4,408 results match your criteria: "the Barcelona Institute of Science and Technology[Affiliation]"

Article Synopsis
  • The regulation of exon inclusion through alternative splicing enhances the diversity of the transcriptome and proteome, impacting cell behavior.
  • Traditional methods struggle to identify splicing factors due to the complexity of their activity being controlled by various regulatory layers.
  • The proposed VIPER approach allows for the measurement of splicing factor activity based on downstream exon transcript inclusion, revealing patterns linked to tumorigenesis that are undetectable through conventional methods.
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Transcription factors (TFs) control specificity and activity of gene transcription, but whether a relationship between these two features exists is unclear. Here we provide evidence for an evolutionary trade-off between the activity and specificity in human TFs encoded as submaximal dispersion of aromatic residues in their intrinsically disordered protein regions. We identified approximately 500 human TFs that encode short periodic blocks of aromatic residues in their intrinsically disordered regions, resembling imperfect prion-like sequences.

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Only 30% of embryos from in vitro fertilized oocytes successfully implant and develop to term, leading to repeated transfer cycles. To reduce time-to-pregnancy and stress for patients, there is a need for a diagnostic tool to better select embryos and oocytes based on their physiology. The current standard employs brightfield imaging, which provides limited physiological information.

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Implications of noncoding regulatory functions in the development of insulinomas.

Cell Genom

August 2024

Endocrine Regulatory Genomics, Department of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain. Electronic address:

Insulinomas are rare neuroendocrine tumors arising from pancreatic β cells, characterized by aberrant proliferation and altered insulin secretion, leading to glucose homeostasis failure. With the aim of uncovering the role of noncoding regulatory regions and their aberrations in the development of these tumors, we coupled epigenetic and transcriptome profiling with whole-genome sequencing. As a result, we unraveled somatic mutations associated with changes in regulatory functions.

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Tailored assemblies of COPII proteins in secretion.

J Cell Biol

August 2024

Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.

Export of secretory cargoes from the endoplasmic reticulum (ER) requires COPII proteins, which were first identified for their ability to coat small vesicles that bud from the ER. Recent data indicate that COPII proteins can also organize into a collar at the necks of tubules, as well as phase-separate into liquid-like condensates. Thus, COPII assemblies seem to be tailored to accommodate variations in the size and quantities of cargo secreted.

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Enhanced binding of methyl alkylammonium cations through preorganization of a water-soluble calix[4]pyrrole.

Org Biomol Chem

July 2024

Institute of Chemical Research of Catalonia (ICIQ)-CERCA, The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans 16, 43007 Tarragona, Spain.

Article Synopsis
  • - The study focuses on creating two water-soluble calix[4]pyrroles (C[4]Ps) with carboxylic end groups, which can form stable complexes with tetra-methylammonium (G1) and pyridine-oxide (PNO) in a specific conformation in water.
  • - The PNO@4a complex shows better binding properties to G1 than the original C[4]P 4a, showcasing its ability to form stable 1:1 complexes with various tetra-alkylammonium salts.
  • - Through thermodynamic experiments and computational modeling, the research identifies cation-π and coulombic interactions as key factors in stabilizing these complexes
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Common genetic variants associated with urinary phthalate levels in children: A genome-wide study.

Environ Int

August 2024

Environment and Health Over the Lifecourse, ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.

Article Synopsis
  • * This study aimed to find genetic variations (SNPs and CNVs) affecting how children metabolize phthalates by analyzing data from 1,044 children in the HELIX cohort.
  • * Significant genetic loci associated with phthalate metabolism were identified, along with genes related to detoxification processes and renal excretion, suggesting a strong genetic component influencing how these compounds are processed in the body.
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We demonstrate in a proof-of-concept experiment spectral-domain optical coherence tomography where steering of the optical beam that probes the sample in a transverse scan does not make use of any mechanical element. Steering is done with the help of a phase-only spatial light modulator, that introduces a spatially-dependent phase between the two orthogonal polarization components of an optical beam, and some optical elements that control the polarization of light. We demonstrate that making use of the non-mechanical beam steering system considered here, we can reproduce the main traits of imaging with standard OCT that makes use of mechanical-assisted optical beam steering.

