Publications by authors named "M Crescenzi"

197 Publications

Structural basis of ubiquitination mediated by protein splicing in early Eukarya.

Biochim Biophys Acta Gen Subj 2021 May 11;1865(5):129844. Epub 2021 Jan 11.

Institute of Molecular Biology and Pathology of The National Research Council of Italy (CNR), P.le A. Moro 5, 00185 Rome, Italy. Electronic address:

Background: Inteins are intervening proteins, which are known to perform protein splicing. The reaction results in the production of an intein domain and an inteinless protein, which shows no trace of the insertion. BIL2 is part of the polyubiquitin locus of Tetrahymena thermophila (BUBL), where two bacterial-intein-like (BIL) domains lacking the C + 1 nucleophile, are flanked by two independent ubiquitin-like domains (ubl4/ubl5).

Methods: We solved the X-ray structures of BIL2 in both the inactive and unprecedented, zinc-induced active, forms. Then, we characterized by mass spectrometry the BUBL splicing products in the absence and in the presence of T.thRas-GTPase. Finally, we investigated the effect of ubiquitination on T.thRas-GTPase by molecular dynamics simulations.

Results: The structural analysis demonstrated that zinc-induced conformational change activates protein splicing. Moreover, mass spectrometry characterization of the splicing products shed light on the possible function of BIL2, which operates as a "single-ubiquitin-dispensing-platform", allowing the conjugation, via isopeptide bond formation (K(εNH)-C-ter), of ubl4 to either ubl5 or T.thRas-GTPase. Lastly, we demonstrated that T.thRas-GTPase ubiquitination occurs in proximity of the nucleotide binding pocket and stabilizes the protein active state.

Conclusions: We demonstrated that BIL2 is activated by zinc and that protein splicing induced by this intein does not take place through classical or aminolysis mechanisms but via formation of a covalent isopeptide bond, causing the ubiquitination of endogenous substrates such as T.thRas-GTPase.

General Significance: In this "enzyme-free" ubiquitination mechanism the isopeptide formation, which canonically requires E1-E2-E3 enzymatic cascade and constitutes the alphabet of ubiquitin biology, is achieved in a single, concerted step without energy consumption.
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http://dx.doi.org/10.1016/j.bbagen.2021.129844DOI Listing
May 2021

Large-area, high-responsivity, fast and broadband graphene/n-Si photodetector.

Nanotechnology 2021 Apr;32(15):155504

Dipartimento di Fisica, Università di Roma 'Tor Vergata', 00133 Roma, Italy. INFN, Università di Roma 'Tor Vergata', 00133 Roma, Italy.

A graphene/Si heterojunction device has been realized to overcome many different requests necessary to make it a versatile, widely used and competitive detector. The obtained photodetectors, which operate at room temperature, are sensitive in the spectral region from ultraviolet (240 nm) to infrared (2000 nm) and they can be used in different configurations that allow a high responsivity up to 10 A W, a rise time of a few nanoseconds, an external quantum efficiency greater than 300%, and a linear response for different light sources. This is allowed by the high quality of the graphene deposited on a large area of 8 mm, and by the interdigitated design of the contacts, both preserving the excellent properties of graphene when switching from nanoscale to macroscopic dimensions of commonly used devices.
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http://dx.doi.org/10.1088/1361-6528/abd789DOI Listing
April 2021

Administration of Human MSC-Derived Extracellular Vesicles for the Treatment of Primary Sclerosing Cholangitis: Preclinical Data in MDR2 Knockout Mice.

Int J Mol Sci 2020 Nov 23;21(22). Epub 2020 Nov 23.

Department of Biomedical Sciences, University of Padova and Fondazione Istituto di Ricerca Pediatrica-Città della Speranza, 35127 Padova, Italy.

Primary Sclerosing Cholangitis (PSC) is a progressive liver disease for which there is no effective medical therapy. PSC belongs to the family of immune-mediated biliary disorders and it is characterized by persistent biliary inflammation and fibrosis. Here, we explored the possibility of using extracellular vesicles (EVs) derived from human, bone marrow mesenchymal stromal cells (MSCs) to target liver inflammation and reduce fibrosis in a mouse model of PSC. Five-week-old male FVB.129P2-Abcb mice were intraperitoneally injected with either 100 µL of EVs (± 9.1 × 10 particles/mL) or PBS, once a week, for three consecutive weeks. One week after the last injection, mice were sacrificed and liver and blood collected for flow cytometry analysis and transaminase quantification. In FVB.129P2-Abcb4 mice, EV administration resulted in reduced serum levels of alkaline phosphatase (ALP), bile acid (BA), and alanine aminotransferase (ALT), as well as in decreased liver fibrosis. Mechanistically, we observed that EVs reduce liver accumulation of both granulocytes and T cells and dampen VCAM-1 expression. Further analysis revealed that the therapeutic effect of EVs is accompanied by the inhibition of NFkB activation in proximity of the portal triad. Our pre-clinical experiments suggest that EVs isolated from MSCs may represent an effective therapeutic strategy to treat patients suffering from PSC.
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http://dx.doi.org/10.3390/ijms21228874DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7700340PMC
November 2020

Gas Sensing with Solar Cells: The Case of NH Detection through Nanocarbon/Silicon Hybrid Heterojunctions.

Nanomaterials (Basel) 2020 Nov 21;10(11). Epub 2020 Nov 21.

I-Lamp and Dipartimento di Matematica e Fisica, Università Cattolica del Sacro Cuore, via dei Musei 41, 25121 Brescia, Italy.

