Books, documents, and art items supported on paper are objects easily attacked and degraded by microorganisms. They are mostly made of organic compounds such as cellulose, an ideal substrate for developing many species of fungi and bacteria. Across the centuries, the probability that an object made of paper is colonised and degraded by some saprophytic microorganism is consistent. The challenge for conservators and those involved in preventing the deterioration of cultural heritage is to slow down these inevitable natural processes as much as possible (Pinzari et Sequeira, 2022). Moreover, the functional and biological diversity of species of microorganisms capable of degrading cellulose is exceptionally high because many species have evolved in the most diverse environments to compete for such a widespread carbon source. Thus, the forms of cellulose degradation, whether in natural settings such as soil or anthropogenic environments such as libraries, can differ significantly depending on the species of microorganisms involved and the microenvironment in which they thrive. Although the processes of paper biodeterioration have been the same since the paper was invented, the investigation techniques have significantly changed. After decades of intensive study, there is a clear sense of the enormous complexity of the mechanisms involved and how difficult it is to standardise diagnosis and intervention methods. This is especially true when biodeterioration affects valuable, unique, artistic objects.

Ochratoxin A (OTA) is a toxic and teratogenic metabolite produced by fungal species of the genera Penicillium and Aspergillus. Analysing OTA in food and monitoring its presence in biological samples is recommended to assess individual exposure to the mycotoxin. The primary technique used for OTA detection in biological samples is LC-MS/MS. However, biosensors provide a viable alternative for mycotoxin detection due to their high portability potential and ease of use. Various types of biosensors have been developed for OTA detection, relying on the specific recognition of OTA by DNA aptamers. DNA's engineering versatility makes it a powerful and programmable element for constructing microscale systems that find numerous applications in biosensing. In our study, we present a DNA-based biosensor for detecting OTA in urine. The sensor consists of a DNA-based capture system and a detection system. We created paramagnetic microbeads carrying a capture aptamer for OTA, enabling its specific capture in liquid samples. A detection complex, which triggers an isothermal rolling circle amplification (RCA), was assembled using the same aptamer annealed to a circularized probe. This complex was used to detect the occurrence of toxin capture. We designed the RCA to generate autocatalytic units with peroxidase activity (DNAzyme). In the presence of OTA, the circular DNA initiates its isothermal amplification at 30°C, producing a single-stranded and tandemly repeated long homologous copy of its sequence. Within the amplified DNA strand, a peroxidase self-catalytic structure induces a colour reaction that is visible to the naked eye. The resulting biosensor exhibited high sensitivity and selectivity for detecting OTA, with a limit of detection as low as 1.09×10-12 ng/ml. Furthermore, we tested the biosensor for OTA detection in naturally contaminated urine. Accuracy and repeatability data obtained from recovery experiments showed recoveries exceeding 95%, with relative standard deviations ranging from 3.6 to 15%. For the first time, an aptasensor has been successfully applied to detect OTA in biological fluids. It can be used for mycotoxin biomonitoring and assessment of individual exposure.

l linguaggio della Vita - Viaggio fantastico dal DNA alle proteine: laboratorio basato su giochi e attività ludiche, pensato in particolare per bambini e ragazzi delle scuole elementari e medie ma adatto a tutti. Lo scopo è illustrare in modo pratico il "linguaggio della vita", raccontando attraverso il gioco come funziona la riproduzione cellulare, dal DNA all'RNA fino agli amminoacidi e alla produzione delle proteine. (Padiglione LEARN)

Protein biosynthesis is a complex process that involves the transcription of DNA into mRNA and the subsequent translation of mRNA into proteins according to the genetic code. To introduce this fundamental process to a broad audience, we developed "The Language of Life", a game-based workshop that was presented at the Genoa Science Festival 2022, the largest science communication event in Italy. The game-based workshop employed jigsaw puzzle-like elements to represent DNA, mRNA, and aminoacyl transfer RNAs, enabling participants to pair them through codon combinations. The game-based workshop lasted for an hour and the framing was a "special mission" inside a cell. It consisted of an initial training phase that incorporated videos, models, and explanations, followed by practical "missions'' in which participants reproduce transcription and translation mechanisms by moving inside the cell and using the provided materials. The workshop was attended by 1,505 participants, primarily students aged 6-18, and received positive feedback. In this paper, we present our experience conducting this workshop and discuss its impact and potential for future use.

