RNA Isolation Method in Marginal Crops with High Agronomic Potential.

Ribonucleic Acid (RNA) isolation is a basic technique in the field of molecular biology. The purpose of RNA isolation is to acquire pure and complete RNA that can be used to evaluate gene expression. Many methods can be used to perform RNA isolation, all of them based on the chemical properties of nucleic acids. However, some of them do not achieve high RNA yields and purity levels when used in a number of marginally studied crops of agronomic importance, such as grain and vegetable amaranth plants. In the method described here, the use of guanidinium thiocyanate and two additional precipitation steps with different reagents designed to obtain high yields and RNA purity levels from diverse plant species employed for plant functional genomics studies is described.

Degradation of thiocyanate by Fe/Cu/C microelectrolysis: Role of pre-magnetization and enhancement mechanism.

Thiocyanate (SCN-), a non-volatile inorganic pollutant, is commonly found in various types of industrial wastewater, which is resistant to hydrolysis and has the potential to be toxic to organisms. Premagnetized iron-copper-carbon ternary micro-electrolytic filler (pre-Fe/Cu/C) was prepared to degrade SCN-. Pre-Fe/Cu/C exhibited the most significant enhancement effect on SCN- removal when magnetized for 5 min with an intensity of 100 mT, and the SCN- removal rate was the highest at an initial pH of 3.0 and an aeration rate of 1.6 L/min. The electrochemical corrosion and electron transfer in the pre-Fe/Cu/C system were confirmed through SEM, XPS, FTIR, XRD, and electrochemical tests. This resulted in the formation of more corrosion products and multiple cycles of Fe2+/Fe3+ and Cu0/Cu+/Cu2+. Additionally, density functional theory (DFT) calculations and electron paramagnetic resonance (EPR) were utilized to illustrate the oxygen adsorption properties of the materials and the participation of reactive oxygen species (1O2, ·O2-, and ·OH) in SCN- removal. The degradation products of SCN- were identified as SO42-, HCO3-, NH4+, and N2. This study introduced the use of permanent magnets for the first time to enhance Fe/Cu/C ternary micro-electrolytic fillers, offering a cost-effective, versatile, and stable approach that effectively effectively enhanced the degradation of SCN-.

The therapeutic potential of thiocyanate and hypothiocyanous acid against pulmonary infections.

Hypothiocyanous acid (HOSCN) is an endogenous oxidant produced by peroxidase oxidation of thiocyanate (SCN-), an ubiquitous sulfur-containing pseudohalide synthesized from cyanide. HOSCN serves as a potent microbicidal agent against pathogenic bacteria, viruses, and fungi, functioning through thiol-targeting mechanisms, independent of currently approved antimicrobials. Additionally, SCN- reacts with hypochlorous acid (HOCl), a highly reactive oxidant produced by myeloperoxidase (MPO) at sites of inflammation, also producing HOSCN. This imparts both antioxidant and antimicrobial potential to SCN-. In this review, we discuss roles of HOSCN/SCN- in immunity and potential therapeutic implications for combating infections.

Characterization of the active site in the thiocyanate-forming protein from Thlaspi arvense (TaTFP) using EPR spectroscopy.

Glucosinolates are plant thioglucosides, which act as chemical defenses. Upon tissue damage, their myrosinase-catalyzed hydrolysis yields aglucones that rearrange to toxic isothiocyanates. Specifier proteins such as thiocyanate-forming protein from Thlaspi arvense (TaTFP) are non-heme iron proteins, which capture the aglucone to form alternative products, e.g. nitriles or thiocyanates. To resolve the electronic state of the bound iron cofactor in TaTFP, we applied continuous wave electron paramagnetic resonance (CW EPR) spectroscopy at X-and Q-band frequencies (∼9.4 and ∼34 GHz). We found characteristic features of high spin and low spin states of a d 5 electronic configuration and local rhombic symmetry during catalysis. We monitored the oxidation states of bound iron during conversion of allylglucosinolate by myrosinase and TaTFP in presence and absence of supplemented Fe2+. Without added Fe2+, most high spin features of bound Fe3+ were preserved, while different g'-values of the low spin part indicated slight rearrangements in the coordination sphere and/or structural geometry. We also examined involvement of the redox pair Fe3+/Fe2 in samples with supplemented Fe2+. The absence of any EPR signal related to Fe3+ or Fe2+ using an iron-binding deficient TaTFP variant allowed us to conclude that recorded EPR signals originated from the bound iron cofactor.

2D-IR spectroscopy of carbohydrates: Characterization of thiocyanate-labeled ß-glucose in CHCl3 and H2O.

