bluuebunny/crossref_metadata_2025 huggingface dataset:
Cell-cell communication controls the timing of gastruloid symmetry-breaking
Authors: Oriola David , Torregrosa-Cortés Gabriel , Arató Krisztina , Fernández-Munuera David , Hahn Elisa Maria , Anlaş Kerim , Garcia-Ojalvo Jordi , Trivedi Vikas
Published: December 2024

In the embryo, morphogenetic signals instruct regional patterning thereby defining the body axes of the future animal. Remarkably, in the absence of such signals, collections of pluripotent stem cells can still self-organise and break symmetryin vitro. One such example is gastruloids, three-dimensional stem cell aggregates that form an anterior-posterior axis through the polarised expression of the gene Brachyury/T. How robust and reproducible cell proportions are achieved in these self-organised embryo-like structures is not understood. Here, through quantitative experiments and theoretical modelling, we dissect tissue rheology and cellular feedback in gastruloids. We show that the initial population of Brachyury-expressing cells critically influences the timing of symmetry-breaking. We propose a cell differentiation model, whereby pluripotent cells inhibit mesoderm differentiation, accounting for the observed cell fate dynamics. Our findings suggest that cell-cell communication dictates temporal cell proportions, while differential tissue mechanics governs spatial pole formation. Our work highlights the importance of initial cell heterogeneity in gastruloid development and offers a framework to identify feedback mechanisms in multicellular systems, advancing our understanding of how embryo-like structures self-organise.
Joining the Conversation with a Dedicated Medical Education Corpus
Authors: Ow Gregory M. , Stetson Geoffrey V. , Costello Joseph A. , Artino Anthony R. , Maggio Lauren A.
Published: December 2024

PROBLEM

Medical education scholars struggle to join ongoing conversations in their field due to the lack of a dedicated medical education corpus. Without such a corpus, scholars must either search too widely across thousands of irrelevant journals, or too narrowly by relying on PubMed’s Medical Subject Headings (MeSH). In our tests, MeSH missed 34% of medical education papers.

APPROACH

We developed the MEC (Medical Education Corpus), the first dedicated collection of medical education papers, through a three-step process. First, using the Core-Periphery model, we created the MEJ (Medical Education Journals), a collection of three groups of journals based on participation and influence in medical education discourse: the MEJ-Core (formerly the MEJ-24, 24 journals), MEJ-Adjacent (127 journals), and MEJ-Peripheral (a theoretical group). Second, we developed and evaluated a machine learning model, the MEC Classifier, trained on 4,032 manually labeled papers to identify medical education content. Finally, we applied the MEC Classifier to extract medical education papers from the MEJ-Core and MEJ-Adjacent journals.

OUTCOMES

The MEC currently contains 119,137 medical education papers from the MEJ-Core (54,927 papers) and MEJ-Adjacent journals (64,210 papers). In our evaluation using 1,358 test papers, the MEC Classifier demonstrated significantly improved sensitivity compared to MeSH (90% vs 66%,p= 0.001), even while maintaining a similar positive predictive value (82% vs 81%).

NEXT STEPS

The MEC provides a focused, searchable corpus that enables medical education scholars to more easily join conversations in the field. Scholars can now rely on the MEC when reviewing literature to frame their work, and the MEC also creates opportunities for field-wide analyses and meta-research. The MEC is freely available in the Supplement and is regularly updated on MedEdMentor (mededmentor.org), where we will also incorporate community feedback to further improve and expand the corpus.
Gene age shapes functional and evolutionary properties of theDrosophilaseminal fluid proteome
Authors: Ranz Jose M. , Flacchi Carolina , Hariyani Imtiyaz E. , Civetta Alberto
Published: December 2024

Seminal fluid proteins (Sfps) are crucial for animal reproductive success, with most Sfps-encoding genes believed to be evolutionarily young and rapidly evolving. By employing estimates of the phylogenetic origin of eachDrosophila melanogasterSfp gene based on genomic resources that include outgroup species to theDrosophilagenus, we examined the functional attributes and evolutionary characteristics of Sfp genes relative to their evolutionary age. Contrary to common belief, 62% of Sfp genes existed in the genome of the ancestor to such genus. These ancient genes have broadened their expression profiles, expanded their biological roles, and formed a denser network of interactions with non-Sfp genes. This increased pleiotropy has imposed constraints on the rate of sequence evolution in ancient Sfp genes compared to younger ones. Within the Sfp interactome, we identified a fast-evolving core sub-network of younger genes with more restricted tissue expression and functions. Our findings uncover a large, previously unrecognized set of ancient Sfp genes with distinct genomic, functional, and evolutionary characteristics compared to the younger, more commonly studied Sfp genes.
The TRX assay for triplet repeat expansions
Authors: O’Brien Thomas , Salciute Karolina , Kieffer Shaylee , Packil Ponraj Nehaa Kandasamy , Richer Madeleine , Marzec Paulina , Benn Caroline , Monckton Darren G. , Dion Vincent , Lahue Robert S.
Published: December 2024

