater molecular insight into PLD.     

Anti-complement effects of lactoferrin-derived peptides

Lactoferrin is an important biological molecule with many functions such as modulation of the inflammatory response, iron metabolism and antimicrobial defense. One effect of lactoferrin is the inhibition of the classical complement pathway. This study reports that antimicrobial peptides derived from the N-terminal region from both human and bovine lactoferrin, lactoferricin H and lactoferricin B, respectively, inhibit the classical complement pathway. No inhibitory effect of these peptides was observed on the alternative complement pathway in an AP50 assay. However, lactoferricin B reduced the inhibitory properties of serum against Escherichia coli in a concentration dependent manner. These results suggest that the N-terminal region of lactoferrin is the important part in the inhibition of complement activation and that these peptides possess other important properties than their antimicrobial effect.     

Alpha1-AR-mediated activation of NKCC in rat cardiomyocytes involves ERK-dependent phosphorylation of the cotransporter

We studied molecular and functional characteristics as well as hormonal regulation of the Na-K-2Cl cotransporter (NKCC) in the isolated rat heart and cardiomyocytes. NKCC activity was measured as bumetanide-sensitive (86)Rb(+) influx in isolated perfused rat hearts and isolated cardiomyocytes. Stimulation of alpha(1)-adrenoceptors (AR) by phenylephrine (30 microM) increased (86)Rb(+) influx. The NKCC inhibitor bumetanide (50 microM) reduced the response to phenylephrine by 45 +/- 13% (n = 12, P < 0.01). PD-98059 (10 microM), an inhibitor of the activation of the mitogen-activated protein kinases extracellular signal-regulated protein kinase 1 and 2 (ERK1/2), reduced the total response to phenylephrine by 51 +/- 13% (n = 10, P < 0.01) and eliminated the bumetanide-sensitive component, indicating that alpha(1)-AR mediated stimulation of NKCC is dependent on activation of ERK1/2. Inhibitors of protein kinase C or phosphatidylinositol 3-kinase had no effect. The presence of NKCC mRNA and protein was demonstrated in isolated rat cardiomyocytes. Phosphorylation of NKCC after alpha(1)-AR stimulation was shown by immunoprecipitation of the phosphoprotein from (32)P(i) prelabeled cardiomyocytes. Increased phosphorylation of the NKCC protein was also abolished by PD-98059. We conclude that the NKCC is present in rat cardiomyocytes and that ion transport by the cotransporter is regulated by alpha(1)-AR stimulation through phosphorylation of this protein involving the ERK pathway.     

Anthocyanin from strawberry (Fragaria ananassa) with the novel aglycone, 5-carboxypyranopelargonidin

An anthocyanin, 1, with the novel 4-substituted aglycone, 5-carboxypyranopelargonidin, was isolated in small amounts from the acidified, methanolic extract of strawberries, Fragaria ananassa Duch., by preparative HPLC after purification by partition against ethyl acetate, Amberlite XAD-7 and Sephadex LH-20 column chromatography. It was identified mainly by 2D NMR spectroscopy and electrospray LC-MS as the 3-O-beta-glucopyranoside of 5-carboxy-2-(4-hydroxyphenyl)-3,8-dihydroxy-pyrano[4,3,2-de]-1-benzopyrylium, an anthocyanidin which is homologous to 5-carboxypyranomalvidin (vitisidin A) reported in red wines and 5-carboxypyranocyanidin recently isolated from red onions. By comparison of UV-Vis absorption spectra, 1 showed in contrast to 2, pelargonidin 3-O-beta-glucopyranoside, a local absorption peak around 360 nm, a hypsochromic shift (8 nm) of the visible absorption maximum, and lack of a distinct UV absorption peak around 280 nm. The similarities between the absorption spectra of 1 in various acidic and neutral buffer solutions implied restricted formation of the instable colourless equilibrium forms, which are typical for most anthocyanins in weakly acidic solutions. The molar absorptivity (epsilon) of 1 varied little with pH contrary to similar values of for instance the major anthocyanin in strawberry, 2. However, 2 revealed higher epsilon-values than 1 at all pH values except 5.1. At pH 5.1, the epsilon-value of 1 (6250) was nearly four times the corresponding value of 2 (1720), which showed the potential of 5-carboxypyranopelargonidin derivatives as colorants in solutions with pH around 5. The colours of 1 and 2 in buffered solutions with pH 1.1 and pH 6.9 have been described by the CIELAB coordinates h(ab) (hue angle), C* (chroma), and L* (lightness).     

Daphnicle dynamics based on kinetic theory: An analogue-modelling of swarming and behaviour of Daphnia

Attempts are presented of an analogue modelling of Daphnia responses to various influences and stimuli, as distribution of food and of predators. An aim of the study is to examine to what extent a statistical-mechanical approach may be useful as a tool in modelling of Daphnia swarms behaviour. In the modelling we follow a line close to test particle studies in physical sciences. A generalized kinetic equation of what we shall call daphnicles is derived. The modelling incorporates individual characteristics of daphnicles, as position, velocity, degree of food saturation and responses daphnicles have to outside influences. Each daphnicle we assume responds to some stimuli in ordered ways and to others in stochastic ways, and the degree or strength of reactions depends on the density of all daphnicles, the density of food available, the saturation level of daphnicles and the threat level in the environment, or background, the daphnicles are living on. Some fluid equations of daphnicle swarms are subsequently derived from the basic equation, and solutions are given of the model-equations, including a food distribution equation, in some particular cases that show peculiarities in reactions of daphnicles to food, degree of saturation and to threat, when these are acting alone, and in combination. The modelling results may be compared to results of laboratory experiments of Daphnia behaviour that soon will be performed.