The enzymatic determination of glucose in carbonated beverages: a useful tool for the undergraduate students to learn the basis of enzymatic analysis and the comparison of two analytical methods

The importance of enzymatic analysis in biochemistry, clinical chemistry and food chemistry is undoubted. The course "Applied Biochemistry" in our Faculty is aimed to undergraduate students of Chemistry and Biochemistry. In this subject, the principles and applications of enzymatic analysis are presented to the students, who receive a theoretical introductory lecture in the classroom before they carry out an experiment that should be feasible to be solved in a short laboratory period. The experimental protocol here presented, based on the enzymatic determination of glucose in carbonated beverages, has been implemented at the University of Málaga and it has been optimized according to the students’ results and commentaries along the last years. It aims to illustrate basic issues relating enzymatic analysis, including its potential application to food chemistry. Although there are several enzymatic methods that can be used for the determination of glucose, we selected the one based on the coupled reactions of glucose oxidase (GOD; EC 1.1.3.4.) and peroxidase (POD; EC 1.11.1.7.) because the kinetic constants of glucose oxidase allow the mentioned enzymatic reactions to be used in both, the end point and the kinetic enzymatic analysis methods. In this way, data for two different protocols for the determination of glucose concentration are obtained by the students from a single reaction mixture. Students construct a calibration curve for each method using a glucose standard solution, and use them to determine the glucose concentration in the problem solutions. The inclusion of replicate samples in the determination of the glucose concentration of an “ideal problem” (glucose in purified water) is used to illustrate the principles of statistics in the lab, and comparison with the “real value” allows an estimation of the accuracy of each method. The evaluation of glucose concentration in four carbonated beverages: coloured coke and uncoloured tonic sodas (regular or sugarless in both cases) makes student to recognise the appearance of interferences that should be either avoided or eliminated. Since all samples are analysed by means of end-point and kinetic methods, students can discuss the applicability of each method to these specific analytical problems. They are also encouraged to compare both analytical methods in terms of sensitivity, selectivity, accuracy, and time consumed. Chemistry and Biochemistry undergraduate students having performed this experiment in our laboratories have found it formative, interesting and challenging.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

A practice project to prevent the cookbook model as modus operandi for biochemistry laboratory learning

Laboratory learning is a crucial component of chemistry and biochemistry instruction and should be conceived as a way to develop students’ reasoning, technical or practical skills, introducing them into the scientific method principles. Nevertheless, the heavily criticized “expository instruction style”, characterized by a cookbook nature, is still the most widespread style of laboratory instruction in our universities. Alternative learning styles based in the inquiry, discovery and problem-based pedagogical approaches, have been reported to promote students’ problem solving skills, critical thought and self-confidence development. We are currently involved in the Educative Innovation Project PIE17-065, funded by University of Malaga, aimed to improve the teaching practice of Biochemistry laboratory to undergraduate students. Based on an enzymatic analysis of glucose in soft-drinks we have developed a laboratory protocol as a part of a full practice project where students must work before and after the lab session, in order to prevent the cookbook model as modus operandi, therefore preventing the situation where the students get a first glimpse of the experiment protocol whereas they put on their lab coat. The learning activities have been designed to move our students from the passive role that characterizes the step-by-step procedures, to an active and critical attitude that starts before and remains after their laboratory session, also minimizing time, space, and equipment resources. Our results have shown that this experiment has improved the learning of both, future biochemists and chemists, which showed a very positive perception of the whole practical project.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech. PIE 17-06

VariScan Software

Linux / Mac OS X : The package includes executables for linux (variscan) and Mac OS X (variscan). For other Unix-based platforms you will have to compile it from the source files included in the VariScan package. Windows: The package includes (src directory), the source code, the project (variscan.dev) and makefile (variscan.win) files to be used, for instance, for the Dev-C++ (a free Integrated Development Environment for the C/C++ programming language)Podeu consultar l'article relacionat a: http://hdl.handle.net/2445/7384Podeu consultar la pàgina de desenvolupament del programari: http://www.ub.edu/softevol/VariScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome scale. Among other features, the software: (1) can conduct many population genetic analyses; (2) incorporates a multiresolution wavelet transform-based method that allows capturing relevant information from DNA polymorphism data; and (3) it facilitates the visualization of the results in the most commonly used genome browsers

Learning contract, co-operative and flipped learning as useful tools for studying metabolism

