Legionella pneumophila pangenome reveals strain-specific virulence factors

<p>Abstract</p> <p>Background</p> <p><it>Legionella pneumophila </it>subsp. <it>pneumophila </it>is a gram-negative <it>γ-Proteobacterium </it>and the causative agent of Legionnaires' disease, a form of epidemic pneumonia. It has a water-related life cycle. In industrialized cities <it>L. pneumophila </it>is commonly encountered in refrigeration towers and water pipes. Infection is always via infected aerosols to humans. Although many efforts have been made to eradicate <it>Legionella </it>from buildings, it still contaminates the water systems. The town of Alcoy (Valencian Region, Spain) has had recurrent outbreaks since 1999. The strain "Alcoy 2300/99" is a particularly persistent and recurrent strain that was isolated during one of the most significant outbreaks between the years 1999-2000.</p> <p>Results</p> <p>We have sequenced the genome of the particularly persistent <it>L. pneumophila </it>strain Alcoy 2300/99 and have compared it with four previously sequenced strains known as Philadelphia (USA), Lens (France), Paris (France) and Corby (England).</p> <p>Pangenome analysis facilitated the identification of strain-specific features, as well as some that are shared by two or more strains. We identified: (1) three islands related to anti-drug resistance systems; (2) a system for transport and secretion of heavy metals; (3) three systems related to DNA transfer; (4) two CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems, known to provide resistance against phage infections, one similar in the Lens and Alcoy strains, and another specific to the Paris strain; and (5) seven islands of phage-related proteins, five of which seem to be strain-specific and two shared.</p> <p>Conclusions</p> <p>The dispensable genome disclosed by the pangenomic analysis seems to be a reservoir of new traits that have mainly been acquired by horizontal gene transfer and could confer evolutionary advantages over strains lacking them.</p

Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome

Metagenomics; Sequencing; ViromeMetagenómica; Secuenciación; ViromaMetagenòmica; Seqüenciació; ViromaStudies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals.This research was funded by Conselleria de Sanitat Universal i Salut Pública, Generalitat Valenciana, grant number CDEI-06/20-E, awarded to V.P.B., as well as by the Asociación Española contra el Cáncer (AECC), project AECC 2017-1485, and the project CIPROM/2021/042 from the Generalitat Valenciana, both awarded to A.M

Effect of Biofumigation on Typical Weeds of Strawberry Fields

This research was conducted to evaluate the effect of biofumigation using fresh organic matter on typical weeds present in strawberry fields of southern Spain. Field experiments consisted of biofumigation (BF) treatment over 45 days, at two locations, with hen droppings or horse manure at a dose of 3 kg m-2, alone or in combination with solarization (BF+S) in an experimental randomized block design. Results showed good control of the main weed species, Poa annua, Portulaca oleracea and Lolium rigidum, with comparative populations of the three species under BF/BF+S of 42/4/8, 18/9/12, and 15/0/1 plants m-2 respectively. In addition, 20 seeds each of several weeds were sown inside cloth bags and were submitted to the treatment. The efficiency of biofumigation combined with solarization in the control of P. oleracea, Cynodon dactilon and Echinochloa crus-galli was 77/0, 50/15, and 30/2, as a percentage of germination of control/BF+S. Laboratory experiments consisted of simulating field conditions using a mix of soil, water and different fresh organic matter in a plastic bag, into which different seeds were sown and kept under controlled conditions over 30 days at 27ºC. Fresh organic matter used was whole strawberry plants, horse manure, hen droppings, and combinations of these. Best results were obtained with hen droppings, which showed effective control of Malva parviflora, Medicago sp., E. crus-galli, Amaranthus retroflesuxus, Chenopodium album and P. oleracea, while strawberry residues and horse manure were not useful as herbicides, sometimes even less so than the solarization treatment. Biofumigation with fresh hen droppings and solarization showed promising results in preliminary experiments

Stability and visual outcomes yielded by three intraocular trifocal lenses with same optical zone design but differing material or toricity

Purpose: To compare rotational stability, centration and visual outcomes provided by three trifocal lens models that have the same optical zone design but different material, composition, and/or toricity. Methods: The study included 78 patients with symmetric bilateral intraocular lens implantation. The lenses under evaluation were trifocal intraocular lenses made of hydrophilic acrylic material: a spherical lens 26% hydrophilic acrylic (POD FineVision), a similar lens but having a toric design (POD Toric FineVision), and a trifocal lens 25% hydrophilic acrylic material (FineVision/MicroF). Moreover, the lenses share the same optical zone design. The lenses’ rotational stability and centration were measured by means of the PIOLET software, which relies on recording and image processing techniques to determine lens rotation and centration based on slit-lamp images. We also assessed patients’ visual quality by means of 25, 40, and 80 cm VA tests. Results: The best centration results were achieved with the POD Toric FineVision model, although the differences were not statistically significant. As for lens rotation, it was below 5° in all cases under study. Regarding VA, all subjects attained at least 0.3 logMAR for far distance uncorrected VA, at 80 cm VA was about 0.2 logMAR, at 40 cm it was above 0.15 logMAR, and at 25 cm it was about 0.3 logMAR for both lens types. Conclusion: All three intraocular lens models yield excellent visual results at far, near as well as intermediate distances. The POD FineVision and POD Toric FineVision models, with double C-loop design, yielded the best results centrationwise and rotation-wise. Differences had no clinical relevance