Photovoltaic (PV) cells based on single-walled carbon nanotube (SWCNT)/silicon (Si) and multiwalled carbon nanotube (MWCNT)/Si junctions were tested under exposure to NH in the 0-21 ppm concentration range. The PV cell parameters remarkably changed upon NH exposure, suggesting that these junctions, while being operated as PV cells, can react to changes in the environment, thereby acting as NH gas sensors. Indeed, by choosing the open-circuit voltage, V, parameter as read-out, it was found that these cells behaved as gas sensors, operating at room temperature with a response higher than chemiresistors developed on the same layers. The sensitivity was further increased when the whole current-voltage (I-V) curve was collected and the maximum power values were tracked upon NH exposure.
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http://dx.doi.org/10.3390/nano10112303DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7700682PMC
November 2020

Spastin recovery in hereditary spastic paraplegia by preventing neddylation-dependent degradation.

Life Sci Alliance 2020 12 26;3(12). Epub 2020 Oct 26.

Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), c/o Sapienza University, Rome, Italy

Hereditary Spastic Paraplegia (HSP) is a neurodegenerative disease most commonly caused by autosomal dominant mutations in the gene encoding the microtubule-severing protein spastin. We hypothesise that -HSP is attributable to reduced spastin function because of haploinsufficiency; thus, therapeutic approaches which elevate levels of the wild-type spastin allele may be an effective therapy. However, until now, how spastin levels are regulated is largely unknown. Here, we show that the kinase HIPK2 regulates spastin protein levels in proliferating cells, in differentiated neurons and in vivo. Our work reveals that HIPK2-mediated phosphorylation of spastin at S268 inhibits spastin K48-poly-ubiquitination at K554 and prevents its neddylation-dependent proteasomal degradation. In a spastin RNAi neuronal cell model, overexpression of HIPK2, or inhibition of neddylation, restores spastin levels and rescues neurite defects. Notably, we demonstrate that spastin levels can be restored pharmacologically by inhibiting its neddylation-mediated degradation in neurons derived from a spastin mouse model of HSP and in patient-derived cells, thus revealing novel therapeutic targets for the treatment of -HSP.
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http://dx.doi.org/10.26508/lsa.202000799DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7652396PMC
December 2020

Functional rewiring across spinal injuries via biomimetic nanofiber scaffolds.

Proc Natl Acad Sci U S A 2020 10 30;117(41):25212-25218. Epub 2020 Sep 30.

Neurobiology Department, International School for Advanced Studies (SISSA/ISAS), Trieste 34136, Italy;

The regrowth of severed axons is fundamental to reestablish motor control after spinal-cord injury (SCI). Ongoing efforts to promote axonal regeneration after SCI have involved multiple strategies that have been only partially successful. Our study introduces an artificial carbon-nanotube based scaffold that, once implanted in SCI rats, improves motor function recovery. Confocal microscopy analysis plus fiber tracking by magnetic resonance imaging and neurotracer labeling of long-distance corticospinal axons suggest that recovery might be partly attributable to successful crossing of the lesion site by regenerating fibers. Since manipulating SCI microenvironment properties, such as mechanical and electrical ones, may promote biological responses, we propose this artificial scaffold as a prototype to exploit the physics governing spinal regenerative plasticity.
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http://dx.doi.org/10.1073/pnas.2005708117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7568334PMC
October 2020

Stoichiometric BiSe topological insulator ultra-thin films obtained through a new fabrication process for optoelectronic applications.

Nanoscale 2020 Jun 3;12(23):12405-12415. Epub 2020 Jun 3.

Dipartimento di Fisica, Università di Roma "Tor Vergata", 00133 Roma, Italy.

A new fabrication process is developed for growing BiSe topological insulators in the form of nanowires/nanobelts and ultra-thin films. It consists of two consecutive procedures: first BiSe nanowires/nanobelts are deposited by standard catalyst free vapour-solid deposition on different substrates positioned inside a quartz tube. Then, the BiSe, stuck on the inner surface of the quartz tube, is re-evaporated and deposited in the form of ultra-thin films on new substrates at a temperature below 100 °C, which is of relevance for flexible electronic applications. The method is new, quick, very inexpensive, easy to control and allows obtaining films with different thickness down to one quintuple layer (QL) during the same procedure. The composition and the crystal structure of both the nanowires/nanobelts and the thin films are analysed by different optical, electronic and structural techniques. For the films, scanning tunnelling spectroscopy shows that the Fermi level is positioned in the middle of the energy bandgap as a consequence of the achieved correct stoichiometry. Ultra-thin films, with thickness in the range 1-10 QLs deposited on n-doped Si substrates, show good rectifying properties suitable for their use as photodetectors in the ultra violet-visible-near infrared wavelength range.
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http://dx.doi.org/10.1039/d0nr02725aDOI Listing
June 2020

Phytoremediation potential of the duckweeds Lemna minuta and Lemna minor to remove nutrients from treated waters.

Environ Sci Pollut Res Int 2020 May 22;27(13):15806-15814. Epub 2020 Feb 22.

Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Via Salaria Km 29,300, 00015, Monterotondo Scalo, Rome, Italy.

