Biology subjects

Jimenez, R.

Publications and source records attributed to Jimenez, R..

12 recordsLinked to original sources

bioRxiv2026

Dark state-mediated photobleaching in mCherry-basedred fluorescent proteins

Developing bright and photostable red fluorescent proteins (RFPs) is one of the holy grails of the protein engineering community. Despite several attempts, finding such fluorescent proteins (FPs) has remained elusive. One bottleneck to engineering next generation RFPs is our lack of understanding of non-fluorescent or dark state properties in such constructs. Here, we develop a theoretical and experimental framework that describes how photobleaching decays in FPs relates to dark state conversion and ground state recovery. Our systematic photophysical investigation of mCherry and mCherry-d, an RFP with enhanced dark state behavior, showed the presence of photodestructive dark states in such FPs. Molecular dynamics simulations reveal enhanced fluctuation around the imidazolinone-end of the chromophore in mCherry-d, potentially facilitating conversion to non-fluorescent states. Collectively, this work quantifies dark state kinetics and gives insights into engineering dark states in RFPs to develop bright yet photostable molecular probes.

biophysics↗

bioRxiv2025

Robust prediction of drug combination side effects in realistic settings

Side effects caused by drug combinations pose a major challenge in healthcare. Knowledge of these side effects is limited because often they are not detected in clinical trials, which typically involve a restricted number of participants and tested drug combinations. We introduce DCSE (Drug Combinations Side Effects), a novel machine learning method for predicting polypharmacy side effects. DCSE learns latent signatures for drugs, drug pairs, and side effects to predict the probability that a side effect occurs in a given drug combination. We first evaluate its performance in the commonly adopted experimental settings in the literature. Then, a key contribution of this paper is the introduction of more realistic experimental settings that incorporate warm-start and cold-start scenarios under a prospective evaluation. Here, we attempt to predict side effects reported between 2009 and 2014 after training only on data available prior to that period. Our results indicate that DCSE consistently outperforms state-of-the-art methods, demonstrating its robustness and efficacy in real-world applications. Author summaryUnderstanding the risks of combining medications is a central problem in healthcare. Clinical trials rarely capture the full range of adverse reactions, and many side effects are identified only after drugs reach the market, leaving many possible drug combinations insufficiently tested. Computational approaches can help fill this gap by predicting which combinations are likely to cause specific side effects. Our approach works by learning signatures for both drugs and side effects, which can be thought of as representations that describe how drugs act and what is required to trigger a side effect. A key challenge is how to combine the signatures of two drugs into one representation for the pair. We show that simple linear models fail to capture the complexity of drug interactions, so we use a deep neural network to combine them in a non-linear way. Our tests, which use reports collected at different points in time to mirror how information about drug pairs becomes available, show that our approach is useful for monitoring risks after drugs have been approved and for exploring new uses of pairs of existing drugs.

bioinformatics↗

bioRxiv2024

Sox9 prevents retinal degeneration and is required for limbal stem cell differentiation in the adult mouse eye

Sox9 is a transcription factor with multiple roles during development and in adult organ homeostasis. In the adult eye, Sox9 expression persists in several cell types, including the retinal pigmented epithelium cells and the Muller glial cells, as well as in the limbal and corneal basal epithelia. To uncover the role of Sox9 in these cell types, we induced the deletion of the gene in adult mice. We found that, after Sox9 ablation, mutant mice undergo a severe process of retinal degeneration characterized by the loss of Muller glial cells and complete depletion of the photoreceptors layer. Moreover, by combining single-cell RNA sequencing and Sox9 lineage tracing, we found that Sox9 is expressed in a basal limbal stem cell population with the ability to form two types of long-lived cell clones involved in stem cell maintenance and homeostasis. Mosaic analysis of Sox9 positive and negative cells confirmed that the gene is essential for limbal stem cell differentiation. Our results show that Sox9 is required for the maintenance of retinal integrity and for limbal stem cell differentiation in the adult mouse eye.

