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

Here we realized a networks-based model representing the process of actin remodelling that occurs during the acquisition of fertilizing ability of human spermatozoa (HumanMade_ActinSpermNetwork, HM_ASN). Then, we compared it with the networks provided by two different text mining tools: Agilent Literature Search (ALS) and PESCADOR. As a reference, we used the data from the online repository Kyoto Encyclopaedia of Genes and Genomes (KEGG), referred to the actin dynamics in a more general biological context. We found that HM_ALS and the networks from KEGG data shared the same scale-free topology following the Barabasi-Albert model, thus suggesting that the information is spread within the network quickly and efficiently. On the contrary, the networks obtained by ALS and PESCADOR have a scale-free hierarchical architecture, which implies a different pattern of information transmission. Also, the hubs identified within the networks are different: HM_ALS and KEGG networks contain as hubs several molecules known to be involved in actin signalling; ALS was unable to find other hubs than “actin,” whereas PESCADOR gave some nonspecific result. This seems to suggest that the human-made information retrieval in the case of a specific event, such as actin dynamics in human spermatozoa, could be a reliable strategy

Graphene and Reproduction: A Love-Hate Relationship

Since its discovery, graphene and its multiple derivatives have been extensively used in many fields and with different applications, even in biomedicine. Numerous efforts have been made to elucidate the potential toxicity derived from their use, giving rise to an adequate number of publications with varied results. On this basis, the study of the reproductive function constitutes a good tool to evaluate not only the toxic effects derived from the use of these materials directly on the individual, but also the potential toxicity passed on to the offspring. By providing a detailed scientometric analysis, the present review provides an updated overview gathering all the research studies focused on the use of graphene and graphene-based materials in the reproductive field, highlighting the consequences and effects reported to date from experiments performed in vivo and in vitro and in different animal species (from Archea to mammals). Special attention is given to the oxidized form of graphene, graphene oxide, which has been recently investigated for its ability to increase the in vitro fertilization outcomes. Thus, the potential use of graphene oxide against infertility is hypothesized here, probably by engineering the spermatozoa and thus manipulating them in a safer and more efficient way

A Scientometric Study on Graphene and Related Graphene- Based Materials in Medicine

Here we carried out a scientometric analysis of scientific literature published referred to the use of graphene and graphene-based materials. We found that in the last 15 years, more than 1200 issues have been produced, with an H-index of 67 cited 2647 times. The countries that have a larger production, in terms of number of issues published, are China, the United States, South Korea, India, and Iran, and the most relevant subject categories in which they are indexed are materials science, chemistry, science and technology, physics, and engineering, while the biological and medical specialties seem to be actually not deeply involved

Membrane remodelling events occurring during mammalian spermatozoa capacitation: A systems biology study

Immediately after ejaculation, mammalian spermatozoa are unable to fertilize the homologous oocyte. They reach their fertilizing ability only after they reside for hours to days, depending on the species, within the female genital tract. Here a complex process, the capacitation, takes place as a consequence of the functional dialogue of activating (hormones, bicarbonate, calcium ions, etc…) and inhibiting (seminal plasma, endocannabinoids) factors present in female genital tract fluids. This process involves virtually all the component of male gametes: the intracellular pH rises, the ionic composition of cytosol changes, the proteins tyrosine phosphorylation pattern modifies, the actin cytoskeleton reorganizes, and the sperm membranes change their physical/chemical proprieties1. In particular, the cholesterol/phospholipids ratio decreases, the microdomains architecture reorganizes, and the plasma membrane (PM) anisotropy decreases, then PM becomes more instable and fluid2. These lasts events attracted the attention of researchers because of their possible implication in the determinism of “idiopathic infertility” of male origin, which is at the present one of the most important causes of fertilization failure. In addition, recently, has emerged the intriguing question of interconnection of signaling systems involved in capacitation and those expressed in apoptosis3. To study the structure of signaling systems involved in the lipid remodeling process that occurs during capacitation, we applied a systems biology approach. In particular, we realized a computational model of lipid remodeling, by using a biological networks-based modeling strategy: each molecule involved in that process was represented as a node, each interaction between molecules was represented as a link4. The database representing the lipid remodeling of spermatozoa and endocannabionid system have been de novo manually compiled. The one concerning apoptosis has been downloaded from Reactome, version v51 (http://www.reactome.org/), a free, open-source, curated and peer reviewed pathways database. All the networks have been realized with Cytoscape 3.1.1 (http://www.cytoscape.org/), an open source software for visualizing and integrating complex networks. All the analysis have been carried out with the plug-in Network Analyzer (http://apps.cytoscape.org/apps/networkanalyzer). As a result, we obtained a network that contains a single connected component composed by 244 nodes and 418 links. The in- and out-node degree, i.e. the probability distribution of the number of connection per node, followed the exponential law (exponent = -1.522 and -1.792 respectively), while the clustering coefficient, i.e. the measure the network tendency to form clusters, was near 0 (0.061). The node degree was correlated with the centrality of nodes within the network (r=0.802), expressed as beetweenness centrality. i.e. as the number of shortest paths from all vertices to all others that pass through a node. The values of characteristic path length was 6.373, while that of the average number of neighbors was 3.287. The statistical analysis of the obtained network clearly showed that it has a scale free topology and a small word structure. This specific feature could lead to take some important biological inferences. Firstly, it implies that the most of nodes is scarcely linked, while only a few nodes, the hubs, are highly connected. In other words the network is robust against random failure4. The low value of clustering coefficient, together with the values of averaged number of neighbors and of characteristic path length suggest that the messages will spread within the networks quickly and efficiently. Finally, it is possible to identify the nodes that show a higher level of control within the networks, i.e. the most connected ad central ones, listed in decreasing order: [Ca2+]I, ATP, Protein tyrosine Phosphorilation, PKA, cholesterol efflux, apoptosis, scramblase, acquisition of fertilizing ability, PKC, cAMP, AEA, membrane symmetry, oxysterols, sAC, cholesterol, pHi rise, PLD1, CaV, acrosome reaction, CB1, NADH. In our opinion, these findings could contribute to the knowledge of such an important event, which leads the spermatozoa to gain their fertilizing ability, and allows identifying the molecular mechanisms involved in the final fate of spermatozoa and in the check points involved

