Enrico Bucci | Temple University (original) (raw)

Papers by Enrico Bucci

Research paper thumbnail of Synthesis, spectroscopic studies and biological activity of a novel nucleopeptide with Moloney murine leukemia virus reverse transcriptase inhibitory activity

Amino Acids, Oct 8, 2009

In this work, we report the synthesis of an alternate nucleo-alpha,epsilon-peptide based on l-lys... more In this work, we report the synthesis of an alternate nucleo-alpha,epsilon-peptide based on l-lysine moieties, an in vitro study of its biological activity, and spectroscopical binding studies between the novel nucleopeptide and Moloney murine leukemia virus reverse transcriptase as well as RNA. An alternate homothymine hexamer was synthesized by a straightforward solid phase route starting from commercial materials, purified by

Research paper thumbnail of Protein-centered biological networks by automatic caption analysis

Research paper thumbnail of Synthesis and aggregation properties of a novel enzymatically resistant nucleoamino acid

Amino Acids, Jan 18, 2012

Research paper thumbnail of 1H Chemical Shift Assignments for Superman Zinc Finger Domain

Journal of Back and Musculoskeletal Rehabilitation, Apr 10, 2003

Research paper thumbnail of Automatic detection of image manipulations in the biomedical literature

Cell Death and Disease, Mar 1, 2018

Research paper thumbnail of Synthesis and characterization of a novel ester-based nucleoamino acid for the assembly of aromatic nucleopeptides for biomedical applications

International Journal of Pharmaceutics, Aug 1, 2011

In this work, we report a technological approach to a novel Fmoc-protected nucleoamino acid, base... more In this work, we report a technological approach to a novel Fmoc-protected nucleoamino acid, based on l-tyrosine, carrying the DNA nucleobase on the hydroxyl group by means of an ester bond, suitable for the solid-phase synthesis of novel aromatic nucleopeptides of potential interest in biomedicine. After ESI-MS and NMR characterization this building block was used for the assembly of a thymine-functionalized tetrapeptide, composed of nucleobase-containing and underivatized l-tyrosine moieties alternated in the backbone.

Research paper thumbnail of Fractal parameters and vascular networks: facts & artifacts

Theoretical Biology and Medical Modelling, Jul 17, 2008

Research paper thumbnail of Parkinson Informative System (ParIS): a pipeline fo the evaluation and clinical validation of Parkinson' disease proteomic biomarkers

Research paper thumbnail of A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots

Genomics, Proteomics & Bioinformatics, Dec 1, 2012

Research paper thumbnail of In vitro characterization of peptides interfering with the hiv-1 nucleocapsid protein (ncp7) functions

Protein & Peptide Letters

: In HIV-I, the nucleocapsid protein (NCp7) play essential roles in several steps of HIV-I replic... more : In HIV-I, the nucleocapsid protein (NCp7) play essential roles in several steps of HIV-I replication. Since NCp7 is required for virion formation and proviral DNA synthesis and is highly conserved, identification of compounds able to inhibit NCp7 activities and functions may lead to the discovery of new anti-HIV drugs. Here we present data showing that peptides derived from the first and second NCp7 zinc finger interfere, in vitro, with NCp7 functions during the early stage of HIV- I reverse transcription.

Research paper thumbnail of A Multicenter Phase 2 Randomized Controlled Study on the Efficacy and Safety of Reparixin in the Treatment of Hospitalized Patients with COVID-19 Pneumonia

Infectious Diseases and Therapy

Research paper thumbnail of Genetic and cell biology discriminants of Sars-CoV2 infection and susceptibility to Covid-19 pulmonary complication

The agent of Covid19, Sars-CoV-2 has caused thousands of fatalities worldwide and overshadowed th... more The agent of Covid19, Sars-CoV-2 has caused thousands of fatalities worldwide and overshadowed the number of deaths of other previous coronavirus outbreaks (Sars-CoV1 2002 and MERS-CoV 2012). Although the new coronavirus pathogenicity is actively under investigation, part of its infectious behavior can be linked to its higher binding affinity to the angiotensin-converting enzyme 2 (ACE2) in the respiratory tracts. However, the expression of ACE2 per se may not be sufficient to justify the individual variability observed among affected patients in terms of clinical outcome in apparently non-immune depressed, non-elders subjects. The present update provides an overview of the most recent scientific findings related to genetic factors involved in the Sars-CoV-2 infectious process and their potential role in affecting the virus pathogenicity. The present update can provide valuable hints towards developing a predictive screening/susceptibility profile testing on individuals not yet infe...

Research paper thumbnail of BCG vaccination policy and preventive chloroquine usage: do they have an impact on COVID-19 pandemic?

Cell Death & Disease, 2020

Coronavirus disease 2019 (COVID-19) is a severe acute respiratory syndrome caused by Coronavirus ... more Coronavirus disease 2019 (COVID-19) is a severe acute respiratory syndrome caused by Coronavirus 2 (SARS-CoV-2). In the light of its rapid global spreading, on 11 March 2020, the World Health Organization has declared it a pandemic. Interestingly, the global spreading of the disease is not uniform, but has so far left some countries relatively less affected. The reason(s) for this anomalous behavior are not fully understood, but distinct hypotheses have been proposed. Here we discuss the plausibility of two of them: the universal vaccination with Bacillus Calmette–Guerin (BCG) and the widespread use of the antimalarial drug chloroquine (CQ). Both have been amply discussed in the recent literature with positive and negative conclusions: we felt that a comprehensive presentation of the data available on them would be useful. The analysis of data for countries with over 1000 reported COVID-19 cases has shown that the incidence and mortality were higher in countries in which BCG vaccina...