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Article Synopsis
  • Long-read RNA sequencing is crucial for accurate eukaryotic genome annotation, but consistent identification of RNA transcripts is still challenging.
  • CapTrap-seq is a new cDNA library preparation method that enhances detection of full-length RNA transcripts by using a Cap-trapping strategy and oligo(dT) priming.
  • In tests comparing CapTrap-seq to other RNA-seq methods on human and mouse tissues, results show it effectively reconstructs full-length RNA molecules and performs well across various sequencing platforms.
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Elucidation of the Epitranscriptomic RNA Modification Landscape of Chikungunya Virus.

Viruses

June 2024

Molecular Virology Group, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain.

The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. Among the 32 distinct RNA modifications analysed by mass spectrometry, inosine was found enriched in the genomic CHIKV RNA.

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FADS1/2 control lipid metabolism and ferroptosis susceptibility in triple-negative breast cancer.

EMBO Mol Med

July 2024

Department of Experimental and Clinical Biomedical Sciences, University of Florence, Viale Morgagni 50, 50134, Florence, Italy.

Triple-negative breast cancer (TNBC) has limited therapeutic options, is highly metastatic and characterized by early recurrence. Lipid metabolism is generally deregulated in TNBC and might reveal vulnerabilities to be targeted or used as biomarkers with clinical value. Ferroptosis is a type of cell death caused by iron-dependent lipid peroxidation which is facilitated by the presence of polyunsaturated fatty acids (PUFA).

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The incidence of infections has increased in the last decade, posing a serious threat to public health. Appropriately facing this challenge requires precise epidemiological data on species and antimicrobial resistance incidence, but many countries lack appropriate surveillance programs. This study aims to bridge this gap for Morocco by identifying and phenotyping a year-long collection of clinical isolates (n = 93) from four clinics in Tetouan.

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Hilbert Space Delocalization under Random Unitary Circuits.

Entropy (Basel)

May 2024

ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Av. Carl Friedrich Gauss 3, 08860 Castelldefels, Barcelona, Spain.

The unitary dynamics of a quantum system initialized in a selected basis state yield, generically, a state that is a superposition of all the basis states. This process, associated with the quantum information scrambling and intimately tied to the resource theory of coherence, may be viewed as a gradual delocalization of the system's state in the Hilbert space. This work analyzes the Hilbert space delocalization under the dynamics of random quantum circuits, which serve as a minimal model of the chaotic dynamics of quantum many-body systems.

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Cell type-specific alternative splicing (AS) enables differential gene isoform expression between diverse neuron types with distinct identities and functions. Current studies linking individual RNA-binding proteins (RBPs) to AS in a few neuron types underscore the need for holistic modeling. Here, we use network reverse engineering to derive a map of the neuron type-specific AS regulatory landscape from 133 mouse neocortical cell types defined by single-cell transcriptomes.

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The pluripotency state of human embryonic stem cells derived from single blastomeres of eight-cell embryos.

Cells Dev

September 2024

Genome Integrity and Reproductive Biology Group, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.

Human embryonic stem cells (hESCs) derived from blastocyst stage embryos present a primed state of pluripotency, whereas mouse ESCs (mESCs) display naïve pluripotency. Their unique characteristics make naïve hESCs more suitable for particular applications in biomedical research. This work aimed to derive hESCs from single blastomeres and determine their pluripotency state, which is currently unclear.

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Optical coupling between propagating light and confined surface polaritons plays a pivotal role in the practical design of nanophotonic devices. However, the coupling efficiency decreases dramatically with the degree of mode confinement due to the mismatch that exists between the light and polariton wavelengths, and despite the intense efforts made to explore different mechanisms proposed to circumvent this problem, the realization of a flexible scheme to efficiently couple light to polaritons remains a challenge. Here, we experimentally demonstrate an efficient coupling of light to surface-plasmon polaritons assisted by engineered dipolar scatterers placed at an optimum distance from the surface.

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Dual electro-/pH-responsive nanoparticle/hydrogel system for controlled delivery of anticancer peptide.

