Comparing reverse complementary genomic words based on their distance distributions and frequencies

In this work we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance distributions are considered, and it is found that the peak dissimilarity works best in this setting. We report the existence of reverse complementary word pairs with very dissimilar distance distributions, as well as word pairs with very similar distance distributions even when both distributions are irregular and contain strong peaks. The association between distribution dissimilarity and frequency discrepancy is explored also, and it is speculated that symmetric pairs combining low and high values of each measure may uncover features of interest. Taken together, our results suggest that some asymmetries in the human genome go far beyond Chargaff's rules. This study uses both the complete human genome and its repeat-masked version.Comment: Post-print of a paper accepted to publication in "Interdisciplinary Sciences: Computational Life Sciences" (ISSN: 1913-2751, ESSN: 1867-1462

Role of protein kinase R in the killing of Leishmania major by macrophages in response to neutrophil elastase and TLR4 via TNF and IFN

In cutaneous leishmaniasis, Leishmania amazonensis activates macrophage double-stranded, RNA-activated protein kinase R (PKR) to promote parasite growth. In our study, Leishmania major grew normally in RAW cells, RAW-expressing dominant-negative PKR (PKR-DN) cells, and macrophages of PKR-knockout mice, revealing that PKR is dispensable for L. major growth in macrophages. PKR activation in infected macrophages with poly I:C resulted in parasite death. Fifty percent of L. major-knockout lines for the ecotin-like serine peptidase inhibitor (ISP2; Δisp2/isp3), an inhibitor of neutrophil elastase (NE), died in RAW cells or macrophages from 129Sv mice, as a result of PKR activation. Inhibition of PKR or NE or neutralization of Toll-like receptor 4 or 2(TLR4 or TLR2) prevented the death of Δisp2/isp3. Δisp2/isp3 grew normally in RAW-PKR-DN cells or macrophages from 129Sv pkr−/−, tlr2−/−, trif−/−, and myd88−/− mice, associating NE activity, PKR, and TLR responses with parasite death. Δisp2/isp3 increased the expression of mRNA for TNF-α by 2-fold and of interferon β (IFNβ) in a PKR-dependent manner. Antibodies to TNF-α reversed the 95% killing by Δisp2/isp3, whereas they grew normally in macrophages from IFN receptor–knockout mice. We propose that ISP2 prevents the activation of PKR via an NE-TLR4-TLR2 axis to control innate responses that contribute to the killing of L. major.—Faria, M. S., Calegari-Silva, T. C., de Carvalho Vivarini, A., Mottram, J. C., Lopes, U. G., Lima, A. P. C. A. Role of protein kinase R in the killing of Leishmania major by macrophages in response to neutrophil elastase and TLR4 via TNFα and IFNβ

Dissimilar Symmetric Word Pairs in the Human Genome

In this work we explore the dissimilarity between symmetric word pairs, by comparing the inter-word distance distribution of a word to that of its reversed complement. We propose a new measure of dissimilarity between such distributions. Since symmetric pairs with different patterns could point to evolutionary features, we search for the pairs with the most dissimilar behaviour. We focus our study on the complete human genome and its repeat-masked version.Comment: Submitted 13-Feb-2017; accepted, after a minor revision, 17-Mar-2017; 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2017, Porto, Portugal, 21-23 June, 201

Cinnamic acid conjugates in the rescuing and repurposing of classical antimalarial drugs

© 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).Cinnamic acids are compounds of natural origin that can be found in many different parts of a wide panoply of plants, where they play the most diverse biological roles, often in a conjugated form. For a long time, this has been driving Medicinal Chemists towards the investigation of the therapeutic potential of natural, semi-synthetic, or fully synthetic cinnamic acid conjugates. These efforts have been steadily disclosing promising drug leads, but a wide chemical space remains that deserves to be further explored. Amongst different reported approaches, the combination or conjugation of cinnamic acids with known drugs has been addressed in an attempt to produce either synergistic or multi-target action. In this connection, the present review will focus on efforts of the past decade regarding conjugation with cinnamic acids as a tool for the rescuing or the repurposing of classical antimalarial drugs, and also on future perspectives in this particular field of research.This research was funded by Fundação para a Ciência e Tecnologia (FCT), Portugal, grants UID/QUI/50006/2019, and PTDC/BTM-SAL/29786/2017.info:eu-repo/semantics/publishedVersio

Experimental and computational study of the energetics of hydantoin and 2-thiohydantoin