Carbohydrates constitute one of the four key classes of biomacromolecules but have not been studied by 2D-IR spectroscopy so far. Similarly as for proteins, a lack of native vibrational reporter groups, combined with their huge structural diversity, leads to spectrally congested infrared spectra already for single carbohydrates. Biophysical studies are further impeded by the strong overlap between water modes and carbohydrate modes. Here, we demonstrate the application of the known vibrational reporter group thiocyanate (SCN) as a label in glucose. In this first study, we are able to perform IR and 2D-IR spectroscopy of ß-glucose with SCN at the C2 position in chloroform. Upon improved synthesis and the removal of all protecting groups, we successfully performed 2D-IR spectroscopy of ß-glucose in H2O. All experimental results are compared to those of methyl-thiocyanate as a reference sample. Overall, we show that the concept of using site-specific vibrational reporter groups can be transferred to carbohydrates. Thus, biophysical studies with 2D-IR spectroscopy can now expand to glycoscience.

On the mechanisms of ion adsorption to aqueous interfaces: air-water vs. oil-water.

The adsorption of ions to water-hydrophobe interfaces influences a wide range of phenomena, including chemical reaction rates, ion transport across biological membranes, and electrochemical and many catalytic processes; hence, developing a detailed understanding of the behavior of ions at water-hydrophobe interfaces is of central interest. Here, we characterize the adsorption of the chaotropic thiocyanate anion (SCN-) to two prototypical liquid hydrophobic surfaces, water-toluene and water-decane, by surface-sensitive nonlinear spectroscopy and compare the results against our previous studies of SCN- adsorption to the air-water interface. For these systems, we observe no spectral shift in the charge transfer to solvent spectrum of SCN-, and the Gibb's free energies of adsorption for these three different interfaces all agree within error. We employed molecular dynamics simulations to develop a molecular-level understanding of the adsorption mechanism and found that the adsorption for SCN- to both water-toluene and water-decane interfaces is driven by an increase in entropy, with very little enthalpic contribution. This is a qualitatively different mechanism than reported for SCN- adsorption to the air-water and graphene-water interfaces, wherein a favorable enthalpy change was the main driving force, against an unfavorable entropy change.

Self-assembly of new cobalt complexes based on [Co (SCN)4], synthesis, empirical, antioxidant activity, and quantum theory investigations.

The cobalt (II) complexes have been synthesized from the reaction of the cationic entities (3,4-dimethylaniline (1) and histamine (2)) with metallic salt CoCl2⋅6H2O and thiocyanate ion (SCN-) as a ligand in H2O/ethanolic solution and processing by the evaporation crystal growth method at room temperature to get crystals. The synthesized complex has been fully characterized by single-crystal X-ray diffraction. UV-Visible, FTIR spectroscopy, TGA analysis, and DFT circulations were also performed. The crystal structural analysis reveals that the solid (1) {[Co(SCN)4] (C8H12N)3}·Cl crystallizes in the monoclinic system with the space group P21/n and the solid (2) {[Co(SCN)4](C5H11N3)2}·2Cl crystallizes in the monoclinic space group P21/m. Metal cations are joined into corrugated chains parallel to the b-axis direction in (1) and (2) by four thiocyanate anions. The crystal structures of (1) and (2) were calculated using XRPD data, indicating that they are closely connected to the DRX mono-crystal results. Different interactions pack the system into a ring formed by N-H⋯Cl and N-H⋯S hydrogen bonds. C-H⋯π and the π⋯π stacking of anilinuim ring for (1) and N-H⋯S intermolecular interactions for (1) and (2) increase the crystals' robustness. Hirshfeld surface analysis cum 2D fingerprint plots visualize the main intermolecular interactions with their contributions in the solid-state phase. The molecular geometries of both complexes obtained from the crystal structure were used for quantum chemical calculation. Here, frontier orbital analysis and electrostatic potential illustrate the chemical reactivities of metal-organic complexes. QTAIM and NCI analysis reveal the strength of interactions at the electronic level.

Total Synthesis of (±)-Fasicularin through Double Consecutive Epimerizations.

The total synthesis of tricyclic marine alkaloid fasicularin (1b) has been accomplished from a novel sterically well-defined α-aminonitrile 7, featuring a novel double consecutive epimerization process and Ir-catalyzed reductive functionalization of a tertiary γ-lactam. The required configuration is obtained through the thermodynamically stereoselectively driven isomerization of a readily available 8a-cyanodecahydroquinoline framework. The strategy allows us to achieve the tricyclic core structures efficiently from affordable starting materials through simple operations.

