Cytotoxicity of Libyan Juniperus phoenicea against Human Cancer Cell Lines A549, EJ138, Hepg2 and MCF7

Background: The current study was undertaken to assess the cytotoxicity of the leaves of Libyan Juniperus phoenicea (Cupressaceae) against human cancer cell lines. Methods: The cytotoxicity of the n-hexane, dichloromethane (DCM) and methanol (MeOH) extracts of the leaves of J. phoenicea (JP), obtained from sequential Soxhlet extractions, was assessed against four human cancer cell lines: EJ138 (human bladder carcinoma), HepG2 (human liver hepatocellular carcinoma), A549 (human lung carcinoma) and MCF7 (human breast adenocarcinoma) using the MTT assay. Results: The cell line A549 was the most sensitive to the JP extracts, with the highest level of cytotoxicity with the IC50 values of 16, 13 and 100 μg/mL for the DCM, n-hexane and MeOH extracts, respectively. However, generally the most potent cytotoxic extract across the other cells tested was the n-hexane extract, followed by the DCM extract, whilst the MeOH extracts showed little or no cytotoxicity. The percentage of viability of cells decreased as the concentration of test compounds increased. The cytotoxicity of various chromatographic fractions from the extracts was also studied against the A459 cells. For the n-hexane fractions, the IC50 values were 160, 62, 90, 30, 9.5 and 40 μg/mL for fractions 1 to 5 and 7, respectively. Fractions 4 and 5 showed the greatest effect. DCM fractions 2, 3 and 4 had the IC50 values of 60, 92 and 19 μg/mL, respectively, and DCM fractions 5 to 8 were non-cytotoxic. Fractions 1 and 2 of the MeOH extract were non-cytotoxic, whereas cytotoxicity was observed for fractions 3 and 4 with IC50 values of 50 and 85 μg/mL, respectively. Conclusion: The outcome of the present study suggested that the JP leaves possess cytotoxic activities. The high level of cytotoxicity of the n-hexane and DCM extracts suggested that lipophilicity might affect the cytotoxicity of JP, where the less polar compounds had the strongest cytotoxicity

G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription

In human and mouse, the promoter of the KRAS gene contains a nuclease hypersensitive polypurine–polypyrimidine element (NHPPE) that is essential for transcription. An interesting feature of the polypurine G-rich strand of NHPPE is its ability to assume an unusual DNA structure that, according to circular dichroism (CD) and DMS footprinting experiments, is attributed to an intramolecular parallel G-quadruplex, consisting of three G-tetrads and three loops. The human and mouse KRAS NHPPE G-rich strands display melting temperature of 64 and 73°C, respectively, as well as a K(+)-dependent capacity to arrest DNA polymerase. Photocleavage and CD experiments showed that the cationic porphyrin TMPyP4 stacks to the external G-tetrads of the KRAS quadruplexes, increasing the T(m) by ∼20°C. These findings raise the intriguing question that the G-quadruplex formed within the NHPPE of KRAS may be involved in the regulation of transcription. Indeed, transfection experiments showed that the activity of the mouse KRAS promoter is reduced to 20% of control, in the presence of the quadruplex-stabilizing TMPyP4. In addition, we found that G-rich oligonucleotides mimicking the KRAS quadruplex, but not the corresponding 4-base mutant sequences or oligonucleotides forming quadruplexes with different structures, competed with the NHPPE duplex for binding to nuclear proteins. When vector pKRS-413, containing CAT driven by the mouse KRAS promoter, and KRAS quadruplex oligonucleotides were co-transfected in 293 cells, the expression of CAT was found to be downregulated to 40% of the control. On the basis of these data, we propose that the NHPPE of KRAS exists in equilibrium between a double-stranded form favouring transcription and a folded quadruplex form, which instead inhibits transcription. Such a mechanism, which is probably adopted by other growth-related genes, provides useful hints for the rational design of anticancer drugs against the KRAS oncogene

The effects of unnatural base pairs and mispairs on DNA duplex stability and solvation

In an effort to develop unnatural DNA base pairs we examined six pyridine-based nucleotides, d3MPy, d4MPy, d5MPy, d34DMPy, d35DMPy and d45DMPy. Each bears a pyridyl nucleobase scaffold but they are differentiated by methyl substitution, and were designed to vary both inter- and intra-strand packing within duplex DNA. The effects of the unnatural base pairs on duplex stability demonstrate that the pyridine scaffold may be optimized for stable and selective pairing, and identify one self pair, the pair formed between two d34DMPy nucleotides, which is virtually as stable as a dA:dT base pair in the same sequence context. In addition, we found that the incorporation of either the d34DMPy self pair or a single d34DMPy paired opposite a natural dA significantly increases oligonucleotide hybridization fidelity at other positions within the duplex. Hypersensitization of the duplex to mispairing appears to result from global and interdependent solvation effects mediated by the unnatural nucleotide(s) and the mispair. The results have important implications for our efforts to develop unnatural base pairs and suggest that the unnatural nucleotides might be developed as novel biotechnological tools, diagnostics, or therapeutics for applications where hybridization stringency is important

Ribosomal scanning on the 5′-untranslated region of the human immunodeficiency virus RNA genome

