Networks Models of Actin Dynamics during Spermatozoa Postejaculatory Life: A Comparison among Human-Made and Text Mining-Based Models

Bernabò, Nicola; Ordinelli, Alessandra; Ramal-Sanchez, Marina; Mattioli, Mauro; Barboni, Barbara

doi:10.1155/2016/9795409

Cited by 6 publications

(7 citation statements)

References 39 publications

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“…The presence of hub nodes indicated a real functional network with multiple biologically relevant pathways associated with the novel coronavirus infection. The text-mining approach in conjunction with Cytoscape has been successfully adopted to illustrate actin dynamics during the post-ejaculatory life of spermatozoa [ 48 ], to demonstrate the synergistic mechanisms of therapeutic herbs for rheumatic arthritis [ 49 ], and to find out the effects of psychological stress on innate immunity and metabolism in human [ 50 ].…”

Section: Resultsmentioning

confidence: 99%

Systematic Network and Meta-analysis on the Antiviral Mechanisms of Probiotics: A Preventive and Treatment Strategy to Mitigate SARS-CoV-2 Infection

Patra

Saxena

Sahu

et al. 2021

Probiotics & Antimicro. Prot.

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With the alarming rise of infected cases and deaths, COVID-19 is a pandemic, affecting 220 countries worldwide. Until now, no specific treatment is available against SARS-CoV-2. The causal virus SARS-CoV-2 primarily infects lung cells, leading to respiratory illness ranging in severity from the common cold to deadly pneumonia. This, with comorbidities, worsens the clinical outcome, particularly for immunosuppressed individuals with COVID-19. Interestingly, the commensal gut microbiota has been shown to improve lung infections by modulating the immune system. Therefore, fine-tuning of the gut microbiome with probiotics could be an alternative strategy for boosting immunity and treating COVID-19. Here, we present a systematic biological network and meta-analysis to provide a rationale for the implementation of probiotics in preventing and/or treating COVID-19. We have identified 90 training genes from the literature analysis (according to PRISMA guidelines) and generated an association network concerning the candidate genes linked with COVID-19 and probiotic treatment. The functional modules and pathway enrichment analysis of the association network clearly show that the application of probiotics could have therapeutic effects on ACE2-mediated virus entry, activation of the systemic immune response, nlrp3 -mediated immunomodulatory pathways, immune cell migration resulting in lung tissue damage and cardiovascular difficulties, and altered glucose/lipid metabolic pathways in the disease prognosis. We also demonstrate the potential mechanistic domains as molecular targets for probiotic applications to combat the viral infection. Our study, therefore, offers probiotics-mediated novel preventive and therapeutic strategies for COVID-19 warfare.

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Section: Resultsmentioning

confidence: 99%

Systematic Network and Meta-analysis on the Antiviral Mechanisms of Probiotics: A Preventive and Treatment Strategy to Mitigate SARS-CoV-2 Infection

Patra

Saxena

Sahu

et al. 2021

Probiotics & Antimicro. Prot.

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“…Each list obtained from manual data mining was matched to create a unique database “WoS_MMivF”, including exclusively mammalian-related manuscripts, which accounts totally for 1,111 papers. The quality control of manually collected data was carried out according to Bernabò et al , ( Bernabò et al, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

In Vitro Folliculogenesis in Mammalian Models: A Computational Biology Study

Bernabò

Berardino

Capacchietti

et al. 2021

Front. Mol. Biosci.

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In vitro folliculogenesis (ivF) has been proposed as an emerging technology to support follicle growth and oocyte development. It holds a great deal of attraction from preserving human fertility to improving animal reproductive biotechnology. Despite the mice model, where live offspring have been achieved,in medium-sized mammals, ivF has not been validated yet. Thus, the employment of a network theory approach has been proposed for interpreting the large amount of ivF information collected to date in different mammalian models in order to identify the controllers of the in vitro system. The WoS-derived data generated a scale-free network, easily navigable including 641 nodes and 2089 links. A limited number of controllers (7.2%) are responsible for network robustness by preserving it against random damage. The network nodes were stratified in a coherent biological manner on three layers: the input was composed of systemic hormones and somatic-oocyte paracrine factors; the intermediate one recognized mainly key signaling molecules such as PI3K, KL, JAK-STAT, SMAD4, and cAMP; and the output layer molecules were related to functional ivF endpoints such as the FSH receptor and steroidogenesis. Notably, the phenotypes of knock-out mice previously developed for hub.BN indirectly corroborate their biological relevance in early folliculogenesis. Finally, taking advantage of the STRING analysis approach, further controllers belonging to the metabolic axis backbone were identified, such as mTOR/FOXO, FOXO3/SIRT1, and VEGF, which have been poorly considered in ivF to date. Overall, this in silico study identifies new metabolic sensor molecules controlling ivF serving as a basis for designing innovative diagnostic and treatment methods to preserve female fertility.

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“…As the data source, we used a validated and curated database [46], which describes the molecular events occurring during the capacitation-dependent actin remodeling process [46] updated with the recent literature from an accurate search in PubMed and Google Scholar.…”

Section: Methodsmentioning

confidence: 99%

Cyclin–CDK Complexes are Key Controllers of Capacitation-Dependent Actin Dynamics in Mammalian Spermatozoa

Bernabò

Ramal-Sanchez

Valbonetti

et al. 2019

IJMS

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Mammalian spermatozoa are infertile immediately after ejaculation and need to undergo a functional maturation process to acquire the competence to fertilize the female egg. During this process, called capacitation, the actin cytoskeleton dramatically changes its organization. First, actin fibers polymerize, forming a network over the anterior part of the sperm cells head, and then it rapidly depolymerizes and disappears during the exocytosis of the acrosome content (the acrosome reaction (AR)). Here, we developed a computational model representing the actin dynamics (AD) process on mature spermatozoa. In particular, we represented all the molecular events known to be involved in AD as a network of nodes linked by edges (the interactions). After the network enrichment, using an online resource (STRING), we carried out the statistical analysis on its topology, identifying the controllers of the system and validating them in an experiment of targeted versus random attack to the network. Interestingly, among them, we found that cyclin-dependent kinase (cyclin–CDK) complexes are acting as stronger controllers. This finding is of great interest since it suggests the key role that cyclin–CDK complexes could play in controlling AD during sperm capacitation, leading us to propose a new and interesting non-genomic role for these molecules.

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Networks Models of Actin Dynamics during Spermatozoa Postejaculatory Life: A Comparison among Human-Made and Text Mining-Based Models

Cited by 6 publications

References 39 publications

Systematic Network and Meta-analysis on the Antiviral Mechanisms of Probiotics: A Preventive and Treatment Strategy to Mitigate SARS-CoV-2 Infection

Systematic Network and Meta-analysis on the Antiviral Mechanisms of Probiotics: A Preventive and Treatment Strategy to Mitigate SARS-CoV-2 Infection

In Vitro Folliculogenesis in Mammalian Models: A Computational Biology Study

Cyclin–CDK Complexes are Key Controllers of Capacitation-Dependent Actin Dynamics in Mammalian Spermatozoa

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