In silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19

Background: There is pressing urgency to identify therapeutic targets and drugs that allow treating COVID-19 patients effectively.Methods: We performed in silico analyses of immune system protein interactome network, single-cell RNA sequencing of human tissues, and artificial neural networks to reveal potential therapeutic targets for drug repurposing against COVID-19.Results: We screened 1,584 high-confidence immune system proteins in ACE2 and TMPRSS2 co-expressing cells, finding 25 potential therapeutic targets significantly overexpressed in nasal goblet secretory cells, lung type II pneumocytes, and ileal absorptive enterocytes of patients with several immunopathologies. Then, we performed fully connected deep neural networks to find the best multitask classification model to predict the activity of 10,672 drugs, obtaining several approved drugs, compounds under investigation, and experimental compounds with the highest area under the receiver operating characteristics.Conclusion: After being effectively analyzed in clinical trials, these drugs can be considered for treatment of severe COVID-19 patients. Scripts can be downloaded at

Los sistemas de dos componentes: circuitos moleculares versátiles

To survive, organisms must adapt to sudden environmental changes that exert a selective pressure and therefore, their chances of survival depend on their ability to respond quickly and accurately. Adapting to these changes is closely linked to the correct perception and transmission of stimuli and the generation of appropriate responses. Two component systems (TCS) allow different bacteria, fungi, slime molds and plants to regulate their physiology according to the environmental conditions. In these molecular circuits, the mechanism of communication between modules is the consecutive phosphorylation of His and Asp residues located in sensor histidine kinase and  response  regulator protein pairs. This review highlights the most relevant features of TCS and their role in the perception and response to diverse stimuli. Finally, the differences between prokaryotic and eukaryotic TCS are illustrated using the osmotic response in Escherichia coli and Saccharomyces cerevisiae.Para sobrevivir, los organismos deben adaptarse a cambios ambientales repentinos que ejercen una presión selectiva y por lo tanto sus posibilidades de supervivencia, dependen de su capacidad para responder en forma rápida y precisa. La adaptación a estos cambios está estrechamente ligada a la correcta percepción y transmisión de los estímulos, así como a la generación de respuestas apropiadas. En diferentes bacterias, hongos, plantas y mohos mucilaginosos, los sistemas de dos componentes (SDC) permiten regular su fisiología de acuerdo a las condiciones ambientales. En estos circuitos moleculares, el mecanismo de comunicación entre módulos es la fosforilación consecutiva de residuos de His y Asp localizados en dos proteínas: una cinasa sensora (CS) y un regulador de la respuesta (RR). En este artículo de revisión, se destacan las características más relevantes de los SDC, así como su participación como sistemas de percepción-respuesta a muy diversos estímulos. Además se resaltan las diferencias entre los SDC en procariontes y eucariontes. Finalmente se ejemplifican algunas diferencias usando los circuitos de regulación osmótica de Escherichia coli y Saccharomyces cerevisiae

Los sistemas de dos componentes: circuitos moleculares versátiles

Para sobrevivir, los organismos deben adaptarse a cambios ambientales repentinos que ejercen una presión selectiva y por lo tanto sus posibilidades de supervivencia, dependen de su capacidad para responder en forma rápida y precisa. La adaptación a estos cambios está estrechamente ligada a la correcta percepción y transmisión de los estímulos, así como a la generación de respuestas apropiadas. En diferentes bacterias, hongos, plantas y mohos mucilaginosos, los sistemas de dos componentes (SDC) permiten regular su fisiología de acuerdo a las condiciones ambientales. En estos circuitos moleculares, el mecanismo de comunicación entre módulos es la fosforilación consecutiva de residuos de His y Asp localizados en dos proteínas: una cinasa sensora (CS) y un regulador de la respuesta (RR). En este artículo de revisión, se destacan las características más relevantes de los SDC, así como su participación como sistemas de percepción-respuesta a muy diversos estímulos. Además se resaltan las diferencias entre los SDC en procariontes y eucariontes. Finalmente se ejemplifican algunas diferencias usando los circuitos de regulación osmótica de Escherichia coli y Saccharomyces cerevisiae

Caracterización de los sistemas de dos componentes de neurospora crassa /\ua0tesis que para obtener el grado de Doctorado en Ciencias Bioquímicas, presenta Carlos Arturo Barba Ostria ; tutor principal de tesis Dimitris Georgellis

