Distinguishing regional from within-codon rate heterogeneity in DNA sequence alignments

We present an improved phylogenetic factorial hidden Markov model (FHMM) for detecting two types of mosaic structures in DNA sequence alignments, related to (1) recombination and (2) rate heterogeneity. The focus of the present work is on improving the modelling of the latter aspect. Earlier papers have modelled different degrees of rate heterogeneity with separate hidden states of the FHMM. This approach fails to appreciate the intrinsic difference between two types of rate heterogeneity: long-range regional effects, which are potentially related to differences in the selective pressure, and the short-term periodic patterns within the codons, which merely capture the signature of the genetic code. We propose an improved model that explicitly distinguishes between these two effects, and we assess its performance on a set of simulated DNA sequence alignments

Unconventional magnetism of non-uniform distribution of Co in TiO2 nanoparticles

High-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD) analysis, electron paramagnetic resonance (EPR), X-ray absorption spectroscopy (XAS), magnetic methods, and density-functional theory (DFT) calculations were applied for the investigations of Co-doped anatase TiO2 nanoparticles (∼20 nm). It was found that high-spin Co2+ ions prefer to occupy the interstitial positions in the TiO2 lattice which are the most energetically favourable in compare to the substitutional those. A quantum mechanical model which operates mainly on two types of Co2+ – Co2+ dimers with different negative exchange interactions and the non-interacting paramagnetic Co2+ ions provides a satisfactorily description of magnetic properties for the TiO2:Co system. © 2020 Elsevier B.V.Russian Foundation for Basic Research. Ministry of Science and Higher Education of the Russian Federatio

Bispyrenylalkane Chemosensor for the Naked-eye Detection of Nitro-explosives

Pyrene-based compounds have a great potential as fluorescent chemosensors for various analytes including common nitro-explosives, such as 2,4,6-trinitrotoluene (TNT). Compounds having two pyrene units in one molecule, such as bispyrenylalkanes, are able to form stable, bright emissive in a visual wavelength region excimers both in non-polar and polar environments. In this work we wish to report that in non-polar solvents the excimer has poor chemosensing properties while in aqueous solutions it provides significant “turn-off” fluorescence response to TNT in the sub-nanomolar concentrations

Metabolism of the viable mammalian embryo: quietness revisited

This review examines the ‘Quiet Embryo Hypothesis’ which proposes that viable preimplantation embryos operate at metabolite or nutrient turnover rates distributed within lower ranges than those of their less viable counterparts. The ‘quieter’ metabolism consistent with this hypothesis is considered in terms of (i) ‘functional’ quietness; the contrasting levels of intrinsic metabolic activity in different cell types as a consequence of their specialized functions, (ii) inter-individual embryo/cell differences in metabolism and (iii) loss of quietness in response to environmental stress. Data are reviewed which indicate that gametes and early embryos function in vivo at a lower temperature than core body temperature, which could encourage the expression of a quiet metabolism. We call for research to determine the optimum temperature for mammalian gamete/embryo culture. The review concludes by examining the key role of reactive oxygen species, which can induce molecular damage, trigger a cellular stress response and lead to a loss of quietness

Accurate Detection of Recombinant Breakpoints in Whole-Genome Alignments

We propose a novel method for detecting sites of molecular recombination in multiple alignments. Our approach is a compromise between previous extremes of computationally prohibitive but mathematically rigorous methods and imprecise heuristic methods. Using a combined algorithm for estimating tree structure and hidden Markov model parameters, our program detects changes in phylogenetic tree topology over a multiple sequence alignment. We evaluate our method on benchmark datasets from previous studies on two recombinant pathogens, Neisseria and HIV-1, as well as simulated data. We show that we are not only able to detect recombinant regions of vastly different sizes but also the location of breakpoints with great accuracy. We show that our method does well inferring recombination breakpoints while at the same time maintaining practicality for larger datasets. In all cases, we confirm the breakpoint predictions of previous studies, and in many cases we offer novel predictions

Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees

Genomic regions participating in recombination events may support distinct topologies, and phylogenetic analyses should incorporate this heterogeneity. Existing phylogenetic methods for recombination detection are challenged by the enormous number of possible topologies, even for a moderate number of taxa. If, however, the detection analysis is conducted independently between each putative recombinant sequence and a set of reference parentals, potential recombinations between the recombinants are neglected. In this context, a recombination hotspot can be inferred in phylogenetic analyses if we observe several consecutive breakpoints. We developed a distance measure between unrooted topologies that closely resembles the number of recombinations. By introducing a prior distribution on these recombination distances, a Bayesian hierarchical model was devised to detect phylogenetic inconsistencies occurring due to recombinations. This model relaxes the assumption of known parental sequences, still common in HIV analysis, allowing the entire dataset to be analyzed at once. On simulated datasets with up to 16 taxa, our method correctly detected recombination breakpoints and the number of recombination events for each breakpoint. The procedure is robust to rate and transition∶transversion heterogeneities for simulations with and without recombination. This recombination distance is related to recombination hotspots. Applying this procedure to a genomic HIV-1 dataset, we found evidence for hotspots and de novo recombination

Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2

Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, despite the availability of unprecedented numbers of SARS-CoV-2 genomes. Here, we present an approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2. We demonstrate that including travel history data yields i) more realistic hypotheses of virus spread and ii) higher posterior predictive accuracy compared to including only sampling location. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts.status: publishe

Evaluation of methods for detecting conversion events in gene clusters

Background: Gene clusters are genetically important, but their analysis poses significant computational challenges. One of the major reasons for these difficulties is gene conversion among the duplicated regions of the cluster, which can obscure their true relationships. Many computational methods for detecting gene conversion events have been released, but their performance has not been assessed for wide deployment in evolutionary history studies due to a lack of accurate evaluation methods. Results: We designed a new method that simulates gene cluster evolution, including large-scale events of duplication, deletion, and conversion as well as small mutations. We used this simulation data to evaluate several different programs for detecting gene conversion events. Conclusions: Our evaluation identifies strengths and weaknesses of several methods for detecting gene conversion, which can contribute to more accurate analysis of gene cluster evolution

Phylogeographic Analysis of HIV-1 Subtype C Dissemination in Southern Brazil

The HIV-1 subtype C has spread efficiently in the southern states of Brazil (Rio Grande do Sul, Santa Catarina and Paraná). Phylogeographic studies indicate that the subtype C epidemic in southern Brazil was initiated by the introduction of a single founder virus population at some time point between 1960 and 1980, but little is known about the spatial dynamics of viral spread. A total of 135 Brazilian HIV-1 subtype C pol sequences collected from 1992 to 2009 at the three southern state capitals (Porto Alegre, Florianópolis and Curitiba) were analyzed. Maximum-likelihood and Bayesian methods were used to explore the degree of phylogenetic mixing of subtype C sequences from different cities and to reconstruct the geographical pattern of viral spread in this country region. Phylogeographic analyses supported the monophyletic origin of the HIV-1 subtype C clade circulating in southern Brazil and placed the root of that clade in Curitiba (Paraná state). This analysis further suggested that Florianópolis (Santa Catarina state) is an important staging post in the subtype C dissemination displaying high viral migration rates from and to the other cities, while viral flux between Curitiba and Porto Alegre (Rio Grande do Sul state) is very low. We found a positive correlation (r2 = 0.64) between routine travel and viral migration rates among localities. Despite the intense viral movement, phylogenetic intermixing of subtype C sequences from different Brazilian cities is lower than expected by chance. Notably, a high proportion (67%) of subtype C sequences from Porto Alegre branched within a single local monophyletic sub-cluster. These results suggest that the HIV-1 subtype C epidemic in southern Brazil has been shaped by both frequent viral migration among states and in situ dissemination of local clades

Conservation prioritization can resolve the flagship species conundrum

Conservation strategies based on charismatic flagship species, such as tigers, lions, and elephants, successfully attract funding from individuals and corporate donors. However, critics of this species-focused approach argue it wastes resources and often does not benefit broader biodiversity. If true, then the best way of raising conservation funds excludes the best way of spending it. Here we show that this conundrum can be resolved, and that the flagship species approach does not impede cost-effective conservation. Through a tailored prioritization approach, we identify places containing flagship species while also maximizing global biodiversity representation (based on 19,616 terrestrial and freshwater species). We then compare these results to scenarios that only maximized biodiversity representation, and demonstrate that our flagship-based approach achieves 79−89% of our objective. This provides strong evidence that prudently selected flagships can both raise funds for conservation and help target where these resources are best spent to conserve biodiversity