bluuebunny/crossref_metadata_2025 huggingface dataset:
A Membrane Lipid Signature Unravels the Dynamic Landscape of Group 1 ILCs
Authors: Frey Halle C. , Sun Xin , Oudeif Fatima , Corona Darleny L. , He Zijun , Won Taejoon , Schultz Tracy L. , Carruthers Vern B. , Laouar Amale , Laouar Yasmina
Published: April 2024

In an era where the established lines between cell identities are blurred by intra-lineage plasticity, distinguishing between stable and transitional states becomes imperative. This challenge is particularly pronounced within the Group 1 ILC lineage, where the similarity and plasticity between NK cells and ILC1s obscure their classification and the assignment of their unique contributions to immune regulation. This study exploits the unique property of Asialo-GM1 (AsGM1)—a membrane lipid associated with cytotoxic attributes absent in ILC1s—as a definitive criterion to distinguish between these cells. By prioritizing cytotoxic potential as the cardinal differentiator, our strategic use of the AsGM1 signature achieved precise delineation of NK cells and ILC1s across tissues, validated by RNA-seq analysis. This capability extends beyond steady-state classifications, adeptly capturing the binary classification of NK cells and ILC1s during acute liver injury. By leveraging two established models of NK-to-ILC1 plasticity driven by TGFβ andToxoplasma gondii, we demonstrate the stability of the AsGM1 signature, which sharply contrasts with the loss of Eomes. This signature identified a spectrum of known and novel NK cell derivatives—ILC1-like entities that bridge traditional binary classifications in aging and infection. The early detection of the AsGM1 signature at the immature NK (iNK) stage, preceding Eomes, and its stability, unaffected by transcriptional reprogramming that typically alters Eomes, position AsGM1 as a unique, site-agnostic marker for fate mapping NK-to-ILC1 plasticity. This provides a powerful tool to explore the expanding heterogeneity within the Group 1 ILC landscape, effectively transcending the ambiguity inherent to the NK-to-ILC1 continuum.
Cleaner gobies can solve a biological market task when the correct cue is larger
Authors: Ranucci Maddalena , Court Mélanie , Pereira Beatriz P. , Romeo Daniele , Paula José Ricardo
Published: April 2024

Animal cognition is deeply influenced by interactions with the environment. A notable example of sophisticated cognition in the animal kingdom is described by the mutualistic relationship between cleaner fish and clients, where decision-making processes play a pivotal role in partner choice and fish survival. In this context, while extensive research has explored the cognition of the cleaner wrasseLabroides dimidiatus, its Caribbean counterparts,Elacatinus spp., have been comparatively inadequately evaluated. In this study, we used plexiglass plates as surrogates for clients and assessed the ability of cleaner gobies,Elacatinus oceanops, to solve a biological market task where prioritising an ephemeral food plate over a permanent one would double the food reward. We varied cue-based decision-making using both ecologically relevant cues (plate size and colour) and non-relevant ones (presentation side). Additionally, we tested their capacity for reversal learning, an indicator of complex cognitive abilities. Notably, cleaner gobies were able to solve the biological markets task when the distinguishing cue was a larger plate size. Given that these gobies tend to prioritise larger predatory clients in nature, our results align with their natural inclination. Furthermore, considering these gobies were bred in captivity and never experienced cleaning interactions in their lifetime, our data might suggest that their intrinsic cognitive abilities are shaped by evolutionary pressures rooted in their ecological roles. In essence, even in the absence of direct ecological interactions, innate cognitive abilities in cleaner gobies seem to be deeply influenced by evolutionary forces tied to their natural ecological functions. However, their inability to solve the same task involving other cues, may be influenced by factors such as captivity-reared fish or limitations in the experimental design. Further research, including wild individuals, is essential to elucidate the cognitive abilities of the studied species and its implications in the ecological context and evolutionary history.
VPS41 deletion triggers progressive loss of insulin stores and downregulation of beta-cell identity
Authors: Yau Belinda , An Yousun , Germanos Mark , Schwarzkopf Patricia , van der Kraan A Gabrielle , Larance Mark , Webster Hayley , Burns Christian , Asensio Cedric S , Kebede Melkam A
Published: April 2024

