Vaginal Microbiome Components as Correlates of Cervical Human Papillomavirus Infection.

BACKGROUND: Interplay between vaginal microbiome and human papillomavirus (HPV) remains unclear, partly due to heterogeneity of microbiota. METHODS: We used data from 546 women enrolled in a cross-sectional study in 5 Brazil. We genotyped vaginal samples for HPV and sequenced V3-V4 region of 16S rRNA gene for vaginal microbiome analysis. We used stepwise logistic regression to construct 2 linear scores to predict high-risk HPV (hrHPV) positivity: one based exclusively on presence of individual bacterial taxa (microbiome-based [MB] score) and the other exclusively on participants' sociodemographic, behavioral, and clinical (SBC) characteristics. MB score combined coefficients of 30 (of 116) species. SBC score retained 6 of 25 candidate variables. We constructed receiver operating characteristic curves for scores as hrHPV correlates and compared areas under the curve (AUC) and 95% confidence intervals (CI). RESULTS: Overall, prevalence of hrHPV was 15.8%, and 26.2% had a Lactobacillus-depleted microbiome. AUCs were 0.8022 (95% CI, .7517-.8527) for MB score and 0.7027 (95% CI, .6419-.7636) for SBC score (P = .0163). CONCLUSIONS: The proposed MB score is strongly correlated with hrHPV positivity-exceeding the predictive value of behavioral variables-suggesting its potential as an indicator of infection and possible value for clinical risk stratification.

QCloud2: An Improved Cloud-based Quality-Control System for Mass-Spectrometry-based Proteomics Laboratories.

QCloud is a cloud-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, and automated data processing. Since its release, QCloud has facilitated automated quality control for proteomics experiments in many laboratories. QCloud provides a quick and effortless evaluation of instrument performance that helps to overcome many analytical challenges derived from clinical and translational research. Here we present an improved version of the system, QCloud2. This new version includes enhancements in the scalability and reproducibility of the quality-control pipelines, and it features an improved front end for data visualization, user management, and chart annotation. The QCloud2 system also includes programmatic access and a standalone local version.

Translatome analysis at the egg-to-embryo transition in sea urchin.

Early embryogenesis relies on the translational regulation of maternally stored mRNAs. In sea urchin, fertilization triggers a dramatic rise in translation activity, necessary for the onset of cell division. Here, the full spectrum of the mRNAs translated upon fertilization was investigated by polysome profiling and sequencing. The translatome of the early sea urchin embryo gave a complete picture of the polysomal recruitment dynamics following fertilization. Our results indicate that only a subset of maternal mRNAs were selectively recruited onto polysomes, with over-represented functional categories in the translated set. The increase in translation upon fertilization depends on the formation of translation initiation complexes following mTOR pathway activation. Surprisingly, mTOR pathway inhibition differentially affected polysomal recruitment of the newly translated mRNAs, which thus appeared either mTOR-dependent or mTOR-independent. Therefore, our data argue for an alternative to the classical cap-dependent model of translation in early development. The identification of the mRNAs translated following fertilization helped assign translational activation events to specific mRNAs. This translatome is the first step to a comprehensive analysis of the molecular mechanisms governing translation upon fertilization and the translational regulatory networks that control the egg-to-embryo transition as well as the early steps of embryogenesis.

mTOR Signaling at the Crossroad between Metazoan Regeneration and Human Diseases.

A major challenge in medical research resides in controlling the molecular processes of tissue regeneration, as organ and structure damage are central to several human diseases. A survey of the literature reveals that mTOR (mechanistic/mammalian target of rapamycin) is involved in a wide range of regeneration mechanisms in the animal kingdom. More particularly, cellular processes such as growth, proliferation, and differentiation are controlled by mTOR. In addition, autophagy, stem cell maintenance or the newly described intermediate quiescence state, Galert, imply upstream monitoring by the mTOR pathway. In this review, we report the role of mTOR signaling in reparative regenerations in different tissues and body parts (e.g., axon, skeletal muscle, liver, epithelia, appendages, kidney, and whole-body), and highlight how the mTOR kinase can be viewed as a therapeutic target to boost organ repair. Studies in this area have focused on modulating the mTOR pathway in various animal models to elucidate its contribution to regeneration. The diversity of metazoan species used to identify the implication of this pathway might then serve applied medicine (in better understanding what is required for efficient treatments in human diseases) but also evolutionary biology. Indeed, species-specific differences in mTOR modulation can contain the keys to appreciate why certain regeneration processes have been lost or conserved in the animal kingdom.