Escherichia coli RclA is a highly active hypothiocyanite reductase.

Hypothiocyanite and hypothiocyanous acid (OSCN-/HOSCN) are pseudohypohalous acids released by the innate immune system which are capable of rapidly oxidizing sulfur-containing amino acids, causing significant protein aggregation and damage to invading bacteria. HOSCN is abundant in saliva and airway secretions and has long been considered a highly specific antimicrobial that is nearly harmless to mammalian cells. However, certain bacteria, commensal and pathogenic, are able to escape damage by HOSCN and other harmful antimicrobials during inflammation, which allows them to continue to grow and, in some cases, cause severe disease. The exact genes or mechanisms by which bacteria respond to HOSCN have not yet been elucidated. We have found, in Escherichia coli, that the flavoprotein RclA, previously implicated in reactive chlorine resistance, reduces HOSCN to thiocyanate with near-perfect catalytic efficiency and strongly protects E. coli against HOSCN toxicity. This is notable in E. coli because this species thrives in the chronically inflamed environment found in patients with inflammatory bowel disease and is able to compete with and outgrow other important commensal organisms, suggesting that HOSCN may be a relevant antimicrobial in the gut, which has not previously been explored. RclA is conserved in a variety of epithelium-colonizing bacteria, implicating its HOSCN reductase activity in a variety of host-microbe interactions. We show that an rclA mutant of the probiotic Limosilactobacillus reuteri is sensitive to HOSCN and that RclA homologs from Staphylococcus aureus, Streptococcus pneumoniae, and Bacteroides thetaiotaomicron all have potent protective activity against HOSCN when expressed in E. coli.

Thiocyanate Ions Form Antiparallel Populations at the Concentrated Electrolyte/Charged Surfactant Interface.

Anions play significant roles in the separation of lanthanides and actinides. The molecular-scale details of how these anions behave at aqueous interfaces are not well understood, especially at high ionic strengths. Here, we describe the interfacial structure of thiocyanate anions at a soft charged interface up to 5 M bulk concentration with combined classical and phase-sensitive vibrational sum frequency generation (PS-VSFG) spectroscopy and molecular dynamics (MD) simulations. At low concentrations thiocyanate ions are mostly oriented with their sulfur end pointing toward the charged surfactants. The VSFG signal reaches a plateau at around 100 mM bulk concentration, followed by significant changes above 1 M. At high concentrations a new thiocyanate population emerges with their sulfur end pointing toward the bulk liquid. The -CN stretch frequency is different for up and down oriented SCN- ions, indicating different coordination environments. These results provide key molecular-level insights for the interfacial behavior of complex anions in highly concentrated solutions.

A Protein Data Bank survey of multimodal binding of thiocyanate to proteins: Evidence for thiocyanate promiscuity.

Over the last one and half century, a myriad of studies has demonstrated that Hofmeister ions have a major impact on protein stability and solubility. Nevertheless, the definition of the physico-chemical basis of their activity has proved to be highly challenging and controversial. Here, by exploiting the enormous information content of the Protein Data Bank, we explored the binding to proteins of thiocyanate, the anion of the series exerting the highest solubilization/destabilization effects. The survey, which led to the identification and characterization of 712 thiocyanate binding sites, provides a comprehensive and atomic-level view of the varied interactions that the ion forms with proteins. The inspection of these sites highlights a limited tendency of thiocyanate to interact with structured water molecules, in line with the reported poor hydration of the ion. On the other hand, the thiocyanate makes interactions with protein nonpolar moieties, especially with the backbone Cα atom. In as many as 104 cases, the ion exclusively makes nonpolar contacts. In conclusion, these findings suggest that the ability of thiocyanate to bind all types of protein exposed patches may lead to the formation of a negatively charged electrostatic barrier that could prevent protein-protein aggregation and promote protein solubility. Moreover, the denaturing action of thiocyanate may be ascribed to its ability to establish multiple attractive interactions with protein surfaces.

NDTP Mediated Direct Rapid Amide and Peptide Synthesis without Epimerization.

Herein, we explored an unprecedented mild, nonirritating, conveniently available, and recyclable coupling reagent NDTP, which could activate the carboxylic acids via acyl thiocyanide and enable the rapid amide and peptide synthesis at very mild conditions. In addition, the methodology was compatible with Fmoc-SPPS, which may provide an alternative to peptide manufacturing.

Cavitas electrochemical sensors for the direct determination of salivary thiocyanate levels.