Research paper thumbnail of Coronavirus 2019 Infectious Disease Epidemic: Where We Are, What Can Be Done and Hope For

Journal of Thoracic Oncology, 2021

Research paper thumbnail of COVID-19 infection: the perspectives on immune responses

Cell Death & Differentiation, 2020

Research paper thumbnail of Correction: P53-regulated miR-320a targets PDL1 and is downregulated in malignant mesothelioma

Cell Death & Disease, 2020

Author Francesca Pentimalli was incorrectly associated with Histopathological Unit, IRCCS-Istitut... more Author Francesca Pentimalli was incorrectly associated with Histopathological Unit, IRCCS-Istituto Tumori “Giovanni Paolo II”, Viale Orazio Flacco 65, 70124 Bari, Italy. The author’s actual affiliation is Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, I-80131 Napoli, Italy.

Research paper thumbnail of P53-regulated miR-320a targets PDL1 and is downregulated in malignant mesothelioma

Cell Death & Disease, 2020

Malignant pleural mesothelioma (MPM) is an aggressive cancer, related to asbestos exposure, which... more Malignant pleural mesothelioma (MPM) is an aggressive cancer, related to asbestos exposure, which has a dismal prognosis. MPM diagnosis is late and often challenging, suggesting the need to identify more reliable molecular biomarkers. Here, we set out to identify differentially expressed miRNAs in epithelioid, biphasic, and sarcomatoid MPMs versus normal mesothelium and explored specific miRNA contribution to mesothelial tumorigenesis. We screened an LNA™-based miRNA-microrray with 14 formalin-fixed paraffin-embedded (FFPE) MPMs and 6 normal controls. Through real-time qRT-PCR we extended the analysis of a miRNA subset and further investigated miR-320a role through state-of-the-art techniques. We identified 16 upregulated and 32 downregulated miRNAs in MPMs versus normal tissue, including the previously identified potential biomarkers miR-21, miR-126, miR-143, miR-145. We showed in an extended series that miR-145, miR-10b, and miR-320a levels can discriminate tumor versus controls w...

Research paper thumbnail of Genomic analysis reveals association of specific SNPs with athletic performance and susceptibility to injuries in professional soccer players

Journal of Cellular Physiology, 2019

The development of specific and individualized training programs is a possible way to improve ath... more The development of specific and individualized training programs is a possible way to improve athletic performance and minimize injuries in professional athletes. The information regarding the sport's physical demands and the athletes’ physical profile have been, so far, considered as exhaustive for the design of effective training programs. However, it is currently emerging that the genetic profile has to be also taken into consideration. By merging medical and genetic data, it is thus possible to identify the athlete's specific attitude to respond to training, diet, and physical stress. In this context, we performed a study in which 30 professional soccer players, subjected to standard sport medical evaluation and practices, were also screened for genetic polymorphism in five key genes (ACTN3, COL5A1, MCT1, VEGF, and HFE). This genetic analysis represents the central point of a multidisciplinary method that can be adopted by elite soccer teams to obtain an improvement in a...

Research paper thumbnail of New mouse models to study HGF/Met role in postnatal heart development and heart disease pathogenesis

Research paper thumbnail of Synthesis of a l-lysine-based alternate alpha,epsilon-peptide: A novel linear polycation with nucleic acids-binding ability

International Journal of Pharmaceutics, Sep 1, 2010

Research paper thumbnail of Synthesis, spectroscopic studies and biological activity of a novel nucleopeptide with Moloney murine leukemia virus reverse transcriptase inhibitory activity

Amino Acids, Oct 8, 2009

In this work, we report the synthesis of an alternate nucleo-alpha,epsilon-peptide based on l-lys... more In this work, we report the synthesis of an alternate nucleo-alpha,epsilon-peptide based on l-lysine moieties, an in vitro study of its biological activity, and spectroscopical binding studies between the novel nucleopeptide and Moloney murine leukemia virus reverse transcriptase as well as RNA. An alternate homothymine hexamer was synthesized by a straightforward solid phase route starting from commercial materials, purified by

Research paper thumbnail of Protein-centered biological networks by automatic caption analysis

Research paper thumbnail of Synthesis and aggregation properties of a novel enzymatically resistant nucleoamino acid

Amino Acids, Jan 18, 2012

Research paper thumbnail of 1H Chemical Shift Assignments for Superman Zinc Finger Domain

Journal of Back and Musculoskeletal Rehabilitation, Apr 10, 2003

Research paper thumbnail of Automatic detection of image manipulations in the biomedical literature

Cell Death and Disease, Mar 1, 2018

Research paper thumbnail of Synthesis and characterization of a novel ester-based nucleoamino acid for the assembly of aromatic nucleopeptides for biomedical applications

International Journal of Pharmaceutics, Aug 1, 2011

In this work, we report a technological approach to a novel Fmoc-protected nucleoamino acid, base... more In this work, we report a technological approach to a novel Fmoc-protected nucleoamino acid, based on l-tyrosine, carrying the DNA nucleobase on the hydroxyl group by means of an ester bond, suitable for the solid-phase synthesis of novel aromatic nucleopeptides of potential interest in biomedicine. After ESI-MS and NMR characterization this building block was used for the assembly of a thymine-functionalized tetrapeptide, composed of nucleobase-containing and underivatized l-tyrosine moieties alternated in the backbone.