developmental biology↗

bioRxiv2023

Complete male-to-female sex reversal in XY mice lacking the miR-17~92 cluster

In mammals, sex determination is controlled by antagonistic gene cascades operating in embryonic undifferentiated gonads1 2. The expression of the Y-linked gene SRY is sufficient to trigger the testicular pathway, whereas its absence in XX embryos leads to ovarian differentiation3 4 5. Despite this strong genetic component, the involvement of non-coding regulation in determining mammalian sex remains unclear6. Here we show that the deletion of a single microRNA cluster, miR-17[~]92, induces complete primary male-to-female sex reversal in XY mice. Time-course analyses revealed that Sry is heterochronically expressed, showing a delay in XY miR-17[~]92 knockout gonads, which subsequently activate the ovarian genetic program. Bulk and single cell RNA-seq analyses showed that Sertoli cell differentiation is reduced, delayed and unable to sustain the testicular fate. This disrupted differentiation results from a transient state of sex ambiguity in pre-supporting cells, which is later resolved towards the ovarian fate. Consistent with known mechanisms of miRNA-mediated gene regulation, the expression of miR-17[~]92 target genes is not stabilized in undifferentiated XY mutant gonads, affecting concomitantly the fine regulation of gene networks with critical roles in developing gonads. Our results demonstrate that microRNAs are key components for mammalian sex determination, controlling the timing of Sry expression and Sertoli cell differentiation.

developmental biology↗

bioRxiv2022

Cell adhesion and immune response, two main functions altered in the transcriptome of seasonally regressed testes of two mammalian species

In species with seasonal breeding, male specimens undergo substantial testicular regression during the non-breeding period of the year. However, the molecular mechanisms that control this biological process are largely unknown. Here, we report a transcriptomic analysis on the Iberian mole, Talpa occidentalis, in which the desquamation of live, non-apoptotic germ cells is the major cellular event responsible for testis regression. By comparing testes at different reproductive states (active, regressing and inactive), we demonstrate that the molecular pathways controlling the cell adhesion function in the seminiferous epithelium, such as the MAPK, ERK and TGF-{beta} signalling, are altered during the regression process. In addition, inactive testes display a global upregulation of genes associated with immune response, indicating a selective loss of the "immune privilege" that normally operates in sexually active testes. Interspecies comparative analyses using analogous data from the Mediterranean pine vole, a rodent species where testis regression is controlled by halting meiosis entry, revealed a common gene expression signature in the regressed testes of these two evolutionary distant species. Our study advances in the knowledge of the molecular mechanisms associated to gonadal seasonal breeding, highlighting the existence of a conserved transcriptional program of testis involution across mammalian clades. Research HighlightsBy comparing the trascriptomes of the testes from males of the iberian mole, Talpa occidentalis (order Eulipotyphla), captured at different stages of the seasonal breeding cycle of this species, we show that two main functions are altered during seasonal testis regression: cell adhesion and immune response. The fact that the same functions alre also altered in the Mediterranean pine vole, Microtus duodecimcostatus (order Rodentia), evidences the existence of a conserved transcriptional program of testis regression across mammalian clades.

molecular biology↗

bioRxiv2021

Phenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria

Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central to defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multi-locus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which still harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors.

microbiology↗

bioRxiv2021

Interpretable Drug Target Predictions using Self-Expressiveness

The identification of missing drug targets is critical for the development of treatments and for the molecular elucidation of drug side effects. Drug targets have been predicted by exploiting molecular, biological or pharmacological features of drugs and protein targets. Yet, developing integrative and interpretable machine learning models for predicting drug targets remains a challenging task. We present Inception, an integrative and interpretable matrix completion model for predicting drug targets. Inception is a self-expressive model that learns two similarity matrices: one for drugs and another for protein targets. These learned similarity matrices are key for our models interpretability: they can explain how a predicted drug-target interaction can be explain in terms of a linear combination of chemical, biological and pharmacological similarities. We develop a novel objective function with efficient closed-form solution. To demonstrate the ability of Inception at recovering missing drug-target interactions (DTIs), we perform cross-validation experiments with stringent controls of data imbalance, chemical similarities between drugs and sequence similarities between targets. We also assess the performance of our model using a simulated prospective approach. Having trained our model with DTIs from a snapshot 2011 of the DrugBank database, we test whether we could predict DTIs from a 2020 snapshot of DrugBank. Inception outperforms two state-of-the-art drug target prediction models in all the scenarios. This suggests that Inception could be useful for predicting missing drug target interactions while providing interpretable predictions.

bioinformatics↗

bioRxiv2020

Structure-guided point mutations on FusionRed produce a brighter red fluorescent protein

