Browsing by Issue Date, starting with "2022-11-11"
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- Repeated out-of-Africa expansions of Helicobacter pylori driven by replacement of deleterious mutationsPublication . Thorpe, Harry A.; Tourrette, Elise; Yahara, Koji; Vale, Filipa F.; Liu, Siqi; Oleastro, Mónica; Alarcon, Teresa; Perets, Tsachi-Tsadok; Latifi-Navid, Saeid; Yamaoka, Yoshio; Martinez-Gonzalez, Beatriz; Karayiannis, Ioannis; Karamitros, Timokratis; Sgouras, Dionyssios N.; Elamin, Wael; Pascoe, Ben; Sheppard, Samuel K.; Ronkainen, Jukka; Aro, Pertti; Engstrand, Lars; Agreus, Lars; Suerbaum, Sebastian; Thorell, Kaisa; Falush, DanielHelicobacter pylori lives in the human stomach and has a population structure resembling that of its host. However, H. pylori fromEurope and the Middle East trace substantially more ancestry from modern African populations than the humans that carry them. Here, we use a collection of Afro-Eurasian H. pylori genomes to show that this African ancestry is due to at least three distinct admixture events. H. pylori from East Asia, which have undergone little admixture, have accumulated many more non-synonymous mutations than African strains. European and Middle Eastern bacteria have elevated African ancestry at the sites of these mutations, implying selection to remove them during admixture. Simulations show that population fitness can be restored after bottlenecks bymigration and subsequent admixture of small numbers of bacteria from non-bottlenecked populations. We conclude that recent spread of African DNA has been driven by deleterious mutations accumulated during the original out-of-Africa bottleneck.
- Molecular detection of Aspergillus in respiratory samples collected from patients at higher risk of chronic pulmonary aspergillosisPublication . Oliveira, M.; Pinto, M.; Simões, H.; Gomes, J.P.; Veríssimo, C.; Sabino, R.Objective: Aspergillosis diagnosis depends on the detection of Aspergillus in biological samples ─ usually using cultural and immunoenzyme techniques ─ but their sensitivity and specificity varies. We aimed to study the prevalence of Aspergillus in patients at higher risk of chronic pulmonary aspergillosis (i.e., HIV-infected patients and individuals with active or previous tuberculosis), and to determine the potential role of molecular approaches to increase detection of Aspergillus in respiratory samples. Methods: The DNA extracted from 43 respiratory samples that had been previously analyzed by immunoenzyme and/or cultural techniques was amplified by real-time multiplex PCR, and the results of these methods were compared. We also sequenced the ITS1 region and the calmodulin gene in 10 respiratory samples to perform a pilot metagenomic study to understand the ability of this methodology to detect potential pathogenic fungi in the lung mycobiome. Results: Real-time Aspergillus PCR test exhibited a higher positivity rate than the conventional techniques used for aspergillosis diagnosis, particularly in individuals at risk for chronic pulmonary aspergillosis. The metagenomic analysis allowed for the detection of various potentially pathogenic fungi. Conclusions: Molecular techniques, including metagenomics, have great ability to detect potentially pathogenic fungi rapidly and efficiently in human biological samples.
- Mitochondrial Fatty Acid β-Oxidation Disorders: From Disease to Lipidomic Studies—A Critical ReviewPublication . Guerra, Inês M.S.; Ferreira, Helena B.; Melo, Tânia; Rocha, Hugo; Moreira, Sónia; Diogo, Luísa; Domingues, Maria Rosário; Moreira, Ana S.P.Fatty acid oxidation disorders (FAODs) are inborn errors of metabolism (IEMs) caused by defects in the fatty acid (FA) mitochondrial β-oxidation. The most common FAODs are characterized by the accumulation of medium-chain FAs and long-chain (3-hydroxy) FAs (and their carnitine derivatives), respectively. These deregulations are associated with lipotoxicity which affects several organs and potentially leads to life-threatening complications and comorbidities. Changes in the lipidome have been associated with several diseases, including some IEMs. In FAODs, the alteration of acylcarnitines (CARs) and FA profiles have been reported in patients and animal models, but changes in polar and neutral lipid profile are still scarcely studied. In this review, we present the main findings on FA and CAR profile changes associated with FAOD pathogenesis, their correlation with oxidative damage, and the consequent disturbance of mitochondrial homeostasis. Moreover, alterations in polar and neutral lipid classes and lipid species identified so far and their possible role in FAODs are discussed. We highlight the need of mass-spectrometry-based lipidomic studies to understand (epi)lipidome remodelling in FAODs, thus allowing to elucidate the pathophysiology and the identification of possible biomarkers for disease prognosis and an evaluation of therapeutic efficacy.