Research paper thumbnail of Fractal parameters and vascular networks: facts & artifacts

Theoretical Biology and Medical Modelling, Jul 17, 2008

Research paper thumbnail of Parkinson Informative System (ParIS): a pipeline fo the evaluation and clinical validation of Parkinson' disease proteomic biomarkers

Research paper thumbnail of A Novel Gaussian Extrapolation Approach for 2D Gel Electrophoresis Saturated Protein Spots

Genomics, Proteomics & Bioinformatics, Dec 1, 2012

Research paper thumbnail of In vitro characterization of peptides interfering with the hiv-1 nucleocapsid protein (ncp7) functions

Protein & Peptide Letters

: In HIV-I, the nucleocapsid protein (NCp7) play essential roles in several steps of HIV-I replic... more : In HIV-I, the nucleocapsid protein (NCp7) play essential roles in several steps of HIV-I replication. Since NCp7 is required for virion formation and proviral DNA synthesis and is highly conserved, identification of compounds able to inhibit NCp7 activities and functions may lead to the discovery of new anti-HIV drugs. Here we present data showing that peptides derived from the first and second NCp7 zinc finger interfere, in vitro, with NCp7 functions during the early stage of HIV- I reverse transcription.

Research paper thumbnail of A Multicenter Phase 2 Randomized Controlled Study on the Efficacy and Safety of Reparixin in the Treatment of Hospitalized Patients with COVID-19 Pneumonia

Infectious Diseases and Therapy

Research paper thumbnail of Genetic and cell biology discriminants of Sars-CoV2 infection and susceptibility to Covid-19 pulmonary complication

The agent of Covid19, Sars-CoV-2 has caused thousands of fatalities worldwide and overshadowed th... more The agent of Covid19, Sars-CoV-2 has caused thousands of fatalities worldwide and overshadowed the number of deaths of other previous coronavirus outbreaks (Sars-CoV1 2002 and MERS-CoV 2012). Although the new coronavirus pathogenicity is actively under investigation, part of its infectious behavior can be linked to its higher binding affinity to the angiotensin-converting enzyme 2 (ACE2) in the respiratory tracts. However, the expression of ACE2 per se may not be sufficient to justify the individual variability observed among affected patients in terms of clinical outcome in apparently non-immune depressed, non-elders subjects. The present update provides an overview of the most recent scientific findings related to genetic factors involved in the Sars-CoV-2 infectious process and their potential role in affecting the virus pathogenicity. The present update can provide valuable hints towards developing a predictive screening/susceptibility profile testing on individuals not yet infe...

Research paper thumbnail of BCG vaccination policy and preventive chloroquine usage: do they have an impact on COVID-19 pandemic?

Cell Death & Disease, 2020

Coronavirus disease 2019 (COVID-19) is a severe acute respiratory syndrome caused by Coronavirus ... more Coronavirus disease 2019 (COVID-19) is a severe acute respiratory syndrome caused by Coronavirus 2 (SARS-CoV-2). In the light of its rapid global spreading, on 11 March 2020, the World Health Organization has declared it a pandemic. Interestingly, the global spreading of the disease is not uniform, but has so far left some countries relatively less affected. The reason(s) for this anomalous behavior are not fully understood, but distinct hypotheses have been proposed. Here we discuss the plausibility of two of them: the universal vaccination with Bacillus Calmette–Guerin (BCG) and the widespread use of the antimalarial drug chloroquine (CQ). Both have been amply discussed in the recent literature with positive and negative conclusions: we felt that a comprehensive presentation of the data available on them would be useful. The analysis of data for countries with over 1000 reported COVID-19 cases has shown that the incidence and mortality were higher in countries in which BCG vaccina...

Research paper thumbnail of Coronavirus 2019 Infectious Disease Epidemic: Where We Are, What Can Be Done and Hope For

Journal of Thoracic Oncology, 2021

Research paper thumbnail of COVID-19 infection: the perspectives on immune responses

Cell Death & Differentiation, 2020

Research paper thumbnail of Correction: P53-regulated miR-320a targets PDL1 and is downregulated in malignant mesothelioma

Cell Death & Disease, 2020

Author Francesca Pentimalli was incorrectly associated with Histopathological Unit, IRCCS-Istitut... more Author Francesca Pentimalli was incorrectly associated with Histopathological Unit, IRCCS-Istituto Tumori “Giovanni Paolo II”, Viale Orazio Flacco 65, 70124 Bari, Italy. The author’s actual affiliation is Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, I-80131 Napoli, Italy.

Research paper thumbnail of P53-regulated miR-320a targets PDL1 and is downregulated in malignant mesothelioma

Cell Death & Disease, 2020

Malignant pleural mesothelioma (MPM) is an aggressive cancer, related to asbestos exposure, which... more Malignant pleural mesothelioma (MPM) is an aggressive cancer, related to asbestos exposure, which has a dismal prognosis. MPM diagnosis is late and often challenging, suggesting the need to identify more reliable molecular biomarkers. Here, we set out to identify differentially expressed miRNAs in epithelioid, biphasic, and sarcomatoid MPMs versus normal mesothelium and explored specific miRNA contribution to mesothelial tumorigenesis. We screened an LNA™-based miRNA-microrray with 14 formalin-fixed paraffin-embedded (FFPE) MPMs and 6 normal controls. Through real-time qRT-PCR we extended the analysis of a miRNA subset and further investigated miR-320a role through state-of-the-art techniques. We identified 16 upregulated and 32 downregulated miRNAs in MPMs versus normal tissue, including the previously identified potential biomarkers miR-21, miR-126, miR-143, miR-145. We showed in an extended series that miR-145, miR-10b, and miR-320a levels can discriminate tumor versus controls w...

