Factors affecting the concordance between orthologous gene trees and species tree in bacteria

<p>Abstract</p> <p>Background</p> <p>As originally defined, orthologous genes implied a reflection of the history of the species. In recent years, many studies have examined the concordance between orthologous gene trees and species trees in bacteria. These studies have produced contradictory results that may have been influenced by orthologous gene misidentification and artefactual phylogenetic reconstructions. Here, using a method that allows the detection and exclusion of false positives during identification of orthologous genes, we address the question of whether putative orthologous genes within bacteria really reflect the history of the species.</p> <p>Results</p> <p>We identified a set of 370 orthologous genes from the bacterial order <it>Rhizobiales</it>. Although manifesting strong vertical signal, almost every orthologous gene had a distinct phylogeny, and the most common topology among the orthologous gene trees did not correspond with the best estimate of the species tree. However, each orthologous gene tree shared an average of 70% of its bipartitions with the best estimate of the species tree. Stochastic error related to gene size affected the concordance between the best estimated of the species tree and the orthologous gene trees, although this effect was weak and distributed unevenly among the functional categories. The nodes showing the greatest discordance were those defined by the shortest internal branches in the best estimated of the species tree. Moreover, a clear bias was evident with respect to the function of the orthologous genes, and the degree of divergence among the orthologous genes appeared to be related to their functional classification.</p> <p>Conclusion</p> <p>Orthologous genes do not reflect the history of the species when taken as individual markers, but they do when taken as a whole. Stochastic error affected the concordance of orthologous genes with the species tree, albeit weakly. We conclude that two important biological causes of discordance among orthologous genes are incomplete lineage sorting and functional restriction.</p

Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: the repABC operon

<p>Abstract</p> <p>Background</p> <p>The <it>repABC </it>plasmid family, which is extensively present within <it>Alphaproteobacteria</it>, and some secondary chromosomes of the <it>Rhizobiales </it>have the particular feature that all the elements involved in replication and partitioning reside within one transcriptional unit, the <it>repABC </it>operon. Given the functional interactions among the elements of the <it>repABC </it>operon, and the fact that they all reside in the same operon, a common evolutionary history would be expected if the entire operon had been horizontally transferred. Here, we tested whether there is a common evolutionary history within the <it>repABC </it>operon. We further examined different incompatibility groups in terms of their differentiation and degree of adaptation to their host.</p> <p>Results</p> <p>We did not find a single evolutionary history within the <it>repABC </it>operon. Each protein had a particular phylogeny, horizontal gene transfer events of the individual genes within the operon were detected, and different functional constraints were found within and between the Rep proteins. When different <it>repABC </it>operons coexisted in the same genome, they were well differentiated from one another. Finally, we found different levels of adaptation to the host genome within and between <it>repABC </it>operons coexisting in the same species.</p> <p>Conclusion</p> <p>Horizontal gene transfer with conservation of the <it>repABC </it>operon structure provides a highly dynamic operon in which each member of this operon has its own evolutionary dynamics. In addition, it seems that different incompatibility groups present in the same species have different degrees of adaptation to their host genomes, in proportion to the amount of time the incompatibility group has coexisted with the host genome.</p

Cancer Mortality in Older Mexican Individuals (2000 – 2010)

Objective: Given the trends in aging worldwide, in Mexico, we determined trends in adjusted mortality rates due to cancer and 11 cancer subtypes in older individuals (>65 years) from 2000 to 2010. Methods: For this retrospective study, we collected data on mortality due to cancer from the registries of the National Institute of Statistics and Geography. Adjusted rates were calculated with a direct method based on the world standard population. Trend analysis was performed with a linear regression of the natural logarithm of the adjusted rate, and trends were evaluated with the Student´s t test. Results: During the studied period, the cancer mortality rates significantly declined from 630.21 to 573.03 (per 100,000 inhabitants) in the overall population. Similar declines were observed in women (from 548.81 to 490.09) and men (from 726.03 to 672.94). Significant declines in mortality rates were observed across several cancer subtypes, including esophageal, gastric, colorectal-anal, liver-biliary, pancreatic, and tracheal-bronchial-lung cancers. Significant increases in mortality rates were observed in colorectal and breast cancer, but no changes were observed in mortality rates due to prostate, ovarian, bladder, and non-Hodgkin lymphoma cancers. Conclusion: Mortality due to cancer in older Mexicans was lower than that observed in developed countries, and it significantly declined over the study period. Men had higher mortality rates than women. The highest mortality rates were due to breast and prostate cancer subtypes in older individuals

