Cell Response to Extracellular DNA and Self-DNA Inhibition

The discovery of DNA beyond the confinement of cell boundaries, generally defined as extracellular DNA, poses questions on its alternative roles that may differ from its being the main repository of genetic information within a cell. DNA can be extruded from cells by active or passive release, remaining in the extracellular context, that can be either the body of multicellular organisms or the natural environment, as free molecule or complexed with inorganic and organic particles, and/or organized in extracellular structures. The presence of extracellular DNA (exDNA) outside cells, either in multicellular organisms or in the environment, has been initially discussed in terms of horizontal gene transfer, nutrient, and then as protective and/or signalling molecule. Recently, a novel and interesting research line revealed for the exDNA additional roles depending on its nature, environmental location and structural organization. Indeed, in 2015, Mazzoleni and his colleagues demonstrated for the first time that the exposure to fragmented self-exDNA (conspecific or similar/homologous DNA) differently from the exposure to nonself-exDNA (heterologous, DNA from phylogenetically unrelated species, or, more in general, distant in sequence similarity terms), inhibits root growth and seed germination in plants in a concentration dependent manner. Later, it has been also demonstrated that it induces intracellular calcium signalling and plasma membrane depolarization and also triggers well-known markers of the immunological response, e.g. H2O2 production and MAPK activation. Following the results on plants, the inhibitory effect of self-exDNA on other species was also demonstrated by Mazzoleni and his group and, on the basis of these findings, they suggested the generality of the observed phenomenon which opens new perspectives in the context of self-inhibition processes. Nevertheless, the mechanism underlying the specific recognition of either self or nonself-exDNA and subsequent responses in plants as well as in other organisms is still poorly understood. The presented project aims at investigating the effects of the exposure of organisms from model species to nonself- and self-exDNA. In particular, one of the main objectives, is to confirm the inhibitory role of self-exDNA when compared to the exposure to nonself-exDNA, as highlighted for the first time in plants and then also in other species by Mazzoleni and colleagues in 2015. In this regard, it will be explored the effect of nonself- and self-exDNA on both terrestrial and aquatic species including representatives of unicellular and multicellular organisms from animals and plants with the purpose of confirming the generality of the phenomenon observed by Mazzoleni et al. in 2015. In particular, as representative of multicellular autotrophs, the early response to either nonself- and self-exDNA will be adressed in the model plant Arabidopsis thaliana through the evaluation of gene expression changes and exDNA spatial distribution at root and cellular levels. Then, to confirm the differential responses also in aquatic environments, it will be also evaluated the effect of nonself- and self-exDNA on cell density and on the morphology of two microalgae Nannochloropsis gaditana and Chlamydomonas reinhardtii, examples of unicellular authothophs, living in marine and freshwater, respectively. Futhermore, aiming at highlighting potential differences and similarities among the responses of cells from different phyla, the effects of nonself- and self-exDNA will be evaluated on the vitality, morphological and physiological features of human cells, considered as a simplified system representing non-photosynthetic species. Finally, to further characterize the phenomenon in multicellular organisms living in marine environment, the chordate Ciona robusta, a model system which is considered the closest living relatives of vertebrates, will be used to investigate the effects of exDNAs on the main stages of the cordate embryos development and, thus, to infer on its potential role on vertebrates developmental processes. The findings of this project will contribute to shed light on the differential responses of organisms of different clades to either self- or nonself-exDNA. This will have relevant ecological implications and will support the unexpected new functional roles of exDNA in species interactions at community and ecosystem levels also deserving high potentiality for the development of biotechnological and industrial applications

Colorectal Cancer Stage at Diagnosis Before vs During the COVID-19 Pandemic in Italy