Noninvasive diagnosis using salivary samples to detect thiocyanate provides vital information on individual health. This article demonstrates the first example of a wearable sensing device to noninvasively assess thiocyanate levels. The customized screen-printed electrode system is integrated into a form of a mouthguard squarewave-voltammetric sensor toward the convenient and fast detection of the salivary biomarker within 15 s. The sensor with a protective film to mitigate the effect of biofouling offers high sensitivity and selectivity toward the detection of thiocyanate ions. Partial least square regression is applied to analyze the high-order squarewave-voltammetric data over the applied potential range of 0-1.75 V vs Ag/AgCl and quantify the thiocyanate concentration in a complex matrix. The mouthguard sensor operating under physiological conditions can monitor a wide range of thiocyanate (up to 11 mM) with a low detection limit of 30 µM. The demonstration introduces a unique approach, that obviates the requirement for blood sampling, to study thiocyanate levels of healthy people, cigarette smokers, or people with other health conditions. It is envisioned that the new cavitas device possesses a substantial promise for diverse biomedical diagnosis applications.

Lepidium graminifolium L.: Glucosinolate Profile and Antiproliferative Potential of Volatile Isolates.

Glucosinolates (GSLs) from Lepidium graminifolium L. were analyzed qualitatively and quantitatively by their desulfo-counterparts using UHPLC-DAD-MS/MS technique and by their volatile breakdown products-isothiocyanates (ITCs) using GC-MS analysis. Thirteen GSLs were identified with arylaliphatic as the major ones in the following order: 3-hydroxybenzyl GSL (glucolepigramin, 7), benzyl GSL (glucotropaeolin, 9), 3,4,5-trimethoxybenzyl GSL (11), 3-methoxybenzyl GSL (glucolimnanthin, 12), 4-hydroxy-3,5-dimethoxybenzyl GSL (3,5-dimethoxysinalbin, 8), 4-hydroxybenzyl GSL (glucosinalbin, 6), 3,4-dimethoxybenzyl GSL (10) and 2-phenylethyl GSL (gluconasturtiin, 13). GSL breakdown products obtained by hydrodistillation (HD) and CH2Cl2 extraction after hydrolysis by myrosinase for 24 h (EXT) as well as benzyl ITC were tested for their cytotoxic activity using MTT assay. Generally, EXT showed noticeable antiproliferative activity against human bladder cancer cell line UM-UC-3 and human glioblastoma cell line LN229, and can be considered as moderately active, while IC50 of benzyl ITC was 12.3 µg/mL, which can be considered as highly active.

A convenient synthesis of branched-chain nucleoside isothiocyanates via aza-Claisen rearrangement.

Stereocontrolled introduction of a nitrogen atom at either C-2' or C-3' positions of nucleosides derived from uridine, 4-N-benzoylcytidine and adenosine was investigated. An efficient and rapid procedure was employed for creating new chiral centers at C-2' and C-3' positions using [3,3]-sigmatropic aza-Claisen rearrangement of allyl thiocyanates under conventional and microwave conditions. Structure of isothiocyanate products was confirmed by 1-D and 2-D NMR spectral analyses including selective 1H 1-D-NOE experiments.

Characterization of hydrophobic interaction of galactomannan in aqueous solutions using fluorescence-based technique.

Fluorescence probing was used to study hydrophobic interactions of galactomannan (GM) obtained from fenugreek gum (FG), guar gum (GG), and locust bean gum (LBG) at different M/G ratios. The I1/I3 ratio of pyrene changed from 1.73 to 1.29, 1.22, and 1.29 for FG, GG and LBG, respectively, as the concentration of GM increased from 0.01 to 8.0 g/L at 30 °C. The critical aggregation concentration of FG, GG, and LBG increased from 1.04 to 3.84 g/L, 1.15 to 3.73 g/L, and 0.94 to 3.63 g/L, respectively, as temperature increased from 10 to 70 °C. Addition of Na2SO4 and NaSCN increased the I1/I3 ratio in dilute solution, but reduced it in semi-dilute solution, whereas adding urea reduced I1/I3 in dilute solution but increased it in semi-dilute solution. These results indicated that the CAC of GM, polarity and number of hydrophobic microdomains were highly dependent on the M/G ratio and galactose distribution.

Synergistic Interaction between 5-FU and an Analog of Sulforaphane-2-Oxohexyl Isothiocyanate-In an In Vitro Colon Cancer Model.