Epigenetics is a rapidly growing field of biology that studies the changes in gene expression that are not due to alterations in the DNA sequence but rather the chemical modifications of DNA and its associated proteins. Epigenetic mechanisms can profoundly influence gene expression, cell differentiation, tissue development, and disease susceptibility. Understanding epigenetic changes is essential to elucidate the mechanisms underlying the increasingly recognized role of environmental and lifestyle factors in health and disease and the intergenerational transmission of phenotypes. Recent studies suggest epigenetics may be critical in various diseases, from cardiovascular disease and cancer to neurodevelopmental and neurodegenerative disorders. Epigenetic modifications are potentially reversible and could provide new therapeutic avenues for treating these diseases using epigenetic modulators. Moreover, epigenetics provide insight into disease pathogenesis and biomarkers for disease diagnosis and risk stratification. Nevertheless, epigenetic interventions have the potential for unintended consequences and may potentially lead to increased risks of unexpected outcomes, such as adverse drug reactions, developmental abnormalities, and cancer. Therefore, rigorous studies are essential to minimize the risks associated with epigenetic therapies and to develop safe and effective interventions for improving human health. This article provides a synthetic and historical view of the origin of epigenetics and some of the most relevant achievements.

Telomere length maintenance is crucial to cancer cell immortality. Up to 15% of cancers utilize a telomerase-independent, recombination-based mechanism termed alternative lengthening of telomeres (ALT). Currently, the primary ALT biomarker is the C-circle, a type of circular DNA with extrachromosomal telomere repeats (cECTRs). How C-circles form is not well characterized. We investigated C-circle formation in the human cen3tel cell line, a long-telomere, telomerase+ (LTT+) cell line with progressively hyper-elongated telomeres (up to ~100 kb). cECTR signal was observed in 2D gels and C-circle assays but not t-circle assays, which also detect circular DNA with extrachromosomal telomere repeats. Telomerase activity and C-circle signal were not separable in the analysis of clonal populations, consistent with C-circle production occurring within telomerase+ cells. We observed similar cECTR results in two other LTT+ cell lines, HeLa1.3 (~23 kb telomeres) and HeLaE1 (~50 kb telomeres). In LTT+ cells, telomerase activity did not directly impact C-circle signal; instead, C-circle signal correlated with telomere length. LTT+ cell lines were less sensitive to hydroxyurea than ALT+ cell lines, suggesting that ALT status is a stronger contributor to replication stress levels than telomere length. Additionally, the DNA repair-associated protein FANCM did not suppress C-circles in LTT+ cells as it does in ALT+ cells. Thus, C-circle formation may be driven by telomere length, independently of telomerase and replication stress, highlighting limitations of C-circles as a stand-alone ALT biomarker.

Purpose of review Gliomas are the most common primary tumors of the central nervous system. They are characterized by a disappointing prognosis and ineffective therapy that has shown no substantial improvements in the past 20 years. The lack of progress in treating gliomas is linked with the inadequacy of suitable tumor samples to plan translational studies and support laboratory developments. To overcome the use of tumor tissue, this commentary review aims to highlight the potential for the clinical application of liquid biopsy (intended as the study of circulating biomarkers in the blood), focusing on circulating tumor cells, circulating DNA and circulating noncoding RNA. Recent findings Thanks to the increasing sensitivity of sequencing techniques, it is now possible to analyze circulating nucleic acids and tumor cells (liquid biopsy). Summary Although studies on the use of liquid biopsy are still at an early stage, the potential clinical applications of liquid biopsy in the study of primary brain cancer are many and have the potential to revolutionize the approach to neuro-oncology, and importantly, they offer the possibility of gathering information on the disease at any time during its history.

