Proteomic and Bioinformatic Investigation of Altered Pathways in Neuroglobin-Deficient Breast Cancer Cells

Neuroglobin (NGB) is a myoglobin-like monomeric globin that is involved in several processes, displaying a pivotal redox-dependent protective role in neuronal and extra-neuronal cells. NGB remarkably exerts its function upon upregulation by NGB inducers, such as 17β-estradiol (E2) and H₂O₂. However, the molecular bases of NGB’s functions remain undefined, mainly in non-neuronal cancer cells. Human MCF-7 breast cancer cells with a knocked-out (KO) NGB gene obtained using CRISPR/Cas9 technology were analyzed using shotgun label-free quantitative proteomics in comparison with control cells. The differential proteomics experiments were also performed after treatment with E2, H₂O₂, and E2 + H₂O₂. All the runs acquired using liquid chromatography–tandem mass spectrometry were elaborated within the same MaxQuant analysis, leading to the quantification of 1872 proteins in the global proteomic dataset. Then, a differentially regulated protein dataset was obtained for each specific treatment. After the proteomic study, multiple bioinformatics analyses were performed to highlight unbalanced pathways and processes. Here, we report the proteomic and bioinformatic investigations concerning the effects on cellular processes of NGB deficiency and cell treatments. Globally, the main processes that were affected were related to the response to stress, cytoskeleton dynamics, apoptosis, and mitochondria-driven pathways.     

Volatiles emission patterns of different plant organs and pollen of Citrus limon

The volatiles emitted in vivo by different plant parts of Citrus limon (Rutaceae) have been identified by mean of head space-solid phase micro extraction (HS-SPME) and gas chromatography coupled with mass spectrometry (GC-MS) analyses. In particular, the profiles of flower buds, mature flowers, petals, stamens, gynaecium, pericarp of unripe and ripe fruits, young and adult leaves and pollen have been examined. Furthermore, the essential oil obtained from expression of ripe pericarp was studied. Volatiles were produced in distinctive amounts by the different plant organs, creating an interesting contrast, particularly within the flower parts: the highest amount of limonene (62.5%) was emitted by gynaecium, followed by stamens (22.9%) and petals (3.1%). Pollen did not produce limonene at all. The same compound is contained in higher amounts in the young leaves than in old ones (65.3% versus 30.1%). A possible defensive role of limonene and other volatiles, mainly terpene aldehydes, produced by young leaves has been hypothesized.     

Synthesis, structural characterization, and biological studies of six- and five-coordinate organotin(IV) complexes with the thioamides 2-mercaptobenzothiazole, 5-chloro-2-mercaptobenzothiazole, and 2-mercaptobenzoxazole

Organotin(IV) complexes with the formulas [(C6H5)3Sn(mbzt)] (1), [(C6H5)3Sn(cmbzt)] (3), and [(C6H5)2Sn(cmbzt)2] (4) (Hmbzt = 2-mercaptobenzothiazole and Hcmbzt = 5-chloro-2-mercaptobenzothiazole) have been synthesized and characterized by elemental analysis; FT-IR, Raman, 1H, 13C, and 119Sn NMR, and M?ssbauer spectroscopic techniques; and X-ray crystallography at various temperatures. The crystal structures of complexes 1, 3, and 4 were determined by X-ray diffraction at room temperature [295(1) or 293(2) K]. The complexes [(C6H5)3Sn(mbzo)] (2) and [(n-C4H9)2Sn(cmbzt)2] (5) (Hmbzo = 2-mercaptobenzoxazole) were synthesized by new improved methods, and their structures were determined at low temperature [100(1) K] and compared to those solved at room temperature. Comparison with {(CH3)2Sn(cmbzt)2]} (6), already reported, was also attempted. The influence of temperature on the geometry of the complexes is discussed. In the cases of complexes 1-3, three carbon atoms from phenyl groups and one sulfur atom and one nitrogen atom from thione ligands form a tetrahedrally distorted trigonal-bipyramidal geometry around the five-coordinate tin(IV) ion. In complexes 4-6, two carbon atoms from aryl groups and two sulfur atoms and two nitrogen atoms from thione ligands form a distorted tetrahedral geometry, tending toward octahedral, around the six-coordinate tin(IV) ions, with trans-C2, cis-N2, and cis-S2 configurations. Although the C-Sn and S-Sn bond distances are found to be constant in compounds 1-6, their N-Sn bond lengths vary significantly (from 2.635 to 3.078 A), with the longer distances found in the cases of five-coordinate complexes 1-3.     

