Using Protein Homology Models for Structure-Based Studies: Approaches to Model Refinement

Homology modeling is a computational methodology to assign a 3-D structure to a target protein when experimental data are not available. The methodology uses another protein with a known structure that shares some sequence identity with the target as a template. The crudest approach is to thread the target protein backbone atoms over the backbone atoms of the template protein, but necessary refinement methods are needed to produce realistic models. In this mini-review anchored within the scope of drug design, we show the validity of using homology models of proteins in the discovery of binders for potential therapeutic targets. We also report several different approaches to homology model refinement, going from very simple to the most elaborate. Results show that refinement approaches are system dependent and that more elaborate methodologies do not always correlate with better performances from built homology models

Stress and Developmental Stability: Vegetation Removal Causes Increased Fluctuating Asymmetry in Shrews

Environmental stress can increase phenotypic variation in populations by affecting developmental stability of individuals. While such increase in variation results from individual differences in ability to buffer stress, groups of individuals and different traits may have different sensitivity to stressful conditions. For example, the sex that is under stronger directional selection for faster growth may be more sensitive to stressful conditions during development. On an individual level, stress-induced variation in a trait may be related to the strength of stabilizing selection that acts on the trait. We experimentally examined sensitivity of mandibular development to stress in a free-living population of common shrews (Sorex cinereus), a short-lived insectivore mammal with very limited dispersal and nearly continuous foraging activity. We found a strong increase in asymmetry in shrews born under stressful conditions. Increased asymmetry was associated with lower physiological condition in both control and stressed populations, although the effect of asymmetry on fitness was more pronounced under stressful conditions. Males\u27 developmental stability was more sensitive to stressful conditions than developmental stability of females, suggesting that their apparently faster and more variable growth is more sensitive to stress than is growth of females. Mandible traits differed in their sensitivity to environmental changes. Preliminary results suggest that this differential sensitivity is proportional to the degree of developmental and functional morphological integration among mandibular traits

Biomarker of Chronic Alcohol Abuse – Carbohydrate-deficient Transferrin (CDT): Methodology Verification

Introduction: Transferrin is a glycoprotein synthesized in hepatocytes that can appear with different isomorphic forms in the plasma, acquiring different levels of sialization (1,2). In a healthy person, penta, tetra and trisial isoforms are detectible in plasma. However, in an alcohol abuse and/or dependence, asialo, monosialo and disialotransferrin isoforms are also present called carbohydrate-deficient transferrin (CDT) (3) . This is considered a specific biomarker of alcohol abusive and/or dependence, being useful in the diagnosis and monitoring of this pathology (4) . Aim: Verify compliance with the requirements of the manufacturer of the capillary electrophoresis method in laboratory practice and its suitability in determining the CDT. Materials and methods: The MiniCap System (Sebia) was used with calibrators traceable to the IFCC international reference procedure and normal and pathological internal control samples. Repeatability and intermediate precision tests were performed on control samples. From participation in External Quality Assessment (EQA) program (5 rounds - 2 samples each), Bias%, Deviation Index (DI) and Total Laboratory Error (TELab) were obtained. The Measurement Uncertainty was calculated by the Top Down Method (combined and expanded with a factor of 1.96), using the internal (CV%) and external (Bias%) quality control results. Results: In the repeatability tests, normal control samples (n=22, mean = 1.4%) were obtained, CV = 5.7%; for the pathological sample (n=24, mean = 5.4%), CV = 2.2%. In intermediate precision tests for the normal control sample, (n= 12, mean = 1.4%), CV = 6.7%; for the pathological sample (n=12, mean = 5.3%), CV = 4.9%. In samples from EQA program, mean Bias = -1.0% and TELab = 11.5. In the evaluation of the method by DI, 1 satisfactory, 7 good and 2 excellent results were obtained. The obtained Expanded Uncertainty (1.3% ± 0.3) is consistent with that indicated by the manufacturer. Conclusion: The TELab obtained meets Westgard`s desirable specifications (5) , being considered an appropriate methodology for use in laboratory practise for diagnosis. However, it is considered important to monitor the method with Internal Control samples, and participate in EQA programs, as well as periodic evaluation of Quality Indicators.N/

Organic acids concentration in citrus juice from conventional versus organic farming