Phytoremediation potential of duckweeds (Lemna minuta, Lemna minor) to remove nutrients from simulated wastewater was analyzed. In two separate experiments, the two species were grown for 28 days in waters enriched with nitrate and phosphate to simulate nutrient concentrations of domestic wastewater. Water physical and chemical measurements (temperature, pH, conductivity, oxygen) and plant physiological and biochemical analysis (biomass, relative growth rate-RGR, nutrient and chlorophyll contents, peroxidative damage, bioconcentration factor-BCF) were made to test and compare the phytoremediation capacity of the two Lemna species. L. minuta biomass increased almost tenfold during the time-course of the treatment resulting in a doubling of the mat thickness and a RGR of 0.083 ± 0.001 g/g day. Maximum frond content of phosphate was reached by day 21 (increase over 165%) and nitrate by day 7 (10%). According to the BCF results (BCF > 1000), L. minuta was a hyperaccumulator for both nutrients. On the other hand, L. minor biomass and mat thickness decreased continuously during incubation (RGR = - 0.039 ± 0.004 g/g day). In L. minor fronds, phosphate content increased until day 14, after which there was a decrease until the end of the incubation. Frond nitrate content significantly decreased by day 7, but then remained relatively constant until the end of the experiment. L. minor proved to be hyperaccumulator for phosphates, but not for nitrates. Results indicated L. minuta has a greater potential than L. minor to remove both nutrients by bioaccumulation, especially phosphates, demonstrated also by better physiological and biochemical responses. However, during the incubation, the chlorophyll content of L. minuta mat did continuously decrease and peroxidative damage had increased until day 14, indicating that the system was under some kind of stress. Strategies to avoid this stress were discussed.
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http://dx.doi.org/10.1007/s11356-020-08045-3DOI Listing
May 2020

Enhanced Expression of CD47 Is Associated With Off-Target Resistance to Tyrosine Kinase Inhibitor Gefitinib in NSCLC.

Front Immunol 2019 31;10:3135. Epub 2020 Jan 31.

Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana," University of Salerno, Baronissi, Italy.

Mutual interactions between cancer cells and the tumor microenvironment importantly contribute to the development of tyrosine kinase inhibitor (TKI) resistance in patients affected by EGFR-mutant NSCLC. In particular, immune recognition-associated proteins with impact on tumor cell clearance through phagocytosis, such as CD47 and calreticulin, could contribute to adaptive resistance and immune escape. Preclinical studies targeting the anti-phagocytic CD47 molecule showed promising results in different cancer types including lung cancer, but no data are available on its role in patients acquiring resistance to EGFR TKI treatment. We analyzed the functional contribution of CD47 and calreticulin to immune surveillance and evasion in a panel of NSCLC cell lines carrying sensitizing or resistant mutations in the EGFR gene, following treatment with the TKI gefitinib and after development of gefitinib resistance. While CD47 and calreticulin protein levels were markedly variable in both EGFR-mutant and wild-type cell lines, analysis of NSCLC transcriptomic dataset revealed selective overexpression of CD47 in patients carrying EGFR mutations. EGFR inhibition significantly reduced CD47 expression on the surface of pre-apoptotic cells, favoring more efficient engulfment of cancer cells by monocyte-derived dendritic cells. This was not necessarily associated with augmented surface exposure of calreticulin or other molecular markers of immunogenic cell death. Moreover, CD47 expression became up-regulated following drug resistance development, and blocking of this protein by a specific monoclonal antibody increased the clearance of EGFR-TKI resistant cells by phagocytes. Our study supports CD47 neutralization by specific monoclonal antibody as a promising immunotherapeutic option for naïve and resistant EGFR-mutant NSCLCs.
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http://dx.doi.org/10.3389/fimmu.2019.03135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7004973PMC
November 2020

Dramatic efficiency boost of single-walled carbon nanotube-silicon hybrid solar cells through exposure to ppm nitrogen dioxide in air: An ab-initio assessment of the measured device performances.

J Colloid Interface Sci 2020 Apr 14;566:60-68. Epub 2020 Jan 14.

Surface Science and Spectroscopy Lab @ I-Lamp, and Dipartimento di Matematica e Fisica, Università Cattolica del Sacro Cuore, Brescia, Italy. Electronic address:

We observed a 73% enhancement of the power conversion efficiency (PCE) of a photovoltaic cell based on a single wall carbon nanotube/Si hybrid junction after exposing the device to a limited amount (10 ppm) of NO diluted in dry air. On the basis of a computational modeling of the junction, this enhancement is discussed in terms of both carbon nanotube (CNT) p-doping, induced by the interaction with the oxidizing molecules, and work function changes across the junction. Unlike studies so far reported, where the PCE enhancement was correlated only qualitatively to CNT doping, our study (i) provides a novel and reversible path to tune and considerably enhance the cell efficiency by a few ppm gas exposure, and (ii) shows computational results that quantitatively relate the observed effects to the electrostatics of the cell through a systematic calculation of the work function. These effects have been cross-checked by exposing the cell to reducing molecules (i.e·NH) that resulted to be detrimental to the cell efficiency, consistently with the theoretical ab-initio calculations.
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http://dx.doi.org/10.1016/j.jcis.2020.01.038DOI Listing
April 2020

No metagenomic evidence of tumorigenic viruses in cancers from a selected cohort of immunosuppressed subjects.

Sci Rep 2019 12 24;9(1):19815. Epub 2019 Dec 24.

Italian National Institute of Health, Core Facilities, Rome, 00161, Italy.

The possible existence of yet undiscovered human tumorigenic viruses is still under scrutiny. The development of large-scale sequencing technologies, coupled with bioinformatics techniques for the characterization of metagenomic sequences, have provided an invaluable tool for the detection of unknown, infectious, tumorigenic agents, as demonstrated by several recent studies. However, discoveries of novel viruses possibly associated with tumorigenesis are scarce at best. Here, we apply a rigorous bioinformatics workflow to investigate in depth tumor metagenomes from a small but carefully selected cohort of immunosuppressed patients. While a variegated bacterial microbiome was associated with each tumor, no evidence of the presence of putative oncoviruses was found. These results are consistent with the major findings of several recent papers and suggest that new human tumorigenic viruses are not common even in immunosuppressed populations.
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http://dx.doi.org/10.1038/s41598-019-56240-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6930283PMC
December 2019

HIPK2 Phosphorylates the Microtubule-Severing Enzyme Spastin at S268 for Abscission.