Research paper thumbnail of Genomic analysis reveals association of specific SNPs with athletic performance and susceptibility to injuries in professional soccer players

Journal of Cellular Physiology, 2019

The development of specific and individualized training programs is a possible way to improve ath... more The development of specific and individualized training programs is a possible way to improve athletic performance and minimize injuries in professional athletes. The information regarding the sport's physical demands and the athletes’ physical profile have been, so far, considered as exhaustive for the design of effective training programs. However, it is currently emerging that the genetic profile has to be also taken into consideration. By merging medical and genetic data, it is thus possible to identify the athlete's specific attitude to respond to training, diet, and physical stress. In this context, we performed a study in which 30 professional soccer players, subjected to standard sport medical evaluation and practices, were also screened for genetic polymorphism in five key genes (ACTN3, COL5A1, MCT1, VEGF, and HFE). This genetic analysis represents the central point of a multidisciplinary method that can be adopted by elite soccer teams to obtain an improvement in a...

Research paper thumbnail of New mouse models to study HGF/Met role in postnatal heart development and heart disease pathogenesis

Research paper thumbnail of Synthesis of a l-lysine-based alternate alpha,epsilon-peptide: A novel linear polycation with nucleic acids-binding ability

International Journal of Pharmaceutics, Sep 1, 2010

Research paper thumbnail of C'è speranza tra gli ulivi

Research paper thumbnail of Xylella, la parola alla scienza

Terra e Vita, 2019

Il punto di partenza è la relazione causale fra batterio e disseccamento rapido, accertata già da... more Il punto di partenza è la relazione causale fra batterio e disseccamento rapido, accertata già da molti anni e da più gruppi di ricerca Xylella, la parola alla scienza L a Xylella avanza, il Governo mette final-mente in atto misure che prevedono ab-battimenti obbligatori delle piante infette, ma c'è ancora qualcuno che si azzarda a mettere in discussione le acquisizioni della scienza. Terra e Vita si è rivolta a Enrico Bucci, professore aggiunto della Temple University di Filadelfia (Usa), per contribuire a liberare la "questione Xylella" dalle mistificazioni di negazionisti e complottisti e metterla final-mente con i piedi per terra, nella terra della scienza seria.

Research paper thumbnail of Xylella oppure no?

All’inizio di quest’anno la Commissione ricerca dell’Accademia nazionale dei Lincei ha chiesto al... more All’inizio di quest’anno la Commissione ricerca dell’Accademia nazionale dei Lincei ha chiesto all’autore di valutare se vi fossero dati sufficienti per provare in maniera solida la correlazione tra infezione del batterio Xylella fastidiosa osservata in olivi pugliesi e presenza di sintomi di della sindrome da disseccamento rapido. Lo studio ha riguardato oltre 5000 campioni di olivo raccolti da inizio 2015 a fine 2016. I campioni sono stati sottoposti a saggi di ricerca del batterio; inoltre, per stabilire un eventuale nesso di causalità il batterio è stato iniettato in olivi di una varietà nota per la sua suscettibilità all’infezione. I risultati hanno mostrato che Xylella fastidiosa è correlata alla sindrome da disseccamento rapido, e non è un semplice opportunista: il batterio è la causa della malattia

Research paper thumbnail of Cattivi Scienziati

In genere si pensa che gli errori nella ricerca scientifica siano commessi in buona fede o dovuti... more In genere si pensa che gli errori nella ricerca scientifica siano commessi in buona fede o dovuti a conoscenze imperfette. Ma non sempre è così. Mistificazioni, asserzioni fondate su osservazioni mai avvenute, selezione di risultati e plagio crescono spinti dalla volontà deliberata di soddisfare interessi individuali avallati da un sistema parzialmente corruttivo. L'estensione del disastro e il danno economico della frode scientifica sono scoraggianti, eppure... Eppure un sistema immunitario nuovo sta emergendo, ed è formato da una comunità sempre più numerosa di ricercatori che dedicano il proprio tempo all'identificazione di metodi utili alla scoperta delle manipolazioni, professionisti indipendenti che applicano questi metodi nell'analisi di ogni manoscritto candidato alla pubblicazione (e di ogni documento prodotto per ottenere finanziamenti o avanzamenti di carriera), comunicatori (con buona formazione scientifica) in grado di esporre con efficacia il pericolo contro cui ci si misura. A noi tutti spetta il compito di difendere il valore e la bellezza di uno strumento culturale - la Scienza che non ha eguali e che rappresenta uno dei fondamenti del nostro vivere odierno. Prefazione di Elena Cattaneo.

Research paper thumbnail of PUBBLICARE IL FALSO E NON CORREGGERLO : IL PECCATO ORIGINALE E LA RESPONSABILITÀ DELLE RIVISTE BIOMEDICHE

Il grande vantaggio dell’indagine scientifica sopra il mondo fisico rispetto a possibili alternat... more Il grande vantaggio dell’indagine scientifica sopra il mondo fisico rispetto a possibili alternative di natura filosofica, religiosa o di ogni altra specie che sia stata finora immaginata, consiste principalmente nell’utilizzare un metodo che, almeno in potenza, è in grado intrinsecamente di individuar debolezze e inconsistenze nel sapere accumulato, attraverso il doppio vaglio del dato sperimentale e della coerenza logico matematica delle teorie elaborate. Purtroppo, però, il tipo di organizzazione che si è oggi data la comunità dei ricercatori, ed in particolare il modo in cui gli editori e le riviste scientifiche agiscono nella pratica dell’impresa scientifica, tendono a rendere sempre più complesso ed in qualche caso apertamente ostacolano il processo di autocorrezione, di fatto trasformando gli articoli scientifici da semplici veicoli del sapere provvisoriamente riconosciuto come vero a certificatori di una realtà scientifica immutabile perché ormai pubblicata, utilizzabili per valutare un ricercatore rispetto ad un altro e dunque preziosi per carriera e finanziamenti. Con ciò, le riviste occupano quello che una volta era il posto delle autorità costituite nel bloccare l’avanzamento della conoscenza, particolarmente quando si tratti di correggere errori ormai accertati. Nel breve testo che segue, si tratterà l’esempio delle scienze biomediche.
Parole

