We share our consolidated views, long-term experiences, and best tips for effective scientific writing. After writing hundreds of manuscripts and thus having battled and succeeded in this “mine-field”, and knowing the importance of guidance for successful science communication, particularly for beginners, we have tried to introduce readers to the art of scientific writing, from A to Ω. To help less experienced scientific writers to learn quickly and overcome some initial barriers, avoiding common mistakes that we ourselves have also made, we discuss the most important techniques we have used in trying to write clear, comprehensible, and concise manuscripts that are as attractive and impacting as possible. This guide therefore offers crucial tips and concepts - from the very first words, initial draft, and on to submission, “battles” with reviewers and finally to acceptance and publication. The ethical use of artificial intelligence tools, along with some best practice suggestions for their application, is also presented and discussed. In the end, readers should have a comprehensive picture to help them understand basic manuscript structures and major features, habits and tips that help ensure excellence in scientific writing.

Progenesis QI (PQI) is a multiplatform bioinformatics tool that facilitates the identification workflow for metabolomics experiments. PQI uses fragmentation data provided by MassBank of North America (MoNA) libraries, among others, for metabolite annotation. However, PQI does not officially support MoNA libraries and other libraries based on structure-data files (.sdf). This paper describes the development and application of a software named MoNA to Progenesis QI Library Converter, allowing PQI and MoNA by correcting the fragmentation data of the library for Progenesis readability. We evaluated several public experimental datasets, including human plasma, plant extracts, cultured cells, bacteria, rat serum, and rat hippocampus. The results showed that it is mandatory to proceed with file conversion of each library to allow PQI to access fragmentation information from .msp (main spectra profile) files. This step is highly recommended to improve the identification level of the metabolites.

Representative tar balls collected in two distinct years (2012 and 2014) in a beach along the State of Bahia, northeastern Brazil, were geochemically characterized in order to identify correlations between them and investigate potential sources. Terpanes and steranes biomarkers (detected by gas chromatography coupled to mass spectrometry, GC-MS), carbon stable isotope ratio (δ13C), Ni and V ratios and polar compounds by Fourier transform ion cyclotron resonance mass spectrometry using electrospray ionization in negative mode (ESI(-) FT-ICR MS) were evaluated. Three Brazilian oil samples from distinct sources were assessed as possible spill sources, comparing their results with the tar ball samples. Using chemometric techniques, it was verified correlation between the two set of tar ball samples, suggesting same source. However, no correlation with the oil samples was observed, with different geochemical profile among them. The heteroatom class distribution displayed severe degradation levels for tar balls and its seems that photo-oxidation and biodegradation processes were further relevant. Tar ball samples show multiple classes, most oxygenated, and with one sample showing considerable relative abundance of N1 class, suggesting it is from a more recent oil spill. In brief, our results suggest that the region, with very sensitive ecosystem, is possibly subjected to frequent spills from the same source.

In order to provide an effective and environmentally correct alternative for oil extraction, subcritical n-propane was used under different temperature and pressure conditions to obtain Brazil nut oil. The composition of the oil was determined and compared to the oils obtained by conventional methods. The result of the extraction yield obtained using subcritical fluid extraction (SFE) at 60 ºC, 6 MPa and granulometry < 1.40 mm (63.13%) presented minor differences to the yield obtained by Soxhlet extraction (SE) (68.44%) and Bligh and Dyer extraction (BD) (59.54%). The composition in fatty acids was similar regardless of the method of extraction used. Oxidized triacylglycerols (TAGs) were found in the oils extracted by SE and BD while they were not detected in the oils extracted by SFE. The quantity of bioactive compounds was higher in the oils obtained by SFE. Thus, the SFE using n-propane preserves the nutritional characteristics and lipophilic components of the oil, besides improving the availability of bioactive compounds from an effective “green extraction” without the use of toxic solvents.

Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) was used to assess the spatial distribution of some key flavonoids in peppermint (Mentha × piperita L.) leaves. The chemical images were generated by applying DESI-MSI on the peppermint leaves imprinting while acquiring the spectra in the negative ion mode. The following key flavonoids were detected and grouped within well-known biosynthetic routes in plants: naringenin route [naringenin, sakuranetin, hesperetin, hesperidin, luteolin, and apigenin]; luteolin route [luteolin, chrysoeriol, luteolin-7-O-D-glucuronide, luteolin-7-O-D-glucoside, luteolin-7-O-neohesperidoside]; apigenin route [apigenin, apigenin-7-O-gentiobioside, apigenin-7-O-neohesperidoside, thymusin/pilosin, pebrellin, acacetin/genkwanin, ladanein, xanthomicrol/pedunculin/nevadensin]. Maps of the spatial distribution of these flavonoids throughout the peppermint leaves within each route were then displayed. The results described herein comprise an important (although still underexplored) subject that certainly will experience a remarkable growth in the next years.

Abstract Hydroalcoholic extracts prepared by conventional methods (in stirred vessel at 25 °C and 1 bar) and, hydroalcoholic and supercritical carbon dioxide (scCO2) extracts prepared in fixed bed extractors (60 ºC and 400 bar) were obtained from pitanga leaves (Eugenia uniflora L.) in order to recover phenolic compounds. Hydroalcoholic and ethanolic extracts obtained in fixed bed were further fractionated in four separators by gradual pressure reduction, using scCO2 as an antisolvent. All extracts and fractions were characterized in terms of extraction yield and the presence of total phenolics and flavonoids. Solvents were found to significantly influence the extraction yields and composition. Yields increased as a function of polarity, whereas the hydroalcoholic extractions displayed the highest yields and the highest amounts of extracted phenols and flavonoids.

Design of experiments (DOE) applied to mass spectrometry (MS), mainly focusing on the optimization of ionization techniques, has been applied to optimize experiments in order to provide the highest amount of information with the lowest number of experiments. However, DOE has not been used in petroleomics. For the first time, we applied DOE to optimize the main parameters associated with the crude oil analysis in a petroleomics approach. For the ionization technique, atmospheric pressure photoionization (APPI) has been selected and data were acquired in a high resolution (400,000 at m/z 400) and high mass accuracy (< 1 ppm) Fourier transform ion cyclotron resonance (FT-ICR) MS. Full and fractional two-level factorial designs were applied for the APPI(±) FT-ICR MS data set from two different crude oil samples with distinct physical and chemical characteristics. The standard ionization parameters that affect the MS responses of the crude oil analysis were optimized for both APPI(+)-MS and APPI(–)-MS. Such ionization parameters were then successfully applied to a crude oil and its saturated, aromatics, resin and asphaltene fractions, all with superior features of merit. Thus, the optimized APPI(±)-MS parameters should serve as reference and can be used as a guide for new studies in petroleomics.

The genus Streptomyces represents one of the largest producers of molecules with antibiotic activity. The whole genome sequencing of the endophytic microorganism Streptomyces sp. CBMAI 2042 revealed 35 gene clusters encoding for secondary metabolism including 3 non-ribosomal peptide synthetases (NRPS) and 7 NRPS-hybrids. Combining genome mining and cultivation profile analysis, the depsipeptide ionophore valinomycin was identified as one of the main metabolites produced by this strain. To better understand the metabolic machinery codified in CBMAI 2042 genome an adenylation domain from a hybrid NRPS cluster was deleted through a double crossing knockout experiment. Though the deletion was not plentiful to elucidate the encoded NRP metabolite related to the adenilation domain, an astounding increase of 10.5-fold in valinomycin production was observed in the mutant. These results suggest a metabolic flux redistribution of common substrates as an outcome of a gene target deletion.

Vegetable oils have properties that are beneficial to the human skin, and so, they are being used increasingly as ingredients of many cosmetic preparations; however, they are targets of adulteration. This study will evaluate the authenticity of Brazilian cosmetics based on vegetable oils (sesame, peanut, sunflower, and almonds) to determine the composition of fatty acids by gas chromatography with flame ionization detection (GC-FID) and the percentage of fatty acids in conjunction with chemometric treatments (principal component analysis), and lipid profiles using direct infusion electrospray ionization mass spectrometry (ESI-MS). The results obtained were compared with the respective pure vegetable oils. Of the seven brands analyzed, three were revealed as authentic, three were found to be adulterated with the addition of large amounts of soybean oil, and one showed no vegetable oils. These results demonstrate the relevance of quality control for cosmetics based on vegetable oils, which are more susceptible to adulteration owing to their higher cost when compared with vegetable oils such as soybean.