The recent development of mRNA vaccines against the SARS-CoV-2 infection has turned the spotlight on the potential of nucleic acids as innovative prophylactic agents and as diagnostic and therapeutic tools. Until now, their use has been severely limited by their reduced half-life in the biological environment and the difficulties related to their transport to target cells. These limiting aspects can now be overcome by resorting to chemical modifications in the drug and using appro-priate nanocarriers, respectively. Oligonucleotides can interact with complementary sequences of nucleic acid targets, forming stable complexes and determining their loss of function. An alternative strategy uses nucleic acid aptamers that, like the antibodies, bind to specific proteins to modulate their activity. In this review, the authors will examine the recent literature on nucleic acids-based strategies in the COVID-19 era, focusing the attention on their applications for the prophylaxis of COVID-19, but also on antisense-and aptamer-based strategies directed to the diagnosis and therapy of the coronavirus pandemic.

Multivalent molecules are a potential group of bioactive compounds endowed with high affinity and specificity in innovative biomolecule-targeting therapeutic approaches. Herein, we report on a new and versatile N,N,N,N-donor ligand L (1R,4R)-N1,N4-bis(quinolin-2-ylmethylene)cyclohexane-1,4-diamine with two coordinating quinoline moieties connected with trans-1,4-diaminocyclohexane. It coordinates Cu forming a [2 × 2] square grid-type complex C1 [CuL] and Ni giving a triangle-type complex C2 [NiL]. We screened their potential as versatile metal-based Serum Albumin (SA), double helical and G-quadruplex DNA binders taking advantage of their shape, size and stability effects using different spectroscopic experiments (UV-Vis, fluorescence, circular dichroism). The findings of our work suggest the potential utility of the metal complexes herein described in the context of the new drug discovery.

G-quadruplex (G4) oligonucleotides are higher-order DNA and RNA secondary structures of enormous relevance due to their implication in several biological processes and pathological states in different organisms. Strategies aiming at modulating human G4 structures and their interrelated functions are first-line approaches in modern research aiming at finding new potential anticancer treatments or G4-based aptamers for various biomedical and biotechnological applications. Plants offer a cornucopia of phytocompounds that, in many cases, are effective in binding and modulating the thermal stability of G4s and, on the other hand, contain almost unexplored G4 motifs in their genome that could inspire new biotechnological strategies. Herein, we describe some G4 structures found in plants, summarizing the existing knowledge of their functions and biological role. Moreover, we review some of the most promising G4 ligands isolated from vegetal sources and report on the known relationships between such phytochemicals and G4-mediated biological processes that make them potential leads in the pharmaceutical sector.

The rising connection of vehicles with the road infrastructure enables the creation of data-driven applications to offer drivers customized services. At the same time, these opportunities require innovative solutions to protect the drivers&#x2019; privacy in a complex environment like an Intelligent Transportation System (ITS). This need is even more relevant when data are used to retrieve personal behaviors or attitudes. In our work, we propose a privacy-preserving solution, called Private Driver DNA, which designs a possible architecture, allowing drivers of an ITS to receive customized services. The proposed solution is based on the concept of Driver DNA as characterization of driver&#x2019;s driving style. To assure privacy, we perform the operations directly on sanitized data, using the Order Revealing Encryption (ORE) method. Besides, the proposed solution is integrated with ITS architecture defined in the European project E-Corridor. The result is an effective privacy-preserving architecture for ITS to offer customized products, which can be used to address drivers&#x2019; behaviors, for example, to environmental-friendly attitudes or a more safe driving style. We test Private Driver DNA using a synthetic dataset generated with the vehicle simulator CARLA. We compare ORE with another encryption method like <italic>Homomorphic Encryption</italic> (HE) and some other privacy-preserving schemas. Besides, we quantify privacy gain and data loss utility after the data sanitization process.