The development of fluorescent proteins (FPs) has revolutionized biological imaging. FusionRed, a monomeric red FP (RFP), is known for its low cytotoxicity and appropriate localization of target fusion proteins in mammalian cells but is limited in application by low fluorescence brightness. We report a brighter variant of FusionRed, FusionRed-MQV, which exhibits an extended fluorescence lifetime (2.8 ns), enhanced quantum yield (0.53), higher extinction coefficient (~140,000 M-1cm-1), increased radiative rate constant and reduced non-radiative rate constant with respect to its precursor. The properties of FusionRed-MQV derive from three mutations - M42Q, C159V and the previously identified L175M. A structure-guided approach was used to identify and mutate candidate residues around the phenol and the acylimine ends of the chromophore. The C159V mutation was identified via lifetime-based flow cytometry screening of a library in which multiple residues adjacent to the phenol end of the chromophore were mutated. The M42Q mutation is located near the acylimine end of the chromophore and was discovered using site-directed mutagenesis guided by x-ray crystal structures. FusionRed-MQV exhibits 3.4-fold higher molecular brightness and a 5-fold increase in the cellular brightness in HeLa cells (based on FACS) compared to FusionRed. It also retains the low cytotoxicity and high-fidelity localization of FusionRed, as demonstrated through assays in mammalian cells.

biophysics↗

bioRxiv2020

Intracranial recordings demonstrate medial temporal lobe engagement in visual search in humans

Visual search is a fundamental human behavior, which has been proposed to include two component processes: inefficient search (Search) and efficient search (Pop-out). According to extant research, these two processes map onto two separable neural systems located in the frontal and parietal association cortices. In the present study, we use intracranial recordings from 23 participants to delineate the neural correlates of Search and Pop-out with an unprecedented combination of spatiotemporal resolution and coverage across cortical and subcortical structures. First, we demonstrate a role for the medial temporal lobe in visual search, on par with engagement in frontal and parietal association cortex. Second, we show a gradient of increasing engagement over anatomical space from dorsal to ventral lateral frontal cortex. Third, we confirm previous work demonstrating nearly complete overlap in neural engagement across cortical regions in Search and Pop-out. We further demonstrate Pop-out selectivity manifesting as activity increase in Pop-out as compared to Search in a distributed set of sites including frontal cortex. This result is at odds with the view that Pop-out is implemented in low-level visual cortex or parietal cortex alone. Finally, we affirm a central role for the right lateral frontal cortex in Search.

neuroscience↗

bioRxiv2019

Unexpected sound omissions are signaled in human posterior superior temporal gyrus: an intracranial study

Context modulates sensory neural activations enhancing perceptual and behavioral performance and reducing prediction errors. However, the mechanism of when and where these high-level expectations act on sensory processing is unclear. Here, we isolate the effect of expectation absent any auditory evoked activity by assessing the response to omitted expected sounds. Electrophysiological signals were recorded directly from the superior temporal gyrus (STG) and superior temporal sulcus (STS) in patients with medically refractory epilepsy. Subjects listened to a predictable sequence of syllables, with some infrequently omitted. We found a high frequency band (HFB, 70-150Hz) response to omissions, which overlap with a posterior subset of auditory active electrodes. This response is distinct from omission activations observed in non-auditory selective sites in STG. Heard syllables could be classified reliably from STG, but not the identity of the omitted stimulus. Both omission- and target detection activations were also observed in prefrontal cortex.\n\nWe propose that the posterior STG and STS are central for implementing predictions in the auditory environment. HFB omission activations in this region appear to index mismatch-signaling or salience detection processes.

neuroscience↗

bioRxiv2017

Identifiers for the 21st century:How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

In many disciplines, data is highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline ten lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers; we also outline important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

bioinformatics↗

bioRxiv2017

Uniform Resolution of Compact Identifiers for Biomedical Data

Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement data citation in accordance with widely accepted principles. Local accessions may however be prefixed with a namespace identifier, providing global uniqueness. Such \"compact identifiers\" have been widely used in biomedical informatics to support global resource identification with local identifier assignment.\n\nWe report here on our project to provide robust support for machine-resolvable, persistent compact identifiers in biomedical data citation, by harmonizing the Identifiers.org and N2T.net (Name-To-Thing) meta-resolvers and extending their capabilities. Identifiers.org services hosted at the European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), and N2T.net services hosted at the California Digital Library (CDL), can now resolve any given identifier from over 600 source databases to its original source on the Web, using a common registry of prefix-based redirection rules.\n\nWe believe these services will be of significant help to publishers and others implementing persistent, machine-resolvable citation of research data.

bioinformatics↗