Clustering analysis of different hop varieties according to their essential oil composition measured by GC/MS

This study describes the analysis of total hops essential oils from 18 cultivated varieties of hops, five of which were bred in Lithuania, and 7 wild hop forms using gas chromatography-mass spectrometry. The study sought to organise the samples of hops into clusters, according to 72 semi-volatile compounds, by applying a well-known method, k-means clustering analysis and to identify the origin of the Lithuanian hop varieties. The bouquet of the hops essential oil was composed of various esters, terpenes, hydrocarbons and ketones. Monoterpenes (mainly β-myrcene), sesquiterpenes (dominated by β-caryophyllene and α-humulene) and oxygenated sesquiterpenes (mainly caryophyllene oxide and humulene epoxide II) were the main compound groups detected in the samples tested. The above compounds, together with a-muurolene, were the only compounds found in all the samples. Qualitative and quantitative differences were observed in the composition of the essential oils of the hop varieties analysed. For successful and statistically significant clustering of the data obtained, expertise and skills in employing chemometric analysis methods are necessary. The result is also highly dependent on the set of samples (representativeness) used for segmentation into groups, the technique for pre-processing the data, the method selected for partitioning the samples according to the similarity measures chosen, etc. To achieve a large and representative data set for clustering analysis from a small number of measurements, numerical simulation was applied using the Monte Carlo method with normal and uniform distributions and several relative standard deviation values. The grouping was performed using the k-means clustering method, employing several optimal number of clusters evaluation techniques (Davies-Bouldin index, distortion function, etc.) and different data pre-processing approaches. The hop samples analysed were separated into 3 and 5 clusters according to the data filtering scenario used. However, the targeted Lithuanian hop varieties were clustered identically in both cases and fell into the same group together with other cultivated hop varieties from Ukraine and Poland.     

XPS spectra of vanadium-doped disulfides CuCrS<Subscript>2</Subscript>

The charged state of atoms in layered cation-substituted disulfides CuCr_1?x V _x S₂ (x = 0?0.4) was studied using X-ray photoelectron spectroscopy. The study was performed with polycrystalline powder and ceramic samples of chromium-copper disulfides. CuCr_1?x V _x S₂ samples were shown to comprise differently charged atoms of chromium, copper and vanadium, the charged state of which varies with the concentration of vanadium cations (x).     

Drought Stress Effects on Growth,ROS Markers,Compatible Solutes,Phenolics, Flavonoids,and Antioxidant Activity in <Emphasis Type="Italic">Amaranthus tricolor</Emphasis>

Four selected Amaranthus tricolor cultivars were grown under four irrigation regimes (25, 50, 80, and 100% field capacity) to evaluate the mechanisms of growth and physiological and biochemical responses against drought stress in randomized complete block design with three replications. Drought stress led to decrease in total biomass, specific leaf area, relative water content (RWC), photosynthetic pigments (chlorophyll a, chlorophyll b, chlorophyll ab), and soluble protein and increase in MDA, H₂O₂, EL, proline, total carotenoid, ascorbic acid, polyphenols, flavonoids, and antioxidant activity. However, responses of these parameters were differential in respect to cultivars and the degree of drought stresses. No significant difference was observed in control and LDS for most of the traits. The cultivars VA14 and VA16 were identified as more tolerant to drought and could be used for further evaluations in future breeding programs and new cultivar release programs. Positively significant correlations among MDA, H₂O₂, compatible solutes, and non-enzymatic antioxidant (proline, TPC, TFC, and TAC) suggested that compatible solutes and non-enzymatic antioxidant played vital role in detoxifying of ROS in A. tricolor cultivar. The increased content of ascorbic acid indicated the crucial role of the ASC–GSH cycle for scavenging ROS in A. tricolor.     

