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Recovering genomics clusters of secondary metabolites from lakes using genome-resolved metagenomics
(2018)
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.
Experimental studies on polysemy have come to contradictory conclusions on whether words with multiple senses are stored as separate or shared mental representations. The present study examined the semantic relatedness and semantic similarity of literal and non-literal (metonymic and metaphorical) senses of three word classes: nouns, verbs, and adjectives. Two methods were used: a psycholinguistic experiment and a distributional analysis of corpus data. In the experiment, participants were presented with 6-12 short phrases containing a polysemous word in literal, metonymic, or metaphorical senses and were asked to classify them so that phrases with the same perceived sense were grouped together. To investigate the impact of professional background on their decisions, participants were controlled for linguistic vs. non-linguistic education. For nouns and verbs, all participants preferred to group together phrases with literal and metonymic senses, but not any other pairs of senses. For adjectives, two pairs of senses were often grouped together: literal with metonymic, and metonymic with metaphorical. Participants with a linguistic background were more accurate than participants with non-linguistic backgrounds, although both groups shared principal patterns of sense classification. For the distributional analysis of corpus data, we used a semantic vector approach to quantify the similarity of phrases with literal, metonymic, and metaphorical senses in the corpora. We found that phrases with literal and metonymic senses had the highest degree of similarity for the three word classes, and that metonymic and metaphorical senses of adjectives had the highest degree of similarity among all word classes. These findings are in line with the experimental results. Overall, the results suggest that the mental representation of a polysemous word depends on its word class. In nouns and verbs, literal and metonymic senses are stored together, while metaphorical senses are stored separately; in adjectives, metonymic senses significantly overlap with both literal and metaphorical senses.
Here, we present novel equations for the large-scale zonal-mean wind as well as those for planetary waves. Together with synoptic parameterization (as presented by Coumou et al., 2011), these form the mathematical description of the dynamical core of Aeolus 1.0. The regions of high azonal wind velocities (planetary waves) are accurately captured for all validation experiments. The zonal-mean zonal wind and the integrated lower troposphere mass flux show good results in particular in the Northern Hemisphere. In the Southern Hemisphere, the model tends to produce too-weak zonal-mean zonal winds and a too-narrow Hadley circulation. We discuss possible reasons for these model biases as well as planned future model improvements and applications.
Background. Metal recycling factories (MRFs) have developed rapidly in Nigeria as recycling policies have been increasingly embraced. These MRFs are point sources for introducing potentially toxic elements (PTEs) into environmental media. Objectives. The aim of this study was to determine the constituents (elemental and mineralogy) of the wastes (slag and particulate matter, (PM)) and soils around the MRFs and to determine the level of pollution within the area. Methods. Sixty samples (30 slag samples, 15 soil samples and 15 PM samples) were collected for this study. The soils, slag and PM samples were analyzed for elemental constituents using inductively coupled plasma optical emission spectrometry. Mineralogy of the PM was determined using scanning electron microscope-energy dispersive spectroscopy (SEM-EDS), and soil mineralogy was determined by an X-ray diffractometer (XRD). Results. The results of the soil analyses revealed the following concentrations for the selected metals in mg/kg include lead (Pb) (21.0-2399.0), zinc (Zn) (56.0-4188.0), copper (Cu) (10.0-1470.0), nickel (Ni) (6.0-215.0), chromium (Cr) (921.0-1737.0) and cadmium (Cd) (below detectable limit (Bdl)-18.1). For the slags the results were Pb (68.0-.333.0), Zn (1364.0-3062), Cu (119.0-1470.0), Ni (12.0-675.0), Cr (297-1737) and Cd (Bdl-15.8). The results in mu g/g for the metal analysis in PM were Pb (4.6-160.0), Zn (18.0-471.0), Cu (2.5-11.0), Ni (0.8-4.2), and Cr (2.5-11.0), while Cd was undetected. The slags are currently utilized for filling the foundations of buildings and roads, providing additional pathways for the introduction of PTEs into the environment from the suspended materials generated from mechanical breakdown of the slags. Conclusions. The MRFs were found to have impacted the quality of environmental media through the introduction of PTEs, impairing soil quality, in addition to PM, which can have detrimental health consequences. Further studies on the health implications of these pollutants and their impacts on human health are needed. Competing Interests. The authors declare no competing financial interests
Background: Pavlovian processes are thought to play an important role in the development, maintenance and relapse of alcohol dependence, possibly by influencing and usurping on- going thought and behavior. The influence of Pavlovian stimuli on on-going behavior is paradigmatically measured by Pavlovian-to-instrumental-transfer (PIT) tasks. These involve multiple stages and are complex. Whether increased PIT is involved in human alcohol
dependence is uncertain. We therefore aimed to establish and validate a modified PIT paradigm that would be robust, consistent, and tolerated by healthy controls as well as by patients suffering from alcohol dependence, and to explore whether alcohol dependence is associated with enhanced Pavlovian-Instrumental transfer.
