The accuracy of several multiple sequence alignment programs for proteins

BACKGROUND: There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences. The "true" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs. RESULTS: We tested nine of the most often used protein alignment programs and compared their results using sequences generated with the simulation software Simprot which creates known alignments under realistic and controlled evolutionary scenarios. We have simulated more than 30000 alignment sets using various evolutionary histories in order to define strengths and weaknesses of each program tested. We found that alignment accuracy is extremely dependent on the number of insertions and deletions in the sequences, and that indel size has a weaker effect. We also considered benchmark alignments from the latest version of BAliBASE and the results relative to BAliBASE- and Simprot-generated data sets were consistent in most cases. CONCLUSION: Our results indicate that employing Simprot's simulated sequences allows the creation of a more flexible and broader range of alignment classes than the usual methods for alignment accuracy assessment. Simprot also allows for a quick and efficient analysis of a wider range of possible evolutionary histories that might not be present in currently available alignment sets. Among the nine programs tested, the iterative approach available in Mafft (L-INS-i) and ProbCons were consistently the most accurate, with Mafft being the faster of the two

SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution

BACKGROUND: General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis and for the computer simulation of artificial sequence data sets. RESULTS: We have developed a new method of simulating protein sequence evolution, including insertion and deletion (indel) events in addition to amino-acid substitutions. The simulation generates both the simulated sequence family and a true sequence alignment that captures the evolutionary relationships between amino acids from different sequences. Our statistical model for indel evolution is based on the empirical indel distribution determined by Qian and Goldstein. We have parameterized this distribution so that it applies to sequences diverged by varying evolutionary times and generalized it to provide flexibility in simulation conditions. Our method uses a Monte-Carlo simulation strategy, and has been implemented in a C++ program named Simprot. CONCLUSION: Simprot will be useful for testing methods of analysis of protein sequence families particularly alignment methods, phylogenetic tree building, detection of recombination and horizontal gene transfer, and homology detection, where knowing the true course of sequence evolution is essential

Genetic diversity of Bursaphelenchus cocophilus in South America

Molecular characterisation of Bursaphelenchus cocophilus, the causal agent of ‘red ring disease’, is imperative for efficient identification procedures in Brazil and Colombia, because quarantine species such as B. xylophilus and B. mucronatus are already listed in both countries. ITS-1/2 region and D2-D3 segment of LSU rDNA were used to characterise isolates of B. cocophilus obtained from coconut plantations in Brazil and Colombia. Results from ITS-1/2 and LSU rDNA regions showed that all isolates of B. cocophilus from Brazil and Colombia formed a monophyletic group. The LSU rDNA region indicated that all isolates formed a single monophyletic group with high Bayesian posterior probability (100%). This is the first study on ITS-1/2 for the characterisation of B. cocophilus populations. A species-specific primer was designed for identification of B. cocophilus

Phylogeny, ultrastructure, histopathology and prevalence of Myxobolus oliveirai sp. nov., a parasite of Brycon hilarii (Characidae) in the Pantanal wetland, Brazil

This paper presents the morphological, histological and ultrastructural characteristics of Myxobolus oliveirai sp. nov., a parasite of the gill filaments in Brycon hilarii from the Brazilian Pantanal. Out of 216 B. hilariispecimens examined (126 wild and 90 cultivated), 38.1% of wild specimens (n = 48) were infected. The parasites form elongated plasmodia primarily in the tip of gill filaments, reaching about 3 mm in length. A thorough comparison with all the Myxobolus species described from South American hosts, as well as nearly all the Myxobolus species described so far is provided. Partial sequencing of the 18S rDNA gene revealed a total of 1,527 bp. The Myxobolus species parasite of B. hilarii did not match any of the Myxozoa available in GenBank. In the phylogenetic analysis, M. oliveirai sp. nov. composed a monophyletic group with eight other species: five species of Myxobolus parasites of mugilid fishes, two parasites of pangasiid and one of centrarchid. Infection prevalence values of the parasite revealed no significant differences between wet and dry seasons or between males and females. The importance of the infection to the farming of the host species is emphasized.FAPESPCEPTA - ICMBioCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES

Modeling the quantum evolution of the universe through classical matter

It is well known that the canonical quantization of the Friedmann-Lema\^itre-Robertson-Walker (FLRW) filled with a perfect fluid leads to nonsingular universes which, for later times, behave as their classical counterpart. This means that the expectation value of the scale factor $(t)$ never vanishes and, as $t\to\infty$, we recover the classical expression for the scale factor. In this paper, we show that such universes can be reproduced by classical cosmology given that the universe is filled with an exotic matter. In the case of a perfect fluid, we find an implicit equation of state (EoS). We then show that this single fluid with an implict EoS is equivalent to two non-interacting fluids, one of them representing stiff matter with negative energy density. In the case of two non-interacting scalar fields, one of them of the phantom type, we find their potential energy. In both cases we find that quantum mechanics changes completely the configuration of matter for small values of time, by adding a fluid or a scalar field with negative energy density. As time passes, the density of negative energy decreases and we recover the ordinary content of the classical universe. The more the initial wave function of the universe is concentrated around the classical big bang singularity, the more it is necessary to add negative energy, since this type of energy will be responsible for the removal of the classical singularity.Comment: updated version as accepted by Gen. Relativ. Gravi

The cognitive interview: comparing face-to-face and video-mediated interviews

Purpose: Eyewitness testimony can determine the outcome of criminal investigations. The cognitive interview (CI) has been widely used to collect informative and accurate accounts. However, face-to-face interviews have been restricted during the current pandemic, raising the need for using video-conferencing. The authors tested whether virtual interviews could produce elaborate accounts from eyewitnesses and if the CI superiority effect against a structured interview (SI) could be fully replicated online. Design/methodology/approach: The authors used a 2 × 2 factorial design with interview condition (CI vs SI) and environment (face-to-face vs virtual) manipulated between-subjects. A total of 88 participants were randomly assigned to one of the four conditions. Participants watched a mock robbery and were interviewed 48 h later using either the SI or the CI. Both interviews contained the same structure and interview phases but only the CI included its key cognitive mnemonics/ instructions. Both sessions were either face-to-face or online. Findings: Participants interviewed with the CI recalled more information than participants interviewed with the SI, regardless of the interview environment. Both environments produced a comparable amount of recall. Report accuracy was high for all groups. Practical implications: This can be crucial to inform police practices and research in this field by suggesting investigative interviews can be conducted virtually in situations such as the current pandemic or when time and resources do not allow for face-to-face interviewing. Originality/value: To the best of the authors’ knowledge, this is the first study showing that the CI superiority effect can be replicated online and that a fully remote CI can produce elaborate accounts

Spatial patterns and temporal variability of drought in Western Iran

An analysis of drought in western Iran from 1966 to 2000 is presented using monthly precipitation data observed at 140 gauges uniformly distributed over the area. Drought conditions have been assessed by means of the Standardized Precipitation Index (SPI). To study the long-term drought variability the principal component analysis was applied to the SPI field computed on 12-month time scale. The analysis shows that applying an orthogonal rotation to the first two principal component patterns, two distinct sub-regions having different climatic variability may be identified. Results have been compared to those obtained for the largescale using re-analysis data suggesting a satisfactory agreement. Furthermore, the extension of the large-scale analysis to a longer period (1948–2007) shows that the spatial patterns and the associated time variability of drought are subjected to noticeable changes. Finally, the relationship between hydrological droughts in the two sub-regions and El Niño Southern Oscillation events has been investigated finding that there is not clear evidence for a link between the two phenomen