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Article ; Online: Assessing the interaction between hemoglobin and the receptor binding domain of SARS-CoV-2 spike protein through MARTINI coarse-grained molecular dynamics.

Gasparello, Jessica / Verona, Marco / Chilin, Adriana / Gambari, Roberto / Marzaro, Giovanni

International journal of biological macromolecules

2023 Volume 253, Issue Pt 5, Page(s) 127088

Abstract: The emergence of different coronavirus-related diseases in the 2000's (SARS, MERS, and Covid-19) warrants the need of a complete understanding of the pathological, biological, and biochemical behavior of this class of pathogens. Great attention has been ... ...

Abstract	The emergence of different coronavirus-related diseases in the 2000's (SARS, MERS, and Covid-19) warrants the need of a complete understanding of the pathological, biological, and biochemical behavior of this class of pathogens. Great attention has been paid to the SARS-CoV-2 Spike protein, and its interaction with the human ACE2 has been thoroughly investigated. Recent findings suggested that the SARS-CoV-2 components may interact with different human proteins, and hemoglobin has very recently been demonstrated as a potential target for the Spike protein. Here we have investigated the interaction between either adult or fetal hemoglobin and the receptor binding domain of the Spike protein at molecular level through advanced molecular dynamics techniques and proposed rational binding modes and energy estimations. Our results agree with biochemical data previously reported in literature. We also demonstrated that co-incubation of pulmonary epithelial cells with hemoglobin strongly reduces the pro-inflammatory effects exerted by the concomitant administration of Spike protein.
MeSH term(s)	Humans ; COVID-19 ; Spike Glycoprotein, Coronavirus/chemistry ; SARS-CoV-2/metabolism ; Molecular Dynamics Simulation ; Binding Sites ; Protein Binding ; Hemoglobins/metabolism
Chemical Substances	spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Hemoglobins
Language	English
Publishing date	2023-09-27
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2023.127088
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Article ; Online: The Cystic Fibrosis Transmembrane Conductance Regulator Gene (CFTR) Is under Post-Transcriptional Control of microRNAs: Analysis of the Effects of agomiRNAs Mimicking miR-145-5p, miR-101-3p, and miR-335-5p.

Papi, Chiara / Gasparello, Jessica / Zurlo, Matteo / Cosenza, Lucia Carmela / Gambari, Roberto / Finotti, Alessia

Non-coding RNA

2023 Volume 9, Issue 2

Abstract: 1) Background: MicroRNAs are involved in the expression of the gene encoding the chloride channel CFTR (Cystic Fibrosis Transmembrane Conductance Regulator); the objective of this short report is to study the effects of the treatment of bronchial ... ...

Abstract	(1) Background: MicroRNAs are involved in the expression of the gene encoding the chloride channel CFTR (Cystic Fibrosis Transmembrane Conductance Regulator); the objective of this short report is to study the effects of the treatment of bronchial epithelial Calu-3 cells with molecules mimicking the activity of pre-miR-145-5p, pre-miR-335-5p, and pre-miR-101-3p, and to discuss possible translational applications of these molecules in pre-clinical studies focusing on the development of protocols of possible interest in therapy; (2) Methods:
Language	English
Publishing date	2023-04-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2813993-8
ISSN	2311-553X ; 2311-553X
ISSN (online)	2311-553X
ISSN	2311-553X
DOI	10.3390/ncrna9020029
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Article ; Online: Differential effects on the miRNome of the treatment of human airway epithelial Calu-3 cells with peptide-nucleic acids (PNAs) targeting microRNAs miR-101-3p and miR-145-5p: Next generation sequencing datasets.

Gasparello, Jessica / Fabbri, Enrica / Gambari, Roberto / Finotti, Alessia

Data in brief

2021 Volume 35, Page(s) 106718

Abstract: Since the demonstration that microRNAs are deeply involved in the regulation of Cystic Fibrosis (CF) Transmembrane Conductance Regulator (CFTR) gene, a great attention has been dedicated to possible alteration of the CFTR gene expression by targeting ... ...

