Biology subjects

Ramirez, J.

Publications and source records attributed to Ramirez, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Three annotated tiger beetle genomes (Coleoptera, Adephaga, Cicindelidae)

Advances and accessibility to next-generation technology provide opportunities to sequence non-model organisms. Despite this increase in whole-genome sequencing data, annotation and the production of reference genomes remain limited. Reference genomes are a critical tool for a variety of studies in evolutionary biology, functional genomics, and conservation genetics. Tiger beetles (Cicindelidae) are a diverse and globally distributed family of beetles that serve as bioindicator taxa and flagship species for insect conservation. Here, we report highly complete, contiguous, and annotated genome assemblies representing draft reference genomes for three species of tiger beetle spanning the phylogeny. These draft reference genomes are for Audouins night-stalking tiger beetle, Omus audouini; the montane giant tiger beetle, Amblycheila baroni; and the western red-bellied tiger beetle, Cicindelidia sedecimpunctata. Article SummaryTiger beetles are a charismatic group with [~]3000 species distributed globally. Despite their popularity among insect enthusiasts and their role as bioindicators of ecosystem health, the group currently lacks a reference genome. This article outlines genome assembly and annotation for three tiger beetle species that span evolutionary relationships within the lineage. Quality control analyses show that the assemblies are reference quality and demonstrate high contiguity, completeness, and accuracy. The resulting draft genome annotations will be a valuable resource for scientific endeavors and allow for continued research on tiger beetles and their allies.

genomics↗

bioRxiv2026

Record-breaking wildfire intensity and nocturnal spread during the extreme 2025 wildfire season in Southwestern Europe: causes and impacts

Southwestern Europe faced an extreme wildfire season in 2025, with nearly 700,000 hectares burned in the Iberian Peninsula (IP) alone. Here, we analyze the drivers and impacts of the 2025 wildfire season in the IP and its significance within the ongoing global pyrocrisis. Decades-long declines in burned area, driven by increased fire suppression, ceased after an inflection point in 2022. Fire intensity has escalated over the last two decades, and the energy emitted in 2025 approached that produced annually by a 1,000MW nuclear reactor. Despite a historically wet spring, an extreme summer heatwave triggered a flash drought, dehydrating fuels below critical thresholds. Remarkably, 29-42% of all wildfires spread faster at night than during the day, a seldom-reported phenomenon likely arising from interactions between surface weather, atmospheric instability, and pyroconvective processes. Global change-induced increases in fire intensity facilitated the overwhelming of suppression efforts during simultaneous fire events that may have been manageable decades ago. Fire activity expanded into previously fire-free high-altitude regions, and there was a marked change in fire-size distributions, with the largest wildfire in record and the largest proportion of burned area by megafires (those burning over 5,000ha). Impacts included over 2,000 premature deaths from smoke exposure and significant effects on protected areas. These results indicate shifts in key components of anthropogenic fire regimes, including unprecedented nocturnal fire acceleration and increased burned area and fire intensity, with escalating impacts on human health and ecosystems.

ecology↗

bioRxiv2026

δ-catenin controls layer-specific transcriptional maturation of astrocytes via Zbtb20

Coordinated maturation of diverse neural cell types drives mammalian cortical circuit development. Disruption of this coordination is a hallmark of human neurodevelopmental disorders, yet mechanisms that synchronize transcriptional maturation across cell types remain poorly understood. Here, we identify {delta}-catenin (Ctnnd2), a component of adherens junctions, that links cell-cell interactions to transcriptional regulation. Using single-nucleus and spatial transcriptomics, we show that {delta}-catenin loss disrupts transcriptional maturation across neural cell types, particularly in astrocytes. {delta}-catenin loss impairs acquisition of layer-specific astrocyte identities and prolongs ocular dominance plasticity, indicating impaired circuit stabilization. Mechanistically, we identify the BTB/POZ transcription factor Zbtb20, which is enriched in glial cells, as a key regulator of this process. {delta}-catenin loss increases Zbtb20 expression, redistributes its genome-wide binding, and dysregulates its target genes. Together, these findings support a model in which {delta}-catenin regulates Zbtb20-dependent transcriptional programs to establish layer-specific astrocyte identities in coordination with developing cortical circuits. SUMMARYSejourne et al report that loss of the adherens junction protein {delta}-catenin prolongs ocular dominance plasticity and disrupts astrocyte and oligodendrocyte transcriptional identity. The underlying mechanism seems to rely on the glia-enriched transcription factor Zbtb20, which is upregulated and redistributed upon {delta}-catenin loss, resulting in altered expression of its target genes.