Expansion mutations of triplet repeat sequences cause numerous inherited neurological diseases. In some diseases, affected individuals display somatic expansions in affected tissues which have been linked to accelerated disease onset and progression. There is currently considerable interest in developing therapies to slow somatic repeat expansions to delay or block disease onset.In vitroassays are particularly important to evaluate potential therapeutic interventions. Current assays typically use physical methods to monitor triplet repeat lengths within a population of cells. While useful, most of these assays are relatively slow (∼six weeks) and are somewhat limited in sensitivity to rare events. Here, a new assay, called TRX, is described to monitor CAG•CTG triplet repeat expansions more rapidly and with better sensitivity. TRX uses human tissue culture cells expressing two fluorescent proteins. Red fluorescent protein TagRFP658 is constitutively expressed and serves as an internal control. GFP is expressed in a CAG•CTG repeat length-dependent manner, with longer repeat lengths predicted to give higher green fluorescence intensity. Standard flow cytometry allows quantification of changes in fluorescent signal as a simple readout with <2% sensitivity. Two independently derived cell lines with 63 or 59 CAG repeats yielded similar rates of TRX activity. Cells with increased green fluorescence were observed within one to two weeks of culture, with longer times leading to additional signal. The appearance of green fluorescence was partly dependent on MutSβ, the DNA MSH2-MSH3 complex, based on siRNA knockdown of MSH3. However, physical analysis of the CAG•CTG repeat tracts by MiSeq deep sequencing or capillary electrophoresis showed limited changes in the length of the repeat tracts. We conclude that the TRX assay is a promising new tool for monitoring CAG•CTG repeat expansions but that further development of the assay is needed to make it fully useful.
Detection of triglyceride metabolism in white blood cells using a novel fluorescently labeled long chain fatty acid analogue
Authors: Hara Yasuhiro , Hirano Ken-ichi
Published: December 2024

123I-15-(p-iodophenyl)-(R,S)-methyl pentadecanoic acid (123I-BMIPP) is a long-chain fatty acid (LCFA) analog developed to examine myocardial LCFA metabolism and has been used as a tracer for nuclear cardiology. However, its use is limited because of the specialized features of cardiac scintigraphy. In this study, a novel BMIPP-based probe, in which iodine-123 was replaced with a fluorescent compound, was used to extend the application of123I-BMIPP toex vivoanalysis of fatty acid metabolism. To confirm that fluorescently labeled BMIPP-based probe (fluorescent BMPP) is effective for the detection of LCFA metabolismex vivo, we performed fluorescence-activated cell sorting (FACS) analysis for the incorporation of fluorescent BMPP using white blood cells from human peripheral blood. FACS analysis showed that the incorporation of fluorescent BMPP into white blood cells was dose-dependent. Fluorescence intensities of cells incorporating fluorescent BMPP were attenuated after incubation in non-fluorescent BMPP medium, suggesting that these cells could export the probe. Neutrophils from a patient with primary triglyceride deposit cardiomyovasculopathy, a rare type of triglyceride (TG) metabolism disorders, showed lower BMPP export and was ameliorated after treatment with tricaprin. These results suggest that fluorescent BMPP could be imported to and exported from cells through the same mechanism as123I-BMIPP, reflecting the mechanism that occurs for LCFAs during TG metabolism. This study shows that fluorescent BMPP has the potential to be used as a probe for the diagnosis of TG metabolic diseasesex vivo.
Oral and faecal viromes of New Zealand calves on pasture with an idiopathic ill-thrift syndrome
Authors: Grimwood Rebecca M. , Darnley Jessica A. , O’Connell John P. , Hunt Hayley , Taylor Harry S. , Lawrence Kevin E. , Abbott Michaela B. W. , Jauregui Ruy , Geoghegan Jemma L.
Published: December 2024

Since 2015, an idiopathic ill-thrift syndrome featuring diarrhoea and, in some cases, gastrointestinal ulceration has been reported in weaned New Zealand dairy calves. Similar syndromes have been described in the British Isles and Australia, but investigations in New Zealand have yet to identify a specific cause. Notably, the viromes of affected calves remain understudied. We conducted metatranscriptomic analyses of oral and faecal viromes in 11 calves from a dairy farm in Taranaki, New Zealand experiencing an outbreak of this syndrome. This included nine symptomatic calves. Our analysis identified 18 bovine-associated viruses across two DNA and three RNA viral families, including five novel species. Oral viromes were dominated byPseudocowpox virus, detected in all calves with oral lesions. Faecal viromes were more diverse, featuring adenoviruses, caliciviruses, astroviruses, and picornaviruses.Bovine bopivirus, from thePicornaviridaefamily and previously unreported in New Zealand, was significantly associated with calves showing oral lesions and diarrhoea, indicating a possible link to disease, though its role remains unclear. The diverse viral communities in the calves complicates identifying a single causative agent. Importantly, no novel viruses were significantly associated with the syndrome, and the viromes closely resembled those found in cattle globally. These findings suggest the syndrome likely has a multifactorial origin involving nutritional, management, and environmental factors rather than being driven primarily by known or novel viruses. Further research across regions and seasons is recommended to clarify the role of viruses in idiopathic ill-thrift among New Zealand calves.
DTPSP: A Deep Learning Framework for Optimized Time Point Selection in Time-Series Single-Cell Studies
Authors: Hijazin Michel , Shi Pumeng , Wang Jingtao , Ding Jun
Published: December 2024

