Electron capture dissociation product ion abundances at the X amino acid in RAAAA-X-AAAAK peptides correlate with amino acid polarity and radical stability

We present mechanistic studies aimed at improving the understanding of the product ion formation rules in electron capture dissociation (ECD) of peptides and proteins in Fourier transform ion cyclotron resonance mass spectrometry. In particular, we attempted to quantify the recently reported general correlation of ECD product ion abundance (PIA) with amino acid hydrophobicity. The results obtained on a series of model H-RAAAAXAAAAK-OH peptides confirm a direct correlation of ECD PIA with X amino acid hydrophobicity and polarity. The correlation factor (R) exceeds 0.9 for 12 amino acids (Ile, Val, His, Asn, Asp, Glu, Gln, Ser, Thr, Gly, Cys, and Ala). The deviation of ECD PIA for seven outliers (Pro is not taken into consideration) is explained by their specific radical stabilization properties (Phe, Trp, Tyr, Met, and Leu) and amino acid basicity (Lys, Arg). Phosphorylation of Ser, Thr, and Tyr decreases the efficiency of ECD around phosphorylated residues, as expected. The systematic arrangement of amino acids reported here indicates a possible route toward development of a predictive model for quantitative electron capture/transfer dissociation tandem mass spectrometry, with possible applications in proteomics.     

Improving the characteristics of the modulation response for fiber Bragg grating Fabry–Perot lasers by optimizing model parameters

A unified and comprehensive study on the small-signal intensity and frequency modulation characteristics of a fiber Bragg grating Fabry–Perot (FBG–FP) laser are numerically investigated. The effect of injection current, temperature, external optical feedback (OFB), nonlinear gain compression factor, fiber grating (FG) parameters and spontaneous emission factor on modulation response characteristics are presented. The rate equations of the laser model are presented in the form that the effect of temperature (T) and external optical feedback (OFB) are included. The temperature dependence (TD) of laser response is calculated according to the TD of laser cavity parameters instead of directly using the well-known Parkove equation. It is shown that the optimum external fiber length (L_ext) is 3.1 cm and the optimum range of working temperature for FGFP laser is within ±2 °C from the FBG reference temperature (T_o). Also, the antireflection (AR) coating reflectivity and the linewidth enhancement factor have no significant effect on the modulation spectra. It is also show that modulation response is extremely sensitive to the OFB level, high injection current and gain compression factor. The study indicates clearly that good dynamic characteristic can be obtained by system parameters optimization.     

Design and construction of Q-switched Nd:YAG laser system for LIBS measurements

A passive, Q-switched pulsed, Nd:YAG laser system was designed and built, which can provide a potential compact robust laser source for portable laser induced breakdown spectroscopy systems.The developed laser system operates at 1064 nm. Each laser shot contains a train of pulses having maximum total output energy of 170 mJ. The number of pulses varies from 1–6 pulses in each laser shot depending on the pump energy. The pulse width of each pulse ranges from 20 to 30 ns. The total duration of the output pulse train is within 300 μs. The multi-pulse nature of the laser shots was employed to enhance the LIBS signal. To validate the system, LIBS measurements and analysis were performed on ancient ceramic samples collected from Al-Fustat excavation in Old Cairo. The samples belong to different Islamic periods in Egypt history. The results obtained are highly indicative that useful information can be provided to archeologists for use in restoring and repairing of precious archeological objects.     

Comment on: “Theoretical calculation of turn-on delay time of VCSEL and effect of carriers recombination” [Opt. Laser Technol. 39 (2007) 997–1001]

Zhang et al. [Opt. Laser Technol. 39 (2007) 997–1001], through theoretical calculation, have shown that the turn-on time delay can be reduced by increasing any of the non-radiative (A_nr), radiative (B), and/or Auger recombination (C) coefficients at a constant injection current over threshold current. Here, we explain that the results presented by that paper are incorrect and the turn-on time delay increases by increasing any of the carrier recombination rate coefficients.     

The Potential Role of Nigella sativa Seed Oil as Epigenetic Therapy of Cancer

Nigella sativa oil, commonly known as black seed oil (BSO), is a well-known Mediterranean food, and its consumption is associated with beneficial effects on human health. A large number of BSO’s therapeutic properties is attributed to its pharmacologically active compound, thymoquinone (TQ), which inhibits cell proliferation and induces apoptosis by targeting several epigenetic players, including the ubiquitin-like, containing plant homeodomain (PHD) and an interesting new gene, RING finger domains 1 (UHRF1), and its partners, DNA methyltransferase 1 (DNMT1) and histone deacetylase 1 (HDAC1). This study was designed to compare the effects of locally sourced BSO with those of pure TQ on the expression of the epigenetic complex UHRF1/DNMT1/HDAC1 and the related events in several cancer cells. The gas chromatographs obtained from GC-MS analyses of extracted BSO showed that TQ was the major volatile compound. BSO significantly inhibited the proliferation of MCF-7, HeLa and Jurkat cells in a dose-dependent manner, and it induced apoptosis in these cell lines. BSO-induced inhibitory effects were associated with a significant decrease in mRNA expression of UHRF1, DNMT1 and HDAC1. Molecular docking and MD simulation showed that TQ had good binding affinity to UHRF1 and HDAC1. Of note, TQ formed a stable metal coordinate bond with zinc tom, found in the active site of the HDAC1 protein. These findings suggest that the use of TQ-rich BSO represents a promising strategy for epigenetic therapy for both solid and blood tumors through direct targeting of the trimeric epigenetic complex UHRF1/DNMT1/ HDAC1.     

