by Keyword: Evolution
Roca, C, Avalos-Padilla, Y, Prieto-Simon, B, Iglesias, V, Ramirez, M, Imperial, S, Fernandez-Busquets, X, (2022). Selection of an Aptamer against the Enzyme 1-deoxy-D-xylulose-5-phosphate Reductoisomerase from Plasmodium falciparum Pharmaceutics 14, 2515
The methyl erythritol phosphate (MEP) pathway of isoprenoid biosynthesis is essential for malaria parasites and also for several human pathogenic bacteria, thus representing an interesting target for future antimalarials and antibiotics and for diagnostic strategies. We have developed a DNA aptamer (D10) against Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), the second enzyme of this metabolic route. D10 binds in vitro to recombinant DXR from P. falciparum and Escherichia coli, showing at 10 mu M a ca. 50% inhibition of the bacterial enzyme. In silico docking analysis indicates that D10 associates with DXR in solvent-exposed regions outside the active center pocket. According to fluorescence confocal microscopy data, this aptamer specifically targets in P. falciparum in vitro cultures the apicoplast organelle where the MEP pathway is localized and is, therefore, a highly specific marker of red blood cells parasitized by Plasmodium vs. naive erythrocytes. D10 is also selective for the detection of MEP+ bacteria (e.g., E. coli and Pseudomonas aeruginosa) vs. those lacking DXR (e.g., Enterococcus faecalis). Based on these results, we discuss the potential of DNA aptamers in the development of ligands that can outcompete the performance of the well-established antibody technology for future therapeutic and diagnostic approaches.
JTD Keywords: 1-deoxy-d-xylulose-5-phosphate reductoisomerase, Apicoplast, Dna aptamers, Drug targets, Evolution, Inhibitors, Isoprenoid biosynthesis, Malaria, Methyl erythritol phosphate pathway, Pathway, Plasmodium, Protein-protein, Web server
Bernabeu, M, Aznar, S, Prieto, A, Huttener, M, Juarez, A, (2022). Differential Expression of Two Copies of the irmA Gene in the Enteroaggregative E. coli Strain 042 Microbiology Spectrum 17, 00454-22
Gene duplications occur in prokaryotic genomes at a detectable frequency. In many instances, the biological function of the duplicates is unknown, and hence, the significance of the presence of multiple copies of these genes remains unclear.; Gene duplications significantly impact the gene repertoires of both eukaryotic and prokaryotic microorganisms. The genomes of pathogenic Escherichia coli strains share a group of duplicated genes whose function is mostly unknown. The irmA gene is one of the duplicates encoded in several pathogenic E. coli strains. The function of its gene product was investigated in the uropathogenic E. coli strain CFT073, which contains a single functional copy. The IrmA protein structure mimics that of human interleukin receptors and likely plays a role during infection. The enteroaggregative E. coli strain 042 contains two functional copies of the irmA gene. In the present work, we investigated their biological roles. The irmA_4509 allele is expressed under several growth conditions. Its expression is modulated by the global regulators OxyR and Hha, with optimal expression at 37 degrees C and under nutritional stress conditions. Expression of the irmA_2244 allele can only be detected when the irmA_4509 allele is knocked out. Differences in the promoter regions of both alleles account for their differential expression. Our results show that under several environmental conditions, the expression of the IrmA protein in strain 042 is dictated by the irmA_4509 allele. The irmA_2244 allele appears to play a backup role to ensure IrmA expression when the irmA_4509 allele loses its function. IMPORTANCE Gene duplications occur in prokaryotic genomes at a detectable frequency. In many instances, the biological function of the duplicates is unknown, and hence, the significance of the presence of multiple copies of these genes remains unclear. In pathogenic E. coli isolates, the irmA gene can be present either as a single copy or in two or more copies. We focused our work on studying why a different pathogenic E. coli strain encodes two functional copies of the irmA gene. We show that under several environmental conditions, one of the alleles dictates IrmA expression, and the second remains silent. The latter allele is only expressed when the former is silenced. The presence of more than one functional copy of the irmA gene in some pathogenic E. coli strains can result in sufficient expression of this virulence factor during the infection process.
