Publications by authors named "Federico Rossi"

75 Publications

Coordinated maintenance of H3K36/K27 methylation by histone demethylases preserves germ cell identity and immortality.

Cell Rep 2021 Nov;37(8):110050

Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark. Electronic address:

Germ cells have evolved unique mechanisms to ensure the transmission of genetically and nongenetically encoded information, whose alteration compromises germ cell immortality. Chromatin factors play fundamental roles in these mechanisms. H3K36 and H3K27 methyltransferases shape and propagate a pattern of histone methylation essential for C. elegans germ cell maintenance, but the role of respective histone demethylases remains unexplored. Here, we show that jmjd-5 regulates H3K36me2 and H3K27me3 levels, preserves germline immortality, and protects germ cell identity by controlling gene expression. The transcriptional and biological effects of jmjd-5 loss can be hindered by the removal of H3K27demethylases, indicating that H3K36/K27 demethylases act in a transcriptional framework and promote the balance between H3K36 and H3K27 methylation required for germ cell immortality. Furthermore, we find that in wild-type, but not in jmjd-5 mutants, alterations of H3K36 methylation and transcription occur at high temperature, suggesting a role for jmjd-5 in adaptation to environmental changes.
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http://dx.doi.org/10.1016/j.celrep.2021.110050DOI Listing
November 2021

Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling.

PLoS One 2021 18;16(11):e0254971. Epub 2021 Nov 18.

Department of Medical and Molecular Genetics, King's College London, London, United Kingdom.

Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability of oak heartwood and hence the availability of samples spanning long time periods of the distant past. Wood formation is regulated in part by epigenetic mechanisms such as DNA methylation. Studies of the methylation state of DNA preserved in oak heartwood thus could identify epigenetic tree ring features informing on past environmental conditions. In this study, we aimed to establish protocols for the extraction of DNA, the high-throughput sequencing of whole-genome DNA libraries (WGS) and the profiling of DNA methylation by whole-genome bisulfite sequencing (WGBS) for oak (Quercus robur) heartwood drill cores taken from the trunks of living standing trees spanning the AD 1776-2014 time period. Heartwood contains little DNA, and large amounts of phenolic compounds known to hinder the preparation of high-throughput sequencing libraries. Whole-genome and DNA methylome library preparation and sequencing consistently failed for oak heartwood samples more than 100 and 50 years of age, respectively. DNA fragmentation increased with sample age and was exacerbated by the additional bisulfite treatment step during methylome library preparation. Relative coverage of the non-repetitive portion of the oak genome was sparse. These results suggest that quantitative methylome studies of oak hardwood will likely be limited to relatively recent samples and will require a high sequencing depth to achieve sufficient genome coverage.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0254971PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8601515PMC
November 2021

Methane and Carbon Dioxide Hydrate Formation and Dissociation in Presence of a Pure Quartz Porous Framework Impregnated with CuSn12 Metallic Powder: An Experimental Report.

Materials (Basel) 2021 Sep 6;14(17). Epub 2021 Sep 6.

Engineering Department, University of Perugia, Via G. Duranti 93, 06125 Perugia, Italy.

Hydrate formation and dissociation processes were carried out in the presence of a pure quartz porous medium impregnated with a metallic powder made with a CuSn12 alloy. Experiments were firstly made in the absence of that powder; then, different concentrations were added to the porous medium: 4.23 wt.%, 18.01 wt.%, and 30.66 wt.%. Then, the hydrate dissociation values were compared with those present in the literature. The porous medium was found to act as an inhibitor in the presence of carbon dioxide, while it did not alter methane hydrate, whose formation proceeded similarly to the ideal trend. The addition of CuSn12 promoted the process significantly. In particular, in concentrations of up to 18.01 wt.%, CO hydrate formed at milder conditions until it moved below the ideal equilibrium curve. For methane, the addition of 30.66 wt.% of powder significantly reduced the pressure required to form hydrate, but in every case, dissociation values remained below the ideal equilibrium curve.
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http://dx.doi.org/10.3390/ma14175115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8433810PMC
September 2021

Synchronization scenarios induced by delayed communication in arrays of diffusively coupled autonomous chemical oscillators.

Phys Chem Chem Phys 2021 Aug 9;23(32):17606-17615. Epub 2021 Aug 9.

Department of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100 Sassari, Italy.

We study the impact of delayed feedbacks in the collective synchronization of ensembles of identical and autonomous micro-oscillators. To this aim, we consider linear arrays of Belousov-Zhabotinsky (BZ) oscillators confined in micro-compartmentalised systems, where the delayed feedback mimics natural lags that can arise due to the confinement properties and mechanisms driving the inter-oscillator communication. The micro-oscillator array is modeled as a set of Oregonator-like kinetics coupled via mass exchange of the chemical messengers. Changes in the synchronization patterns are explored by varying the delayed feedback introduced in the messenger species Br2. A direct transition from anti-phase to in-phase synchronization and back to the initial anti-phase scheme is observed by progressively increasing the time delay from zero to the value T, which is the oscillation period characterising the system without any delayed coupling. The route from anti- to in-phase oscillations (and back) consists of regimes where windows of in-phase oscillations are periodically broken by anti-phase beats. Similarities between these phase transition dynamics and synchronization scenarios characterising the coordination of oscillatory limb movements are finally discussed.
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http://dx.doi.org/10.1039/d1cp02221kDOI Listing
August 2021

Effect of the Membrane Composition of Giant Unilamellar Vesicles on Their Budding Probability: A Trade-Off between Elasticity and Preferred Area Difference.

