19 results on '"Riccardo Zecchi"'
Search Results
2. Mass spectrometry imaging as a tool for evaluating the pulmonary distribution of exogenous surfactant in premature lambs
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Riccardo Zecchi, Pietro Franceschi, Laura Tigli, Francesca Ricci, Francesca Boscaro, Barbara Pioselli, Valentina Mileo, Xabier Murgia, Federico Bianco, Fabrizio Salomone, Augusto F. Schmidt, Noah H. Hillman, Matthew W. Kemp, and Alan H. Jobe
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Surfactant ,CHF5633 ,Mass spectrometry imaging ,Respiratory distress syndrome ,Premature lambs ,Diseases of the respiratory system ,RC705-779 - Abstract
Abstract Background The amount of surfactant deposited in the lungs and its overall pulmonary distribution determine the therapeutic outcome of surfactant replacement therapy. Most of the currently available methods to determine the intrapulmonary distribution of surfactant are time-consuming and require surfactant labelling. Our aim was to assess the potential of Mass Spectrometry Imaging (MSI) as a label-free technique to qualitatively and quantitatively evaluate the distribution of surfactant to the premature lamb. Methods Twelve preterm lambs (gestational age 126-127d, term ~150d) were allocated in two experimental groups. Seven lambs were treated with an intratracheal bolus of the synthetic surfactant CHF5633 (200 mg/kg) and 5 lambs were managed with mechanical ventilation for 120 min, as controls. The right lung lobes of all lambs were gradually frozen while inflated to 20 cmH2O pressure for lung cryo-sections for MSI analysis. The intensity signals of SP-C analog and SP-B analog, the two synthetic peptides contained in the CHF5633 surfactant, were used to locate, map and quantify the intrapulmonary exogenous surfactant. Results Surfactant treatment was associated with a significant improvement of the mean arterial oxygenation and lung compliance (p
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- 2019
- Full Text
- View/download PDF
3. Surfactant-Assisted Distal Pulmonary Distribution of Budesonide Revealed by Mass Spectrometry Imaging
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Riccardo Zecchi, Pietro Franceschi, Laura Tigli, Barbara Pioselli, Valentina Mileo, Xabier Murgia, Fabrizio Salomone, Giuseppe Pieraccini, Haruo Usada, Augusto F. Schmidt, Noah H. Hillman, Matthew W. Kemp, and Alan H. Jobe
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budesonide ,Poractant alfa ,mass spectrometry imaging ,bronchopulmonary dysplasia ,neonatal respiratory distress syndrome ,premature lambs ,Pharmacy and materia medica ,RS1-441 - Abstract
Direct lung administration of budesonide in combination with surfactant reduces the incidence of bronchopulmonary dysplasia. Although the therapy is currently undergoing clinical development, the lung distribution of budesonide throughout the premature neonatal lung has not yet been investigated. Here, we applied mass spectrometry imaging (MSI) to investigate the surfactant-assisted distal lung distribution of budesonide. Unlabeled budesonide was either delivered using saline as a vehicle (n = 5) or in combination with a standard dose of the porcine surfactant Poractant alfa (n = 5). These lambs were ventilated for one minute, and then the lungs were extracted for MSI analysis. Another group of lambs (n = 5) received the combination of budesonide and Poractant alfa, followed by two hours of mechanical ventilation. MSI enabled the label-free detection and visualization of both budesonide and the essential constituent of Poractant alfa, the porcine surfactant protein C (SP-C). 2D ion intensity images revealed a non-uniform distribution of budesonide with saline, which appeared clustered in clumps. In contrast, the combination therapy showed a more homogeneous distribution of budesonide throughout the sample, with more budesonide distributed towards the lung periphery. We found similar distribution patterns for the SP-C and budesonide in consecutive lung tissue sections, indicating that budesonide was transported across the lungs associated with the exogenous surfactant. After two hours of mechanical ventilation, the budesonide intensity signal in the 2D ion intensity maps dropped dramatically, suggesting a rapid lung clearance and highlighting the relevance of achieving a uniform surfactant-assisted lung distribution of budesonide early after delivery to maximize the anti-inflammatory and maturational effects throughout the lung.