Time-series studies are critical for uncovering dynamic biological processes, but achieving comprehensive profiling and resolution across multiple time points and modalities (multi-omics) remains challenging due to cost and scalability constraints. Current methods for studying temporal dynamics, whether at the bulk or single-cell level, often require extensive sampling, making it impractical to deeply profile all time points and modalities. To overcome these limitations, we present DTPSP, a deep learning framework designed to identify the most informative time points in any time-series study, enabling resource-efficient and targeted analyses. DTPSP models temporal gene expression patterns using readily obtainable data, such as bulk RNA-seq, to select time points that capture key system dynamics. It also integrates a deep generative module to infer data for non-sampled time points based on the selected time points, reconstructing the full temporal trajectory. This dual capability enables DTPSP to prioritize key time points for in-depth profiling, such as single-cell sequencing or multi-omics analyses, while filling gaps in the temporal landscape with high fidelity. We apply DTPSP to developmental and disease-associated time courses, demonstrating its ability to optimize experimental designs across bulk and single-cell studies. By reducing costs, enabling strategic multi-omics profiling, and enhancing biological insights, DTPSP provides a scalable and generalized solution for investigating dynamic systems.
Contribution of front-line, standard of care drugs to bactericidal responses, resistance emergence, and cure in murine models of easy- or hard-to-treat tuberculosis disease
Authors: Peroutka-Bigus Nathan , Brooks Elizabeth J. , Ramey Michelle E. , D’Erasmo Hope , Ernest Jacqueline P. , Bauman Allison A. , Woolhiser Lisa K , Savic Radojka M. , Lenaerts Anne J. , Aldridge Bree B. , Sarathy Jansy P. , Robertson Gregory T.
Published: December 2024

By assessing the standard of care regimen for tuberculosis (TB) in BALB/c and C3HeB/FeJ mice, we demonstrate that rifampin, with or without pyrazinamide, is essential to effective bactericidal response and resistance suppression. Potency measurements in anin vitrolipid-rich model and rabbit caseum assay recapitulate the significance of rifampin as a sterilizing agent. These outcomes align with clinical performance, thus emphasizing the value ofin vitropredictive tools and murine TB models with human-like pathology.
Quantum chemical properties of chlorinated polycyclic aromatic hydrocarbons for delta machine learning
Authors: Frolov Dmitry , Ibraev Ilya , Sedov Igor
Published: December 2024

Promising Δ-machine learning approaches aim to correct the values of molecular properties obtained with computationally inexpensive methods to the accuracy of higher levels of theory. Training such models requires datasets containing the results of calculations at several different levels of quantum chemical theory. While several large and chemically diverse datasets have been published, studies in many areas require specialized datasets of structurally related molecules. Chlorinated polycyclic aromatic hydrocarbons (Cl-PAHs), the products of incomplete combustion of organic substances and materials, are hazardous pollutants with carcinogenic and mutagenic activity. Quantum chemistry methods are important to understand their formation mechanisms and properties. We describe a dataset, PACHQA, containing the results of quantum chemical calculations including properties, geometries, wavefunctions, and electron densities for 3551 molecules including 3417 Cl-PAHs with up to 6 rings and a different number of chlorine atoms in their structure as well as 134 parent polycyclic aromatic hydrocarbons (PAHs). The major part of these molecules have previously not been included in any quantum chemical datasets. The calculations were performed at three different levels of theory including geometry optimization with GFN2-xTB and r2SCAN-3c methods and single-point energy calculation at ωB97X-D4/def2-TZVP DFT level. The dataset can be useful to develop and validate the computational, machine learning, or experimental, approaches and study the structure-property relationships for Cl-PAHs.
DNMT1 loss leads to hypermethylation of a subset of late replicating domains by DNMT3A
Authors: Kafetzopoulos Ioannis , Taglini Francesca , Davidson-Smith Hazel , Sproul Duncan
Published: December 2024

Loss of DNA methylation is a hallmark of cancer that is proposed to promote carcinogenesis through gene expression alterations, retrotransposon activation and induction of genomic instability. Cancer-associated hypomethylation does not occur across the whole genome but leads to the formation of partially methylated domains (PMDs). However, the mechanisms underpinning PMD formation remain unclear. PMDs replicate late in S-phase leading to the proposal that they become hypomethylated due to incomplete re-methylation by the maintenance methyltransferase DNMT1 during cell division. Here we investigate the role of DNMT1 in the formation of PMDs in cancer by conducting whole genome bisulfite sequencing (WGBS), repli-seq and ChIP-seq on DNMT1 knockout HCT116 colorectal cancer cells (DNMT1 KO cells). We find that DNMT1 loss leads to preferential hypomethylation in late replicating, heterochromatic PMDs marked by the constitutive heterochromatic mark H3K9me3 or the facultative heterochromatic mark H3K27me3. However, we also observe that a subset of H3K9me3-marked PMDs gain methylation in DNMT1 KO cells. We find that, in DNMT1 KO cells, these hypermethylated PMDs remain late replicating but gain DNMT3A localisation. This is accompanied by loss of heterochromatic H3K9me3 and specific gain of euchromatic H3K36me2. Our observations suggest that hypermethylated PMDs lose their heterochromatic state, enabling their methylation by DNMT3A and the establishment of a hypermethylated, non-PMD state, despite their late replication timing. More generally, our findings suggest that thede novoDNMTs play a key role in establishing domain level DNA methylation patterns in cancer cells.
Genomic insights intoPlasmodium vivaxandPlasmodium simiumhost shifts in Latin America
Authors: Lefebvre Margaux J. M. , Degrugillier Fanny , Arnathau Céline , González Camila , Rondón Silvia , Link Andrés , Chaves A. , Benavides Julio A. , Campos Aline Alves Scarpellini , dos Santos Edmilson , Huff Rosana , Silva Cláudia Maria Dornelles , Vanderhoeven Ezequiel , De Thoisy Benoit , Fontaine Michael C. , Prugnolle Franck , Rougeron Virginie
Published: December 2024

