Divergent evolution and purifying selection of the flaA gene sequences in Aeromonas

<p>Abstract</p> <p>Background</p> <p>The bacterial flagellum is the most important organelle of motility in bacteria and plays a key role in many bacterial lifestyles, including virulence. The flagellum also provides a paradigm of how hierarchical gene regulation, intricate protein-protein interactions and controlled protein secretion can result in the assembly of a complex multi-protein structure tightly orchestrated in time and space. As if to stress its importance, plants and animals produce receptors specifically dedicated to the recognition of flagella. Aside from motility, the flagellum also moonlights as an adhesion and has been adapted by humans as a tool for peptide display. Flagellar sequence variation constitutes a marker with widespread potential uses for studies of population genetics and phylogeny of bacterial species.</p> <p>Results</p> <p>We sequenced the complete flagellin gene <it>(flaA</it>) in 18 different species and subspecies of <it>Aeromonas</it>. Sequences ranged in size from 870 (<it>A. allosaccharophila</it>) to 921 nucleotides (<it>A. popoffii</it>). The multiple alignment displayed 924 sites, 66 of which presented alignment gaps. The phylogenetic tree revealed the existence of two groups of species exhibiting different FlaA flagellins (FlaA1 and FlaA2). Maximum likelihood models of codon substitution were used to analyze <it>flaA </it>sequences. Likelihood ratio tests suggested a low variation in selective pressure among lineages, with an ω ratio of less than 1 indicating the presence of purifying selection in almost all cases. Only one site under potential diversifying selection was identified (isoleucine in position 179). However, 17 amino acid positions were inferred as sites that are likely to be under positive selection using the branch-site model. Ancestral reconstruction revealed that these 17 amino acids were among the amino acid changes detected in the ancestral sequence.</p> <p>Conclusion</p> <p>The models applied to our set of sequences allowed us to determine the possible evolutionary pathway followed by the <it>flaA </it>gene in <it>Aeromonas</it>, suggesting that this gene have probably been evolving independently in the two groups of <it>Aeromonas </it>species since the divergence of a distant common ancestor after one or several episodes of positive selection.</p> <p>Reviewers</p> <p>This article was reviewed by Alexey Kondrashov, John Logsdon and Olivier Tenaillon (nominated by Laurence D Hurst).</p

2018 consensus statement by the Spanish Society of Pathology and the Spanish Society of Medical Oncology on the diagnosis and treatment of cancer of unknown primary

Cancer of unknown primary (CUP) is defned as a heterogeneous group of tumours that present with metastasis, and in which attempts to identify the original site have failed. They difer from other primary tumours in their biological features and how they spread, which means that they can be considered a separate entity. There are several hypotheses regarding their origin, but the most plausible explanation for their aggressiveness and chemoresistance seems to involve chromosomal instability. Depending on the type of study done, CUP can account for 2–9% of all cancer patients, mostly 60–75 years old. This article reviews the main clinical, pathological, and molecular studies conducted to analyse and determine the origin of CUP.The main strategies for patient management and treatment, by both clinicians and pathologists, are also addressed.The authors are grateful for the editorial assistance of Dr. Fernando Sánchez-Barbero of HealthCo (Madrid, Spain) in the production of this manuscript. SEOM and SEAP are grateful for the fnancial support for this project in the form of unrestricted grants from Ferrer Diagnostic, OncoDNA and Foundation Medicine/Roche

2018 consensus statement by the Spanish Society of Pathology and the Spanish Society of Medical Oncology on the diagnosis and treatment of cancer of unknown primary

Cancer of unknown primary (CUP) is defined as a heterogeneous group of tumours that present with metastasis, and in which attempts to identify the original site have failed. They differ from other primary tumours in their biological features and how they spread, which means that they can be considered a separate entity. There are several hypotheses regarding their origin, but the most plausible explanation for their aggressiveness and chemoresistance seems to involve chromosomal instability. Depending on the type of study done, CUP can account for 2-9% of all cancer patients, mostly 60-75years old. This article reviews the main clinical, pathological, and molecular studies conducted to analyse and determine the origin of CUP. The main strategies for patient management and treatment, by both clinicians and pathologists, are also addressed

