Systems Biology of Aromatic Compound Catabolism in Facultative Anaerobic Aromatoleum aromaticum EbN1T.

Members of the genus Aromatoleum thrive in diverse habitats and use a broad range of recalcitrant organic molecules coupled to denitrification or O2 respiration. To gain a holistic understanding of the model organism A. aromaticum EbN1T, we studied its catabolic network dynamics in response to 3-(4-hydroxyphenyl)propanoate, phenylalanine, 3-hydroxybenzoate, benzoate, and acetate utilized under nitrate-reducing versus oxic conditions. Integrated multi-omics (transcriptome, proteome, and metabolome) covered most of the catabolic network (199 genes) and allowed for the refining of knowledge of the degradation modules studied. Their substrate-dependent regulation showed differing degrees of specificity, ranging from high with 3-(4-hydroxyphenyl)propanoate to mostly relaxed with benzoate. For benzoate, the transcript and protein formation were essentially constitutive, contrasted by that of anoxia-specific versus oxia-specific metabolite profiles. The matrix factorization of transcriptomic data revealed that the anaerobic modules accounted for most of the variance across the degradation network. The respiration network appeared to be constitutive, both on the transcript and protein levels, except for nitrate reductase (with narGHI expression occurring only under nitrate-reducing conditions). The anoxia/nitrate-dependent transcription of denitrification genes is apparently controlled by three FNR-type regulators as well as by NarXL (all constitutively formed). The resequencing and functional reannotation of the genome fostered a genome-scale metabolic model, which is comprised of 655 enzyme-catalyzed reactions and 731 distinct metabolites. The model predictions for growth rates and biomass yields agreed well with experimental stoichiometric data, except for 3-(4-hydroxyphenyl)propanoate, with which 4-hydroxybenzoate was exported. Taken together, the combination of multi-omics, growth physiology, and a metabolic model advanced our knowledge of an environmentally relevant microorganism that differs significantly from other bacterial model strains. IMPORTANCE Aromatic compounds are abundant constituents not only of natural organic matter but also of bulk industrial chemicals and fuel components of environmental concern. Considering the widespread occurrence of redox gradients in the biosphere, facultative anaerobic degradation specialists can be assumed to play a prominent role in the natural mineralization of organic matter and in bioremediation at contaminated sites. Surprisingly, differential multi-omics profiling of the A. aromaticum EbN1T studied here revealed relaxed regulatory stringency across its four main physiological modi operandi (i.e., O2-independent and O2-dependent degradation reactions versus denitrification and O2 respiration). Combining multi-omics analyses with a genome-scale metabolic model aligned with measured growth performances establishes A. aromaticum EbN1T as a systems-biology model organism and provides unprecedented insights into how this bacterium functions on a holistic level. Moreover, this experimental platform invites future studies on eco-systems and synthetic biology of the environmentally relevant betaproteobacterial Aromatoleum/Azoarcus/Thauera cluster.

Evaluating the accuracy of facial expressions as emotion indicators across contexts in dogs.

Facial expressions potentially serve as indicators of animal emotions if they are consistently present across situations that (likely) elicit the same emotional state. In a previous study, we used the Dog Facial Action Coding System (DogFACS) to identify facial expressions in dogs associated with conditions presumably eliciting positive anticipation (expectation of a food reward) and frustration (prevention of access to the food). Our first aim here was to identify facial expressions of positive anticipation and frustration in dogs that are context-independent (and thus have potential as emotion indicators) and to distinguish them from expressions that are reward-specific (and thus might relate to a motivational state associated with the expected reward). Therefore, we tested a new sample of 28 dogs with a similar set-up designed to induce positive anticipation (positive condition) and frustration (negative condition) in two reward contexts: food and toys. The previous results were replicated: Ears adductor was associated with the positive condition and Ears flattener, Blink, Lips part, Jaw drop, and Nose lick with the negative condition. Four additional facial actions were also more common in the negative condition. All actions except the Upper lip raiser were independent of reward type. Our second aim was to assess basic measures of diagnostic accuracy for the potential emotion indicators. Ears flattener and Ears downward had relatively high sensitivity but low specificity, whereas the opposite was the case for the other negative correlates. Ears adductor had excellent specificity but low sensitivity. If the identified facial expressions were to be used individually as diagnostic indicators, none would allow consistent correct classifications of the associated emotion. Diagnostic accuracy measures are an essential feature for validity assessments of potential indicators of animal emotion.

The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases.

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (Metano Modeling Toolbox), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens.

The influence of human interaction on guinea pigs: Behavioral and thermographic changes during animal-assisted therapy.

