Pangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity

Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N2 into ammonia (nitrogen-fixation). The pangenome of 12 nitrogen-fixing plant symbionts of the Rhizobiales was analyzed yielding total 37,364 loci, with a core genome constituting 700 genes. The percentage of core genes averaged 10.2% over single genomes, and between 5% to 7% were found to be plasmid-associated. The comparison between a representative reference genome and the core genome subset, showed the core genome highly enriched in genes for macromolecule metabolism, ribosomal constituents and overall translation machinery, while membrane/periplasm-associated genes, and transport domains resulted under-represented. The analysis of protein functions revealed that between 1.7% and 4.9% of core proteins could putatively have different functions.This work was supported in part by grant “Progetto di Ateneo PRAT CPDA154841/15” from the University of Padova

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon

The analysis of environmental microbial communities has largely relied on a PCR-dependent amplification of genes entailing species identity as 16S rRNA. This approach is susceptible to biases depending on the level of primer matching in different species. Moreover, possible yet-to-discover taxa whose rRNA could differ enough from known ones would not be revealed. DNA-based methods moreover do not provide information on the actual physiological relevance of each taxon within an environment and are affected by the variable number of rRNA operons in different genomes. To overcome these drawbacks we propose an approach of direct sequencing of 16S ribosomal RNA without any primer- or PCR-dependent step. The method was tested on a microbial community developing in an anammox bioreactor sampled at different time-points. A conventional PCR-based amplicon pyrosequencing was run in parallel. The community resulting from direct rRNA sequencing was highly consistent with the known biochemical processes operative in the reactor. As direct rRNA-seq is based not only on taxon abundance but also on physiological activity, no comparison between its results and those from PCR-based approaches can be applied. The novel principle is in this respect proposed not as an alternative but rather as a complementary methodology in microbial community studies

Application of latent class analysis in assessing the awareness, attitude, practice and satisfaction of paediatricians on sleep disorder management in children in Italy.

AIM: To identify subgroups regarding paediatricians' awareness, attitude, practice and satisfaction about management of Sleep-Disordered Breathing (SDB) in Italy using Latent Class Analysis (LCA). METHODS: A cross-sectional study was conducted on a large sample of Italian paediatricians. Using a self-administered questionnaire, the study collected information on 420 Paediatric Hospital Paediatricians (PHPs) and 594 Family Care Paediatricians (FCPs). LCA was used to discover underlying response patterns, thus allowing identification of respondent groups with similar awareness, attitude, practice and satisfaction. A logistic regression model was used to investigate which independent variables influenced latent class membership. Analyses were performed using R 3.5.2 software. A p-value<0.05 was considered statistically significant. RESULTS: Two classes were identified: Class 1 (n = 368, 36.29%) "Untrained and poorly satisfied" and Class 2 (n = 646, 63.71%) "Trained and satisfied." Involving paediatric pneumologists or otorhinolaryngologists in clinical practice was associated with an increased probability of Class 2 membership (OR = 5.88, 95%CI [2.94-13.19]; OR = 15.95, 95% CI [10.92-23.81] respectively). Examining more than 20 children with SDB during the last month decreased the probability of Class 2 membership (OR = 0.29, 95% CI [0.14-0.61]). FCPs showed a higher probability of Class 2 membership than PHPs (OR = 4.64, 95% CI [3.31-6.55]). CONCLUSIONS: These findings suggest that the LCA approach can provide important information on how education and training could be tailored for different subgroups of paediatricians. In Italy standardized educational interventions improving paediatricians' screening of SDB are needed in order to guarantee efficient management of children with SDB and reduce the burden of disease

Crucial and fragile: a multi-methods and multi-disciplinary study of cooperation in the aftermath of the COVID-19 pandemic

In addressing global pandemics, robust cooperation across nations, institutions, and individuals is paramount. However, navigating the complexities of individual versus collective interests, diverse group objectives, and varying societal norms and cultures makes fostering such cooperation challenging. This research delves deep into the dynamics of interpersonal cooperation during the COVID-19 pandemic in Canton Ticino, Switzerland, using an integrative approach that combines qualitative and experimental methodologies. Through a series of retrospective interviews and a lab-in-the-field experiment, we gained insights into the cooperation patterns of healthcare and manufacturing workers. Within healthcare, professionals grappled with escalating emergencies and deteriorating work conditions, resisting the “new normalcy” ushered in by the pandemic. Meanwhile, manufacturing workers adapted to the altered landscape, leveraging smart working strategies to carve out a fresh professional paradigm amidst novel challenges and opportunities. Across these contrasting narratives, the centrality of individual, institutional, and interpersonal factors in galvanizing cooperation was evident. Key drivers like established relational dynamics, mutual dependencies, and proactive leadership were particularly salient. Our experimental findings further reinforced some of these qualitative insights, underscoring the pivotal role of recognition and the detrimental effects of uncertainty on cooperative behaviors. While contextual and sample-related constraints exist, this study illuminates vital facets of cooperation during crises and lays the groundwork for future explorations into cooperative decision-making

Foreign rule?: transnational, national, and local perspectives on Venice and Venetia within the “multinational” empire

The history of the Habsburg Empire in the post-Napoleonic era is frequently approached from the perspective of its various component nationalities. These were traditionally portrayed in the historiography as engaged in more-or-less open struggle with control from Vienna. This article argues that the over-privileging of such national categories can distort the picture. By looking at a number of case studies – the naming of Lombardy-Venetia, the Biblioteca italiana, the Panteon veneto – the relationship between Venice (and its Terraferma) and Habsburg rule during the second Austrian domination is examined. It will be argued that it is more profitable to see Venetian identities (municipal, local, Italian, and as part of a wider transnational European culture) as capable of working for as well as against the empire, and that Habsburg policy was as often concerned with managing potential local rivalries (notably between Lombards and Venetians) as with controlling a perceived Italian threat. It is also suggested that, while cultivation of local identity was often used to reinforce the national, the Austrian authorities were also happy to annex both to further imperial interests