Every day consumers make choices about what to eat and ask themselves “Should I be buying organic food?” For producers, is very important to have technical information about the quality of organic products. It can facilitate to demonstrate the quality of organic products, in comparison with conventional ones. The purpose of our work was to compare internal and external characteristics of citrus, produced in organic versus conventional farming. The study was carried out in the south of Portugal. Fruits of different orchards have been harvested and submitted to physical and chemical analyses, as well as to a sensorial test. The analyses showed that the farming system affected fruit quality. Special attention was paid to the concentration of vitamin C, a compound which plays an important role in human health. Fruits from organic farming had a higher level of vitamin C, compared with fruits from conventional production. However, this result was not obtained in all cultivars. The concentration of other organic acids was also evaluated. Results showed clear differences between cultivars and between the two farming systems. In most cases, concentration of organic acids was higher in the citrus fruits from organic farming

Comparison of harvesting methods for the cyanobacteria Microcystis aeruginosa

BioTech 2017 and 7th Czech-Swiss Symposium with ExhibitionMicrocystis aeruginosa is a wellknown cyanobacterium that has been spreading all over the world due to increased temperatures and eutrophication of water bodies caused by intensive anthropogenic activities. This toxin-producing microorganism is frequently responsible for diminishing water quality and causing intoxication of humans and animals. Due to this, its intracellular cyanotoxin – microcystin (MC) – is commonly used as tool for molecular and cell biology studies or as a standard in human and environmental risk assessment assays. Moreover, MC is a promising anticancer/antitumor drug candidate and a possible antimicrobial, antifungal, antialgal and insecticide agent. Despite MC’s potential application in several biotechnological fields, its high production costs significantly contribute for the prohibitive selling prices (28000 e/mg). Thus, improvements in process’ cost-effectiveness is needed, especially in terms of downstream processing techniques which are probably the major bottlenecks of cyanobacteria production at large scale, commonly representing 20-30 % of the total costs. Bearing this in mind, this study aimed at optimizing harvesting of M. aeruginosa induced by pH change and compares the optimal conditions obtained with the use of three different flocculant agents: chitosan, ferric chloride, and aluminium chloride. Harvesting induced by pH was assessed by testing pH values ranging between 2 and 14. Despite the fact that harvesting efficiencies above 90 % were obtained for most pH values, pH 2 was the one where higher sedimentation rate was observed and consequently the chosen method to compare with the three flocculants. Aluminium chloride addition was found to be the most efficient method, reaching 93 % of sedimentation efficiency within the first 2 h. These results are in agreement with zeta potential measurements where cells presented nearly neutral (approx. 0 mV) charge, while positive or negative charges where achieved using the other three methodologies.This research work was supported by the grant SFRH/BPD/98694/2013 (Bruno Fernandes) and SFRH/BD/52335/2013 (Pedro Geada) from Fundação para a Ciência e a Tecnologia (Portugal). Luís Loureiro is recipient of a fellowship supported by a doctoral advanced training (call NORTE-69-2015-15) funded by the European Social Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684), Project UID/Multi/04423/2013, Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462), FCT Strategic Project of UID/BIO/04469/2013 unit, by the project NOVELMAR (reference NORTE-01-0145-FEDER-000035), co-financed by the North Portugal Regional Operational Programme (Norte 2020) under the National Strategic Reference Framework (NSRF), through the ERDF, and by BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersio

Design of a new test chamber for evaluation of the toxicity of rubber infill

A test chamber was projected and built (according to ISO 16000-9 Standard) to simulate atmospheric conditions experienced by rubber infill (when applied in synthetic turf pitches) and measure accurately the airborne emissions of pollutants such as dusts and volatile organic compounds (VOC), as well as pollutants present in leachates. It should be pointed out that standard ISO 16000-9 is only concerned with the determination of the emission of VOC from building products and furnishing (not specific of synthetic turf materials), whereas other standards are concerned with the emission of leachates only. This procedure is to be considered as a technical option to the lysimeter "global turf system evaluation" when the rubber infill alone is to be evaluated. The advantage of the proposed option considering this "test chamber" is its simplicity and economy. This test chamber is actually installed and being used for tests in LAIST

The amino acids motif-32GSSYN36-in the catalytic domain of E. coli flavorubredoxin NO reductase is essential for its activity