. 97 páginas :\ua0ilustraciones. Doctorado en Ciencias Bioquímicas\ua0Universidad Nacional Autónoma de México,\ua02013\ua0Programa de Posgrado en Ciencias Bioquímica

The Neurospora crassa DCC-1 Protein, a Putative Histidine Kinase, Is Required for Normal Sexual and Asexual Development and Carotenogenesis▿

Two-component signaling pathways based on phosphoryl group transfer between histidine kinase and response regulator proteins regulate environmental responses in bacteria, archaea, plants, slime molds, and fungi. Here we characterize a mutant form of DCC-1, a putative histidine kinase encoded by the NCU00939 gene of the filamentous fungus Neurospora crassa. We show that this protein participates in the regulation of processes such as conidiation, perithecial development, and, to a certain degree, carotenogenesis. Furthermore, DCC-1 is suggested to exert its effect by promoting cyclic AMP production, thereby placing this protein within the context of a signaling pathway

Engineering <i>Escherichia coli</i> for Conversion of Glucose to Medium-Chain ω‑Hydroxy Fatty Acids and α,ω-Dicarboxylic Acids

In search of sustainable approaches to plastics production, many efforts have been made to engineer microbial conversions of renewable feedstock to short-chain (C2–C8) bifunctional polymer precursors (e.g., succinic acid, cadaverine, 1,4-butanediol). Less attention has been given to medium-chain (C12–C14) monomers such as ω-hydroxy fatty acids (ω-OHFAs) and α,ω-dicarboxylic acids (α,ω-DCAs), which are precursors to high performance polyesters and polyamides. Here we engineer a complete microbial conversion of glucose to C12 and C14 ω-OHFAs and α,ω-DCAs, with precise control of product chain length. Using an expanded bioinformatics approach, we screen a wide range of enzymes across phyla to identify combinations that yield complete conversion of intermediates to product α,ω-DCAs. Finally, through optimization of culture conditions, we enhance production titer of C12 α,ω-DCA to nearly 600 mg/L. Our results indicate potential for this microbial factory to enable commercially relevant, renewable production of C12 α,ω-DCAa valuable precursor to the high-performance plastic, nylon-6,12

Engineering xylose metabolism for production of polyhydroxybutyrate in the non-model bacterium Burkholderia sacchari

Abstract Background Despite its ability to grow and produce high-value molecules using renewable carbon sources, two main factors must be improved to use Burkholderia sacchari as a chassis for bioproduction at an industrial scale: first, the lack of molecular tools to engineer this organism and second, the inherently slow growth rate and poly-3-hydroxybutyrate [P(3HB)] production using xylose. In this work, we have addressed both factors. Results First, we adapted a set of BglBrick plasmids and showed tunable expression in B. sacchari. Finally, we assessed growth rate and P(3HB) production through overexpression of xylose transporters, catabolic or regulatory genes. Overexpression of xylR significantly improved growth rate (55.5% improvement), polymer yield (77.27% improvement), and resulted in 71% of cell dry weight as P(3HB). Conclusions These values are unprecedented for P(3HB) accumulation using xylose as a sole carbon source and highlight the importance of precise expression control for improving utilization of hemicellulosic sugars in B. sacchari

Developing a Cas9-Based Tool to Engineer Native Plasmids in Synechocystis sp. PCC 6803

The oxygenic photosynthetic bacterium Synechocystis sp. PCC 6803 (S6803) is a model cyanobacterium widely used for fundamental research and biotechnology applications. Due to its polyploidy, existing methods for genome engineering of S6803 require multiple rounds of selection to modify all genome copies, which is time consuming and inefficient. In this study, we engineered the Cas9 tool for onestep, segregationfree genome engineering. We further used our Cas9 tool to delete three of seven S6803 native plasmids. Our results show that all three smallsize native plasmids, but not the largesize native plasmids, can be deleted with this tool. To further facilitate heterologous gene expression in S6803, a shuttle vector based on the native plasmid pCC5.2 was created. The shuttle vector can be introduced into Cas9containing S6803 in one step without requiring segregation and can be stably maintained without antibiotic pressure for at least 30 days. Moreover, genes encoded on the shuttle vector remain functional after 30 days of continuous cultivation without selective pressure. Thus, this study provides a set of new tools for rapid modification of the S6803 genome and for stable expression of heterologous genes, potentially facilitating both fundamental research and biotechnology applications using S6803