La equidad de género en la educación física: El uso del lenguaje

This study analyzed Spanish teachers' behavior and the transmission of gender stereotypes. We observed 48 physical education lessons given by four Spanish teachers (two men and two women). Descriptive codes, which were generated iteratively, were clustered, categorized, integrated, recoded, and recategorized. They allowed us to identify four major themes related to the transmission of gender stereotypes of teachers: male generics, stereotyped expressions, nominative attention, and priority order. We used a coding sheet as well as audio and video recordings to register the categories. The KruskalWallis test produced significance levels lower than .05, resulting in the rejection of the null hypothesis. Sexist behavior was found in the male generics, nominative attention, and priority order. However, we found no difference in stereotyped expressions.“Igualdade de gênero em educação física: O uso da linguagem.” O objetivo do estudo foi analisar o comportamento dos professores espanhóis na transmissão de estereótipos de gênero para os seus alunos. Observou-se 48 aulas de educação física dadas por quatro professores espanhóis (dois homens e duas mulheres). Os códigos descritivos, que foram gerados de forma iterativa, foram agrupados, categorizados, integrados, recodificados e reclassificados. Identificou-se quatro variáveis relacionando o professorado e a sua transmissão dos estereótipos de gênero: masculinos genéricos, expressões estereotipadas, atenção nominativa e ordem de prioridade. Utilizou-se uma folha de codificação, bem como gravações de áudio e vídeo para os registros. Níveis de significância no teste de Kruskal-Wallis inferiores 0,05 permitiram rejeitar a hipótese nula. Comportamentos sexistas foram encontrados no uso de masculino genérico, a atenção nominativa e ordem de prioridade. No entanto, não foi encontrada diferenças nas expressões estereotipadas

Silyl and siloxanediyl cyclopentadienyl titanium and zirconium complexes: synthesis and reactivity. X-ray molecular structure of [Zr{η5-C5H4SiMe2(μ-OH)}(μ-Cl)Cl2]2

Chloro(dimethyl)silyl-η5-cyclopentadienyl group 4 metal complexes of the type [M(η5-C5H4Cl)Cl3] (Full-size image (<1 K)) react with thallium salts Tl(C5H4R) (R = H, SiMe3) to give mixed dicyclopentadienyl derivatives [M(η5-C5H4R)(η5-C5H4SiMe2Cl)Cl2], (M = Ti, R = H 3, R = SiMe34; M = Zr, R = H 5, R = SiMe36) in high yield. Hydrolysis of complexes 3 and 4 affords the dinuclear complexes [Ti(η5-C5H4R)Cl2]2{μ-[(η5-C5H4SiMe2)2O]}] [R = H 7, R = SiMe38) containing a siloxanyl bridge, by elimination of two equivalents of HCl. Reactions of complexes 1 with hydroxo containing reagents such as anhydrous LiOH and SiPh2(OH)2 give the derivatives [Ti(η5-C5H4SiMe2Cl)Cl2]2(μ-O)], 9 and Ti[μ-(η5-C5H4SiMe2OSiPh2-η1-O)]Cl2, 10 identified by analytical, spectrometric and spectroscopic data. Treatment of analogous complex 2 with water produces the dimeric monocyclopentadienyl zirconium trichloride adduct [Zr(η5-C5H4SiMe2OH)Cl3]2, 11. Compound 11 has been characterized by X-ray crystallography.Universidad de AlcaláConsejería de Educación de la Comunidad de Madri

The Impact of Recombination on dN/dS within Recently Emerged Bacterial Clones

The development of next-generation sequencing platforms is set to reveal an unprecedented level of detail on short-term molecular evolutionary processes in bacteria. Here we re-analyse genome-wide single nucleotide polymorphism (SNP) datasets for recently emerged clones of methicillin resistant Staphylococcus aureus (MRSA) and Clostridium difficile. We note a highly significant enrichment of synonymous SNPs in those genes which have been affected by recombination, i.e. those genes on mobile elements designated “non-core” (in the case of S. aureus), or those core genes which have been affected by homologous replacements (S. aureus and C. difficile). This observation suggests that the previously documented decrease in dN/dS over time in bacteria applies not only to genomes of differing levels of divergence overall, but also to horizontally acquired genes of differing levels of divergence within a single genome. We also consider the role of increased drift acting on recently emerged, highly specialised clones, and the impact of recombination on selection at linked sites. This work has implications for a wide range of genomic analyses