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- 2021
- Full Text
- View/download PDF
4. Mass spectrometry imaging as a tool for evaluating the pulmonary distribution of exogenous surfactant in premature lambs
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Francesca Ricci, Noah H. Hillman, Valentina Mileo, Xabier Murgia, Federico Bianco, Laura Tigli, Barbara Pioselli, Fabrizio Salomone, Francesca Boscaro, Pietro Franceschi, Alan H. Jobe, Matthew W. Kemp, Riccardo Zecchi, and Augusto F. Schmidt
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0301 basic medicine ,medicine.medical_specialty ,Settore CHIM/01 - CHIMICA ANALITICA ,Respiratory distress syndrome ,medicine.medical_treatment ,Pulmonary compliance ,Mass Spectrometry ,Mass spectrometry imaging ,Premature lambs ,03 medical and health sciences ,0302 clinical medicine ,Pulmonary surfactant ,Internal medicine ,Surfactant ,medicine ,Animals ,Distribution (pharmacology) ,Tissue Distribution ,Lung ,Mechanical ventilation ,lcsh:RC705-779 ,Pulmonary Surfactant-Associated Protein B ,Sheep ,Chemistry ,Research ,Pulmonary Surfactants ,Oxygenation ,lcsh:Diseases of the respiratory system ,respiratory system ,Pulmonary Surfactant-Associated Protein C ,Peptide Fragments ,030104 developmental biology ,medicine.anatomical_structure ,Animals, Newborn ,030228 respiratory system ,Phosphatidylcholines ,Cardiology ,CHF5633 ,Bolus (digestion) - Abstract
Background The amount of surfactant deposited in the lungs and its overall pulmonary distribution determine the therapeutic outcome of surfactant replacement therapy. Most of the currently available methods to determine the intrapulmonary distribution of surfactant are time-consuming and require surfactant labelling. Our aim was to assess the potential of Mass Spectrometry Imaging (MSI) as a label-free technique to qualitatively and quantitatively evaluate the distribution of surfactant to the premature lamb. Methods Twelve preterm lambs (gestational age 126-127d, term ~150d) were allocated in two experimental groups. Seven lambs were treated with an intratracheal bolus of the synthetic surfactant CHF5633 (200 mg/kg) and 5 lambs were managed with mechanical ventilation for 120 min, as controls. The right lung lobes of all lambs were gradually frozen while inflated to 20 cmH2O pressure for lung cryo-sections for MSI analysis. The intensity signals of SP-C analog and SP-B analog, the two synthetic peptides contained in the CHF5633 surfactant, were used to locate, map and quantify the intrapulmonary exogenous surfactant. Results Surfactant treatment was associated with a significant improvement of the mean arterial oxygenation and lung compliance (p
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- 2019
5. Sample preparation strategy for the detection of steroid-like compounds using MALDI mass spectrometry imaging: pulmonary distribution of budesonide as a case study
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Valentina Mileo, Laura Tigli, Barbara Pioselli, Giuseppe Pieraccini, Davide Amidani, Riccardo Zecchi, Fabrizio Salomone, Pietro Franceschi, Francesca Ricci, and Chiara Catozzi
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Budesonide ,Settore CHIM/01 - CHIMICA ANALITICA ,On-tissue derivatization ,Biochemistry ,Mass spectrometry imaging ,Analytical Chemistry ,Matrix (chemical analysis) ,chemistry.chemical_compound ,medicine ,Distribution (pharmacology) ,Animals ,Sample preparation ,Derivatization ,Glucocorticoids ,Lung ,Asthma ,Chromatography ,Chemistry ,Ferulic acid ,medicine.disease ,Girard reagent ,Pulmonary drug distribution ,medicine.anatomical_structure ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Indicators and Reagents ,Steroids ,Rabbits ,medicine.drug ,Research Paper - Abstract
Graphical abstract Corticosteroids as budesonide can be effective in reducing topic inflammation processes in different organs. Therapeutic use of budesonide in respiratory diseases, like asthma, chronic obstructive pulmonary disease, and allergic rhinitis is well known. However, the pulmonary distribution of budesonide is not well understood, mainly due to the difficulties in tracing the molecule in lung samples without the addition of a label. In this paper, we present a matrix-assisted laser desorption/ionization mass spectrometry imaging protocol that can be used to visualize the pulmonary distribution of budesonide administered to a surfactant-depleted adult rabbit. Considering that budesonide is not easily ionized by MALDI, we developed an on-tissue derivatization method with Girard’s reagent P followed by ferulic acid deposition as MALDI matrix. Interestingly, this sample preparation protocol results as a very effective strategy to raise the sensitivity towards not only budesonide but also other corticosteroids, allowing us to track its distribution and quantify the drug inside lung samples. Supplementary Information The online version contains supplementary material available at 10.1007/s00216-021-03393-6.