Abstract	Since the demonstration that microRNAs are deeply involved in the regulation of Cystic Fibrosis (CF) Transmembrane Conductance Regulator (CFTR) gene, a great attention has been dedicated to possible alteration of the CFTR gene expression by targeting miRNAs causing down-regulation of CFTR and CFTR-associated proteins. The data here presented are related to previously published studies on the effects of treatment of human bronchial cells of PNAs targeting miR-101-3p and miR-145-5p (microRNAs shown to regulate the CFTR mRNA). These data here presented are relative to two companion articles "Treatment of human airway epithelial Calu-3 cells with a Peptide-Nucleic Acid (PNA) targeting the microRNA miR-101-3p is associated with increased expression of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene" (published in European Journal of Medicinal Chemistry, 2020) and "Peptide Nucleic Acids for MicroRNA Targeting" (published in Methods in Molecular Biology, 2020). The data obtained indicate that, while the expression of most microRNAs is not affected by PNA treatment, some of them are strongly modulated. In particular, some microRNAs involved in CF and/or CFTR regulation are co-inhibited by miR-101-3p and miR-145-5p. Among them, miR-155-5p, miR-125b-5p, miR-132-3p and miR-6873-3p. This has been demonstrated by Next Generation Sequencing (NGS) followed by RT-qPCR and RT-ddPCR validation.
Language	English
Publishing date	2021-01-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2021.106718
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Article: Differential effects on the miRNome of the treatment of human airway epithelial Calu-3 cells with peptide-nucleic acids (PNAs) targeting microRNAs miR-101-3p and miR-145-5p: Next generation sequencing datasets

Gasparello, Jessica / Fabbri, Enrica / Gambari, Roberto / Finotti, Alessia

Data in Brief. 2021 Apr., v. 35

2021

Abstract	Since the demonstration that microRNAs are deeply involved in the regulation of Cystic Fibrosis (CF) Transmembrane Conductance Regulator (CFTR) gene, a great attention has been dedicated to possible alteration of the CFTR gene expression by targeting miRNAs causing down-regulation of CFTR and CFTR-associated proteins. The data here presented are related to previously published studies on the effects of treatment of human bronchial cells of PNAs targeting miR-101-3p and miR-145-5p (microRNAs shown to regulate the CFTR mRNA). These data here presented are relative to two companion articles “Treatment of human airway epithelial Calu-3 cells with a Peptide-Nucleic Acid (PNA) targeting the microRNA miR-101-3p is associated with increased expression of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene” (published in European Journal of Medicinal Chemistry, 2020) and “Peptide Nucleic Acids for MicroRNA Targeting” (published in Methods in Molecular Biology, 2020). The data obtained indicate that, while the expression of most microRNAs is not affected by PNA treatment, some of them are strongly modulated. In particular, some microRNAs involved in CF and/or CFTR regulation are co-inhibited by miR-101-3p and miR-145-5p. Among them, miR-155-5p, miR-125b-5p, miR-132-3p and miR-6873-3p. This has been demonstrated by Next Generation Sequencing (NGS) followed by RT-qPCR and RT-ddPCR validation.
Keywords	chemistry ; cystic fibrosis ; cystic fibrosis transmembrane conductance regulator ; data collection ; epithelium ; gene expression ; genes ; humans ; microRNA ; molecular biology ; peptides
Language	English
Dates of publication	2021-04
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	2786545-9
ISSN	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2021.106718
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Article ; Online: Tackling the COVID-19 "cytokine storm" with microRNA mimics directly targeting the 3'UTR of pro-inflammatory mRNAs.

Gasparello, Jessica / Finotti, Alessia / Gambari, Roberto

Medical hypotheses

2020 Volume 146, Page(s) 110415

Abstract: COVID-19 is characterized by two major clinical phases, the SARS-CoV-2 infection of target cells and tissues, and a deep inflammatory state, known as "cytokine storm", caused by activation of pro-inflammatory genes, such as NF-kB, STAT-3, IL-6, IL-8, IL- ... ...