Guinea pigs are often involved in animal-assisted therapy (AAT) but there is little knowledge about the effects of human contact on guinea pigs involved in AAT. The aim of this study was to investigate effects of availability of a retreat, presence of conspecifics, prior experience with AAT, and human interaction on indicators of welfare in guinea pigs involved in AAT. Guinea pigs of both sexes and different ages (n=20) were assigned to a randomized, controlled within-subject trial with repeated measurements. Each guinea pig was tested in four settings: (I) therapy with retreat possibility with conspecifics, (II) therapy with retreat possibility without conspecifics, (III) therapy without retreat possibility, and (IV) setting without human interaction. We measured changes in eye temperature, as a proxy to infer stress levels, at 5-s intervals with a thermographic camera. All sessions were video recorded and the guinea pigs' behavior was coded using continuous recording and focal animal sampling. For the statistical analysis we used generalized linear mixed models, with therapy setting as a fixed effect and individual guinea pig as a random effect. We observed a temperature increase relative to baseline in settings (I) therapy with retreat with conspecifics present and (III) therapy without retreat. The percentage of time a guinea pig was petted was positively correlated with a rise in the eye temperature independent of the setting. Time spent eating was reduced in all therapy settings (I-III) compared to the setting without HAI (human animal interaction) (IV). In the setting with retreat (I), guinea pigs showed more active behaviors such as locomotive behavior or startling compared to the setting without retreat (III) and the setting without HAI (IV). When no retreat was available (III), they showed more passive behaviors, such as standing still or freezing compared to therapy with retreat (I). Based on our results we identified the behaviors "reduced eating", "increased startle" and "increased freezing" as indicators of an increased stress level. Petting the guinea pigs was correlated with a rise in the eye temperature and might be a factor which can cause stress. Our results support the suggestion that guinea pigs involved in AAT should have a retreat possibility, should have access to conspecifics, and should be given time to adapt to a new setting. In this way, stress might be reduced.

Simplified and age-appropriate recommendations for added sugars in children.

Excess sugar intake increases risk for obesity and related comorbidities among children. The World Health Organization (WHO), American Heart Association (AHA) and the 2015 USDA dietary recommendations have proposed guidelines for added sugar intake to reduce risk for disease. WHO and USDA recommendations are presented as a percentage of daily calories from added sugar. This approach is not easily understood or translated to children, where energy needs increase with age. The AHA recommendation is based on a fixed value of 25 g of added sugar for all children 2-19 years of age. This approach does not take into account the different levels of intake across this wide age range. Due to these limitations, we adapted current recommendations for added sugars based on daily energy needs of children 2-19 years. We used those values to derive simple regression equations to predict grams or teaspoons of added sugars per day based on age that would be equivalent to 10% of daily energy needs. This proposed approach aligns with the changing nutritional needs of children and adolescents during growth.

Depolymerization of lignosulfonates by submerged cultures of the basidiomycete Irpex consors and cloning of a putative versatile peroxidase.

Lignosulfonates are abundantly available byproducts of the paper and pulping industry, and they therefore represent a promising feedstock for new sustainable processes. For industrial applications of lignosulfonates, their molecular weight distribution is a critical factor. In order to decrease the average molecular weight of lignosulfonates, Seventeen basidiomycetes were screened for their capability to depolymerize lignosulfonates from spent sulfite liquor (SSL) in surface and liquid cultures. Five basidiomycetes polymerized the lignosulfonates under the selected conditions. Only Irpex consors was found to efficiently degrade calcium lignosulfonates when SSL (0.5%, w/w) was used as the sole carbon and nitrogen source. The average molecular weight of the lignosulfonates was reduced from ∼26 to ∼4 kDa as determined by size exclusion chromatography (SEC) within two weeks. Various extracellular enzyme activities of I. consors were determined over the culture period. High peroxidase activities were correlating with a high degradation rate and the culture was harvested at the day of highest peroxidase activity. A putative versatile peroxidase was isolated by fast protein liquid chromatography (FPLC) and its encoding cDNA was cloned.

A metabolite-centric view on flux distributions in genome-scale metabolic models.

