A new procedure to analyze RNA non-branching structures

RNA structure prediction and structural motifs analysis are challenging tasks in the investigation of RNA function. We propose a novel procedure to detect structural motifs shared between two RNAs (a reference and a target). In particular, we developed two core modules: (i) nbRSSP_extractor, to assign a unique structure to the reference RNA encoded by a set of non-branching structures; (ii) SSD_finder, to detect structural motifs that the target RNA shares with the reference, by means of a new score function that rewards the relative distance of the target non-branching structures compared to the reference ones. We integrated these algorithms with already existing software to reach a coherent pipeline able to perform the following two main tasks: prediction of RNA structures (integration of RNALfold and nbRSSP_extractor) and search for chains of matches (integration of Structator and SSD_finder)

Relevant and selective activity of Pancratium illyricum L. against Candida albicans clinical isolates: a combined effect on yeast growth and virulence

BACKGROUND: Alkaloids present in plants of the Amaryllidaceae family are secondary metabolites of high biological interest, possessing a wide range of pharmacological activities. In the search for new plant-derived compounds with antimicrobial activities, two alkaloid extracts obtained from bulbs and leaves of Pancratium illyricum L., a plant of the Amarillydaceae family, were tested for their effect on bacterial and yeast growth. METHODS: The broth microdilution susceptibility test was applied to study the effect of plant extracts on the growth of reference bacterial strains and Candida albicans reference and clinical isolates strains. Extracts obtained from the different parts of the plant were tested and compared with the pure components identified in the extracts. Since matrix metalloproteinase enzymes play a role in the dissemination process of Candida albicans, the effect of the bulb extract and pure alkaloids on in vitro collagenase activity was tested. Cell viability test was carried out on human embryo lung fibroblasts (HEL 299). RESULTS: Whilst both extracts did not show any inhibitory activity against neither Gram positive nor Gram negative bacteria, a strong antifungal activity was detected, in particular for the bulb extract. All clinical isolates were susceptible to the growth inhibitory activity of the bulb extract, with endpoint IC50 values ranging from 1.22 to 78 μg/mL. The pure alkaloids lycorine and vittatine, identified as components of the extract, were also assayed for their capacity of inhibiting the yeast growth, and lycorine turned very active, with endpoint IC50 values ranging from 0.89 to 28.5 μg/mL. A potent inhibition of the in vitro collagenase activity was found in the presence of the bulb extract, and this effect was much higher than that exerted by the pure alkaloids. Viability of cell lines tested was not affected by the extract. CONCLUSIONS: Taken together, results suggest that the extract of Pancratium illyricum may act as antifungal agent both directly on the yeast growth and by altering the tissue invasion process

Relaxed selection on male mitochondrial genes in DUI bivalves eases the need for mitonuclear coevolution

Mitonuclear coevolution is an important prerequisite for efficient energy production in eukaryotes. However, many bivalve taxa experience doubly uniparental inheritance (DUI) and have sex-specific mitochondrial (mt) genomes, providing a challenge for mitonuclear coevolution. We examined possible mechanisms to reconcile mitonuclear coevolution with DUI. No nuclear-encoded, sex-specific OXPHOS paralogs were found in the DUI clam Ruditapes philippinarum, refuting OXPHOS paralogy as a solution in this species. It is also unlikely that mt changes causing disruption of nuclear interactions are strongly selected against because sex-specific mt-residues or those under positive selection in M mt genes were not depleted for contacting nuclear-encoded residues. However, M genomes showed consistently higher dN/dS ratios compared to putatively ancestral F genomes in all mt OXPHOS genes and across all DUI species. Further analyses indicated that this was consistently due to relaxed, not positive selection on M vs. F mt OXPHOS genes. Similarly, selection was relaxed on the F genome of DUI species compared to species with strict maternal inheritance. Coupled with recent physiological and molecular evolution studies, we suggest that relaxed selection on M mt function limits the need to maintain mitonuclear interactions in M genomes compared to F genomes. We discuss our findings with regard to OXPHOS function and the origin of DUI

Immunolocalization of Vasa, PIWI, and TDRKH proteins in male germ cells during spermatogenesis of the teleost fish Poecilia reticulata