Abstract	COVID-19 is characterized by two major clinical phases, the SARS-CoV-2 infection of target cells and tissues, and a deep inflammatory state, known as "cytokine storm", caused by activation of pro-inflammatory genes, such as NF-kB, STAT-3, IL-6, IL-8, IL-1ß. Among possible anti-inflammatory agents, the "microRNA targeting" should be carefully considered, since it is well known that microRNAs are deeply involved in the expression of cytokines, chemokines and growth factors. The working general hypothesis is that targeting the microRNA network might be important for the development of therapeutic approaches to counteract the COVID-19 induction of inflammatory response. This hypothesis is based on several publications demonstrating the use of miRNA mimics for inhibitory effects on the production of proteins characterizing the COVID-19 "cytokine storm".
MeSH term(s)	3' Untranslated Regions/genetics ; Anti-Inflammatory Agents/pharmacology ; COVID-19/genetics ; COVID-19/immunology ; COVID-19/therapy ; Cytokine Release Syndrome/genetics ; Cytokine Release Syndrome/immunology ; Cytokine Release Syndrome/therapy ; Humans ; Inflammation/genetics ; Inflammation/immunology ; Inflammation/therapy ; MicroRNAs/genetics ; MicroRNAs/therapeutic use ; Models, Biological ; Molecular Mimicry ; RNA, Messenger/antagonists & inhibitors ; RNA, Messenger/genetics ; SARS-CoV-2
Chemical Substances	3' Untranslated Regions ; Anti-Inflammatory Agents ; MIRN200 microRNA, human ; MicroRNAs ; RNA, Messenger
Language	English
Publishing date	2020-11-25
Publishing country	United States
Document type	Journal Article
ZDB-ID	193145-3
ISSN	1532-2777 ; 0306-9877
ISSN (online)	1532-2777
ISSN	0306-9877
DOI	10.1016/j.mehy.2020.110415
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Article ; Online: Synergistic Effects of A Combined Treatment of Glioblastoma U251 Cells with An Anti-miR-10b-5p Molecule and An AntiCancer Agent Based on 1-(3',4',5'-Trimethoxyphenyl)-2-Aryl-1

Zurlo, Matteo / Romagnoli, Romeo / Oliva, Paola / Gasparello, Jessica / Finotti, Alessia / Gambari, Roberto

International journal of molecular sciences

2022 Volume 23, Issue 11

Abstract: 1) Background: In the development of new and more effective anticancer approaches, combined treatments appear of great interest. Combination therapy could be of importance in the management of glioblastoma (GBM), a lethal malignancy that accounts for 42% ...

Abstract	(1) Background: In the development of new and more effective anticancer approaches, combined treatments appear of great interest. Combination therapy could be of importance in the management of glioblastoma (GBM), a lethal malignancy that accounts for 42% of cancer of the central nervous system, with a median survival of 15 months. This study aimed to verify the activity on a glioblastoma cancer cell line of one of the most active compounds of a novel series of tubulin polymerization inhibitors based on the 1-(3',4',5'-trimethoxyphenyl)-2-aryl-1
MeSH term(s)	Antagomirs ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Brain Neoplasms/metabolism ; Cell Line, Tumor ; Cell Proliferation ; Gene Expression Regulation, Neoplastic ; Glioblastoma/drug therapy ; Glioblastoma/genetics ; Glioblastoma/metabolism ; Humans ; Imidazoles/pharmacology ; MicroRNAs/metabolism
Chemical Substances	Antagomirs ; Antineoplastic Agents ; Imidazoles ; MicroRNAs
Language	English
Publishing date	2022-05-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23115991
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Article: The Long Scientific Journey of Sirolimus (Rapamycin): From the Soil of Easter Island (Rapa Nui) to Applied Research and Clinical Trials on β-Thalassemia and Other Hemoglobinopathies.