Physicochemical changes and chilling injury disorders in 'Tango' mandarins stored at low temperatures.

BACKGROUND: The susceptibility to chilling injury and quality changes of 'Tango' mandarins stored at different temperatures was evaluated in fruit grown at two locations in Andalusia (Spain) and grafted on Carrizo Citrange or FA5 rootstock. The peel disorders were also characterized by a microstructural study. RESULTS: Fruit developed chilling injuries, manifested as pitting lesions affecting the equatorial area of the fruit stored at 1 °C or 5 °C; fruit growing on FA5 rootstock showed a slightly lower incidence. The microstructural study revealed that only the upper layers of flavedo were affected in the damaged fruit, the epidermal and hypodermal tissues being dramatically collapsed. Although the fruit was prone to accumulate ethanol, especially after the shelf life that followed the different periods of cold storage, the ethanol did not compromise the overall flavor. CONCLUSIONS: Storage of 'Tango' fruit was limited by chilling injuries when stored at 1 °C or 5 °C for more than 20 days. Moreover, at these temperatures, the fruit was prone to accumulate ethanol and develop off flavors. At 9° C, the fruit could be stored for 30 days without compromising external or internal quality. Growing location and rootstock influenced some quality attributes at harvest but not during storage. © 2020 Society of Chemical Industry.

Analysis of translation using polysome profiling.

During the past decade, there has been growing interest in the role of translational regulation of gene expression in many organisms. Polysome profiling has been developed to infer the translational status of a specific mRNA species or to analyze the translatome, i.e. the subset of mRNAs actively translated in a cell. Polysome profiling is especially suitable for emergent model organisms for which genomic data are limited. In this paper, we describe an optimized protocol for the purification of sea urchin polysomes and highlight the critical steps involved in polysome purification. We applied this protocol to obtain experimental results on translational regulation of mRNAs following fertilization. Our protocol should prove useful for integrating the study of the role of translational regulation in gene regulatory networks in any biological model. In addition, we demonstrate how to carry out high-throughput processing of polysome gradient fractions, for the simultaneous screening of multiple biological conditions and large-scale preparation of samples for next-generation sequencing.

Translational Control of Canonical and Non-Canonical Translation Initiation Factors at the Sea Urchin Egg to Embryo Transition.

Sea urchin early development is a powerful model to study translational regulation under physiological conditions. Fertilization triggers an activation of the translation machinery responsible for the increase of protein synthesis necessary for the completion of the first embryonic cell cycles. The cap-binding protein eIF4E, the helicase eIF4A and the large scaffolding protein eIF4G are assembled upon fertilization to form an initiation complex on mRNAs involved in cap-dependent translation initiation. The presence of these proteins in unfertilized and fertilized eggs has already been demonstrated, however data concerning the translational status of translation factors are still scarce. Using polysome fractionation, we analyzed the impact of fertilization on the recruitment of mRNAs encoding initiation factors. Strikingly, whereas the mRNAs coding eIF4E, eIF4A, and eIF4G were not recruited into polysomes at 1 h post-fertilization, mRNAs for eIF4B and for non-canonical initiation factors such as DAP5, eIF4E2, eIF4E3, or hnRNP Q, are recruited and are differentially sensitive to the activation state of the mechanistic target of rapamycin (mTOR) pathway. We discuss our results suggesting alternative translation initiation in the context of the early development of sea urchins.

MAPK/ERK activity is required for the successful progression of mitosis in sea urchin embryos.