cell biology↗

bioRxiv2025

PKC-dependent MYRF dysregulation links Aβ pathology to oligodendrocyte, myelin and cognitive alterations in Alzheimer's disease

Alzheimers disease (AD) is characterized not only by neuronal loss and synaptic dysfunction but also by emerging evidence of oligodendrocyte and myelin pathology. Amyloid-{beta} (A{beta}), a hallmark of AD, disrupts oligodendrocyte homeostasis through mechanisms that remain poorly understood. Here, we investigated the role of the myelin regulatory factor (MYRF), a transcription factor essential for oligodendrocyte maturation, in AD-related glial dysfunction. Using the 3xTg-AD mouse model, we observed aberrantly induced maturation dynamics and reduced oligodendrocyte lineage cell density at 12 months in the dentate gyrus, accompanied by increased MYRF expression. Interestingly, sustained MYRF overexpression was found to be toxic for oligodendrocytes in vitro. Moreover, in vitro and in vivo experiments further demonstrated that A{beta} exposure elevates MYRF protein levels and enhances its transcriptional activity, pointing to post-translational regulation. Mechanistically, A{beta} impaired GSK3-dependent phosphorylation and Fbxw7-mediated ubiquitination of MYRF, prolonging N-MYRF stability, an effect prevented by PKC inhibition in vitro. Intracerebroventricular infusion of PKC inhibitor Go6983 normalized MYRF levels, restored oligodendrocyte populations and myelin integrity, and improved hippocampal-dependent spatial learning in 3xTg-AD mice, with locomotor activity and anxiety-like behavior remaining unaffected. Together, these findings identify MYRF dysregulation as a mechanistic link between A{beta}/PKC signaling and oligodendrocyte pathology, and highlight PKC inhibition as a potential strategy to restore oligodendroglial function and cognition in AD.

neuroscience↗

bioRxiv2025

A secreted fatty acid- and retinol- binding protein from Heligmosomoides polygyrus suppresses host macrophage polarization

Parasitic nematodes are major pathogens of humans, animals, and plants, contributing to global health challenges and substantial agricultural losses. Fatty acid- and retinol-binding proteins (FARs), secreted by parasitic nematodes, are believed to play key roles in host-pathogen interactions, including immune modulation and nutrient acquisition. In this study, we characterize a FAR protein from the gastrointestinal nematode Heligmosomoides polygyrus, Hp-FAR-2. Unlike FARs from Caenorhabditis elegans, Steinernema carpocapsae, and Ancylostoma ceylanicum, Hp-FAR-2 did not influence immunity or survival in a Drosophila melanogaster infection model, suggesting functional divergence within the FAR family. Competitive lipid-binding assays revealed a preference for omega-3 and omega-6 polyunsaturated fatty acids, indicating selective binding to bioactive lipids that may modulate immunity. Using RAW 264.7 macrophages, we found that Hp-FAR-2 suppresses the expression of both M1-associated (TNF-, IL-6) and M2-associated (Chil3) markers during polarization, implicating it as a broad immunomodulator that may inhibit inflammatory responses and tissue repair mechanisms to promote chronic infection. Our findings support a model in which Hp-FAR-2 disrupts host lipid signaling and immune function to favor parasite persistence, suggesting its potential role in the excretory/secretory products of H. polygyrus. Together, these data enhance our understanding of FAR-mediated host manipulation and may inform the development of novel anthelmintic or immunoregulatory therapies.

