Search Results (82)

Genomic instability has been increasingly recognized over the past decade as a fundamental driver of cancer initiation and progression, largely owing to its association with specific genes and cellular mechanisms that offer therapeutic potential. However, a comprehensive molecular framework that captures the interconnected processes underlying this phenomenon remains elusive. In this study, we focused on polo-like kinase 1 (PLK1), a key cell cycle regulator frequently overexpressed in diverse human tumors, to reconstruct a regulatory network that consolidates pre-existing biological knowledge exclusively related to pathways involved in genome stability maintenance and cancer. The resulting model integrates nine biological processes, 1030 reactions, and 716 molecular species to form a literature-supported network in which PLK1 serves as a central regulatory node. However, rather than depicting an isolated PLK1-centric system, this network reflects a broader and more complex architecture of interrelated genomic instability mechanisms. As expected, the simulations reproduced known behaviors associated with PLK1 dysregulation, reinforcing the well-established role of the kinase in genome destabilization. Importantly, this model also enables the exploration of additional, less-characterized dynamics, including the potential involvement of genes such as kif2c, incenp, and other regulators of chromosomal segregation and DNA repair, which appear to contribute to instability events downstream of PLK1. While these findings are grounded in mechanistic simulations and require further experimental validation, gene expression and survival analyses across tumor types support their clinical relevance by linking them to poor prognosis in specific cancers. Overall, the model provides a systemic and adaptable foundation for studying PLK1-related genomic instability, enabling both the reinforcement of known mechanisms and discovery of candidate genes and circuits that may drive tumorigenesis through compromised genome integrity across distinct cancer contexts. Full article

Since the development of recombinant DNA technologies, the need to establish biosafety and biosecurity measures to control genetically modified organisms has been clear. Auxotrophies, or conditional suicide switches, have been used as firewalls to avoid horizontal or vertical gene transfer, but their efficacy has important limitations. The use of xenobiological systems has been proposed as the ultimate biosafety tool to circumvent biosafety problems in genetically modified organisms. Xenobiology is a subfield of Synthetic Biology that aims to construct orthogonal biological systems based on alternative biochemistries. Establishing true orthogonality in cell-based or cell-free systems promises to improve and assure that we can progress in synthetic biology safely. Although a wide array of strategies for orthogonal genetic systems have been tested, the construction of a host harboring fully orthogonal genetic system, with all parts operating in an orchestrated, integrated, and controlled manner, still poses an extraordinary challenge for researchers. In this study, we have performed a thorough review of the current literature to present the main advances in the use of xenobiology as a strategy for biocontainment, expanding on the opportunities and challenges of this field of research. Full article

Nano solutions are widely used in medicine and also have the potential to be used when performing allelopathy screening studies. The present experiment aimed to test the effectiveness of colloidal nano silver Silver–Amber© with nanoparticles of 20 nm (>20 mg/L at a purity level of 99.99%) as a carrier of allelochemicals in laboratory conditions. The influence of eleven concentrations of Silver–Amber© (0.10, 0.20, 0.39, 0.78, 1.56, 3.13, 6.25, 12.5, 25.0, 50.0 and 100.0% v/v) on the germination and initial development of test plant Lactuca sativa L. in 0.75% agar medium was studied. Data revealed that when increasing the quantitative ratio of Silver–Amber©, an inhibitory effect on seed germination (from 37.8 to 94.3%) and on the plant growth (from 54.0 to 98.9%) appeared. Lower concentrations (0.63 to 0.04 ppm) had an indifferent to statistically unproven stimulatory effect on the germination and initial development of L. sativa (GI ranged from 88.7–94.6%). Therefore, nano silver can be used as carrier of allelochemicals in allelopathic studies in laboratory conditions. Full article

In many plant species, flowering is promoted by the cold treatment or vernalization. The mechanism of vernalization-induced flowering has been extensively studied in Arabidopsis but remains largely unknown in legumes. The orthologs of the FLC gene, a major regulator of vernalization response in Arabidopsis, are absent or non-functional in the vernalization-sensitive legume species. Nevertheless, the legume integrator genes FT and SOC1 are involved in the transition of the vernalization signal to meristem identity genes, including PIM (AP1 ortholog). However, the regulatory contribution of these genes to PIM activation in legumes remains elusive. Here, we presented the theoretical and data-driven analyses of a feed-forward regulatory motif that includes a vernalization-responsive FT gene and several SOC1 genes, which independently activate PIM and thereby mediate floral transition. Our theoretical model showed that the multiple regulatory branches in this regulatory motif facilitated the elimination of no-sense signals and amplified useful signals from the upstream regulator. We further developed and analyzed four data-driven models of PIM activation in Medicago trancatula in vernalized and non-vernalized conditions in wild-type and fta1-1 mutants. The model with FTa1 providing both direct activation and indirect activation via three intermediate activators, SOC1a, SOC1b, and SOC1c, resulted in the most relevant PIM dynamics. In this model, the difference between regulatory inputs of SOC1 genes was nonessential. As a result, in the M. trancatula model, the cumulative action of SOC1a, SOC1b, and SOC1c was favored. Overall, in this study, we first presented the in silico analysis of vernalization-induced flowering in legumes. The considered vernalization network motif can be supplemented with additional regulatory branches as new experimental data become available. Full article