Discovery of novel inhibitors for <Emphasis Type="Italic">Leishmania</Emphasis> nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization

Nucleoside diphosphate kinases (NDKs) are ubiquitous enzymes that catalyze the transfer of the γ-phosphate moiety from an NTP donor to an NDP acceptor, crucial for maintaining the cellular level of nucleoside triphosphates (NTPs). The inability of trypanosomatids to synthesize purines de novo and their dependence on the salvage pathway makes NDK an attractive target to develop drugs for the diseases they cause. Here we report the discovery of novel inhibitors for Leishmania NDK based on the structural and functional characterization of purified recombinant NDK from Leishmania amazonensis. Recombinant LaNDK possesses auto-phosphorylation, phosphotransferase and kinase activities with Histidine 117 playing an essential role. LaNDK crystals were grown by hanging drop vapour diffusion method in a solution containing 18% PEG-MME 500, 100 mM Bis-Tris propane pH 6.0 and 50 mM MgCl₂. It belongs to the hexagonal space group P6₃22 with unit cell parameters a?=?b?=?115.18, c?=?62.18 Å and α?=?β?=?90°, γ?=?120°. The structure solved by molecular replacement methods was refined to crystallographic R-factor and R_free values of 22.54 and 26.52%, respectively. Molecular docking and dynamics simulation-based virtual screening identified putative binding compounds. Protein inhibition studies of selected hits identified five inhibitors effective at micromolar concentrations. One of the compounds showed ~45% inhibition of Leishmania promastigotes proliferation. Analysis of inhibitor-NDK complexes reveals the mode of their binding, facilitating design of new compounds for optimization of activities as drugs against leishmaniasis.     

Modification of silica nanoparticles with stereisomers of <Emphasis Type="Italic">p</Emphasis>-<Emphasis Type="Italic">tert</Emphasis>-butylthiacalix[4]arene containing four 2-oxo-2-{[3-(triethoxysilyl)prop-1-yl]amino}ethoxy substituents at the lower rim

Three stereoisomers (cone, partial cone, and 1,3-alternate) of p-tert-butylthiacalix[4]arene bearing four anchor propyltriethoxysilane substituents at the lower rim were synthesized for the first time. Surface modification of silica nanoparticles (d = 12 nm) with the synthesized macrocycles gave novel hybride thiacalix [4]arene?SiO₂ particles. The obtained nanostructured adsorbents were found to efficiently extract nitroaromatic compounds from aqueous solutions. The partial cone and 1,3-alternate thiacalix[4]arene–SiO₂ hybrid particles showed affinity to nitrophenols.     

Dicarboxylic acids and hydroxy fatty acids in different species of fungi

Secondary metabolites of fungi can be responsible for allergies; therefore, the identification of compounds produced by these organisms is very important. Fungi produce large amounts of secondary metabolites, which belong to groups of chemicals such as: dicarboxylic acids, hydroxy acids, alcohols, hydrocarbons, esters, fatty acids, sterols, amino acids and mycotoxins. The presence of all these compounds in human proximity contributes to many diseases. Therefore, the aim of the study was a qualitative and quantitative analysis of hydroxy and dicarboxylic acids produced by fungi occurring in student hostel in Poland, in the province of Pomerania. The following species of fungi were subjected to extraction: Aspergillus niger, Aspergillus fumigatus, Aspergillus candidus, Rhizopus sp., Geotrichum candidum, and Penicillium chrysogenum. A mixture of ethyl acetate and methanol was used for the extraction. The obtained extracts were further analyzed by gas chromatography mass spectrometry (GC–MS). In all samples of fungi, the presence of a total of 22 acids, including 13 dicarboxylic and 9 hydroxy acids, was confirmed. Most acids (17 different acids) were identified in A. fumigatus. Only 10 acids were identified in the mycelium of G. candidum and A. niger. Acids which were identified in all samples of the mycelium were 22-hydroxydocosanoic acid, 24-hydroxytetracosanoic acid and adipic acid. The most abundant compounds were 22-hydroxydocosanoic acid in A. fumigatus, A. candidus, Rhizopus sp., G. candidum and P. chrysogenum, and succinic acid in A. niger. More experiments are needed to understand the physiological role of hydroxy and dicarboxylic acids. We hope that our results are an important contribution to further studies on the human health.     

