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To better understand the potential of drug repurposing in COVID-19, we analyzed control strategies over essential host factors for SARS-CoV-2 infection. We constructed comprehensive directed protein-protein interaction (PPI) networks integrating the top-ranked host factors, the drug target proteins and directed PPI data. We analyzed the networks to identify drug targets and combinations thereof that offer efficient control over the host factors. We validated our findings against clinical studies data and bioinformatics studies. Our method offers a new insight into the molecular details of the disease and into potentially new therapy targets for it. Our approach for drug repurposing is significant beyond COVID-19 and may be applied also to other diseases.

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Current advances in computational modelling and simulation have led to the inclusion of computer scientists as partners in the process of engineering of new nanomaterials and nanodevices. This trend is now, more than ever, visible in the field of deoxyribonucleic acid (DNA)-based nanotechnology, as DNA's intrinsic principle of self-assembly has been proven to be highly algorithmic and programmable. As a raw material, DNA is a rather unremarkable fabric. However, as a way to achieve patterns, dynamic behavior, or nano-shape reconstruction, DNA has been proven to be one of the most functional nanomaterials. It would thus be of great potential to pair up DNA's highly functional assembly characteristics with the mechanic properties of other well-known bio-nanomaterials, such as graphene, cellulos, or fibroin. In the current study, we perform projections regarding the structural properties of a fibril mesh (or filter) for which assembly would be guided by the controlled aggregation of DNA scaffold subunits. The formation of such a 2D fibril mesh structure is ensured by the mechanistic assembly properties borrowed from the DNA assembly apparatus. For generating inexpensive pre-experimental assessments regarding the efficiency of various assembly strategies, we introduced in this study a computational model for the simulation of fibril mesh assembly dynamical systems. Our approach was based on providing solutions towards two main circumstances. First, we created a functional computational model that is restrictive enough to be able to numerically simulate the controlled aggregation of up to 1000s of elementary fibril elements yet rich enough to provide actionable insides on the structural characteristics for the generated assembly. Second, we used the provided numerical model in order to generate projections regarding effective ways of manipulating one of the the key structural properties of such generated filters, namely the average size of the openings (gaps) within these meshes, also known as the filter's aperture. This work is a continuation of Amarioarei et al., 2018, where a preliminary version of this research was discussed.

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Since its introduction in the early 2000s, DNA origami had a big impact on the development of nanotechnology by gathering numerous applications. During this time, many tools were designed and used to generate arbitrary shapes capable of self-assembly which make this technique more approachable. In this paper, we have created the map of Romania at nanoscale dimensions by using a new open-source software - PERDIX. For this purpose, we used a scaffold strand with a length of 6959 nucleotides and 162 staple strands with a variable length ranging between 20 and 63 nucleotides. All the computational tools that were used in this experiment are open-source and user-friendly.

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The Tile Assembly Model, and its many variants, is one of the most fundamental algorithmic assembly formalism within DNA nanotechnology. Most of the research in this field is focused on the complexity of assembling different shapes and patterns. In many cases, the assembly process is intrinsically deterministic and the final product is unique, while the assembly process might evolve through several possible assembly strategies. In this study we consider the controlled assembly of one dimensional tile structures according to predefined assembly graphs. We provide algorithmic approaches for developing such controlled assembly protocols, using the signal-passing Tile Assembly Model, as well as probabilistic approaches for investigating the assembly of such tile-based one-dimensional structures. As a byproduct, we build a generalized TAS (tile assembly system) which generate specific non-local non-associative algebraic computations and we assamble n x n squares using only one tile, which is a better efficiency compared to the staged assembly model. (C) 2019 The Authors. Published by Elsevier B.V.

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This paper presents the latest trends and approaches used for constructing nanoscale structures of 2D objects through DNA folding based on the DNA origami technology developed by Rothemund. The Rothemund method has been used in the construction of various shapes, such as the development of the nanoscale structure for the United States map. Following the steps of Rothemund's technique, we simulate the construction of the Romanian map nanoscale 2D structure, embedding the number 100 into it.