JTD Keywords: 042, Adaptation, Aec69, Aggregative adherence, Chromosomal genes, Coli, Duplication, Enteroaggregative e, Escherichia-coli, Evolution, Gene duplications, Hha/ymoa, Irma, Mechanism, Outer-membrane, Protein
Sans J, Arnau M, Sanz V, Turon P, Alemán C, (2022). Hydroxyapatite-based biphasic catalysts with plasticity properties and its potential in carbon dioxide fixation Chemical Engineering Journal 433, 133512
The design of catalysts with controlled selectivity at will, also known as catalytic plasticity, is a very attractive approach for the recycling of carbon dioxide (CO2). In this work, we study how catalytically active hydroxyapatite (HAp) and brushite (Bru) interact synergistically, allowing the production of formic acid or acetic acid depending on the HAp/Bru ratio in the catalyst. Raman, wide angle X-ray scattering, X-ray photoelectron spectroscopy, scanning electron microscopy and electrochemical impedance spectroscopy studies, combined with an exhaustive revision of the crystalline structure of the catalyst at the atomic level, allowed to discern how the Bru phase can be generated and stabilized at high temperatures. Results clearly indicate that the presence of OH– groups to maintain the crystalline structural integrity in conjunction with Ca2+ ions less bonded to the lattice fixate carbon into C1, C2 and C3 molecules from CO2 and allow the evolution from formic to acetic acid and acetone. In this way, the plasticity of the HAp-Bru system is demonstrated, representing a promising green alternative to the conventional metal-based electrocatalysts used for CO2 fixation. Thus, the fact that no electric voltage is necessary for the CO2 reduction has a very favorable impact in the final energetic net balance of the carbon fixation reaction. © 2021 ethanol production & nbsp
ethanol production & nbsp, brushite, co2 reduction, conversion, electrocatalytic reduction, electrode, formate, heterogeneous catalysis & nbsp, hydrogen evolution, insights, monetite, polarized hydroxyapatite,
Puiggalí-Jou A, Molina BG, Lopes-Rodrigues M, Michaux C, Perpète EA, Zanuy D, Alemán C, (2021). Self-standing, conducting and capacitive biomimetic hybrid nanomembranes for selective molecular ion separation Physical Chemistry Chemical Physics 23, 16157-16164
Hybrid free-standing biomimetic materials are developed by integrating the VDAC36 β-barrel protein into robust and flexible three-layered polymer nanomembranes. The first and third layers are prepared by spin-coating a mixture of poly(lactic acid) (PLA) and poly(vinyl alcohol) (PVA). PVA nanofeatures are transformed into controlled nanoperforations by solvent-etching. The two nanoperforated PLA layers are separated by an electroactive layer, which is successfully electropolymerized by introducing a conducting sacrificial substrate under the first PLA nanosheet. Finally, the nanomaterial is consolidated by immobilizing the VDAC36 protein, active as an ion channel, into the nanoperforations of the upper layer. The integration of the protein causes a significant reduction of the material resistance, which decreases from 21.9 to 3.9 kΩ cm2. Electrochemical impedance spectroscopy studies using inorganic ions and molecular metabolites (i.e.l-lysine and ATP) not only reveal that the hybrid films behave as electrochemical supercapacitors but also indicate the most appropriate conditions to obtain selective responses against molecular ions as a function of their charge. The combination of polymers and proteins is promising for the development of new devices for engineering, biotechnological and biomedical applications.
JTD Keywords: channels, evolution, filter, Outer-membrane proteins
Vilanova, E., Ciodaro, P. J., Bezerra, F. F., Santos, G. R. C., Valle-Delgado, J. J., Anselmetti, D., Fernàndez-Busquets, X., Mourão, P. A. S., (2020). Adhesion of freshwater sponge cells mediated by carbohydrate-carbohydrate interactions requires low environmental calcium Glycobiology 30, (9), 710-721
Marine ancestors of freshwater sponges had to undergo a series of physiological adaptations to colonize harsh and heterogeneous limnic environments. Besides reduced salinity, river-lake systems also have calcium concentrations far lower than seawater. Cell adhesion in sponges is mediated by calcium-dependent multivalent self-interactions of sulfated polysaccharide components of membrane-bound proteoglycans named aggregation factors. Cells of marine sponges require seawater average calcium concentration (10 mM) to sustain adhesion promoted by aggregation factors. We demonstrate here that the freshwater sponge Spongilla alba can thrive in a calcium-poor aquatic environment and that their cells are able to aggregate and form primmorphs with calcium concentrations 40-fold lower than that required by marine sponges cells. We also find that their gemmules need calcium and other micronutrients to hatch and generate new sponges. The sulfated polysaccharide purified from S. alba has sulfate content and molecular size notably lower than those from marine sponges. Nuclear magnetic resonance analyses indicated that it is composed of a central backbone of non- and 2-sulfated α- and β-glucose units decorated with branches of α-glucose. Assessments with atomic force microscopy/single-molecule force spectroscopy show that S. alba glucan requires 10-fold less calcium than sulfated polysaccharides from marine sponges to self-interact efficiently. Such an ability to retain multicellular morphology with low environmental calcium must have been a crucial evolutionary step for freshwater sponges to successfully colonize inland waters.