Cells 2019 07 5;8(7). Epub 2019 Jul 5.

Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR), c/o Sapienza University, 00185 Rome, Italy.

Abscission is the final step of cell division, mediating the physical separation of the two daughter cells. A key player in this process is the microtubule-severing enzyme spastin that localizes at the midbody where its activity is crucial to cut microtubules and culminate the cytokinesis. Recently, we demonstrated that HIPK2, a multifunctional kinase involved in several cellular pathways, contributes to abscission and prevents tetraploidization. Here, we show that HIPK2 binds and phosphorylates spastin at serine 268. During cytokinesis, the midbody-localized spastin is phosphorylated at S268 in HIPK2-proficient cells. In contrast, no spastin is detectable at the midbody in HIPK2-depleted cells. The non-phosphorylatable spastin-S268A mutant does not localize at the midbody and cannot rescue HIPK2-depleted cells from abscission defects. In contrast, the phosphomimetic spastin-S268D mutant localizes at the midbody and restores successful abscission in the HIPK2-depleted cells. These results show that spastin is a novel target of HIPK2 and that HIPK2-mediated phosphorylation of spastin contributes to its midbody localization for successful abscission.
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http://dx.doi.org/10.3390/cells8070684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6678495PMC
July 2019

Type E Botulinum Neurotoxin-Producing Clostridium butyricum Strains Are Aerotolerant during Vegetative Growth.

mSystems 2019 Mar-Apr;4(2). Epub 2019 Apr 30.

Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy.

Clostridium butyricum, the type species of the genus , is considered an obligate anaerobe, yet it has been shown to grow in the presence of oxygen. strains atypically producing the botulinum neurotoxin type E are the leading cause of type E human botulism in Italy. Here, we show that type E botulinum neurotoxin-producing strains growing exponentially were able to keep growing and producing toxin upon exposure to air, although less efficiently than under ideal oxygen-depleted conditions. Bacterial growth in air was maintained when the initial cell density was higher than 10 cells/ml. No spores were detected in the cultures aerated for 5 h. To understand the biological mechanisms allowing the adaptation of vegetative cells of type E to oxygen, we compared the proteome and metabolome profiles of the clostridial cultures grown for 5 h under either aerated or anaerobic conditions. The results indicated that bacterial cells responded to oxygen stress by slowing growth and modulating the expression of proteins involved in carbohydrate uptake and metabolism, redox homeostasis, DNA damage response, and bacterial motility. Moreover, the ratio of acetate to butyrate was significantly higher under aeration. This study demonstrates for the first time that a botulinum neurotoxin-producing can withstand oxygen during vegetative growth. Botulinum neurotoxins, the causative agents of the potentially fatal disease of botulism, are produced by certain strains during vegetative growth, usually in anaerobic environments. Our findings indicate that, contrary to current understanding, the growth of neurotoxigenic strains and botulinum neurotoxin type E production can continue upon transfer from anaerobic to aerated conditions and that adaptation of strains to oxygenated environments requires global changes in proteomic and metabolic profiles. We hypothesize that aerotolerance might constitute an unappreciated factor conferring physiological advantages on some botulinum toxin-producing clostridial strains, allowing them to adapt to otherwise restrictive environments.
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http://dx.doi.org/10.1128/mSystems.00299-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6495232PMC
April 2019

Scanning tunneling microscopy and Raman evidence of silicene nanosheets intercalated into graphite surfaces at room temperature.

Nanoscale 2019 Mar;11(13):6145-6152

V. E. Lashkaryov Institute of Semiconductor Physics, National Academy of Sciences of Ukraine, Ukraine.

Highly oriented pyrolytic graphite (HOPG) is an inert substrate with a structural honeycomb lattice, well suited for the growth of a two-dimensional (2D) silicene layer. It was reported that when Si atoms are deposited on the HOPG surface at room temperature, they arrange into two configurations: silicene nanosheets and three-dimensional clusters. In this work we demonstrate, by using scanning tunneling microscopy (STM) and Raman spectroscopy, that a third configuration stabilizes in the form of Si 2D nanosheets intercalated below the first top layer of carbon atoms. The Raman spectra reveal a structure located at 538 cm-1 which we ascribe to the presence of sp2 Si hybridization. Moreover, the silicon deposition induces several modifications in the graphite D and G Raman modes, which we interpret as experimental evidence of the intercalation of the silicene nanosheets. The Si atom intercalation at room temperature takes place at the HOPG step edges and it detaches only the outermost graphite layer inducing a strong tensile strain mainly concentrated on the edges of the silicene nanosheets. Theoretical calculations of the structure and energetic viability of the silicene nanosheets and of the strain distribution on the outermost graphite layer and its influence on the Raman resonances support the STM and Raman observations.
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http://dx.doi.org/10.1039/c9nr00343fDOI Listing
March 2019

Carbon nanotube sponges as tunable materials for electromagnetic applications.

Nanotechnology 2018 Sep 26;29(37):375202. Epub 2018 Jun 26.

Institute for Nuclear Problems, Belarusian State University, Bobruiskaya 11, 220050 Minsk, Belarus. Tomsk State University, Lenin Avenue 36, 634050, Tomsk, Russia.