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

The human gut is the natural habitat for a large and dynamic bacterial community that has a great relevance for health. Metagenomics is increasing our knowledge of gene content as well as of functional and genetic variability in this microbiome. However, little is known about the active bacteria and their function(s) in the gastrointestinal tract. We performed a metatranscriptomic study on ten healthy volunteers to elucidate the active members of the gut microbiome and their functionality under conditions of health. First, the microbial cDNAs obtained from each sample were sequenced using 454 technology. The analysis of 16S transcripts showed the phylogenetic structure of the active microbial community. Lachnospiraceae, Ruminococcaceae, Bacteroidaceae, Prevotellaceae, and Rickenellaceae were the predominant families detected in the active microbiota. The characterization of mRNAs revealed a uniform functional pattern in healthy individuals. The main functional roles of the gut microbiota were carbohydrate metabolism, energy production and synthesis of cellular components. In contrast, housekeeping activities such as amino acid and lipid metabolism were underrepresented in the metatranscriptome. Our results provide new insights into the functionality of the complex gut microbiota in healthy individuals. In this RNA-based survey, we also detected small RNAs, which are important regulatory elements in prokaryotic physiology and pathogenicity

Valorisation of Persimmon and Blueberry By-Products to Obtain Functional Powders: in vitro Digestion and Fermentation by Gut Microbiota

This document is the unedited Author's version of a Submitted Work that was subsequently accepted for publication in Journal of Agricultural and Food Chemistry, copyright © American Chemical Society after peer review. To access the final edited and published work see https://doi.org/10.1021/acs.jafc.0c02088[EN] Globalization of fruit and vegetable markets generates overproduction, surpluses, and potentially valuable residues. The valorization of these byproducts constitutes a challenge, to ensure sustainability and reintroduce them into the food chain. This work focuses on blueberry and persimmon residues, rich in polyphenols and carotenoids, to obtain powders with high added value to be used as ingredients in food formulation. These powders have been characterized, and the changes in the bioactive compounds in in vitro gastrointestinal digestion have been evaluated. The results indicated that the type of residue, the drying process, as well as the content and type of fiber determine the release of antioxidants during digestion. In vitro colonic fermentations were also performed, and it was observed that the characteristics of digested powders had an effect on the composition of the growing microbial community. Thus, carotenoids and anthocyanins maintain an interplay with microbiota that could be beneficial for human health.This study was supported by the Polisabio grant (P32) from Universitat Politecnica de Valencia and FISABIO and also financially supported by the Generalitat Valenciana (Project AICO/2017/049).Bas-Bellver, C.; Andrés, C.; Seguí Gil, L.; Barrera Puigdollers, C.; Jiménez-Hernández, N.; Artacho, A.; Betoret Valls, N.... (2020). Valorisation of Persimmon and Blueberry By-Products to Obtain Functional Powders: in vitro Digestion and Fermentation by Gut Microbiota. 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Efecto de la biofumigación sobre flora arvense del cultivo del fresón

Debido a la biodescomposición de la materia orgánica, se producen una serie de compuestos capaces de controlar plagas, patógenos y flora arvense. Este proceso ha sido definido como biofumigación (BF). El objetivo de esta investigación fue evaluar el efecto de la biofumigación con materia orgánica fresca sobre flora arvense típica de los cultivos de fresón. Los experimentos de campo consistieron en el tratamiento con gallinaza o estiércol de caballo a la dosis de 3 kg m-2 durante 45 días. La biofumigación se combinó también con solarización (BF+S), en un diseño experimental de bloques al azar. Los resultados con gallinaza mostraron un buen control de las principales adventicias Poa annua, Portulaca oleracea y Lolium rigidum con resultados de control/BF/BF+S de 42/4/8, 18/9/12, y 15/0/1 plants m-2 respectivamente. Por otra parte, 20 semillas de varias arvenses se introdujeron en bolsas de tela y fueron sometidas a biofumigación con solarización. La eficacia del tratamiento BF+S fue claro en el control de P. oleracea, Cynodon dactilon y Echinochloa crus-galli con un porcentaje de germinación control/BF+S de 77/0, 50/15 y 30/2. Los experimentos de laboratorio consistieron en simular las condiciones de campo usando una mezcla de suelo, agua y diferentes materias orgánicas frescas. Las materias orgánicas utilizadas fueron restos de fresa, estiércol de caballo y gallinaza. Los mejores resultados se obtuvieron con gallinaza que mostró un control eficaz de Malva parviflora, Medicago sp., E. crus-galli, Amaranthus retroflexus, Chenopodium album y P. oleracea mientras que los residuos de fresa y el estiércol no mostraron inhibición de la germinación. En conclusión, los resultados obtenidos con los tratamientos de gallinaza se encuentran bajo investigación con resultados prometedores en los experimentos realizados hasta la fech

