by Keyword: region

Cuervo, R, Rodriguez-Lázaro, MA, Farré, R, Gozal, D, Solana, G, Otero, J, (2023). Low-cost and open-source neonatal incubator operated by an Arduino microcontroller Hardwarex 15, e00457

An unacceptably large number of newborn infants die in developing countries. For a considerable number of cases (particularly in preterm infants), morbidity and mortality can be reduced by simply maintaining newborn thermal homeostasis during the first weeks of life. Unfortunately, deaths caused by prematurity remain inordinately common in low- and middle-income countries (LMICs) due to reduced access to incubators in light of the high cost of commercially available devices. We herein describe and test a low-cost and easy-to-assemble neonatal incubator created with inexpensive materials readily available in LMICs. The incubator is based on an Arduino microcontroller. It maintains controlled temperature and relative humidity inside the main chamber while continuously measuring newborn weight progress. Moreover, the incubator has a tilting bed system and an additional independent safety temperature alarm. The performance of the novel low-cost neonatal incubator was evaluated and successfully passed the IEC 60601-2-19 standards. In the present work, we provide all the necessary technical information, which is distributed as open source. This will enable assembly of very low-cost (<250 €) and fully functional incubators in LMICs that should help reduce neonatal mortality.© 2023 The Authors. Published by Elsevier Ltd.

JTD Keywords: arduino, control systems, developing countries, low-cost, low-resource regions, noise, preterm infant, Arduino, Control systems, Developing countries, Low-cost, Low-resource regions, Mortality, Neonatal incubator, Preterm infant

Pietroforte, S, Monasterio, MB, Ferrer-Vaquer, A, Irimia, M, Ibáñez, E, Popovic, M, Vassena, R, Zambelli, F, (2023). Specific processing of meiosis-related transcript is linked to final maturation in human oocytes Molecular Human Reproduction 29, gaad021

Human meiosis in oocytes entails an intricate regulation of the transcriptome to support late oocyte growth and early embryo development, both crucial to reproductive success. Currently, little is known about the co- and post-transcriptional mRNA processing mechanisms regulating the last meiotic phases, which contribute to transcriptome complexity and influence translation rates. We analyzed gene expression changes, splicing and pre-mRNA processing in an RNA sequencing set of 40 human oocytes at different meiotic maturation stages, matured both in vivo and in vitro. We found abundant untranslated region (UTR) processing, mostly at the 3' end, of meiosis-related genes between the germinal vesicle (GV) and metaphase II (MII) stages, supported by the differential expression of spliceosome and pre-mRNA processing related genes. Importantly, we found very few differences among GV oocytes across several durations of IVM, as long as they did not reach MII, suggesting an association of RNA processing and successful meiosis transit. Changes in protein isoforms are minor, although specific and consistent for genes involved in chromosome organization and spindle assembly. In conclusion, we reveal a dynamic transcript remodeling during human female meiosis, and show how pre-mRNA processing, specifically 3'UTR shortening, drives a selective translational regulation of transcripts necessary to reach final meiotic maturation.© The Author(s) 2023. Published by Oxford University Press on behalf of European Society of Human Reproduction and Embryology. All rights reserved. For permissions, please email:

JTD Keywords: 3 & prime, alternative splicing, gene expression, meiosis, oocyte competence, program, rna, splicing, untranslated region processing, untranslated regions, 3′ untranslated region processing, 3′ untranslated regions, Alternative splicing, Expression, Gene expression, Human oocytes, Meiosis, Oocyte competence, Splicing

Pintado-Grima, C, Santos, J, Iglesias, V, Manglano-Artuñedo, Z, Pallarès, I, Ventura, S, (2023). Exploring cryptic amyloidogenic regions in prion-like proteins from plants Frontiers In Plant Science 13, 1060410

Prion-like domains (PrLDs) are intrinsically disordered regions (IDRs) of low sequence complexity with a similar composition to yeast prion domains. PrLDs-containing proteins have been involved in different organisms' regulatory processes. Regions of moderate amyloid propensity within IDRs have been shown to assemble autonomously into amyloid fibrils. These sequences tend to be rich in polar amino acids and often escape from the detection of classical bioinformatics screenings that look for highly aggregation-prone hydrophobic sequence stretches. We defined them as cryptic amyloidogenic regions (CARs) and recently developed an integrated database that collects thousands of predicted CARs in IDRs. CARs seem to be evolutionary conserved among disordered regions because of their potential to stablish functional contacts with other biomolecules. Here we have focused on identifying and characterizing CARs in prion-like proteins (pCARs) from plants, a lineage that has been poorly studied in comparison with other prionomes. We confirmed the intrinsic amyloid potential for a selected pCAR from Arabidopsis thaliana and explored functional enrichments and compositional bias of pCARs in plant prion-like proteins.Copyright © 2023 Pintado-Grima, Santos, Iglesias, Manglano-Artuñedo, Pallarès and Ventura.

