An integrative approach for codon repeats evolutionary analyses

The relationship between genome characteristics and several human diseases has been a central research goal in genomics. Many studies have shown that specific gene patterns, such as amino acid repetitions, are associated with human diseases. However, several open questions still remain, such as, how these tandem repeats appeared in the evolutionary path or how they have evolved in orthologous genes of related organisms. In this paper, we present a computational solution that facilitates comparative studies of orthologous genes from various organisms. The application uses various web services to gather gene sequence information, local algorithms for tandem repeats identification and similarity measures for gene clustering.publishe

Computational and statistical methodologies for ORFeome primary structure analysis

Codon usage and context are biased in open reading frames (ORFs) of most genomes. Codon usage is largely influenced by biased genome G+C pressure, in particular in prokaryotes, but the general rules that govern the evolution of codon context remain largely elusive. In order to shed new light into this question we have developed computational, statistical and graphical tools for analysis of codon context on an ORFeome wide scale. In here, we describe these methodologies in detail and show how they can be used for analysis of ORFs of any genome sequenced.publishe

Ants Sleep, Plants do not: The Variation in Species’ Activity Influences the Topology of Interaction Networks

The emergence of graph theory allowed using the complex network approach to aggregate detailed information about interactions between species. Although the use of the complex network approach has improved the understanding about community structuring, few aspects such as the temporal variation in the species’ activity pattern in the networks’ topology were explored so far. The current study used the ecological network approach to investigate ants interacting in the extrafloral nectary (EFN) of plants in order to test the hypothesis that the temporal variation in the foraging behavior of these animals affects the networks’ topology. In order to assess the temporal effect on the interaction networks, 24-hour collections divided in two 12-hour shifts (day and night) were performed in 20 plots, thus totaling 288 collection hours over 6 months. The ant-plant interaction networks presented similarity among the topological metrics assessed throughout the day. Different ant species presented distinct foraging times. Thus, two modules referring to the day and night shifts emerged from the network and presented specific species at each foraging shift. On the other hand, the plants kept on providing the resource (active EFNs) throughout the day. The results found in the current study have shown that ecological networks keep their structures constant; however, the ecological processes ruling these networks can better respond to the effects caused, for example, by the temporal variation in species’ activity. Therefore, it is worth always taking into consideration the importance of ecological processes at the time to analyze interactions in the nature

Treatment of effluents containing 2-chlorophenol by adsorption onto chemically and physically activated biochars

The application of adsorption using biochars for the remediation of effluents containing emerging contaminants, including chlorophenols, is a hotspot and trend development in the literature. This treatment is more interesting when using readily available wastes and at no cost, such as malt bagasse, for example. Here, the biochars were produced from malt bagasse, by physical and chemical activation (with CO2 and ZnCl2, respectively) and employed as adsorbents in the remediation of effluents containing 2-chlorophenol. Results revealed that the activated biochars have mesoporous structures and surface areas of 161 m² g-1 (CO2) and 545 m² g-1 (ZnCl2). For both activated biochars, adsorption of 2-chlorophenol was favored under acid conditions, with the highest adsorption capacities found using ZnCl2-activated biochar. The maximum adsorption capacity using ZnCl2-activated biochar was 150 mg g-1. The process was endothermic and spontaneous. ZnCl2-activated biochar exhibited an efficiency of 98% (using a dosage of 10 g L-1) in the treatment of industrial effluents containing 2-chlorophenol.La aplicación de la adsorción mediante biocarros para la remediación de efluentes que contienen contaminantes emergentes, incluidos los clorofenoles, es un punto crítico y un desarrollo de tendencia en la literatura. Este tratamiento es más interesante cuando se utilizan residuos fácilmente disponibles y sin costo, como el bagazo de malta, por ejemplo. Aquí, los biocarros se produjeron a partir de bagazo de malta, mediante activación física y química (con CO2 y ZnCl2, respectivamente) y se emplearon como adsorbentes en la remediación de efluentes que contienen 2-clorofenol. Los resultados revelaron que los biocarros activados tienen estructuras mesoporosas y áreas superficiales de 161 m² g-1 (CO2) y 545 m² g-1 (ZnCl2). Para ambos biocarros activados, la adsorción de 2-clorofenol se vio favorecida en condiciones ácidas, con las capacidades de adsorción más altas encontradas utilizando biocarbón activado con ZnCl2. La capacidad máxima de adsorción usando biocarbón activado con ZnCl2 fue de 150 mg g-1. El proceso fue endotérmico y espontáneo. El biocarbón activado con ZnCl2 exhibió una eficiencia del 98% (usando una dosis de 10 g L-1) en el tratamiento de efluentes industriales que contienen 2-clorofenol