The microwave conductivity and permittivity of both single-walled and multi-walled carbon nanotube (SWCNT and MWCNT) sponges were measured while compressing the samples. Compression leads to a huge variation of the absorptance, reflectance, and transmittance of the samples. The dependence of the microwave conductivity on the sponge density follows a power-law relation with exponents 1.7 ± 0.1 and 2.0 ± 0.2 for MWCNT and SWCNT sponges, respectively. These exponents can be decreased slightly by the addition of a non-conducting component which partly electrically separates adjacent tubes within the samples. The conductivity of MWCNT sponge was measured in the terahertz range while heating in air from 300 to 513 K and it increased due to an increase of a number of conducting channels in MWCNTs.
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http://dx.doi.org/10.1088/1361-6528/aacf3cDOI Listing
September 2018

HIPK2 and extrachromosomal histone H2B are separately recruited by Aurora-B for cytokinesis.

Oncogene 2018 06 22;37(26):3562-3574. Epub 2018 Mar 22.

Unit of Cellular Networks and Molecular Therapeutic Targets, Regina Elena National Cancer Institute-IRCCS, Rome, 00144, Italy.

Cytokinesis, the final phase of cell division, is necessary to form two distinct daughter cells with correct distribution of genomic and cytoplasmic materials. Its failure provokes genetically unstable states, such as tetraploidization and polyploidization, which can contribute to tumorigenesis. Aurora-B kinase controls multiple cytokinetic events, from chromosome condensation to abscission when the midbody is severed. We have previously shown that HIPK2, a kinase involved in DNA damage response and development, localizes at the midbody and contributes to abscission by phosphorylating extrachromosomal histone H2B at Ser14. Of relevance, HIPK2-defective cells do not phosphorylate H2B and do not successfully complete cytokinesis leading to accumulation of binucleated cells, chromosomal instability, and increased tumorigenicity. However, how HIPK2 and H2B are recruited to the midbody during cytokinesis is still unknown. Here, we show that regardless of their direct (H2B) and indirect (HIPK2) binding of chromosomal DNA, both H2B and HIPK2 localize at the midbody independently of nucleic acids. Instead, by using mitotic kinase-specific inhibitors in a spatio-temporal regulated manner, we found that Aurora-B kinase activity is required to recruit both HIPK2 and H2B to the midbody. Molecular characterization showed that Aurora-B directly binds and phosphorylates H2B at Ser32 while indirectly recruits HIPK2 through the central spindle components MgcRacGAP and PRC1. Thus, among different cytokinetic functions, Aurora-B separately recruits HIPK2 and H2B to the midbody and these activities contribute to faithful cytokinesis.
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http://dx.doi.org/10.1038/s41388-018-0191-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6021368PMC
June 2018

The enzymatic processing of α-dystroglycan by MMP-2 is controlled by two anchoring sites distinct from the active site.

PLoS One 2018 15;13(2):e0192651. Epub 2018 Feb 15.

CNR Institute for Molecular Recognition, Roma Italy.

Dystroglycan (DG) is a membrane receptor, belonging to the dystrophin-glycoprotein complex (DGC) and formed by two subunits, α-dystroglycan (α-DG) and β-dystroglycan (β -DG). The C-terminal domain of α-DG and the N-terminal extracellular domain of β -DG are connected, providing a link between the extracellular matrix and the cytosol. Under pathological conditions, such as cancer and muscular dystrophies, DG may be the target of metalloproteinases MMP-2 and MMP-9, contributing to disease progression. Previously, we reported that the C-terminal domain α-DG (483-628) domain is particularly susceptible to the catalytic activity of MMP-2; here we show that the α-DG 621-628 region is required to carry out its complete digestion, suggesting that this portion may represent a MMP-2 anchoring site. Following this observation, we synthesized an α-DG based-peptide, spanning the (613-651) C-terminal region. The analysis of the kinetic and thermodynamic parameters of the whole and the isolated catalytic domain of MMP-2 (cdMMP-2) has shown its inhibitory properties, indicating the presence of (at least) two binding sites for the peptide, both located within the catalytic domain, only one of the two being topologically distinct from the catalytic active groove. However, the different behavior between whole MMP-2 and cdMMP-2 envisages the occurrence of an additional binding site for the peptide on the hemopexin-like domain of MMP-2. Interestingly, mass spectrometry analysis has shown that α-DG (613-651) peptide is cleavable even though it is a very poor substrate of MMP-2, a feature that renders this molecule a promising template for developing a selective MMP-2 inhibitor.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0192651PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813964PMC
April 2018

Sex-dependent differences in inflammatory responses during liver regeneration in a murine model of acute liver injury.

Clin Sci (Lond) 2018 01 25;132(2):255-272. Epub 2018 Jan 25.

Department of Surgery, Oncology and Gastroenterology, Gastroenterology/Multivisceral Transplant Section, University/Hospital Padova, via Giustiniani 2, 35128, Padova, Italy

