Mapping research on biochemistry education: A bibliometric analysis.

The purpose of this study was to map the research literature on Biochemistry education, covering the scientific production indexed on the Web of Science over the past 66 years. The open-source Bibliometrix R-package, an R-tool, was used to carry out the bibliometric analysis. Our results describe (1) how many articles were published per year and what is the annual average growth rate; (2) which are the core journals, authors, and publications in the field; (3) which countries and funding agencies contribute most to the development of research in the area; (4) the leading collaborative research and co-citation networks; (5) which articles were the most cited in the past 10 years; and (6) which are the trending topics in the field. Our main contribution is offering insights into the evolution of the field. Also, the use of a quantitative methodological design, which covers a large volume of publications, and could identify possible gaps in the area.

Copper and Neurotoxicity in Autism Spectrum Disorder.

Free radicals (FR) act on living organisms and present unpaired electrons in the molecular orbitals of oxygen or nitrogen species. They are classified as redox reactions and account for a wide range of processes in biological systems. Genetic and environmental factors may alter the levels of FR in the cell, leading to deleterious consequences such as membrane lipid peroxidation, protein nitration, enzyme, carbohydrate and DNA damage, ultimately resulting in premature aging and a pro-inflammatory microenvironment as observed in Alzheimer's disease (AD) and autism spectrum disorder (ASD). O2 radical ability to act as a Lewis base and to form a complex with metal transition such as iron and copper (Lewis acids) leads to biomolecules oxidation at physiological pH, thus increasing the possibility of injury and oxidative damage in biological tissues. In this review, we discuss the role of metals, like copper, and the amyloid precursor protein (APP) derivative (s-APP-alpha) as an antioxidant and a possible adjuvant in the treatment of some autistic spectrum disorder symptoms (ASD).

Using augmented reality to teach and learn biochemistry.

Understanding metabolism and metabolic pathways constitutes one of the central aims for students of biological sciences. Learning metabolic pathways should be focused on the understanding of general concepts and core principles. New technologies such Augmented Reality (AR) have shown potential to improve assimilation of biochemistry abstract concepts because students can manipulate 3D molecules in real time. Here we describe an application named Augmented Reality Metabolic Pathways (ARMET), which allowed students to visualize the 3D molecular structure of substrates and products, thus perceiving changes in each molecule. The structural modification of molecules shows students the flow and exchange of compounds and energy through metabolism. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):417-420, 2017.

SUR1 Receptor Interaction with Hesperidin and Linarin Predicts Possible Mechanisms of Action of Valeriana officinalis in Parkinson.

Parkinson's disease (PD) is one of the most common neurodegenerative disorders. A theoretical approach of our previous experiments reporting the cytoprotective effects of the Valeriana officinalis compounds extract for PD is suggested. In addiction to considering the PD as a result of mitochondrial metabolic imbalance and oxidative stress, such as in our previous in vitro model of rotenone, in the present manuscript we added a genomic approach to evaluate the possible underlying mechanisms of the effect of the plant extract. Microarray of substantia nigra (SN) genome obtained from Allen Brain Institute was analyzed using gene set enrichment analysis to build a network of hub genes implicated in PD. Proteins transcribed from hub genes and their ligands selected by search ensemble approach algorithm were subjected to molecular docking studies, as well as 20 ns Molecular Dynamics (MD) using a Molecular Mechanic Poison/Boltzman Surface Area (MMPBSA) protocol. Our results bring a new approach to Valeriana officinalis extract, and suggest that hesperidin, and probably linarin are able to relieve effects of oxidative stress during ATP depletion due to its ability to binding SUR1. In addition, the key role of valerenic acid and apigenin is possibly related to prevent cortical hyperexcitation by inducing neuronal cells from SN to release GABA on brain stem. Thus, under hyperexcitability, oxidative stress, asphyxia and/or ATP depletion, Valeriana officinalis may trigger different mechanisms to provide neuronal cell protection.

The evolution of the Krebs cycle: A promising subject for meaningful learning of biochemistry.