Gambari, Roberto / Zuccato, Cristina / Cosenza, Lucia Carmela / Zurlo, Matteo / Gasparello, Jessica / Finotti, Alessia / Gamberini, Maria Rita / Prosdocimi, Marco

Biology

2023 Volume 12, Issue 9

Abstract: In this review article, we present the fascinating story of rapamycin (sirolimus), a drug able to induce γ-globin gene expression and increased production of fetal hemoglobin (HbF) in erythroid cells, including primary erythroid precursor cells (ErPCs) ... ...

Abstract	In this review article, we present the fascinating story of rapamycin (sirolimus), a drug able to induce γ-globin gene expression and increased production of fetal hemoglobin (HbF) in erythroid cells, including primary erythroid precursor cells (ErPCs) isolated from β-thalassemia patients. For this reason, rapamycin is considered of great interest for the treatment of β-thalassemia. In fact, high levels of HbF are known to be highly beneficial for β-thalassemia patients. The story of rapamycin discovery began in 1964, with METEI, the Medical Expedition to Easter Island (Rapa Nui). During this expedition, samples of the soil from different parts of the island were collected and, from this material, an antibiotic-producing microorganism (
Language	English
Publishing date	2023-09-02
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2661517-4
ISSN	2079-7737
ISSN	2079-7737
DOI	10.3390/biology12091202
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Article ; Online: Differential effects on the miRNome of the treatment of human airway epithelial Calu-3 cells with peptide-nucleic acids (PNAs) targeting microRNAs miR-101-3p and miR-145-5p

Jessica Gasparello / Enrica Fabbri / Roberto Gambari / Alessia Finotti

Data in Brief, Vol 35, Iss , Pp 106718- (2021)

Next generation sequencing datasets

2021

Abstract	Since the demonstration that microRNAs are deeply involved in the regulation of Cystic Fibrosis (CF) Transmembrane Conductance Regulator (CFTR) gene, a great attention has been dedicated to possible alteration of the CFTR gene expression by targeting miRNAs causing down-regulation of CFTR and CFTR-associated proteins. The data here presented are related to previously published studies on the effects of treatment of human bronchial cells of PNAs targeting miR-101-3p and miR-145-5p (microRNAs shown to regulate the CFTR mRNA). These data here presented are relative to two companion articles “Treatment of human airway epithelial Calu-3 cells with a Peptide-Nucleic Acid (PNA) targeting the microRNA miR-101-3p is associated with increased expression of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene” (published in European Journal of Medicinal Chemistry, 2020) and “Peptide Nucleic Acids for MicroRNA Targeting” (published in Methods in Molecular Biology, 2020). The data obtained indicate that, while the expression of most microRNAs is not affected by PNA treatment, some of them are strongly modulated. In particular, some microRNAs involved in CF and/or CFTR regulation are co-inhibited by miR-101-3p and miR-145-5p. Among them, miR-155-5p, miR-125b-5p, miR-132-3p and miR-6873-3p. This has been demonstrated by Next Generation Sequencing (NGS) followed by RT-qPCR and RT-ddPCR validation.
Keywords	Peptide nucleic acids ; Cystic fibrosis ; MicroRNAs ; miR-101-3p ; miR-145-5p ; NGS ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Science (General) ; Q1-390
Subject code	500
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Effects of Mithramycin on BCL11A Gene Expression and on the Interaction of the BCL11A Transcriptional Complex to γ-Globin Gene Promoter Sequences.

Finotti, Alessia / Gasparello, Jessica / Zuccato, Cristina / Cosenza, Lucia Carmela / Fabbri, Enrica / Bianchi, Nicoletta / Gambari, Roberto

Genes

2023 Volume 14, Issue 10

Abstract: The anticancer drug mithramycin (MTH), has been proposed for drug repurposing after the finding that it is a potent inducer of fetal hemoglobin (HbF) production in erythroid precursor cells (ErPCs) from β-thalassemia patients. In this respect, previously ...