Vacuolar protein sorting-associated protein 41 (VPS41) has been established as a requirement for normal insulin secretory function in pancreatic beta-cells. Genetic deletion of VPS41 in mouse pancreatic beta-cells results in diabetes, though the mechanisms are not understood. Presently, we show that VPS41 deletion results in rapid mature insulin degradation and downregulation of beta-cell identity. This phenotype is observedin vivo,with VPS41KO mice displaying progressive loss of insulin content and beta-cell function with age. In acute VPS41 depletionin vitro, the loss of insulin is associated with increased degradative pathway activity, increased Adapter Protein 3 complex colocalisation with lysosomes, increased nuclear localisation of transcription factor E3, and downregulation of PDX1 and INS mRNA expression. Inhibition of lysosomal degradation rescues the rapidly depleted insulin content. These data evidence a VPS41-dependent mechanism for both insulin content degradation and loss of beta-cell identity in beta-cells.
3D bioprinting of Liver Microenvironment Model Using Photocrosslinkable Decellularized Extracellular Matrix based Hydrogel
Authors: Tabatabaei Rezaei Nima , Kumar Hitendra , Liu Hongqun , Rajeev Ashna , Natale Giovanniantonio , Lee Samuel S. , Park Simon S. , Kim Keekyoung
Published: April 2024

The liver, as one of the vital organs in the body, plays a crucial role in various bodily functions. Numerous factors can cause liver damage, that the sole remedy for severe liver conditions is the transplantation of healthy liver tissue. In response to the transplantation challenges, innovative approaches involving hydrogel-based technologies have emerged, leading to the creation of highly functionalized tissues. The development of three-dimensional printing and patterning of cell-laden biomaterial matrices offers promising advances for creating tissue-specific structures in tissue engineering and bioprinting. However, the matrix materials currently employed in bioprinting liver microtissue often fail to capture the complexity of the natural extracellular matrix (ECM), hindering their ability to restore innate cellular shapes and functions. Liver ECM-based hydrogels are increasingly recognized for their potential as biomimetic 3D cell culture systems that facilitate the exploration of liver disease, metabolism, and toxicity mechanisms. Yet, the conventional production of these hydrogels relies on slow thermal gelation processes, which restrict the manipulation of their mechanical characteristics. In this research, we introduce a novel approach with a functionalized photocrosslinkable liver decellularized extracellular matrix (dECM). By combining liver dECM methacrylate (LdECMMA) with gelatin methacrylate (GelMA), we achieved accelerated crosslinking under visible light irradiation and the ability to tune the mechanical, rheological, and physiological properties of the material. We encapsulated human hepatocellular carcinoma cells within an optimal concentration of the GelMA-LdECMMA hybrid hydrogel and examined cell proliferation and function over an extended period. The findings revealed that the GelMA-LdECMMA hybrid hydrogel enhances liver cell proliferation and function, holding significant promise for applications in drug screening and liver cancer metastasis research.
Pinging the Hidden Attentional Priority Map: Suppression Needs Attention
Authors: Huang Changrun , van Moorselaar Dirk , Foster Joshua J. , Donk Mieke , Theeuwes Jan
Published: April 2024