RESUMO: A espectrometria de massas (MALDI-TOF MS) tem mostrado ser um método alternativo para a identificação de bactérias, sendo capaz de identificar as bactérias causadoras de mastite em gênero, espécie ou até mesmo subespécie. Com o objetivo de identificar os patógenos causadores de mastite em grande-escala por esta plataforma, um total de 305 isolados bacterianos oriundos de vacas com mastite subclínica foram analisados pela cultura microbiológica convencional (CM) e pela MALDI-TOF MS acoplada ao software Biotyper. Aproximadamente 89% das identificações realizadas pela MALDI-TOF MS foram consistentes com os resultados obtidos pela CM. Do restante de isolados bacterianos (11%), 6,3% foram classificados como identificação errônea (discordância de gênero e espécie), e 4,7% apresentaram concordância de gênero, mas discordância da espécie. Os resultados que apresentaram divergência estavam mais associados com a identificação das espécies de Streptococcus spp. e Enterococcus spp. devido à similaridade fenotípica entre os dois gêneros. Estes resultados divergentes sugerem que os ensaios bioquímicos podem ser propensos a erros de identificação, por isso a MALDI-TOF MS pode ser considerada um método alternativo para superar os erros de identificação da CM. A cultura microbiológica padrão e os ensaios bioquímicos utilizados na identificação de agentes causadores de mastite são demorados, trabalhosos e propensos a erros quando utilizados na identificação em nível de espécie. No presente estudo, demonstramos que a MALDI-TOF MS acoplada ao software Biotyper pode ser considerada um método alternativo de identificação de bactérias causadoras de mastite em grande-escala quando comparado com a cultura microbiológica convencional.

ABSTRACT: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been shown to be an alternative method for identification of bacteria via their protein profile spectra, being able to identify bacteria at the genus, species and even at subspecies level. With the aim of large-scale identification of pathogens causing mastitis by this platform, a total of 305 isolates of bacteria identified from cows with subclinical mastitis were analyzed by conventional microbiological culture (MC) as well as by MALDI-TOF MS coupled with Biotyper data processing. Approximately 89% of the identifications performed by MALDI-TOF MS were consistent with results obtained by MC. From the remaining isolates (11%), 6.3% of isolates were classified as misidentified (discordance for both genus and species level), and 4.7% showed identification agreement at the genus level but not at the species level, being classified as unidentified at species level. The disagreement results were mostly associated with identification of Streptococcus and Enterococcus species probably due to the narrow phenotypic similarity between these two genera. These disagreement results suggest that biochemical assays might be prone to identification errors and, MALDI-TOF MS therefore may be an alternative to overcome incorrect species-specific identification. Standard microbiological methods for bovine mastitis diagnosis are time consuming, laborious and prone to errors for some bacteria genera. In our study, we showed that MALDI-TOF MS coupled with Biotyper may be an alternative method for large-scale identification of bacteria isolated from milk samples compared to classical microbiological routine protocols.

Amino acids/ureides and carbohydrates are the main nutrients for the plants growth. These metabolites are continuously translocated through the plant organism via well-known transportation mechanisms. The well-established source-to-sink relationship involves the transfer of these nutrients from mature (source) to young (sink) leaves. Desorption electrospray ionization mass spectrometry imaging (DESI-MSI) is used herein to determine the spatial distribution of amino acids/ureides and carbohydrates in the imprintings of Mentha × piperita L. leaves at three distinct maturation stages: young, expanding, and mature. Hence, chemical images of some typical carbohydrates (glucose, sucrose, sorbitol/mannitol) and free amino acids/ureides (phenylalanine, leucine, histidine, aspartate, asparagine, tyrosine, glutamate, allantoic acid) clearly point to a source-to-sink relationship, as the young leaves are the final destination for some of these key metabolites. These results therefore reveal the high potential of DESI-MSI to investigate biochemical processes in plants, a still underexplored area.