Funding Information: Funding: This study was financially supported by the Portuguese Fundação para a Ciência e Tec-nologia (FCT), grants PTDC/BIA-BQM/27959/2017 and PTDC/BIA-BQM/0562/2020, and Project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement 810856. MCM is the recipient of FCT grant SFRH/BD/143651/2019. BAS is the recipient of FCT grant DFA/BD/8066/2020. Funding Information: This study was financially supported by the Portuguese Funda??o para a Ci?ncia e Tecnologia (FCT), grants PTDC/BIA-BQM/27959/2017 and PTDC/BIA-BQM/0562/2020, and Project MOSTMICRO-ITQB with references UIDB/04612/2020 and UIDP/04612/2020. This project has also received funding from the European Union?s Horizon 2020 research and innovation program under grant agreement 810856. MCM is the recipient of FCT grant SFRH/BD/143651/2019. BAS is the recipient of FCT grant DFA/BD/8066/2020. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Flavodiiron proteins (FDPs) are a family of modular and soluble enzymes endowed with nitric oxide and/or oxygen reductase activities, producing N2O or H2O, respectively. The FDP from Escherichia coli, which, apart from the two core domains, possesses a rubredoxin-like domain at the C-terminus (therefore named flavorubredoxin (FlRd)), is a bona fide NO reductase, exhibiting O2 reducing activity that is approximately ten times lower than that for NO. Among the flavorubredoxins, there is a strictly conserved amino acids motif,-G[S,T]SYN-, close to the catalytic diiron center. To assess its role in FlRd’s activity, we designed several site-directed mutants, replacing the conserved residues with hydrophobic or anionic ones. The mutants, which maintained the general characteristics of the wild type enzyme, including cofactor content and integrity of the diiron center, revealed a decrease of their oxygen reductase activity, while the NO reductase activity—specifically, its physiological function—was almost completely abolished in some of the mutants. Molecular modeling of the mutant proteins pointed to subtle changes in the predicted structures that resulted in the reduction of the hydration of the regions around the conserved residues, as well as in the elimination of hydrogen bonds, which may affect proton transfer and/or product release.publishe

Benefits Of Therapeutic Horticulture In Institutionalized Patients With Mental Health Disorders Within An Organic Environment

Therapeutic horticulture (TH) is a non-pharmacological approach to assist other psychiatric treatments and should be carried out according to organic principles for health reasons. The benefits of TH in individuals with mental health conditions can be found in the literature. However, it is scarce the information to understand if TH activities have advantages when compared to more conventional occupational therapies (OT), and this is the main objective of the present study. It was led in a psychiatric hospital in Portugal with 25 patients attending TH amongst other OT and 15 patients attending only OT. The instruments used were two questionnaires of sociodemographic and clinical data and patients’ preferences, and two evaluation instruments, the ‘Subjective Happiness Scale’ (SHS) and the short form of the ‘Social and Emotional Loneliness Scale for Adults’ (SELSA-S).The scores of the SHS and SELSA-S were generally similar for TH and OT groups, except the 'optimism about life' with a lower optimistic perception of life for the TH patients. It was found that the activities of TH were preferred to other OT by 48% of the patients in the TH group. The changes perceived by some of these TH patients included the perception of feeling more relaxed and happier. In this group, a greater number of days per week with activities provided lower loneliness and a greater happiness perspective compared to peers. For all patients, visits by family or friends also had a positive effect as revealed by the lower level of family emotional loneliness, compared to patients without visits. The findings and the benefits reported in the literature suggest that TH is an integrative treatment option, which merits further study and can be better tailored to maximize TH effectiveness

P-Sulfonic acid calix[4]arene-functionalized alkyl-bridged organosilica in esterification reactions

Two new p-sulfonic acid calix[4]arene- and p-sulfonic acid calix[6]arene-functionalized organosilica have been synthesized using a sol-gel method and applied as heterogeneous catalysts in esterification reactions. The catalytic performance was evaluated using the esterification of carboxylic acids with ethanol, and good catalytic activity (i.e., 55-88%) was observed under the optimum reaction conditions. This study reports the first promising example of the successful employment of calix[n]arenes as a heterogeneous catalyst for catalytic esterification. The catalyst was easily separated by filtration and reused five times without any significant loss of activity.Fil: De Assis, J. V.. Universidade Federal de Viçosa; BrasilFil: Abranches, P. A. S.. Universidade Federal de Viçosa; BrasilFil: Braga, I. B.. Universidade Federal de Viçosa; BrasilFil: Portilla Zúñiga, Omar Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Ciencias Aplicadas "Dr. Jorge J. Ronco". Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Ciencias Aplicadas; ArgentinaFil: Sathicq, Angel Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Ciencias Aplicadas "Dr. Jorge J. Ronco". Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Ciencias Aplicadas; ArgentinaFil: Romanelli, Gustavo Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Ciencias Aplicadas "Dr. Jorge J. Ronco". Universidad Nacional de la Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Ciencias Aplicadas; ArgentinaFil: Sato, A. G.. Universidade Federal de Viçosa; BrasilFil: Fernandes, S. A.. Universidade Federal de Viçosa; Brasi