Vasa, PIWI and TDRKH are conserved components of germ granules that in metazoans are involved in germline specification and differentiation, as documented by mutational experiments in some model animals. So far, investigations on PIWI during spermatogenesis of fish has been limited to a few species, and no information is available for TDRKH, another protein involved in the piRNA pathway. In this study, the immunolocalization of these three germline determinants was analyzed in male gonads of the teleost fish Poecilia reticulata to document their localization pattern in the different stages of germ cell differentiation. To analyze their distribution pattern during the different stages of spermatogenesis we performed immunohistochemistry (IHC) and immunofluorescence (IF) assays using primary polyclonal antibodies after testing their specificity with Western Blot. Moreover, sections of testis stained with haematoxylin and eosin clarified the structural organization of P. reticulata testis, while the use of the confocal microscope and the nuclear staining clarified the different stages of germ cell differentiation during spermatogenesis. The results showed that Vasa, PIWI and TDRKH were specifically immunolocalized in the germ cells of P. reticulata, with no specific signal detected in Sertoli cells and in other somatic cells of the gonad. These markers were detected in all stages of differentiation from early spermatogonia to advanced spermatids. Vasa staining was the strongest in spermatogonia, and then decreases throughout differentiation. Instead, both PIWI and TDRKH staining increases during differentiation, and their distribution pattern, similar to what observed in the mouse, suggests their concerted participation in the piRNA pathway also in this fish

Pivotal role of boron supplementation on bone health: A narrative review

Background: Boron is a trace element that plays an important role in numerous biological functions, including calcium metabolism, growth and maintenance of bone tissue. However, there are still no precise indications regarding a possible role of boron supplementation, and its amount of supplementation, to maintain bone health. So the aim of this narrative review was to consider the state of the art on the effectiveness of boron supplementation (alone or with other micronutrients) on growth and maintenance of bone in humans through control of calcium, vitamin D and sex steroid hormone metabolism in order to suggest a daily dosage of boron supplementation. Main findings: This review included 11 eligible studies: 7 regarding the supplementation with boron alone and 4 regarding supplementation with boron and other nutrients. Despite the number of studies considered being low, the number of subjects studied is high (594) and the results are interesting. Conclusions: The studies considered in this narrative review have evaluated the positive effectiveness on bone, in humans, through control of calcium, vitamin D and sex steroid hormone metabolism, considering a dietary supplementation of 3 mg/day of boron (alone or with other nutrients); this supplementation is demonstrably useful to support bone health (in order to prevent and maintain adequate bone mineral density), also considering the daily dose of 3 mg is much lower than the Upper Level indicated by EFSA in the daily dose of 10 mg

Radicalization in Correctional Systems: A Scoping Review of the Literature Evaluating the Effectiveness of Preventing and Countering Interventions

Although several prevention and countering radicalization programs in correctional institutions have been carried out in Europe and worldwide, little is known about their effectiveness. Thus, the current scoping review aimed at reporting on the state of the art of the literature assessing and evaluating such actions, identifying knowledge gaps, and examining methods used to assess their successfulness and impact. A total of eight studies that met eligibility criteria were reviewed after performing a search on Scopus, Web of Science, and PsychInfo (Ebsco) databases: Two studies evaluated a reintegration initiative based in the Netherlands; four focused on an Australian disengagement program; and two offered insights on a rehabilitation program carried out in Sri Lanka. Findings were discussed according to their evaluation methods (qualitative, mixed-methods, and quantitative) and instruments. Results highlighted that the evaluation process is still confronted with several methodological difficulties, such as a lack of agreement on how to univocally define and measure success and the identification of uniform indicators of deradicalization and disengagement. Additionally, results revealed that the effectiveness of these interventions is predominantly based on anecdotal evidence rather than on rigorous, empirical proofs. As such, it was not possible to compare these programs and determine which worked best. Suggestions for future research and practical implications for policymakers, prison governors, and practitioners are offered in the concluding section of this work

The interplay between risk and protective factors during the initial height of the COVID-19 crisis in Italy: The role of risk aversion and intolerance of ambiguity on distress

The present study aimed to test a model of relations to ascertain the determinants of distress caused by lockdown for COVID- 19. It was hypothesized that the exposure to the COVID-19 increased distress directly and through the mediation of worry, health-related information seeking, and perception of the utility of the lockdown. It was also expected that higher levels of ambiguity intolerance corresponded to higher distress directly and through the mediation of worry, health information seeking behaviors, and perceived utility of the lockdown. Finally, it was expected that risk aversion positively influenced distress directly and through the increasing of worry, health-related information seeking behavior, and more positive perception of the utility of the lockdown The study was conducted in Italy during the mandatory lockdown for COVID-19 pandemic on 240 individuals (age range 18\u201376). Data recruitment was conducted via snowball sampling. COVID-19 exposure was positively associated with worry and health-related information seeking. Risk-aversion was positively associated with health-related information seeking and perceived utility of the lockdown to contain the spread of the virus. Worry and health-related information seeking were positively associated with distress, whereas the perceived utility of the lockdown was negatively associated with distress. Intolerance for the ambiguity was directly linked to distress with a positive sign. Findings suggest that risk aversion represents both a risk factor and a protective factor, based on what kind of variable mediates the relationship with distress, and that the intolerance to the ambiguity is a risk factor that busters distress