Oxidation of elemental gold in alcohol solutions

Gold is designated as the noblest metal because of its chemical inertness. It is known to dissolve in cyanide solutions in the presence of air or H2O2 or in halogen-containing solutions, aqua regia being the most famous example. Herein, we report a unique thiol, especially 4-pyridinethiol (4-PS), assisted dissolution of Au in alcohol solutions. Although dissolution was found to be very selective for pyridinethiols, such a phenomenon is astonishing since thiols are commonly used as etch resists for Au and even 4-PS is extensively used as a surface modifier for Au. To gain further understanding of the dissolution process, the influence of the reaction conditions was extensively studied. On the basis of the obtained results, a mechanism for the dissolution reaction is proposed. Fascinatingly, by tuning of the reaction conditions, this phenomenon can be applied in selective preparation of self-supporting nanometer-thick Au foils.     

A new long-step interior point algorithm for linear programming based on the algebraic equivalent transformation

In this paper, we investigate a new primal-dual long-step interior point algorithm for linear optimization. Based on the step size, interior point algorithms can be divided into two main groups, short-step, and long-step methods. In practice, long-step variants perform better, but usually, a better theoretical complexity can be achieved for the short-step methods. One of the exceptions is the large-update algorithm of Ai and Zhang. The new wide neighborhood and the main characteristics of the presented algorithm are based on their approach. In addition, we use the algebraic equivalent transformation technique of Darvay to determine new modified search directions for our method. We show that the new long-step algorithm is convergent and has the best known iteration complexity of short-step variants. We present our numerical results and compare the performance of our algorithm with two previously introduced Ai-Zhang type interior point algorithms on a set of linear programming test problems from the Netlib library.

     

New Sn(IV) and Ti(IV) bis(trimethylsilyl)amides in d,l-lactide polymerization, SEM characterization of polymers

Ring-opening polymerization of d,l-lactide initiated with new chlorotris(bis(trimethylsilyl) amido) tin(IV), tetrakis(bis(trimethylsilyl)amido) tin(IV) and titanium(IV) was investigated. New complexes reveal practically quantitative conversion degrees and produced polymers with higher molecular weight with respect to reference alkoxo-species.The X-ray crystal structure of chlorotris(bis(trimethylsilyl)amido) tin (IV) was investigated. Axial enantiomerism of [SnCl{N(SiMe₃)₂}₃] molecules in solution was studied by high-field dynamic NMR, the value of Gibbs activation energy ΔG^‡ = 59.5 kJ/mol.Field emission SEM investigation of bulk polymer samples and thin films on conductive Al foil revealed a stratified fibrous textures in the bulk polymers, as well as nanoscaled topographical features due to coils and entanglements of individual macromolecules in thin films.     

Surface modification of thermoplastics by atomic layer deposition of Al2O3 and TiO2 thin films

Al₂O₃ and TiO₂ thin films were deposited by atomic layer deposition at 80-250 °C on various polymeric substrates such as polymethylmethacrylate (PMMA), polyetheretherketone (PEEK), polytetrafluoroethylene (PTFE) and ethylenetetrafluoroethylene (ETFE). The films were studied with FESEM, EDX, XRD, contact angle measurements and adhesion tests. The film growth rates on the thermoplastics were close to the corresponding growth rates on Si substrates. The adhesion of the films was good on PEEK and poor on PTFE. All coated surfaces showed lower water contact angles than the uncoated thermoplastics. Furthermore, the water contact angles on all TiO₂-coated surfaces decreased upon UV illumination, most efficiently with crystalline TiO₂ coatings.     

