From local bacterial communities to energy: application of microbial fuel cells in laboratory experimentation.

It is well known that bacterial communities are an essential component to maintain the balance of terrestrial ecosystems due to the functions and services performed by microorganisms in the environment. The research seeking on alternative energy sources has shown that bacterial communities can bioconvert the chemical energy of an organic substrate into electrical energy, within devices known as microbial fuel cells. For this reason, this class project allows students of Biotechnology, Environmental Science, and Microbiology to apply the appropriate methodology to develop a class project throughout an environmental bacterial community capable of generating electrical energy.

GUSignal: An Informatics Tool to Analyze Glucuronidase Gene Expression in Arabidopsis Thaliana Roots.

The uidA gene codifies for a glucuronidase (GUS) enzyme which has been used as a biotechnological tool during the last years. When uidA gene is fused to a gene's promotor region, it is possible to evaluate the activity of this one in response to a stimulus. Arabidopsis thaliana has served as the biological platform to elucidate molecular and regulatory signaling responses in plants. Transgenic lines of A. thaliana, tagged with the uidA gene, have allowed explaining how plants modify their hormonal pathways depending on the environmental conditions. Although the information extracted from microscopic images of these transgenic plants is often qualitative and in many publications is not subjected to quantification, in this paper we report the development of an informatics tool focused on computer vision for processing and analysis of digital images in order to analyze the expression of the GUS signal in A. thaliana roots, which is strongly correlated with the intensity of the grayscale images. This means that the presence of the GUS-induced color indicates where the gene has been actively expressed, such as our statistical analysis has demonstrated after treatment of A. thaliana DR5::GUS with naphtalen-acetic acid (0.0001 mM and 1 mM). GUSignal is a free informatics tool that aims to be fast and systematic during the image analysis since it executes specific and ordered instructions, to offer a segmented analysis by areas or regions of interest, providing quantitative results of the image intensity levels.

Marine Arthropods as a Source of Antimicrobial Peptides.

Peptide therapeutics play a key role in the development of new medical treatments. The traditional focus on endogenous peptides has shifted from first discovering other natural sources of these molecules, to later synthesizing those with unique bioactivities. This review provides concise information concerning antimicrobial peptides derived from marine crustaceans for the development of new therapeutics. Marine arthropods do not have an adaptive immune system, and therefore, they depend on the innate immune system to eliminate pathogens. In this context, antimicrobial peptides (AMPs) with unique characteristics are a pivotal part of the defense systems of these organisms. This review covers topics such as the diversity and distribution of peptides in marine arthropods (crustacea and chelicerata), with a focus on penaeid shrimps. The following aspects are covered: the defense system; classes of AMPs; molecular characteristics of AMPs; AMP synthesis; the role of penaeidins, anti-lipopolysaccharide factors, crustins, and stylicins against microorganisms; and the use of AMPs as therapeutic drugs. This review seeks to provide a useful compilation of the most recent information regarding AMPs from marine crustaceans, and describes the future potential applications of these molecules.

NIFtHool: an informatics program for identification of NifH proteins using deep neural networks.

Atmospheric nitrogen fixation carried out by microorganisms has environmental and industrial importance, related to the increase of soil fertility and productivity. The present work proposes the development of a new high precision system that allows the recognition of amino acid sequences of the nitrogenase enzyme (NifH) as a promising way to improve the identification of diazotrophic bacteria. For this purpose, a database obtained from UniProt built a processed dataset formed by a set of 4911 and 4782 amino acid sequences of the NifH and non-NifH proteins respectively. Subsequently, the feature extraction was developed using two methodologies: (i) k-mers counting and (ii) embedding layers to obtain numerical vectors of the amino acid chains. Afterward, for the embedding layer, the data was crossed by an external trainable convolutional layer, which received a uniform matrix and applied convolution using filters to obtain the feature maps of the model. Finally, a deep neural network was used as the primary model to classify the amino acid sequences as NifH protein or not. Performance evaluation experiments were carried out, and the results revealed an accuracy of 96.4%, a sensitivity of 95.2%, and a specificity of 96.7%. Therefore, an amino acid sequence-based feature extraction method that uses a neural network to detect N-fixing organisms is proposed and implemented. NIFtHool is available from: https://nifthool.anvil.app/.