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- 2021
6. Surfactant lung delivery with LISA and InSurE in adult rabbits with respiratory distress
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Ilia Bresesti, Costanza Casiraghi, Laura Tigli, Virgilio P. Carnielli, Xabier Murgia, Arianna Mersanne, Chiara Catozzi, Pietro Franceschi, Matteo Storti, Riccardo Zecchi, Gianluca Lista, Manuela Simonato, Fabrizio Salomone, Paola Cogo, Paola Azzurra Maria LaVerde, and Francesca Ricci
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Settore CHIM/01 - CHIMICA ANALITICA ,medicine.medical_treatment ,Lung injury ,03 medical and health sciences ,0302 clinical medicine ,Pulmonary surfactant ,030225 pediatrics ,Medicine ,Animals ,Humans ,Continuous positive airway pressure ,Mechanical ventilation ,Respiratory Distress Syndrome, Newborn ,Lung ,Respiratory distress ,Continuous Positive Airway Pressure ,business.industry ,Surfactant protein C ,Pulmonary Surfactants ,respiratory system ,Basic Science Article ,Respiration, Artificial ,Disease Models, Animal ,medicine.anatomical_structure ,Anesthesia ,Pediatrics, Perinatology and Child Health ,Breathing ,Rabbits ,business ,030217 neurology & neurosurgery - Abstract
Background In preterm infants, InSurE (Intubation-Surfactant-Extubation) and LISA (less invasive surfactant administration) techniques allow for exogenous surfactant administration while reducing lung injury associated with mechanical ventilation. We compared the acute pulmonary response and lung deposition of surfactant by LISA and InSurE in surfactant-depleted adult rabbits. Methods Twenty-six spontaneously breathing surfactant-depleted adult rabbits (6-7 weeks old) with moderate RDS and managed with nasal continuous positive airway pressure were randomized to 3 groups: (1) 200 mg/kg of surfactant by InSurE; (2) 200 mg/kg of surfactant by LISA; (3) no surfactant treatment (Control). Gas exchange and lung mechanics were monitored for 180 min. After that, surfactant lung deposition and distribution were evaluated monitoring disaturated-phosphatidylcholine (DSPC) and surfactant protein C (SP-C), respectively. Results No signs of recovery were found in the untreated animals. After InSurE, oxygenation improved more rapidly compared to LISA. However, at 180' LISA and InSurE showed comparable outcomes in terms of gas exchange, ventilation parameters, and lung mechanics. Neither DSPC in the alveolar pool nor SP-C signal distributions in a frontal lung section were significantly different between InSurE and LISA groups. Conclusions In an acute setting, LISA demonstrated efficacy and surfactant lung delivery similar to that of InSurE in surfactant-depleted adult rabbits. Impact Although LISA technique is gaining popularity, there are still several questions to address. This is the first study comparing LISA and InSurE in terms of gas exchange, ventilation parameters, and lung mechanics as well as surfactant deposition and distribution. In our animal study, three hours post-treatment, LISA method seems to be as effective as InSurE and showed similar surfactant lung delivery. Our findings provide some clarifications on a fair comparison between LISA and InSurE techniques, particularly in terms of surfactant delivery. They should reassure some of the concerns raised by the clinical community on LISA adoption in neonatal units.
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- 2021
7. Ultra-rapid brain uptake of subcutaneous sumatriptan in the rat: Implication for cluster headache treatment
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Francesco De Cesaris, Matteo Urru, Alessandro Panconesi, Alberto Chiarugi, Mirko Muzzi, Riccardo Zecchi, Lorenzo Tofani, and Giuseppe Antonio Ranieri
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Male ,Time Factors ,Injections, Subcutaneous ,Symptomatic treatment ,Cluster Headache ,Triptans ,Pharmacology ,Disease cluster ,Mass Spectrometry ,03 medical and health sciences ,0302 clinical medicine ,Pharmacokinetics ,Medicine ,Animals ,Rats, Wistar ,030304 developmental biology ,Brain uptake ,0303 health sciences ,business.industry ,Sumatriptan ,Cluster headache ,Brain ,General Medicine ,Serotonin 5-HT1 Receptor Agonists ,medicine.disease ,Rats ,Editorial ,Migraine ,cardiovascular system ,Neurology (clinical) ,business ,030217 neurology & neurosurgery ,medicine.drug ,Chromatography, Liquid - Abstract
BackgroundIn spite of the substantial therapeutic efficacy of triptans, their site of action is still debated. Subcutaneous sumatriptan is the most efficacious symptomatic treatment for cluster headache (CH) patients, showing therapeutic onset within a few minutes after injection even in migraine patients. However, whether subcutaneous sumatriptan is able to reach the CNS within this short time frame is currently unknown.MethodsHere, by means of liquid chromatography/mass spectrometry, we investigated peripheral and brain distribution of subcutaneous sumatriptan soon after injection in rats at a dose equivalent to that used in patients. Tissue sumatriptan contents were compared to those of oxazepam, a prototypical lipophilic, neuroactive drug.ResultsWe report that sumatriptan accumulated within brain regions of relevance to migraine and CH pathogenesis such as the hypothalamus and the brainstem as soon as 1 and 5 minutes after injection. Notably, sumatriptan brain distribution was faster than that of oxazepam, reaching concentrations exceeding its reported binding affinity for 5HT1B/Dreceptors, and in the range of those able to inhibit neurotransmitter release in vivo.ConclusionOur findings indicate that sumatriptan distributes within the CNS soon after injection, and are in line with prompt pain relief by parenteral sumatriptan in CH patients.