SHORT-TERM SOCIAL ISOLATION DOES NOT REDUCE ELEVATED PLUS-MAZE EXPLORATION IN EARLY PROTEIN MALNOURISHED RATS

An increased number of visits and time spent in the open arms of the elevated plus-maze by malnourished rats has been used as indicative of lower anxiety or impulsiveness. In order to study how this behavior profile responds to an anxiogenic procedure (short-term social isolation), control (16% protein) and malnourished (6% protein) rats were socially isolated prior to the test in the maze. Litters (dam plus 6 male 2 female pups) were fed the diets from birth to 49 days of age. From 50 days on, all rats were fed a lab chow diet. Social isolation consists in removing the rats from the group and placing in individual cages for 2h before the test. During the test each rat was individually placed on the center of the maze and allowed to explore for 5 min. The results showed higher open arms exploration and lower attempts to enter open arms by the malnourished rats than by the controls. Social isolation decreased open arm exploration and increased time spent on the central platform in control animals, but had no effect on the malnourished rats. The results reinforce the lower anxiety or higher impulsiveness of malnourished rats, as well as the anxiogenic effect of social isolation in control rats. However, the malnourished rats were unresponsive to the anxiogenic effects of social isolation, indicating that protein deficiency early in life not only induces lower anxiety or higher impulsiveness in the maze, but also changes the behavior of these animals in response to another environmentally-induced procedure of anxiety (social isolation). Keywords: Early protein malnutrition, Social isolation, Anxiety, Impulsiveness, Stress, Rats.

Adsorption of ibuprofen, ketoprofen, and paracetamol onto activated carbon prepared from effluent treatment plant sludge of the beverage industry

The presence of emerging contaminants such as pharmaceuticals in aquatic means presents as a serious threat, since their real consequences for the environment and human health are not well known. Therefore, this work consisted of preparing and characterize sludge-derived activated carbons (beverage sludge activated carbon – BSAC and acid-treated beverage sludge activated carbon - ABSAC) to investigate their use in the pharmaceuticals adsorption in aqueous media. The morphology study has demonstrated that ABSAC, unlike BSAC, exhibited an abundant porous structure, with smaller particles and bigger roughness. Adsorption results indicated that the ABSAC was more effective that BSAC, since it presented superior surface area (642 m2 g-1) and total pore volume (0.485 cm3 g-1) values. Pseudo-second-order kinetic model was more suitable to predict experimental data. Sips model best described the equilibrium data, with maximum adsorption capacities of 145, 105, and 57 mg g-1 for paracetamol, ibuprofen, and ketoprofen, respectively. Besides, the sludge-derived adsorbent was highly efficient in the treatment of a simulated drug effluent, removing 85.16% of the pharmaceutical compounds. Therefore, the material prepared in this work possesses intrinsic characteristics that make it a remarkable adsorbent to be applied in the treatment of pharmaceutical contaminants contained in industrial wastewater

Enhanced sweet taste perception in obesity: joint analysis of gustatory data from multiple studies

Copyright © 2022 Ribeiro, Torres, Fernandes, Camacho, Branco, Martins, Raimundo and Oliveira-Maia. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.Introduction: While sweet taste perception is a potential determinant of feeding behavior in obesity, the supporting evidence is inconsistent and is typically associated with methodological limitations. Notably, possible associations between sweet taste perception and measures of food reward remain undetermined. Materials and methods: We conducted a cross-sectional analysis comparing 246 individuals with severe obesity and 174 healthy volunteers using a validated method for taste perception assessment. We included gustatory variables, namely intensity and pleasantness ratings of sour, salt, sweet, and bitter tastants, and taste thresholds assessed by electrogustometry. Reward-related feeding behavior, including hedonic hunger, food addiction, feeding behavior traits, and acceptance of foods and alcohol, was evaluated using self-rated scales for comparison with gustatory measures. Result: In logistic regressions adjusted for age, gender, educational level, and research center, we found that a greater likelihood of belonging to the obesity group was associated with higher sweet intensity ratings (OR = 1.4, P = 0.01), hedonic hunger, food addiction symptoms, restrained and emotional eating (1.7 < OR ≤ 4.6, all P ≤ 0.001), and lower alcohol acceptance (OR = 0.6, P = 0.0002). Using principal component analysis, we found that while hedonic hunger, food addiction, and emotional eating were strongly interrelated, they were not associated with sweet intensity perception that, in turn, had a closer relationship with alcohol acceptance and restrained eating. Conclusion: We found that individuals with obesity report higher sweet taste intensity ratings than healthy controls. Furthermore, while psychological measures of reward-related feeding behavior assess a common construct, sweet intensity perception may represent a different obesity-related dimension.AJO-M was supported by grants from the BIAL Foundation (176/10), from Fundação para a Ciência e Tecnologia (FCT), through a Junior Research and Career Development Award from the Harvard Medical Portugal Program (HMSP/ICJ/0020/2011), and by a Starting Grant from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 950357). ST was funded by the Center for Psychology at the University of Porto (FCT UIDB/00050/2020). AF was funded by a postdoctoral fellowship from FCT (SFRH/BPD/880972/2012). GR was funded by doctoral fellowships from Universidade de Lisboa (BD/2015Call) and FCT (SFRH/BD/128783/2017).info:eu-repo/semantics/publishedVersio