Involvement of Phytochemical-Encapsulated Nanoparticles’ Interaction with Cellular Signalling in the Amelioration of Benign and Malignant Brain Tumours

Brain tumours have unresolved challenges that include delay prognosis and lower patient survival rate. The increased understanding of the molecular pathways underlying cancer progression has aided in developing various anticancer medications. Brain cancer is the most malignant and invasive type of cancer, with several subtypes. According to the WHO, they are classified as ependymal tumours, chordomas, gangliocytomas, medulloblastomas, oligodendroglial tumours, diffuse astrocytomas, and other astrocytic tumours on the basis of their heterogeneity and molecular mechanisms. The present study is based on the most recent research trends, emphasising glioblastoma cells classified as astrocytoma. Brain cancer treatment is hindered by the failure of drugs to cross the blood–brain barrier (BBB), which is highly impregnableto foreign molecule entry. Moreover, currently available medications frequently fail to cross the BBB, whereas chemotherapy and radiotherapy are too expensive to be afforded by an average incomeperson and have many associated side effects. When compared to our current understanding of molecularly targeted chemotherapeutic agents, it appears that investigating the efficacy of specific phytochemicals in cancer treatment may be beneficial. Plants and their derivatives are game changers because they are efficacious, affordable, environmentally friendly, faster, and less toxic for the treatment of benign and malignant tumours. Over the past few years, nanotechnology has made a steady progress in diagnosing and treating cancers, particularly brain tumours. This article discusses the effects of phytochemicals encapsulated in nanoparticles on molecular targets in brain tumours, along with their limitations and potential challenges.     

In-Silico Screening and Molecular Dynamics Simulation of Drug Bank Experimental Compounds against SARS-CoV-2

For the last few years, the world has been going through a difficult time, and the reason behind this is severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), one of the significant members of the Coronaviridae family. The major research groups have shifted their focus towards finding a vaccine and drugs against SARS-CoV-2 to reduce the infection rate and save the life of human beings. Even the WHO has permitted using certain vaccines for an emergency attempt to cut the infection curve down. However, the virus has a great sense of mutation, and the vaccine’s effectiveness remains questionable. No natural medicine is available at the community level to cure the patients for now. In this study, we have screened the vast library of experimental drugs of Drug Bank with Schrodinger’s maestro by using three algorithms: high-throughput virtual screening (HTVS), standard precision, and extra precise docking followed by Molecular Mechanics/Generalized Born Surface Area (MMGBSA). We have identified 3-(7-diaminomethyl-naphthalen-2-YL)-propionic acid ethyl ester and Thymidine-5′-thiophosphate as potent inhibitors against the SARS-CoV-2, and both drugs performed impeccably and showed stability during the 100 ns molecular dynamics simulation. Both of the drugs are among the category of small molecules and have an acceptable range of ADME properties. They can be used after their validation in in-vitro and in-vivo conditions.     

Screen-printed electrochemical sensors for label-free potentiometric and impedimetric detection of human serum albumin

Herein, two electrochemical methods based on potentiometric and impedimetric transductions were presented for albumin targeting, employing screen-printed platforms (SPEs) to make easy and cost-effective sensors with good detection merits. The SPEs incorporated ion-to-electron multi-walled carbon nanotubes (MWCNTs) transducer. Sensors were constructed using either tridodecyl methyl-ammonium chloride (TDMACl) (sensor I) or aliquate 336S (sensor II) in plasticized polymeric matrices of carboxylated poly (vinyl chloride) (PVC-COOH). Analytical performances of the sensors were evaluated using the above-mentioned electrochemical techniques. For potentiometric assay, constructed sensors responded to albumin with −81.7 ± 1.7 (r² = 0.9986) and −146.2 ± 2.3 mV/decade (r² = 0.9991) slopes over the linearity range 1.5 μM–1.5 mM with 0.8 and 1.0 μM detection limits for respective TDMAC- and aliquate-based sensors. Interference study showed apparent selectivity for both sensors. Impedimetric assays were performed at pH = 7.5 in 10 mM PBS buffer solution with a 0.02 M [Fe(CN)₆]^−3/−4 redox-active electrolyte. Sensors achieved detection limits of 4.3 × 10⁻⁸ and 1.8 × 10⁻⁷ M over the linear ranges of 5.2×10⁻⁸–1.0×10⁻⁴ M and 1.4×10⁻⁶–1.4×10⁻³ M, with 0.09 ± 0.004 and 0.168 ± 0.009 log Ω/decade slopes for sensors based on TDMAC and aliquate, respectively. These sensors are characterized with simple construction, high sensitivity and selectivity, fast response time, single-use, and cost-effectiveness. The methods were successfully applied to albumin assessment in different biological fluids.     

Acylphosphonamidates and α-hydroxyiminophosphonamidates. Synthesis of N-acylphosphordiamidates by Beckmann rearrangement. Crystal structure of (E)-α-hydroxyiminobenzyl-1-pyrrolidinylphosphinate

Reaction of methyl benzoylphosphonochloridate (3) with a secondary or primary series of amines yielded methyl benzoylphosphonamidates, 4a-e. The latter compounds reacted with hydroxylamine to yield a-hydroxyiminobenzylphosphonamidates (5a-e), largely as (E)-isomers. The structure of methyl (E)-a-hydroxyimino-benzyl-1-pyrrolidinylphosphinate (5b) was determined by single-crystal X-ray crystallography. Heating oximes 5a-e in boiling toluene caused them to undergo Beckmann rearrangement to N-benzoylphosphordiamidates 6a-e. © 1996 John Wiley & Sons, Inc.