Translation initiation on most eukaryotic mRNAs occurs via a cap-dependent scanning mechanism and its efficiency is modulated by their 5′-untranslated regions (5′-UTR). The human immunodeficiency virus type 1 (HIV-1) 5′-UTR contains a stable TAR hairpin directly at its 5′-end, which possibly masks the cap structure. In addition, the 5′-UTR is relatively long and contains several stable RNA structures that are essential for viral replication. These characteristics may interfere with ribosomal scanning and suggest that translation is initiated via internal entry of ribosomes. Literature on the HIV-1 5′-UTR-driven translation initiation mechanism is controversial. Both scanning and internal initiation have been shown to occur in various experimental systems. To gain further insight in the translation initiation process, we determined which part of the 5′-UTR is scanned. To do so, we introduced upstream AUGs at various positions across the 5′-UTR and determined the effect on expression of a downstream reporter gene that was placed under control of the gag start codon. This strategy allowed us to determine the window of ribosomal scanning on the HIV-1 5′-UTR

Performance of wide-area power system stabilizers during major system upsets: investigation and proposal of solutions

© 2021 Springer Nature Switzerland AG. This is a post-peer-review, pre-copyedit version of Benasla, M., Denaï, M., Liang, J. et al. Performance of wide-area power system stabilizers during major system upsets: investigation and proposal of solutions. Electr Eng (2021). The final authenticated version is available online https://doi.org/10.1007/s00202-020-01168-3Wide-area damping controllers (WADCs) are effective means of improving the damping of inter-area oscillations and thereby ensuring a secure operation of modern highly stressed interconnected power systems; however, their implementation costs are high. Therefore, the controller must be well configured and designed to ensure its cost-effectiveness. Several techniques have been proposed in the literature to design effective controllers and good results have been achieved. However, some important practical aspects that could potentially impact the performance of the designed controller have not been addressed or studied in sufficient detail in these previous works. One such aspect is assessing the performance of the designed controllers under major system upsets resulting in large deviations in the frequency and fluctuations in the power. These may lead to controller saturation which could negatively impact its damping performance or even cause instability. In this paper, the impact of such large upsets is investigated on several test systems via extensive small- and large-signal analyses and it is shown that, during severe transients, controller saturation may occur and persist over a long period of time, posing a potential threat to the power system stability. This paper presents a very effective solution to alleviate this problem and help design more robust WADCs. The simulation results show that the proposed solution works well and leads to improved power system stabilisers performance during transient upsets.Peer reviewedFinal Accepted Versio

Insecticide susceptibility status of Phlebotomus (Paraphlebotomus) sergenti and Phlebotomus (Phlebotomus) papatasi in endemic foci of cutaneous leishmaniasis in Morocco

<p>Abstract</p> <p>Background</p> <p>In Morocco, cutaneous leishmaniasis is transmitted by <it>Phlebotomus sergenti </it>and <it>Ph. papatasi</it>. Vector control is mainly based on environmental management but indoor residual spraying with synthetic pyrethroids is applied in many foci of <it>Leishmania tropica</it>. However, the levels and distribution of sandfly susceptibility to insecticides currently used has not been studied yet. Hence, this study was undertaken to establish the susceptibility status of <it>Ph. sergenti </it>and <it>Ph. papatasi </it>to lambdacyhalothrin, DDT and malathion.</p> <p>Methods</p> <p>The insecticide susceptibility status of <it>Ph. sergenti </it>and <it>Ph. papatasi </it>was assessed during 2011, following the standard WHO technique based on discriminating dosage. A series of twenty-five susceptibility tests were carried out on wild populations of <it>Ph. sergenti </it>and <it>Ph. papatasi </it>collected by CDC light traps from seven villages in six different provinces. Knockdown rates (KDT) were noted at 5 min intervals during the exposure to DDT and to lambdacyhalothrin. After one hour of exposure, sandflies were transferred to the observation tubes for 24 hours. After this period, mortality rate was calculated. Data were analyzed by Probit analysis program to determine the knockdown time 50% and 90% (KDT50 and KDT90) values.</p> <p>Results</p> <p>Study results showed that <it>Ph.sergenti </it>and <it>Ph. papatasi </it>were susceptible to all insecticides tested. Comparison of KDT values showed a clear difference between the insecticide knockdown effect in studied villages. This effect was lower in areas subject to high selective public health insecticide pressure in the framework of malaria or leishmaniasis control.</p> <p>Conclusion</p> <p><it>Phlebotomus sergenti </it>and <it>Ph. papatasi </it>are susceptible to the insecticides tested in the seven studied villages but they showed a low knockdown effect in Azilal, Chichaoua and Settat. Therefore, a study of insecticide susceptibility of these vectors in other foci of leishmaniasis is recommended and the level of their susceptibility should be regularly monitored.</p

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field

RNAstructure: software for RNA secondary structure prediction and analysis

<p>Abstract</p> <p>Background</p> <p>To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence.</p> <p>Results</p> <p>RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained.</p> <p>Conclusion</p> <p>The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at <url>http://rna.urmc.rochester.edu/RNAstructure.html</url>.</p