Environmental transcriptome analysis reveals physiological differences between biofilm and planktonic modes of life of the iron oxidizing bacteria Leptospirillum spp. in their natural microbial community

<p>Abstract</p> <p>Background</p> <p>Extreme acidic environments are characterized by their high metal content and lack of nutrients (oligotrophy). Macroscopic biofilms and filaments usually grow on the water-air interface or under the stream attached to solid substrates (streamers). In the Río Tinto (Spain), brown filaments develop under the water stream where the Gram-negative iron-oxidizing bacteria <it>Leptospirillum </it>spp. (<it>L. ferrooxidans </it>and <it>L. ferriphilum</it>) and <it>Acidithiobacillus ferrooxidans </it>are abundant. These microorganisms play a critical role in bioleaching processes for industrial (biominery) and environmental applications (acid mine drainage, bioremediation). The aim of this study was to investigate the physiological differences between the free living (planktonic) and the sessile (biofilm associated) lifestyles of <it>Leptospirillum </it>spp. as part of its natural extremely acidophilic community.</p> <p>Results</p> <p>Total RNA extracted from environmental samples was used to determine the composition of the metabolically active members of the microbial community and then to compare the biofilm and planktonic environmental transcriptomes by hybridizing to a genomic microarray of <it>L. ferrooxidans</it>. Genes up-regulated in the filamentous biofilm are involved in cellular functions related to biofilm formation and maintenance, such as: motility and quorum sensing (<it>mqsR, cheAY, fliA, motAB</it>), synthesis of cell wall structures (<it>lnt, murA, murB</it>), specific proteases (<it>clpX/clpP</it>), stress response chaperons (<it>clpB, clpC, grpE-dnaKJ, groESL</it>), etc. Additionally, genes involved in mixed acid fermentation (<it>poxB</it>, <it>ackA</it>) were up-regulated in the biofilm. This result, together with the presence of small organic acids like acetate and formate (1.36 mM and 0.06 mM respectively) in the acidic (pH 1.8) water stream, suggests that either <it>L. ferrooxidans </it>or other member of the microbial community are producing acetate in the acidophilic biofilm under microaerophilic conditions.</p> <p>Conclusions</p> <p>Our results indicate that the acidophilic filaments are dynamic structures in which different mechanisms for biofilm formation/dispersion are operating. Specific transcriptomic fingerprints can be inferred for both planktonic and sessile cells, having the former a more active TCA cycle, while the mixed acid fermentation process dominate in the latter. The excretion of acetate may play a relevant ecological role as a source of electron donor for heterotrophic Fe³⁺reducers like some Alphaproteobacteria, <it>Acidobacterium </it>spp. and <it>Sulfobacillus </it>spp., also present in the biofilm. Additionally, acetate may have a negative effect on bioleaching by inhibiting the growth of chemolithotrophic bacteria.</p

Perspective Chapter: Real-Time Genomic Surveillance for SARS-CoV-2 on Center Stage

The course of the COVID-19 pandemic depends not only on how the SARS-CoV-2 virus mutates but on the actions taken to respond to it. Important public health decisions can only be taken if we know viral dynamics, viral variants distribution, and whether new variants are emerging that may be more transmissible or/and more virulent, displaying evasion to vaccines or antiviral treatments. This situation has put the use of different approaches, such as molecular techniques and real-time genomic sequencing, to support public health decision-making on center stage. To achieve this, robust programs based on: (i) diagnostic capacity; (ii) high-throughput sequencing technologies; and (iii) high-performance bioinformatic resources, need to be established. This chapter focuses on how SARS-CoV-2 evolved since its discovery and it summarizes the scientific efforts to obtain genomic data as the virus spread throughout the globe

El teatro escolar como estrategia didáctica en el desarrollo de la comprensión lectora en el 3er grado, turno matutino en la Escuela Pública Santa Clara del Municipio de Ciudad Darío, departamento de Matagalpa durante el II semestre del año lectivo 2021

Dentro de la presente investigación se plantea el teatro escolar como estrategia didáctica que favorece a la comprensión de los estudiantes del 3er grado de la Escuela Pública Santa Clara durante el año lectivo 2021. Teniendo en cuenta como objetivo principal el desarrollo de la comprensión lectora en los estudiantes del tercer grado se desarrolla el plan de acción con el fin de dar respuesta a la hipótesis planteada dentro de la investigación y de esta forma dar alternativas de solución a la problemática del comprender textos en estudiantes del tercer grado. Para la recopilación de la información presentada en el presente documento se hizo uso de técnicas e instrumentos tales como el conversatorio, guía de observación, clases demostrativas, monitoreo y seguimiento a la estrategia. Fue posible recolectar la información y gracias a eso tener un mejor panorama acerca de las dificultades y problemáticas que se encuentran dentro del salón de clases. Como parte del marco referencial que acompaña la investigación se presentan las contextualizaciones del teatro como estrategia didáctica y sus elementos para ponerla en práctica en el aula de clases. De tal forma que se diseña la estrategia didáctica, con el fin de brindar una estrategia nueva a la docente y que los estudiantes alcancen el objetivo de la clase, el cual es mejorar la comprensión lectora, ya que fue posible encontrar dificultades al comprender lo que leían, por otro lado, fue posible apreciar clases desarrolladas de forma tradicional. Se pretende que la implementación del teatro como estrategia didáctica, de respuestas factibles a las problemáticas encontradas en el aula de clas