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- 2019
8. Dexpramipexole improves bioenergetics and outcome in experimental stroke
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Daniela Buonvicino, Francesco Resta, Emidio Camaioni, Alberto Chiarugi, Riccardo Zecchi, Guido Mannaioni, Laura Formentini, Alessio Masi, Mirko Muzzi, Domenico E. Pellegrini-Giampietro, Daniele Bani, Elisabetta Gerace, Elisabetta Coppi, Daniele Guasti, Anna Maria Pugliese, Martina Ferri, and Laura Tigli
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0301 basic medicine ,Pharmacology ,Penumbra ,Depolarization ,Biology ,Hippocampal formation ,medicine.disease ,Cytoprotection ,Neuroprotection ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,medicine.artery ,Middle cerebral artery ,medicine ,Amyotrophic lateral sclerosis ,Dexpramipexole ,Neuroscience ,030217 neurology & neurosurgery ,medicine.drug - Abstract
Background and purpose Dexpramipexole, a drug recently tested in patients with amyotrophic lateral sclerosis (ALS,) is able to bind F1Fo ATP synthase and increase mitochondrial ATP production. Here, we have investigated its effects on experimental ischaemic brain injury. Experimental approach The effects of dexpramipexole on bioenergetics, Ca2+ fluxes, electrophysiological functions and death were evaluated in primary neural cultures and hippocampal slices exposed to oxygen-glucose deprivation (OGD). Effects on infarct volumes and neurological functions were also evaluated in mice following proximal or distal middle cerebral artery occlusion (MCAo). Distribution of dexpramipexole within the ischaemic brain was evaluated by means of mass spectrometry imaging. Key results Dexpramipexole increased mitochondrial ATP production in cultured neurons or glia and reduces energy failure, prevents intracellular Ca2+ overload and affords cytoprotection when cultures are exposed to OGD. This compound also counteracted ATP depletion, mitochondrial swelling, anoxic depolarization, loss of synaptic activity and neuronal death in hippocampal slices subjected to OGD. Post-ischaemic treatment with dexpramipexole, at doses consistent with those already used in ALS patients, reduced brain infarct size and ameliorated neuroscore in mice subjected to transient or permanent MCAo. Notably, the concentrations of dexpramipexole reached within the ischaemic penumbra equalled those found neuroprotective in vitro. Conclusion and implications Dexpramipexole, a compound able to increase mitochondrial F1Fo ATP-synthase activity reduced ischaemic brain injury. These findings, together with the excellent brain penetration and favourable safety profile in humans, make dexpramipexole a drug with realistic translational potential for the treatment of stroke. Linked articles This article is part of a themed section on Inventing New Therapies Without Reinventing the Wheel: The Power of Drug Repurposing. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.2/issuetoc.
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- 2017
9. Electrospray MS and MALDI imaging show that non-specific lipid-transfer proteins (LTPs) in tomato are present as several isoforms and are concentrated in seeds
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Arnaldo Dossena, Mariangela Bencivenni, Riccardo Zecchi, Gloriano Moneti, Francesca Boscaro, Andrea Faccini, and Stefano Sforza
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MALDI imaging ,Gene isoform ,Chromatography ,Biochemistry ,Non specific ,Liquid chromatography–mass spectrometry ,Chemistry ,food and beverages ,Ultracentrifuge ,Electrospray ms ,Plant lipid transfer proteins ,Spectroscopy ,Cysteine - Abstract
Non-specific lipid-transfer proteins (nsLTPs) are major human allergens in many plant species, albeit their role in plant biochemistry is still undefined. They are found in many plant species, either as one or several isoforms according to the species, and usually they are found to concentrate in the outer part of the fruits. In this work, the characterization of tomato nsLTP isoforms was performed on the three main fractions of Piccadilly tomato fruit (peel, pulp and seeds) by using ultracentrifuge devices with molecular cut-off able to retain proteins with molecular weight typical of plant LTPs. The isolated proteins were further analysed by LC-MS, in order to investigate the occurrence and the localization of tomato LTP isoforms. The chromatographic retention times, the molecular masses, the presence of eight cysteine residues in their tertiary structures and the sequence information obtained by MS, although not complete yet, allowed us to identify four different LTP isoforms, not yet reported in the literature, which were found to be concentrated in the seed fractions. None of the molecular masses of these potential LTPs was already present in the UniProtKB/SwissProt database. MALDI imaging experiments confirmed their presence and main localization in seeds, although the actual data hinted at their presence around seeds, rather than exactly in them. These data hint to a complicated scenario concerning LTP proteins in tomato.