Critical Involvement of the ATM-Dependent DNA Damage Response in the Apoptotic Demise of HIV-1-Elicited Syncytia

DNA damage can activate the oncosuppressor protein ataxia telangiectasia mutated (ATM), which phosphorylates the histone H2AX within characteristic DNA damage foci. Here, we show that ATM undergoes an activating phosphorylation in syncytia elicited by the envelope glycoprotein complex (Env) of human immunodeficiency virus-1 (HIV-1) in vitro. This was accompanied by aggregation of ATM in discrete nuclear foci that also contained phospho-histone H2AX. DNA damage foci containing phosphorylated ATM and H2AX were detectable in syncytia present in the brain or lymph nodes from patients with HIV-1 infection, as well as in a fraction of blood leukocytes, correlating with viral status. Knockdown of ATM or of its obligate activating factor NBS1 (Nijmegen breakage syndrome 1 protein), as well as pharmacological inhibition of ATM with KU-55933, inhibited H2AX phosphorylation and prevented Env-elicited syncytia from undergoing apoptosis. ATM was found indispensable for the activation of MAP kinase p38, which catalyzes the activating phosphorylation of p53 on serine 46, thereby causing p53 dependent apoptosis. Both wild type HIV-1 and an HIV-1 mutant lacking integrase activity induced syncytial apoptosis, which could be suppressed by inhibiting ATM. HIV-1-infected T lymphoblasts from patients with inactivating ATM or NBS1 mutations also exhibited reduced syncytial apoptosis. Altogether these results indicate that apoptosis induced by a fusogenic HIV-1 Env follows a pro-apoptotic pathway involving the sequential activation of ATM, p38MAPK and p53

The ISES Project subsidence monitoring of the catchment basin south of the Venice Lagoon (Italy)

The catchment located south of the Venice Lagoon experienced during the last century a general land settlement owing to groundwater pumping, oxidation of organically rich soils enhanced by agricultural activities, and natural sediment compaction. High land subsidence rates (2-4 cm/year) have been estimated in the area comprised between the lagoon edge and the Adige River and located between two leveling lines of the Italian national network (IGM lines n 7 and n 19). Only a partial knowledge on the behavior of land elevation is available in this region. To overcome this lack of information, a new fine leveling and GPS network has been established in the area within the ISES Project funded by National/Local water and administrative Authorities. The first field measurement carried out in 1999 have produced as a major result an accurate knowledge of the geoid height in this part of the Po River plain and has pointed out the stability of the area located along the lagoon boundaries during the six-year period from 1993 to now

Monitoring of abandoned quarries by remote sensing and in situ surveying

In Italy quarrying causes relevant environmental damages and alterations to the land and the ecosystems. Despite the present Italian legislation requiring the restoration of the sites after exploitation, most of the quarries, both the abandoned and the still operational ones, are not restored. The objective of this work is to indicate a monitoring methodology in order to survey the present state of the quarry sites and their evolution in time, which are the basic data needed to implement an adequate land reclamation project. Such methodology has been applied to several abandoned limestone quarries in the Latina province (close to Rome), characterised by a typical Mediterranean vegetation, but it can be applied to any other kind of litology and vegetation. The land monitoring has been realised both by using remote sensing techniques, supported by a Geographic Information System of the studied area, and by in situ surveying. The in situ surveying was able to assess the capability of the remote sensing model to describe the state of each site. (C) 2003 Elsevier B.V. All rights reserved

The Thyme oil pickering emulsion for the biological cleaning of historical stone surfaces

The Thymus genus is one of the most taxonomically complex genera in the Lamiaceae family and includes 250–350 taxa (species and varieties) of wild growing evergreen species of herbaceous perennials and subshrubs, native to Southern Europe, Africa and Asia. Thyme is a largely used medicinal plant for its expectorant, spasmolytic and antiseptic properties and infusions are employed for treating ulcers, dermatitis and rheumatic pains. The essential oil of Thymus ssp. shows a broad spectrum of bioactivities. In fact, its application as food preservative, as antioxidant, and as additive to enhance organoleptic characteristics has been reported. Thymus capitatus (L.) Hoffmanns. & Link. [syn. Coridothymus capitatus (L.) Reichenb. fil; Thymbra capitata (L.) Cav.; Satureja capitata L.] (Lamiaceae) is a Mediterranean endemic plant commonly used as a condiment for typical Mediterranean cuisine in Portugal, Spain, Italy, Cyprus, and Greece (Facciola, 1990). It is very rich in the terpenes thymol, carvacrol, and p-cymene. Chemotypes thymol, thymol-carvacrol, and carvacrol have been described, the latter being the most abundant (Bounatirou et al., 2007).Several heterotrophic microorganisms (bacteria and fungi) have the ability to interact with historical material such as textile, leather, paper, paintings, wood, papyri. Species of bacteria, fungi and algas can cause deep deteriorations of the items. Also stone monuments, in moderate and humid climates, can be colonized by fungal communities. The surfaces of stone monuments can be altered by fungal activity via hyphal penetration through the porous stone matrix and by production of organic acids and pigments (Stupar et al., 2014). Herein we reports on Maltese accession of Thymus capitatus essential oil as anti-microbial agent against several microorganism, infesting historical stone surfaces