Life (Basel) 2021 Jun 29;11(7). Epub 2021 Jun 29.

Department of Earth, Environmental and Physical Sciences-DEEP Sciences, University of Siena, Pian dei Mantellini 44, 53100 Siena, Italy.

The budding and division of artificial cells engineered from vesicles and droplets have gained much attention in the past few decades due to an increased interest in designing stimuli-responsive synthetic systems. Proper control of the division process is one of the main challenges in the field of synthetic biology and, especially in the context of the origin of life studies, it would be helpful to look for the simplest chemical and physical processes likely at play in prebiotic conditions. Here we show that pH-sensitive giant unilamellar vesicles composed of mixed phospholipid/fatty acid membranes undergo a budding process, internally fuelled by the urea-urease enzymatic reaction, only for a given range of the membrane composition. A gentle interplay between the effects of the membrane composition on the elasticity and the preferred area difference of the bilayer is responsible for the existence of a narrow range of membrane composition yielding a high probability for budding of the vesicles.
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http://dx.doi.org/10.3390/life11070634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8306738PMC
June 2021

Effects of the Quinone Oxidoreductase WrbA on Biofilm Formation and Oxidative Stress.

Antioxidants (Basel) 2021 Jun 6;10(6). Epub 2021 Jun 6.

Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, 20133 Milano, Italy.

The effects of natural compounds on biofilm formation have been extensively studied, with the goal of identifying biofilm formation antagonists at sub-lethal concentrations. Salicylic and cinnamic acids are some examples of these compounds that interact with the quinone oxidoreductase WrbA, a potential biofilm modulator and an antibiofilm compound biomarker. However, WrbA's role in biofilm development is still poorly understood. To investigate the key roles of WrbA in biofilm maturation and oxidative stress, wild-type and ∆A mutant strains were used. Furthermore, we reported the functional validation of WrbA as a molecular target of salicylic and cinnamic acids. The lack of WrbA did not impair planktonic growth, but rather affected the biofilm formation through a mechanism that depends on reactive oxygen species (ROS). The loss of WrbA function resulted in an ROS-sensitive phenotype that showed reductions in biofilm-dwelling cells, biofilm thickness, matrix polysaccharide content, and HO tolerance. Endogenous oxidative events in the mutant strain generated a stressful condition to which the bacterium responded by increasing the catalase activity to compensate for the lack of WrbA. Cinnamic and salicylic acids inhibited the quinone oxidoreductase activity of purified recombinant WrbA. The effects of these antibiofilm molecules on WrbA function was proven for the first time.
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http://dx.doi.org/10.3390/antiox10060919DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8229589PMC
June 2021

BAP1 enhances Polycomb repression by counteracting widespread H2AK119ub1 deposition and chromatin condensation.

Mol Cell 2021 09 28;81(17):3526-3541.e8. Epub 2021 Jun 28.

IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Via A. di Rudini 8, Department of Health Sciences, 20142 Milan, Italy. Electronic address:

BAP1 is mutated or deleted in many cancer types, including mesothelioma, uveal melanoma, and cholangiocarcinoma. It is the catalytic subunit of the PR-DUB complex, which removes PRC1-mediated H2AK119ub1, essential for maintaining transcriptional repression. However, the precise relationship between BAP1 and Polycombs remains elusive. Using embryonic stem cells, we show that BAP1 restricts H2AK119ub1 deposition to Polycomb target sites. This increases the stability of Polycomb with their targets and prevents diffuse accumulation of H2AK119ub1 and H3K27me3. Loss of BAP1 results in a broad increase in H2AK119ub1 levels that is primarily dependent on PCGF3/5-PRC1 complexes. This titrates PRC2 away from its targets and stimulates H3K27me3 accumulation across the genome, leading to a general chromatin compaction. This provides evidence for a unifying model that resolves the apparent contradiction between BAP1 catalytic activity and its role in vivo, uncovering molecular vulnerabilities that could be useful for BAP1-related pathologies.
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http://dx.doi.org/10.1016/j.molcel.2021.06.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8428331PMC
September 2021

Metal-Promoted Heterocyclization: A Heterosynthetic Approach to Face a Pandemic Crisis.

Molecules 2021 Apr 29;26(9). Epub 2021 Apr 29.

Chemistry Division, School of Science and Technology, University of Camerino, 62032 Camerino, Italy.

The outbreak of SARS-CoV-2 has drastically changed our everyday life and the life of scientists from all over the world. In the last year, the scientific community has faced this worldwide threat using any tool available in order to find an effective response. The recent formulation, production, and ongoing administration of vaccines represent a starting point in the battle against SARS-CoV-2, but they cannot be the only aid available. In this regard, the use of drugs capable to mitigate and fight the virus is a crucial aspect of the pharmacological strategy. Among the plethora of approved drugs, a consistent element is a heterocyclic framework inside its skeleton. Heterocycles have played a pivotal role for decades in the pharmaceutical industry due to their high bioactivity derived from anticancer, antiviral, and anti-inflammatory capabilities. In this context, the development of new performing and sustainable synthetic strategies to obtain heterocyclic molecules has become a key focus of scientists. In this review, we present the recent trends in metal-promoted heterocyclization, and we focus our attention on the construction of heterocycles associated with the skeleton of drugs targeting SARS-CoV-2 coronavirus.
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http://dx.doi.org/10.3390/molecules26092620DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8124705PMC
April 2021

Congenital Adrenal Hyperplasia (CAH) and Gitelman Syndrome (GS): Overlapping Symptoms in an Uncommon Association.