Evolution has been recognized as a key concept for biologists. To enhance comprehension and motivate biology undergraduates for the contents of central energetic metabolism, we addressed the Krebs cycle structure and functions in an evolutionary view. To this end, we created a study guide that contextualizes the emergence of the cyclic pathway, in light of the prokaryotic influence since the early anaerobic condition of the Earth to increase oxygen in the atmosphere. The study guide is composed of three interrelated sections: (1) a problem, designed to arouse curiosity, inform and motivate students, (2) a text about life evolution, including early microorganisms and the emergence of the Krebs cycle, and (3) questions for debate. The activity consisted on individual reading and peer discussion based on this written material, under the guidance of the instructors. The questions were designed to foster debate in an ever-increasing level of complexity and to strengthen the main contextual aspects leading to emergence, evolving, and permanency of a complex metabolic pathway. Based on classroom observation, analysis of student's written responses, and individual interviews, we noticed they were engaged and motivated by the task, especially during group discussion. The whole experience suggests that the study guide was a stimulus to broaden the comprehension of the Krebs cycle, reinforcing the evolutionary approach as an important subject for learning purposes. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:288-296, 2016.

Metabolic pathways visualization skills development by undergraduate students.

We have developed a metabolic pathways visualization skill test (MPVST) to gain greater insight into our students' abilities to comprehend the visual information presented in metabolic pathways diagrams. The test is able to discriminate students' visualization ability with respect to six specific visualization skills that we identified as key to the understanding of metabolic map diagrams. Application of the MPVST to B. S. Biochemistry students showed that their visualization skills develop informally and progressively during their college years. Furthermore, the complex nature of biochemical pathways, together with students' lack of familiarity with metabolic maps, suggests that it is important for instructors to spend more time than usual explaining visual representations to their students.

Effects of the protonation state in the interaction of an HIV-1 reverse transcriptase (RT) amino acid, Lys101, and a non nucleoside RT inhibitor, GW420867X.

Interactions between an inhibitor and amino acids from a binding pocket could help not only to understand the nature of these interactions, but also to support the design of new inhibitors. In this paper, we explore the key interaction between a second generation non-nucleoside reverse transcriptase inhibitor (NNRTI), GW420867X, and HIV-1 RT amino acid Lys101 (K101), by quantum mechanical methods. The neutral, protonated, and zwitterionic complexes of GW420867X-K101 were studied. The interaction energies were determined by SCS-MP2/def2-cc-pVQZ, and the electron density was analyzed by natural bond orbital (NBO), atoms in molecules (AIM) and reduced gradient analysis. A large increase in the interaction was observed with the tautomerization of neutral or neutral protonated species. The monomers interact by two medium-strength hydrogen bonds, one partially covalent and another noncovalent. There are some van der Waals intramolecular interactions that are topologically unstable. The nature of the intermolecular interactions was also analyzed using quantitative molecular orbital (MO) theory in combination with an energy decomposition analysis (EDA) based on dispersion-corrected density functional theory (DFT) at BLYP-D/TZ2P.

Chave de identificação de espécies do estrato arbóreo da Mata Atlântica em Ubatuba (SP), com base em caracteres vegetativos / Key for the identification of the arboreal stratum species of the Atlantic Rain Forest in Ubatuba (SP) based on vegetative characters

The identification key was developed taking into account the herbarium specimens from the species of the arboreal stratum sampled, with at least 4.8 cm DBH, in two stretches of Lower Montane Rain Forest. Only morphological vegetative characters were used, such as phyllotaxy, leaf shape, presence or absence of stipules, trichomes and glands, and other aspects relevant to the species identification, besides field observations. The key comprises 193 (4 without identification) species belonging to 114 genera and 50 botanical families, and an interactive electronic version is available online at the site http://www.gama.ib.unicamp.br/gama/index.php.

A chave de identificação foi elaborada com base no material herborizado das espécies do estrato arbóreo amostradas com pelo menos 4,8 cm de DAP, em dois trechos de Floresta Ombrófila Densa Submontana. Foram utilizadas apenas características morfológicas vegetativas, como a filotaxia, forma das folhas, presença ou ausência de estípulas, indumento e glândulas, dentre outros aspectos relevantes para a identificação das espécies, e observações de campo. A chave consta de 193 espécies (4 indeterminadas), distribuídas em 114 gêneros e 50 famílias botânicas, e uma versão eletrônica interativa está disponível para consulta on line (http://www.gama.ib.unicamp.br/gama/index.php ).

Phosphoproteome reveals an atlas of protein signaling networks during osteoblast adhesion.