Transferability of coarse-grained force fields: the polymer case

A key question for all coarse-graining methodologies is the degree of transferability of the resulting force field between various systems and thermodynamic conditions. Here we present a detailed study of the transferability over different thermodynamic states of a coarse-grained (CG) force field developed using the iterative Boltzmann inversion method. The force field is optimized against distribution functions obtained from atomistic simulations. We analyze the polymer case by investigating the bulk of polystyrene and polyamide-6,6 whose coarse-grained models differ in the chain length and in the number of atoms lumped in one bead. The effect of temperature and pressure on static, dynamic, and thermodynamic properties is tested by comparing systematically the coarse-grain results with the atomistic ones. We find that the CG model describing the polystyrene is transferable only in a narrow range of temperature and it fails in describing the change of the bulk density when temperature is 80 K lower than the optimization one. Moreover the calculation of the self-diffusion coefficient shows that the CG model is characterized by a faster dynamics than the atomistic one and that it overestimates the isothermal compressibility. On the contrary, the polyamide-6,6 CG model turns out to be fully transferable between different thermodynamic conditions. The transferability is checked by changing either the temperature or the pressure of the simulation. We find that, in this case, the CG model is able to follow all the intra- and interstructural rearrangements caused by the temperature changes. In addition, while at low temperature the difference between the CG and atomistic dynamics is remarkable due to the presence of hydrogen bonds in the atomistic systems, for high temperatures, the speedup of the CG dynamics is strongly reduced, leading to a CG diffusion coefficient only six times bigger than the atomistic one. Moreover, the isothermal compressibility calculated at different temperatures agrees very well with the experimental one. We find that the polymer chain length does not affect the transferability of the force field and we attribute such transferability mainly to the finer model used in describing the polyamide-6,6 than the polystyrene.     

Chemistry of nitrated lipids: remarkable instability of 9-nitrolinoleic acid in neutral aqueous medium and a novel nitronitrate ester product by concurrent autoxidation/nitric oxide-release pathways

Despite the mounting interest in nitrolinoleic acids and related nitrated polyunsaturated fatty acids as a novel class of bioactive signaling lipids, their chemistry and metabolic fate have remained poorly elucidated. Herein, we report an expedient nitroselenenylation/oxidation route to 9-nitrolinoleic acid (1) and 10-nitrolinoleic acid (2), which enabled comparative product studies under physiologically relevant conditions. Under biomimetic conditions, 1 decayed at an unusually fast rate to give the hydroxy-, keto-, and nitronitrate ester derivatives 3, 4, and 5 as main products, identified by ESI-MS and 2D NMR spectroscopy, including (1)H, (15)N HMBC experiments on the (15)N-labeled derivatives. The 13-nitrato functionality in 5 suggested partitioning of 1 between concurrent peroxidation and nitric oxide (NO)-release pathways. Lipid 2 decayed at a much slower rate giving only the hydroxynitro derivative 6 as an isolable product. Diphenylpicrylhydrazide (DPPH) radical quenching experiments and DFT computations concurred to support a higher H-atom donating ability of 1 versus 2, due to more effective stabilization of the resulting pentadienyl radical by the terminal nitro group. The markedly different stability of isomeric nitrolinoleic acids disclosed in the present study may provide an explanation for the previous identification of 2, but not 1, in body fluids and offers a key for future insights into the biological activities of nitrated lipids.     

Further syphonosides from the sea hare Syphonota geographica and the sea-grass Halophila stipulacea

The unusual structural features of syphonoside (1), recently reported from the marine mollusc Syphonota geographica and its prey Halophila stipulacea, stimulated further investigations on the minor secondary metabolites of both organisms. The three novel macrocyclic glycoterpenoids 2-4, structurally related to the main co-occurring metabolite 1, have been isolated and chemically characterized mainly by NMR spectroscopic techniques and degradation methods. Compounds 2 and 3 were found only in the mollusc whereas compound 4 was isolated in trace quantities exclusively from the sea-grass.