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- 2014
10. Identification of the Nicotinamide Salvage Pathway as a New Toxification Route for Antimetabolites
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Mirko Muzzi, Emidio Camaioni, Alberto Chiarugi, Daniela Buonvicino, Barbara Stecca, Federica Zamporlini, Massimo Calamante, Giuseppe Antonio Ranieri, Giuseppe Pieraccini, Riccardo Zecchi, Francesca Mazzola, Mathias Ziegler, Francesco Resta, Christian Dölle, Nadia Raffaelli, and Gianluca Bartolucci
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Models, Molecular ,Niacinamide ,0301 basic medicine ,Antimetabolites, Antineoplastic ,NAD, NAMPT, NMNAT2, Vacor, glycolysis, dehydrogenases, neuroblastoma cells, melanoma cells, xenograft ,nicotinamide adenine dinucleotide (NAD) ,nicotinamide phosphoribosyl transferase (NAMPT) inhibitors ,Cell Survival ,Clinical Biochemistry ,Mice, Nude ,NMNAT2 ,neuroblastoma cells ,Biology ,Nicotinamide adenine dinucleotide ,NAMPT ,Biochemistry ,Neuroblastoma ,03 medical and health sciences ,chemistry.chemical_compound ,Cell Line, Tumor ,Drug Discovery ,Metabolome ,Animals ,Humans ,Glycolysis ,xenograft ,Nicotinamide Phosphoribosyltransferase ,Melanoma ,Molecular Biology ,Nucleotide salvage ,Nicotinamide mononucleotide ,Pharmacology ,chemistry.chemical_classification ,Nicotinamide ,Vacor ,Phenylurea Compounds ,dehydrogenases ,NAD ,030104 developmental biology ,Enzyme ,chemistry ,Molecular Medicine ,NAD+ kinase ,melanoma cells - Abstract
Interest in the modulation of nicotinamide adenine dinucleotide (NAD) metabolome is gaining great momentum because of its therapeutic potential in different human disorders. Suppression of nicotinamide salvage by nicotinamide phosphoribosyl transferase (NAMPT) inhibitors, however, gave inconclusive results in neoplastic patients because several metabolic routes circumvent the enzymatic block converging directly on nicotinamide mononucleotide adenylyl transferases (NMNATs) for NAD synthesis. Unfortunately, NMNAT inhibitors have not been identified. Here, we report the identification of Vacor as a substrate metabolized by the consecutive action of NAMPT and NMNAT2 into the NAD analog Vacor adenine dinucleotide (VAD). This leads to inhibition of both enzymes, as well as NAD-dependent dehydrogenases, thereby causing unprecedented rapid NAD depletion, glycolytic block, energy failure, and necrotic death of NMNAT2-proficient cancer cells. Conversely, lack of NMNAT2 expression confers complete resistance to Vacor. Remarkably, Vacor prompts VAD formation and growth suppression in NMNAT2-positive neuroblastoma and melanoma xenografts. Our data show the first evidence of harnessing the entire nicotinamide salvage pathway for antimetabolic strategies. Synthesis and consumption of the pyridine nucleotide NAD are increased in cancer cells and contribute to cell proliferation and neoplastic transformation. Buonvicino et al. identified Vacor as a new structure interfering with NAD metabolome which may lead to the development of new antineoplastic molecules.
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- 2018
11. Electrospray MS and MALDI imaging show that non-specific lipid-transfer proteins (LTPs) in tomato are present as several isoforms and are concentrated in seeds
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Mariangela, Bencivenni, Andrea, Faccini, Riccardo, Zecchi, Francesca, Boscaro, Gloriano, Moneti, Arnaldo, Dossena, and Stefano, Sforza
- Abstract
Non-specific lipid-transfer proteins (nsLTPs) are major human allergens in many plant species, albeit their role in plant biochemistry is still undefined. They are found in many plant species, either as one or several isoforms according to the species, and usually they are found to concentrate in the outer part of the fruits. In this work, the characterization of tomato nsLTP isoforms was performed on the three main fractions of Piccadilly tomato fruit (peel, pulp and seeds) by using ultracentrifuge devices with molecular cut-off able to retain proteins with molecular weight typical of plant LTPs. The isolated proteins were further analysed by LC-MS, in order to investigate the occurrence and the localization of tomato LTP isoforms. The chromatographic retention times, the molecular masses, the presence of eight cysteine residues in their tertiary structures and the sequence information obtained by MS, although not complete yet, allowed us to identify four different LTP isoforms, not yet reported in the literature, which were found to be concentrated in the seed fractions. None of the molecular masses of these potential LTPs was already present in the UniProtKB/SwissProt database. MALDI imaging experiments confirmed their presence and main localization in seeds, although the actual data hinted at their presence around seeds, rather than exactly in them. These data hint to a complicated scenario concerning LTP proteins in tomato.