IMPORTANCE Delays in screening programs and the reluctance of patients to seek medical attention because of the outbreak of SARS-CoV-2 could be associated with the risk of more advanced colorectal cancers at diagnosis. OBJECTIVE To evaluate whether the SARS-CoV-2 pandemic was associated with more advanced oncologic stage and change in clinical presentation for patients with colorectal cancer. DESIGN, SETTING, AND PARTICIPANTS This retrospective, multicenter cohort study included all 17 938 adult patients who underwent surgery for colorectal cancer from March 1, 2020, to December 31, 2021 (pandemic period), and from January 1, 2018, to February 29, 2020 (prepandemic period), in 81 participating centers in Italy, including tertiary centers and community hospitals. Follow-up was 30 days from surgery. EXPOSURES Any type of surgical procedure for colorectal cancer, including explorative surgery, palliative procedures, and atypical or segmental resections. MAIN OUTCOMES AND MEASURES The primary outcome was advanced stage of colorectal cancer at diagnosis. Secondary outcomes were distant metastasis, T4 stage, aggressive biology (defined as cancer with at least 1 of the following characteristics: signet ring cells, mucinous tumor, budding, lymphovascular invasion, perineural invasion, and lymphangitis), stenotic lesion, emergency surgery, and palliative surgery. The independent association between the pandemic period and the outcomes was assessed using multivariate random-effects logistic regression, with hospital as the cluster variable. RESULTS A total of 17 938 patients (10 007 men [55.8%]; mean [SD] age, 70.6 [12.2] years) underwent surgery for colorectal cancer: 7796 (43.5%) during the pandemic period and 10 142 (56.5%) during the prepandemic period. Logistic regression indicated that the pandemic period was significantly associated with an increased rate of advanced-stage colorectal cancer (odds ratio [OR], 1.07; 95%CI, 1.01-1.13; P = .03), aggressive biology (OR, 1.32; 95%CI, 1.15-1.53; P < .001), and stenotic lesions (OR, 1.15; 95%CI, 1.01-1.31; P = .03). CONCLUSIONS AND RELEVANCE This cohort study suggests a significant association between the SARS-CoV-2 pandemic and the risk of a more advanced oncologic stage at diagnosis among patients undergoing surgery for colorectal cancer and might indicate a potential reduction of survival for these patients

Global disparities in surgeons’ workloads, academic engagement and rest periods: the on-calL shIft fOr geNEral SurgeonS (LIONESS) study

: The workload of general surgeons is multifaceted, encompassing not only surgical procedures but also a myriad of other responsibilities. From April to May 2023, we conducted a CHERRIES-compliant internet-based survey analyzing clinical practice, academic engagement, and post-on-call rest. The questionnaire featured six sections with 35 questions. Statistical analysis used Chi-square tests, ANOVA, and logistic regression (SPSS® v. 28). The survey received a total of 1.046 responses (65.4%). Over 78.0% of responders came from Europe, 65.1% came from a general surgery unit; 92.8% of European and 87.5% of North American respondents were involved in research, compared to 71.7% in Africa. Europe led in publishing research studies (6.6 ± 8.6 yearly). Teaching involvement was high in North America (100%) and Africa (91.7%). Surgeons reported an average of 6.7 ± 4.9 on-call shifts per month, with European and North American surgeons experiencing 6.5 ± 4.9 and 7.8 ± 4.1 on-calls monthly, respectively. African surgeons had the highest on-call frequency (8.7 ± 6.1). Post-on-call, only 35.1% of respondents received a day off. Europeans were most likely (40%) to have a day off, while African surgeons were least likely (6.7%). On the adjusted multivariable analysis HDI (Human Development Index) (aOR 1.993) hospital capacity > 400 beds (aOR 2.423), working in a specialty surgery unit (aOR 2.087), and making the on-call in-house (aOR 5.446), significantly predicted the likelihood of having a day off after an on-call shift. Our study revealed critical insights into the disparities in workload, access to research, and professional opportunities for surgeons across different continents, underscored by the HDI

From geometric rules to ribbed vaults procedural modeling Parametric tools to study star vaults geometry in St-Eustache

The definition of adaptive parametric models to automate modelling architectural elements is one of the main goal for heritage documentation, dissemination and management in HBIM process. Parametric objects library of historical architectural elements is a very important step in more than one process, starting from 3D Point Clouds segmentation with Deep Learning (DL) techniques to 3D modelling from Point Cloud. Following the state of the art we have defined an adaptive parametric model for ribbed vaults modelling that allow us to generate a 3D model based on geometric rules and\or from point cloud data.. Starting from geometric rules we defined the main parameters to use to generate different “ideal models” and the specific parameters from point cloud data to use to generate a “reality based model”. We compared the different 3D models based on geometric rules from literature, 3D reality based model with mesh model from point cloud data to evaluate the process, to improve it and to verify the design hypothesis. We are going to test this workflow on a case study: Saint-Eustache church in Paris. There are some different kind of star vaults in Saint-Eustache, in this paper we show the parametric model definition process from French literature for the five keystone vault samples

Identification of Novel Potential Genes Involved in Cancer by Integrated Comparative Analyses