Research paper thumbnail of Introducing an unbiased software procedure for image checking in a large research institution

The status of relative " objectivity " attributed to photographic documents was severely challeng... more The status of relative " objectivity " attributed to photographic documents was severely challenged in the transition from classical photography to digital imaging, because the same software used for producing and analysing digital images was very early used to retouch the images to be published. While this can be acceptable in principle – for example, intensity calibration of a digital image can be required for a quantitative analysis – it is also true that image manipulation aiming to deceive the readers of a scientific paper unfortunately became extremely easy. The once difficult photographic retouching is today technically available to anyone; thus, an easy prediction would be that illicit manipulation of scientific images should be highly prevalent. In particular, once the original obstacle (i.e. technical feasibility) has been lifted, there are certain conditions which would lead to a higher number of misconduct cases connected to image manipulation, namely: 1) the manipulation confers some strong advantages to the person committing it; 2) the probability of being discovered is low; 3) even after an actual fraud is discovered, the consequences for the offender are mild, if any. Indirect evidence for the hypothesis that fraudulent image manipulations are indeed increasingly common comes from the U.S. Office for Research Integrity (ORI) database. In fact, since the introduction of Photoshop in 1988, the number of ORI cases with questioned images has been growing exponentially. 1 However, image manipulations which surfaced in ORI cases are by definition originating from a tiny selection of research groups – only cases involving US Federal Funding are reported to and considered by ORI – and, even for the population considered, ORI cases are suspected to be only the tip of the iceberg. 2 In recognition of this problem, we thus decided to measure the actual extent of suspect image manipulation in the biomedical literature by performing an unbiased, automated analysis of a large image sample obtained from recent scientific publications, supplemented by expert analysis for verification of the findings. To this aim, we tweaked some home-made software with available open-source and commercial tools, to get an efficient pipeline for the extraction and processing of images from the scientific literature on a bulk scale. Briefly, we proceed through the following steps using the specified tools: a) Using a home-made software to process the different pdf format efficiently, we first performed an image-extraction step, used to extract all figures from each article and then to break down figures into single panels representing the results of specific experiments; b) Using a commercially-available tool to identify duplicated panels, both in the same paper and among the papers included in the sample;

Research paper thumbnail of Structural NMR studies of zinc finger domains

Research paper thumbnail of Die Klassifikation porziner Enteroviren auf der Basis molekularbiologischer Daten

Research paper thumbnail of Structure of an RNA Involved in Enteroviral Replication

Enteroviruses are human pathogens responsible for a number of acute and chronic diseases. The ini... more Enteroviruses are human pathogens responsible for a number of acute and chronic diseases. The initiation of enteroviral positive-strand synthesis requires a ribonucleoprotein complex consisting of a cloverleaf-like RNA structure at the 5´-end of the viral positive-strand RNA, and a set of proteins including the viral protease 3C pro . The 5´-cloverleaf RNA comprises one stem (A) and three stemloop subdomains (B, C, D). In vitro binding experiments using the 3C of coxsackievirus B3 revealed that the subdomain D of the 5´-cloverleaf is necessary and sufficient for specific 3C pro binding. Binding analysis using a set of cloverleaf and stemloop D mutants, together with CD spectroscopy, suggested that the apical loop of subdomain D is a major determinant for the specific RNA-protein interactions here (1). To elucidate the structural basis of the recognition of subdomain D by 3C pro we have determined the structure of a 30-mer RNA from subdomain D by heteronuclear multidimensional NMR spectroscopy. Hydrogen bonds indicating the presence of canonical base pairs and one unusual U:C base pair have been directly detected by the HNN-COSY experiment. Resonance assignments have been obtained using standard triple resonance experiments and a new experiment to link the exchangeable with the H5/H6 protons in pyrimidine bases simultaneously. The stem of stemloop D is in an all-helical conformation and includes a central base paired triple pyrimidine (U:U-U:C-U:U) mismatched region. The apical tetraloop has a defined structure closed by a U:G base pair. Even though the sequence and the closing base pair of the apical tetraloop differ from known stable tetraloops its structure is surprisingly similar to the structure of one of the known stable tetraloops. pro

Research paper thumbnail of Peptide Nucleic Acids targeting the 5´-nontranslated region of the Coxsackievirus B3 genomic RNA

Research paper thumbnail of PNA targeting the 5'-non traslated region of Coxsackievirus B3

Research paper thumbnail of Chimere PNA/DNA: nuove strategie per la sintesi di monomeri di PNA

Research paper thumbnail of TARGETING OF PNA TO A CYTOPLASMIC VIRUS

Peptide nucleic acids (PNA) are among the most powerful oligonucleotides analogues, with a N-(2-a... more Peptide nucleic acids (PNA) are among the most powerful oligonucleotides analogues, with a N-(2-amino-ethyl)-glycine unit replacing the sugar- phosphate backbone. They show strong a nd sequence specific hybridization to complementary single stranded DNA and RNA as well as to double stranded DNA by triplex formation. In additi on, this type of DNA mimic is not degraded by nucleases and proteas es and was shown to have both good antisense and antigene activity. Recen tly we have reported the design, synthesis and characterization of a PNA able to bind specifically to a control region of Coxsackievirus. In particular, the target system is the 5 ́- nontranslated region (5 ́-NTR) of Coxsackievirus B3 (CVB3), which is an important human pathogen. Regulatory regions often are unique in sequence and/or structure, suited for specific recognition with a low risk of nonspecific side effects. The 5 ́-NTR of CVB3 is a key player in the assembly of the viral replication complex which contains also viral and host cell proteins. We have demonstrated that the synthesised PNA binds to the target RNA disrupting its native structure and inhibits the inte raction with the RNA of a key viral protein, the protease 3Cpro. We report here the PNA entrance in HeLa cells and its antiviral activity.