biochemistry↗

bioRxiv2025

Genetic Code Expansion and Enzymatic Modifications as Accessible Methods for Studying Site-Specific Post-Translational Modifications of Alpha-Synuclein and Tau

Alpha-synuclein (S) and tau play important roles in the pathology of Parkinsons Disease and Alzheimers Disease, respectively, as well as numerous other neurodegenerative diseases. Both proteins are classified as intrinsically disordered proteins (IDPs), as they have no stable structure that underlies their function in healthy tissue, and both proteins are prone to aggregation in disease states. There is substantial interest in understanding the roles that post-translational modifications (PTMs) play in regulating the structural dynamics and function of S and tau monomers, as well as their propensity to aggregate. While there have been many valuable insights into site-specific effects of PTMs garnered through chemical synthesis and semi-synthesis, these techniques are often outside of the expertise of biochemistry and biophysics laboratories wishing to study S and tau. Therefore, we have assembled a primer on genetic code expansion and enzymatic modification approaches to installing PTMs into S and tau site-specifically, including isotopic labeling for NMR and fluorescent labeling for biophysics and microscopy experiments. These methods should be enabling for those wishing to study authentic PTMs in S or tau as well as the broader field of IDPs and aggregating proteins.

biochemistry↗

bioRxiv2025

Investigation of All Disease-Relevant Lysine Acetylation Sites in α-Synuclein Enabled by Non-canonical Amino Acid Mutagenesis

Aggregates of -synuclein (S) are hallmarks of synucleinopathies, including Parkinsons Disease (PD) and Multiple System Atrophy (MSA). We have recently shown that S lysine acetylation in the soluble monomer pool varies between healthy controls, PD, and MSA patients. We used non-canonical amino acid (ncAA) mutagenesis to express and purify all 12 currently known disease-relevant variants of S and studied their binding to membranes as well as their aggregation propensities. We found that acetylation of lysine 12, 43, and 80 had particularly strong effects. To understand the implications for acetylation of monomeric S found in healthy cells, we performed NMR experiments to study protein conformation and fluorescence correlation spectroscopy experiments to quantify lipid binding. We also investigated the effects of acetylation at lysine 12, 43, and 80 on fibril seeding in neurons. Collectively, our biochemical and cell biological investigations indicated that acetylation of K80 could inhibit aggregation without conferring negative effects on monomer function in healthy cells. Therefore, we studied the structures of fibrils with K80 acetylation through cryo-electron microscopy to uncover the structural basis for these effects. Finally, we identified inhibition of HDAC8 as a way of potentially increasing acetylation at K80 and other inhibitory sites for therapeutic benefit.

biochemistry↗

bioRxiv2024

Fbxo42 promotes the degradation of Ataxin-2 granules to trigger terminal Xbp1 signaling

The Unfolded Protein Response (UPR) is composed by homeostatic signaling pathways that are activated by the accumulation of misfolded proteins in the Endoplasmic Reticulum (ER), a condition known as ER stress. Prolonged ER stress and activation of the UPR causes cell death, by mechanisms that remain poorly understood. Here, we report that regulation of Ataxin-2 by Fbxo42 is a crucial step during UPR-induced cell death. From a genetic screen in Drosophila, we identified loss of function mutations in Fbxo42 that suppress cell death and retinal degeneration induced by the overexpression of Xbp1spliced, an important mediator of the UPR. We identified the RNA binding protein Ataxin-2 as a substrate of Fbxo42, which, as part of a Skp-A/Cullin-1 complex, promotes the ubiquitylation and degradation of Ataxin-2. Upon ER-stress, the mRNA of Xbp1 is not immediately translated but instead it is sequestered and stabilized in Ataxin-2 granules, until the Fbxo42 recruitment to these granules promotes the degradation of Ataxin-2, allowing the translation of Xbp1 mRNA at later stages of UPR activation. Our results identify Fbxo42-mediated degradation of Ataxin-2 as a key mechanism regulating the levels of Xbp1 mRNA and protein, to trigger cell death during the terminal stages of UPR activation.

cell biology↗

bioRxiv2024

Data-driven insights into the association between oxidative stress and calcium-regulating proteins in cardiovascular disease.