The present study aimed to determine whether autophagy contributes to radiofrequency-induced adaptive response. To this purpose, SH-SY5Y human neuroblastoma cells were exposed for 20 hours to 1950 MHz, UMTS signal, and then treated with menadione, a DNA damage inducer. The results obtained indicated a reduction of menadione-induced DNA damage in samples that were pre-exposed to radiofrequency field, as assessed by the comet assay. Such a reduction was negated when autophagy was inhibited by Bafilomycin A1 and E64d. Moreover, CRISPR SHSY-5Y cell lines defective for ATG7 or ATG5 genes also did not show adaptive response. These findings suggest the involvement of autophagy in the radiofrequency-induced adaptive response, although further investigation is required to extend such observation at molecular level.

ConspectusThe interaction between light and multichromophoric assemblies (MCAs) is the primary event of many fundamental processes, from photosynthesis to organic photovoltaics, and it triggers dynamical processes that share remarkable similarities at the molecular scale: light absorption, energy and charge transfer, internal conversions, emission, and so on. Those events often involve many chromophores and different excited electronic states that are coupled on an ultrafast time scale. This Account aims to discuss some of the chemical physical effects ruling these processes, a fundamental step toward their control, based on our experience on nucleic acids.In the last 15 years, we have, indeed, studied the photophysics and photochemistry of DNA and its components. By combining different quantum mechanical methods, we investigated the molecular processes responsible for the damage of the genetic code or, on the contrary, those preventing it by dissipating the excess energy deposited in the system by UV absorption. Independently of its fundamental biological role, DNA, with its fluctuating closely stacked bases stabilized by weak nonbonding interactions, can be considered a prototypical MCA. Therefore, it allows one to tackle within a single system many of the conceptual and methodological challenges involved in the study of photoinduced processes in MCA.In this Account, by using the outcome of our studies on oligonucleotides as a guideline, we thus highlight the most critical modellistic issues to be faced when studying, either experimentally or computationally, the interaction between UV light and DNA and, at the same time, bring out their general relevance for the study of MCAs.We first discuss the rich photoactivated dynamics of nucleobases (the chromophores), highlighting the main effects modulating the interplay between their excited states and how the latter can affect the photoactivated dynamics of the polynucleotides, either providing effective monomer-like nonradiative decay routes or triggering reactive processes (e.g., triplet generation).We then tackle the reaction paths involving multiple bases, showing that in the DNA duplex the most important ones involve two stacked bases, forming a neutral excimer or a charge transfer (CT) state, which exhibit different spectral signatures and photochemical reactivity. In particular, we analyze the factors affecting the dynamic equilibrium between the excimer and CT, such as the fluctuations of the backbone or the rearrangement of the solvent.Next, we highlight the importance of the effects not directly connected to the chromophores, such as the flexibility of the backbone or the solvent effect. The former, affecting the stacking geometry of the bases, can determine the preference between different deactivation paths. The latter is particularly influential for CT states, making very important an accurate treatment of dynamical solvation effects, involving both the solvent bulk and specific solute-solvent interactions.In the last section, we describe the main methodological challenges related to the study of polynucleotide excited states and stress the benefits derived by the integration of complementary approaches, both computational and experimental. Only exploiting different point of views, in our opinion, it is possible to shed light on the complex phenomena triggered by light absorption in DNA, as in every MCA.