Attentional capture by an irrelevant salient distractor is attenuated when the distractor is presented more frequently in one location compared to other locations, suggesting that people learn to suppress an irrelevant salient location. However, to date it is unclear whether this suppression is proactive, applied before attention has been directed to the distractor location, or reactive, occurring after attention has been directed to that specific location. The aim of the present study is to investigate how suppression is accomplished by using the pinging technique, which allows one to probe how attention is distributed across the visual field prior to the presentation of the search display. In an EEG experiment, participants performed a visual search task wherein they were tasked with identifying a shape singleton in the presence of an irrelevant color singleton. Compared to all other locations, this color singleton appeared more frequently at a specific location, which was termed the high-probability location. Prior to the search task, we introduced a continuous recall spatial memory task to reveal the hidden attentional priority map. Participants had to memorize the location of a memory cue continuously and report this location after the visual search task. Critically, after the presentation of the memory cue but before the onset of the search display, a neutral placeholder display was presented to probe how the hidden priority map is reconfigured by the learned distractor suppression. Behaviorally, there was clear evidence that the high-probability location was suppressed, as search was more efficient when the distractor appeared at this location. To examine the priority map prior to search, we adopted an inverted encoding approach to reconstruct the tuning profile of the memorized position in the spatial memory task. Inverted modeling resulted in reliable tuning profiles during memory maintenance that gradually decayed and that were revived again by the onset of a neutral placeholder display preceding search. After the onset of the placeholders, the tuning profile observed was characterized by a spatial gradient centered over the high-probability location, with tuning being most pronounced at the-to-be suppressed location. This finding suggests that while learned suppression is initiated prior to search display onset, it is preceded by an initial phase of spatial selection, which is in line with a reactive suppression account. Together these results further our understanding of the mechanism of spatial distractor suppression.
Multiscale modelling of neuronal dynamics in hippocampus CA1
Authors: Tesler Federico , Lorenzi Roberta Maria , Ponzi Adam , Castellato Claudia , Palesi Fulvia , Gandolfi Daniela , Gandini Wheeler Kingshott Claudia A.M. , Mapelli Jonathan , D’Angelo Egidio , Migliore Michele , Destexhe Alain
Published: April 2024

The development of biologically realistic models of brain microcircuits and regions is currently a very relevant topic in computational neuroscience. From basic research to clinical applications, there is an increasing demand for accurate models that incorporate local cellular and network specificities, able to capture a broad range of dynamics and functions associated with given brain regions. One of the main challenges of these models is the passage between different scales, going from the microscale (cellular) to the meso (microcircuit) and macroscale (region or whole-brain level), while keeping at the same time a constraint on the demand of computational resources. One novel approach to this problem is the use of mean-field models of neuronal activity to build large-scale simulations. This provides an effective solution to the passage between scales with relatively low computational demands, which is achieved by a drastic reduction in the dimensionality of the system. In this paper we introduce a multiscale modelling framework for the hippocampal CA1, a region of the brain that plays a key role in functions such as learning, memory consolidation and navigation. Our modelling framework goes from the single cell level to the macroscale and makes use of a novel mean-field model of CA1, introduced in this paper, to bridge the gap between the micro and macro scales. To develop the mean-field model we make use of a recently introduced formalism based on a bottom-up approach that is easily applicable to different neuronal models and cell types. We test and validate the model by analyzing the response of the system to the main brain rhythms observed in the hippocampus and comparing our results with the ones of the corresponding spiking network model of CA1. In addition, we show an example of the implementation of our model to study a stimulus propagation at the macro-scale, and we compare the results obtained from our model with the corresponding spiking network model of the whole CA1 area.
Activity based proteome profiling of serum serine hydrolases: application in pediatric abusive head trauma
Authors: Maret Estelle , Wiskott Kim , Shipley Tobias , Gilardi Federica , Augsburger Marc , Thomas Aurelien , Fracasso Tony , Sajic Tatjana
Published: April 2024

Purpose

Traumatic brain injury (TBI), including pediatric abusive head trauma (AHT), is the leading cause of death and disability in children and young adults worldwide. The current understanding of trauma-induced molecular changes in the brain of human subjects with intracranial haemorrhage (ICH) remains inadequate and requires further investigation to improve the outcome and management of TBI in the clinic. Calcium-mediated damage at the site of brain injury has been shown to activate several catalytic enzymes.

Experimental design

Serine hydrolases (SHs) are major catalytic enzymes involved in the biochemical pathways of blood coagulation, systemic inflammation and neuronal signaling. Here we investigated activity-based protein profiling (ABPP) by measuring the activity status of SH enzymes in the serum of infants with severe ICH as a consequence of AHT or atraumatic infants who died of sudden infant death syndrome (SIDS).

Results

Our proof-of-principle study revealed significantly reduced physiological activity of dozens of metabolic SHs in the serum of infants with severe AHT compared to the SIDS group, with some of the enzymes being related to neurodevelopment and basic brain metabolism.