Plasmodium vivaxcauses >70% of malaria cases in Latin America. The emergence ofPlasmodium simium, transmitted from humans to monkeys, increased the malaria burden, notably after an outbreak in 2015 in Brazil. To investigateP. simiumevolutionary history, we screened 646 monkey samples and analyzed whole genome variations for 19P. simiumand 408P. vivaxisolates.P. vivaxstrains were identified in Colombian (n=3) and Brazilian monkeys (n=1), suggesting host reinvasion in Colombia and genetic exchange betweenP. vivaxandP. simiumin Brazil. Genetic analysis indicates thatP. simiumoriginated from a host jump approximately a century ago, possibly linked toP. vivaxmigration from Mexico to Brazil. Genome-wide scans identified selection in genes interacting with primate hosts and vectors. These findings highlightP. simiumevolutionary history and zoonotic malaria risks, and underscore the need to include monkeys in malaria prevention measures while ensuring human-wildlife coexistence.
Prefrontal gamma oscillations and fear extinction learning require early postnatal interneuron-oligodendroglia communication
Authors: Plaisier Fabrice , Ibaceta-González Cristóbal , Khelfaoui Hasni , Watson Adrianne E S , Poilbout Corinne , Voronova Anastassia , Angulo María Cecilia
Published: December 2024

Emerging evidence links oligodendrocyte (OL) lineage cells and myelin to cognitive processes, yet the role of myelination in shaping neuronal networks critical for cognitive tasks remains unknown. We demonstrate that early postnatal GABAergic signaling between interneurons and oligodendrocyte precursor cells (OPCs) is crucial for myelination of parvalbumin (PV) interneurons, which facilitatesin vivolow-gamma oscillations in the medial prefrontal cortex (mPFC) and supports fear extinction learning. Disruption of this signaling resulted in PV interneuron dysmyelination, decreased low-gamma power, and impaired tone fear extinction. These deficits were specific to PV interneuron dysmyelination, as overall mPFC myelination, high-gamma oscillations and context fear extinction remained unaffected. Increasing PV interneuron activity or enhancing myelination did not reverse the deficits, indicating the long-term consequences of these early myelination impairments. Our findings reveal critical roles of OPC GABAergic signaling in PV interneuron myelination and mPFC circuit maturation, with lasting impacts on gamma rhythms and cognitive function.
Heat stress drives rapid viral and antiviral innate immunity activation in Hexacorallia
Authors: Sharoni Ton , Becerra Adrian Jaimes , Lewandowska Magda , Aharoni Reuven , Voolstra Christian R. , Fine Maoz , Moran Yehu
Published: December 2024

The cnidarian class Hexacorallia, encompassing stony corals and sea anemones, plays a critical role in marine ecosystems. Coral bleaching, the disruption of the symbiosis between stony corals and zooxanthellate algae, is driven by climate change-induced seawater warming and further exacerbated by pathogenic microbes. However, how pathogens, especially viruses, contribute to accelerated bleaching remains poorly understood. The present study utilizes the model sea anemoneNematostella vectensisto explore these dynamics by creating a transgenic line with a reporter gene regulated by sequences from two RIG-I-like receptor (RLR) genes involved in antiviral responses. Under heat stress, the reporter gene showed significant upregulation, indicating that these regulatory sequences are indeed responsive to thermal stress. Analyses of transcriptome data ofN. vectensis,Exaiptasia diaphana(another sea anemone), and the stony coralStylophora pistillatarevealed stress-induced activation of a set ofbona fideimmune-related genes conserved between the three species. Population-specific differences in stress-induced transcriptional responses of immune-related genes were evident in bothNematostellaandStylophora, depending on geographic origin. InExaiptasia, the presence or absence of zooxanthellae also influenced stress-induced immune gene expression. To test whether the viruses themselves may contribute to this immune response under stress, we subjectedNematostellapolyps to variable periods of heat stress and measured the transcript levels of resident viruses as well as selected antiviral genes. While the antiviral genes responded within 1-3 hours of heat stress, viral gene expression was already upregulated within 30 minutes, suggesting that their increase might be contributing to the elevated immune response under stress, and consequentially, the further demise of organismal homeostasis. These findings highlight the complex interplay between environmental stress, viruses, immune responses, and symbiotic states in Hexacorallia. Better understanding of these mechanisms could provide insights into the role of immune pathways in coral resilience and bleaching in a changing climate.
Hormone-regulated dynamics of mRNA distribution on ribosomes in Sertoli cells
Authors: Leray Xavier , Morales Julia , Tréfier Aurélie , León Kelly , Bourquard Thomas , Musnier Astrid , Pecnard Emmanuel , Drobecq Lucile , Boulben Sandrine , Azzopardi Nicolas , Coulaud Rémi , Ouchène Hamza , Jaszczyszyn Yan , Reiter Eric , Guillou Florian , Pellissier Lucie P. , Poupon Anne , Yvinec Romain , Crépieux Pascale
Published: December 2024

The effects of hormone stimulation on the cell translational profile remain poorly understood. Here, using polysome profiling combined to RNA sequencing, we analyzed the translational response to follicle-stimulating hormone (FSH) of primary rat Sertoli cells, that exhibit an active anabolic activity regulated by reproductive hormones in the male gonad. We first established that mRNA distribution to polysomes follows a bimodal pattern, with 15% of mRNAs enriched in polysomes and exhibiting high expression. Critically, this basal polysomal enrichment had a major impact on FSH-induced mRNA recruitment to the polysomes, since FSH stimulation promoted the release of polysome-enriched mRNAs, while mRNAs that were the least associated to polysomes were preferentially recruited to polysomes upon stimulation. The FSH signal did not alter the core biological functions of Sertoli cells, but shifted the proteins involved in these functions, suggesting a molecular rewiring of the FSH-induced gene expression. These findings underscore how ribosomal reallocation dynamically adapts the cellular translatome to microenvironmental changes, enabling cells to fine-tune protein production in response to external stimuli.