Methods: 32 recently detoxified alcohol-dependent patients and 32 age and gender matched healthy controls performed a PIT task with instrumental go/no-go approach behaviours. The task involved both Pavlovian stimuli associated with monetary rewards and losses, and images of drinks.
Results: Both patients and healthy controls showed a robust and temporally stable PIT effect. Strengths of PIT effects to drug-related and monetary conditioned stimuli were highly correlated. Patients more frequently showed a PIT effect and the effect was stronger in response to aversively conditioned CSs (conditioned suppression), but there was no group difference in response to appetitive CSs.
Conclusion: The implementation of PIT has favorably robust properties in chronic alcohol- dependent patients and in healthy controls. It shows internal consistency between monetary and drug-related cues. The findings support an association of alcohol dependence with an increased propensity towards PIT.
Two decades ago, sphingosine 1-phosphate (S1P) was discovered as a novel bioactive molecule that regulates a variety of cellular functions. The plethora of S1P-mediated effects is due to the fact that the sphingolipid not only modulates intracellular functions but also acts as a ligand of G protein-coupled receptors after secretion into the extracellular environment. In the plasma, S1P is found in high concentrations, modulating immune cell trafficking and vascular endothelial integrity. The liver is engaged in modulating the plasma S1P content, as it produces apolipoprotein M, which is a chaperone for the S1P transport. Moreover, the liver plays a substantial role in glucose and lipid homeostasis. A dysfunction of glucose and lipid metabolism is connected with the development of liver diseases such as hepatic insulin resistance, non-alcoholic fatty liver disease, or liver fibrosis. Recent studies indicate that S1P is involved in liver pathophysiology and contributes to the development of liver diseases. In this review, the current state of knowledge about S1P and its signaling in the liver is summarized with a specific focus on the dysregulation of S1P signaling in obesity-mediated liver diseases. Thus, the modulation of S1P signaling can be considered as a potential therapeutic target for the treatment of hepatic diseases.
The article describes the surface modification of 3D printed poly(lactic acid) (PLA) scaffolds with calcium phosphate (CP)/gelatin and CP/chitosan hybrid coating layers. The presence of gelatin or chitosan significantly enhances CP co-deposition and adhesion of the mineral layer on the PLA scaffolds. The hydrogel/CP coating layers are fairly thick and the mineral is a mixture of brushite, octacalcium phosphate, and hydroxyapatite. Mineral formation is uniform throughout the printed architectures and all steps (printing, hydrogel deposition, and mineralization) are in principle amenable to automatization. Overall, the process reported here therefore has a high application potential for the controlled synthesis of biomimetic coatings on polymeric biomaterials.
High-throughput sequence data retrieved from ancient or other degraded samples has led to unprecedented insights into the evolutionary history of many species, but the analysis of such sequences also poses specific computational challenges. The most commonly used approach involves mapping sequence reads to a reference genome. However, this process becomes increasingly challenging with an elevated genetic distance between target and reference or with the presence of contaminant sequences with high sequence similarity to the target species. The evaluation and testing of mapping efficiency and stringency are thus paramount for the reliable identification and analysis of ancient sequences. In this paper, we present ‘TAPAS’, (Testing of Alignment Parameters for Ancient Samples), a computational tool that enables the systematic testing of mapping tools for ancient data by simulating sequence data reflecting the properties of an ancient dataset and performing test runs using the mapping software and parameter settings of interest. We showcase TAPAS by using it to assess and improve mapping strategy for a degraded sample from a banded linsang (Prionodon linsang), for which no closely related reference is currently available. This enables a 1.8-fold increase of the number of mapped reads without sacrificing mapping specificity. The increase of mapped reads effectively reduces the need for additional sequencing, thus making more economical use of time, resources, and sample material.