Structural and epigenetic dysfunctions of telomeric chromatin in cancer cells

Telomeres are nucleoprotein structures that protect chromosome termini in eukaryotes. Functional telomeres need the establishment of a protective chromatin structure based on the interplay between the specific complex named shelterin and a tight nucleosomal organization. In somatic cells, progressive telomere reduction brings to the destabilization of the telomere capping structure and to the activation of a DNA damage response (DDR) signalling. Then, cells enter into replicative senescence, which constitute a protective barrier against unlimited proliferation. A crucial step in cancer development is the acquirement of a telomere maintenance mechanism that gives the neoplastic cell unlimited replicative potential, one of the main hallmarks of cancer. Despite the crucial role that telomeres play in cancer development, little is known about the epigenetic alterations of telomeric chromatin that affect telomere protection and are associated with tumorigenesis. Here, we explore two different aspects of this wide issue that involves telomeric chromatin and its dysfunctions in cancer development. The first aspect involves the interaction between SIRT6 and TRF2 in heterochromatin stability and cancer. Based on previous evidences reporting the telomeric protein TRF2 as a novel substrate of SIRT6, and that an inverse correlation between SIRT6 and TRF2 protein expression levels was present in a cohort of CRC patients (Rizzo et al., 2017), we decided to investigate the dynamic and the effects of this interaction. We performed several in vitro binding assays which showed that SIRT6 has the capability of stabilize the interaction of TRF2 with the telomeric nucleosome in vitro. Additionally, chromatin extractions after silencing SIRT6 showed that this stabilization is recapitulated also in HCT cancer cell line. Then, we performed chromatin immunoprecipitation of TRF2 coupled with sequencing (ChIP-seq) in HCT-116 upon SIRT6 silencing. We found that TRF2 delocalize both from telomeres and from pericentromeres. Furthermore, we also found TRF2 bound on several gene promoters involved in cancer development. Collectively these data unveil new interesting elements about the interplay of SIRT6 and TRF2 with heterochromatin in colon cancer cells, which could be relevant for a deeper understanding of the mechanisms of tumour onset and potentially brings to the development of new anti-cancer therapies. The second aspect regards the role played by the histone variant H3.3 at telomeres. Among the histone variants, H3.3 is the most common non-centromeric variant of histone H3. Despite being enriched in transcriptionally active regions, it has also been found at pericentromeres and telomeres. Some dominant mutations in the H3F3A/B genes have been described in several paediatric cancers. Interestingly, a positive correlation with mutations in chaperones responsible for H3.3 deposition at telomeres and pericentromeres, and an association with ALT phenotype was also reported. In light of these evidences, unravelling H3.3 function(s) at telomeres could be pivotal for the purposes of both basic and applied research. Telomeric sequences, together with the limitations of a classical methodologies used for studies on telomeres, complicated the analyses of the telomeric nucleosome spacing, and in general of the repeated long sequences. Therefore, we directed the second part of this project towards the development of a novel approach to precisely map H3.3-containing nucleosomes at human telomeres. We generated transgenic cell lines expressing a H3.3Q85C mutated gene. This particular mutation made chromatin sensitive to phenantroline, which cuts the DNA generating short DNA fragments after the addition of copper and hydrogen peroxide which catalyse the formation of short-lived hydroxyl radicals. Then, to overcome the difficulties generated by the uniformly repeated telomeric sequence, we developed a strategy to map nucleosome positions using subtelomeric sequences as starting point. To characterize the fragments of different length emerging from MNase or chemical cleavage, we took advantage of Oxford Nanopores, a technique that can handle very long fragments and does not require any amplification step sequencing. We performed pilot sequencing runs of MNase digested DNA to test the feasibility of nanopores to map telomeric nucleosome positions and spacing. The analysis of the read lengths showed clearly that nucleosome spacing at telomeres is shorter than in the rest of chromatin, but the number of reads obtained is too small to allow nucleosome mapping of single telomeres. For this reason, we developed a protocol to enrich telomeric DNA, by using biotinylated telomeric probes and streptavidin magnetic beads to capture telomeric sequences. With the application of these tools, we aim – in the near future - to obtain a detailed map of telomeric (and genome wide) H3.3 containing nucleosomes and to develop a reliable method to study the H3.3 mutations found in ALT and paediatric cancer

Supply chain network design for the diffusion of a new product

Supply Chain Network Design (SCND) deals with the determination of the physical configuration and infrastructures of the supply chain. Specifically, facility location is one of the most critical decisions: transportation, inventory and information sharing decisions can be readily re-optimized in response to changes in the context, while facility location is often fixed and difficult to change even in the medium term. On top of this, when designing a supply network to support a new product diffusion (NPD), the problem becomes both dynamic and stochastic. While literature concentrated on approaching SCND for NPD separately coping with dynamic and stochastic issues, we propose an integrated optimisation model, which allows warehouse positioning decisions in concert with the demand dynamics during the diffusion stage of an innovative product/service. A stochastic dynamic model, which integrates a Stochastic Bass Model (SBM) in order to better describe and capture demand dynamics, is presented. A myopic policy is elaborated in order to solve and validate on the data of a real case of SCND with 1,400 potential market points and 28 alternatives for logistics platforms

Integrating MRP in production systems simulation tools

Literature review suggests concentrating on the development of new reference model for manufacturing system simulation, which may implement an operation logic much closer to real industrial contexts. A production system modelling tool should be designed with the aim of standardizing and simplifying the simulation of manufacturing processes and to widespread this approach in SMEs. With this aim, the authors got committed in designing a reference model for providing a structural framework to support shop-floor simulation and optimization. This paper presents the basic framework logic and structure of the simulation tool, showing how it is possible to represent it in Business Process Modelling Notation (BPMN). On top of this, the efforts of implementing an MRP module on top of a simulation took which was originally conceived to embed look-back material handling policies area described, together with the operative solutions chosen to reach the integration