Abstract In a previous study, we reported the antispasmodic and gastroprotective effects of the Serjania caracasana (Jacq.) Willd., Sapindaceae, extract. In the present study, we evaluated the LD50, hemolytic and antispasmodic activities of its fractions and characterized its major constituents by isolation and GC–MS. The animals showed non-toxic symptoms with oral doses up to 2000 mg/kg, suggesting a safe oral administration. Furthermore, a low hemolytic activity was detected for the saponin fraction. Antispasmodic activity of the fractions was evaluated through carbachol-induced contractions in rat ileum. The hexane fraction was the most potent (IC50 68.4 ± 5.9 µg/ml) followed by the dichloromethane fraction (IC50 161.3.4 ± 40.7 µg/ml). Butanol fraction was the less effective (IC50 219.8 ± 60.3 µg/ml). The phytochemical study of the S. caracasana fractions afforded the isolation of friedelin, β-amyrin, allantoin and quercitrin. This is the first time that the presence of allantoin and quercitrin in the Serjania genus has been reported. Among the isolated compounds and those characterized by GC–MS, β-amyrin and β-sitosterol were present in the most active fractions, hexane and dichloromethane, and they may be related to its antispasmodic activity. In addition, spathulenol was only found in the hexane fraction and its presence might justify the highest antispasmodic activity observed for this fraction.

The Itajaí-Açu estuarine system, located in southern Brazil, has great economic importance due to the presence of two ports (Itajaí and Navegantes). This system is affected by industrial and dredging activities, which can cause the remobilization of pollutants accumulated over time in the sediment. In this context, hydrocarbons were assessed in twelve surface sediment samples. n-Alkane and polycyclic aromatic hydrocarbons (PAH) concentrations were determined by gas chromatography and their sources assessed. Total concentrations ranged between 0.50 ± 0.04 and 69.70 ± 3.90 μg g-1 dry weight (d.w.) for n-alkanes and from 63.9 ± 12.1 to 1459.0 ± 43.5 ng g-1 d.w. for PAH. Most of the sediment samples presented carbon preference index (CPI) values close to unity, indicating that the area is submitted to petroleum-related sources, mainly close to Itajaí harbor, where an intense unresolved complex mixture (UCM) was observed. The presence at all stations of αβ-hopane biomarkers also indicated petrogenic input. Based on selected PAH ratios, the sedimentary PAH composition reflects a mixture of both petrogenic and pyrolytic sources. A comparison of the PAH concentrations found in this study with those listed in the sediment quality guidelines (SQGs) indicated that adverse biological effects on the biota are rarely expected.

Cyanobacteria are among the most ancient forms of life, yet they are known to synthesize highly sophisticated defense molecules, such as the highly hepatotoxic cyclic peptides microcystins and nodularins produced by the genera Microcystis, Anabaena and Nodularia. These metabolites are released by cyanobacteria to water environments causing episodes of fatalities among animals and humans. To better understand the releasing of these metabolites, imaging mass spectrometry (IMS) using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) was herein applied to determine the spatial distribution of such toxins directly on agar-based cultures. Other key metabolites such as aeruginosin 602 and the siderophore anachelin were also mapped in mixed cyanobacterial cultures, showing the great potential of IMS to spatially monitor the biochemical details of cyanobacterial defense and interactions.

Correct interpretation of mass spectra is essential to our understanding of the ion chemistry occurring in the gas phase inside mass spectrometers and for constructing a solid knowledge from which mass spectrometry (MS) data of novel molecules will be interpreted. Assignments of product ions leading to incorrect dissociation mechanisms can also be dangerous in several disciplines such as in forensic chemistry and clinical diagnostics. Main fragmentation routes for rhodamines B and 6G were investigated by high accuracy Orbitrap tandem mass spectrometry (MS/MS). Isobars were properly resolved and molecular formulas were correctly attributed to all major product ions. This proper evaluation of ions composition and formula allowed us to propose a detailed mechanism for their dissociation. A comprehensive mechanistic fragmentation is proposed for rhodamine B and 6G using product ion assignments resulting from high resolution and accuracy tandem MS data, which should serve as a guide for MS and MS/MS data interpretation of homologues molecules.