Conclusions and clinical relevance

To our knowledge, this is the first study to investigate the ABPP of the SHs enzyme family to detect changes in their physiological activity in blood serum in severe TBI. We used antemortem (AM) serum from infants under the age of 2 years who were victims of AHT with a severe form of ICH. The analytical approach used in the proof-of-principle study shows reduced activities of serum serine lipases in AHT cases and could be further investigated in mild forms of AHT, which currently show 30% of misdiagnosed cases in clinics.
Unraveling the phylogenetic signal of gene expression from single-cell RNA-seq data
Authors: Alves Joao M , Tomás Laura , Posada David
Published: April 2024

Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of phenotypic heterogeneity. Although the predominant focus of scRNA-seq analyses has been assessing gene expression changes, several approaches have been proposed in recent years to identify changes at the DNA level from scRNA-seq data. In this study, we evaluated the relative performance of six strategies for calling single-nucleotide variants from scRNA-seq data using 381 single-cell transcriptomes from five cancer patients. Specifically, we focused on the quality of the inferred genotypes and the resulting single-cell phylogenies. We found that scAllele, Monopogen, and Monovar consistently returned phylogenetically informative genotype calls, providing more precise signals of discrimination between tumor and normal cells within heterogeneous samples and among distinct subclonal lineages in longitudinal samples. In addition, we evaluated the evolution of gene expression along the cell phylogenies. While most transcriptomic variation was very plastic and did not correlate with the cell phylogeny, a group of genes associated with cell cycle processes showed a strong phylogenetic signal in one of the patients, underscoring a potential link between gene expression patterns and lineage-specific traits in the context of cancer progression. In summary, our study highlights the potential of scRNA-seq data for inferring cell phylogenies to decipher the evolutionary dynamics of cell populations.
Knowledge Graph-based Thought: a knowledge graph enhanced LLMs framework for pan-cancer question answering
Authors: Feng Yichun , Zhou Lu , Ma Chao , Zheng Yikai , He Ruikun , Li Yixue
Published: April 2024

Background

In recent years, Large Language Models (LLMs) have shown promise in various domains, notably in biomedical sciences. However, their real-world application is often limited by issues like erroneous outputs and hallucinatory responses.

Results

We developed the Knowledge Graph-based Thought (KGT) framework, an innovative solution that integrates LLMs with Knowledge Graphs (KGs) to improve their initial responses by utilizing verifiable information from KGs, thus significantly reducing factual errors in reasoning. The KGT framework demonstrates strong adaptability and performs well across various open-source LLMs. Notably, KGT can facilitate the discovery of new uses for existing drugs through potential drug-cancer associations, and can assist in predicting resistance by analyzing relevant biomarkers and genetic mechanisms. To evaluate the Knowledge Graph Question Answering (KGQA) task within biomedicine, we utilize a pan-cancer knowledge graph to develop a pan-cancer question answering benchmark, named the Pan-cancer Question Answering (PcQA).

Conclusions

The KGT framework substantially improves the accuracy and utility of LLMs in the biomedical field. This study serves as a proof-of-concept, demonstrating its exceptional performance in biomedical question answering.

Key Points

We introduce a framework combining LLMs with KGs to improve factual accuracy in LLM reasoning.

Our system is a flexible architecture that seamlessly integrates various LLMs.

Utilizing a pan-cancer knowledge graph, we have proposed the first KGQA benchmark in the field of biomedicine.

Case studies reveal our method enhanced LLMs in addressing biomedical challenges such as drug repositioning, resistance research, individualized treatment, and biomarker analysis.

The method performs favorably in comparison to existing methods.
Multi-omic profiling of squamous cell lung cancer identifies metabolites and related genes associated with squamous cell carcinoma
Authors: Staaf Johan , Ehinger Daniel , Brunnström Hans , Jönsson Mats , Rosengren Frida , Kotevska Marija , Karlsson Anna , Aine Mattias , Frezza Christian , Planck Maria , Arbajian Elsa
Published: April 2024

Background

Squamous cell lung carcinoma (SqCC) is the second most common histological subtype of lung cancer. Besides -tumor-initiating and promoting DNA, RNA, and epigenetic alterations, aberrant tumor cell metabolism has been identified as one of the hallmarks of carcinogenesis. The aim of the current study was to identify SqCC-specific metabolites and key gene regulators that could eventually be used as new anticancer targets.

