Dealing with repetitions in sequencing by hybridization

DNA sequencing by hybridization (SBH) induces errors in the biochemical experiment. Some of them are random and disappear when the experiment is repeated. Others are systematic, involving repetitions in the probes of the target sequence. A good method for solving SBH problems must deal with both types of errors. In this work we propose a new hybrid genetic algorithm for isothermic and standard sequencing that incorporates the concept of structured combinations. The algorithm is then compared with other methods designed for handling errors that arise in standard and isothermic SBH approaches. DNA sequences used for testing are taken from GenBank. The set of instances for testing was divided into two groups. The first group consisted of sequences containing positive and negative errors in the spectrum, at a rate of up to 20%, excluding errors coming from repetitions. The second group consisted of sequences containing repeated oligonucleotides, and containing additional errors up to 5% added into the spectra. Our new method outperforms the best alternative procedures for both data sets. Moreover, the method produces solutions exhibiting extremely high degree of similarity to the target sequences in the cases without repetitions, which is an important outcome for biologists. The spectra prepared from the sequences taken from GenBank are available on our website http://bio.cs.put.poznan.pl/.     

Modulating Properties of Piroxicam,Meloxicam and Oxicam Analogues against Macrophage-Associated Chemokines in Colorectal Cancer

The mechanisms underlying the antineoplastic effects of oxicams have not been fully elucidated. We aimed to assess the effect of classic and novel oxicams on the expression/secretion of macrophage-associated chemokines (RTqPCR/Luminex xMAP) in colorectal adenocarcinoma cells, and on the expression of upstream the non-steroidal anti-inflammatory drug (NSAID)-activated genes NAG1, NFKBIA, MYD88, and RELA, as well as at the chemokine profiling in colorectal tumors. Meloxicam downregulated CCL4 9.9-fold, but otherwise the classic oxicams had a negligible/non-significant effect. Novel analogues with a thiazine ring substituted with arylpiperazine and benzoyl moieties significantly modulated chemokine expression to varying degree, upregulated NAG1 and NFKBIA, and downregulated MYD88. They inhibited CCL3 and CCL4, and their effect on CCL2 and CXCL2 depended on the dose and exposure. The propylene linker between thiazine and piperazine nitrogens and one arylpiperazine fluorine substituent characterized the most effective analogue. Only CCL19 and CXCL2 were not upregulated in tumors, nor was CXCL2 in tumor-adjacent tissue compared to normal mucosa. Compared to adjacent tissue, CCL4 and CXCL2 were upregulated, while CCL2, CCL8, and CCL19 were downregulated in tumors. Tumor CCL2 and CCL7 increased along with advancing T and CCL3, and CCL4 along with the N stage. The introduction of arylpiperazine and benzoyl moieties into the oxicam scaffold yields effective modulators of chemokine expression, which act by upregulating NAG1 and interfering with NF-κB signaling.     

New insights into the reaction of zinc alkyls with dioxygen

Studies on the reaction of zinc alkyls with O2 are reported which demonstrate that the selective oxygenation of organozinc compound is viable. The reaction of [EtZn(azol)]n (azol = deprotonated 1-aziridineethanol) with an excess of dry O2 in toluene affords the zinc ethylperoxide [EtOOZn(azol)]2[EtZn(azol)]2, while the analogous reaction between Me2Zn and O2 results in the isolation of the Me6Zn7(OMe)8 cluster in high yield.     

May GSH and L-His contribute to intracellular binding of zinc? Thermodynamic and solution structural study of a ternary complex

GSH and L-His are abundant biomolecules and likely biological ligands for Zn(II) under certain conditions. Potentiometric titrations provide evidence of formation of ternary Zn(II) complexes with GSH and L-His or D-His with slight stereoselectivity in favour of L-His (ca. 1 log unit of stability constant). The solution structure of the ZnH(GSH)(L-His)(H2O) complex at pH 6.8, determined by NMR, includes tridentate L-His, monodentate (sulfur) GSH, and weak interligand interactions. Calculations of competitivity of this complex for Zn(II) binding at pH 7.4 indicate that it is likely to be formed in vivo under conditions of GSH depletion. Otherwise, GSH alone emerges as a likely Zn(II) carrier.     

Enantioselective synthesis of 5-methylidenedihydrouracils as potential anticancer agents

An efficient, versatile, enantioselective synthesis of 1,3-disubstituted and 1,3,6-trisubstituted 5-methylidenedihydrouracils applying Horner-Wadsworth Emmons methodology was developed. Starting 1,3-disubstituted 5-diethoxyphosphoryluracils were subjected to reduction of the double bond or addition of various Grignard reagents and obtained Horner-Wadsworth Emmons reagents were used for the olefination of formaldehyde. Enantioselective synthesis of 1,3,6-trisubstituted 5-methylidenedihydrouracils was accomplished by introducing (R,R)- or (S,S)-di(1-phenylethylamino)phosphoryl groups as chiral auxiliary. Additions of Grignard reagents in the presence of these groups were highly and complimentary diastereoselective (de?～?80%). Further separation of the diastereomeric mixtures by column chromatography enabled synthesis of (R)- and (S)-1,3,6-trisubstituted-5-methylidenedihydrouracils with ee?≥?98%. Furthermore, absolute configuration of the adducts and final products was established using single crystal X-ray analysis. Stereochemical course of the addition reactions is also discussed.     

Beyond Oxides: Nitride as a Ligand in a Neutral IrIXNO3 Molecule Bearing a Transition Metal at High Oxidation State

Theoretical calculations utilizing relativistic ZORA Hamiltonian point to the conceivable existence of an IrNO₃ molecule in C_3v geometry. This minimum is shown to correspond to genuine nonavalent iridium nitride trioxide, which is a neutral analogue of cationic [IrO₄]⁺ species detected recently. Despite the presence of nitride anion, the molecule is protected by substantial barriers exceeding 200 kJ mol⁻¹ against transformations leading, for example, to global minimum (O=)₂Ir−NO, which contains metal at a lower formal oxidation state.