Abstract	The anticancer drug mithramycin (MTH), has been proposed for drug repurposing after the finding that it is a potent inducer of fetal hemoglobin (HbF) production in erythroid precursor cells (ErPCs) from β-thalassemia patients. In this respect, previously published studies indicate that MTH is very active in inducing increased expression of γ-globin genes in erythroid cells. This is clinically relevant, as it is firmly established that HbF induction is a valuable approach for the therapy of β-thalassemia and for ameliorating the clinical parameters of sickle-cell disease (SCD). Therefore, the identification of MTH biochemical/molecular targets is of great interest. This study is inspired by recent robust evidence indicating that the expression of γ-globin genes is controlled in adult erythroid cells by different transcriptional repressors, including Oct4, MYB, BCL11A, Sp1, KLF3 and others. Among these, BCL11A is very important. In the present paper we report evidence indicating that alterations of BCL11A gene expression and biological functions occur during MTH-mediated erythroid differentiation. Our study demonstrates that one of the mechanisms of action of MTH is a down-regulation of the transcription of the BCL11A gene, while a second mechanism of action is the inhibition of the molecular interactions between the BCL11A complex and specific sequences of the γ-globin gene promoter.
MeSH term(s)	Humans ; gamma-Globins/genetics ; gamma-Globins/metabolism ; beta-Thalassemia/genetics ; Plicamycin/pharmacology ; Repressor Proteins/genetics ; Transcription Factors/genetics ; Fetal Hemoglobin/genetics ; Fetal Hemoglobin/metabolism ; Gene Expression ; Kruppel-Like Transcription Factors/genetics
Chemical Substances	gamma-Globins ; Plicamycin (NIJ123W41V) ; Repressor Proteins ; Transcription Factors ; Fetal Hemoglobin (9034-63-3) ; KLF3 protein, human ; Kruppel-Like Transcription Factors ; BCL11A protein, human
Language	English
Publishing date	2023-10-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14101927
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Article ; Online: Production and Characterization of K562 Cellular Clones Hyper-Expressing the Gene Encoding α-Globin: Preliminary Analysis of Biomarkers Associated with Autophagy.

Zurlo, Matteo / Gasparello, Jessica / Cosenza, Lucia Carmela / Breveglieri, Giulia / Papi, Chiara / Zuccato, Cristina / Gambari, Roberto / Finotti, Alessia

Genes

2023 Volume 14, Issue 3

Abstract: One of the most relevant pathophysiological hallmarks of β-thalassemia is the accumulation of toxic α-globin chains inside erythroid cells, which is responsible for their premature death (hemolysis). In this context, the availability of an experimental ... ...

Abstract	One of the most relevant pathophysiological hallmarks of β-thalassemia is the accumulation of toxic α-globin chains inside erythroid cells, which is responsible for their premature death (hemolysis). In this context, the availability of an experimental model system mimicking the excess in α-globin chain production is still lacking. The objective of the present study was to produce and characterize K562 cellular clones forced to produce high amounts of α-globin, in order to develop an experimental model system suitable for studies aimed at the reduction of the accumulation of toxic α-globin aggregates. In the present study, we produced and characterized K562 cellular clones that, unlike the original K562 cell line, stably produced high levels of α-globin protein. As expected, the obtained clones had a tendency to undergo apoptosis that was proportional to the accumulation of α-globin, confirming the pivotal role of α-globin accumulation in damaging erythroid cells. Interestingly, the obtained clones seemed to trigger autophagy spontaneously, probably to overcome the accumulation/toxicity of the α-globin. We propose this new model system for the screening of pharmacological agents able to activate the full program of autophagy to reduce α-globin accumulation, but the model may be also suitable for new therapeutical approaches targeted at the reduction of the expression of the α-globin gene.
MeSH term(s)	Humans ; alpha-Globins/biosynthesis ; alpha-Globins/genetics ; Autophagy/genetics ; Biomarkers ; Clone Cells ; K562 Cells
Chemical Substances	alpha-Globins ; Biomarkers
Language	English
Publishing date	2023-02-23
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes14030556
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