A sexual dimorphism in liver inflammation and repair was previously demonstrated. Its cellular dissection in the course of acute liver injury (ALI) was explored. BALB/c mice were treated with carbon tetrachloride (CCl) by intraperitoneal injection and killed after 3, 5, and 8 days. Histological and hepatic cell population analyses were performed. The correlation between androgen receptor (AR) expression and liver recruited inflammatory cells was investigated by treatment with the AR antagonist flutamide. Additionally, patients with a diagnosis of drug induced liver injury (DILI) were included in the study, with a particular focus on gender dimorphism in circulating monocytes. A delayed resolution of necrotic damage and a higher expression of proinflammatory cytokines were apparent in male mice along with a slower recruitment of inflammatory monocytes. F4/80CD11b macrophages and CD11bGr-1 monocytes expressed AR and were recruited later in male compared with female livers after CCl treatment. Moreover, CD11bARGr-1 recruitment was negatively modulated by flutamide in males. Analysis of DILI patients showed overall a significant reduction in circulating mature monocytes compared with healthy subjects. More interestingly, male patients had higher numbers of immature monocytes compared with female patients.A stronger cytotoxic tissue response was correlated with an impaired recruitment of CD11bARGr-1 cells and F4/80CD11b macrophages in the early inflammatory phase under AR signaling. During DILI, a dimorphic immune response was apparent, characterized by a massive recruitment of monocytes to the liver both in males and females, but only in males was this recruitment sustained by a turnover of immature monocytes.
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http://dx.doi.org/10.1042/CS20171260DOI Listing
January 2018

Coating ZnO nanoparticle films with DNA nanolayers for enhancing the electron extracting properties and performance of polymer solar cells.

Nanoscale 2017 Dec;9(48):19031-19038

CHOSE (Centre for Hybrid and Organic Solar Energy), Department of Electronic Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy.

Here we present for the first time polymer solar cells that incorporate biological material that show state of the art efficiencies in excess of 8%. The performance of inverted polymer solar cells was improved significantly after deposition of ZnO nanoparticles (ZnO-NPs) together with a thin deoxyribonucleic acid nanolayer and used as an electron extraction layer (EEL). The ZnO-NPs/DNA double layer improved the rectifying ratio, shunt resistance of the cells as well as lowering the work function of the electron-collecting contact. Importantly, the ZnO-NPs/DNA bilayer enhanced the power conversion efficiency of cells considerably compared to cells with EELs made of only DNA (improvement of 56% in relative terms) or only ZnO-NPs (improvement of 19% in relative terms) reaching a best power conversion efficiency of 8.5%. The ZnO-NPs/DNA double layer cells also outperformed ones made with one of the most efficient previous synthetic composite EELs (i.e. ZnO/PEIE(poly(ethyleneimine)-ethoxylated)). Since all fabrication procedures were carried out at low (<150 °C) or room temperature, we have applied the findings to flexible substrates as well as on glass obtaining a high PCE of 7.2%. The solar cells with the biological/metal-oxide composite EELs also delivered an improvement in the stability (∼20% in relative term) compared to that with ZnO-NPs only. All these findings show that natural materials, in this case DNA, the premium biological material, can be incorporated in organic semiconductor devices in tandem with inorganic devices delivering uncompromising levels of performance as well as significant improvements.
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http://dx.doi.org/10.1039/c7nr06982kDOI Listing
December 2017

Separase prevents genomic instability by controlling replication fork speed.

Nucleic Acids Res 2018 01;46(1):267-278

Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy.

Proper chromosome segregation is crucial for preserving genomic integrity, and errors in this process cause chromosome mis-segregation, which may contribute to cancer development. Sister chromatid separation is triggered by Separase, an evolutionary conserved protease that cleaves the cohesin complex, allowing the dissolution of sister chromatid cohesion. Here we provide evidence that Separase participates in genomic stability maintenance by controlling replication fork speed. We found that Separase interacted with the replication licensing factors MCM2-7, and genome-wide data showed that Separase co-localized with MCM complex and cohesin. Unexpectedly, the depletion of Separase increased the fork velocity about 1.5-fold and caused a strong acetylation of cohesin's SMC3 subunit and altered checkpoint response. Notably, Separase silencing triggered genomic instability in both HeLa and human primary fibroblast cells. Our results show a novel mechanism for fork progression mediated by Separase and thus the basis for genomic instability associated with tumorigenesis.
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http://dx.doi.org/10.1093/nar/gkx1172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5758895PMC
January 2018

Heparanase and macrophage interplay in the onset of liver fibrosis.

Sci Rep 2017 11 2;7(1):14956. Epub 2017 Nov 2.

University of Padova, Dept. Biomedical Sciences, 35121, Padova, Italy.

The heparan sulfate endoglycosidase heparanase (HPSE) is involved in tumor growth, chronic inflammation and fibrosis. Since a role for HPSE in chronic liver disease has not been demonstrated to date, the current study was aimed at investigating the involvement of HPSE in the pathogenesis of chronic liver injury. Herein, we revealed that HPSE expression increased in mouse livers after carbon tetrachloride (CCl)-mediated chronic induction of fibrosis, but with a trend to decline during progression of the disease. In mouse fibrotic liver tissues HPSE immunostaining was restricted in necro-inflammatory areas, co-localizing with F4/80 macrophage marker and TNF-α. TNF-α treatment induced HPSE expression as well as HPSE secretion in U937 macrophages. Moreover, macrophage-secreted HPSE regulated the expression of α-SMA and fibronectin in hepatic stellate LX-2 cells. Finally, HPSE activity increased in the plasma of patients with liver fibrosis but it inversely correlated with liver stiffness. Our results suggest the involvement of HPSE in early phases of reaction to liver damage and inflammatory macrophages as an important source of HPSE. HPSE seems to play a key role in the macrophage-mediated activation of hepatic stellate cells (HSCs), thus suggesting that HPSE targeting could be a new therapeutic option in the treatment of liver fibrosis.
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http://dx.doi.org/10.1038/s41598-017-14946-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668295PMC
November 2017

Single walled carbon nanotube/Si heterojunctions for high responsivity photodetectors.

Nanotechnology 2017 Oct 22;28(43):435201. Epub 2017 Aug 22.