Research paper thumbnail of Preliminary report on a radiofrequency controlled biosensor

Research paper thumbnail of Palaeobiology of Pietraroia fishes as inferred from phosphorus determination in coprolites

Research paper thumbnail of First occurrence of the ichthyodectid Cladocyclus sp. in the Lower Cretaceous Plattenkalk of Pietraroja (Southern Italy)

Research paper thumbnail of A mathematical descriptor for theropod forelimb claws: methods and implications

Research paper thumbnail of OPTIMAL RECOGNITION OF THE LENGTH OF DNA INSERTION/DELETION PATTERNS BY HMGB1

Research paper thumbnail of PHARMACOLOGICAL STRATEGIES TO ANTAGONIZE / INHIBIT HMGB1, AN EMERGING CHEMOTCYTOKINE, AS RELEVANT TARGET IN INFLAMMATORY PATHOLOGIES

Research paper thumbnail of dabPNA: synthesis, characterization and nucleic acid binding studies

Research paper thumbnail of Remote control of biomolecules by radiofrequency: A test study

Research paper thumbnail of A family of RF exposure systems for monitoring conformational changes of biomolecules induced by electromagnetic fields

Research paper thumbnail of From dsDNA a novel class of therapeutic HMGB1 inhibitors

Research paper thumbnail of Magnetic nanoparticles as effective energy transducers to activate biological nanomachines by means of RF electromagnetic signals

Research paper thumbnail of Predator-prey interaction of Brazilian Cretaceous toothed pterosaurs: a case example.

Elewa A.M.T. (eds) Predation in Organisms. Springer, Berlin, Heidelberg, 2007

This chapter presents an overview of evidence of predator-prey relationships in pterosaurs, with ... more This chapter presents an overview of evidence of predator-prey relationships in pterosaurs, with a focus on the Cretaceous (Santana Formation) pterosaurs from Chapado do Araripe, northeastern Brazil. The examples from the fossil record of pterosaurs as prey is scanty; the situation of pterosaurs as predators is not much better. However, especially for pterosaurs as predator, secondary evidence provides much insight in the life of these extinct predators. Here, we present a simple geometric model that proves the suggested way of predations of the toothed and crested taxa of the Anhangueridae.

Research paper thumbnail of Il finanziamento della ricerca scientifica e le politiche dell’UE

Europa. Le sfide della Scienza., Rome: Treccani, 2018, pp. 420–428., 2018

420 Per lungo tempo, in Europa, il finanziamento e la pro-mozione della ricerca scientifica e del... more 420 Per lungo tempo, in Europa, il finanziamento e la pro-mozione della ricerca scientifica e dell'attività cultu-rale in genere sono rimasti appannaggio di singoli me-cenati o gruppi di potere, i quali selezionavano i migliori 'dilettanti' disponibili, ovvero quegli indivi-dui che per proprio diletto coltivavano questo o quel settore del sapere. Lo scopo era quello di imprezio-sire con le discussioni dei 'filosofi'-cioè degli amanti della saggezza-le corti dei principi, 'arruolando' gli individui più meritevoli in circolazione, al pari di quanto si faceva con artisti e altri specialisti. Il sapere, come estremo ornamento, veniva mostrato ed esibito attraverso le opere di munificenza che il signore era in grado di finanziare. Rarissimi-e comunque risa-lenti alla volontà di singoli individui come l'impera-tore Federico II di Svevia-erano i finanziamenti di intere istituzioni, quali le università; fatta forse ecce-zione per i monasteri e le istituzioni ecclesiastiche, co-munque limitate nel campo d'azione delle proprie ri-cerche, le strutture di governo esistenti non prevedevano la presenza stabile di istituzioni di ri-cerca autonome dalla volontà di singoli individui o piccoli gruppi di potere. Questo stato di cose aveva un indubbio vantaggio per chi entrava nelle grazie di un mecenate. Quando però, in epoca moderna, al fa-coltoso mecenate si è sostituito lo Stato, cioè il citta-dino che finanzia la ricerca e la cultura attraverso le sue tasse, le cose sono profondamente cambiate. Innanzitutto, le risorse destinate alla ricerca scien-tifica hanno assunto il carattere di 'prelievo forzoso', molto più che quello di elargizione liberale: al citta-dino non viene infatti chiesto se intenda finanziare università, ricerca scientifica o altre imprese cultu-rali, perché-come riconosciuto anche nella nostra Costituzione-l'avanzamento del sapere è conside-rato un bene superiore e irrinunciabile per l'intera so-cietà. Alla base del reperimento delle risorse neces-sarie a finanziare la ricerca, al mecenate sono subentrate le leggi dei singoli Stati, cui nessuno si può sottrarre. In secondo luogo, è emersa una larga comunità di ri-cercatori pubblici, afferenti cioè a strutture e istituzioni finanziate con le tasse prelevate ai cittadini e i cui sti-pendi sono finanziati dallo Stato. È ben comprensi-bile infatti che la società nel suo complesso, anziché affidare le proprie risorse destinate alla ricerca scien-tifica a soggetti privati (potenzialmente latori di inte-ressi confliggenti con quello pubblico), decida di do-tarsi di pubbliche strutture e di pubblici ricercatori che abbiano per obiettivo predefinito nulla di più del-l'avanzamento della conoscenza e che non rispondano ad altri che allo Stato. Infine, la combinazione dei due punti appena di-scussi fa sì che, contrariamente a quanto accadeva in epoche precedenti, il singolo ricercatore o intellet-tuale che voglia dedicarsi a studi finanziati dal pub-blico non disponga in partenza delle risorse necessa-rie per portare avanti con successo il progetto che ha in mente, ma debba accettare regole e procedimenti che tutelino il sistema pubblico nell'ottenimento del risultato per il quale ha investito. Con queste premesse, si arriva alla vexata quaestio che è argomento di questo saggio: in presenza di ri-sorse limitate rispetto alla richiesta proveniente dai ricercatori, come possono le istituzioni pubbliche fi-nanziatrici distribuire al meglio quanto disponibile per la ricerca scientifica e per le attività di avanza-mento della conoscenza? Questa domanda può scomporsi in un insieme di punti, tutti connessi in sequenza logica. Si tratta di decidere: a) come distribuire le risorse disponibili e, in parti-colare, se concentrare o ripartire omogeneamente le risorse; b) cosa finanziare e in che modo prendere questa de-cisione; c) chi finanziare e su che base; d) come valutare l'efficacia e l'efficienza del finan-ziamento. Prima di affrontare tali questioni di teoria e me-todo dell'agire politico in tema di finanziamento della ricerca, è opportuno tuttavia ripercorrere brevemente, da un punto di vista storico-istituzionale, le politiche