Using sea urchin embryos, we demonstrate that the MEK/MAPK/ERK cascade is essential for the proper progression of the cell cycle. Activation of a limited fraction of MAPK/ERK is required between S-phase and M-phase. Neither DNA replication nor CDK1 activation are impacted by the inhibition of this small active MAPK/ERK fraction. Nonetheless, the chromatin and spindle organisations are profoundly altered. Early morphological disorders induced by the absence of MAPK/ERK activation are correlated with an important inhibition of global protein synthesis and modification in the cyclin B accumulation profile. After appearance of morphological disorders, there is an increase in the level of the inhibitor of protein synthesis, 4E-BP, and, ultimately, an activation of the spindle checkpoint. Altogether, our results suggest that MAPK/ERK activity is required for the synthesis of (a) protein(s) implicated in an early step of chromatin /microtubule attachment. If this MAPK/ERK-dependent step is not achieved, the cell activates a new checkpoint mechanism, involving the reappearance of 4E-BP that maintains a low level of protein translation, thus saving cellular energy.

Reading comprehension and immersion schooling: evidence from component skills.

The present research aims to assess literacy acquisition in children becoming bilingual via second language immersion in school. We adopt a cognitive components approach, assessing text-level reading comprehension, a complex literacy skill, as well as underlying cognitive and linguistic components in 144 children aged 7 to 14 (72 immersion bilinguals, 72 controls). Using principal component analysis, a nuanced pattern of results was observed: although emergent bilinguals lag behind their monolingual counterparts on measures of linguistic processing, they showed enhanced performance on a memory and reasoning component. For reading comprehension, no between-group differences were evident, suggesting that selective benefits compensate costs at the level of underlying cognitive components. Overall, the results seem to indicate that literacy skills may be modulated by emerging bilingualism even when no between-group differences are evident at the level of complex skill, and the detection of such differences may depend on the focus and selectivity of the task battery used.

Model of the delayed translation of cyclin B maternal mRNA after sea urchin fertilization.

Sea urchin eggs exhibit a cap-dependent increase in protein synthesis within minutes after fertilization. This rise in protein synthesis occurs at a constant rate for a great number of proteins translated from the different available mRNAs. Surprisingly, we found that cyclin B, a major cell-cycle regulator, follows a synthesis pattern that is distinct from the global protein population, so we developed a mathematical model to analyze this dissimilarity in biosynthesis kinetic patterns. The model includes two pathways for cyclin B mRNA entry into the translational machinery: one from immediately available mRNA (mRNAcyclinB) and one from mRNA activated solely after fertilization (XXmRNAcyclinB). Two coefficients, α and ß, were added to fit the measured scales of global protein and cyclin B synthesis, respectively. The model was simplified to identify the synthesis parameters and to allow its simulation. The calculated parameters for activation of the specific cyclin B synthesis pathway after fertilization included a kinetic constant (ka ) of 0.024 sec-1 , for the activation of XXmRNAcyclinB, and a critical time interval (t2 ) of 42 min. The proportion of XXmRNAcyclinB form was also calculated to be largely dominant over the mRNAcyclinB form. Regulation of cyclin B biosynthesis is an example of a select protein whose translation is controlled by pathways that are distinct from housekeeping proteins, even though both involve the same cap-dependent initiation pathway. Therefore, this model should help provide insight to the signaling utilized for the biosynthesis of cyclin B and other select proteins. Mol. Reprod. Dev. 83: 1070-1082, 2016. © 2016 Wiley Periodicals, Inc.

The Ectocarpus genome and the independent evolution of multicellularity in brown algae.

Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.

Magnetic resonance imaging structural alterations in brain of alcohol abusers and its association with impulsivity.

Despite the suggestion that impulsivity plays a central role in the transfer from a recreational drug use to a substance use disorder, very few studies focused on neurobiological markers for addiction. This study aimed to identify volumetric alterations in a sample of patients with mild alcohol use disorder with a short history of alcohol use, compared with a control group, and also focused on its association with impulsivity levels. Most magnetic resonance imaging studies have focused on severe alcohol use disorder, formerly called alcohol-dependent patients, showing alcohol-related structural alterations and their association with alcohol use history variables but not with personality parameters like impulsivity. Our hypothesis is that our group of alcohol users may already display structural alterations especially in brain regions related to inhibitory control like medial-prefrontal regions, and that those structural alterations could be more associated to personality traits like impulsivity than to drug use variables. Our results clearly demonstrate that our population showed lower regional grey and white matter volumes in the medial-prefrontal and orbitofrontal cortices, as well as higher regional white matter volume in the ventral striatum and the internal capsule. Volumetric alterations were associated to the Barratt's impulsivity score: the more impulsive the subjects, the lower the medial-prefrontal cortex grey matter volume.

