Understanding Water Equilibration Fundamentals as a Step for Rational Protein Crystallization

Background: Vapor diffusion is the most widely used technique for protein crystallization and the rate of water evaporation plays a key role on the quality of the crystals. Attempts have been made in the past to solve the mass transfer problem governing the evaporation process, either analytically or by employing numerical methods. Despite these efforts, the methods used for protein crystallization remain based on trial and error techniques rather than on fundamental principles. Methodology/Principal Findings: Here we present a new theoretical model which describes the hanging drop method as a function of the different variables that are known to influence the evaporation process. The model is extensively tested against experimental data published by other authors and considering different crystallizing conditions. Aspects responsible for the discrepancies between the existing theories and the measured evaporation kinetics are especially discussed; they include the characterization of vapor-liquid equilibrium, the role of mass transfer within the evaporating droplet, and the influence of the droplet-reservoir distance. Conclusions/Significance: The validation tests show that the proposed model can be used to predict the water evaporation rates under a wide range of experimental conditions used in the hanging drop vapor-diffusion method, with no parameter fitting or computational requirements. This model combined with protein solubility data is expected to become a usefu

Tracing Back the History of Pepper (Capsicum annuum) in the Iberian Peninsula from a Phenomics Point of View

[Abstract] The Iberian Peninsula was the place where pepper (Capsicum annuum) entered Europe and dispersed to other continents but was also an important secondary center for its diversification. The current work evaluated the phenotypic diversity existing in this region and investigated how that evolved from Capsicum native areas (Mexico and Andean Region). For that purpose, the high-throughput phenotyping tool Tomato Analyzer was employed. Descriptors related to size and shape were the most distinctive among fruit types, reflecting a broad diversity for Iberian peppers. These traits likely reflected those suffering from more intensive human selections, driving the worldwide expansion of C. annuum. Iberian peppers maintained close proximity to the American accessions in terms of fruit phenomics. The highest similarities were observed for those coming from the southeastern edge of the Peninsula, while northwestern accessions displayed more significant differences. Common fruit traits (small, conical) suggested that Portuguese and Spanish landraces may have arisen from an ancient American population that entered the south of Spain and promptly migrated to the central and northern territories, giving rise to larger, elongated, and blocky pods. Such lineages would be the result of adaptations to local soil–climate factors prevailing in different biogeographic provinces.This research was funded by the Spanish Institute for Agricultural and Food Research and Technology (INIA), co-financed by the European Regional Development Fund (FEDER) (Project RTA2015-00042-C02-02), and by the Xunta de Galicia (Project ED431C 2018/57)Xunta de Galicia; ED431C 2018/5

Biosurfactant-mediated biodegradation of straight and methyl-branched alkanes by Pseudomonas aeruginosa ATCC 55925

Accidental oil spills and waste disposal are important sources for environmental pollution. We investigated the biodegradation of alkanes by Pseudomonas aeruginosa ATCC 55925 in relation to a rhamnolipid surfactant produced by the same bacterial strain. Results showed that the linear C11-C21 compounds in a heating oil sample degraded from 6% to 100%, whereas the iso-alkanes tended to be recalcitrant unless they were exposed to the biosurfactant; under such condition total biodegradation was achieved. Only the biodegradation of the commercial C12-C19 alkanes could be demonstrated, ranging from 23% to 100%, depending on the experimental conditions. Pristane (a C19 branched alkane) only biodegraded when present alone with the biosurfactant and when included in an artificial mixture even without the biosurfactant. In all cases the biosurfactant significantly enhanced biodegradation. The electron scanning microscopy showed that cells depicted several adaptations to growth on hydrocarbons, such as biopolymeric spheres with embedded cells distributed over different layers on the spherical surfaces and cells linked to each other by extracellular appendages. Electron transmission microscopy revealed transparent inclusions, which were associated with hydrocarbon based-culture cells. These patterns of hydrocarbon biodegradation and cell adaptations depended on the substrate bioavailability, type and length of hydrocarbon

Analysis of long period gratings inscribed by CO2 laser irradiation and estimation of the refractive index modulation

Long period gratings (LPGs) inscribed in single mode fibers (SMFs) using CO2 laser irradiation were modelled numerically using the coupled mode method. The model considers the specifications of the inscription technique, such as the shape of the refractive index modulation that mimics the circularly symmetric point-to-point laser irradiation profile. A simple expression for predicting the resonant wavelength was obtained assuming a two-mode coupling model. However, to explain the spectra of the experimental LPGs, it was necessary to assume a reasonably high refractive index change and a multimode coupling model. Furthermore, using the developed model and a genetic algorithm to fit experimental resonances to simulated ones, we were able to estimate the maximum refractive index change, obtaining a value of 2.2 × 10-3, confirming the high refractive index change. The proposed model also predicts a second order resonance for this high value of refractive index change that was confirmed experimentally. Hence, with this model, we found some significant differences in the LPGs behavior when compared with conventional ones, namely, the emergence of coupling between different cladding modes and the competition of first and second order resonances which change the LPG transmission spectrum.publishe

Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages characterizing protein interaction (ISS) in full text documents. We approached the abstract classification task with a novel, lightweight linear model inspired by spam-detection techniques, as well as an uncertainty-based integration scheme. We also used a Support Vector Machine and the Singular Value Decomposition on the same features for comparison purposes. Our approach to the full text subtasks (protein pair and passage identification) includes a feature expansion method based on word-proximity networks. Our approach to the abstract classification task (IAS) was among the top submissions for this task in terms of the measures of performance used in the challenge evaluation (accuracy, F-score and AUC). We also report on a web-tool we produced using our approach: the Protein Interaction Abstract Relevance Evaluator (PIARE). Our approach to the full text tasks resulted in one of the highest recall rates as well as mean reciprocal rank of correct passages. Our approach to abstract classification shows that a simple linear model, using relatively few features, is capable of generalizing and uncovering the conceptual nature of protein-protein interaction from the bibliome. Since the novel approach is based on a very lightweight linear model, it can be easily ported and applied to similar problems. In full text problems, the expansion of word features with word-proximity networks is shown to be useful, though the need for some improvements is discussed

On local convergence of stochastic global optimization algorithms

In engineering optimization with continuous variables, the use of Stochastic Global Optimization (SGO) algorithms is popular due to the easy availability of codes. All algorithms have a global and local search character, where the global behaviour tries to avoid getting trapped in local optima and the local behaviour intends to reach the lowest objective function values. As the algorithm parameter set includes a final convergence criterion, the algorithm might be running for a while around a reached minimum point. Our question deals with the local search behaviour after the algorithm reached the final stage. How fast do practical SGO algorithms actually converge to the minimum point? To investigate this question, we run implementations of well known SGO algorithms in a final local phase stage.- This paper has been supported by The Spanish Ministry (RTI2018-095993-B-I00) in part financed by the European Regional Development Fund (ERDF) and by FCT Fundacao para a Ciencia e Tecnologia within the Project Scope: UIDB/00319/2020

Evaluation of the Simulated Annealing and the Discrete Artificial Bee Colony in the Weight Tardiness Problem with Taguchi Experiments Parameterization

Meta-Heuristics (MH) are the most used optimization techniques to approach Complex Combinatorial Problems (COPs). Their ability to move beyond the local optimums make them an especially attractive choice to solve complex computational problems, such as most scheduling problems. However, the knowledge of what Meta-Heuristics perform better in certain problems is based on experiments. Classic MH, as the Simulated Annealing (SA) has been deeply studied, but newer MH, as the Discrete Artificial Bee Colony (DABC) still need to be examined in more detail. In this paper DABC has been compared with SA in 30 academic benchmark instances of the weighted tardiness problem (1 parallel to Sigma w(j)T(j)). Both MH parameters were fine-tuned with Taguchi Experiments. In the computational study DABC performed better and the subsequent statistical study demonstrated that DABC is more prone to find near-optimum solutions. On the other hand SA appeared to be more efficient.This work is supported by FEDER Funds through the "Programa Operacional Factores de Competitividade - COMPETE" program and by National Funds through FCT "Fundacao para a Ciencia e a Tecnologia" under the project: PEst-OE/EEI/UI0760/2014, and PEst2015-2020.info:eu-repo/semantics/publishedVersio

Mathematics achievement in engineering : an exploratory study with MIEGI students

Mathematics is a discipline that appears on the syllabus of many courses, including courses in engineering, where it is an essential discipline to the formation of all future engineers, whatever their field of study and work. Despite that, engineering students tend to reveal difficulties with courses based on mathematics. The factors that influence learning mathematics have been the subject of study for several researchers around the world. Researchers attempt to identify variables that explain mathematics achievement, but fail to address university students. In this paper, we present the results of an exploratory study based on industrial engineering students of University of Minho, concerning their grades in the courses of statistics and numerical methods. The preliminary results show that gender is an unexpected and significant factor.Fundação para a Ciência e a Tecnologia (FCT

On the correlation between physicochemical properties of agar and its performance as edible coating and film to enhance shelf-life of fresh fruit

Agar is a biopolymer extensively used as gel and stabilizer. Depending on red seaweeds and agar extraction protocols, different physicochemical properties are attained. This research aimed at a better understanding the agar’s physicochemical properties effect on agar coatings performance to improve shelf-life of fresh fruits. Agar was extracted from red algae Gracilaria vermiculophylla in presence or absence of a pre-treatment with aqueous sodium hydroxide prior to extraction and purification. Agar extracts were characterized regarding molecular weight (Mw), sulphates, 3,6-anidrogalactoses (LA), gelation and melting point, extraction yield, gel strength, microstructure (via crio-SEM) and water content. Distinct agar-based coating and film formulations were prepared resorting to native and low sulphate and high anydrogalactose content-commercial agars. Glycerol and tween-80 were used as plasticizer and surfactant, respectively. Agar-based coatings were employed in fresh strawberries, which were further packed and stored at 10ºC, 80%RH and 25%van during 7-d, and shelf-life evaluated via several physicochemical, mechanical and nutritional parameters. Significant differences were observed in some properties, e.g. LA, sulphates, Mw, gel strength and microstructure – particularly in comparison to commercial agar. Coating data showed minor differences between native agar extracts and formulations but significant variations with commercial ones. Nevertheless, shelflife improvement was apparent in coated fruits when analysing colour and phenolics. Commercial agar led to slightly stronger films but native agar produced appropriated ones. This study confirms high correlations between extraction procedure and some properties of final agar which, in turn, have some key effects when used as edible coatings and films. Finally, potential use of G. vermiculophylla agar in coatings and films was established, contributing to the valorisation of environmental by-products