Case Rep Pediatr 2021 8;2021:6633541. Epub 2021 Mar 8.

Department of Pediatrics, Children's Hospital "V. Buzzi", 20157 Milano, Italy.

Background: Classical salt-wasting (SW) congenital adrenal hyperplasia (CAH) and Gitelman syndrome (GS) are two genetic conditions in which dyselectrolytemia may occur. No association between the two conditions has been previously described. . We present the case of a boy with a neonatal diagnosis of SW-CAH who showed low potassium blood levels from the age of 15 years. This electrolytic alteration was, at first, attributed to an excessive action of mineralocorticoid drugs. Due to persistence of hypokalemia, SLC12A3 whole genome sequencing was performed, showing a heterozygous C to base pair substitution at position 965 in gene SLC12A3. This mutation is related to Gitelman syndrome with autosomal recessive transmission.

Conclusions: SW-CAH and GS determine opposite values of potassium in the absence of specific therapy, with a natural tendency to compensate each other. The symptom overlap makes diagnosis difficult. Organic causes of hypokalemia in patients undergoing life-saving therapy should not be excluded.
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http://dx.doi.org/10.1155/2021/6633541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7964118PMC
March 2021

Shape changes and budding of giant vesicles induced by an internal chemical trigger: an interplay between osmosis and pH change.

Phys Chem Chem Phys 2021 Feb;23(7):4262-4270

Department of Physics, Budapest University of Technology and Economics 1111, Budafoki út 8, Budapest, Hungary.

Shape transformation and budding of phospholipid/fatty acid giant hybrid vesicles can be induced by an internal chemical stimulus (pH change) when coupled with an osmotic shock. In particular, an autocatalytic enzymatic reaction set (urea-urease system), confined in the lumen of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/oleic acid (HOA) vesicles, can force the budding of the hosting vesicle, when properly fed by a trans-membrane substrate infusion. Herein, we elucidate the budding mechanism by simulating the shape changes of a vesicle during the enzymatic reaction. The area-difference-elasticity (ADE) theory is thus implemented to minimize the surface elastic energy and obtain the equilibrium shape at different values of the reduced volume and different values of the reduced preferred area difference (Δa0). Simulations, together with control experiments, unambiguously show that to obtain an effective vesicle shape transformation, the osmotic stress and the pH change in the lumen of the vesicle must act in synergy at the same timescale. Osmotic pressure induces a vesicle deflation (volume loss), while the pH change affects the preferred area difference between the outer and the inner membrane leaflets.
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http://dx.doi.org/10.1039/d0cp05952hDOI Listing
February 2021

Spatial connectivity matches direction selectivity in visual cortex.

Nature 2020 12 11;588(7839):648-652. Epub 2020 Nov 11.

UCL Institute of Ophthalmology, University College London, London, UK.

The selectivity of neuronal responses arises from the architecture of excitatory and inhibitory connections. In the primary visual cortex, the selectivity of a neuron in layer 2/3 for stimulus orientation and direction is thought to arise from intracortical inputs that are similarly selective. However, the excitatory inputs of a neuron can have diverse stimulus preferences, and inhibitory inputs can be promiscuous and unselective. Here we show that the excitatory and inhibitory intracortical connections to a layer 2/3 neuron accord with its selectivity by obeying precise spatial patterns. We used rabies tracing to label and functionally image the excitatory and inhibitory inputs to individual pyramidal neurons of layer 2/3 of the mouse visual cortex. Presynaptic excitatory neurons spanned layers 2/3 and 4 and were distributed coaxial to the preferred orientation of the postsynaptic neuron, favouring the region opposite to its preferred direction. By contrast, presynaptic inhibitory neurons resided within layer 2/3 and favoured locations near the postsynaptic neuron and ahead of its preferred direction. The direction selectivity of a postsynaptic neuron was unrelated to the selectivity of presynaptic neurons, but correlated with the spatial displacement between excitatory and inhibitory presynaptic ensembles. Similar asymmetric connectivity establishes direction selectivity in the retina. This suggests that this circuit motif might be canonical in sensory processing.
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http://dx.doi.org/10.1038/s41586-020-2894-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7116721PMC
December 2020

Beneficial biofilms for land rehabilitation and fertilization.

Authors:
Federico Rossi

FEMS Microbiol Lett 2020 11;367(21)

Department of Environmental Sciences, Informatics and Statistics (DAIS), Cà Foscari University of Venice, Via Torino 155, 30172 Mestre, Venice, Italy.