Capacitation-Related Lipid Remodeling of Mammalian Spermatozoa Membrane Determines the Final Fate of Male Gametes: A Computational Biology Study

To become fully fertile, mammalian spermatozoa must undergo a complex process of biochemical maturation within the female genital tract, which determines a marked lipid remodeling (LR) of membranes. Here, we represent this process as a biological network, which is a graph constituted by nodes (the molecules involved in LR) and by edges (their interactions). As a result, we found that LR network has a scale-free and small world topology. This implies that it is robust against random damage and that it allows a fast and specific transmission of information. In addition, the hubs in the network allow identification of the control mechanisms involved in membrane-related signaling, which could concur in determining the fate of ejaculated spermatozoa. Interestingly, different pathways involved in LR (maintenance of functional incompetence, reaching of fertilizing ability, apoptosis) are overlapped and some molecules take part in different signalling cascades; thus their role in sperm biology needs to be interpreted in a more large context. In addition, it was possible to differentiate, either based on their topological and biological characteristics, the molecules acting as global or local controller in LR. These findings may contribute to the understanding of capacitation-related signaling and of sperm physiopathology

Human sperm Interactome: a first step toward the personalized male Reproductive Medicine.

Despite the continuously growing effort of researchers, often the most common diagnostic and therapeutic approaches are not effective in treating male infertility. This, in one hand, causes the worsening of living conditions and of physical and psychological wellness of several couples and, in the other one, it determines the healthcare costs rising. The personalised medicine could address these challenges, by characterizing individuals’ phenotypes and genotypes. As a first step toward the adoption of a personalized medicine-based approach in the study of male infertility, we have realized a network that describes the Human Spermatozoa Interactome (HSI), by adopting Python scripting and biological networks-based approach. As data source, we used Pathway Commons and Reactome databases. All the networks have been realized, visualized, and analysed with Cytoscape 3.2.0. The analysis of HSI network topology, pointing out a scale-free and ultra-small world architecture, has led to infer important characteristics of the biological system: the network is robust against random failure; the low value of clustering coefficient, together with the values of averaged number of neighbours and of characteristic path length suggests that the messages will spread within the networks quickly and efficiently; it is possible to identify the nodes that shows a higher level of control within the networks, i.e. the most connected and central ones. This work could represent a first step to identify potential diagnostic markers and to concur in explaining “idiopathic infertility” of male origin with tailor-made prevention and treatment strategies

The maturation of murine spermatozoa membranes within the epididymis, a computational biology perspective

