Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

A Field Trial of Alternative Targeted Screening Strategies for Chagas Disease in Arequipa, Peru

In the wake of emerging T. cruzi infection in children of periurban Arequipa, Peru, we conducted a prospective field trial to evaluate alternative targeted screening strategies for Chagas disease across the city. Using insect vector data that is routinely collected during Ministry of Health insecticide application campaigns in 3 periurban districts of Arequipa, we separated into 4 categories those households with 1) infected vectors; 2) high vector densities; 3) low vector densities; and 4) no vectors. Residents of all infected-vector households and a random sample of those in the other 3 categories were invited for serological screening for T. cruzi infection. Subsequently, all residents of households within a 15-meter radius of detected seropositive individuals were invited to be screened in a ring case-detection scheme. Of 923 participants, 21 (2.28%) were seropositive. There were no significant differences in prevalence across the 4 screening strategies, indicating that household entomologic factors alone could not predict the risk of infection. Indeed, the most predictive variable of infection was the number of years a person lived in a location with triatomine insects. Therefore, a simple residence history questionnaire may be a useful screening tool in large, diverse urban environments with emerging Chagas disease

Physicochemical and textural quality attributes of gluten-free bread formulated with guar gum

The objective of this study was to assess the combined effect of guar gum (GG) and water content (WC) on the rheological properties of batter, and the physicochemical and textural properties of bread. Batches of gluten-free bread used a base formulation of rice (50%), maize (30%) and quinoa flour (20%), with different levels of GG (2.5, 3.0 or 3.5%) and water (90, 100 or 110%) in a full factorial design. Higher GG doses (p<0.001) tended to produce batters of lower stickiness, work of adhesion and cohesive strength; yet, of higher firmness, consistency, cohesiveness and viscosity index. These batters yielded loaves of lower (p<0.001) specific volume and baking loss; and crumbs of lower (p<0.001) aw, pH, mean cell area, void fraction, mean cell aspect ratio; and higher (p<0.001) hardness, adhesiveness, springiness, cohesiveness, chewiness, resilience, mean cell density, cell size uniformity and mean cell compactness. The sticker and less consistent batters produced with higher WC rendered larger bread loaves of softer and more cohesive and springy/resilient crumbs with greater mean cell size and void fraction. Gluten-free loaves of good appearance in terms of higher specific volume, lower crumb hardness, higher crumb springiness, and open grain visual texture were obtained in formulations with 110% WC and GG doses between 2.5 and 3.0%.Eng. Encina-Zelada acknowledges the financial aid provided by the Peruvian National Programme of Scholarships and Student Loans (PRONABEC) in the mode of PhD grants (Presidente de la República-183308). The authors are grateful to Eng. Andrea Oliveira from Prodipani, Portugal, for her kind advice and providing breadmaking ingredients.info:eu-repo/semantics/publishedVersio

Thermorheological and textural behaviour of gluten-free gels obtained from chestnut and rice flours

Nowadays, as celiac disease is becoming more common the consumers’ demand for gluten-free products with high nutritional and taste quality is increasing. This work deals with the study of the impact of four novelty gluten-free sources: chestnut flour (Cf), whole rice flour (Rw), Carolino rice flour (Rc) and Agulha rice flour (Ra). Textural, thermorheological and stability performance of gluten-free gels using different experimental techniques were evaluated. Mixed gels were also produced for comparison. Texture parameters were determined from the texture profile analysis using a texturometer. Thermorheological oscillatory measurements were conducted in a stresscontrolled rheometer in order to clarify the kinetics of gel formation and to characterise the structure of the matured gels. The stability of the gels was evaluated using transmittance profiling of the gels under gravitational fields (LUMiSizer®). Texture studies suggested that gels from mixtures of chestnut flour at 30 % and rice flour at 20 % showed the right texture to develop gel-based new desserts. Rheological results showed that the thermal profiles on heating of Cf gels were similar to those obtained for Rw and Ra, whereas Rc gels exhibited a particular pattern. Once the final gelatinisation temperature was achieved, no significant differences on the viscoelastic properties were noticed for all the tested gels. Stability tests showed that gels with Rc should present an industrial advantage over the other assayed formulations, since the stability of these gels is of the order of four times larger

Significant variation in transformation frequency in Streptococcus pneumoniae

The naturally transformable bacterium Streptococcus pneumoniae is able to take up extracellular DNA and incorporate it into its genome. Maintaining natural transformation within a species requires that the benefits of transformation outweigh its costs. Although much is known about the distribution of natural transformation among bacterial species, little is known about the degree to which transformation frequencies vary within species. Here we find that there is significant variation in transformation frequency between strains of Streptococcus pneumoniae isolated from asymptomatic carriage, and that this variation is not concordant with isolate genetic relatedness. Polymorphism in the signalling system regulating competence is also not causally related to differences in transformation frequency, although this polymorphism does influence the degree of genetic admixture experienced by bacterial strains. These data suggest that bacteria can evolve new transformation frequencies over short evolutionary timescales. This facility may permit cells to balance the potential costs and benefits of transformation by regulating transformation frequency in response to environmental conditions

Discovery of Ongoing Selective Sweeps within Anopheles Mosquito Populations Using Deep Learning