Dipartimento di Fisica, Università di Roma 'Tor Vergata', Via della Ricerca Scientifica 1, I-00133 Roma, Italy. CNR-SPIN Salerno, Università degli Studi di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Italy.

Single walled carbon nanotube/n-Si (SWCNT/n-Si) hetero-junctions have been obtained by depositing SWCNT ultra-thin films on the surface of an n-Si substrate by dry transfer method. The as obtained junctions are photo sensitive in the measured wavelength range (300-1000 nm) and show zero bias responsivity and detectivity values of the order of 1 A W and 10 Jones respectively, which are higher than those previously observed in carbon based devices. Moreover, under on-off light excitation, the junctions show response speed as fast as 1 μs or better and noise equivalent powers comparable to commercial Si photomultipliers. Current-voltage measurements in dark and under illumination suggest that the devices consist of Schottky and semiconductor/semiconductor junctions both contributing to the fast and high responses observed.
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http://dx.doi.org/10.1088/1361-6528/aa8797DOI Listing
October 2017

Structural and photoluminescence properties of silicon nanowires extracted by means of a centrifugation process from plasma torch synthesized silicon nanopowder.

Nanotechnology 2017 Jul 6;28(28):285702. Epub 2017 Jun 6.

Institut national de la recherche scientifique, Centre-Énergie, Matériaux et Télécommunications, 1650 Blvd. Lionel Boulet, Varennes, QC, J3X 1S2, Canada.

We report on a method for the extraction of silicon nanowires (SiNWs) from the by-product of a plasma torch based spheroidization process of silicon. This by-product is a nanopowder which consists of a mixture of SiNWs and silicon particles. By optimizing a centrifugation based process, we were able to extract substantial amounts of highly pure Si nanomaterials (mainly SiNWs and Si nanospheres (SiNSs)). While the purified SiNWs were found to have typical outer diameters in the 10-15 nm range and lengths of up to several μm, the SiNSs have external diameters in the 10-100 nm range. Interestingly, the SiNWs are found to have a thinner Si core (2-5 nm diam.) and an outer silicon oxide shell (with a typical thickness of ∼5-10 nm). High resolution transmission electron microscopy (HRTEM) observations revealed that many SiNWs have a continuous cylindrical core, whereas others feature a discontinuous core consisting of a chain of Si nanocrystals forming a sort of 'chaplet-like' structures. These plasma-torch-produced SiNWs are highly pure with no trace of any metal catalyst, suggesting that they mostly form through SiO-catalyzed growth scheme rather than from metal-catalyzed path. The extracted Si nanostructures are shown to exhibit a strong photoluminescence (PL) which is found to blue-shift from 950 to 680 nm as the core size of the Si nanostructures decreases from ∼5 to ∼3 nm. This near IR-visible PL is shown to originate from quantum confinement (QC) in Si nanostructures. Consistently, the sizes of the Si nanocrystals directly determined from HRTEM images corroborate well with those expected by QC theory.
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http://dx.doi.org/10.1088/1361-6528/aa7769DOI Listing
July 2017

Hybridized C-O-Si Interface States at the Origin of Efficiency Improvement in CNT/Si Solar Cells.

ACS Appl Mater Interfaces 2017 May 5;9(19):16627-16634. Epub 2017 May 5.

I-LAMP and Dipartimento di Matematica e Fisica, Università Cattolica del Sacro Cuore , 25121 Brescia, Italy.

Despite the astonishing values of the power conversion efficiency reached, in just less than a decade, by the carbon nanotube/silicon (CNT/Si) solar cells, many doubts remain on the underlying transport mechanisms across the CNT/Si heterojunction. Here, by combining transient optical spectroscopy in the femtosecond timescale, X-ray photoemission, and a systematic tracking of I-V curves across all phases of the interlayer SiO growth at the interface, we grasp the mechanism that adequately preserves charge separation at the junction, hindering the photoexcited carrier recombination. Moreover, supported by ab initio calculations aimed to model the complex CNT-Si heterointerface, we show that oxygen-related states at the interface act as entrapping centers for the photoexcited electrons, thus preventing recombination with holes that can flow from Si to CNT across the SiO layer.
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http://dx.doi.org/10.1021/acsami.7b01766DOI Listing
May 2017

Self-assembly of silicon nanowires studied by advanced transmission electron microscopy.

Beilstein J Nanotechnol 2017 15;8:440-445. Epub 2017 Feb 15.

CNR IMM-MATIS, Via S. Sofia 64, Catania 95123, Italy.

Scanning transmission electron microscopy (STEM) was successfully applied to the analysis of silicon nanowires (SiNWs) that were self-assembled during an inductively coupled plasma (ICP) process. The ICP-synthesized SiNWs were found to present a Si-SiO core-shell structure and length varying from ≈100 nm to 2-3 μm. The shorter SiNWs (maximum length ≈300 nm) were generally found to possess a nanoparticle at their tip. STEM energy dispersive X-ray (EDX) spectroscopy combined with electron tomography performed on these nanostructures revealed that they contain iron, clearly demonstrating that the short ICP-synthesized SiNWs grew via an iron-catalyzed vapor-liquid-solid (VLS) mechanism within the plasma reactor. Both the STEM tomography and STEM-EDX analysis contributed to gain further insight into the self-assembly process. In the long-term, this approach might be used to optimize the synthesis of VLS-grown SiNWs via ICP as a competitive technique to the well-established bottom-up approaches used for the production of thin SiNWs.
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http://dx.doi.org/10.3762/bjnano.8.47DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5331248PMC
February 2017

A cross-functional nanostructured platform based on carbon nanotube-Si hybrid junctions: where photon harvesting meets gas sensing.