Cell adhesion on surfaces is a fundamental process in the emerging biomaterials field and developmental events as well. However, the mechanisms regulating this biological process in osteoblasts are not fully understood. Reversible phosphorylation catalyzed by kinases is probably the most important regulatory mechanism in eukaryotes. Therefore, the goal of this study is to assess osteoblast adhesion through a molecular prism under a peptide array technology, revealing essential signaling proteins governing adhesion-related events. First, we showed that there are main morphological changes on osteoblast shape during adhesion up to 3 h. Second, besides classical proteins activated upon integrin activation, our results showed a novel network involving signaling proteins such as Rap1A, PKA, PKC, and GSK3beta during osteoblast adhesion on polystyrene. Third, these proteins were grouped in different signaling cascades including focal adhesion establishment, cytoskeleton rearrangement, and cell-cycle arrest. We have thus provided evidence that a global phosphorylation screening is able to yield a systems-oriented look at osteoblast adhesion, providing new insights for understanding of bone formation and improvement of cell-substratum interactions. Altogether, these statements are necessary means for further intervention and development of new approaches for the progress of tissue engineering.

Insulin and leptin relations in obesity: a multimedia approach.

Obesity has been recognized as a worldwide public health problem. It significantly increases the chances of developing several diseases, including Type II diabetes. The roles of insulin and leptin in obesity involve reactions that can be better understood when they are presented step by step. The aim of this work was to design software with data from some of the most recent publications on obesity, especially those concerning the roles of insulin and leptin in this metabolic disturbance. The most notable characteristic of this software is the use of animations representing the cellular response together with the presentation of recently discovered mechanisms on the participation of insulin and leptin in processes leading to obesity. The software was field tested in the Biochemistry of Nutrition web-based course. After using the software and discussing its contents in chatrooms, students were asked to answer an evaluation survey about the whole activity and the usefulness of the software within the learning process. The teaching assistants (TA) evaluated the software as a tool to help in the teaching process. The students' and TAs' satisfaction was very evident and encouraged us to move forward with the software development and to improve the use of this kind of educational tool in biochemistry classes.

Adapting a biochemistry course to distance education.

Internet-based distance education seems to be an attractive alternative to offer courses dealing with specific topics that are not conveniently explored in undergraduate courses. This is a good way to provide access to the recent and updated discoveries in this research area and to reach people who could not take the classes in the traditional mode. Using the communication advantages available via the Internet, we adapted the course "Biochemistry of Nutrition," first offered as a summer course to be entirely carried out at distance. The adaptation explored the use of online tools such as E-mail communication among students and teachers, computer conferencing in small groups to discuss specific subjects, and texts and software downloads to be used as main references. Graduate students had their first real experience as teachers, which proved to be very productive for both the development of the Internet version of the course and their integration with undergraduate students.

Proteome analysis of the plant pathogen Xylella fastidiosa reveals major cellular and extracellular proteins and a peculiar codon bias distribution.

The bacteria Xylella fastidiosa is the causative agent of a number of economically important crop diseases, including citrus variegated chlorosis. Although its complete genome is already sequenced, X. fastidiosa is very poorly characterized by biochemical approaches at the protein level. In an initial effort to characterize protein expression in X. fastidiosa we used one- and two-dimensional gel electrophoresis and mass spectrometry to identify the products of 142 genes present in a whole cell extract and in an extracellular fraction of the citrus isolated strain 9a5c. Of particular interest for the study of pathogenesis are adhesion and secreted proteins. Homologs to proteins from three different adhesion systems (type IV fimbriae, mrk pili and hsf surface fibrils) were found to be coexpressed, the last two being detected only as multimeric complexes in the high molecular weight region of one-dimensional electrophoresis gels. Using a procedure to extract secreted proteins as well as proteins weakly attached to the cell surface we identified 30 different proteins including toxins, adhesion related proteins, antioxidant enzymes, different types of proteases and 16 hypothetical proteins. These data suggest that the intercellular space of X. fastidiosa colonies is a multifunctional microenvironment containing proteins related to in vivo bacterial survival and pathogenesis. A codon usage analysis of the most expressed proteins from the whole cell extract revealed a low biased distribution, which we propose is related to the slow growing nature of X. fastidiosa. A database of the X. fastidiosa proteome was developed and can be accessed via the internet (URL: www.proteome.ibi.unicamp.br).