The acquisition of a biofilm lifestyle is common in nature for microorganisms. It increases their biotic and abiotic stress tolerance and their capability to provide ecosystem services. Although diminutive communities, soil beneficial biofilms are essential for nutrient cycling, soil stabilization and direct or indirect promotion of plant development. Some biofilms represent valid biotechnological tools to deal with problems related to soil degradation, which threat food quality and the maintenance of ecosystem functions. Three genres of biofilms: rhizobacterial biofilms, fungal-bacterial biofilms and biocrusts are reviewed, and their beneficial effects on the environment outlined. Their induction by microbial inoculation represents a potential eco-friendly and sustainable approach to restore lost ecosystem functions and counteract the effects of soil erosion. Yet, some existing knowledge and methodological gaps, that will be discussed here, still hamper the optimization of this technology, and its application at its full potential.
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http://dx.doi.org/10.1093/femsle/fnaa184DOI Listing
November 2020

Hofmeister Effect in Self-Organized Chemical Systems.

J Phys Chem B 2020 10 29;124(43):9658-9667. Epub 2020 Sep 29.

Department of Chemistry and Pharmacy, University of Sassari, Sassari (SS) 07100, Italy.

We studied the effect of spectator ions in the prototype of far-from-equilibrium self-organized chemical systems, the Belousov-Zhabotinsky (BZ) reaction. In particular, we investigated the specific ion effect of alkali metal cations, connoted for their kosmotropic and chaotropic properties. By means of combined experimental and numerical approaches, we could show a neat and robust evidence for the Hofmeister effect in this system. Spectator cations induce a marked increment of the induction period that preludes regular oscillations and decrease the oscillation amplitude following the sequence Li < Na ≪ K ∼ Cs. These ions affect the system kinetics by interfering in the interaction between the oxidized form of the catalyst and the organic substrate, responsible for resetting the BZ system to pre-autocatalytic (reduced) conditions. The specific ion effect on these key reactive steps is systematically characterized and correlated with different parameters which describe the interaction of the cations with the solvent.
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http://dx.doi.org/10.1021/acs.jpcb.0c06956DOI Listing
October 2020

Microfluidic compartmentalization of diffusively coupled oscillators in multisomes induces a novel synchronization scenario.

Chem Commun (Camb) 2020 Oct;56(79):11771-11774

Sorbonne Université, CNRS UMR 8234, PHysico-chimie des Electrolytes et Nanosystèmes InterfaciauX (PHENIX), Paris F-75005, France.

Stable cell-like multisomes encapsulating the chemical oscillator Belousov-Zhabotinsky were engineered and organized in a linear network of diffusively-coupled chemical oscillators by using microfluidics. The multi-compartmentalization and the spatial configuration resulted in a new global synchronization scenario. After an initial induction interval, all the oscillators started to pulsate in phase with a halved period with respect to the natural one.
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http://dx.doi.org/10.1039/d0cc05046fDOI Listing
October 2020

A Flavone-Based Solvatochromic Probe with A Low Expected Perturbation Impact on the Membrane Physical State.

Molecules 2020 Jul 29;25(15). Epub 2020 Jul 29.

Department of Pharmacy, University of Salerno, 84084 Fisciano, Italy.

The study of the cell membrane is an ambitious and arduous objective since its physical state is regulated by a series of processes that guarantee its regular functionality. Among the different methods of analysis, fluorescence spectroscopy is a technique of election, non-invasive, and easy to use. Besides, molecular dynamics analysis (MD) on model membranes provides useful information on the possibility of using a new probe, following its positioning in the membrane, and evaluating the possible perturbation of the double layer. In this work, we report the rational design and the synthesis of a new fluorescent solvatochromic probe and its characterization in model membranes. The probe consists of a fluorescent aromatic nucleus of a 3-hydroxyflavone moiety, provided with a saturated chain of 18 carbon atoms and a zwitterionic head so to facilitate the anchoring to the polar heads of the lipid bilayer and avoid the complete internalization. It was possible to study the behavior of the probe in GUV model membranes by MD analysis and fluorescence microscopy, demonstrating that the new probe can efficiently be incorporated in the lipid bilayer, and give a color response, thanks to is solvatochromic properties. Moreover, MD simulation of the probe in the membrane supports the hypothesis of a reduced perturbation of the membrane physical state.
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http://dx.doi.org/10.3390/molecules25153458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7436088PMC
July 2020

Synthesis of PEG-Functionalized Amines Using Ruthenium-Catalyzed Hydrogen Borrowing.

Org Lett 2020 08 24;22(15):5890-5894. Epub 2020 Jul 24.

Pfizer Worldwide R&D, Eastern Point Road, Groton, Connecticut 06340, United States.

The polyethylene glycol (PEG) moiety has become increasingly important in medicinal chemistry. Herein, we describe the PEG functionalization of amines via hydrogen borrowing reductive amination. This was accomplished using the [Ru(-cymene)Cl] catalyst and phosphorus-containing ligand dppf or DPE to yield a variety of PEGylated primary and secondary amine products. Furthermore, we illustrate the utility of this method with the synthesis of quetiapine (Seroquel) in 62% isolated yield.
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http://dx.doi.org/10.1021/acs.orglett.0c01965DOI Listing
August 2020

Environmental and economic optima of solar home systems design: A combined LCA and LCC approach.

Sci Total Environ 2020 Nov 11;744:140569. Epub 2020 Jul 11.

University of Siena, R(2)ES Lab, Department of Biotechnology, Chemistry and Pharmacy, Via A. Moro, 2, Siena, Italy; CSGI, Center for Colloid and Surface Science, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Institute of Chemistry of Organometallic Compounds (CNR-ICCOM), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy.