Sci Rep 2017 03 15;7:44413. Epub 2017 Mar 15.

Surface Science and Spectroscopy Lab @ I-Lamp and Dipartimento di Matematica e Fisica, Università Cattolica del Sacro Cuore, Brescia, Italy.

A combination of the functionalities of carbon nanotube (CNT)-Si hybrid heterojunctions is presented as a novel method to steer the efficiency of the photovoltaic (PV) cell based on these junctions, and to increase the selectivity and sensitivity of the chemiresistor gas sensor operated with the p-doped CNT layer. The electrical characteristics of the junctions have been tracked by exposing the devices to oxidizing (NO) and reducing (NH) molecules. It is shown that when used as PV cells, the cell efficiency can be reversibly steered by gas adsorption, providing a tool to selectively dope the p-type layer through molecular adsorption. Tracking of the current-voltage curve upon gas exposure also allowed to use these cells as gas sensors with an enhanced sensitivity as compared to that provided by a readout of the electrical signal from the CNT layer alone. In turn, the chemiresistive response was improved, both in terms of selectivity and sensitivity, by operating the system under illumination, as the photo-induced charges at the junction increase the p-doping of CNTs making them more sensitive to NH and less to NO.
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http://dx.doi.org/10.1038/srep44413DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5353639PMC
March 2017

Estrogens enhance myoblast differentiation in facioscapulohumeral muscular dystrophy by antagonizing DUX4 activity.

J Clin Invest 2017 Apr 6;127(4):1531-1545. Epub 2017 Mar 6.

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant neuromuscular disorder that is characterized by extreme variability in symptoms, with females being less severely affected than males and presenting a higher proportion of asymptomatic carriers. The sex-related factors involved in the disease are not known. Here, we have utilized myoblasts isolated from FSHD patients (FSHD myoblasts) to investigate the effect of estrogens on muscle properties. Our results demonstrated that estrogens counteract the differentiation impairment of FSHD myoblasts without affecting cell proliferation or survival. Estrogen effects are mediated by estrogen receptor β (ERβ), which reduces chromatin occupancy and transcriptional activity of double homeobox 4 (DUX4), a protein whose aberrant expression has been implicated in FSHD pathogenesis. During myoblast differentiation, we observed that the levels and activity of DUX4 increased progressively and were associated with its enhanced recruitment in the nucleus. ERβ interfered with this recruitment by relocalizing DUX4 in the cytoplasm. This work identifies estrogens as a potential disease modifier that underlie sex-related differences in FSHD by protecting against myoblast differentiation impairments in this disease.
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http://dx.doi.org/10.1172/JCI89401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373881PMC
April 2017

A defective dNTP pool hinders DNA replication in cell cycle-reactivated terminally differentiated muscle cells.

Cell Death Differ 2017 05 10;24(5):774-784. Epub 2017 Feb 10.

Department of Cell Biology and Neurosciences, Italian National Institute of Health, Rome, Italy.

Terminally differentiated cells are defined by their inability to proliferate. When forced to re-enter the cell cycle, they generally cannot undergo long-term replication. Our previous work with myotubes has shown that these cells fail to proliferate because of their intrinsic inability to complete DNA replication. Moreover, we have reported pronounced modifications of deoxynucleotide metabolism during myogenesis. Here we investigate the causes of incomplete DNA duplication in cell cycle-reactivated myotubes (rMt). We find that rMt possess extremely low levels of thymidine triphosphate (dTTP), resulting in very slow replication fork rates. Exogenous administration of thymidine or forced expression of thymidine kinase increases deoxynucleotide availability, allowing extended and faster DNA replication. Inadequate dTTP levels are caused by selective, differentiation-dependent, cell cycle-resistant suppression of genes encoding critical synthetic enzymes, chief among which is thymidine kinase 1. We conclude that lack of dTTP is at least partially responsible for the inability of myotubes to proliferate and speculate that it constitutes an emergency barrier against unwarranted DNA replication in terminally differentiated cells.
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http://dx.doi.org/10.1038/cdd.2017.4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423118PMC
May 2017

Trends in tissue repair and regeneration.

Development 2017 02;144(3):357-364

Department of Developmental & Stem Cell Biology, Stem Cells & Development Unit, CNRS UMR 3738, Institut Pasteur, 75015 Paris, France.

The 6th EMBO conference on the Molecular and Cellular Basis of Regeneration and Tissue Repair took place in Paestum (Italy) on the 17th-21st September, 2016. The 160 scientists who attended discussed the importance of cellular and tissue plasticity, biophysical aspects of regeneration, the diverse roles of injury-induced immune responses, strategies to reactivate regeneration in mammals, links between regeneration and ageing, and the impact of non-mammalian models on regenerative medicine.
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http://dx.doi.org/10.1242/dev.144279DOI Listing
February 2017

MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.

Bioinformatics 2017 Jun;33(11):1730-1732

Institute of Biomembranes and Bioenergetics, Consiglio Nazionale delle Ricerche, Bari, Italy.

Summary: Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing data is still extremely challenging in terms of both overall accuracy and computational efficiency, and current methodologies show substantial variability in misclassification rate and resolution at lower taxonomic ranks or are limited to specific life domains (e.g. only bacteria). We present here MetaShot, a workflow for assessing the total microbiome composition from host-associated shotgun sequence data, and show its overall optimal accuracy performance by analyzing both simulated and real datasets.

Availability And Implementation: https://github.com/bfosso/MetaShot.

Contact: graziano.pesole@uniba.it.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btx036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5447231PMC
June 2017