Lateral phase separation within lipid bilayer membranes has attracted considerable attention in the fields of biophysics and cell biology. Living cells organize laterally segregated compartments, such as raft domains in an ordered phase, and regulate their dynamic structures under isothermal conditions to promote cellular functions. Model membrane systems with minimum components are powerful tools for investigating the basic phenomena of membrane phase separation. With the use of such model systems, several physicochemical characteristics of phase separation have been revealed. This review focuses on the isothermal triggering of membrane phase separation from a physical point of view. We consider the free energy of the membrane that describes lateral phase separation and explain the experimental results of model membranes to regulate domain formation under isothermal conditions. Three possible regulation factors are discussed: electrostatic interactions, chemical reactions and membrane tension. These findings may contribute to a better understanding of membrane lateral organization within living cells that function under isothermal conditions and could be useful for the development of artificial cell engineering. Full article

Silver nanoparticles (Ag NPs) with antibacterial activity can be prepared in different ways. In our case, we used ecological green synthesis with Agrimonia eupatoria L. The plant extract was used with Ag NPs for the first time to prepare termosensitive in situ gels (ISGs). Such gels are used to heal human or animal skin and mucous membranes, as they can change from a liquid to solid state after application. Ag NPs were characterized with various techniques (FTIR, TEM, size distribution, zeta potential) and their antibacterial activity was tested against Staphylococcus aureus and Escherichia coli. In accordance with the TEM data, we prepared monodispersed spherical Ag NPs with an average size of about 20 nm. Organic active compounds from Agrimonia eupatoria L. were found on their surfaces using FTIR spectroscopy. Surprisingly, only the in situ gel with Ag NPs showed antibacterial activity against Escherichia coli, while Ag NPs alone did not. Ag NPs prepared via green synthesis using plants with medicinal properties and incorporated into ISGs have great potential for wound healing due to the antibacterial activity of Ag NPs and the dermatological activity of organic substances from plants. Full article

Cancer is a fatal disease with a complex pathophysiology. Lack of specificity and cytotoxicity, as well as the multidrug resistance of traditional cancer chemotherapy, are the most common limitations that often cause treatment failure. Thus, in recent years, significant efforts have concentrated on the development of a modernistic field called nano-oncology, which provides the possibility of using nanoparticles (NPs) with the aim to detect, target, and treat cancer diseases. In comparison with conventional anticancer strategies, NPs provide a targeted approach, preventing undesirable side effects. What is more, nanoparticle-based drug delivery systems have shown good pharmacokinetics and precise targeting, as well as reduced multidrug resistance. It has been documented that, in cancer cells, NPs promote reactive oxygen species (ROS) production, induce cell cycle arrest and apoptosis, activate ER (endoplasmic reticulum) stress, modulate various signaling pathways, etc. Furthermore, their ability to inhibit tumor growth in vivo has also been documented. In this paper, we have reviewed the role of silver NPs (AgNPs) in cancer nanomedicine, discussing numerous mechanisms by which they render anticancer properties under both in vitro and in vivo conditions, as well as their potential in the diagnosis of cancer. Full article

Ratio sensing is a fundamental biological function observed in signal transduction and decision making. In the synthetic biology context, ratio sensing presents one of the elementary functions for cellular multi-signal computation. To investigate the mechanism of the ratio-sensing behavior, we explored the topological characteristics of biological ratio-sensing networks. With exhaustive enumeration of three-node enzymatic and transcriptional regulatory networks, we found that robust ratio sensing was highly dependent on network structure rather than network complexity. Specifically, a set of seven minimal core topological structures and four motifs were deduced to be capable of robust ratio sensing. Further investigations on the evolutionary space of robust ratio-sensing networks revealed highly clustered domains surrounding the core motifs which suggested their evolutionary plausibility. Our study revealed the network topological design principles of ratio-sensing behavior and provided a design scheme for constructing regulatory circuits with ratio-sensing behavior in synthetic biology. Full article

Within many chemical and biological systems, both synthetic and natural, communication via chemical messengers is widely viewed as a key feature. Often known as molecular communication, such communication has been a concern in the fields of synthetic biologists, nanotechnologists, communications engineers, and philosophers of science. However, interactions between these fields are currently limited. Nevertheless, the fact that the same basic phenomenon is studied by all of these fields raises the question of whether there are unexploited interdisciplinary synergies. In this paper, we summarize the perspectives of each field on molecular communications, highlight potential synergies, discuss ongoing challenges to exploit these synergies, and present future perspectives for interdisciplinary efforts in this area. Full article