GRAPHICAL ABSTRACT

Bullet points

• In Sertoli cells, most mRNAs distribute similarly between monosomes and polysomes, but a sub-population is specifically enriched in polysomes

• Basal polysomal enrichment level has a major impact on FSH-induced mRNA recruitment or release from the polysomes

• The FSH signal induced a global rewiring of the proteins involved in Sertoli cell basal activity

• FSH-induced reassignment of ribosomes to specific mRNAs has to comply with a tightly maintained mRNA distribution landscape
Genomic signals of local adaptation in Eleginops maclovinus from Northern Chilean Patagonia
Authors: Claure C. Eliza , McKinney Garrett J. , Rocha J. Dellis , Yanez Jose M , Perez-Santos Ivan , Canales-Aguirre Cristian B.
Published: December 2024

Understanding the evolutionary mechanisms that shape the adaptive divergence across spatially heterogeneous environments is a challenging task for evolutionary ecologists. The Chilean marine Patagonia is a complex ecosystem with diverse geomorphology and physical-chemical oceanographic conditions. There is limited research evaluating the interactions between selective forces and environmental conditions in this area. This study focuses on identifying the genomic signals of local adaptation of the endemic marine fish, Eleginops maclovinus from Chilean North Patagonia. To achieve this goal, we used an environmental marine database (temperature, salinity, oxygen, phosphate nitrate and silicate concentration) with collected from 1995 to 2018 and 11,961 SNPs obtained from 246 individuals from 10 sampling locations across this area. We identified putative adaptive loci using ten bioinformatic software tools, where five were based on population genetic differentiation (PGD) and five based on the genotype-environment association (GEA). We identified 392 adaptative loci using PGD and 2,164 associated with at least one of the six environmental variables analyzed using GEA. A total of 131 loci were shared between the PGD and GEA approaches, of which 37 were associated with genes involved in the growth, metabolism and homeostasis. Then, we evaluated the variation of adaptive loci with environmental variables using polygenic scores and found significant correlations with temperature, salinity, and oxygen, indicating polygenic selection along environmental gradients. This study highlights how polygenic selection drives local adaptation in Eleginops maclovinus and underscores the value of integrating genomic and environmental data for conservation in the Patagonian ecosystem.
SOD1 controls neutrophil oxidative burst and microbial killing
Authors: Brinkmann Volker , Goosmann Christian , Meier Andre , Majer Thomas , Foti Alessandro
Published: December 2024

Abstract

Neutrophils are immune cells specialized in producing large amounts of reactive oxygen species (ROS) to kill microbes. However, the mechanisms by which these cells regulate the balance of different ROS species and mitigate oxidative stress remain unclear. Here, we demonstrate that superoxide dismutase 1 (SOD1) plays a crucial role in ROS formation and antimicrobial activity in neutrophils. Our findings reveal that SOD1 modulates the ratio of superoxide (O2-) to hydrogen peroxide (H2O2) during the ROS burst, thereby supporting myeloperoxidase (MPO) enzymatic activity. By employing biochemical, cell biological, and genetic approaches, we show that SOD1 is crucial for ROS formation during NETosis and microbial infections, as it reduces oxidative stress and enables complete neutrophil activation. Impairment of SOD1 activity increases cysteine oxidation and lipid peroxidation. Neutrophils isolated from a patient with a SOD1 mutation exhibit decreased ROS production and impaired neutrophil extracellular trap (NET) formation. Our findings suggest that SOD1 is a novel regulatory factor in the oxidative burst that enables the full immunological response of neutrophils.
PI3Kγ pathway contributes to neuroinflammation and neuronal death induced by Zika virus infection
Authors: Teixeira Danielle Cunha , Campolina-Silva Gabriel , Marim Fernanda Martins , Santos Felipe Rocha da Silva , Queiroz-Junior Celso Martins , Costa Pedro Augusto Carvalho , Tana Fernanda de Lima , Costa-Souza Luiz Pedro , Pimenta Jordane Clarisse , Carvalho Júlia Gomes , Beltrami Vinícius Amorim , Rocha Felipe Emanuel Oliveira , Vieira Drielle Viana , Dornelas Evandro Gonçalves , Ferreira Giovana Cougo , Dias Felipe Ferraz , Guimarães Pedro Pires Goulart , Ribas Vinícius Toledo , Teixeira Antonio Lucio , Miranda Aline Silva de , Teixeira Mauro Martins , Souza Daniele da Glória , Costa Vivian Vasconcelos
Published: December 2024