JTD Keywords: aggregation, aromatic residues, bioinformatics, domains, functional interactions, identify proteins, plants, prediction, prion-like domains, q/n-rich, regulator, sup35, yeast, Bioinformatics, Cryptic amyloidogenic regions, Functional interactions, Plants, Prion-like domains, Rna-binding proteins

Bonilla-Pons, SA, Nakagawa, S, Bahima, EG, Fernández-Blanco, A, Pesaresi, M, D'Antin, JC, Sebastian-Perez, R, Greco, D, Domínguez-Sala, E, Gómez-Riera, R, Compte, RIB, Dierssen, M, Pulido, NM, Cosma, MP, (2022). Müller glia fused with adult stem cells undergo neural differentiation in human retinal models Ebiomedicine 77, 103914

Visual impairments are a critical medical hurdle to be addressed in modern society. Müller glia (MG) have regenerative potential in the retina in lower vertebrates, but not in mammals. However, in mice, in vivo cell fusion between MG and adult stem cells forms hybrids that can partially regenerate ablated neurons.We used organotypic cultures of human retina and preparations of dissociated cells to test the hypothesis that cell fusion between human MG and adult stem cells can induce neuronal regeneration in human systems. Moreover, we established a microinjection system for transplanting human retinal organoids to demonstrate hybrid differentiation.We first found that cell fusion occurs between MG and adult stem cells, in organotypic cultures of human retina as well as in cell cultures. Next, we showed that the resulting hybrids can differentiate and acquire a proto-neural electrophysiology profile when the Wnt/beta-catenin pathway is activated in the adult stem cells prior fusion. Finally, we demonstrated the engraftment and differentiation of these hybrids into human retinal organoids.We show fusion between human MG and adult stem cells, and demonstrate that the resulting hybrid cells can differentiate towards neural fate in human model systems. Our results suggest that cell fusion-mediated therapy is a potential regenerative approach for treating human retinal dystrophies.This work was supported by La Caixa Health (HR17-00231), Velux Stiftung (976a) and the Ministerio de Ciencia e Innovación, (BFU2017-86760-P) (AEI/FEDER, UE), AGAUR (2017 SGR 689, 2017 SGR 926).Published by Elsevier B.V.

JTD Keywords: cell fusion, expression, fusion, ganglion-cells, in-vitro, mouse, müller glia, neural differentiation, organoids, regeneration, retina regeneration, stem cells, stromal cells, transplantation, 4',6 diamidino 2 phenylindole, 5' nucleotidase, Agarose, Alcohol, Arpe-19 cell line, Article, Beta catenin, Beta tubulin, Bone-marrow-cells, Bromophenol blue, Buffer, Calcium cell level, Calcium phosphate, Calretinin, Canonical wnt signaling, Cd34 antigen, Cell culture, Cell fusion, Cell viability, Coculture, Complementary dna, Confocal microscopy, Cornea transplantation, Cryopreservation, Cryoprotection, Crystal structure, Current clamp technique, Dimethyl sulfoxide, Dodecyl sulfate sodium, Edetic acid, Electrophysiology, Endoglin, Fetal bovine serum, Fibroblast growth factor 2, Flow cytometry, Fluorescence activated cell sorting, Fluorescence intensity, Glyceraldehyde 3 phosphate dehydrogenase, Glycerol, Glycine, Hoe 33342, Immunofluorescence, Immunohistochemistry, Incubation time, Interleukin 1beta, Lentivirus vector, Matrigel, Mercaptoethanol, Microinjection, Mueller cell, Müller glia, N methyl dextro aspartic acid, Nerve cell differentiation, Neural differentiation, Nitrogen, Nonhuman, Organoids, Paraffin, Paraffin embedding, Paraformaldehyde, Patch clamp technique, Penicillin derivative, Phenolsulfonphthalein, Phenotype, Phosphate buffered saline, Phosphoprotein phosphatase inhibitor, Polyacrylamide gel electrophoresis, Potassium chloride, Povidone iodine, Promoter region, Proteinase inhibitor, Real time polymerase chain reaction, Receptor type tyrosine protein phosphatase c, Restriction endonuclease, Retina, Retina dystrophy, Retina regeneration, Retinol, Rhodopsin, Rna extraction, Stem cell, Stem cells, Subcutaneous fat, Tunel assay, Visual impairment, Western blotting

Prieto, A, Bernabeu, M, Sánchez-Herrero, JF, Pérez-Bosque, A, Mir, L, Bäuer, C, Colladcy, C, Hüttener, M, Juárez, A, (2021). Modulation of AggR levels reveals features of virulence regulation in enteroaggregative E. coli Commun Biol 4, 1295