Impaired wound healing affects hundreds of million people around the world; therefore, chronic wounds are a major problem not only for the patient, but also for already overloaded healthcare systems. Chronic wounds are always very susceptible to infections. Billions of dollars are spent to discover new antibiotics as quickly as possible; however, bacterial resistance against antibiotics is rising even faster. For this reason, a complete shift of the antibacterial treatment paradigm is necessary. The development of technology has allowed us to rediscover well-known agents presenting antimicrobial properties with a better outcome. In this context, silver nanoparticles are a promising candidate for use in such therapy. Silver has many useful properties that can be used in the treatment of chronic wounds, such as anti-bacterial, anti-inflammatory, and anti-oxidative properties. In the form of nanoparticles, silver agents can work even more effectively and can be more easily incorporated into various dressings. Silver-based dressings are already commercially available; however, innovative combinations are still being discovered and very promising results have been described. In this review article, the authors focused on describing experimental and clinical studies exploring dressings containing either silver or silver nanoparticles, the results of which have been published in recent years. Full article

In the present study, the anti-proliferative and apoptotic potential of Tabebuia roseo-alba in lung cancer was assessed. Silver nanoparticles (AgNPs) of T. roseo-alba were synthesized using an ethanolic extract and characterized by adopting various parameters. Herein, the eco-friendly, cost-effective, and green synthesis of AgNPs was evaluated using an ethanolic extract of T. roseo-alba. The as-synthesized AgNPs were then characterized using various characterization techniques, such as UV-visible spectroscopy (UV-vis), X-ray powder diffraction (XRD), dynamic light scattering (DLS), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The AgNPs are crystalline, spherical, and highly stable AgNPs of varying sizes in the range of 5–20 nm. The anticancer activity of the ethanolic extract of T. roseo-alba and its AgNPs was determined using an MTT assay. The results indicated that, although both samples showed prominent anti-proliferative activity on lung cancer cell lines, the AgNPs of T. roseo-alba were found to be more potent than the ethanolic extract. Further, apoptosis induction ability was evaluated by FITC Annexin V and PI staining, the results of which demonstrated the efficiency of the ethanolic extract of T. roseo-alba and its AgNPs in causing oxidative stress and subsequent cellular death. This was subsequently further confirmed by measuring the mitochondrial membrane potential after staining the cells with JC1. The apoptotic mode of cell death was further confirmed by DNA fragmentation and caspase assays using Western blot analysis. Full article

In this review, we discuss various methods of reproducing life dynamics using a constructive approach. An increase in the structural complexity of a model protocell is accompanied by an increase in the stage of reproduction of a compartment (giant vesicle; GV) from simple reproduction to linked reproduction with the replication of information molecules (DNA), and eventually to recursive proliferation of a model protocell. An encounter between a plural protic catalyst (C) and DNA within a GV membrane containing a plural cationic lipid (V) spontaneously forms a supramolecular catalyst (C@DNA) that catalyzes the production of cationic membrane lipid V. The local formation of V causes budding deformation of the GV and equivolume divisions. The length of the DNA strand influences the frequency of proliferation, associated with the emergence of a primitive information flow that induces phenotypic plasticity in response to environmental conditions. A predominant protocell appears from the competitive proliferation of protocells containing DNA with different strand lengths, leading to an evolvable model protocell. Recently, peptides of amino acid thioesters have been used to construct peptide droplets through liquid–liquid phase separation. These droplets grew, owing to the supply of nutrients, and were divided repeatedly under a physical stimulus. This proposed chemical system demonstrates a new perspective of the origins of membraneless protocells, i.e., the “droplet world” hypothesis. Proliferative model protocells can be regarded as autonomous supramolecular machines. This concept of this review may open new horizons of “evolution” for intelligent supramolecular machines and robotics. Full article

Although numerous reports using methods such as molecular dynamics, cellular automata, and artificial chemistry have clarified the process connecting non-life and life on protocell simulations, none of the models could simultaneously explain the emergence of cell shape, continuous self-replication, and replication control solely from molecular reactions and diffusion. Herein, we developed a model to generate all three conditions, except evolution ability, from hypothetical chains of chemical and molecular polymerization reactions. The present model considers a 2D lattice cell space, where virtual molecules are placed in each cell, and molecular reactions in each cell are based on a multiset rewriting rule, indicating stochastic transition of molecular species. The reaction paths of virtual molecules were implemented by replacing the rules of cellular automata that generate Turing patterns with molecular reactions. The emergence of a cell-like form with all three conditions except evolution ability was modeled and demonstrated using only molecular diffusion, reaction, and polymerization for modeling the chemical reactions of 15 types of molecules and 2 types of polymerized molecules. Furthermore, controlling self-replication is possible by changing the initial arrangement of a specific molecule. In summary, the present model is capable of investigating and refining existing hypotheses on the emergence of life. Full article

Light-driven synthetic biology refers to an autotrophic microorganisms-based research platform that remodels microbial metabolism through synthetic biology and directly converts light energy into bio-based chemicals. This technology can help achieve the goal of carbon neutrality while promoting green production. Cyanobacteria are photosynthetic microorganisms that use light and CO₂ for growth and production. They thus possess unique advantages as “autotrophic cell factories”. Various fuels and chemicals have been synthesized by cyanobacteria, indicating their important roles in research and industrial application. This review summarized the progresses and remaining challenges in light-driven cyanobacterial cell factory. The choice of chassis cells, strategies used in metabolic engineering, and the methods for high-value CO₂ utilization will be discussed. Full article