Phylogenetic analysis reveals an ancient gene duplication as the origin of the MdtABC efflux pump.

The efflux pumps from the Resistance-Nodulation-Division family, RND, are main contributors to intrinsic antibiotic resistance in Gram-negative bacteria. Among this family, the MdtABC pump is unusual by having two inner membrane components. The two components, MdtB and MdtC are homologs, therefore it is evident that the two components arose by gene duplication. In this paper, we describe the results obtained from a phylogenetic analysis of the MdtBC pumps in the context of other RNDs. We show that the individual inner membrane components (MdtB and MdtC) are conserved throughout the Proteobacterial species and that their existence is a result of a single gene duplication. We argue that this gene duplication was an ancient event which occurred before the split of Proteobacteria into Alpha-, Beta- and Gamma- classes. Moreover, we find that the MdtABC pumps and the MexMN pump from Pseudomonas aeruginosa share a close common ancestor, suggesting the MexMN pump arose by another gene duplication event of the original Mdt ancestor. Taken together, these results shed light on the evolution of the RND efflux pumps and demonstrate the ancient origin of the Mdt pumps and suggest that the core bacterial efflux pump repertoires have been generally stable throughout the course of evolution

Beyond Gross-Pitaevskii equation for 1D gas: Quasiparticles and solitons

Describing properties of a strongly interacting quantum many-body system poses a serious challenge both for theory and experiment. In this work, we study excitations of one-dimensional repulsive Bose gas for arbitrary interaction strength using a hydrodynamic approach. We use linearization to study particle (type-I) excitations and numerical minimization to study hole (type-II) excitations. We observe a good agreement between our approach and exact solutions of the Lieb-Liniger model for the particle modes and discrepancies for the hole modes. Therefore, the hydrodynamical equations find to be useful for long-wave structures like phonons and of a limited range of applicability for short-wave ones like narrow solitons. We discuss potential further applications of the method.Comment: 27 pages, 11 figures. Submission to SciPos

Front-face fluorescence spectroscopy and chemometrics for quality control of cold-pressed rapeseed oil during storage

The aim of this study was to test the usability of fluorescence spectroscopy to evaluate the stability of cold-pressed rapeseed oil during storage. Freshly-pressed rapeseed oil was stored in colorless and green glass bottles exposed to light, and in darkness for a period of 6 months. The quality deterioration of oils was evaluated on the basis of several chemical parameters (peroxide value, acid value, K232 and K270, polar compounds, tocopherols, carotenoids, pheophytins, oxygen concentration) and fluorescence. Parallel factor analysis (PARAFAC) of oil excitation-emission matrices revealed the presence of four fluorophores that showed different evolution throughout the storage period. The fluorescence study provided direct information about tocopherol and pheophytin degradation and revealed formation of a new fluorescent product. Principal component analysis (PCA) performed on analytical and fluorescence data showed that oxidation was more advanced in samples exposed to light due to the photo-induced processes; only a very minor effect of the bottle color was observed. Multiple linear regression (MLR) and partial least squares regression (PLSR) on the PARAFAC scores revealed a quantitative relationship between fluorescence and some of the chemical parameters.Funding Agency Ministry of Science and Higher Education, Poland NN312428239 Poznan University of Economics and Businessinfo:eu-repo/semantics/publishedVersio

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem

<p>Abstract</p> <p>Background</p> <p>Evolutionary methods are increasingly challenged by the wealth of fast growing resources of genomic sequence information. Evolutionary events, like gene duplication, loss, and deep coalescence, account more then ever for incongruence between gene trees and the actual species tree. Gene tree reconciliation is addressing this fundamental problem by invoking the minimum number of gene duplication and losses that reconcile a rooted gene tree with a rooted species tree. However, the reconciliation process is highly sensitive to topological error or wrong rooting of the gene tree, a condition that is not met by most gene trees in practice. Thus, despite the promises of gene tree reconciliation, its applicability in practice is severely limited.</p> <p>Results</p> <p>We introduce the problem of reconciling unrooted and erroneous gene trees by simultaneously rooting and error-correcting them, and describe an efficient algorithm for this problem. Moreover, we introduce an error-corrected version of the gene duplication problem, a standard application of gene tree reconciliation. We introduce an effective heuristic for our error-corrected version of the gene duplication problem, given that the original version of this problem is NP-hard. Our experimental results suggest that our error-correcting approaches for unrooted input trees can significantly improve on the accuracy of gene tree reconciliation, and the species tree inference under the gene duplication problem. Furthermore, the efficiency of our algorithm for error-correcting reconciliation is capable of handling truly large-scale phylogenetic studies.</p> <p>Conclusions</p> <p>Our presented error-correction approach is a crucial step towards making gene tree reconciliation more robust, and thus to improve on the accuracy of applications that fundamentally rely on gene tree reconciliation, like the inference of gene-duplication supertrees.</p

