Quadra-Stable Dynamics of p53 and PTEN in the DNA Damage Response.

Cell fate determination is a complex process that is frequently described as cells traveling on rugged pathways, beginning with DNA damage response (DDR). Tumor protein p53 (p53) and phosphatase and tensin homolog (PTEN) are two critical players in this process. Although both of these proteins are known to be key cell fate regulators, the exact mechanism by which they collaborate in the DDR remains unknown. Thus, we propose a dynamic Boolean network. Our model incorporates experimental data obtained from NSCLC cells and is the first of its kind. Our network's wild-type system shows that DDR activates the G2/M checkpoint, and this triggers a cascade of events, involving p53 and PTEN, that ultimately lead to the four potential phenotypes: cell cycle arrest, senescence, autophagy, and apoptosis (quadra-stable dynamics). The network predictions correspond with the gain-and-loss of function investigations in the additional two cell lines (HeLa and MCF-7). Our findings imply that p53 and PTEN act as molecular switches that activate or deactivate specific pathways to govern cell fate decisions. Thus, our network facilitates the direct investigation of quadruplicate cell fate decisions in DDR. Therefore, we concluded that concurrently controlling PTEN and p53 dynamics may be a viable strategy for enhancing clinical outcomes.

Network analysis reveals that the tumor suppressor lncRNA GAS5 acts as a double-edged sword in response to DNA damage in gastric cancer.

The lncRNA GAS5 acts as a tumor suppressor and is downregulated in gastric cancer (GC). In contrast, E2F1, an important transcription factor and tumor promoter, directly inhibits miR-34c expression in GC cell lines. Furthermore, in the corresponding GC cell lines, lncRNA GAS5 directly targets E2F1. However, lncRNA GAS5 and miR-34c remain to be studied in conjunction with GC. Here, we present a dynamic Boolean network to classify gene regulation between these two non-coding RNAs (ncRNAs) in GC. This is the first study to show that lncRNA GAS5 can positively regulate miR-34c in GC through a previously unknown molecular pathway coupling lncRNA/miRNA. We compared our network to several in-vivo/in-vitro experiments and obtained an excellent agreement. We revealed that lncRNA GAS5 regulates miR-34c by targeting E2F1. Additionally, we found that lncRNA GAS5, independently of p53, inhibits GC proliferation through the ATM/p38 MAPK signaling pathway. Accordingly, our results support that E2F1 is an engaging target of drug development in tumor growth and aggressive proliferation of GC, and favorable results can be achieved through tumor suppressor lncRNA GAS5/miR-34c axis in GC. Thus, our findings unlock a new avenue for GC treatment in response to DNA damage by these ncRNAs.

2D Dumbbell Silicene as a High Storage Capacity and Fast Ion Diffusion Anode for Li-Ion Batteries.

First-principles calculations within DFT have been performed to investigate the use of a recently synthesized form of silicene, the dumbbell (DB) silicene as an anode material for Li-ion batteries (LiBs). The energetically most stable geometries for Li adsorption on DB silicene were investigated, and the energy barriers for Li-ion diffusion among the possible stable adsorption sites were calculated. We found that DB silicene can be lithiated up to a ratio of 1.05 Li per Si atom, resulting in a high storage capacity of 1002 mA h g-1 and an average open-circuit potential of 0.38 V, which makes DB silicene suitable for applications as an anode in LiBs. The energy barrier for Li-ion diffusion was calculated to be as low as 0.19 eV, suggesting that the Li ions can easily diffuse on the entire DB silicene surface, decreasing the time for the charge/discharge process of the LiBs. Our detailed investigations show that the most stable form of two-dimensional silicon has characteristic features suitable for application in high-performance LiBs.

Dynamical modeling of miR-34a, miR-449a, and miR-16 reveals numerous DDR signaling pathways regulating senescence, autophagy, and apoptosis in HeLa cells.

Transfection of tumor suppressor miRNAs such as miR-34a, miR-449a, and miR-16 with DNA damage can regulate apoptosis and senescence in cancer cells. miR-16 has been shown to influence autophagy in cervical cancer. However, the function of miR-34a and miR-449a in autophagy remains unknown. The functional and persistent G1/S checkpoint signaling pathways in HeLa cells via these three miRNAs, either synergistically or separately, remain a mystery. As a result, we present a synthetic Boolean network of the functional G1/S checkpoint regulation, illustrating the regulatory effects of these three miRNAs. To our knowledge, this is the first synthetic Boolean network that demonstrates the advanced role of these miRNAs in cervical cancer signaling pathways reliant on or independent of p53, such as MAPK or AMPK. We compared our estimated probability to the experimental data and found reasonable agreement. Our findings indicate that miR-34a or miR-16 may control senescence, autophagy, apoptosis, and the functional G1/S checkpoint. Additionally, miR-449a can regulate just senescence and apoptosis on an individual basis. MiR-449a can coordinate autophagy in HeLa cells in a synergistic manner with miR-16 and/or miR-34a.

Theoretical Evidence behind Bifunctional Catalytic Activity in Pristine and Functionalized Al2 C Monolayers.

First principles electronic structure calculations based on the density functional theory (DFT) framework are performed to investigate hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) on two-dimensional Al2 C monolayers. In addition to the pristine Al2 C monolayer, monolayers doped with Nitrogen (N), Phosphorous (P), Boron (B), and Sulphur (S) are also investigated. After determining the individual adsorption energy of hydrogen and oxygen on the different functionalized Al2 C monolayers, the adsorption free energies are predicted for each of the functionalized monolayers in order to assess their suitability for HER or OER. The density of states and optical absorption spectra calculations along with the work function of the functionalized Al2 C monolayers enable us to gain a profound understanding of the electronic structure for the individual system and their relation to the water splitting mechanism.

Rationalizing the Hydrogen and Oxygen Evolution Reaction Activity of Two-Dimensional Hydrogenated Silicene and Germanene.

We have undertaken first-principles electronic structure calculations to show that the chemical functionalization of two-dimensional hydrogenated silicene (silicane) and germanene (germanane) can become a powerful tool to increase the photocatalytic water-splitting activity. Spin-polarized density functional theory within the GGA-PBE and HSE06 types of exchange correlation functionals has been used to obtain the structural, electronic, and optical properties of silicane and germanane functionalized with a series of nonmetals (N, P, and S), alkali metals (Li, Na, and K) and alkaline-earth metals (Mg and Ca). The surface-adsorbate interaction between the functionalized systems with H2 and O2 molecules that leads to envisaged hydrogen and oxygen evolution reaction activity has been determined.

The effect of impurities in ultra-thin hydrogenated silicene and germanene: a first principles study.

Spin polarized density functional theory within the GGA-PBE and HSE06 approach for the exchange correlation term has been used to investigate the stability and electronic properties of nitrogen and boron impurities in single layers of silicane and germanane. We have observed that these impurities have lower formation energies in silicane and germanane when compared to their counterparts in graphane. We have also noticed that the adsorption of H atoms in the vicinity of defects stabilizes the system. In addition, we have shown that the electronic properties of silicane and germanane can be tuned when N and B are incorporated in the Si and Ge network. N-doping and B-doping give rise to n-type and p-type semiconductor properties. However, the adsorption of H atoms quenches the doping effects.