To become fertile, mammalian spermatozoa require completing a complex biochemical maturation that begins in the testis and ends within the female oviduct. Here, we paid attention to the events occurring at the membrane level during the epididymal transit. Indeed, in the epididymis, the molecular composition and the physical-chemical proprieties of sperm membranes markedly change, with functional cross talking among the spermatozoa, the epithelium, and the luminal content (particularly the epididymosomes). To study this process, we undertook a biological networks study, representing the involved molecules as nodes and their interactions as links. The analysis of network topology revealed that it has a scale free and small world architecture and it is robust against random failure. That assures a fast and efficient transmission of information and it leads to identifying the molecules exerting a higher level of control on the system, among which cholesterol plays a pivotal role. The reactome enrichment analysis allowed the reconstruction of the biochemical pathways involved in sperm epididymal maturation and STRING analysis permitted the identification of molecular events possibly involved in that process. In conclusion, this approach allows inferring interesting information, thus contributing to the knowledge on this process and suggesting staring points for further research

Putative human sperm Interactome: A networks study

Background: For over sixty years, it has been known that mammalian spermatozoa immediately after ejaculation are virtually infertile. They became able to fertilize only after they reside for long time (hours to days) within female genital tract where they complete their functional maturation, the capacitation. This process is finely regulated by the interaction with the female environment and involves, in spermatozoa, a myriad of molecules as messengers and target of signals. Since, to date, a model able to represent the molecular interaction that characterize sperm physiology does not exist, we realized the Human Sperm Interactme Network3.0 (HSIN3.0) and its main component (HSNI3.0_MC), starting from the pathway active in male germ cells. Results: HSIN3.0 and HSIN3.0_MC are scale free networks, adherent to the Barabasi-Albert model, and are characterised by an ultra-small world topology. We found that they are resistant to random attacks and that are designed to respond quickly and specifically to external inputs. In addition, it has been possible to identify the most connected nodes (the hubs) and the bottlenecks nodes. This result allowed us to explore the control mechanisms active in driving sperm biochemical machinery and to verify the different levels of controls: party vs. date hubs and hubs vs. bottlenecks, thanks the availability of data from KO mice. Finally, we found that several key nodes represent molecules specifically involved in function that are thought to be not present or not active in sperm cells, such as control of cell cycle, proteins synthesis, nuclear trafficking, and immune response, thus potentially open new perspectives on the study of sperm biology. Conclusions: For the first time we present a network representing putative human sperm interactome. This result gives very intriguing biological information and could contribute to the knowledge of spermatozoa, either in physiological or pathological conditions

ROLE OF THE ENDOCANNABINOID SYSTEM IN SPERMATOGENESIS: SYSTEMS BIOLOGY APPROACH

The spermatogenesis is a complex process that requires the differentiation of male gametes within the male genital tract. It involves a series of cellular events including mitosis, meiosis, cell migration, apoptosis, and differentiation of diploid germ cells (spermatogonia) to form haploid germ cells (spermatozoa). Recently, the endocannabinoid system (ECS) has been proposed to be involved in this process. It is composed by endogenous bioactive lipids, the N-arachidonoyl ethanolammine (AEA, anandamide) and the 2 arachidonoyl glycerol (2-AG), that recognize intracellular and extracellular receptors and by the enzymes responsible for their synthesis, degradation and transport (1). An innovative, computational modeling- based, approach was adopted to investigate the role of the ECS in control of spermatogenesis. In particular, we realized a network (the endocannabinoid system in spermatogenesis, ECSS) in which the nodes represented the molecules of ECS involved in spermatogenesis and the links were the interaction among them (2). The information on ECS molecules involved in spermatogenesis, from peer-reviewed papers from PubMed, published in last 10 years, were used to realize a database (Microsoft Office Excel 2003). The data were used to build the ECSS network and the statistical analysis of main topological parameters was carried out (Cytoscape 3.0.1 software) (3, 4). In particular the node degree (the number of links per node) distribution, the clustering coefficient (the presence of nodes clusters), the network diameter (the longest shortest path among all pairs of nodes), the mean number of neighbors (the mean number of connections per node), and the characteristic path length (the expected distance between two connected nodes) were assessed. It was found that ECSS network follows a scale free topology, characterized by a low clustering and easy navigability. In addition, the most connected ECS molecules (the hubs) are: AEA (25 links) CB1 and CB2 receptors (19 and 17 links), FAAH (11 links), NO (8 links). Thus, showing that AEA and the molecules directly involved in its signaling (its hydrolyzing enzyme, the FAAH, its receptors CB1 and CB2, and the related second messengers cAMP, Ca2+ and NO) play the key role in controlling spermatogenesis. From these data it is possible to infer some relevant information, not otherwise obtainable, and to achieve an important goal, the understanding of the role of ECS in spermatogenesis, potentially opening new prospective in drug discovery, diagnosis and clinical application. The ECS appears to be a new potential target for improving reproductive health in humans