Transposase interaction with the β sliding clamp: Effects on insertion sequence proliferation and transposition rate

Insertion sequences (ISs) are ubiquitous and abundant mobile genetic elements in prokaryotic genomes. ISs often encode only one protein, the transposase, which catalyzes their transposition. Recent studies have shown that transposases of many different IS families interact with the β sliding clamp, a DNA replication factor of the host. However, it was unclear to what extent this interaction limits or favors the ability of ISs to colonize a chromosome from a phylogenetically-distant organism, or if the strength of this interaction affects the transposition rate. Here we describe the proliferation of a member of the IS1634 family in Acidiphilium over ~600 generations of cultured growth. We demonstrate that the purified transposase binds to the β sliding clamp of Acidiphilium, Leptospirillum and E. coli. Further, we also demonstrate that the Acidiphilium IS1634 transposase binds to the archaeal sliding clamp (PCNA) from Methanosarcina, and that the transposase encoded by Methanosarcina IS1634 binds to Acidiphilium β. Finally, we demonstrate that increasing the strength of the interaction between β and transposase results in a higher transposition rate in vivo. Our results suggest that the interaction could determine the potential of ISs to be mobilized in bacterial populations and also their ability to proliferate within chromosomesThis work was funded by the Subdirección General de Proyectos de Investigación of the Spanish Ministry for Economy and Competitiveness Grants No. CGL2010-17384 and AYA2011-24803, and by the European Research Council (ERC) Advanced Grant No. 250350 (IPBSL). HDM has a FPI fellowship from the Spanish Governmen

Immunoanalytical Approach for Detecting and Identifying Ancestral Peptide Biomarkers in Early Earth Analogue Environments

Several mass spectrometry and spectroscopic techniques have been used in the search for molecular biomarkers on Mars. A major constraint is their capability to detect and identify large and complex compounds such as peptides or other biopolymers. Multiplex immunoassays can detect these com-pounds, but antibodies must be produced for a large number of sequence-dependent molecular targets. Ancestral Sequence Re-construction (ASR) followed by protein "resurrection" in the lab can help to narrow the selection of targets. Herein, we propose an immunoanalytical method to identify ancient and universally conserved protein/peptide sequences as targets for identifying ancestral biomarkers in nature. We have developed, tested, and validated this approach by producing antibodies to eight previously described ancestral resurrected proteins (three beta-lactamases, three thioredoxins, one Elongation Factor Tu, and one RuBisCO, all of them theoretically dated as Precambrian), and used them as a proxy to search for any potential feature of them that could be present in current natural environments. By fluorescent sandwich microarray immunoassays (FSMI), we have detected positive immunoreactions with antibodies to the oldest beta-lactamase and thioredoxin proteins (ca. 4 Ga) in samples from a hydrothermal environment. Fine epitope mapping and inhibitory immunoassays allowed the identification of well-conserved epitope peptide sequences that resulted from ASR and were present in the sample. We corroborated these results by metagenomic sequencing and found several genes encoding analogue proteins with significant matches to the peptide epitopes identified with the antibodies. The results demonstrated that peptides inferred from ASR studies have true counterpart analogues in Nature, which validates and strengthens the well-known ASR/protein resurrection technique and our immunoanalytical approach for investigating ancient environments and metabolisms on Earth and elsewhere

Temperature increase prevails over acidification in gene expression modulation of amastigote differentiation in Leishmania infantum