Microbiologically Induced Carbonate Precipitation in the Restoration and Conservation of Cultural Heritage Materials.

Microbiologically induced carbonate precipitation (MICP) is a well-known biogeochemical process that allows the formation of calcium carbonate deposits in the extracellular environment. The high concentration of carbonate and calcium ions on the bacterial surface, which serves as nucleation sites, promotes the calcium carbonate precipitation filling and binding deteriorated materials. Historic buildings and artwork, especially those present in open sites, are susceptible to enhanced weathering resulting from environmental agents, interaction with physical-chemical pollutants, and living organisms, among others. In this work, some published variations of a novel and ecological surface treatment of heritage structures based on MICP are presented and compared. This method has shown to be successful as a restoration, consolidation, and conservation tool for improvement of mechanical properties and prevention of unwanted gas and fluid migration from historical materials. The treatment has revealed best results on porous media matrixes; nevertheless, it can also be applied on soil, marble, concrete, clay, rocks, and limestone. MICP is proposed as a potentially safe and powerful procedure for efficient conservation of worldwide heritage structures.

[ß-lactam antibiotics resistance in Latin American countries]. / Resistencia de los antibióticos ß-lactámicos en países latinoamericanos.

Ever since antimicrobial activity was observed at the end of the XIX century and antibiotics were produced on a large scale in the 40s, microorganisms have developed multiple resistance mechanisms, making treatment of infectious diseases difficult. For instance, several Gram-positive and Gram-negative bacteria lowered their sensitivity to ß-Lactam antibiotics as a result of their inadequate use and abuse. For this reason, microbial resistance to these drugs represents an increasing health problem in Latin America due to the emergence of drug-resistant bacterial strains. This review aims to summarize and analyze scientific literature reporting resistance to ß-lactam antibiotics in Latin America. We compiled scientific papers published during the last five years from PubMed, SciELO, and LILACS-BIREME. We found that: (i) it is common to identify resistance genes for ß-lactams in the soil and animal farms, and (ii) over 40% of strains isolated from clinical samples developed resistance against ß-lactam antibiotics.

A partir de la observación de la actividad antimicrobiana a finales del siglo XIX y la producción a gran escala de los antibióticos en la década de 1940, los microorganismos han desarrollado múltiples mecanismos de resistencia a estos compuestos, debido a su uso indiscriminado y al paso de los años. Todo ello, dificulta el tratamiento de las enfermedades infecciosas. Este es el caso de varias especies de bacterias grampositivas y gramnegativas las cuales han disminuido su sensibilidad a los antibióticos ß-lactámicos como resultado del empleo inadecuado y abuso de su administración. Es por ello que la resistencia bacteriana a estos medicamentos representa un problema de salud pública que va en aumento en Latinoamérica, como consecuencia del surgimiento de cepas resistentes a varios de estos compuestos. Frente a estos antecedentes, y a que son escasos los análisis sistemáticos que se han efectuado sobre dicho tema, esta revisión bibliográfica tiene como objetivo resumir y analizar las publicaciones científicas sobre la resistencia a los antibióticos ß-lactámicos en algunos países de América Latina. Para esto se estudiaron publicaciones realizadas en los últimos cinco años e indexadas en las bases de datos PubMed, SciELO y LILACS-BIREME. Los resultados del análisis señalan que resulta común la identificación de genes de resistencia para los antibióticos ß-lactámicos en el medio ambiente, especialmente en el suelo y en las granjas de crianza de animales; y más del 40% de las cepas aisladas a partir de muestras clínicas presentan algún mecanismo de resistencia a esta familia de antibióticos.