2022 Oregon State University Student Textbooks and Course Materials Survey: Results and Findings

The summary and findings of the 2022 OSU student textbook and course materials survey. This survey was run in March 2022 by the Open Education Resources Unit. It is a derivative of the Florida Virtual Libraries 2018 Student Textbook and COurse Materials survey. The survey inquires about student access to their course materials, the cost of their textbooks, and what the implications are when student do not purchase their textbooks

Changes in Pharmacy Students After Experiencing Interprofessional Education Activities

Background: Interprofessional education (IPE) has become increasingly important among healthcare professionals. The purpose of this study was to assess the impact of IPE experiences on pharmacy students’ perceived level of comfort with and level of reliability regarding other healthcare professionals. Methods and Findings: A survey of third- and fourth-year pharmacy students (N = 190) was analyzed using descriptive statistics and bivariate analyses to address the study objectives. Students experienced a significant increase in their level of comfort with questioning other professions after IPE (pre IPE: 5.45 ± 2.24 and post IPE: 7.22 ± 1.62, p<0.01) and being questioned by other professions (pre IPE: 5.39 ± 2.24 and post IPE: 7.04 ± 1.68, p<0.01). Students also experienced a significant increase in the perceived reliability and accuracy of information from nurses after IPE (pre IPE: 5.91 ± 1.82 and post IPE: 6.41 ± 1.62, p = 0.01). Conclusions: Pharmacy students who experienced any IPE perceived themselves as more comfortable with questioning and being questioned by other healthcare professionals than students without IPE. Additional research is needed to more clearly define the benefits of IPE and how it should be designed

Model theory of finite and pseudofinite groups

This is a survey, intended both for group theorists and model theorists, concerning the structure of pseudofinite groups, that is, infinite models of the first-order theory of finite groups. The focus is on concepts from stability theory and generalisations in the context of pseudofinite groups, and on the information this might provide for finite group theory

Long- and short-range correlations and their event-scale dependence in high-multiplicity pp collisions at 1as = 13 TeV

Two-particle angular correlations are measured in high-multiplicity proton-proton collisions at s = 13 TeV by the ALICE Collaboration. The yields of particle pairs at short-( 06\u3b7 3c 0) and long-range (1.6 < | 06\u3b7| < 1.8) in pseudorapidity are extracted on the near-side ( 06\u3c6 3c 0). They are reported as a function of transverse momentum (pT) in the range 1 < pT< 4 GeV/c. Furthermore, the event-scale dependence is studied for the first time by requiring the presence of high-pT leading particles or jets for varying pT thresholds. The results demonstrate that the long-range \u201cridge\u201d yield, possibly related to the collective behavior of the system, is present in events with high-pT processes as well. The magnitudes of the short- and long-range yields are found to grow with the event scale. The results are compared to EPOS LHC and PYTHIA 8 calculations, with and without string-shoving interactions. It is found that while both models describe the qualitative trends in the data, calculations from EPOS LHC show a better quantitative agreement for the pT dependency, while overestimating the event-scale dependency. [Figure not available: see fulltext.

f0(980) production in inelastic pp collisions at s = 5.02 TeV

The measurement of the production of f0(980) in inelastic pp collisions at sqrt(s) = 5.02 TeV is presented. This is the first reported measurement of inclusive f0(980) yield at LHC energies. The production is measured at midrapidity, |y| pi+pi- hadronic decay channel using the ALICE detector. The pT-differential yields are compared to those of pions, protons and ϕ mesons as well as to predictions from the HERWIG 7.2 QCD-inspired Monte Carlo event generator and calculations from a coalescence model that uses the AMPT model as an input. The ratio of the pT-integrated yield of f0(980) relative to pions is compared to measurements in e+e- and pp collisions at lower energies and predictions from statistical hadronisation models and HERWIG 7.2. A mild collision energy dependence of the f0(980) to pion production is observed in pp collisions from SPS to LHC energies. All considered models underpredict the pT-integrated 2f0(980)/(pi+ + pi-) ratio. The prediction from the canonical statistical hadronisation model assuming a zero total strangeness content of f0(980) is consistent with the data within 1.9σ and is the closest to the data. The results provide an essential reference for future measurements of the particle yield and nuclear modification in p–Pb and Pb–Pb collisions, which have been proposed to be instrumental to probe the elusive nature and quark composition of the f0(980) scalar meson

Measurement of the production of (anti)nuclei in p–Pb collisions at sNN=8.16TeV

Measurements of (anti)proton, (anti)deuteron, and (anti)3He production in the rapidity range -1 > y > 0 as a function of the transverse momentum and event multiplicity in p–Pb collisions at a center-of-mass energy per nucleon–nucleon pair sqrt(sNN) = 8.16 TeV are presented. The coalescence parameters B2 and B3, measured as a function of the transverse momentum per nucleon and of the mean charged-particle multiplicity density, confirm a smooth evolution from low to high multiplicity across different collision systems and energies. The ratios between (anti)deuteron and (anti)3He yields and those of (anti)protons are also reported as a function of the mean charged-particle multiplicity density. A comparison with the predictions of the statistical hadronization and coalescence models for different collision systems and center-of-mass energies favors the coalescence description for the deuteron-to-proton yield ratio with respect to the canonical statistical model