Es el Abstract de una comunicación a un congreso internacional sobre educaciónUndergraduate students in Biology identify Metabolic Biochemistry as a particularly difficult subject. This is due to the fact that students need to interconnect properly all the contents of its syllabus throughout their study of the subject in order to get a global insight of the complex regulatory features controlling metabolic pathways within the metabolic network under different physiologic and pathologic conditions, as well as metabolism as a whole. Due to these objective difficulties, a high percentage of our students face the study of this subject as a very hard task beyond their forces and capacities. This perception leads to high rates of premature dropout. In previous years, less than 40% of all the registered students attended the examinations of Metabolic Biochemistry (a subject in the second year of the Degree of Biology at our University). Even worse, less than 25% of our students passed the exams. From the academic year 2015/16 on, we are developing innovative teaching projects (PIE15-163 and PIE17-145, funded by University of Malaga) aimed to increase our student loyalty to the subject (and hence to increase their attendance to exams) and to help them to learn more effectively metabolism and its regulation. These innovative teaching projects are based on the use of several powerful tools: a learning contract and problem-based learning within the framework of group tasks promoting an actual collaborative learning in a flipped classroom. The present communication will show the implementation of the PIE15-163 and PIE17-145 projects and some results obtained from them.This work was supported by Malaga University funds granted to the educational innovation project PIE17-145. The attendance to the END2018 International Conference on Education and New Developments (June 2018, Budapest, Hungary) has received a grant from "I Plan Propio Integral de Docencia. Universidad de Málaga"]

Promiscuous mismatch extension by human DNA polymerase lambda

DNA polymerase lambda (Pol λ) is one of several DNA polymerases suggested to participate in base excision repair (BER), in repair of broken DNA ends and in translesion synthesis. It has been proposed that the nature of the DNA intermediates partly determines which polymerase is used for a particular repair reaction. To test this hypothesis, here we examine the ability of human Pol λ to extend mismatched primer-termini, either on ‘open’ template-primer substrates, or on its preferred substrate, a 1 nt gapped-DNA molecule having a 5′-phosphate. Interestingly, Pol λ extended mismatches with an average efficiency of ≈10−2 relative to matched base pairs. The match and mismatch extension catalytic efficiencies obtained on gapped molecules were ≈260-fold higher than on template-primer molecules. A crystal structure of Pol λ in complex with a single-nucleotide gap containing a dG·dGMP mismatch at the primer-terminus (2.40 Å) suggests that, at least for certain mispairs, Pol λ is unable to differentiate between matched and mismatched termini during the DNA binding step, thus accounting for the relatively high efficiency of mismatch extension. This property of Pol λ suggests a potential role as a ‘mismatch extender’ during non-homologous end joining (NHEJ), and possibly during translesion synthesis

Medida de glucosa en refrescos: una útil herramienta para ilustrar el aprendizaje de los fundamentos del análisis enzimático

Es indudable la relevancia que el análisis enzimático tiene en el ámbito de la Bioquímica, la Química Clínica y la Química de la Alimentación, entre otras. En la asignatura “Bioquímica Aplicada” de cuarto curso del grado en Química de nuestra Universidad, los alumnos aprenden los fundamentos teóricos del análisis enzimático, que luego ponen en práctica en el laboratorio, en un contexto cotidiano, mediante la determinación de glucosa en diferentes refrescos carbonatados. Aunque existen diversos métodos enzimáticos para la valoración de la concentración de glucosa, hemos elegido para la sesión práctica el que se basa en las reacciones acopladas de la glucosa oxidasa (EC 1.1.3.4.) y la peroxidasa (EC 1.11.1.7.) por ser especialmente ilustrativo a la hora de afianzar los conceptos teóricos desarrollados en clase, así como para despertar su espíritu crítico al enfrentarles a la resolución de problemas “del mundo real” y hacerles elegir qué método analítico puede ser mejor para un caso concreto. Los alumnos usan dos protocolos distintos (métodos cinético y a punto final) para determinar la concentración de glucosa, inicialmente en una muestra de glucosa en agua, familiarizándose con ambos métodos y permitiéndoles construir las rectas de calibrado, mediante las que deberán establecer el rango de aplicación para cada método. La medida de las variaciones de absorbancia con el tiempo, que en el método cinético son proporcionales a la concentración de glucosa, permite ilustrar aspectos metodológicos de la estimación de la velocidad inicial de una reacción enzimática. Posteriormente los alumnos se enfrentan al problema de la medida de la concentración de glucosa en una serie de bebidas que incluyen refrescos de cola y tónicas, con o sin azúcar (refrescos “cero”), encontrándose con nuevas dificultades como son la necesidad de diluir en varios órdenes de magnitud las muestras (lo que les familiariza con el uso de las diluciones seriadas), y la aparición de interferencias debidas al color de la muestra, decantándose por uno u otro método en función de la naturaleza del problema analítico planteado.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Mitochondrial DNA (mtDNA) haplogroups and serum levels of anti-oxidant enzymes in patients with osteoarthritis