Methods

Transcriptional (n=156), proteomics (n=118), and mass spectrometry-based metabolomic data (n=73) were gathered for a cohort of resected early-stage lung cancers representing all major histological subgroups. SqCC-specific differentially expressed genes were integrated with proteogenomic and metabolic data using genome scale metabolic models (GEMs). Findings were validated in cohorts of tumors, normal specimens, and cancer cell lines. In situ protein expression of SLC6A8 was investigated in 213 tumors.

Results

Differential gene expression analysis identified 280 SqCC-specific genes, of which 57 were connected to metabolites through GEMs. Metabolic profiling identified 7 SqCC-specific metabolites, of which increased creatine and decreased phosphocholine levels matched to SqCC-specific elevated expression ofSLC6A8and decreased expression ofCHKA,part of respective GEMs. Expression of both genes appeared tumor cell-associated, and in particular the elevated expression ofSLC6A8identified SqCC also in stage IV disease.

Conclusion

Elevated creatine levels and the overexpression of its transporter protein SLC6A8 appear as a distinct metabolic feature of SqCC. Considering ongoing clinical trials focused on SLC6A8 inhibition in other malignancies, exploring SLC6A8 inhibition in SqCC appears motivated based on a metabolic addiction hypothesis.
Gill regeneration in the mayflyCloeonuncovers new molecular pathways in insect regeneration
Authors: Martin-Blanco Carlos A. , Navarro Pablo , Esteban-Collado José , Serras Florenci , Almudi Isabel , Casares Fernando
Published: April 2024

The capacity to regenerate lost or damaged organs is widespread among animals, and yet, the species in which regeneration has been experimentally probed using molecular and functional assays is very small. This is also the case for insects, for which we still lack a complete picture of their regeneration mechanisms and the extent of conservation of these mechanisms. Here we contribute to filling this gap by investigating regeneration in the mayflyCloeon dipterum.Mayflies, or Ephemeroptera, appeared early in the evolution of insects. We focus on the abdominal gills ofCloeonnymphs, which are critical for osmoregulation and gas exchange. After amputation, gills re-grow faster than they do during normal development. Direct cell count and EdU proliferation assays indicate that growth acceleration involves an uniform increase in cell proliferation throughout the gill, rather than a localized growth zone. Transcriptomic analysis reveals an early enrichment in cell cycle-related genes, in agreement with fast proliferation. Several other gene classes are also enriched in regenerating gills, including protein neddylation and other proteostatic processes. We then showed that protein neddylation, the activin signaling pathway or the mRNA-binding protein Lin28, among other genes and processes, are required forDrosophilalarval/pupal wing regeneration, and that some of these genes may have a regeneration-specific function in the wing. Globally, our results contribute to elucidating regeneration mechanisms in mayflies and suggest a conservation of regeneration mechanisms across insects, as evidenced by the regenerative role of candidate genes identified inCloeonin the distantDrosophila.
Loss of developmentally derived Irf8+ macrophages promotes hyperinnervation and arrhythmia in the adult zebrafish heart
Authors: Paquette Shannon E. , Oduor Cliff I. , Gaulke Amy , Stefan Sabina , Bronk Peter , Dafonseca Vanny , Barulin Nikolai , Lee Cadence , Carley Rachel , Morrison Alan R. , Choi Bum-Rak , Bailey Jeffrey A. , Plavicki Jessica S.
Published: April 2024

Recent developments in cardiac macrophage biology have broadened our understanding of the critical functions of macrophages in the heart. As a result, there is further interest in understanding the independent contributions of distinct subsets of macrophage to cardiac development and function. Here, we demonstrate that genetic loss of interferon regulatory factor 8 (Irf8)-positive embryonic-derived macrophages significantly disrupts cardiac conduction, chamber function, and innervation in adult zebrafish. At 4 months post-fertilization (mpf), homozygousirf8st96/st96mutants have significantly shortened atrial action potential duration and significant differential expression of genes involved in cardiac contraction. Functionalin vivoassessments via electro- and echocardiograms at 12 mpf reveal thatirf8mutants are arrhythmogenic and exhibit diastolic dysfunction and ventricular stiffening. To identify the molecular drivers of the functional disturbances inirf8null zebrafish, we perform single cell RNA sequencing and immunohistochemistry, which reveal increased leukocyte infiltration, epicardial activation, mesenchymal gene expression, and fibrosis.Irf8null hearts are also hyperinnervated and have aberrant axonal patterning, a phenotype not previously assessed in the context of cardiac macrophage loss. Gene ontology analysis supports a novel role for activated epicardial-derived cells (EPDCs) in promoting neurogenesis and neuronal remodelingin vivo. Together, these data uncover significant cardiac abnormalities following embryonic macrophage loss and expand our knowledge of critical macrophage functions in heart physiology and governing homeostatic heart health.
Neural and computational mechanisms of effort under the pressure of a deadline
Authors: Pisauro M. Andrea , Pollicino Daniele , Fisher Lucy , Apps Matthew A. J.
Published: April 2024