A growing body of biomedical literature suggests a bidirectional regulatory relationship between cardiac calcium (Ca2+)-regulating proteins and reactive oxygen species (ROS), which is integral to the pathogenesis of various cardiac disorders via oxidative stress signaling. To address the challenge of finding hidden connections within the growing volume of biomedical research, we developed a data science pipeline for efficient data extraction, transformation, and loading. Employing the CaseOLAP (Context-Aware Semantic Analytic Processing) algorithm, our pipeline quantifies interactions between 128 human cardiomyocyte Ca2+-regulating proteins and eight cardiovascular disease (CVD) categories. Our machine learning analysis of CaseOLAP scores reveals that the molecular interfaces of Ca2+-regulating proteins uniquely associate with cardiac arrhythmias and diseases of the cardiac conduction system, distinguishing them from other CVDs. Additionally, a knowledge graph analysis identified 59 of the 128 Ca2+-regulating proteins as involved in OS-related cardiac diseases, with cardiomyopathy emerging as the predominant category. By leveraging a link prediction algorithm, our research illuminates interactions between Ca2+-regulating proteins, OS, and CVDs. The insights gained from our study provide a deeper understanding of the molecular interplay between cardiac ROS and Ca2+-regulating proteins in the context of CVDs. Such understanding is essential for the innovation and development of targeted therapeutic strategies.

bioinformatics↗

bioRxiv2024

Chemically-informed coarse-graining of electrostatic forces in charge-richbiomolecular condensates

Biomolecular condensates composed of highly charged biomolecules like DNA, RNA, chromatin, and nucleic-acid binding proteins are ubiquitous in the cell nucleus. The biophysical properties of these charge-rich condensates are largely regulated by electrostatic interactions. Residue-resolution coarse-grained models that describe solvent and ions implicitly are widely used to gain mechanistic insights into the biophysical properties of condensates, offering transferability, computational efficiency, and accurate predictions for many systems. However, their predictive accuracy diminishes for charge-rich condensates due to the implicit treatment of solvent and ions. Here, we present the Mpipi-Recharged model, a residue-resolution coarse-grained model that improves the description of charge effects in biomolecular condensates containing disordered proteins, multi-domain proteins, and/or disordered RNAs. Mpipi-Recharged maintains the computational efficiency of its predecessor--the Mpipi model--by still treating solvent and ions implicitly, but improves its accuracy by incorporating a pair-specific asymmetric electrostatic potential informed by atomistic simulations in explicit solvent and ions. We show that such asymmetric coarse-graining of electrostatic forces is needed to recapitulate the stronger mean-field impact of associative interactions between opposite-charge pairs over the repulsion among equally charged pairs revealed by our atomistic simulations. Mpipi-Recharged shows excellent agreement with the experimental phase behavior of highly charged systems, capturing subtle effects challenging to model without explicit solvation, such as the impact of charge blockiness, stoichiometry changes, and salt concentration variation. By offering improved predictions for charge-rich biomolecular condensates, Mpipi-Recharged extends the computational tools available to investigate the physicochemical mechanisms regulating biomolecular condensates.

biophysics↗

bioRxiv2023

Virulence and transmission biology of the widespread, ecologically important pathogen of zooplankton, Spirobacillus cienkowskii