BACKGROUND: Genome-scale metabolic models are important tools in systems biology. They permit the in-silico prediction of cellular phenotypes via mathematical optimisation procedures, most importantly flux balance analysis. Current studies on metabolic models mostly consider reaction fluxes in isolation. Based on a recently proposed metabolite-centric approach, we here describe a set of methods that enable the analysis and interpretation of flux distributions in an integrated metabolite-centric view. We demonstrate how this framework can be used for the refinement of genome-scale metabolic models. RESULTS: We applied the metabolite-centric view developed here to the most recent metabolic reconstruction of Escherichia coli. By compiling the balance sheets of a small number of currency metabolites, we were able to fully characterise the energy metabolism as predicted by the model and to identify a possibility for model refinement in NADPH metabolism. Selected branch points were examined in detail in order to demonstrate how a metabolite-centric view allows identifying functional roles of metabolites. Fructose 6-phosphate aldolase and the sedoheptulose bisphosphate bypass were identified as enzymatic reactions that can carry high fluxes in the model but are unlikely to exhibit significant activity in vivo. Performing a metabolite essentiality analysis, unconstrained import and export of iron ions could be identified as potentially problematic for the quality of model predictions. CONCLUSIONS: The system-wide analysis of split ratios and branch points allows a much deeper insight into the metabolic network than reaction-centric analyses. Extending an earlier metabolite-centric approach, the methods introduced here establish an integrated metabolite-centric framework for the interpretation of flux distributions in genome-scale metabolic networks that can complement the classical reaction-centric framework. Analysing fluxes and their metabolic context simultaneously opens the door to systems biological interpretations that are not apparent from isolated reaction fluxes. Particularly powerful demonstrations of this are the analyses of the complete metabolic contexts of energy metabolism and the folate-dependent one-carbon pool presented in this work. Finally, a metabolite-centric view on flux distributions can guide the refinement of metabolic reconstructions for specific growth scenarios.

Genome-scale reconstruction and analysis of the metabolic network in the hyperthermophilic archaeon Sulfolobus solfataricus.

We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon Sulfolobus solfataricus, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2-4 (optimum 3.5) and a temperature of 75-80°C (optimum 80°C). The genome of Sulfolobus solfataricus P2 contains 2,992,245 bp on a single circular chromosome and encodes 2,977 proteins and a number of RNAs. The network comprises 718 metabolic and 58 transport/exchange reactions and 705 unique metabolites, based on the annotated genome and available biochemical data. Using the model in conjunction with constraint-based methods, we simulated the metabolic fluxes induced by different environmental and genetic conditions. The predictions were compared to experimental measurements and phenotypes of S. solfataricus. Furthermore, the performance of the network for 35 different carbon sources known for S. solfataricus from the literature was simulated. Comparing the growth on different carbon sources revealed that glycerol is the carbon source with the highest biomass flux per imported carbon atom (75% higher than glucose). Experimental data was also used to fit the model to phenotypic observations. In addition to the commonly known heterotrophic growth of S. solfataricus, the crenarchaeon is also able to grow autotrophically using the hydroxypropionate-hydroxybutyrate cycle for bicarbonate fixation. We integrated this pathway into our model and compared bicarbonate fixation with growth on glucose as sole carbon source. Finally, we tested the robustness of the metabolism with respect to gene deletions using the method of Minimization of Metabolic Adjustment (MOMA), which predicted that 18% of all possible single gene deletions would be lethal for the organism.

[How good are clinical investigative procedures for diagnosing meniscus lesions?]. / Wie gut sind klinische Untersuchungsverfahren zur Diagnostik von Meniskusläsionen?

AIM: The purpose of this study was to evaluate different clinical meniscus tests. METHOD: During 13 months we evaluated 64 patients with a suspected meniscus lesion in a prospective study. The age ranged from 16 to 76 years (average: 38.5 years). 66 % were male patients. Between the clinical examination and the arthroscopy there was no additional trauma to the knee. All patients were clinically examined in a standard manner by two independent orthopaedic surgeons. Clinical findings of the menisci were documented according to 12 well-described and commonly used meniscus tests. The arthroscopy was performed by a single surgeon who was not aware of the results of the clinical examination. This surgeon documented the intraarticular findings in a standardized operating report. A meniscus lesion/degeneration was documented when this was evident either by inspection or by palpation. RESULTS: The results showed either clinical meniscus tests with a high specificity and a low sensitivity or tests with a high sensitivity, but only a low specificity. We were not able to identify meniscus tests which showed both a high sensitivity and a high specificity. CLINICAL RELEVANCE: Even with access to MRI the clinical findings in knee joint with injured menisci still have a high diagnostic value. However, it seems to be necessary to combine different tests.

Chemosensitizers of the multixenobiotic resistance in amorphous aggregates (marine snow): etiology of mass killing on the benthos in the Northern Adriatic?