Spectrometric analysis,phenolics isolation and cytotoxic activity of <Emphasis Type="Italic">Stipagrostis plumosa</Emphasis> (Family Poaceae)

Grasses (family Poaceae) are economically important plants; they are used as crops and animal foods. Stipagrostis plumosa (L.) Munro ex T. Anderson is a member of this family and subjected to chemical and biological studies. The chromatographic techniques,  LC–ESI–MS and GC/MS were used for identification of polar and non-polar compounds in its extract. Ten compounds, including one new flavone glycoside; tricin 7-O-galactoside, three known flavones, three C-glycosyl flavones and three phenolic acids, were isolated from S. plumosa for the first time except tricin. Their structures were elucidated on the basis of extensive spectroscopic interpretation. In addition to the isolated compounds, eleven compounds were tentatively identified using LC–ESI–MS, five of them were detected for the first time from this species. 29 non polar compounds were identified using GC–MS analysis, representing 83.13% of S. plumosa diethyl ether extract. In addition to the DPPH activity evaluation, the crude extract and the isolated compounds were investigated against five human carcinoma cell lines; A549, HCT-116, HepG2, MCF-7 and PC3 at a concentration of 100 μg/ml. From the isolated compounds tricin and luteolin 6,8-di-C-glucoside could be considered as natural-free radical scavenging agents.     

Expression of miRNAs Targeting <Emphasis Type="Italic">mTOR</Emphasis> and <Emphasis Type="Italic">S6K1</Emphasis> Genes of mTOR Signaling Pathway Including miR-96, miR-557, and miR-3182 in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) is a highly aggressive form of breast cancer. Aberrant expression of genes in mTOR pathway and their targeting miRNAs plays an important role in TNBC. The aim of this study was to determine the expression of mTOR and S6K1 and their targeting miRNAs in breast cancer cell lines and clinical samples. miRNAs targeting 3′-UTR of mTOR and S6K1 mRNAs were predicted using bioinformatic algorithms. MDA-MB-231, MCF-7, and MCF-10A as well as 20 TNBC samples were analyzed for gene and miRNA expression using quantitative real-time PCR (RT-qPCR). A receiver operating characteristic (ROC) curve analysis was performed for evaluation of candidate miRNAs as diagnostic biomarkers. miR-96 and miR-557 targeting mTOR and S6K1 mRNAs, respectively, were selected, and miR-3182 was selected as the miRNA targeting both genes. The miRNAs were down-regulated in cell lines, while their target mRNAs were up-regulated. Similar findings were observed in clinical samples. The ROC curve analysis revealed decline in expression of these miRNAs. We suggest that miR-96, miR-557, and miR-3182 can be used as inhibitory agents for mTOR and S6K1 in TNBC-targeted therapy.     

Fatty acids and amino acids of entomopathogenic fungus <Emphasis Type="Italic">Conidiobolus coronatus</Emphasis> grow on minimal and rich media

Entomopathogenic fungi are referred to as potential candidates as insect pest control agents. The objective of the study was to identify fatty acids and amino acids from Conidiobolus coronatus cultured on two different media. Each medium was extracted with ethyl acetate and its mixtures with isopropanol, acetonitrile and methanol. Analyses of fatty acids and amino acids of entomopathogenic fungus C. coronatus were performed by means of gas chromatography coupled with mass spectrometry. The analysis showed that the fungus C. coronatus produces the following groups of compounds: fatty acids and amino acids; α- and β-glucopyranose were also identified. The identified fatty acids included 12–20, 22 and 24 carbon atoms per chain. The highest content of fatty acids was detected in a mycelium sample cultured in a liquid minimal medium extracted with ethyl acetate. The lowest content of these organic compounds was identified in mycelium cultured in a liquid nutrient-rich medium extracted with ethyl acetate–methanol mixture. Fatty acids were found to account for 62.0 mass % to 94.4 mass % of all organic compounds in the analyzed mycelia. C18:1 acids were detected in the highest amounts when ethyl acetate was used as the extracting agent. The identified amino acids accounted for 4 mass % to 21 mass % of all organic compounds. Upon extraction of C. coronatus mycelium samples with the ethyl acetate—methanol mixture, two anomeric forms of glucose were also identified. An analysis of the studied material confirmed, that the entomopathogenic fungus C. coronatus is a very rich source of organic compounds, which might encourage its further research so as to identify an even larger number of compounds being produced by this species.     