Complete Genome Sequence of a bla OXA-58 -Producing Acinetobacter baumannii Strain Isolated from a Mexican Hospital

ABSTRACT In this study, we present the complete genome sequence of a blaOXA-58- producing Acinetobacter baumannii strain, sampled from a Mexican hospital and not related to the international clone

Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts

<p>Abstract</p> <p>Background</p> <p>Fabaceae (legumes) is one of the largest families of flowering plants, and some members are important crops. In contrast to what we know about their great diversity or economic importance, our knowledge at the genomic level of chloroplast genomes (cpDNAs or plastomes) for these crops is limited.</p> <p>Results</p> <p>We sequenced the complete genome of the common bean (<it>Phaseolus vulgari</it>s cv. Negro Jamapa) chloroplast. The plastome of <it>P. vulgaris </it>is a 150,285 bp circular molecule. It has gene content similar to that of other legume plastomes, but contains two pseudogenes, <it>rpl</it>33 and <it>rps</it>16. A distinct inversion occurred at the junction points of <it>trn</it>H-GUG/<it>rpl</it>14 and <it>rps</it>19/<it>rps</it>8, as in adzuki bean <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. These two pseudogenes and the inversion were confirmed in 10 varieties representing the two domestication centers of the bean. Genomic comparative analysis indicated that inversions generally occur in legume plastomes and the magnitude and localization of insertions/deletions (indels) also vary. The analysis of repeat sequences demonstrated that patterns and sequences of tandem repeats had an important impact on sequence diversification between legume plastomes and tandem repeats did not belong to dispersed repeats. Interestingly, <it>P. vulgaris </it>plastome had higher evolutionary rates of change on both genomic and gene levels than <it>G. max</it>, which could be the consequence of pressure from both mutation and natural selection.</p> <p>Conclusion</p> <p>Legume chloroplast genomes are widely diversified in gene content, gene order, indel structure, abundance and localization of repetitive sequences, intracellular sequence exchange and evolutionary rates. The <it>P. vulgaris </it>plastome is a rapidly evolving genome.</p

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

Background: Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently developed Bayesian approach, BRATNextGen, for detecting recombination on an expanded NGS dataset of the globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clone ST239. Results: The data confirm strong geographical clustering at continental, national and city scales and demonstrate that the rate of recombination varies significantly between phylogeographic sub-groups representing independent introductions from Europe. These differences are most striking when mobile non-core genes are included, but remain apparent even when only considering the stable core genome. The monophyletic ST239 sub-group corresponding to isolates from South America shows heightened recombination, the sub-group predominantly from Asia shows an intermediate level, and a very low level of recombination is noted in a third sub-group representing a large collection from Turkey. Conclusions: We show that the rapid global dissemination of a single pathogenic bacterial clone results in local variation in measured recombination rates. Possible explanatory variables include the size and time since emergence of each defined sub-population (as determined by the sampling frame), variation in transmission dynamics due to host movement, and changes in the bacterial genome affecting the propensity for recombination

Acinetobacter baumannii IC2 and IC5 isolates with co-existing blaOXA-143-like and blaOXA-72 and exhibiting strong biofilm formation in a Mexican hospital

Acinetobacter baumannii is an opportunistic pathogen responsible for healthcare-associated infections (HAIs) and outbreaks. Antimicrobial resistance mechanisms and virulence factors allow it to survive and spread in the hospital environment. However, the molecular mechanisms of these traits and their association with international clones are frequently unknown in low- and middle-income countries. Here, we analyze the phenotype and genotype of seventy-six HAIs and outbreak-causing A. baumannii isolates from a Mexican hospital over ten years, with special attention to the carbapenem resistome and biofilm formation. The isolates belonged to the global international clone (IC) 2 and the Latin America endemic IC5 and were predominantly extensively drug-resistant (XDR). Oxacillinases were identified as a common source of carbapenem resistance. We noted the presence of the blaOXA-143-like family (not previously described in Mexico), the blaOXA-72 and the blaOXA-398 found in both ICs. A low prevalence of efflux pump overexpression activity associated with carbapenem resistance was observed. Finally, strong biofilm formation was found, and significant biofilm-related genes were identified, including bfmRS, csuA/BABCDE, pgaABCD and ompA. This study provides a comprehensive profile of the carbapenem resistome of A. baumannii isolates belonging to the same pulse type, along with their significant biofilm formation capacity. Furthermore, it contributes to a better understanding of their role in the recurrence of infection and the endemicity of these isolates in a Mexican hospital