This paper compares the economic and environmental optimal design of Solar Home Systems (SHSs) and explores the role of economic incentives (such as tariffs and technology costs) in approximating the two optima. To achieve that, we present a methodology for the environmental and economic evaluation of grid-connected SHSs: user-scale electric systems involving a photovoltaic (PV) power system and a battery energy storage system. The proposed methodology is based on a mixed integer linear programming (MILP) optimization, life cycle assessment and life cycle costing. This methodological framework is applied to a case study involving a typical SHS installation in Italy. The results of the environmental optimal design brought to the evaluation of a 3.25 kW PV assisted by 8.66 kWh of nickel cobalt manganese batteries, whereas the costs of the SHS are minimized by a small PV system (less than 1 kW). Results underline that the environmental optimal configurations rely on battery technologies, which entails a significant cost compared to the grid connection. In contrast, the economic optimal design solutions is less impactful than the grid mix both from an environmental and economic points of view. Thanks to a reduction of batteries and PV costs, the environmental impact of the economic optimal design is expected to decrease in the future.
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http://dx.doi.org/10.1016/j.scitotenv.2020.140569DOI Listing
November 2020

Hybrid giant lipid vesicles incorporating a PMMA-based copolymer.

Biochim Biophys Acta Gen Subj 2021 04 7;1865(4):129611. Epub 2020 Apr 7.

Department of Earth, Environmental and Physical Sciences - DEEP Sciences - Pian dei Mantellini 44, 53100 Siena, Italy.

Background: In recent years, there has been a growing interest in the formation of copolymer-lipid hybrid self-assemblies, which allow combining and improving the main features of pure lipid-based and copolymer-based systems known for their potential applications in the biomedical field. As the most common method used to obtain giant vesicles is electroformation, most systems so far used low T polymers for their flexibility at room temperature.

Methods: Copolymers used in the hybrid vesicles have been synthesized by a modified version of the ATRP, namely the Activators ReGenerated by Electron Transfer ATRP and characterized by NMR and DSC. Giant hybrid vesicles have been obtained using electroformation and droplet transfer method. Confocal fluorescence microscopy was used to image the vesicles.

Results: Electroformation enabled to obtain hybrid vesicles in a narrow range of compositions (15 mol% was the maximum copolymer content). This range could be extended by the use of a droplet transfer method, which enabled obtaining hybrid vesicles incorporating a methacrylate-based polymer in a wide range of compositions. Proof of the hybrid composition was obtained by fluorescence microscopy using labeled lipids and copolymers.

Conclusions: This work describes for the first time, to the best of our knowledge, the formation of giant hybrid polymer/lipid vesicles formed with such a content of a polymethylmethacrylate copolymer, the glass temperature of which is above room temperature.

General Significance: This work shows that polymer structures, more complex than the ones mostly employed, can be possibly included in giant hybrid vesicles by using the droplet transfer method. This will give easier access to functionalized and stimuli-responsive giant vesicles and to systems exhibiting a tunable permeability, these systems being relevant for biological and technological applications.
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http://dx.doi.org/10.1016/j.bbagen.2020.129611DOI Listing
April 2021

Fast Approximations of Activation Functions in Deep Neural Networks when using Posit Arithmetic.

Sensors (Basel) 2020 Mar 10;20(5). Epub 2020 Mar 10.

Department of Information Engineering, Università di Pisa, Via Girolamo Caruso, 16, 56122 Pisa PI, Italy.

With increasing real-time constraints being put on the use of Deep Neural Networks (DNNs) by real-time scenarios, there is the need to review information representation. A very challenging path is to employ an encoding that allows a fast processing and hardware-friendly representation of information. Among the proposed alternatives to the IEEE 754 standard regarding floating point representation of real numbers, the recently introduced Posit format has been theoretically proven to be really promising in satisfying the mentioned requirements. However, with the absence of proper hardware support for this novel type, this evaluation can be conducted only through a software emulation. While waiting for the widespread availability of the Posit Processing Units (the equivalent of the Floating Point Unit (FPU)), we can already exploit the Posit representation and the currently available Arithmetic-Logic Unit (ALU) to speed up DNNs by manipulating the low-level bit string representations of Posits. As a first step, in this paper, we present new arithmetic properties of the Posit number system with a focus on the configuration with 0 exponent bits. In particular, we propose a new class of Posit operators called L1 operators, which consists of fast and approximated versions of existing arithmetic operations or functions (e.g., hyperbolic tangent (TANH) and extended linear unit (ELU)) only using integer arithmetic. These operators introduce very interesting properties and results: (i) faster evaluation than the exact counterpart with a negligible accuracy degradation; (ii) an efficient ALU emulation of a number of Posits operations; and (iii) the possibility to vectorize operations in Posits, using existing ALU vectorized operations (such as the scalable vector extension of ARM CPUs or advanced vector extensions on Intel CPUs). As a second step, we test the proposed activation function on Posit-based DNNs, showing how 16-bit down to 10-bit Posits represent an exact replacement for 32-bit floats while 8-bit Posits could be an interesting alternative to 32-bit floats since their performances are a bit lower but their high speed and low storage properties are very appealing (leading to a lower bandwidth demand and more cache-friendly code). Finally, we point out how small Posits (i.e., up to 14 bits long) are very interesting while PPUs become widespread, since Posit operations can be tabulated in a very efficient way (see details in the text).
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http://dx.doi.org/10.3390/s20051515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7085555PMC
March 2020

Self-division of giant vesicles driven by an internal enzymatic reaction.