Enteroaggregative Escherichia coli (EAEC) strains are one of the diarrheagenic pathotypes. EAEC strains harbor a virulence plasmid (pAA2) that encodes, among other virulence determinants, the aggR gene. The expression of the AggR protein leads to the expression of several virulence determinants in both plasmids and chromosomes. In this work, we describe a novel mechanism that influences AggR expression. Because of the absence of a Rho-independent terminator in the 3?UTR, aggR transcripts extend far beyond the aggR ORF. These transcripts are prone to PNPase-mediated degradation. Structural alterations in the 3?UTR result in increased aggR transcript stability, leading to increased AggR levels. We therefore investigated the effect of increased AggR levels on EAEC virulence. Upon finding the previously described AggR-dependent virulence factors, we detected novel AggR-regulated genes that may play relevant roles in EAEC virulence. Mutants exhibiting high AggR levels because of structural alterations in the aggR 3?UTR show increased mobility and increased pAA2 conjugation frequency. Furthermore, among the genes exhibiting increased fold change values, we could identify those of metabolic pathways that promote increased degradation of arginine, fatty acids and gamma-aminobutyric acid (GABA), respectively. In this paper, we discuss how the AggR-dependent increase in specific metabolic pathways activity may contribute to EAEC virulence.

JTD Keywords: aggregative adherence, arginine metabolism, biofilm formation, escherichia-coli, gene-expression, messenger-rna, operon, persistent diarrhea, untranslated region, Fimbria-i expression

Santos-Pata, D, Amil, AF, Raikov, IG, Rennó-Costa, C, Mura, A, Soltesz, I, Verschure, PFMJ, (2021). Entorhinal mismatch: A model of self-supervised learning in the hippocampus Iscience 24, 102364

The hippocampal formation displays a wide range of physiological responses to different spatial manipulations of the environment. However, very few attempts have been made to identify core computational principles underlying those hippocampal responses. Here, we capitalize on the observation that the entorhinal-hippocampal complex (EHC) forms a closed loop and projects inhibitory signals “countercurrent” to the trisynaptic pathway to build a self-supervised model that learns to reconstruct its own inputs by error backpropagation. The EHC is then abstracted as an autoencoder, with the hidden layers acting as an information bottleneck. With the inputs mimicking the firing activity of lateral and medial entorhinal cells, our model is shown to generate place cells and to respond to environmental manipulations as observed in rodent experiments. Altogether, we propose that the hippocampus builds conjunctive compressed representations of the environment by learning to reconstruct its own entorhinal inputs via gradient descent.

JTD Keywords: cognitive neuroscience, grid cells, long-term, networks, neural networks, novelty, oscillations, pattern separation, region, representation, working-memory, Cognitive neuroscience, Neural networks, Rat dentate gyrus, Systems neuroscience

Valenti, S., Yousefzade, O., Puiggalí, J., Macovez, R., (2020). Phase-selective conductivity enhancement and cooperativity length in PLLA/TPU nanocomposite blends with carboxylated carbon nanotubes Polymer 191, 122279

Transmission electron microscopy, temperature-modulated differential scanning calorimetry, and broadband dielectric spectroscopy were employed to characterize ternary nanocomposites consisting of carboxylated carbon nanotubes (CNT) dispersed in a blend of two immiscible polymers, poly(L,lactide) (PLLA) and thermoplastic polyurethane (TPU). The nanocomposite blends were obtained by melt-compounding of PLLA and TPU in the presence of 0.2 wt-% CNT, either in the presence or absence of a Joncryl® ADR chain extender for PLLA, leading to reactive and non-reactive melt mixed samples. In both cases, the binary PLLA/TPU blend is characterized by phase separation into submicron TPU droplets dispersed in the PLLA matrix, and displays two separate glass transition temperatures. The carbon nanotubes are present either inside the TPU phase (samples obtained without chain extender), or at their boundaries (reactive-melt mixed samples). The effect of the sub-micron confinement of the TPU component is to decrease the cooperativity length of the primary segmental relaxation of this polymer, which is accentuated by the presence of the CNT fillers. Depending on the type of sample, five or six distinct relaxations are observed by means of dielectric spectroscopy, which we are able to assign to different dielectric phenomena. Our dielectric data show that the CNT fillers do not contribute directly to the long-range charge transport in the nanocomposite blends, consistent with the nanocomposites morphology, but rather result in a shift of the Maxwell-Wagner-Sillars space-charge frequency associated with charge accumulation at the PLLA/TPU boundary. Such shift testifies to a selective conductivity enhancement of the TPU phase due to the filler.

JTD Keywords: Conductivity enhancement, Cooperatively rearranging region, Dielectric spectroscopy, Glass transition, Maxwell-Wagner-Sillars relaxation, Nanofiller