Evidence of Recombination in Intrapatient Populations of Hepatitis C Virus

Hepatitis C virus (HCV) is a major cause of liver disease worldwide and a potential cause of substantial morbidity and mortality in the future. HCV is characterized by a high level of genetic heterogeneity. Although homologous recombination has been demonstrated in many members of the family Flaviviridae, to which HCV belongs, there are only a few studies reporting recombination on natural populations of HCV, suggesting that these events are rare in vivo. Furthermore, these few studies have focused on recombination between different HCV genotypes/subtypes but there are no reports on the extent of intra-genotype or intra-subtype recombination between viral strains infecting the same patient. Given the important implications of recombination for RNA virus evolution, our aim in this study has been to assess the existence and eventually the frequency of intragenic recombination on HCV. For this, we retrospectively have analyzed two regions of the HCV genome (NS5A and E1-E2) in samples from two different groups: (i) patients infected only with HCV (either treated with interferon plus ribavirin or treatment naïve), and (ii) HCV-HIV co-infected patients (with and without treatment against HIV). The complete data set comprised 17712 sequences from 136 serum samples derived from 111 patients. Recombination analyses were performed using 6 different methods implemented in the program RDP3. Recombination events were considered when detected by at least 3 of the 6 methods used and were identified in 10.7% of the amplified samples, distributed throughout all the groups described and the two genomic regions studied. The resulting recombination events were further verified by detailed phylogenetic analyses. The complete experimental procedure was applied to an artificial mixture of relatively closely viral populations and the ensuing analyses failed to reveal artifactual recombination. From these results we conclude that recombination should be considered as a potentially relevant mechanism generating genetic variation in HCV and with important implications for the treatment of this infection

Association of Self-Reported Physical Fitness during Late Pregnancy with Birth Outcomes and Oxytocin Administration during Labour—The GESTAFIT Project

We explored (a) the associations between self-reported maternal physical fitness and birth outcomes; (b) whether self-reported maternal physical fitness (PF) is related to the administration of oxytocin to induce or stimulate labour. Pregnant women from the GESTAFIT project randomized controlled trial (n = 117) participated in this prospective longitudinal study. Maternal physical fitness was assessed through the International Fitness Scale at the 34th gestational week. Maternal and neonatal birth outcomes and oxytocin administration were collected from the obstetric medical records. Umbilical arterial and venous cord blood gas were analysed immediately after birth. Selfreported overall fitness, cardiorespiratory fitness, muscular strength and flexibility were not related to any maternal and neonatal birth outcomes (all p > 0.05). Greater speed-agility was associated with a more alkaline arterial (p = 0.04) and venous (p = 0.02) pH in the umbilical cord blood. Women who were administered oxytocin to induce or stimulate labour reported lower cardiorespiratory fitness (p = 0.013, Cohen’s d = 0.55; 95% confidence interval (CI): 0.14, 0.93) and flexibility (p = 0.040, Cohen´s d = 0.51; 95% CI: 0.09, 0.89) compared to women who were not administered oxytocin. Greater maternal physical fitness during pregnancy could be associated with better neonatal birth outcomes and lower risk of needing oxytocin administration.Regional Ministry of Health of the Junta de Andalucía (PI-0395-2016)Research and Knowledge Transfer Fund (PPIT) 2016, Excellence Actions Programme: Scientific Units of Excellence (UCEES)Regional Ministry of Economy, Knowledge, EnterprisesUniversity, European Regional Development Funds (ref. SOMM17/6107/UGR)Spanish Ministry of Education, Culture and Sports (Grant number FPU17/03715

Association of Self-Reported Physical Fitness with Pregnancy Related Symptoms the GESTAFIT Project

We explored the association of physical fitness (PF) with pregnancy-related symptoms, at the 16th and 34th gestational weeks (g.w.). The International Fitness Scale and the Pregnancy Symptoms Inventory were employed to assess self-reported PF and pregnancy-related symptoms, respectively. At the 16th g.w. greater self-reported overall PF was associated with lower incidence of urinary frequency (p = 0.020); greater overall PF, cardiorespiratory fitness (CRF), muscular strength and speed-agility were associated with lower incidence of tiredness-fatigue (all, p < 0.05); greater overall PF and speed-agility were associated with lower incidence of poor sleep (both, p < 0.05); greater CRF and flexibility were associated with lower limitations by tiredness-fatigue (both, p < 0.05); and greater flexibility was associated with lower limitations by poor sleep (p = 0.021). At the 34th g.w. greater self-reported overall PF, CRF and muscular strength were associated with lower incidence of tiredness-fatigue (all, p < 0.05); greater CRF was associated with lower incidence of poor sleep (p = 0.019); and, greater flexibility was associated with lower incidence of increased vaginal discharge (p = 0.023). Adequate levels of PF, especially CRF, may help women to cope with the most endorsed pregnancy-related symptoms and its limitations, especially tiredness-fatigue and poor sleep