Zika virus (ZIKV) is an emerging arbovirus belonging to the Flaviviridae family and Orthoflavivirus genus, with a pronounced tropism for the central nervous system (CNS), where it induces neuroinflammation and neuronal death. ZIKV is known to exploit host cellular mechanisms, including the activation of survival pathways such as the PI3K/AKT signaling cascade, to evade apoptosis and enhance its replication. The phosphatidylinositol 3-kinase γ (PI3Kγ) pathway regulates critical cellular processes, including differentiation, recruitment, and survival, and is abundantly expressed in both brain tissue and leukocytes. This study aimed to investigate the role of the PI3Kγ pathway during ZIKV infection. Primary neuronal cultures from PI3Kγ-deficient mice (PI3Kγkd/kd) and human neuroblastoma SH-SY5Y cells treated with the PI3Kγ inhibitor AS605240 were infected with ZIKV to assess the impact of PI3Kγ signaling on viral replication and neuronal survival. Additionally, interferon α/β receptor knockout (A129) mice were treated with AS605240 either before or after ZIKV infection to evaluate the pathway’s role in neuroinflammation. In vitro, both genetic ablation and pharmacological inhibition of PI3Kγ suppressed ZIKV replication and prevented neuronal death. In vivo, mice treated with the PI3Kγ inhibitor exhibited enhanced protection against ZIKV infection, characterized by reduced viral load, and diminished brain and optic nerve damage. This neuroprotective effect correlated with altered astrocyte and microglia activation, marked by reduced TNF production in microglia. Furthermore, inhibition of PI3Kγ curtailed the recruitment and activation of CD8+ T cells and decreased the production of pro-inflammatory mediators, including IFN-γ and IL-17, in the brains of ZIKV-infected mice. These findings suggest that PI3Kγ activation facilitates ZIKV infection and exacerbates neuroinflammation. Pharmacological inhibition of the PI3Kγ pathway may offer therapeutic benefits by limiting viral replication and alleviating neuroinflammatory responses during ZIKV infection.
An improved neural network model enables worm tracking in challenging conditions and increases signal-to-noise ratio in phenotypic screens
Authors: Weheliye Weheliye H , Rodriguez Javier , Feriani Luigi , Javer Avelino , Uhlmann Virginie , Brown André EX
Published: December 2024

High-resolution posture tracking ofC. eleganshas applications in genetics, neuroscience, and drug screening. While classic methods can reliably track isolated worms on uniform backgrounds, they fail when worms overlap, coil, or move in complex environments. Model-based tracking and deep learning approaches have addressed these issues to an extent, but there is still significant room for improvement in tracking crawling worms. Here we train a version of the DeepTangle algorithm developed for swimming worms using a combination of data derived from Tierpsy tracker and hand-annotated data for more difficult cases. DeepTangleCrawl (DTC) outperforms existing methods, reducing failure rates and producing more continuous, gap-free worm trajectories that are less likely to be interrupted by collisions between worms or self-intersecting postures (coils). We show that DTC enables the analysis of previously inaccessible behaviours and increases the signal-to-noise ratio in phenotypic screens, even for data that was specifically collected to be compatible with legacy trackers including low worm density and thin bacterial lawns. DTC broadens the applicability of high-throughput worm imaging to more complex behaviours that involve worm-worm interactions and more naturalistic environments including thicker bacterial lawns.
Discovery and Biosynthesis of Nyuzenamides D and E by Genome Mining inStreptomyces hygroscopicus
Authors: Lum Kah Yean , Kumar Rohitesh , Yang Zhijie , Souza Luciano D. O. , Jarmusch Scott A. , Moreira José M. A. , Morth Jens Preben , Ding Ling
Published: December 2024

Nyuzenamides belong to the class of bioactive cinnamoyl moiety containing non-ribosomal peptides (NRPs). However, their biosynthetic gene cluster (BGC) remains unconfirmed. Genome-mining revealed a putativenyuBGC inStreptomyces hygroscopicusDSM 40578. Nyuzenamides D (1) and E (2) were subsequently isolated, and the structures were elucidated by detailed NMR spectroscopic and MS spectrometric data analyses. The absolute configuration of1was determined by a single-crystal X-ray diffraction study. Through retro-biosynthesis and CRISPR-genome editing, the non-ribosomal peptide synthetase biosynthetic gene cluster for nyuzenamides was confirmed. Our discovery enriches the diversity of cinnamoyl-containing nonribosomal peptides and validates the biosynthetic gene clusters for future genome-mining research.
A simple method to efficiently generate structural variation in plants
Authors: Bechen Lindsey L. , Ahsan Naiyara , Bahrainwala Alefiyah , Gehring Mary , Satyaki PRV
Published: December 2024

Phenotypic variation is essential for the selection of new traits of interest. Structural variants, consisting of deletions, duplications, inversions, and translocations, have greater potential for phenotypic consequences than single nucleotide variants. Pan-genome studies have highlighted the importance of structural variation in the evolution and selection of novel traits. Here, we describe a simple method to induce structural variation in plants. We demonstrate that a short period of growth on the topoisomerase II inhibitor etoposide induces heritable structural variation and altered phenotypes inArabidopsis thalianaat high frequency. Using long-read sequencing and genetic analyses, we identified deletions and inversions underlying semi-dominant and recessive phenotypes. This method requires minimal resources, is potentially applicable to any plant species, and can replace irradiation as a source of induced large-effect structural variation.
Advances in magnetic particle imaging: evaluating magnetic microspheres and optimized acquisition parameters for high sensitivity cell tracking
Authors: Flood Samantha N. , Foster Paula J.
Published: December 2024

Motivation

The sensitivity and resolution of magnetic particle imaging (MPI) depend on the choice of tracer and specific imaging parameters. For cell tracking applications with MPI, both the superparamagnetic iron oxide (SPIO) tracer and the cell labeling efficiency have a significant impact on MPI sensitivity and vary for different tracers.

Objective

This study compared three commercially available SPIO tracers (VivoTrax, Synomag-D and ProMag) and SPIO-labeled cells using magnetic particle relaxometry (MPR) and imaging. Further, the effect of imaging parameters (gradient field strength and drive field amplitude) on MPI signal strength, resolution, and cell detection limits, was evaluated.