The use of micro- and nanoparticles in biological applications has dramatically grown during the last few decades due to the ease of protocols development and compatibility with microfluidics devices. Particles can be composed by different materials, i.e., polymers, inorganic dielectrics, and metals. Among them, silica is a suitable material for the development of biosensing applications. Depending on their final application, the surface properties of particles, including silica, are tailored by means of chemical modification or polymeric coating. The latter strategy represents a powerful tool to create a hydrophilic environment that enables the functionalization of particles with biomolecules and the further interaction with analytes. Here, the use of MCP-6, a dimethylacrylamide (DMA)-based ter-copolymer, to coat silica microspheres is presented. MCP-6 offers unprecedented ease of coating, imparting silica particles a hydrophilic coating with antifouling properties that is able to provide high-density immobilization of biological probes.

The coverage density of oligonucleotides on the surface of gold nanoparticles (AuNPs) is crucial for optimizing the sensitivity of AuNPs-based biosensors and evaluating the interactions between thiol-functionalized oligonucleotides and AuNPs. In this study, we report a novel approach based on a miniaturized gel electrophoresis chip (MGEC) integrated with online thermal lens detection for monitoring the amount of DNA on the surface of AuNPs. The microcontroller-based digitization board platform enables simultaneous measurement and recording of data. AuNPs were functionalized with a mixed thiol-terminated monolayer containing single stranded DNA at variable density, which is able to load binders for high sensitivity biorecognition. Due to high spatial and temporal resolution of the thermal lens detection system, our approach enables extremely small differences in the electrophoretic mobility of the particles to be resolved. Hence, small differences in the DNA surface density (55-275 nM) on the particles can be easily distinguished in short time (<6 min), not otherwise detectable using conventional UV-Vis spectrophotometers. In addition, the analytical capability of the proposed MGEC was validated measuring the low detection limit for standard AuNPs solutions using a 80 mu L buffer, 100 mu L gel, and a 37.5 V/cm electrical field. The result showed that the thermal lens signal linearly increased with the concentration of AuNPs over the range of 0.1-10 nM. The detection limit and relative standard deviation were 23 pM and 4%, respectively. We envisage that the system has potential as an advanced instrumental platform for designing biosensors in nanotechnology.

Efficient humoral responses rely on DNA damage, mutagenesis and error-prone DNA repair. Diversification of B cell receptors through somatic hypermutation and class-switch recombination are initiated by cytidine deamination in DNA mediated by activation-induced cytidine deaminase (AID) and by the subsequent excision of the resulting uracils by uracil DNA glycosylase (UNG) and by mismatch repair proteins. Although uracils arising in DNA are accurately repaired, how these pathways are co-opted to generate mutations and double-strand DNA breaks in the context of somatic hypermutation and class-switch recombination is unknown. Here we performed a genome-wide CRISPR-Cas9 knockout screen for genes involved in class-switch recombination and identified FAM72A, a protein that interacts with the nuclear isoform of UNG (UNG2) and is overexpressed in several cancers. We show that the FAM72A-UNG2 interaction controls the levels of UNG2 and that class-switch recombination is defective in Fam72a B cells due to the upregulation of UNG2. Moreover, we show that somatic hypermutation is reduced in Fam72a B cells and that its pattern is skewed upon upregulation of UNG2. Our results are consistent with a model in which FAM72A interacts with UNG2 to control its physiological level by triggering its degradation, regulating the level of uracil excision and thus the balance between error-prone and error-free DNA repair. Our findings have potential implications for tumorigenesis, as reduced levels of UNG2 mediated by overexpression of Fam72a would shift the balance towards mutagenic DNA repair, rendering cells more prone to acquire mutations.