Deadlines fundamentally shape the motivation for effort. Research examining effort-based choices finds high effort is an avoided cost. However, this work overlooks the fact that effort can be valuable when it makes progress on long-term goals before deadlines. We test a new framework where motivation depends on deadline pressure (work remaining / time remaining). Across three studies we use computational modelling on novel tasks examining effort-based decisions when effort makes progress on goals with deadlines. In support of hypotheses, deadline pressure significantly impacts decision-making, shifting people from avoiding effort, to seeking and valuing it. Using ultra-high-field fMRI, we show that functionally connected putamen and midcingulate cortex (MCC) sub-regions process and update estimates of deadline pressure, with distinct anterior cingulate and putamen sub-regions processing the costs or added value of effort. We show the neurocomputational mechanisms for how deadline pressure shapes motivation, and that keep us ‘on track’ for our goals.
Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1
Authors: Isu Ugochi H. , Polasa Adithya , Moradi Mahmoud
Published: April 2024

Cannabinoid receptor 1 (CB1) is a G protein-coupled receptor (GPCR) that regulates critical physiological processes including pain, appetite, and cognition. Understanding the confor- mational dynamics of CB1 associated with transitions between inactive and active signaling states is imperative for developing targeted modulators. Using microsecond-level all-atom molecular dynamics (MD) simulations, we identified marked differences in the conformational ensembles of inactive and active CB1 inapo. The inactive state exhibited substantially in- creased structural heterogeneity and plasticity compared to the more rigidified active state in the absence of stabilizing ligands. Transmembrane helices TM3 and TM7 were identified as distinguishing factors modulating the state-dependent dynamics. TM7 displayed amplified fluctuations selectively in the inactive state simulations attributed to disruption of conserved electrostatic contacts anchoring it to surrounding helices in the active state. Additionally, we identified significant reorganizations in key salt bridge and hydrogen bond networks con- tributing to the CB1 activation/inactivation. For instance, D213-Y224 hydrogen bond and D184-K192 salt bridge showed marked rearrangements between the states. Collectively, these findings reveal the specialized role of TM7 in directing state-dependent CB1 dynamics through electrostatic switch mechanisms. By elucidating the intrinsic enhanced flexibility of inactive CB1, this study provides valuable insights into the conformational landscape enabling functional transitions. Our perspective advances understanding of CB1 activation mechanisms and offers opportunities for structure-based drug discovery targeting the state- specific conformational dynamics of this receptor.

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A cross-species framework for investigating perceptual evidence accumulation
Authors: Chakravarty Sucheta , Delgado-Sallent Cristina , Kane Gary A. , Xia Hongjie , Do Quan H. , Senne Ryan A. , Scott Benjamin B.
Published: April 2024

Cross-species studies are important for a comprehensive understanding of brain functions. However, direct quantitative comparison of behaviors across species presents a significant challenge. To enable such comparisons in perceptual decision-making, we developed a synchronized evidence accumulation task for human and non-human animals, by aligning mechanics, stimuli, and training. The task was readily learned by rats, mice and humans, with each species exhibiting qualitatively similar performance. Quantitative model comparison revealed that all three species employed an evidence accumulation strategy, but differed in speed, accuracy, and key decision parameters. Human performance prioritized accuracy, whereas rodent performance was limited by internal time-pressure. Rats optimized reward rate, while mice appeared to switch between evidence accumulation and other strategies trial-to-trial. Together, these results reveal striking similarities and species-specific priorities in decision-making. Furthermore, the synchronized behavioral framework we present may facilitate future studies involving cross-species comparisons, such as evaluating the face validity of animal models of neuropsychiatric disorders.