Identification of partial sweeps, which include both hard and soft sweeps that have not currently reached fixation, provides crucial information about ongoing evolutionary responses. To this end, we introduce partialS/HIC, a deep learning method to discover selective sweeps from population genomic data. partialS/HIC uses a convolutional neural network for image processing, which is trained with a large suite of summary statistics derived from coalescent simulations incorporating population-specific history, to distinguish between completed versus partial sweeps, hard versus soft sweeps, and regions directly affected by selection versus those merely linked to nearby selective sweeps. We perform several simulation experiments under various demographic scenarios to demonstrate partialS/HIC's performance, which exhibits excellent resolution for detecting partial sweeps. We also apply our classifier to whole genomes from eight mosquito populations sampled across sub-Saharan Africa by the Anopheles gambiae 1000 Genomes Consortium, elucidating both continent-wide patterns as well as sweeps unique to specific geographic regions. These populations have experienced intense insecticide exposure over the past two decades, and we observe a strong overrepresentation of sweeps at insecticide resistance loci. Our analysis thus provides a list of candidate adaptive loci that may be relevant to mosquito control efforts. More broadly, our supervised machine learning approach introduces a method to distinguish between completed and partial sweeps, as well as between hard and soft sweeps, under a variety of demographic scenarios. As whole-genome data rapidly accumulate for a greater diversity of organisms, partialS/HIC addresses an increasing demand for useful selection scan tools that can track in-progress evolutionary dynamics

Perfil de salud bucal de niños que concurrieron a Servicios Odontológicos Universitarios en Porto Alegre (Brasil) y Córdoba (Argentina)

Resumen: OBJETIVO: Comparar las condiciones de salud bucal de niños en relación con aspectos socio-demográficos-culturales maternos y perinatales. MÉTODOS: Se realizó examen clínico odontológico a 92 niños ≤3 años, concurrentes a la Clínica Odontológica de la Facultad de Odontología, UNC Córdoba-Argentina (n=32) y a la Clínica del Bebé, Facultad Odontología, UFRG Porto Alegre-Brasil (n=60). Las madres dieron consentimiento informado por escrito. Se aplicó una entrevista semiestructurada diseñada ad-hoc, a las madres o acompañantes del niño, para indagar aspectos socio-demográficos-culturales, hábitos de higiene bucal, gestación, dieta, tipo de parto y lactancia. Se aplicó Chi2 de Pearson y Fisher para evaluar la significación (p<0,05) de las diferencias entre cohortes. La importancia de diversos factores en relación a experiencia de caries y cohorte, se evaluó aplicando regresión logística binaria. RESULTADOS: El motivo de consulta resultó significativamente diferente entre cohortes, 100% preventivo en Argentina frente 8,3% en Brasil (p<0,001), igualmente al considerar la experiencia de caries (p<0,05). El modelo de regresión logística binaria mostró que las variables cohorte y libre de caries resultaron los factores más significativamente asociados a la experiencia de caries. Nivel de estudios de la madre bajo, dieta cariogénica del bebé y tipo de parto indicaron mayor riesgo cariogénico. Respecto a las cohortes se destacaron como estadísticamente significativos, higiene, edad, dieta del bebé y tipo de parto. CONCLUSIÓN: El nivel de instrucción de la madre y la dieta cariogénica del bebé muestran mayor riesgo de actividad de caries para ambas cohortes. Higiene bucal, dieta del bebé y tipo de parto se diferencian significativamente entre las cohortes

YBa<inf>2</inf>Cu<inf>3</inf>O<inf>7</inf> films grown onto SrTiO<inf>3</inf> and YSZ substrates by chemical solution deposition of trifluoroacetates

AbstractWe report the preparation and characterization of YBa2Cu3O7 (YBCO) films grown onto SrTiO3 and YSZ substrates by the trifluoroacetates chemical solution deposition method and following sintering with oxygen atmosphere at 860 °C. The X-ray diffraction (XRD) reveals (00ℓ) – oriented crystallites indicating epitaxial growth of the films in the c-direction. Despite granular morphology and the presence of Y2BaCuO5 and CuO as minor secondary phases, the technique shows the successful formation of the superconducting YBCO and preventing the formation of the unwanted BaCO3 phase. Rocking curve measurements of the (005) reflection for the YBCO/SrTiO3 was fitted with one Gaussian function with full width at the half maximum (FWHM) of 0.44° confirming that it consists of YBCO crystallites with different texture. For the sample grown on YSZ, the rocking curve was fitted with two Gaussian functions, one corresponding to the YBCO layer (FWHM = 0.4°) and another to the substrate (FWHM = 0.3°). The magnetic measurements taken in zero field cooling and field cooling modes confirm the formation of the superconducting YBCO with critical temperatures (TC) 91.8 and 85.7 K for the samples grown onto YSZ and SrTiO3, respectively. The critical current density (JC) curves indirectly calculated by using the Bean´s model from the M(T) loops were JC ~ 109 A/cm2 for the sample deposited onto YSZ and JC ~ 107A/cm2 for the YBCO deposited onto SrTiO3. Overall, the difference in TC and JC values between both samples could be related to their difference in oxygen content, porosity, hole concentration per Cu ion and the presence of secondary phases.</jats:p