Chem Sci 2020 Mar 4;11(12):3228-3235. Epub 2020 Mar 4.

Department of Chemistry and Biology "A. Zambelli", University of Salerno Via Giovanni Paolo II 132, 84084 - Fisciano SA Italy

Self-division is one of the most common phenomena in living systems and one of the most important properties of life driven by internal mechanisms of cells. Design and engineering of synthetic cells from abiotic components can recreate a life-like function thus contributing to the understanding of the origin of life. Existing methods to induce the self-division of vesicles require external and non-autonomous triggers (temperature change and the addition of membrane precursors). Here we show that pH-responsive giant unilamellar vesicles on the micrometer scale can undergo self-division triggered by an internal autonomous chemical stimulus driven by an enzymatic (urea-urease) reaction coupled to a cross-membrane transport of the substrate, urea. The bilayer of the artificial cells is composed of a mixture of phospholipids (POPC, 1-palmitoyl-2-oleoyl--glycero-3-phosphatidylcholine) and oleic acid molecules. The enzymatic reaction increases the pH in the lumen of the vesicles, which concomitantly changes the protonation state of the oleic acid in the inner leaflet of the bilayer causing the removal of the membrane building blocks into the lumen of the vesicles thus decreasing the inner membrane area with respect to the outer one. This process coupled to the osmotic stress (responsible for the volume loss of the vesicles) leads to the division of a mother vesicle into two smaller daughter vesicles. These two processes must act in synergy; none of them alone can induce the division. Overall, our self-dividing system represents a step forward in the design and engineering of a complex autonomous model of synthetic cells.
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http://dx.doi.org/10.1039/c9sc05195cDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8157745PMC
March 2020

Membrane Structure Drives Synchronization Patterns in Arrays of Diffusively Coupled Self-Oscillating Droplets.

J Phys Chem Lett 2020 Mar 27;11(6):2014-2020. Epub 2020 Feb 27.

Department of Physical Science, Earth and Environment, University of Siena, Pian dei Mantellini, 44 53100 Siena (SI), Italy.

Networks of diffusively coupled inorganic oscillators, confined in nano- and microcompartments, are effective for predicting and understanding the global dynamics of those systems where the diffusion of activatory or inhibitory signals regulates the communication among different individuals. By taking advantage of a microfluidic device, we study the dynamics of arrays of diffusively coupled Belousov-Zhabotinsky (BZ) oscillators encapsulated in water-in-oil single emulsions. New synchronization patterns are induced and controlled by modulating the structural and chemical properties of the phospholipid-based biomimetic membranes via the introduction of specific dopants. Doping molecules do not alter the membrane basic backbone, but modify the lamellarity (and, in turn, the permeability) or interact chemically with the reaction intermediates. A transition from two-period clusters showing 1:2 period-locking to one-period antiphase synchronization is observed by decreasing the membrane lamellarity. An unsynchronized scenario is found when the dopant is able to interfere with chemical communication by reacting with the chemical messengers.
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http://dx.doi.org/10.1021/acs.jpclett.0c00072DOI Listing
March 2020

Life Cycle Inventory datasets for nano-grid configurations.

Data Brief 2020 Feb 28;28:104895. Epub 2019 Nov 28.

University of Siena, RES Lab, Department of Biotechnology, Chemistry and Pharmacy, Via A. Moro,2, Siena, Italy.

Datasets concerning some user-scale Smart Grids, named Nano-grids, are reported in this paper. First several Solar Home Systems composed of a photovoltaic plant, a backup generator and different types of lithium-ion batteries are provided. Then, the inventory analysis of hybrid Nano-grids integrating batteries and hydrogen storage is outlined according to different scenarios. These data inventory could be useful for any academic or stakeholder interested in reproducing this analysis and/or developing environmental sustainability assessment in the field of Smart Grids. For more insight, please see "Environmental analysis of a Nano-Grid: a Life Cycle Assessment" by Rossi F, Parisi M.L., Maranghi S., Basosi R., Sinicropi A. [1].
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http://dx.doi.org/10.1016/j.dib.2019.104895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6911934PMC
February 2020

Catalyst-Free Synthesis of Polysubstituted 5-Acylamino-1,3-Thiazoles via Hantzsch Cyclization of α-Chloroglycinates.

Molecules 2019 Oct 25;24(21). Epub 2019 Oct 25.

School of Science and Technology, Chemistry Division, University of Camerino, Camerino 62032, Italy.

A catalyst-free heterocyclization reaction of α-chloroglycinates with thiobenzamides or thioureas leading to 2,4-disubstituted-5-acylamino-1,3-thiazoles has been developed. The methodology provides straightforward access to valuable building blocks for pharmaceutically relevant compounds.
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http://dx.doi.org/10.3390/molecules24213846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864457PMC
October 2019

Environmental analysis of a nano-grid: A Life Cycle Assessment.

Sci Total Environ 2020 Jan 21;700:134814. Epub 2019 Oct 21.

University of Siena, R(2)ES Lab, Department of Biotechnology, Chemistry and Pharmacy, Via A. Moro, 2, Siena, Italy; CSGI, Center for Colloid and Surface Science, via della Lastruccia 3, 50019 Sesto Fiorentino, Italy; Institute of Chemistry of Organometallic Compounds (CNR-ICCOM), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy.