Enhanced sweet taste perception in obesity: joint analysis of gustatory data from multiple studies

Copyright © 2022 Ribeiro, Torres, Fernandes, Camacho, Branco, Martins, Raimundo and Oliveira-Maia. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.Introduction: While sweet taste perception is a potential determinant of feeding behavior in obesity, the supporting evidence is inconsistent and is typically associated with methodological limitations. Notably, possible associations between sweet taste perception and measures of food reward remain undetermined. Materials and methods: We conducted a cross-sectional analysis comparing 246 individuals with severe obesity and 174 healthy volunteers using a validated method for taste perception assessment. We included gustatory variables, namely intensity and pleasantness ratings of sour, salt, sweet, and bitter tastants, and taste thresholds assessed by electrogustometry. Reward-related feeding behavior, including hedonic hunger, food addiction, feeding behavior traits, and acceptance of foods and alcohol, was evaluated using self-rated scales for comparison with gustatory measures. Result: In logistic regressions adjusted for age, gender, educational level, and research center, we found that a greater likelihood of belonging to the obesity group was associated with higher sweet intensity ratings (OR = 1.4, P = 0.01), hedonic hunger, food addiction symptoms, restrained and emotional eating (1.7 < OR ≤ 4.6, all P ≤ 0.001), and lower alcohol acceptance (OR = 0.6, P = 0.0002). Using principal component analysis, we found that while hedonic hunger, food addiction, and emotional eating were strongly interrelated, they were not associated with sweet intensity perception that, in turn, had a closer relationship with alcohol acceptance and restrained eating. Conclusion: We found that individuals with obesity report higher sweet taste intensity ratings than healthy controls. Furthermore, while psychological measures of reward-related feeding behavior assess a common construct, sweet intensity perception may represent a different obesity-related dimension.AJO-M was supported by grants from the BIAL Foundation (176/10), from Fundação para a Ciência e Tecnologia (FCT), through a Junior Research and Career Development Award from the Harvard Medical Portugal Program (HMSP/ICJ/0020/2011), and by a Starting Grant from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 950357). ST was funded by the Center for Psychology at the University of Porto (FCT UIDB/00050/2020). AF was funded by a postdoctoral fellowship from FCT (SFRH/BPD/880972/2012). GR was funded by doctoral fellowships from Universidade de Lisboa (BD/2015Call) and FCT (SFRH/BD/128783/2017).info:eu-repo/semantics/publishedVersio

Morphology dependence degradation of electro- and magnetoactive poly(3-hydroxybutyrate-co-hydroxyvalerate) for tissue engineering applications

Poly(hydroxybutyrate-co-hydroxyvalerate) (PHBV) is a piezoelectric biodegradable and biocompatible polymer suitable for tissue engineering applications. The incorporation of magnetostrictive cobalt ferrites (CFO) into PHBV matrix enables the production of magnetically responsive composites, which proved to be effective in the differentiation of a variety of cells and tissues. In this work, PHBV and PHBV with CFO nanoparticles were produced in the form of films, fibers and porous scaffolds and subjected to an experimental program allowing to evaluate the degradation process under biological conditions for a period up to 8 weeks. The morphology, physical, chemical and thermal properties were evaluated, together with the weight loss of the samples during the in vitro degradation assays. No major changes in the mentioned properties were found, thus proving its applicability for tissue engineering applications. Degradation was apparent from week 4 and onwards, leading to the conclusion that the degradation ratio of the material is suitable for a large range of tissue engineering applications. Further, it was found that the degradation of the samples maintain the biocompatibility of the materials for the pristine polymer, but can lead to cytotoxic effects when the magnetic CFO nanoparticles are exposed, being therefore needed, for magnetoactive applications, to substitute them by biocompatible ferrites, such as an iron oxide (Fe3O4).This work was supported by the Portuguese Foundation for Science and Technology (FCT) in the framework of the Strategic Funding UID/FIS/04650/2020, UID/BIO/04469/2020 and UID/QUI/00686/2020, and projects PTDC/BTM-MAT/28237/2017 and PTDC/EMD-EMD/28159/2017 and Associate Laboratory for Green Chemistry—LAQV, financed by national funds from FCT/MCTES (UIDB/50006/2020). The authors also thank the FCT for the SFRH/BPD/121526/2016 (DMC) grant. The authors acknowledge funding by the Spanish Ministry of Economy and Competitiveness (MINECO) through the project MAT2016-76039-C4-3-R (AEI/FEDER, UE) and from the Basque Government Industry and Education Departments under the ELKARTEK, HAZITEK and PIBA (PIBA-2018-06) programs, respectively.info:eu-repo/semantics/publishedVersio