Spirobacillus cienkowskii (Spirobacillus, hereafter) is a widely distributed bacterial pathogen that has significant impacts on the population dynamics of zooplankton (Daphnia spp.), particularly in months when Daphnia are asexually reproducing. Yet little is known about Spirobacillus virulence, transmission mode and dynamics. As a result, we cannot explain the dynamics of Spirobacillus epidemics in nature or use Spirobacillus as a model pathogen, despite Daphnias tractability as a model-host. Here, we work to fill these knowledge gaps experimentally. We found that Spirobacillus is among the most virulent of Daphnia pathogens, killing its host within a week and reducing host fecundity. We further found that Spirobacillus did not transmit horizontally among hosts unless the host died or was destroyed (i.e., it is an "obligate killer"). In experiments aimed at quantifying the dynamics of horizontal transmission among asexually reproducing Daphnia, we demonstrated that Spirobacillus transmits poorly in the laboratory. In mesocosms, Spirobacillus failed to generate epidemics; in experiments wherein individual Daphnia were exposed, Spirobacillus transmission success was low. In the (limited) set of conditions we considered, Spirobacillus transmission success did not change with host density or pathogen dose and declined following environmental incubation. Lastly, we conducted a field survey of Spirobacillus prevalence within egg-cases (ephippia) made by sexually reproducing Daphnia. We found Spirobacillus DNA in [~]40% of ephippia, suggesting that, in addition to transmitting horizontally among asexually reproducing Daphnia, Spirobacillus may transmit vertically from sexually reproducing Daphnia. Our work fills critical gaps in the biology of Spirobacillus and illuminates new hypotheses vis-a-vis its life-history. ImportanceSpirobacillus cienkowskii is a bacterial pathogen of zooplankton, first described in the 19th Century and recently placed in a new family of bacteria, the Silvanigrellaceae. Spirobacillus causes epidemics in lake zooplankton populations and increases the probability that zooplankton will be eaten by predators. However, little is known about how Spirobacillus transmits among hosts, its impact on host survival and reproduction (i.e., how virulent it is) in laboratory conditions and what role virulence plays in Spirobacillus life cycle. Here, we experimentally quantified Spirobacillus virulence and showed that Spirobacillus must kill its host to transmit horizontally. We also found evidence that Spirobacillus may transmit vertically via Daphnias seed-like egg cases. Our work will help scientists to (i) understand Spirobacillus epidemics, (ii) use Spirobacillus as a model pathogen for the study of host-parasite interactions and (iii) better understand the unusual group of bacteria to which Spirobacillus belongs.

microbiology↗

bioRxiv2023

In-vitro reconstitution of Herpes Simplex Virus 1 fusion identifies low pH as a fusion co-trigger

Membrane fusion mediated by Herpes Simplex virus 1 (HSV-1) is a complex, multi-protein process that is receptor-triggered and can occur both at the cell surface and in endosomes. To deconvolute this complexity, we reconstituted HSV-1 fusion with synthetic lipid vesicles in vitro. Using this simplified, controllable system, we discovered that HSV-1 fusion required not only a cognate host receptor but also low pH. On the target membrane side, efficient fusion required cholesterol, negatively charged lipids found in the endosomal membranes, and an optimal balance of lipid order and disorder. On the virion side, the four HSV-1 entry glycoproteins gB, gD, gH, and gL were sufficient for fusion. We propose that low pH is a biologically relevant co-trigger for HSV-1 fusion. The dependence of fusion on low pH and endosomal lipids could explain why HSV-1 enters most cell types by endocytosis. We hypothesize that under neutral pH conditions, other, yet undefined, cellular factors may serve as fusion co-triggers. The in-vitro fusion system established here can be employed to systematically investigate HSV-1-mediated membrane fusion. IMPORTANCEHerpes simplex virus 1 (HSV-1) causes life-long, incurable infections and diseases ranging from mucocutaneous lesions to fatal encephalitis. Fusion of viral and host membranes is a critical step in HSV-1 infection of target cells that requires multiple factors on both the viral and host sides. Due to this complexity, many fundamental questions remain unanswered, such as the viral and host factors that are necessary and sufficient for HSV-1-mediated membrane fusion and the nature of the fusion trigger. Here, we developed a simplified in-vitro fusion assay to examine the fusion requirements and identified low pH as a co-trigger for virus-mediated fusion in vitro. We hypothesize that low pH has a critical role in cell entry and, potentially, pathogenesis.

microbiology↗

bioRxiv2023

SynBot: An open-source image analysis software for automated quantification of synapses