JTD Keywords: Carbohydrate interactions, Evolutionary adaptation, Porifera, Proteoglycans, Sulfated polysaccharides
Moulin-Frier, C., Puigbò, J. Y., Arsiwalla, X. D., Sanchez-Fibla, M., Verschure, P., (2018). Embodied artificial intelligence through distributed adaptive control: An integrated framework ICDL-EpiRob 2017 7th Joint IEEE International Conference on Development and Learning and on Epigenetic Robotics , IEEE (Lisbon, Portugal) , 324-330
In this paper, we argue that the future of Artificial Intelligence research resides in two keywords: integration and embodiment. We support this claim by analyzing the recent advances in the field. Regarding integration, we note that the most impactful recent contributions have been made possible through the integration of recent Machine Learning methods (based in particular on Deep Learning and Recurrent Neural Networks) with more traditional ones (e.g. Monte-Carlo tree search, goal babbling exploration or addressable memory systems). Regarding embodiment, we note that the traditional benchmark tasks (e.g. visual classification or board games) are becoming obsolete as state-of-the-art learning algorithms approach or even surpass human performance in most of them, having recently encouraged the development of first-person 3D game platforms embedding realistic physics. Building on this analysis, we first propose an embodied cognitive architecture integrating heterogeneous subfields of Artificial Intelligence into a unified framework. We demonstrate the utility of our approach by showing how major contributions of the field can be expressed within the proposed framework. We then claim that benchmarking environments need to reproduce ecologically-valid conditions for bootstrapping the acquisition of increasingly complex cognitive skills through the concept of a cognitive arms race between embodied agents.
JTD Keywords: Cognitive Architectures, Embodied Artificial Intelligence, Evolutionary Arms Race, Unified Theories of Cognition
Torrents, Eduard, (2014). Ribonucleotide reductases: Essential Enzymes for bacterial life Frontiers in Cellular and Infection Microbiology , 4, 1-9
Ribonucleotide reductase (RNR) is a key enzyme that mediates the synthesis of deoxyribonucleotides, the DNA precursors, for DNA synthesis in every living cell. This enzyme converts ribonucleotides to deoxyribonucleotides, the building blocks for DNA replication, and repair. Clearly, RNR enzymes have contributed to the appearance of genetic material that exists today, being essential for the evolution of all organisms on Earth. The strict control of RNR activity and dNTP pool sizes is important, as pool imbalances increase mutation rates, replication anomalies, and genome instability. Thus, RNR activity should be finely regulated allosterically and at the transcriptional level. In this review we examine the distribution, the evolution, and the genetic regulation of bacterial RNRs. Moreover, this enzyme can be considered an ideal target for anti-proliferative compounds designed to inhibit cell replication in eukaryotic cells (cancer cells), parasites, viruses, and bacteria.
JTD Keywords: Anaerobiosis, Transcription Factors, Evolution, Gene regulation, Ribonucleotide reductase, DNA Synthesis, NrdR,nrd
Juanola-Feliu, E., Colomer-Farrarons, J., Miribel-Català , P., Samitier, J., Valls-Pasola, J., (2012). Market challenges facing academic research in commercializing nano-enabled implantable devices for in-vivo biomedical analysis Technovation , 32, (3-4), 193-204
This article reports on the research and development of a cutting-edge biomedical device for continuous in-vivo glucose monitoring. This entirely public-funded process of technological innovation has been conducted at the University of Barcelona within a context of converging technologies involving the fields of medicine, physics, chemistry, biology, telecommunications, electronics and energy. The authors examine the value chain and the market challenges faced by in-vivo implantable biomedical devices based on nanotechnologies. In so doing, they trace the process from the point of applied research to the final integration and commercialization of the product, when the social rate of return from academic research can be estimated. Using a case-study approach, the paper also examines the high-tech activities involved in the development of this nano-enabled device and describes the technology and innovation management process within the value chain conducted in a University-Hospital-Industry-Administration-Citizens framework. Here, nanotechnology is seen to represent a new industrial revolution, boosting the biomedical devices market. Nanosensors may well provide the tools required for investigating biological processes at the cellular level in vivo when embedded into medical devices of small dimensions, using biocompatible materials, and requiring reliable and targeted biosensors, high speed data transfer, safely stored data, and even energy autonomy.
JTD Keywords: Biomedical device, Diabetes, Innovation management, Nanobiosensor, Nanotechnology, Research commercialization, Technology transfer, Academic research, Applied research, Barcelona, Biocompatible materials, Biological process, Biomedical analysis, Biomedical devices, Cellular levels, Converging technologies, Glucose monitoring, High-speed data transfer, Implantable biomedical devices, Implantable devices, In-vivo, Industrial revolutions, Innovation management, Medical Devices, Nanobiosensor, Rate of return, Research and development, Technological innovation, Value chains, Biological materials, Biomedical engineering, Biosensors, Commerce, Data transfer, Earnings, Engineering education, Glucose, Implants (surgical), Industrial research, Innovation, Medical problems, Nanosensors, Nanotechnology, Technology transfer, Equipment