Binuclear copper(II) complexes with acyldihydrazones of <Emphasis Type="Italic">N</Emphasis>-benzenesulfonyl-<Emphasis Type="Italic">L</Emphasis>-aspartic acid

The structure and the EPR spectra of copper(II) coordination compounds with acyldihydrazones of N-benzenesulfonyl-L-aspartic acid and salicylaldehyde (2-hydroxyacetophenone) were described. The compounds were studied by chemical and thermal analyses, IR spectroscopy, and EPR. The molecular and crystal structures of copper(II) complexes with N-benzenesulfonyl-L-aspartic acid bis(salicylidene)hydrazone (H₄L¹) [Cu₂L¹ · 2Py] · 1.5 H₂O was determined by X-ray diffraction. The crystals are triclinic: a = 10.4714(4) Å, b = 12.9702(5) Å, c = 14.6187(9) Å, α = 104.763(2)°, β = 93.082(2)°, γ = 111.4240(10)°, space group P \(\bar 1\), Z = 2. The binuclear complexes containing copper cations whose coordination polyhedra are connected by an aliphatic spacer (Cu...Cu, 8.669 Å) are additionally linked by phenoxy bridges (Cu...Cu, 3.398 Å). The EPR spectra of these compounds in solutions exhibit an isotropic signal of seven HFS lines due to two equivalent copper ions with the spin Hamiltonian parameters g = 2.115?2.120, a _Cu = (35.5?38.0) × 10^?4 cm^?1, which is indicative of weak exchange interactions between the paramagnetic sites.     

SAMPL6: calculation of macroscopic p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values from ab initio quantum mechanical free energies

Macroscopic pK_a values were calculated for all compounds in the SAMPL6 blind prediction challenge, based on quantum chemical calculations with a continuum solvation model and a linear correction derived from a small training set. Microscopic pK_a values were derived from the gas-phase free energy difference between protonated and deprotonated forms together with the Conductor-like Polarizable Continuum Solvation Model and the experimental solvation free energy of the proton. pH-dependent microstate free energies were obtained from the microscopic pK_as with a maximum likelihood estimator and appropriately summed to yield macroscopic pK_a values or microstate populations as function of pH. We assessed the accuracy of three approaches to calculate the microscopic pK_as: direct use of the quantum mechanical free energy differences and correction of the direct values for short-comings in the QM solvation model with two different linear models that we independently derived from a small training set of 38 compounds with known pK_a. The predictions that were corrected with the linear models had much better accuracy [root-mean-square error (RMSE) 2.04 and 1.95 pK_a units] than the direct calculation (RMSE 3.74). Statistical measures indicate that some systematic errors remain, likely due to differences in the SAMPL6 data set and the small training set with respect to their interactions with water. Overall, the current approach provides a viable physics-based route to estimate macroscopic pK_a values for novel compounds with reasonable accuracy.     

Synthesis processes and transport properties of solid solutions in the Bi<Subscript>2</Subscript>O<Subscript>3</Subscript>-GeO<Subscript>2</Subscript>-V<Subscript>2</Subscript>O<Subscript>5</Subscript> system

The results of studies of solid solutions with the overall composition of Bi₄V_{2 ? x} Ge _x O_{11 ? δ} and Bi₄Ge_{3 ? x} V _x O_{12 + δ} are presented. The process of phase formation are studied during the synthesis of solid solution using the ceramic method and through liquid precursors. Crystallochemical parameters of the obtained compounds are determined. The size distribution of the particles is studied. Conductivity of annealed of polycrystalline samples as a function of temperature and composition is studied using the impedance spectroscopy method. The shape of impedance complex plane plots of the samples obtained in different ways is studied and analyzed.     