<p>Abstract</p> <p>Background</p> <p>The extracellular promastigote and the intracellular amastigote stages alternate in the digenetic life cycle of the trypanosomatid parasite <it>Leishmania</it>. Amastigotes develop inside parasitophorous vacuoles of mammalian phagocytes, where they tolerate extreme environmental conditions. Temperature increase and pH decrease are crucial factors in the multifactorial differentiation process of promastigotes to amastigotes. Although expression profiling approaches for axenic, cell culture- and lesion-derived amastigotes have already been reported, the specific influence of temperature increase and acidification of the environment on developmental regulation of genes has not been previously studied. For the first time, we have used custom <it>L. infantum </it>genomic DNA microarrays to compare the isolated and the combined effects of both factors on the transcriptome.</p> <p>Results</p> <p>Immunofluorescence analysis of promastigote-specific glycoprotein gp46 and expression modulation analysis of the amastigote-specific A2 gene have revealed that concomitant exposure to temperature increase and acidification leads to amastigote-like forms. The temperature-induced gene expression profile in the absence of pH variation resembles the profile obtained under combined exposure to both factors unlike that obtained for exposure to acidification alone. In fact, the subsequent fold change-based global iterative hierarchical clustering analysis supports these findings.</p> <p>Conclusions</p> <p>The specific influence of temperature and pH on the differential regulation of genes described in this study and the evidence provided by clustering analysis is consistent with the predominant role of temperature increase over extracellular pH decrease in the amastigote differentiation process, which provides new insights into <it>Leishmania </it>physiology.</p

Detecting Nonvolatile Life- and Nonlife-Derived Organics in a Carbonaceous Chondrite Analogue with a New Multiplex Immunoassay and Its Relevance for Planetary Exploration

Potential martian molecular targets include those supplied by meteoritic carbonaceous chondrites such as amino acids and polycyclic aromatic hydrocarbons and true biomarkers stemming from any hypothetical martian biota (organic architectures that can be directly related to once-living organisms). Heat extraction and pyrolysis-based methods currently used in planetary exploration are highly aggressive and very often modify the target molecules, making their identification a cumbersome task. We have developed and validated a mild, nondestructive, multiplex inhibitory microarray immunoassay and demonstrated its implementation in the SOLID (Signs of Life Detector) instrument for simultaneous detection of several nonvolatile life- and nonlife-derived organic molecules relevant in planetary exploration and environmental monitoring. By utilizing a set of highly specific antibodies that recognize D- or L-aromatic amino acids (Phe, Tyr, Trp), benzo[a]pyrene (B[a]P), pentachlorophenol, and sulfone-containing aromatic compounds, respectively, the assay was validated in the SOLID instrument for the analysis of carbon-rich samples used as analogues of the organic material in carbonaceous chondrites or even Mars samples. Most of the antibodies enabled sensitivities at the 1–10 ppb level and some even at the part-per-trillion level. The multiplex immunoassay allowed the detection of B[a]P as well as aromatic sulfones in a water/methanol extract of an Early Cretaceous lignite sample (ca. 140 Ma) representing type IV kerogen. No L- or D-aromatic amino acids were detected, reflecting the advanced diagenetic stage and the fossil nature of the sample. The results demonstrate the ability of the liquid extraction by ultrasonication and the versatility of the multiplex inhibitory immunoassays in the SOLID instrument to discriminate between organic matter derived from life and nonlife processes, an essential step toward life detection outside EarthThis work was supported by granted projects AYA2011-24803, ESP2014-51989-P, and ESP2015-69540-R, from the Ministry of Economy and Competitiveness (MINECO) of Spain, and by Grant No. ST/N000803/1 (United Kingdom). A. G-C was a fellow of ‘‘Plan de Formación from INTA.Peer reviewe

Detecting Nonvolatile Life- and Nonlife-Derived Organics in a Carbonaceous Chondrite Analogue with a New Multiplex Immunoassay and Its Relevance for Planetary Exploration

[EN] Potential martian molecular targets include those supplied by meteoritic carbonaceous chondrites such as amino acids and polycyclic aromatic hydrocarbons and true biomarkers stemming from any hypothetical martian biota (organic architectures that can be directly related to once living organisms). Heat extraction and pyrolysis-based methods currently used in planetary exploration are highly aggressive and very often modify the target molecules making their identification a cumbersome task. We have developed and validated a mild, nondestructive, multiplex inhibitory microarray immunoassay and demonstrated its implementation in the SOLID (Signs of Life Detector) instrument for simultaneous detection of several nonvolatile life- and nonlife-derived organic molecules relevant in planetary exploration and environmental monitoring. By utilizing a set of highly specific antibodies that recognize D- or L- aromatic amino acids (Phe, Tyr, Trp), benzo[a]pyrene (B[a]P), pentachlorophenol, and sulfone-containing aromatic compounds, respectively, the assay was validated in the SOLID instrument for the analysis of carbon-rich samples used as analogues of the organic material in carbonaceous chondrites or even Mars samples. Most of the antibodies enabled sensitivities at the 1-10ppb level and some even at the ppt level. The multiplex immunoassay allowed the detection of B[a]P as well as aromatic sulfones in a water/methanol extract of an Early Cretaceous lignite sample (c.a., 140 Ma) representing type IV kerogen. No L- or D-aromatic amino acids were detected, reflecting the advanced diagenetic stage and the fossil nature of the sample. The results demonstrate the ability of the liquid extraction by ultrasonication and the versatility of the multiplex inhibitory immunoassays in the SOLID instrument to discriminate between organic matter derived from life and nonlife processes, an essential step toward life detection outside Earth.This work was supported by granted projects AYA2011-24803, ESP2014-51989-P, and ESP2015-69540-R, from the Ministry of Economy and Competitiveness (MINECO) of Spain, and by Grant No. ST/N000803/1 (United Kingdom). A. G-C was a fellow of Plan de Formación from INTA.Moreno-Paz, M.; Gómez-Cifuentes, A.; Ruiz-Bermejo, M.; Hofstetter, O.; Maquieira Catala, A.; Manchado, JM.; Morais, S.... (2018). Detecting Nonvolatile Life- and Nonlife-Derived Organics in a Carbonaceous Chondrite Analogue with a New Multiplex Immunoassay and Its Relevance for Planetary Exploration. Astrobiology. 18(8):1041-1056. https://doi.org/10.1089/ast.2017.1747S1041105618