Results

The peak MPI signal measured by MPR was much higher for Synomag-D compared to VivoTrax and ProMag. However, the signal for intracellular Synomag-D was significantly reduced. In contrast, the signal for ProMag, a micron-sized iron oxide (MPIO) particle, was not significantly different for free and intracellular particles. The cellular iron loading was higher for ProMag compared to Synomag-D. The total MPI signal measured from images of free and intracellular SPIOs was highest for ProMag. Varying imaging parameters confirmed that a lower gradient field strength and higher drive field amplitude improved tracer and cellular sensitivity.

Conclusion

These results show that the evaluation of tracers by MPR is not sufficient to predict the performance of all SPIO tracers; in particular, not for larger, polymer-encapsulated iron particles such as ProMag, or for SPIO tracers internalized in cells. Improvements in MPI sensitivity through lower gradient field strength and higher drive field amplitudes are associated with a trade-off in image resolution.
Discovery of a Potent and Selective Inhibitor of Human NLRP3 with a Novel Binding Modality and Mechanism of Action
Authors: Wilhelmsen Kevin , Deshpande Aditi , Tronnes Sarah , Mahanta Maitriyee , Banicki Matthew , Cochran Mary , Cowdin Samantha , Fortney Kristen , Hartman George , Hughes Robert , Montgomery Rusty , Portillo Claudia , Rubin Paul , Wang Yan , Yan Shijun , Morgan Barry A , Duisembekova Assem , Riou Romane , Marleaux Michael , Hochheiser Inga V. , Buthmann Hannes , Ferber Dominic , Wang Wei , Cranston Melanie , McKee Chloe M. , Mawhinney Thea , McKay Emma , Py Bénédicte F. , Geyer Matthias , Coll Rebecca C.
Published: December 2024

The NLRP3 inflammasome is an intracellular protein complex that causes inflammation via the release of IL-1β and pyroptosis. NLRP3 activation is associated with many age-related inflammatory diseases, and NLRP3 inhibition is a promising therapeutic strategy. We previously performed a DNA encoded library screen to identify novel NLRP3 binding molecules. Herein we describe the characterization of BAL-0028 as a potent and specific inhibitor of NLRP3 signaling. Notably, BAL-0028 is a poor inhibitor of mouse NLRP3 but inhibits human and primate NLRP3 with nanomolar potency. Using cellular and biochemical analyses we demonstrate that BAL-0028 binds to the NLRP3 NACHT domain at a site that is distinct from the MCC950 binding pocket. Using humanized NLRP3 mice we show that a derivative of BAL-0028 inhibits NLRP3 activationin vivoin a peritonitis model. Finally, we demonstrate that BAL-0028 inhibits select hyperactive NLRP3 mutations associated with autoinflammatory diseases more potently than does MCC950. BAL-0028 thus represents a new modality for NLRP3 inhibition in inflammatory diseases.

NLRP3 is a target for anti-inflammatory therapies and can be inhibited by the tool compound MCC950. We describe the characterization of a new small molecule inhibitor of NLRP3 BAL-0028 that has a distinct mechanism of action and binding site.
Exploration of mScarlet for development of a red lifetime sensor for calcium imaging
Authors: van der Linden Franka H. , Gadella Theodorus W.J. , Goedhart Joachim
Published: December 2024

The past decades, researchers have worked on the development of genetically encoded biosensors, including over 60 genetically encoded calcium indicators (GECIs) containing a single fluorescent protein (FP). Red fluorescent GECIs provide advantages in terms of imaging depths and reduced cell toxicity. Most of GECIs respond with a fluorescence intensity change, and researchers have strived to improve the sensors in terms of brightness and fold-change. Unfortunately, fluorescence intensity is influenced by many factors other than the desired sensor response. GECIs with a fluorescence lifetime contrast overcome this drawback, but so far, no bright red GECI has been developed that shows a fluorescence lifetime contrast. We tried to tackle this challenge by using the brightest red fluorescent proteins from the mScarlet family to develop a new sensor. We did succeed in creating remarkable bright probes, but the fluorescence lifetime contrast we observed in bacterial lysates was lost in mammalian cells. Based on our results, and the success of others to develop a pH and a voltage sensor of mScarlet, we are confident that a GECI with mScarlet is feasible. To this end, we propose to continue development using a mammalian cell-based screening, instead of screening in bacterial lysates.
Characterization of a heterogenous activated B cell compartment arising early after antigen exposure preceding long-lived memory B cell formation
Authors: Fernandez Blanco L , Kuijper LH , Kummer LYL , Verstegen NJM , Bos A , Claireaux M , Duurland MC , Jorritsma T , Steenhuis M , Kerster G , Garcia Vallejo JJ , van Gils MJ , van Dam PJ , Stalmam EW , Wieske L , Boekel L , Wolbink GJ , Tas SW , Rispens T , Kuijpers TW , Eftimov F , ten Brinke A , van Ham SM
Published: December 2024

Once formed, plasma cells and memory B cells (MBCs) are difficult to eradicate, posing a problem in the context of unwanted antibody responses. Characterizing early B cell differentiation stages after antigen encounter is thus crucial to target and prevent unwanted antibody formation. Here, we unravelled in-depth antigen-specific B cell responses longitudinally after SARS-CoV-2 mRNA vaccination in healthy individuals using multiparameter spectral flow cytometry. The early antigen-specific B cell response was dominated by spike-specific IgG+CD27+CD71+activated B cells (ActBCs), previously assigned as germinal center-derived and DN2 extrafollicular B cells. Within the early IgG+ActBC compartment, six distinct clusters were identified with specific contraction dynamics, whereby some of these clusters were more closely related to pre-ASCs and others more to long-lived MBCs. Some of the highly contracting ActBC clusters expressed CD11c, a marker previously used to define atypical B cells. The transient presence of different ActBC clusters could also be observed in total B cells when gated in an antigen- independent manner. Our results thus delineate the early stages of the antigen-specific B cell response, with a further dissection of the CD71+ActBC compartment. Detection of ActBC clusters early after antigen encounter in total B cells opens avenues for future evaluation of their potential to serve as a proxy for antigen-reactive B cells in autoimmunity or other unwanted B cell responses.
Acoustic tumor paint for real-time imaging, surgical guidance and recurrence monitoring of brain tumors with ultrasound
Authors: Rabut Claire , Daghlian George H. , Barturen-Larrea Pierina , Li Hongyi Richard , Bruegge Ruth Vorder , Jones Rebecca M. , Malounda Dina , Pinton Gianmarco F. , Shapiro Mikhail G.
Published: December 2024