The main hallmarks of cancer diseases are the evasion of programmed cell death, uncontrolled cell division, and the ability to invade adjacent tissues. The explosion of omics technologies offers challenging opportunities to identify molecular agents and processes that may play relevant roles in cancer. They can support comparative investigations, in one or multiple experiments, exploiting evidence from one or multiple species. Here, we analyzed gene expression data from induction of programmed cell death and stress response in Homo sapiens and compared the results with Saccharomyces cerevisiae gene expression during the response to cell death. The aim was to identify conserved candidate genes associated with Homo sapiens cell death, favored by crosslinks based on orthology relationships between the two species. We identified differentially-expressed genes, pathways that are significantly dysregulated across treatments, and characterized genes among those involved in induced cell death. We investigated on co-expression patterns and identified novel genes that were not expected to be associated with death pathways, that have a conserved pattern of expression between the two species. Finally, we analyzed the resulting list by HumanNet and identified new genes predicted to be involved in cancer. The data integration and the comparative approach between distantly-related reference species that were here exploited pave the way to novel discoveries in cancer therapy and also contribute to detect conserved genes potentially involved in programmed cell death

Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae

Programmed cell death involves complex molecular pathways in both eukaryotes and prokaryotes. In Escherichia coli, the toxin–antitoxin system (TA-system) has been described as a programmed cell death pathway in which mRNA and ribosome organizations are modified, favoring the production of specific death-related proteins, but also of a minor portion of survival proteins, determining the destiny of the cell population. In the eukaryote Saccharomyces cerevisiae, the ribosome was shown to change its stoichiometry in terms of ribosomal protein content during stress response, affecting the relative proportion between ohnologs, i.e., the couple of paralogs derived by a whole genome duplication event. Here, we confirm the differential expression of ribosomal proteins in yeast also during programmed cell death induced by acetic acid, and we highlight that also in this case pairs of ohnologs are involved. We also show that there are different trends in cytosolic and mitochondrial ribosomal proteins gene expression during the process. Moreover, we show that the exposure to acetic acid induces the differential expression of further genes coding for products related to translation processes and to rRNA post-transcriptional maturation, involving mRNA decapping, affecting translation accuracy, and snoRNA synthesis. Our results suggest that the reprogramming of the overall translation apparatus, including the cytosolic ribosome reorganization, are relevant events in yeast programmed cell death induced by acetic acid

Multi-sensor data acquisition and integration processes for the study and documentation of the church of Santa Maria degli Angeli in Pizzofalcone in Naples

The paper presents the results of a research carried out on the Church of Santa Maria degli Angeli in Pizzofalcone in Naples, in which multi-sensor surveys have been performed in order to assess the architectonical, geometrical and colorimetric characteristics of the majestic basilica. The use of integrated technologies made it possible to realize 3D digital models that allowed the complete representation of the building, integrating data and filling the gaps of the different previous surveys. The performances of the various reality-based technologies employed have been subjected to critical analysis in order to maximize their potential, optimize survey and data elaboration phases, and obtain the expected results. These latter have been defined through the derived digital re-elaborations and representations. Hence, the objective of the research is to carry out a comparative analysis on the 3D models generated through the different active and passive sensors employed in order to proceed with their integration and achieve an accurate, original and updated methodology of building survey

Effects of Extracellular Self- and Nonself-{DNA} on the Freshwater Microalga Chlamydomonas reinhardtii and on the Marine Microalga Nannochloropsis gaditana

: The role of extracellular DNA (exDNA) in soil and aquatic environments was mainly discussed in terms of source of mineral nutrients and of genetic material for horizontal gene transfer. Recently, the self-exDNA (conspecific) has been shown to have an inhibitory effect on the growth of that organism, while the same was not evident for nonself-exDNA (non conspecific). The inhibitory effect of self-exDNA was proposed as a universal phenomenon, although evidence is mainly reported for terrestrial species. The current study showed the inhibitory effect of self-exDNA also on photosynthetic aquatic microorganisms. We showed that self-exDNA inhibits the growth of the microalgae Chlamydomonas reinhardtii and Nannochloropsis gaditana, a freshwater and a marine species, respectively. In addition, the study also revealed the phenotypic effects post self-exDNA treatments. Indeed, Chlamydomonas showed the formation of peculiar heteromorphic aggregates of palmelloid cells embedded in an extracellular matrix, favored by the presence of DNA in the environment, that is not revealed after exposure to nonself-exDNA. The differential effect of self and nonself-exDNA on both microalgae, accompanied by the inhibitory growth effect of self-exDNA are the first pieces of evidence provided for species from aquatic environments