Time series classification with ensembles of elastic distance measures

Several alternative distance measures for comparing time series have recently been proposed and evaluated on time series classification (TSC) problems. These include variants of dynamic time warping (DTW), such as weighted and derivative DTW, and edit distance-based measures, including longest common subsequence, edit distance with real penalty, time warp with edit, and move–split–merge. These measures have the common characteristic that they operate in the time domain and compensate for potential localised misalignment through some elastic adjustment. Our aim is to experimentally test two hypotheses related to these distance measures. Firstly, we test whether there is any significant difference in accuracy for TSC problems between nearest neighbour classifiers using these distance measures. Secondly, we test whether combining these elastic distance measures through simple ensemble schemes gives significantly better accuracy. We test these hypotheses by carrying out one of the largest experimental studies ever conducted into time series classification. Our first key finding is that there is no significant difference between the elastic distance measures in terms of classification accuracy on our data sets. Our second finding, and the major contribution of this work, is to define an ensemble classifier that significantly outperforms the individual classifiers. We also demonstrate that the ensemble is more accurate than approaches not based in the time domain. Nearly all TSC papers in the data mining literature cite DTW (with warping window set through cross validation) as the benchmark for comparison. We believe that our ensemble is the first ever classifier to significantly outperform DTW and as such raises the bar for future work in this area

Chiral [MnIIMnIII3M'] (M' = NaI, CaII, MnII) and [MnIIMnIII6NaI2] clusters built from an enantiomerically pure Schiff base: synthetic, chiroptical and magnetic properties

From the reaction of manganese halides with the chiral Schiff bases obtained by condensation of o-vanillin and (R)- or (S)-phenylglycinol, 11 complexes based on pentanuclear cages with trigonal bipyramidal [MnIIMnIII3M'] (M'=NaI, CaII, MnII) or enneanuclear [MnIIMnIII6NaI2] cores were synthesized. Structural, supramolecular chirality, and optical properties were explored. The magnetic properties of related systems were reviewed, and the magnetic response of the new systems was rationalized to the bond parameters

Syntheses, structures, chiroptical and magnetic properties of chiral clusters built from Schiff bases: a novel [MnIIMnIII6NaI2] core

Chiral clusters with MnIIMnIII3NaI and the new MnIIMnIII6NaI2 cores have been synthesised employing enantiomerically pure Schiff bases and halide ligands. The new compounds have been characterized by electronic circular dichroism (ECD) and magnetic susceptibility

Trinuclear Complexes Derived from R/S Schiff Bases - Chiral Single-Molecule Magnets

The employment of enantiomerically pure Schiff bases in manganese chemistry is revealed to be an excellent method to obtain chiral single-molecule magnets and has allowed the characterization of several pairs of enantiomers, for which the magnetic properties were investigated. The reported systems consist of Mn-III-Mn-II-Mn-III linear trimers or Mn-3(III) cations in a triangular arrangement including the first example of a mu(3)-Cl bridge in an isolated manganese triangle

Behaviour of domestic rabbits during 2 weeks after weaning

Thirty three rabbits from five litters that were weaned at the age of 5 weeks were observed. The animals were kept in pens that were enriched with an elevation made of bricks. In total, 150&thinsp;h of observations made at feeding time (07:30–10:00 and 18:00–20:30&thinsp;LT, local time) were analysed. A number of affiliative, exploratory, comfort, eating, resting and locomotor behaviours were observed. Agonistic behaviour was not observed. Rabbits showed companion and location preferences: 56&thinsp;% of animals had a preferred companion, and 84&thinsp;% preferred a particular place in the pen. Significant effects of group size and time of day on the frequency of some forms of behaviour were found, e.g. rabbits performed comfort behaviours more often in the morning. Sex did not influence the rabbits' behaviour. Correlations were also found between different forms of behaviour, e.g. animals that performed more exploratory behaviours also showed more locomotor behaviours and affiliative interactions.</p