Renewable energy sources are fundamental to face the problem of climate changes. Unfortunately, some resources, such as wind and solar radiation, have fluctuations affecting the electrical grids stability. Energy storage systems can be used for a smart energy management to accumulate power from renewable sources. For such reason, these devices play a key role to achieve a sustainable electric system. On the other hand, they are affected by some environmental drawbacks mainly connected with the depletion of rare and expensive materials. Based on these considerations, in this study a nano-grid composed by a photovoltaic plant, a backup generator and an energy storage system is analysed by an environmental Life Cycle Assessment approach. A Solar Home System is designed, and its environmental profile is evaluated considering several Lithium-ion batteries. Among them, nickel-cobalt aluminium oxide cells resulted to be the most suitable solution for a Solar Home System (46.66 Pts/MWh). Moreover, a sensitivity analysis of the Solar Home System is performed and a hybrid energy storage plant integrating hydrogen and batteries is proposed to face the problem of seasonal solar radiation variability. Four scenarios having different gas pressure levels and lifespan of the devices are considered. Results show that currently the most sustainable configuration is represented by the Solar Home System, but in the future a hybrid nano-grid equipped with 700 bar hydrogen storage might be the best off-grid configuration for minimizing the impact on the environment (37.77 Pts/MWh). Extending the perspective of our analysis to future on-grid potential configurations, an efficient connection of the Solar Home System with a smart-grid is assessed as it looks more sustainable than other off-grid solutions (22.81 Pts/MWh).
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http://dx.doi.org/10.1016/j.scitotenv.2019.134814DOI Listing
January 2020

A Novel Platform to Define Chemotherapy Templates and Their Prescriptions.

Stud Health Technol Inform 2019 Aug;264:1739-1740

Software Engineer at Cloodie S.A., Buenos Aires, Argentina.

Medication errors have been identified as a major type of medical errors. Chemotherapy medication errors that occur in the prescription phase appear to be related to more significant adverse outcomes. The use of pre-printed templates increases patient safety. The functionalities required for the prescription of chemotherapy are not usually part of Clinical Physician Order Entry. The implementation of electronic chemotherapy templates will reduce the prescription errors.
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http://dx.doi.org/10.3233/SHTI190624DOI Listing
August 2019

Multivariate statistical analysis of chemical and electrochemical oscillators for an accurate frequency selection.

Phys Chem Chem Phys 2019 Aug 30;21(30):16423-16434. Epub 2019 May 30.

Institute of Chemistry, University of Campinas, CEP 13083-970, Campinas, SP, Brazil. and Center for Innovation on New Energies, University of Campinas, CEP 13083-841, Campinas, SP, Brazil.

The effect of experimental parameters on the frequency of chemical oscillators has been systematically studied since the first observations of clock reactions. The approach is mainly based on univariate changes in one specific parameter while others are kept constant. The frequency is then monitored and the effect of each parameter is discussed separately. This type of analysis, however, does not take into account the multiple interactions among the controllable parameters and the synergic responses on the oscillation frequency. We have carried out a multivariate statistical analysis of chemical (BZ-ferroin catalyzed reaction) and electrochemical (Cu/CuO cathodic deposition) oscillators and identified the contributions of the experimental parameters on frequency variations. The BZ reaction presented a strong dependence on the initial concentration of sodium bromate and temperature, resulting in a frequency increase. The concentration of malonic acid, the organic substrate, affects the system but with lower intensity compared with the combination of sodium bromate and temperature. On the other hand, the Cu/CuO electrochemical oscillator was shown to be less sensitive to changes in the temperature. The applied current density and pH were the two parameters which most perturbed the system. Interestingly, the frequency behaved nonmonotonically with a quadratic dependence. The multivariate analysis of both oscillators exhibited significant differences - while the homogenous oscillator displayed a linear dependence with the factors, the heterogeneous one revealed a more complex dependence with quadratic terms. Our results may contribute, for instance, in the synthesis of self-organized materials in which an accurate frequency selection is required and, depending on its value, different physicochemical properties are obtained.
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http://dx.doi.org/10.1039/c9cp01998gDOI Listing
August 2019

ADHD in adults: clinical subtypes and associated characteristics.

Riv Psichiatr 2019 Mar-Apr;54(2):84-89

Dipartimento di Salute Mentale e Dipendenze, ASST Fatebenefratelli-Sacco, Milan, Italy.

Introduction: Attention Deficit Hyperactivity Disorder (ADHD) is an early onset clinical condition characterized by attention difficulties, hyperactivity and impulsivity which can persist across the lifespan, significantly influencing the evolutionary course and facilitating the rise of psychiatric comorbidities. The presence of different ADHD subtypes in adults is a heterogeneity factor to be recognized in order to orient prognosis and treatment, as indicated by studies that described differences in the characterization of different subtypes in relation to both severity and comorbidities.

Materials And Methods: In the present study we evaluated the socio-demographic and clinical characteristics of a sample of adults with ADHD and the characteristics associated with the different disorder subtypes. We described 60 patients aged between 18 and 65 years (mean age 34.1) with primary diagnosis of ADHD consecutively admitted to the Regional Centre for diagnosis and treatment of ADHD in adults in Milan.