Metal-support interaction and charge distribution in ceria-supported Au particles exposed to CO

Understanding how reaction conditions affect metal-support interactions in catalytic materials is one of the most challenging tasks in heterogeneous catalysis research. Metal nanoparticles and their supports often undergo changes in structure and oxidation state when exposed to reactants, hindering a straightforward understanding of the structure-activity relations using only ex situ or ultrahigh vacuum techniques. Overcoming these limitations, we explored the metal-support interaction between gold nanoparticles and ceria supports in ultrahigh vacuum and after exposure to CO. A combination of in situ methods (on powder and model Au/CeO2 samples) and theoretical calculations was applied to investigate the gold/ceria interface and its reactivity toward CO exposure. X-ray photoelectron spectroscopy measurements rationalized by first-principles calculations reveal a distinctly inhomogeneous charge distribution, with Au+ atoms in contact with the ceria substrate and neutral Au0 atoms at the surface of the Au nanoparticles. Exposure to CO partially reduces the ceria substrate, leading to electron transfer to the supported Au nanoparticles. Transferred electrons can delocalize among the neutral Au atoms of the particle or contribute to forming inert Auδ− atoms near oxygen vacancies at the ceria surface. This charge redistribution is consistent with the evolution of the vibrational frequencies of CO adsorbed on Au particles obtained using diffuse reflectance infrared Fourier transform spectroscopy

High intrapatient variability of tacrolimus exposure associated with poorer outcomes in liver transplantation

Liver transplantation; Tacrolimus; Liver diseasesTrasplante de hígado; Tacrolimús; Enfermedades del hígadoTrasplantament hepàtic; Tacrolimús; Malalties del fetgeTacrolimus (TAC) is a dose-dependent immunosuppressor with considerable intrapatient variability (IPV) in its pharmacokinetics. The aim of this work is to ascertain the association between TAC IPV at 6 months after liver transplantation (LT) and patient outcome. This single-center cohort study retrospectively analyzed adult patients who underwent transplantation from 2015 to 2019 who survived the first 6 months with a functioning graft. The primary end point was the patient’s probability of death and the secondary outcome was the loss of renal function between month 6 and the last follow-up. TAC IPV was estimated by calculating the coefficient of variation (CV) of the dose-corrected concentration (C0/D) between the third and sixth months post-LT. Of the 140 patients who underwent LT included in the study, the low-variability group (C0/D CV < 27%) comprised 105 patients and the high-variability group (C0/D CV ≥ 27%) 35 patients. One-, 3-, and 5-year patient survival rates were 100%, 82%, and 72% in the high-variability group versus 100%, 97%, and 93% in the low-variability group, respectively (p = 0.005). Moreover, significant impaired renal function was observed in the high-variability group at 1 year (69 ± 16 ml/min/1.73 m2 vs. 78 ± 16 ml/min/1.73 m2, p = 0.004) and at 2 years post-LT (69 ± 17 ml/min/1.73 m2 vs. 77 ± 15 ml/min/1.73 m2, p = 0.03). High C0/D CV 3–6 months remained independently associated with worse survival (hazard ratio = 3.57, 95% CI = 1.32–9.67, p = 0.012) and loss of renal function (odds ratio = 3.47, 95% CI = 1.30–9.20, p = 0.01). Therefore, high IPV between the third and sixth months appears to be an early and independent predictor of patients with poorer liver transplant outcomes.Isabel Campos-Varela’s research activity is funded by grant PI19/00330 from Instituto de Salud Carlos III. CIBERehd is supported by Instituto de Salud Carlos III. The work was independent of all funding

Search for coherent charged pion production in neutrino-carbon interactions

We report the result from a search for charged-current coherent pion production induced by muon neutrinos with a mean energy of 1.3 GeV. The data are collected with a fully active scintillator detector in the K2K long-baseline neutrino oscillation experiment. No evidence for coherent pion production is observed and an upper limit of $0.60 \times 10^{-2}$ is set on the cross section ratio of coherent pion production to the total charged-current interaction at 90% confidence level. This is the first experimental limit for coherent charged pion production in the energy region of a few GeV.Comment: 5 pages, 4 figure