BACKGROUND: Oxidative stress play a main role in the initiation and progression of the OA disease and leads to the degeneration of mitochondria. To prevent this, the chondrocytes possess a well-coordinated enzymatic antioxidant system. Besides, the mitochondrial DNA (mtDNA) haplogroups are associated with the OA disease. Thus, the main goal of this work is to assess the incidence of the mtDNA haplogroups on serum levels of two of the main antioxidant enzymes, Manganese Superoxide Dismutase (Mn-SOD or SOD2) and catalase, and to test the suitability of these two proteins for potential OA-related biomarkers. METHODS: We analyzed the serum levels of SOD2 and catalase in 73 OA patients and 77 healthy controls carrying the haplogroups J, U and H, by ELISA assay. Knee and hip radiographs were classified according to Kellgren and Lawrence (K/L) scoring from Grade 0 to Grade IV. Appropriate statistical analyses were performed to test the effects of clinical variables, including gender, body mass index (BMI), age, smoking status, diagnosis, haplogroups and radiologic K/L grade on serum levels of these enzymes. RESULTS: Serum levels of SOD2 appeared statistically increased in OA patients when compared with healthy controls (p < 0.001). Even in those OA patients with higher OA severity (K/L grade IV), the serum levels of this antioxidant enzyme appeared more significantly increased than in OA patients with lower K/L grade (p < 0.001). The mtDNA haplogroups showed an influence on serum levels of catalase (p = 0.054), being carriers of the mtDNA haplogroup J those who showed higher serum levels than non-J carriers (p = 0.057). CONCLUSIONS: The increased levels of SOD2 in OA patients indicate an increased oxidative stress OA-related, therefore this antioxidant enzyme could be a suitable candidate biomarker for diagnosis of OA. Mitochondrial haplogroups significantly correlates with serum levels of catalase

Laboratory Assessment of Water Permeability Loss of Geotextiles Due to Their Installation in Pervious Pavements

During the last decades, the importance of sustainable development in society has increased considerably. Sustainable Urban Drainage Systems (SUDS) are a group of techniques that aim to improve the management of rain and run-off water while reducing their pollution. Many of these systems incorporate geotextiles in their structures, which act as a layer separation and water filter. Some authors defend the idea that by simply being installed, geotextiles partially or totally lose their separation and filtering capacities. This study proposes a testing methodology that can reproduce this effect and obtain a reduction factor for the water permeability of the material after its installation, which is defined here as the ?new condition factor?. The procedure simulated the real installation conditions in the laboratory by causing the specimen to undergo both mechanical and hydraulic damage and subsequently measuring the loss of water permeability that it provoked on the geotextile. Two different nonwoven geotextiles were tested in order to validate the procedure and to obtain initial results that could confirm the need for the new condition factor in the design of pervious pavements with geotextiles. Analysis of variance (ANOVA) was used to determine the statistical significance of the test variableshis research was funded by the Spanish Ministry of Economy and Competitiveness, grant number BIA2012-32463, and by the Dirección de Investigación of the Universidad Católica de la Santísima Concepción, fund FAA 02/2018. The authors would like to thank the support and collaboration from the Construction Technology Research Group (Grupo de Investigación de Tecnología de la Construcción - GITECO), the Geosynthetics Laboratory of the University of Cantabria (LAGUC), Grupo de Caminos de Santander (GCS) and the Geotechnical Group of the University of Cantabria

Relationship between solar radiation on watercore on apple fruit assessed with MRI

This work is a preliminary studio of the possibility of assess a relationship between solar radiation and watercore development on apple fruit, during maturation, using a non destructive method such as Magnetic Resonance Imaging (MRI). For such purpose, several low cost solar radiation sensors were designed for the trial and placed at 2 different heights (1.5 and 2.5 m) on 6 adult ?Esperiega? apple trees, in a commercial orchard in Ademuz (Valencia). Sensors were connected along 27 days, during the end of the growth period and start of the fruit maturation process, and radiation measurements of the a-Si sensors were recorded every 1 minute. At the end of this period, fruits from the upper and the lower part of the canopy of each tree were harvested. In all, 152 apples were collected and images with MRI. A Principal Component Analysis, perfomed over the histograms of the images, as well as segmentation methods were performed on the MR images in order to find a pattern involving solar radiation and watercore incidence

Assessment of watercore development in apples with MRI: Effect offruit location in the canopy

tWatercore distribution inside apple fruit (block or radial), and its incidence (% of tissue) were relatedto the effect of solar radiation inside the canopy as measured by a set of low-cost irradiation sensors.221 samples were harvested in two seasons from the top and the bottom of the canopy and submittedto the non-invasive and non-destructive technique of magnetic resonance imaging (MRI) in order toobtain 20 inner tomography slices from each fruit and analyze the damaged areas using an interactive3D segmentation method. The number of fruit corresponding to each type of damage and the relevantpercentage were calculated and it was found that apples from the top of the tree were mainly of the radialtype (84%) and had more watercore (approx. 5% more) than apples from the bottom (65% radial). From theimage segmentation, the Euler number, a morphometric parameter, was extracted from the segmentedimages and related to the type of watercore symptoms. Apples with block watercore were grouped inEuler numbers between −400 and 400 with a small evolution. For apples with radial development, theEuler number was highly negative: up to −1439. Significant differences were also found regarding sugarcomposition, with higher fructose and total sugar contents in apples from the upper canopy, compared tothose in the lower canopy location. In the seasons studied (2011 and 2012), significantly higher sorbitoland lower sucrose and fructose contents were found in watercore-affected tissue compared to the healthytissue of affected apples and also compared to healthy apples