Results: We observed high severity of symptoms and low quality of life, in particular in the "life outlook" dimension. The subtypes distribution was the following: 18.3% inattentive subtype, 8.3% hyperactive/impulsive subtype and 70% combined subtype. The hyperactive/impulsive subtype showed a significantly higher frequency in females, while the inattentive subtype was more frequent in males. Patients with the hyperactive/impulsive subtype showed worse quality of life and more frequent anxiety disorders.

Conclusions: Considering the different clinical profiles among various subtypes, these data add relevance to subtypes classification of adult ADHD.
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http://dx.doi.org/10.1708/3142.31249DOI Listing
December 2019

The role of the tyrosine kinase Wzc (Sll0923) and the phosphatase Wzb (Slr0328) in the production of extracellular polymeric substances (EPS) by Synechocystis PCC 6803.

Microbiologyopen 2019 06 23;8(6):e00753. Epub 2019 Jan 23.

i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.

Many cyanobacteria produce extracellular polymeric substances (EPS) mainly composed of heteropolysaccharides with unique characteristics that make them suitable for biotechnological applications. However, manipulation/optimization of EPS biosynthesis/characteristics is hindered by a poor understanding of the production pathways and the differences between bacterial species. In this work, genes putatively related to different pathways of cyanobacterial EPS polymerization, assembly, and export were targeted for deletion or truncation in the unicellular Synechocystis sp. PCC 6803. No evident phenotypic changes were observed for some mutants in genes occurring in multiple copies in Synechocystis genome, namely ∆wzy (∆sll0737), ∆wzx (∆sll5049), ∆kpsM (∆slr2107), and ∆kpsM∆wzy (∆slr2107∆sll0737), strongly suggesting functional redundancy. In contrast, Δwzc (Δsll0923) and Δwzb (Δslr0328) influenced both the amount and composition of the EPS, establishing that Wzc participates in the production of capsular (CPS) and released (RPS) polysaccharides, and Wzb affects RPS production. The structure of Wzb was solved (2.28 Å), revealing structural differences relative to other phosphatases involved in EPS production and suggesting a different substrate recognition mechanism. In addition, Wzc showed the ATPase and autokinase activities typical of bacterial tyrosine kinases. Most importantly, Wzb was able to dephosphorylate Wzc in vitro, suggesting that tyrosine phosphorylation/dephosphorylation plays a role in cyanobacterial EPS production.
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http://dx.doi.org/10.1002/mbo3.753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6562117PMC
June 2019

Influence of the synthesis method on the catalytic activity of mayenite for the oxidation of gas-phase trichloroethylene.

Sci Rep 2019 Jan 23;9(1):425. Epub 2019 Jan 23.

Instituto de Tecnología Química, Universitat Politècnica de València-CSIC, Valencia, 46022, Spain.

Catalytic oxidation of trichloroethylene (TCE) in heterogeneous phase (gas-solid) is an effective strategy for the conversion of this pollutant in less harmful compounds, namely CO, CO and HCl. In this work, we have studied the use of mayenite, a cost-effective material, as an active catalyst for the TCE conversion. In particular, we have assessed the influence of the mayenite synthesis method (hydrothermal, sol-gel and ceramic) on the reaction performance. The materials have been characterized by different techniques, such as XRD, N-sorption (BET), TPR, Raman spectroscopy, FESEM-EDX and TEM. The analysis of the light-off curves and product distribution, has shown that the use of the hydrothermal method for the mayenite synthesis results in the most active and selective catalyst. This has been related with a higher surface area and with a higher concentration of oxygen anions in the mayenite prepared by this method. It has been found that the presence of water in the stream do not influence the catalytic performance of the material. A mechanism for the reaction and for the partial deactivation of the catalyst has been proposed.
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http://dx.doi.org/10.1038/s41598-018-36708-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344594PMC
January 2019

Bioactivity and Structural Properties of Novel Synthetic Analogues of the Protozoan Toxin Climacostol.

Toxins (Basel) 2019 01 15;11(1). Epub 2019 Jan 15.

Laboratory of Protistology and Biology Education, Department of Education, Cultural Heritage, and Tourism (ECHT), Università degli Studi di Macerata, 62100 Macerata, Italy.

Climacostol (5-[(2)-non-2-en-1-yl]benzene-1,3-diol) is a resorcinol produced by the protozoan for defence against predators. It exerts a potent antimicrobial activity against bacterial and fungal pathogens, inhibits the growth of several human and rodent tumour cells, and is now available by chemical synthesis. In this study, we chemically synthesized two novel analogues of climacostol, namely, 2-methyl-5 [(2)-non-2-en-1-yl]benzene-1,3-diol (AN1) and 5-[(2)-non-2-en-1-yl]benzene-1,2,3-triol (AN2), with the aim to increase the activity of the native toxin, evaluating their effects on prokaryotic and free-living protists and on mammalian tumour cells. The results demonstrated that the analogue bearing a methyl group (AN1) in the aromatic ring exhibited appreciably higher toxicity against pathogen microbes and protists than climacostol. On the other hand, the analogue bearing an additional hydroxyl group (AN2) in the aromatic ring revealed its ability to induce programmed cell death in protistan cells. Overall, the data collected demonstrate that the introduction of a methyl or a hydroxyl moiety to the aromatic ring of climacostol can effectively modulate its potency and its mechanism of action.
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http://dx.doi.org/10.3390/toxins11010042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356496PMC
January 2019
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