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The TAM (Model Tile Assembly Model) is a mathematical paradigm for modeling DNA self-assembling according to various given shapes, using DNA-tiles (rectangular shape) with sticky ends on each of the four edges that bound together on various shapes desired by the researcher. Although there are various models in the literature, the focus in this manuscript is on a rule based model, specifically the authors present an overview of the one-dimensional hierarchical self-assembly model of DNA tiles. The authors also present the evolution of number of tiles in partial assemblies, the average assembly size and of the number of partial assemblies of sizes 2 through 10 over the total running time. All simulations were run using the NFSim simulator on a preset period of time.

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According to European Commission reports published between 2010 - 2013, the development of European economy depends crucially on access to critical raw materials. Following the analysis performed by experts at European level, in 2011 was compiled and published a list of 14 critical raw materials, the so-called EU-14. In 2014 the list was updated with several new elements and one element (tantalum), was withdrawn from the list. The current list, being renamed EU-20, covers 20 critical raw materials including several high tech critical metals. Traditional mine exploitations are concentrated on using the deposits of ore extracted and processed by conventional techniques. The efficiency of metal recovery was variable over time and as a result, a significant amount of metal was discarded, most concentrations exceeding the current minimal permissible threshold. On the other hand, it is necessary the recovery of recyclable waste for reducing the risk of shortage of high tech critical metals. Therefore, it is necessary to develop new technologies for obtaining high tech critical metals, which is applicable to both primary and secondary sources of raw materials. Recovery of high-tech critical metals by processing ore, tailings or mine wastes, and recyclable materials can be successfully done with help of consortia or individual isolates of microorganisms, bacteria or fungi. Microorganisms interact with metals thus altering their physical and chemical condition. Isolation of individual strains and identification of microbial consortia that can be used in the design and development of effective biotechnological processes for the extraction of high tech critical metals is a current challenge of the scientific research in Europe. © 2016 Vasile Goldis University Press.

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Transfusion medicine relies on the possibility of storing red blood cells (RBCs) for a prolonged period of time. A better understanding of the nature of changes in stored RBCs may provide new strategies to improve the balance of benefits and transfusion's risks. In the light of recent results on the mechanism of programmed cell death of RBCs (erythroptosis), where numerous cellular changes are common hallmarks of the apoptotic phenomenon, we have developed new flow cytometric criteria to evaluate the viability of stored erythrocytes. In order to evaluate the possible benefic effect of low-intensity laser irradiation for increasing the blood preservation period, we irradiated the whole blood from healthy donors in specially designed bags for research purposes by MacoPharma Company containing SAGM medium, and conserved it for 3 weeks. LED (Light emitting diode) (lambda=465nm, P=60mW, P/S=100mW/cm(2)) and laser diode (lambda=660nm, P=30mW, P/S= 50mW/cm(2)) in continuous wave have been used as sources of irradiation. Doses were ranged between 0 and 2J/cm(3). After that period RBCs were analyzed by flow cytometry for morphological changes (FSC/SSC), apoptosis/necrosis analysis (FITC-annexin-V labeling/PI) and viability using an original Calcein-AM method on a FACScan cytometer using CellQuest Pro software for acquisition and analysis. Complementary, the RBCs integrity was analyzed by scanning electron microscopy (SEM). Morphological changes assessment of red blood cells by flow cytometry and scanning electron microscopy showed a good preservation of the discoidal shape for the irradiated cells compared with control.

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The paper refers to a bioactive matrix in membrane shape, with a thickness of 0.5 - 1.0 mm, and consisting of gelatine, chitosan, and α-chymotrypsin, with or without addition of glutaraldehyde as a cross-linking agent. The bioproduct is a biomaterial with biomedical applications as biocompatible membrane with anti-inflammatory action due to coupling of the proteolytic enzyme. Bioproducts have complex implications in the treatment of traumatized tissue, accelerating the pus cleansing of infected wound, blood clots and other cellular debris, secretions liquefaction and cleansing of necrotic tissue, and also stimulating tissue regeneration and a faster healing of open infected wounds. In order to establish the influence of cross- linking process and membrane’s thickness on mechanical properties, ultrastructural studies were carried out on obtained biomaterials by electron microscopy analysis. To demonstrate the biological qualities of new enzymatic biomaterials, the membrane’s biological effect was analyzed in a cell culture model (mouse fibroblasts NCTC). © 2014 Vasile Goldis University Press.