The formation of precise numbers of neuronal connections, known as synapses, is crucial for brain function. Therefore, synaptogenesis mechanisms have been one of the main focuses of neuroscience. Immunohistochemistry is a common tool for visualizing synapses. Thus, quantifying the numbers of synapses from light microscopy images enables screening the impacts of experimental manipulations on synapse development. Despite its utility, this approach is paired with low throughput analysis methods that are challenging to learn and results are variable between experimenters, especially when analyzing noisy images of brain tissue. We developed an open-source ImageJ-based software, SynBot, to address these technical bottlenecks by automating the analysis. SynBot incorporates the advanced algorithms ilastik and SynQuant for accurate thresholding for synaptic puncta identification, and the code can easily be modified by users. The use of this software will allow for rapid and reproducible screening of synaptic phenotypes in healthy and diseased nervous systems. MotivationLight microscopy imaging of pre- and post-synaptic proteins from neurons in tissue or in vitro allows for the effective identification of synaptic structures. Previous methods for quantitative analysis of these images were time-consuming, required extensive user training, and the source code could not be easily modified. Here, we describe SynBot, a new open-source tool that automates the synapse quantification process, decreases the requirement for user training, and allows for easy modifications to the code.

neuroscience↗

bioRxiv2023

Nanomolar interactions of alpha-synuclein fibrils to tau determined by FCS

Age-related neurodegenerative disorders like Alzheimers disease (AD) and Parkinsons disease (PD) are characterized by deposits of protein aggregates, or amyloid, in various regions of the brain. Traditionally, aggregation of a single protein was observed to be correlated with these different pathologies: tau in AD and -synuclein (S) in PD. However, there is increasing evidence that the pathologies of these two diseases overlap, and the individual proteins may promote each others aggregation. Both tau and S are intrinsically disordered proteins (IDPs), lacking stable secondary and tertiary structure under physiological conditions. In this study we used a combination of biochemical and biophysical techniques to interrogate the interaction of tau with both soluble and fibrillar S. Fluorescence correlation spectroscopy (FCS) was used to assess the interactions of specific domains of fluorescently labeled tau with full length and C-terminally truncated S in both monomeric and fibrillar forms. We found that full-length tau as well as individual tau domains interact with monomer S weakly, but this interaction is much more pronounced with S seeds. This interaction does not impact tau aggregation or fibril formation. These findings provide insight into the nature of interactions between tau and S as well as the domains responsible.

biochemistry↗

bioRxiv2023

Integration of genetic fine-mapping and multi-omics data reveals candidate effector genes for hypertension

Genome-wide association studies of blood pressure (BP) have identified >1000 loci but the effector genes and biological pathways at these loci are mostly unknown. Using published meta-analysis summary statistics, we conducted annotation-informed fine-mapping incorporating tissue-specific chromatin segmentation to identify causal variants and candidate effector genes for systolic BP, diastolic BP, and pulse pressure. We observed 532 distinct signals associated with [≥]2 BP traits and 84 with all three. For >20% of signals, a single variant accounted for >75% posterior probability, 65 were missense variants in known (SLC39A8, ADRB2, DBH) and previously unreported BP candidate genes (NRIP1, MMP14). In disease-relevant tissues, we colocalized >80 and >400 distinct signals for each BP trait with cis-eQTLs, and regulatory regions from promoter capture Hi-C, respectively. Integrating mouse, human disorder, tissue expression data and literature review, we provide consolidated evidence for 394 BP candidate genes for future functional validation and identifies several new drug targets.

genetics↗

bioRxiv2022

Reordering of aromatic-rich segments in FUS inhibits ageing of FUS-RNA condensates