Desarrollo de la inteligencia emocional en los estudiantes del grado sexto a través de las expresiones artísticas

La presente propuesta de investigación está centrada en el desarrollo de la inteligencia emocional en los estudiantes (preadolescentes) del grado sexto del colegio Técnico Industrial de la vereda Verganzo de Tocancipá, mediado por la implementación de diferentes expresiones artísticas como estrategia didáctica, para mejorar y transformar los entornos sociales, mantener un ambiente favorable de participación, comunicación y sana convivencia. Esta investigación está apoyada bajo el enfoque cualitativo con el tipo de investigación acción para la recolección de datos e información, obteniendo criterios para proponer el diseño de una secuencia didáctica que busca poner en práctica y promover el desarrollo de la inteligencia emocional de forma dinámica, motivadora y participativa.This research proposal is focused on the development of emotional intelligence in students (preadolescents) of the sixth grade of the Industrial Technical College of the small town Verganzo de Tocancipá, mediated by the implementation of different artistic expressions as a didactic strategy, to improve and transform social environments, maintain a favorable environment of participation, communication and healthy coexistence. This research is supported under the qualitative approach with the type of action research for the collection of data and information, obtaining criteria to propose the design of a didactic sequence that seeks to put into practice and promote the development of emotional intelligence in a dynamic, motivating way. and participator

Prokaryotic Community Structure and Metabolisms in Shallow Subsurface of Atacama Desert Playas and Alluvial Fans After Heavy Rains: Repairing and Preparing for Next Dry Period

The Atacama Desert, the oldest and driest desert on Earth, displays significant rains only once per decade. To investigate how microbial communities take advantage of these sporadic wet events, we carried out a geomicrobiological study a few days after a heavy rain event in 2015. Different physicochemical and microbial community analyses were conducted on samples collected from playas and an alluvial fan from surface, 10, 20, 50, and 80 cm depth. Gravimetric moisture content peaks were measured in 10 and 20 cm depth samples (from 1.65 to 4.1% w/w maximum values) while, in general, main anions such as chloride, nitrate, and sulfate concentrations increased with depth, with maximum values of 13-1,125; 168-10,109; and 9,904-30,952 ppm, respectively. Small organic anions such as formate and acetate had maximum concentrations from 2.61 to 3.44 ppm and 6.73 to 28.75 ppm, respectively. Microbial diversity inferred from DNA analysis showed Actinobacteria and Alphaproteobacteria as the most abundant and widespread bacterial taxa among the samples, followed by Chloroflexi and Firmicutes at specific sites. Archaea were mainly dominated by Nitrososphaerales, Methanobacteria, with the detection of other groups such as Halobacteria. Metaproteomics showed a high and even distribution of proteins involved in primary metabolic processes such as energy production and biosynthetic pathways, and a limited but remarkable presence of proteins related to resistance to environmental stressors such as radiation, oxidation, or desiccation. The results indicated that extra humidity in the system allows the microbial community to repair, and prepare for the upcoming hyperarid period. Additionally, it supplies biomarkers to the medium whose preservation potential could be high under strong desiccation conditions and relevant for planetary exploration.Spanish Ministerio de Economia y Competitividad/Fondo Europeo de Desarrollo Regional Grants [ESP2014-58494-R, ESP2015-69540-R, ESP2017-89053-C2-2-P]; NASA ASTEP "Life in the Atacama (LITA)" project [NNX11AJ87G]; NASA Astrobiology Institute Colaborative Agreement 7 (CAN-7) project [NNX15BB01A]; Comunidad de Madrid/European Union YEI program; Spanish Ministry of Economy and Competitivity (MINECO); "Maria de Maeztu" program [MDM-2017-0737]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]