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- 2014
12. Impact of drug administration route on drug delivery and distribution into the lung: an imaging mass spectrometry approach
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Maria Pittelli, Gloriano Moneti, Riccardo Zecchi, Marcello Trevisani, Francesco Amadei, Pamela Pedretti, Silvia Catinella, Barbara Pioselli, Maria Elena Manni, and Giuseppe Pieraccini
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Drug ,Male ,media_common.quotation_subject ,Guinea Pigs ,Scopolamine Derivatives ,Pharmacology ,Mass spectrometry imaging ,Cholinergic Antagonists ,Pulmonary Disease, Chronic Obstructive ,Drug Delivery Systems ,In vivo ,Administration, Inhalation ,Drug Discovery ,medicine ,Animals ,Tissue Distribution ,Tiotropium Bromide ,Lung ,Spectroscopy ,media_common ,Aerosols ,Inhalation ,business.industry ,Drug Administration Routes ,Nebulizers and Vaporizers ,General Medicine ,Tiotropium bromide ,Atomic and Molecular Physics, and Optics ,Matrix-assisted laser desorption/ionization ,medicine.anatomical_structure ,Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ,Drug delivery ,business ,medicine.drug - Abstract
During the last decade, significant technological improvements in mass spectrometry have had a great impact on drug discovery. The development of matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) has set a new frontier for the study of the distribution of endogenous and exogenous molecules present within a tissue. MALDI-IMS is a surface sampling technique that allows not only the detection of multiple analytes but also gives the spatial distribution of those analytes. Active compounds for pulmonary disease need an optimal and well-studied delivery into the lungs, in order to assure distribution with greater penetration into the peripheral or the alveolar region of the lung to maximize the therapeutic effects. IMS is very useful in the field of drug discovery, showing drug delivery and distribution in the body and organs. In this study, we present a comparison between two different ways of carrying out pulmonary drug administration: inhalation of a nebulized aerosol of aqueous drug solutions and intratracheal administration, which is much simpler, not expensive and commonly used during in vivo screening. Tiotropium bromide is a long-acting anticholinergic medicine used for maintenance treatment of chronic obstructive pulmonary disease. In the present work, tiotropium was administered by nebulization and by intratracheal instillation to guinea pigs at doses able to induce significant anti-bronchoconstrictive activity. Lung samples were dissected, frozen, cryosectioned and coated with matrix ( α-hydroxy-cinnamic acid). IMS analyses were performed using a MALDI-LTQ-Orbitrap XL. Using this technique we were able to compare different distributions of the drug depending on the method of administration.
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- 2014
13. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22
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Agostinho Carvalho, Cristina Massi-Benedetti, Luigina Romani, Giuseppe Pieraccini, Paolo Puccetti, Francesca Fallarino, Carmen D'Angelo, Rossana G. Iannitti, Riccardo Zecchi, Gloria Giovannini, Teresa Zelante, Cristina Cunha, and Antonella De Luca
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0303 health sciences ,Catabolism ,Immunology ,Tryptophan ,Colonisation resistance ,Biology ,biology.organism_classification ,Aryl hydrocarbon receptor ,Interleukin 22 ,03 medical and health sciences ,Metabolic pathway ,0302 clinical medicine ,Infectious Diseases ,Biochemistry ,030220 oncology & carcinogenesis ,biology.protein ,Immunology and Allergy ,Candida albicans ,Energy source ,030304 developmental biology - Abstract
Summary Endogenous tryptophan (Trp) metabolites have an important role in mammalian gut immune homeostasis, yet the potential contribution of Trp metabolites from resident microbiota has never been addressed experimentally. Here, we describe a metabolic pathway whereby Trp metabolites from the microbiota balance mucosal reactivity in mice. Switching from sugar to Trp as an energy source (e.g., under conditions of unrestricted Trp availability), highly adaptive lactobacilli are expanded and produce an aryl hydrocarbon receptor (AhR) ligand—indole-3-aldehyde—that contributes to AhR-dependent Il22 transcription. The resulting IL-22-dependent balanced mucosal response allows for survival of mixed microbial communities yet provides colonization resistance to the fungus Candida albicans and mucosal protection from inflammation. Thus, the microbiota-AhR axis might represent an important strategy pursued by coevolutive commensalism for fine tuning host mucosal reactivity contingent on Trp catabolism.