Tracking a refined eIF4E-binding motif reveals Angel1 as a new partner of eIF4E.

The initiation factor 4E (eIF4E) is implicated in most of the crucial steps of the mRNA life cycle and is recognized as a pivotal protein in gene regulation. Many of these roles are mediated by its interaction with specific proteins generally known as eIF4E-interacting partners (4E-IPs), such as eIF4G and 4E-BP. To screen for new 4E-IPs, we developed a novel approach based on structural, in silico and biochemical analyses. We identified the protein Angel1, a member of the CCR4 deadenylase family. Immunoprecipitation experiments provided evidence that Angel1 is able to interact in vitro and in vivo with eIF4E. Point mutation variants of Angel1 demonstrated that the interaction of Angel1 with eIF4E is mediated through a consensus eIF4E-binding motif. Immunofluorescence and cell fractionation experiments showed that Angel1 is confined to the endoplasmic reticulum and Golgi apparatus, where it partially co-localizes with eIF4E and eIF4G, but not with 4E-BP. Furthermore, manipulating Angel1 levels in living cells had no effect on global translation rates, suggesting that the protein has a more specific function. Taken together, our results illustrate that we developed a powerful method for identifying new eIF4E partners and open new perspectives for understanding eIF4E-specific regulation.

Low involvement of preexisting associations makes retrieval-induced forgetting long lasting.

Research has shown that selective retrieval of episodic memories usually leads to forgetting of related memories that compete for retrieval [a phenomenon known as retrieval-induced forgetting (RIF)]. However, there are conflicting data regarding the duration of this incidental kind of forgetting. While some studies have found that this forgetting effect disappears within 24 h after selective retrieval, others suggest that it may last for as long as at least a week. In two experiments, we explored whether discrepancies in the durability of RIF may be due to variations in the type of relationships (preexisting vs. novel) that are present between items associated with a given cue. We explored this issue by manipulating the degree of involvement of preexisting/novel associations among competing items as well as the delay between retrieval practice and test (immediate in Experiment 1 and 24-h delay test in Experiment 2). The results suggest that forgetting lasts longer when the degree of preexisting associations among targets and competitors is low.

Dephosphorylation of eIF2α is essential for protein synthesis increase and cell cycle progression after sea urchin fertilization.

The eukaryotic Initiation Factor 2 (eIF2) is a key regulator of protein synthesis in eukaryotic cells, implicated in the initiation step of translation. Fertilization of the sea urchin eggs triggers a rapid increase in protein synthesis activity, which is necessary for the progress into embryonic cell cycles. Here we demonstrate that fertilization triggers eIF2α dephosphorylation, concomitant with an increase in protein synthesis and that induction of the eIF2α phosphorylation is intimately linked with an inhibition of protein synthesis and cell cycle arrest. Using a phospho-mimetic protein microinjected into sea urchin eggs, we showed that dephosphorylation of eIF2α is necessary for protein synthesis activity and cell division progression following fertilization. Our results demonstrate that regulation of eIF2α plays an important role in the protein synthesis rise that occurs during early development following fertilization.

Working memory development in monolingual and bilingual children.

Two studies are reported comparing the performance of monolingual and bilingual children on tasks requiring different levels of working memory. In the first study, 56 5-year-olds performed a Simon-type task that manipulated working memory demands by comparing conditions based on two rules and four rules and manipulated conflict resolution demands by comparing conditions that included conflict with those that did not. Bilingual children responded faster than monolinguals on all conditions and bilinguals were more accurate than monolinguals in responding to incongruent trials, confirming an advantage in aspects of executive functioning. In the second study, 125 children 5- or 7-year-olds performed a visuospatial span task that manipulated other executive function components through simultaneous or sequential presentation of items. Bilinguals outperformed monolinguals overall, but again there were larger language group effects in conditions that included more demanding executive function requirements. Together, the studies show an advantage for bilingual children in working memory that is especially evident when the task contains additional executive function demands.

Spatial and temporal distribution of Alternaria spores in the Iberian Peninsula atmosphere, and meteorological relationships: 1993-2009.