Maturation of functional liquid-like biomolecular condensates into solid-like aggregates has been linked to the onset of several neurodegenerative disorders. Low-complexity aromatic-rich kinked segments (LARKS) contained in numerous RNA-binding proteins can promote aggregation by forming inter-protein {beta}-sheet fibrils that accumulate over time and ultimately drive the liquid-to-solid transition of the condensates. Here, we combine atomistic molecular dynamics simulations with sequence-dependent coarse-grained models of various resolutions to investigate the role of LARKS abundance and position within the amino acid sequence in the maturation of condensates. Remarkably, proteins with tail-located LARKS display much higher viscosity over time than those in which the LARKS are placed towards the center. Yet, at very long timescales, proteins with a single LARKS--independently of its location--can still relax and behave as high viscous liquids. However, phase-separated condensates of proteins containing two or more LARKS become kinetically trapped due to the formation of percolated {beta}-sheet networks that display gel-like behaviour. Furthermore, as a work case example, we demonstrate how shifting the location of the LARKS-containing low-complexity domain of FUS protein towards its center effectively precludes the accumulation of {beta}-sheet fibrils in FUS-RNA condensates, maintaining functional liquid-like behaviour without ageing.

biophysics↗

bioRxiv2022

Time-dependent material properties of ageing biomolecular condensates from different viscoelasticity measurements in molecular dynamics simulations

Biomolecular condensates are important contributors to the internal organization of the cell material. While initially described as liquid-like droplets, the term biomolecular condensates is now used to describe a diversity of condensed phase assemblies with material properties extending from low to high viscous liquids, gels, and even glasses. Because the material properties of condensates are determined by the intrinsic behaviour of their molecules, characterising such properties is integral to rationalising the molecular mechanisms that dictate their functions and roles in health and disease. Here, we apply and compare three distinct computational methods to measure the viscoelasticity of biomolecular condensates in molecular simulations. These methods are the shear stress relaxation modulus integration (SSRMI), the oscillatory shear (OS) technique, and the bead tracking (BT) method. We find that, although all of these methods provide consistent results for the viscosity of the condensates, the SSRMI and OS techniques outperform the BT method in terms of computational efficiency and statistical uncertainty. We, thus, apply the SSRMI and OS techniques for a set of 12 different protein/RNA systems using a sequence-dependent high-resolution coarse-grained model. Our results reveal a strong correlation between condensate viscosity and density, as well as with protein/RNA length and the number of stickers vs. spacers in the amino-acid protein sequence. Moreover, we couple the SSRMI and the OS technique to nonequilibrium molecular dynamics simulations that mimic the progressive liquid-to-gel transition of protein condensates due to the accumulation of inter-protein {beta}-sheets. We compare the behaviour of three different protein condensates--i.e., those formed by either hnRNPA1, FUS, or TDP-43 proteins--whose liquid-to-gel transitions are associated with the onset of amyotrophic lateral sclerosis and frontotemporal dementia. We find that both SSRMI and OS techniques successfully predict the transition from functional liquid-like behaviour to kinetically arrested states once the network of inter-protein {beta}-sheets has percolated through the condensates. Overall, our work provides a comparison of different modelling rheological techniques to assess the viscosity of biomolecular condensates, a critical magnitude that provides information on the behaviour of biomolecules inside condensates.

biophysics↗

bioRxiv2022

Tissue-specific overexpression of the double-stranded RNA transporter SID-1 limits lifespan in C. elegans

Intertissue RNA transport has emerged as a novel signaling mechanism. In C. elegans, this is conferred by the systemic RNAi pathway, in which the limiting step is the cellular import of extracellular RNAs via SID-1. To better understand the physiological role of systemic RNAi in vivo, we modified the function of SID-1 through loss-of-function mutation and tissue-specific overexpression of sid-1 in C. elegans. We observed that sid-1 loss-of-function mutants are as healthy as wild-type worms. Conversely, overexpression of sid-1 in intestine, muscle, or neurons rendered worms short-lived. The effects of intestinal sid-1 overexpression were reversed by silencing the components of the systemic RNAi pathway sid-1, sid-2 and sid-5, thus implicating RNA transport. Moreover, silencing the miRNA biogenesis proteins pash-1 and dcr-1 rendered the lifespan of worms with intestinal sid-1 overexpression similar to controls. Lastly, we observed that the lifespan decrease produced by tissue-specific sid-1 overexpression was dependent on the bacterial food source. Collectively, our data support the notion that systemic RNA signaling is tightly regulated, and unbalancing that process provokes a reduction in lifespan.

molecular biology↗