The rapid growth, invasiveness, and resistance to treatment of glioblastoma multiforme (GBM) underscore the urgent need for improved diagnostics and therapies. Current surgical practice is limited by challenges with intraoperative imaging, while recurrence monitoring requires expensive magnetic resonance or nuclear imaging scans. Here we introduce “acoustic tumor paint”, an approach to labeling brain tumors for ultrasound imaging – a widely accessible imaging modality. We show that gas vesicles (GVs), natural air-filled protein nanostructures, preferentially accumulate in brain tumors following systemic administration in syngeneic and xenograft mouse models of GBM. This enables real-time tumor visualization during surgery and postoperative monitoring of recurrence. We characterize GV uptake and breakdown by tumors and their resident cells and support clinical translatability by documenting non-toxic repeated administration. We also demonstrate the potential for post-operative monitoring in humans by imaging GVs through a human skull and an FDA-approved skull prosthesis. Acoustic tumor paint has the potential to enhance diagnostic accuracy, improve surgical outcomes, make monitoring more accessible, and extend survival in GBM patients.
Differential expression of sex regulatory genes in gonads ofAstyanax mexicanussurface fish and cavefish
Authors: Webster Kaitlyn A. , Ponte Bethany , Vasquez-Gross Hans , Petereit Juli , Hutchinson John , Riddle Misty R.
Published: December 2024

Background

Astyanax mexicanusis a single species of fish that consists of river-dwelling (surface) and cave-dwelling morphotypes. Little is known about how sexual determination, differentiation or reproduction have evolved in the surface morphs or cavefish, though divergence in reproductive strategy is expected as the latter have adapted to the novel cave environment. Evolution of the gonad transcriptome may underlie the differences in gamete morphology, fertility, and fecundity previously reported between morphotypes.

Results

We compared the ovary and testis transcriptome of surface fish and cavefish at juvenile and adult stages. We found that samples clustered by developmental stage, sex, and morphotype identity. Several key genes that are typically associated with the female gonad in other vertebrates showed a reversal in sexual dimorphism or were not differentially expressed between sexes inA. mexicanus. In contrast, while gene expression typically associated with male gonads was largely conserved and consistent with vertebrate testicular expression profiles. Transcriptional and physiological differences between surface fish and cavefish morphotypes were observed in gonads from both sexes. Cavefish ovaries exhibited unique upregulation of neuron development and differentiation genes, and extensive innervation of the ovarian epithelium, while cavefish testes showed increased expression of angiogenesis regulating genes, and greater vasculature density compared to surface fish testes.

Conclusions

These results reveal significant gene expression differences betweenA. mexicanussurface fish and cavefish morphotypes that may have functional consequences in gonad morphogenesis and fertility. Our findings provide a foundation for investigating the evolution of sex regulatory pathways and reproductive strategies in animals adapting to new and challenging environments in which nutrient availability, temperature, and mate selection are suboptimal.
Cryogenic light microscopy with Ångstrom precision deciphers structural conformations of PIEZO1
Authors: Mazal Hisham , Schambony Alexandra , Sandoghdar Vahid
Published: December 2024

Despite the impressive progress in molecular biochemistry and biophysics, many questions regarding the conformational states of large (transmembrane) protein complexes persist. In the case of the PIEZO protein, investigations by cryogenic electron microscopy (Cryo-EM) and atomic force microscopy (AFM) have established a symmetric trimer structure with three long-bladed domains in a propeller-like configuration. A transition of PIEZO protein from curved to flat conformation is hypothesized to actuate closed and open channels for the flow of ions. However, conclusive high-resolution data on the molecular organization of PIEZO in its native form are lacking. To address this shortcoming, we exploit single-particle cryogenic light microscopy (spCryo-LM) to decipher the conformational states of the mouse PIEZO1 protein (mPIEZO1) in the cell membrane. Here, we implement a high-vacuum cryogenic shuttle to transfer shock-frozen unroofed cell membranes in and out of a cryostat for super-resolution microscopy at liquid helium temperature. By localizing fluorescent labels placed at the extremities of the three blades with Ångstrom precision, we ascertain three configurations of the protein with radii of 6, 12, and 20 nm as projected onto the membrane plane. Our data suggest that in the smallest configuration, the blades form a nano-dome structure that is more strongly curved than previously observed and predicted by AlphaFold-3. In the largest conformation, we believe the structure must fully unbend in an anticlockwise manner to form a flat extended state. We attribute the 12 nm conformation, the most frequently occupied state, to an intermediate state and discuss our results in the context of the findings from other groups. Combination of spCryo-LM and Cryo-EM measurements together within situphotothermal stimulation promises to provide quantitative insight into the interplay between structure and function of PIEZO and other biomolecular complexes in their native environments.