This paper provides an updated of airborne Alternaria spore spatial and temporal distribution patterns in the Iberian Peninsula, using a common non-viable volumetric sampling method. The highest mean annual spore counts were recorded in Sevilla (39,418 spores), Mérida (33,744) and Málaga (12,947), while other sampling stations never exceeded 5,000. The same cities also recorded the highest mean daily spore counts (Sevilla 109 spores m(-3); Mérida 53 spores m(-3) and Málaga 35 spores m(-3)) and the highest number of days on which counts exceeded the threshold levels required to trigger allergy symptoms (Sevilla 38 % and Mérida 30 % of days). Analysis of annual spore distribution patterns revealed either one or two peaks, depending on the location and prevailing climate of sampling stations. For all stations, average temperature was the weather parameter displaying the strongest positive correlation with airborne spore counts, whilst negative correlations were found for rainfall and relative humidity.

Factors associated with bacterial vaginosis in women with homosexual, bisexual and heterosexual practices.

BACKGROUND: The factors associated with bacterial vaginosis in women with homosexual, bisexual and heterosexual practices are still poorly explored. Thus, the aim of this study was to analyze the factors associated with bacterial vaginosis in women with different sexual practices. METHODS: Cross-sectional study that included 453 women, 149 Women with Homosexual practice (WSW); 80 bisexual Women (WSWM) and 224 Women with heterosexual practice (WSM). The diagnosis of bacterial vaginosis was performed by microscopic examination of the vaginal smears stained by Gram method and classified according to the Nugent et al. (1991) score. Data analysis was performed by Cox multiple regression. RESULTS: Bacterial vaginosis was associated to years of education among WSW (0.91 [95% CI 0.82‒0.99]; p = 0.048) and non-white skin color (2.34 [95% CI 1.05‒5.19]; p = 0.037) between WSWM. Changing partners in the last 3-months (2.09 [95% CI 1.14‒3.82]; p = 0.017), inconsistent use of condoms (2.61 [95% CI 1.10‒6.20]; p = 0.030) and positive diagnosis of Chlamydia trachomatis (2.40 [95% CI 1.01‒5.73]; p = 0.048) were associated with bacterial vaginoses only in WSH. CONCLUSIONS: The factors associated to bacterial vaginosis differ between different sexual practices, suggesting that the type of sexual partner may influence the risk of developing this classic dysbiosis.

Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes.

Sea urchins are emblematic models in developmental biology and display several characteristics that set them apart from other deuterostomes. To uncover the genomic cues that may underlie these specificities, we generated a chromosome-scale genome assembly for the sea urchin Paracentrotus lividus and an extensive gene expression and epigenetic profiles of its embryonic development. We found that, unlike vertebrates, sea urchins retained ancestral chromosomal linkages but underwent very fast intrachromosomal gene order mixing. We identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes have been recruited in novel structures (water vascular system, Aristotle's lantern, and skeletogenic micromere lineage). Finally, we identified gene-regulatory modules conserved between sea urchins and chordates. Our results suggest that gene-regulatory networks controlling development can be conserved despite extensive gene order rearrangement.

eIF4B mRNA Translation Contributes to Cleavage Dynamics in Early Sea Urchin Embryos.

During the first steps of sea urchin development, fertilization elicits a marked increase in protein synthesis essential for subsequent cell divisions. While the translation of mitotic cyclin mRNAs is crucial, we hypothesized that additional mRNAs must be translated to finely regulate the onset into mitosis. One of the maternal mRNAs recruited onto active polysomes at this stage codes for the initiation factor eIF4B. Here, we show that the sea urchin eIF4B orthologs present the four specific domains essential for eIF4B function and that Paracentrotus lividus eIF4B copurifies with eIF4E in a heterologous system. In addition, we investigated the role of eIF4B mRNA de novo translation during the two first embryonic divisions of two species, P. lividus and Sphaerechinus granularis. Our results show that injection of a morpholino directed against eIF4B mRNA results in a downregulation of translational activity and delays cell division in these two echinoids. Conversely, injection of an mRNA encoding for P. lividus eIF4B stimulates translation and significantly accelerates cleavage rates. Taken together, our findings suggest that eIF4B mRNA de novo translation participates in a conserved regulatory loop that contributes to orchestrating protein synthesis and modulates cell division rhythm during early sea urchin development.