Research paper thumbnail of Analysis of Scortichini et al. 2018

“Comunicare la scienza: La Xylella e il deperimento rapido degli ulivi”

Recently, Scortichini et al. reported the efficacy of Dentamet, a copper-zinc fertilizer, in the ... more Recently, Scortichini et al. reported the efficacy of Dentamet, a copper-zinc fertilizer, in the treatment of X.fastidiosa infected olive trees in Southern Italy. However, after reading the paper I have several doubts on the real efficacy of the compound and on the study setting, as explained in the presentation.

Research paper thumbnail of Scientific fraud as an industry

CM1406 Workshop for ECI, 2018

Until recently, the existence of scientific fraud has been related to the misbehaviour of single ... more Until recently, the existence of scientific fraud has been related to the misbehaviour of single researchers or research groups, cutting the corners to achieve recognition, grants and academic power. Circa 2014, however, the scientific community became aware of a florid Chinese market connected to the sale of authorship in international scientific papers, mainly powered by researchers struggling to publish something at whatever cost. After discovering the so-called " Chinese papermills " , it has been widely assumed that the main problem caused by them laid in the misattribution of papers to authors which did not contribute. Nevertheless, some relevant aspects of the phenomenon had so far escaped investigation. In particular, one might wonder whether: 1) the business of ghost-writing and scientific authorship selling are limited to Chinese papermills or are also based in Western countries; 2) the leaking of papermills papers into scientific journals is limited to low-quality and predatory journals; 3) in light of their relatively low cost, the papers produced by papermills are genuine or contain fabricated, falsified or plagiarized data; 4) papers and data fabrication and selling are limited to biomedical disciplines; 5) the overall impact of papermills fraudulent scientific papers over the scientific record is significant or not. After a thorough investigation of the phenomenon, it was clear to me that the main assumption of scientific fraud as an ethical or even criminal misbehavior, restricted to the scientific community, is far from complete. The reality is that, after scientific papers became a career commodity and a status symbol (with bibliometrics raised from the position of an obscure academic discipline to the level of a research evaluation instrument) both in Western and Eastern countries a new market was born for scientific fraud, one which will potentially inundate the scientific record with fraudulent data, will erode the shares of legitimate publishers and journals and ultimately may lead to a drastic loss of reliability of scientific journals. This market is dominated by digital companies outside the Academia, which is reduced to the role of customer, instead of the main actor, in the production of fraudulent papers; moreover, the size of this market starts to rival those of more respectful research-connected ones. To face this threat, a new model is needed: one in which scientific publishers will invest in quality checks, institutions and governments will abandon purely bibliometric evaluations and scientists will compete for the better idea, not for fragile mountains of papers.

Research paper thumbnail of ENTROPIA DI BIANCONI NELLE RETI BIOLOGICHE: DEFINIZIONE E STUDIO

L'entropia di Bianconi di un insieme di reti è il logaritmo del numero dei grafi che possiedono c... more L'entropia di Bianconi di un insieme di reti è il logaritmo del numero dei grafi che possiedono certe caratteristiche strutturali definite. Più piccola è l'entropia di un insieme di reti (di cui una rete reale rappresenta un'istanza), maggiore è il contenuto di informazione estraibile dai vincoli che lo definiscono. Questa semplicissima definizione di entropia strutturale delle reti permette alcune considerazioni interessanti quando si paragonino reti biologiche che cambiano nel tempo a seguito di eventi fisiologici o patologici, permettendo di ipotizzare l'esistenza di alcune leggi generali non altrimenti formalizzabili in maniera così semplice. Nell'ambito del presente seminario saranno presentati alcuni dati preliminari per illustrare la potenza e la semplicità dell'approccio ideato da Bianconi.