Periodically appearing amorphous aggregates, `marine snow', are formed in the sea and if settled as mats on the sea bottom cause death of benthic metazoans. Especially those animals are killed which are sessile filter feeders, e.g. sponges, mussels, or Anthozoa. The etiology of the toxic principle(s) is not yet well understood. Gel-like marine snow aggregates occurred in the Northern Adriatic during summer 1997. Samples of these aggregates were collected during the period July to September and the outer as well as the inner zones were analyzed for (i) cell toxicity, and (ii) chemosensitizing activity of the multixenobiotic resistance (MXR) mechanism. Organic extracts were prepared and cell toxicity was determined using mouse lymphoma cells. The experiments revealed that the major activity is seen in the center of the mats of the gel-like aggregates; a growth inhibitory activity of up to 54% (correlated to 5 ml of snow sample) was determined. The same extracts were used to determine the inhibition of the P-glycoprotein (Pgp) extrusion pump which confers the multixenobiotic resistance. The analyses were performed with cells from the sponge Suberites domuncula and with gills from the clam Corbicula fluminea in situ. Both systems have been shown to express the Pgp extrusion pump. The data show that extracts from the outer zone of the gel-like aggregate samples display pronounced inhibitory activity on the MXR extrusion pump and hence act as chemosensitizers by reversing the MXP property. These findings indicate that gel-like aggregates contain compounds in the outer zone, chemosensitizer of the Pgp extrusion pump, which lower the level of protection of metazoan animals towards dissolved compounds in their surrounding milieu, and in the center toxic compounds which are-very likely-even in the absence of chemosensitizers hazardous for the invertebrates.

Detection of STEC and epidemiological investigations in surrounding of a HUS patient.

After occurrence of a case of HUS infection in a 2-year-old infant from a dairy farmer's family living near Oldenburg, investigations were performed in the infant's surrounding in order to elucidate the route of infection. Since hospitalization took place at a late stage, it was not possible to isolate EHEC from the patient's stool samples. However, E. coli O157 antibody determinations in serum were positive. Since STEC of serogroup O157 were found in faeces from the 34 dairy cows of the farm, stool samples were taken from 6 members of the child's family and examined. Non-O157 STEC could be isolated from the stools of 2 family members. Determination of other virulence factors and other characteristics such as serotype, biotype and phage type showed identity of the agent for 3 isolates (2 from animals, 1 from humans). By means of pulsed-field gel electrophoresis of the restricted DNA of the isolates and by means of RAPD-PCR it was not possible to establish any differences in the band patterns. It can be assumed, therefore, that the organisms had been transmitted from animals to humans.

Effects of particulate matter on rates of membrane uptake of polynuclear aromatic hydrocarbons.

Investigations of the mechanism of particle-enhanced uptake of benzo [a] pyrene into model membranes and microsomes have been extended by studying the effects of particulates on the rates of uptake of four additional polynuclear aromatic hydrocarbons (PAH) into model membranes. Adsorption of dibenzo [a, h] anthracene, benzo [g,h,i] perylene, and 3-methylcholanthrene to the surface of particles resulted in enhanced rates of membrane uptake of these PAH. Adsorption to the fibrous asbestos minerals (chrysotile and anthophyllite) produced the greatest enhancement in membrane uptake rates compared to uptake from microcrystalline dispersions of the PAH. Adsorption of these PAH to nonfibrous minerals resulted in uptake rates intermediate between those of the asbestos-adsorbed and microcrystalline states. In contrast, adsorption of dibenzo-[c,g] carbazole to particles did not result in enhanced uptake. In this case, the rates of uptake in the absence and presence of particles were all extremely high, presumably as a result of the high water solubility of this PAH. The methods described in this paper permit characterization of particles-PAH mixtures in terms of the rate of PAH uptake into membranes.

Transport of a carcinogen, benzo[a]pyrene, from particulates to lipid bilayers: a model for the fate of particle-adsorbed polynuclear aromatic hydrocarbons which are retained in the lungs.

Fluorescence spectroscopic methods were used to investigate the effects of adsorption of benzo[a]pyrene to particulate matter on its rate of uptake into model membranes composed of dipalmitoyl L-alpha-phosphatidylcholine. From these experiments we conclude the following: 1. Adsorption of benzo[a]pyrene to four types of asbestos (anthophyllite, crocidolite, chrysotile, and amosite) and a variety of non-fibrous particles (hematite, silica, titanium dioxide, porous glass and talc) results in increased rates of membrane uptake when compared with aqueous suspensions of benzo[a]pyrene microcrystals. Benzo[a]pyrene was not released from carbon black. 2. Asbestos-adsorbed benzo[a]pyrene was transferred to the membranes most rapidly. 3. Adsorption of benzo[a]pyrene to the surface of the particles is necessary for its enhanced transport into membranes. That is, simple mixtures of benzo[a]pyrene microcrystals and particulates do not show enhanced transport. 4. Particle-enhanced transport of benzo[a]pyrene is not correlated with the effects of the particles on vesicle integrity, binding of vesicles to the particles, or the concentrations of either particles or vesicles. The rate limiting step for transport of benzo[a]pyrene into vesicles appears to be its rate of desorption from the surface of the particle. Following desorption, membrane uptake of benzo[a]pyrene is rapid.