- Published
- 2013
14. A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks.
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Alireza Alemi, Carlo Baldassi, Nicolas Brunel, and Riccardo Zecchina
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Biology (General) ,QH301-705.5 - Abstract
Understanding the theoretical foundations of how memories are encoded and retrieved in neural populations is a central challenge in neuroscience. A popular theoretical scenario for modeling memory function is the attractor neural network scenario, whose prototype is the Hopfield model. The model simplicity and the locality of the synaptic update rules come at the cost of a poor storage capacity, compared with the capacity achieved with perceptron learning algorithms. Here, by transforming the perceptron learning rule, we present an online learning rule for a recurrent neural network that achieves near-maximal storage capacity without an explicit supervisory error signal, relying only upon locally accessible information. The fully-connected network consists of excitatory binary neurons with plastic recurrent connections and non-plastic inhibitory feedback stabilizing the network dynamics; the memory patterns to be memorized are presented online as strong afferent currents, producing a bimodal distribution for the neuron synaptic inputs. Synapses corresponding to active inputs are modified as a function of the value of the local fields with respect to three thresholds. Above the highest threshold, and below the lowest threshold, no plasticity occurs. In between these two thresholds, potentiation/depression occurs when the local field is above/below an intermediate threshold. We simulated and analyzed a network of binary neurons implementing this rule and measured its storage capacity for different sizes of the basins of attraction. The storage capacity obtained through numerical simulations is shown to be close to the value predicted by analytical calculations. We also measured the dependence of capacity on the strength of external inputs. Finally, we quantified the statistics of the resulting synaptic connectivity matrix, and found that both the fraction of zero weight synapses and the degree of symmetry of the weight matrix increase with the number of stored patterns.
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- 2015
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15. Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.
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Carlo Baldassi, Marco Zamparo, Christoph Feinauer, Andrea Procaccini, Riccardo Zecchina, Martin Weigt, and Andrea Pagnani
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Medicine ,Science - Abstract
In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our method aims at extracting such constraints from rapidly accumulating sequence data, and thereby at inferring protein structure and function from sequence information alone. Recently, global statistical inference methods (e.g. direct-coupling analysis, sparse inverse covariance estimation) have achieved a breakthrough towards this aim, and their predictions have been successfully implemented into tertiary and quaternary protein structure prediction methods. However, due to the discrete nature of the underlying variable (amino-acids), exact inference requires exponential time in the protein length, and efficient approximations are needed for practical applicability. Here we propose a very efficient multivariate Gaussian modeling approach as a variant of direct-coupling analysis: the discrete amino-acid variables are replaced by continuous Gaussian random variables. The resulting statistical inference problem is efficiently and exactly solvable. We show that the quality of inference is comparable or superior to the one achieved by mean-field approximations to inference with discrete variables, as done by direct-coupling analysis. This is true for (i) the prediction of residue-residue contacts in proteins, and (ii) the identification of protein-protein interaction partner in bacterial signal transduction. An implementation of our multivariate Gaussian approach is available at the website http://areeweb.polito.it/ricerca/cmp/code.
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- 2014
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16. Shape similarity, better than semantic membership, accounts for the structure of visual object representations in a population of monkey inferotemporal neurons.
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Carlo Baldassi, Alireza Alemi-Neissi, Marino Pagan, James J Dicarlo, Riccardo Zecchina, and Davide Zoccolan
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Biology (General) ,QH301-705.5 - Abstract
The anterior inferotemporal cortex (IT) is the highest stage along the hierarchy of visual areas that, in primates, processes visual objects. Although several lines of evidence suggest that IT primarily represents visual shape information, some recent studies have argued that neuronal ensembles in IT code the semantic membership of visual objects (i.e., represent conceptual classes such as animate and inanimate objects). In this study, we investigated to what extent semantic, rather than purely visual information, is represented in IT by performing a multivariate analysis of IT responses to a set of visual objects. By relying on a variety of machine-learning approaches (including a cutting-edge clustering algorithm that has been recently developed in the domain of statistical physics), we found that, in most instances, IT representation of visual objects is accounted for by their similarity at the level of shape or, more surprisingly, low-level visual properties. Only in a few cases we observed IT representations of semantic classes that were not explainable by the visual similarity of their members. Overall, these findings reassert the primary function of IT as a conveyor of explicit visual shape information, and reveal that low-level visual properties are represented in IT to a greater extent than previously appreciated. In addition, our work demonstrates how combining a variety of state-of-the-art multivariate approaches, and carefully estimating the contribution of shape similarity to the representation of object categories, can substantially advance our understanding of neuronal coding of visual objects in cortex.
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- 2013
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17. Perturbation biology: inferring signaling networks in cellular systems.