Combination therapy is based on the beneficial effects of pharmacodynamic interaction (synergistic or additive) between combined drugs or substances. A considerable group of candidates for combined treatments are natural compounds (e.g., isothiocyanates) and their analogs, which are tested in combination with anticancer drugs. We tested the anticancer effect of the combined treatment of isothiocyanate 2-oxohexyl isothiocyanate and 5-fluorouracil in colon and prostate cancer cell lines. The type of interaction was described using the Chou-Talalay method. The cytostatic and cytotoxic activities of the most promising combined treatments were investigated. In conclusion, we showed that combined treatment with 5-fluorouracil and 2-oxohexyl isothiocyanate acted synergistically in colon cancer. This activity is dependent on the cytostatic properties of the tested compounds and leads to the intensification of their individual cytotoxic activity. The apoptotic process is considered to be the main mechanism of cytotoxicity in this combined treatment.

Site-Specific Conversion of Cysteine in a Protein to Dehydroalanine Using 2-Nitro-5-thiocyanatobenzoic Acid.

Dehydroalanine exists natively in certain proteins and can also be chemically made from the protein cysteine. As a strong Michael acceptor, dehydroalanine in proteins has been explored to undergo reactions with different thiolate reagents for making close analogues of post-translational modifications (PTMs), including a variety of lysine PTMs. The chemical reagent 2-nitro-5-thiocyanatobenzoic acid (NTCB) selectively modifies cysteine to form S-cyano-cysteine, in which the S-Cß bond is highly polarized. We explored the labile nature of this bond for triggering E2 elimination to generate dehydroalanine. Our results indicated that when cysteine is at the flexible C-terminal end of a protein, the dehydroalanine formation is highly effective. We produced ubiquitin and ubiquitin-like proteins with a C-terminal dehydroalanine residue with high yields. When cysteine is located at an internal region of a protein, the efficiency of the reaction varies with mainly hydrolysis products observed. Dehydroalanine in proteins such as ubiquitin and ubiquitin-like proteins can serve as probes for studying pathways involving ubiquitin and ubiquitin-like proteins and it is also a starting point to generate proteins with many PTM analogues; therefore, we believe that this NTCB-triggered dehydroalanine formation method will find broad applications in studying ubiquitin and ubiquitin-like protein pathways and the functional annotation of many PTMs in proteins such as histones.

Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate.

In daily practice, different types of biomolecules are usually extracted for large-scale "omics" analysis with tailored protocols. However, when sample material is limited, an all-in-one strategy is preferable. Although lysis of cells and tissues with urea is widely used for phosphoproteomic applications, DNA, RNA, and proteins can be simultaneously extracted from small samples using acid guanidinium thiocyanate-phenol-chloroform (AGPC). Use of AGPC for mass spectrometry-based phosphoproteomics was reported but has not yet been thoroughly evaluated against a classical phosphoproteomic protocol. Here we compared urea- with AGPC-based protein extraction, profiling phosphorylations in the DNA damage response pathway after ionizing irradiation of U2OS cells as proof of principle. On average we identified circa 9000 phosphosites per sample with both extraction methods. Moreover, we observed high similarity of phosphosite characteristics (e.g., 94% shared class 1 identifications) and deduced kinase activities (e.g., ATM, ATR, CHEK1/2, PRKDC). We furthermore extended our comparison to murine and human tissue samples yielding similar and highly correlated results for both extraction protocols. AGPC-based sample extraction can thus replace common cell lysates for phosphoproteomic workflows and may thus be an attractive way to obtain input material for multiple omics workflows, yielding several data types from a single sample.

Antioxidant activity of two edible isothiocyanates: Sulforaphane and erucin is due to their thermal decomposition to sulfenic acids and methylsulfinyl radicals.

Sulforaphane(SFN) and erucin(ERN) are isothiocyanates (ITCs) bearing, respectively, methylsulfinyl and methylsulfanyl groups. Their chemopreventive and anticancer activity is attributed to ability to modulate cellular redox status due to induction of Phase 2 cytoprotective enzymes (indirect antioxidant action) but many attempts to connect the bioactivity of ITCs with their radical trapping activity failed. Both ITCs are evolved from their glucosinolates during food processing of Cruciferous vegetables, therefore, we studied antioxidant behaviour of SFN/ERN at elevated temperature in two lipid systems. Neither ERN nor SFN inhibit the oxidation of bulk linolenic acid (below 100  °C) but both ITCs increase oxidative stability of soy lecithin (above 150 °C). On the basis of GC-MS analysis we verified our preliminary hypothesis (Antioxidants2020, 9, 1090) about participation of sulfenic acids and methylsulfinyl radicals as radical trapping agents responsible for the antioxidant effect of edible ITCs during thermal oxidation of lipids at elevated temperatures (above 140 °C).