Synthesis of N-aryl- and <Emphasis Type="Italic">N</Emphasis>,<Emphasis Type="Italic">N</Emphasis>-diethyl-9-methyl-11-sulfanylidene-8-oxa-10,12-diazatricyclo[7.3.1.0<Superscript>2,7</Superscript>]trideca-2,4,6-triene-13-carboxamides

Three-component condensation of N-aryl- and N,N-diethyl-3-oxobutanamides with salicylaldehyde and thiourea in ethanol in the presence of sodium hydrogen sulfate afforded N-aryl- and N,N-diethyl-9-methyl-11-sulfanylidene-8-oxa-10,12-diazatricyclo[7.3.1.0^2,7]trideca-2,4,6-triene-13-carboxamides. Reaction of the same compounds in the absence of a catalyst under solvent-free conditions gave N-aryl-6-(2-hydroxyphenyl)-4-methyl-2-sulfanylidene-1,2,3,6-tetrahydropyrimidine-5-carboxamides.     

Synthesis of New Cyclopenta[<Emphasis Type="Italic">b</Emphasis>]quinoline Derivatives

A series of new 11-(R-phenyl)-8,9-dihydro-7H-benzo[f]cyclopenta[b]quinolin-10(11H)-ones and 7,14-bis(R-phenyl)-2,3,9,10,11,14-hexahydrocyclopenta[2,3]quinolino[8,7-h]cyclopenta[b]quinoline-1,8(4H,7H)-diones were synthesized by three-component condensation of naphthalen-2-amine or naphthalene- 1,5-diamine with substituted benzaldehydes and cyclopentane-1,3-dione in one step through intermediate formation of unstable arylaminoketoenol.     

Crystal structure and conduction of BICUTIVOX

Existence boundaries, structure, and transport parameters were studied for Bi₄V_{2 ? x} Cu _x/2Ti _x/2O_{11 ? x} solid solutions. Doping levels within x = 0.025–0.15 distort the C2/m crystal lattice (this lattice is characteristic of individual the Bi₄V₂O₁₁ phase) and lowers its symmetry to triclinic. The solid solutions with 0.25 ≤ x ≤ 0.30 crystallize in tetragonal space group I4/mmm. High-temperature X-ray diffraction and dilatometry measurements for Bi₄V_{2 ? x} Cu _x/2Ti _x/2O_{11 ? x} (x ≤ 0.35) solid solutions verified the existence of three structural varieties within 298–1023 K. Electrical conductivity of BICUTIVOX was studied by impedance spectroscopy as a function of temperature, composition, and oxygen partial pressure. Equivalent circuits of cells were analyzed. Features of electrical conductivity versus temperature for the structural varieties are noted. Above 873 K, the solid solutions samples with x = 0.05 have the highest conductivity. At lower temperatures, higher conductivities are in the solid solutions that retain the γ phase in the low-temperature region. The dominant oxygen-ion conduction mechanism was discovered in the solid solutions.     

Synthesis and piezoelectric properties of <Emphasis Type="Italic">N</Emphasis>-phthaloylglutamic acid derivatives

The (S,S)- and (R,R)-enantiomers of dimethyl 2,4-diphthalimidoglutarate were synthesized by nucleophilic substitution of bromine in dimethyl (2S,4RS)-4-bromo-N-phthaloyl-glutamate upon treatment with potassium phthalimide, followed by separation. The crystal structure of the obtained compounds was studied by X-ray diffraction. Crystals of enantiomerically pure dimethyl 4-hydroxy- and 4-phthalimido-N-phthaloylglutamates were found to possess a noticeable piezoelectric activity.