Biomater Adv

September 2024

Departament d'Enginyeria Química and Barcelona Research Center for Multiscale Science and Engineering, EEBE, Universitat Politècnica de Catalunya, C/ Eduard Maristany 10-14, 08019 Barcelona, Spain; Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain. Electronic address:

An electro-chemo-responsive carrier has been engineered for the controlled release of a highly hydrophilic anticancer peptide, CR(NMe)EKA (Cys-Arg- N-methyl-Glu-Lys-Ala). Remotely controlled on demand release of CR(NMe)EKA, loaded in electro-responsive poly(3,4-ethylenedioxythiophene) (PEDOT) nanoparticles, has been achieved by applying electrical stimuli consisting of constant positive (+0.50 V) or negative voltages (-0.

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Metabolic alterations in cancer precipitate in associated dependencies that can be therapeutically exploited. To meet this goal, natural product-inspired small molecules can provide a resource of invaluable chemotypes. Here, we identify orpinolide, a synthetic withanolide analog with pronounced antileukemic properties, via orthogonal chemical screening.

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The interaction between free electrons and optical fields constitutes a unique platform to investigate ultrafast processes in matter and explore fundamental quantum phenomena. Specifically, optically modulated electrons in ultrafast electron microscopy act as noninvasive probes that push space-time-energy resolution to the picometer-attosecond-microelectronvolt range. Electron energies well above the involved photon energies are commonly used, rendering a low electron-light coupling and, thus, only providing limited access to the wealth of quantum nonlinear phenomena underlying the dynamical response of nanostructures.

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Beclomethasone loaded liposomes enriched with mucin: A suitable approach for the control of skin disorders.

Biomed Pharmacother

August 2024

Department of Life and Environmental Sciences, University of Cagliari, University Campus, S.P. Monserrato-Sestu Km 0.700, Monserrato, CA 09042, Italy.

Inflammatory skin disorders are the fourth leading cause of chronic non-fatal conditions, which have a serious impact on the patient quality of life. Due to their treatment with conventional corticosteroids, which often result in poor therapeutic efficacy, relapses and systemic side effects from prolonged therapy, these diseases represent a global burden that negatively impacts the global economy. To avoid these problems and optimize corticosteroid benefits, beclomethasone was loaded into liposome formulations specifically tailored for skin delivery.

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The oxygen evolution reaction is the bottleneck to energy-efficient water-based electrolysis for the production of hydrogen and other solar fuels. In proton exchange membrane water electrolysis (PEMWE), precious metals have generally been necessary for the stable catalysis of this reaction. In this work, we report that delamination of cobalt tungstate enables high activity and durability through the stabilization of oxide and water-hydroxide networks of the lattice defects in acid.

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Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work presents a collection of FAIR notebooks covering various areas of the biomolecular simulation field, such as molecular dynamics (MD), protein-ligand docking, molecular checking/modeling, molecular interactions, and free energy perturbations.

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Stereochemistry plays a fundamental role in pharmacology. Here, we systematically investigate the relationship between stereoisomerism and bioactivity on over 1 M compounds, finding that a very significant fraction (~ 40%) of spatial isomer pairs show, to some extent, distinct bioactivities. We then use the 3D representation of these molecules to train a collection of deep neural networks (Signaturizers3D) to generate bioactivity descriptors associated to small molecules, that capture their effects at increasing levels of biological complexity (i.

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Photochemical Synthesis of Thioesters from Aryl Halides and Carboxylic Acids.

Angew Chem Int Ed Engl

September 2024

University of Bologna, Department of Industrial Chemistry 'Toso Montanari', via Piero Gobetti, 85-, 40129, Bologna, Italy.

Thioesters are important in synthesis, materials science, and biology, and their preparation traditionally relies on the use of disagreeable thiols. Here, we report a thiol-free protocol that stitches together widespread carboxylic acids and aryl halides, producing a diverse array of thioesters. Crucial to this strategy is the discovery that tetramethylthiourea can serve as both a sulfur source and, upon direct excitation by purple light, as a strong reductant, suitable for activating aryl halides via single-electron transfer.

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