This work reports an experimental and a theoretical study of two imidazolidine derivatives, hydantoin (CAS No. 461-72-3) and 2-thiohydantoin (CAS No. 503-87-7). The standard (p degrees = 0.1 MPa) molar energies of combustion of hydantoin and 2-thiohydantoin were measured by static and rotating bomb combustion calorimetry, respectively. The standard molar enthalpies of sublimation, at T = 298.15 K, were derived from the temperature dependence of the vapour pressures of these compounds, measured by the Knudsen-effusion technique, and from high temperature Calvet microcalorimetry. The conjugation of these experimental results enables the calculation of the standard molar enthalpies of formation in the gaseous state, at T = 298.15 K, which are discussed in terms of structural contributions. We have also estimated the gas-phase enthalpy of formation from high-level ab initio molecular orbital calculations at the G3MP2B3 level of theory, being the computed values in good agreement with the experimental ones. Furthermore, this composite approach was also used to obtain information about the gas-phase basicities, proton and electron affinities and adiabatic ionization enthalpies

Antimicrobial and cytotoxic activities of 1,2,3-triazole-sucrose derivatives

A library of 1-(1′,2,3,3′,4,4′,6-hepta-O-acetyl-6′-deoxy-sucros-6′-yl)-1,2,3-triazoles have been investigated for their antibacterial, antifungal and cytotoxic activities. Most of the target compounds showed good inhibitory activity against a variety of clinically and food contaminant important microbial pathogens. In particular, 1-(1′,2,3,3′,4,4′,6-hepta-O-acetyl-6′-deoxy-sucros-6′-yl)-4-(4-pentylphenyl)-1,2,3- triazole (5) was highly active against all the tested bacteria with minimal inhibitory concentrations (MICs) ranging between 1.1 and 4.4 μM and bactericidal concentrations (MBCs) from 2.2 and 8.4 μM. The compound 1-(1′,2,3,3′,4,4′,6-hepta-O-acetyl-6′-deoxy-sucros-6′-yl)-4-(4-bromophenyl)-1,2,3-triazole (3) showed antifungal activity with MICs from 0.6 to 4.8 μM and minimal fungicidal concentrations (MFCs) ranging between 1.2 and 8.9 μM. Furthermore, some of the compounds possessed moderate cytotoxicity against human breast, lung, cervical and hepatocellular carcinoma cell lines, without showing toxicity for nontumor liver cells. The above mentioned derivatives represent promising leads for the development of new generation of sugar-triazole anti fungal agents.This work has been supported by Fundação para a Ciência e a Tecnologia through grant Nos. PEst-C/EQB/LA0006/2013 and PEst-OE/AGR/UI0690/2014. T.M. Potewar and R.C. Calhelha are grateful to Fundação para a Ciência e a Tecnologia for their pos-doctoral Grant Nos. SFRH/ BPD/65173/2009 and SFRH/BPD/68344/2010, respectively. The authors thank to Serbian Ministry of Education, Science and Technological Development for financial support (grant number 173032). The NMR spectrometers are part of The National NMR Facility, supported by Fundação para a Ciência e a Tecnologia (RECI/BBB-BQB/0230/2012)

Determination of Kresoxim-Methyl in Water and in Grapes by High-Performance Liquid Chromatography (HPLC) Using PhotochemicalInduced Fluorescence and Dispersive Liquid-Liquid Microextraction (DLLME)

A high-performance chromatographic method was developed to determine the fungicide kresoxim-methyl. Off-line photochemical derivatization was used to induce the formation of a stable and fluorescent product since the fungicide does not present natural fluorescence. Intense fluorescence at 370/430nm was achieved by treating the analyte in solution at pH 6 to ultraviolet light for 45s. The chromatographic conditions included isocratic elution with 50/ 50% (v/v) acetonitrile/water and the photochemical product appeared at a retention time of 7.2min. The short and long term stabilities of the photoproduct were evaluated and variation of less than 5% was achieved. The limits of detection in water samples and in grapes samples were 0.019mg kg1 and 0.065mg kg1 of kresoxim-methyl residue, respectively. The linear response covered three orders of magnitude up to 10.6mg kg1 of kresoxim-methyl. The robustness was evaluated through a Box–Behnken experimental design showing the insignificance of all factors and their interactions. The potential interference of tebuconazole for the determination of kresoxim-methyl was studied. The use of the dispersive liquid-liquid microextraction (DLLME) allowed recoveries between 80% and 101% depending on concentration with the minimum generation of waste products

Characterization of organic matter at different stages of a composting process

The characterization of the organic matter from raw organic wastes, unmatured compost and maturated compost was performed by different techniques: gravimetric, FTIR-ATR, TGA and from the ability of their extracts to bind Cd2+ (evaluating the free cadmium ion by AGNES). Although the amount of humic-like and fulvic-like acids did not change significantly, the structure and properties of the organic matter changed with composting and maturation. These changes resulted in an increase of the stability of the organic material toward thermal decomposition and in an increase of the capacity to bind cadmium.0366_RES2VALHUM_1_P - Valorização de resíduos orgânicos: produção de substâncias húmicas, cofinanciada pelo Fundo Europeu de Desenvolvimento regional (FEDER) através do Programa INTERREG V-A Espanha-Portugal (POCTEP) 2014-2020