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The use of nanoparticles for biological and medical applications has rapidly increased and the potential for human and ecological toxicity is a growing area of investigation. For assessing cytotoxicity of nanoparticles we developed a new experimental cell system based on the use of nucleated erythrocytes (RBCs) from fish and batrachians, which are directly exposed to pollutants or nanoparticles absorbed by different ways and we have evaluated the toxic effects by flow cytometric analysis. The two modes of cell death (apoptosis and necrosis) differ fundamentally in their morphology, biochemistry and biological relevance. We and others have recently shown that programmed cell death of nucleated erythrocytes is related to an apoptotic mechanism. The toxicological analysis were performed comparatively on porphyrin base or metalloporphyrin and for each porphyrin bare derivative on two correspondent porphyrin-silica-hybrid nanomaterials obtained by one step acid catalysis and by two steps acid-base catalysis. To evaluate cell-nanoparticles interactions, nucleated RBCs were exposed to different concentrations of nanocomposites and analyzed by flow cytometry, after 24h incubation endpoints for morphological changes (FSC/SSC), apoptosis/necrosis analysis (FITC-annexin-V labeling/PI) and viability (using calcein-AM method). The investigation showed that the type of cellular death of nucleated erythrocytes is related to an apoptotic mechanism and that flow cytometric analysis of nucleated RBCs viability and cell death discrimination could provide a rapid and accurate analytical tool for evaluating in vitro the biological responses towards of nanoparticles for environmental protection. Nucleated erythrocytes can be a new experimental cellular model easy to use, with no costs for culture and for maintaining in the culture. The results reported in the present study indicate that our new flow cytometric protocols can be used to create dose-response curves which allow us to determine EC50 for toxicity or ecotoxicity tests. It is also generally applicable for identifying harmful effects associated with general antropic impact for the aquatic environment and for its biomonitoring.

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Polycythemia vera (PV) is characterized by an absolute increase in the red blood cell mass, but the mechanisms are not completely understood. In this study, we identified by flow cytometric analysis morphological forms that deviate from the classical discoid shape, who had level. Measurement of glycoconjugate sialylation using lectines demonstrates but which is close to normal after treatment and an increased percentage of cells with active caspase-8 and -3 compared to normal RBCs, showing that the organism tries to restore the apoptotic mechanism for maintaining the normal hematocrit. may contribute elucidation of the mechanism this diseasea more viability determined by Calcein-AM method and a normal phosphatidylserine exposure a low degree of sialilation of membrane glycoconjugates of Polycythemia vera RBCs Our observations for understanding the survival of RBCs in Polycythemia vera and may also participate in elucidation of the mechanism this diseasein pathogenesis of this disease. © 2011 Vasile Goldis University Press.

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The human activities have a negative impact to the environment, consisting in the water contamination with toxic products, heavy metals or with xenobiotic substances. Manufactured nanomaterials (nanoparticles, nanotubes, nanosheets and nanowires) have recent applications in drug delivery, medical devices, cosmetics, chemical catalysts, optoelectronics, electronics and magnetics. Some nanomaterials have been found to be toxic to humans and other organisms either upon contact or after persistent environmental exposure. In present, the measurements of the pollution degree are made with two methods: phisyco-chemical methods and ecotoxicological test (bioassay or environmental biosensors). Our results indicate that flow cytometric analysis of nucleated red blood cells viability using calcein-AM and cell death discrimination could provide a rapid and accurate experimental cellular model for effectively screening and evaluating biological responses for in vitro nanotoxicology and can be used in ecotoxicology as bioassays for the ecological monitoring of aquatic environment. In the some time, our results indicate that the use of nucleated erythocytes could be potentially useful for the development of rapid and low cost safety tests to assess fisheries product quality. © 2011 Vasile Goldis University Press.