Phenanthriplatin (PtPPH) is a monovalent platinum(II)-based complex with a large cytotoxicity against cancer cells. Although the aqua-activated drug has been assumed to be the precursor for DNA damage, it is still under debate whether the way in which that metallodrug attacks to DNA is dominated by a direct binding to a guanine base or rather by an intercalated intermediate product. Aiming to capture the mechanism of action of PtPPH, the present contribution used theoretical tools to systematically assess the sequence of all possible mechanisms on drug activation and reactivity, for example, hydrolysis, intercalation, and covalent damage to DNA. Ab initio quantum mechanical (QM) methods, hybrid QM/QM' schemes, and independent gradient model approaches are implemented in an unbiased protocol. The performed simulations show that the cascade of reactions is articulated in three well-defined stages: (i) an early and fast intercalation of the complex between the DNA bases, (ii) a subsequent hydrolysis reaction that leads to the aqua-activated form, and (iii) a final formation of the covalent bond between PtPPH and DNA at a guanine site. The permanent damage to DNA is consequently driven by that latter bond to DNA but with a simultaneous pi-pi intercalation of the phenanthridine into nudeobases. The impact of the DNA sequence and the lateral backbone was also discussed to provide a more complete picture of the forces that anchor the drug into the double helix.

We demonstrate here the use of 2-(4-chlorophenyl)-2-cyanopropanoic acid (CPA) and nitroacetic acid (NAA) as convenient chemical fuels to drive the dissipative operation of DNA-based nanodevices. Addition of either of the fuel acids to a water solution initially causes a rapid transient pH decrease, which is then followed by a slower pH increase. We have employed such low-to-high pH cycles to control in a dissipative way the operation of two model DNA-based nanodevices: a DNA nanoswitch undergoing time-programmable open-close-open cycles of motion, and a DNA-based receptor able to release-uptake a DNA cargo strand. The kinetics of the transient operation of both systems can be easily modulated by varying the concentration of the acid fuel added to the solution and both acid fuels show an efficient reversibility which further supports their versatility.

Evento divulgativo dell'IFT-CNR tenutosi presso l'Area di Ricerca Roma2 Tor Vergata il 28 settembre 2021, nell'ambito della European Biotech Week (EBW) 2021, manifestazione divulgativa mondiale organizzata in Italia da Associazione Nazionale per lo sviluppo delle Biotecnologie (Assobiotec )- Federchimica e da EuropaBio (Associazione europea delle biotecnologie).

Il castagno europeo (Castanea sativa Mill.) è una specie arborea ad alto fusto, appartenente alla famiglia delle Fagaceae, di notevole interesse agroforestale per il nostro Paese (Nunziata et al. 2020). In Campania, il castagno ha un importante ruolo economico, producendo più del 50% di castagne a livello nazionale, oltre all'utilizzo del fusto (Castellotti et al. 2011). Dal 2005, con l'arrivo accidentale in Campania della specie invasiva Dryocosmus kuriphilus Y. (cinipide galligeno), la produzione di frutti commerciabili si è ridotta drasticamente (Calandrelli et al. 2019). La suscettibilità dei castagneti al parassita è stata dimostrata dipendere principalmente dagli specifici genotipi di castagno presenti sul territorio (Dini et al. 2012; Nugnes et al. 2018). Per tale ragione, nel presente studio, è stata condotta una ricognizione degli strumenti molecolari e delle applicazioni GIS (Geographic Information System) disponibili per una mappatura della distribuzione della biodiversità castanicola. Gli strumenti molecolari basati sul DNA sono stati testati sui principali genotipi varietali di castagno presenti nell'area protetta del vulcano spento di Roccamonfina in Campania (Nunziata et al. 2020): Lucente, Marzatica, Mercogliana, Napoletana, Olefarella, Paccuta, San Pietro, e Tempestiva tradizionalmente coltivati e apprezzati soprattutto per la qualità dei loro frutti. I sistemi informativi geografici (Burrough et al. 1998) consentono di visualizzare la distribuzione della variabilità genetica nello spazio geografico (Miller et al. 2006) correlandola alla posizione di ciascun albero di castagno. L'uso combinato di tali strumenti permette di valutare le caratteristiche del paesaggio associate a modelli di diversità genetica. Il presente lavoro ha indagato la fattibilità della mappatura mediante rappresentazione GIS della distribuzione della diversità genetica di varietà tradizionali di castagno sul territorio di Roccamonfina col fine di estrarre informazioni utili per la gestione della biodiversità castanicola campana a rischio.