Research paper thumbnail of Fabbricazione, Falsificazione e Plagio: la letteratura scientifica e i suoi tre peccati capitali

Research paper thumbnail of Identificazione e frequenza di immagini alterate

L'immagine scientifica, e nella fattispecie i diversi tipi di immagine acquisiti attraverso macch... more L'immagine scientifica, e nella fattispecie i diversi tipi di immagine acquisiti attraverso macchinari via via più sofisticati, lungi dall'essere una semplice illustrazione, è stata ormai assunta come una delle possibili forme del dato scientifico, utilizzabile per dimostrare una gran varietà di fenomeni e per misurare una quantità di variabili sperimentali differenti. Per questo sua funzione multiforme e centrale nella documentazione scientifica, in particolare nelle discipline biologiche e mediche la figura pubblicata è anzi assurta ben presto al ruolo di principale dato sperimentale, perché, in mancanza di una esauriente teoria matematica alla base dell'interpretazione della realtà in queste discipline, il dato sperimentale " visibile " ha un ruolo fondamentale nel provare o confutare le ipotesi del ricercatore. A fronte di questo ruolo centrale dell'immagine, e della crescente spinta a pubblicare a tutti i costi cui sono sottoposti i ricercatori di tutte le discipline per ottenere finanziamenti e fare carriera, è naturale attendersi che, almeno nelle citate discipline, le figure scientifiche siano le prime a subire manipolazione fraudolenta, dato che su di esse riposa la possibilità di veder accettato un manoscritto sottoposto al meccanismo della peer review tipico delle discipline scientifiche. Questo è infatti precisamente quello che accade: sempre di più la frode scientifica, in settori disparati, vede al suo centro e come suo meccanismo la manipolazione di una o più immagini cruciali per la dimostrazione di una determinata ipotesi, tanto che nei casi analizzati dall'Office for Research Integrity degli Stati Uniti la manipolazione di immagini è alla base di oltre il 70% delle frodi scoperte. Contrariamente all'idea che i meccanismi auto-correttivi della Scienza possano funzionare, nella realtà queste manipolazioni passano il controllo dei revisori degli articoli scientifici, sia perché questi non sono abituati a metter in dubbio i dati (quanto le conclusioni che se ne traggono), sia perché le manipolazioni spesso sfruttano alcuni limiti intrinseci alla visione umana (un po' come nei giochi di prestigio). Con ciò, si accumulano sempre più lavori nella letteratura scientifica che contengono dati manipolati, con gravi danni per l'economia, la credibilità ed in ultima analisi la sostenibilità stessa dell'impresa scientifica. Eppure, proprio quello che è il mezzo attraverso cui viene commesso un gran numero di frodi ne costituisce il limite principale: metodi moderni di analisi delle immagini sono infatti in grado di stabilire in maniera obiettiva la presenza di manipolazioni, allertando i revisori di eventuali problemi e consentendo quindi una successiva indagine mirata e più approfondita. Questi metodi sono allo studio proprio nel nostro Paese, ed hanno potuto portare già al raggiungimento di qualche risultato nel settore dell'individuazione delle immagini manipolate, nella quantificazione generale del fenomeno e nella prima definizione di alcune misure di contenimento. Auspicabilmente, sfruttando il vantaggio accumulato, l'Italia e la sua comunità accademica e scientifica potranno giocare un ruolo di primo piano nell'affrontare il problema, a partire dalla sua analisi e dalla definizione dei suoi confini tecnici.

Research paper thumbnail of Research Integrity and Misconduct: General Considerations and Notable Cases in Plant Biology

When I started my activity in biomedical data analysis, I was fully convinced that Science could ... more When I started my activity in biomedical data analysis, I was fully convinced that Science could correct itself – and researchers as a community were motivated into telling the truth, notwithstanding some notable exception. In Science, every researcher builds upon trusted results obtained by others; which was exactly what I wanted to do, albeit on a scale larger than usual – aggregating the full biomedical literature in a single database, crossing data from different sources and finding new potential answers to diverse scientific problems using the power of informatics to get it quick and easy. Trusting each other experimental findings is the usual habit of researchers in every discipline – and I used to perceive errors in Science as honest or due to sloppy science, not to some bad and concealed purpose. It then came as a shock to me, when with my small group and armed with the proper technology, we discovered that, far from being an exception, the three cardinal sins of scientific fraud – data and experiment fabrication, falsification and plagiarism – are largely diffuse in the current scientific record, at such a rate that scientific fraud is becoming a serious issue. I started writing to scientific journals, to uncover potential frauds, ending up into involving the police for investigating some serious case. That because Science is not simply a cultural exercise; it must help all of us in discriminating facts from fictions and in making the right predictions, not to mention its role in the technological development and in the general progress of humanity. The human society as a whole, cannot allow the poisoning of the very essence of Science – i.e. the unbiased collection of facts to be screened with a method able to discriminate whether a given hypothesis is true or not. While fraud in science is not a new thing nor unexpected, given the human nature of scientists, the scale at which today is occurring is previously unseen – simply because there are too many incentives and very little risks given the current organization of the scientific enterprise. The result? More and more dishonest researchers are ruining Science – and if we will allow this, it will be very hard to step back. Plant Biology is not exempt; while one could think that most of the dishonest behaviour would be limited to those research fields where larger funding is available, such as biomedical sciences, in facts some of the most notable cases of recent scientific misconduct are to be found among people pretending to study plant molecular biology. I think that all of us should know what is going on – what are we risking, who are the fraudsters, what we can do and what responsibility every single citizen has in knowing what Science really is – and what is not.