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Evan J Molinelli, Anil Korkut, Weiqing Wang, Martin L Miller, Nicholas P Gauthier, Xiaohong Jing, Poorvi Kaushik, Qin He, Gordon Mills, David B Solit, Christine A Pratilas, Martin Weigt, Alfredo Braunstein, Andrea Pagnani, Riccardo Zecchina, and Chris Sander
- Subjects
Biology (General) ,QH301-705.5 - Abstract
We present a powerful experimental-computational technology for inferring network models that predict the response of cells to perturbations, and that may be useful in the design of combinatorial therapy against cancer. The experiments are systematic series of perturbations of cancer cell lines by targeted drugs, singly or in combination. The response to perturbation is quantified in terms of relative changes in the measured levels of proteins, phospho-proteins and cellular phenotypes such as viability. Computational network models are derived de novo, i.e., without prior knowledge of signaling pathways, and are based on simple non-linear differential equations. The prohibitively large solution space of all possible network models is explored efficiently using a probabilistic algorithm, Belief Propagation (BP), which is three orders of magnitude faster than standard Monte Carlo methods. Explicit executable models are derived for a set of perturbation experiments in SKMEL-133 melanoma cell lines, which are resistant to the therapeutically important inhibitor of RAF kinase. The resulting network models reproduce and extend known pathway biology. They empower potential discoveries of new molecular interactions and predict efficacious novel drug perturbations, such as the inhibition of PLK1, which is verified experimentally. This technology is suitable for application to larger systems in diverse areas of molecular biology.
- Published
- 2013
- Full Text
- View/download PDF
18. Modelling Competing Endogenous RNA Networks.
- Author
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Carla Bosia, Andrea Pagnani, and Riccardo Zecchina
- Subjects
Medicine ,Science - Abstract
MicroRNAs (miRNAs) are small RNA molecules, about 22 nucleotide long, which post-transcriptionally regulate their target messenger RNAs (mRNAs). They accomplish key roles in gene regulatory networks, ranging from signaling pathways to tissue morphogenesis, and their aberrant behavior is often associated with the development of various diseases. Recently it has been experimentally shown that the way miRNAs interact with their targets can be described in terms of a titration mechanism. From a theoretical point of view titration mechanisms are characterized by threshold effect at near-equimolarity of the different chemical species, hypersensitivity of the system around the threshold, and cross-talk among targets. The latter characteristic has been lately identified as competing endogenous RNA (ceRNA) effect to mark those indirect interactions among targets of a common pool of miRNAs they are in competition for. Here we propose a stochastic model to analyze the equilibrium and out-of-equilibrium properties of a network of [Formula: see text] miRNAs interacting with [Formula: see text] mRNA targets. In particular we are able to describe in detail the peculiar equilibrium and non-equilibrium phenomena that the system displays in proximity to the threshold: (i) maximal cross-talk and correlation between targets, (ii) robustness of ceRNA effect with respect to the model's parameters and in particular to the catalyticity of the miRNA-mRNA interaction, and (iii) anomalous response-time to external perturbations.
- Published
- 2013
- Full Text
- View/download PDF
19. Protein 3D structure computed from evolutionary sequence variation.
- Author
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Debora S Marks, Lucy J Colwell, Robert Sheridan, Thomas A Hopf, Andrea Pagnani, Riccardo Zecchina, and Chris Sander
- Subjects
Medicine ,Science - Abstract
The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. Deciphering the evolutionary record held in these sequences and exploiting it for predictive and engineering purposes presents a formidable challenge. The potential benefit of solving this challenge is amplified by the advent of inexpensive high-throughput genomic sequencing.In this paper we ask whether we can infer evolutionary constraints from a set of sequence homologs of a protein. The challenge is to distinguish true co-evolution couplings from the noisy set of observed correlations. We address this challenge using a maximum entropy model of the protein sequence, constrained by the statistics of the multiple sequence alignment, to infer residue pair couplings. Surprisingly, we find that the strength of these inferred couplings is an excellent predictor of residue-residue proximity in folded structures. Indeed, the top-scoring residue couplings are sufficiently accurate and well-distributed to define the 3D protein fold with remarkable accuracy.We quantify this observation by computing, from sequence alone, all-atom 3D structures of fifteen test proteins from different fold classes, ranging in size from 50 to 260 residues, including a G-protein coupled receptor. These blinded inferences are de novo, i.e., they do not use homology modeling or sequence-similar fragments from known structures. The co-evolution signals provide sufficient information to determine accurate 3D protein structure to 2.7-4.8 Å C(α)-RMSD error relative to the observed structure, over at least two-thirds of the protein (method called EVfold, details at http://EVfold.org). This discovery provides insight into essential interactions constraining protein evolution and will facilitate a comprehensive survey of the universe of protein structures, new strategies in protein and drug design, and the identification of functional genetic variants in normal and disease genomes.
- Published
- 2011
- Full Text
- View/download PDF
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