Highlights

Development of an evidence accumulation task for rats and mice

Synchronized video game allows direct comparisons with humans

Rat, mouse and human behavior are well fit by the same decision models

Model parameters reveal species-specific priorities in accumulation strategy
Enhancements in Squid Retinal Responses to Change of Polarizations in a Caustic Shallow Water
Authors: Cai Jing , Nikonov Sergei , Sweeney Alison M.
Published: April 2024

Marine animals with polarization vision are able to effectively detect moving objects in shallow waters, which are illuminated by dynamic fluctuations of downwelling light known as caustics. While behavioral studies across different animal species have demonstrated the support of polarization vision in moving object detection within this noisy environment, little is known about how their retinal photoreceptors, absorbing polarized photons, respond to moving objects, or how each photoreceptor contributes to the collective retinal reaction to changes in polarization. In this study, we employed multi-electrode array recordings to examine the retinal neural response of squid to polarized light stimuli that were designed to simulate caustics environment. Extracellular retinal recordings not only exhibit neural activities selective to the direction of polarization but also demonstrate a significant enhancement in response to stimuli with changing polarization compared to constant polarization. This enhancement is robust in almost all recording channels, but absent in a random permutation of the recordings from different trial types. These results suggest that the retinal photoreceptors directly encode the change of polarization stimuli, thereby contributing to signal detections with polarization vision. Together, our research represents a novel neural exploration of cephalopod polarization vision in a caustic environment, and advances our understanding of how nature parses scenes with salient, dynamic polarization in animal vision.
Placental malaria is associated with a TLR–Endothelin-3–oxidative damage response in human placenta tissues
Authors: Chenge Samuel , Mbalitsi Melvin , Ngure Harrison , Obimbo Moses , Singoei Mercy , Kangogo Mourine , Kanoi Bernard N. , Gitaka Jesse , Kobia Francis M.
Published: April 2024

Placental malaria, which is mainly caused by the sequestration ofPlasmodium falciparum- infected erythrocytes in the placenta, is an important driver of poor pregnancy outcomes, including fetal growth restriction, preterm birth, and stillbirth. However, the mechanisms underlying its adverse outcomes are unclear. Mouse models have shown that placental malaria triggers a proinflammatory response in the placenta, which is accompanied by a fetal Toll-like receptor (TLR)4-mediated innate immune response associated with improved fetal outcomes. Here, we used hematoxylin and eosin staining to identify placental malaria positive and negative samples in our biobank of placentas donated by women living in a malaria-endemic region of Kenya and assessed the impact of placental malaria on the expression of TLRs, Endothelins, and oxidative damage. RT-qPCR analysis revealed that placental malaria was associated with an upregulation of TLR4, TLR7, and Endothelin-3. Moreover, immunohistochemistry showed that placental malaria was associated with elevated expression levels of the oxidative DNA damage marker, 8- hydroxy-2’-deoxyguanosine, while RT-qPCR revealed that this was accompanied by an upregulation of p21, an inhibitor of cell cycle progression and marker of cellular response to DNA damage. These findings allude to a novel mechanism of placental malaria pathogenesis driven by a TLR–Endothelin-3–oxidative DNA damage signaling axis.
Nuclear size-regulated emergence of topological packing order on growing human lung alveolospheres
Authors: Tang Wenhui , Huang Jessie , Pegoraro Adrian F. , Zhang James H. , Tang Yiwen , Bi Dapeng , Kotton Darrell N. , Guo Ming
Published: April 2024

Within multicellular living systems, cells coordinate their positions with spatiotemporal accuracy to form various structures, setting the clock to control developmental processes and trigger maturation. These arrangements can be regulated by tissue topology, biochemical cues, as well as mechanical perturbations. However, the fundamental rules of how local cell packing order is regulated in forming three-dimensional (3D) multicellular architectures remain unclear. Furthermore, how cellular coordination evolves during developmental processes, and whether this cell patterning behavior is indicative of more complex biological functions, is largely unknown. Here, using human lung alveolospheres as a model system, by combining experiments and numerical simulations, we find that, surprisingly, cell packing behavior on alveolospheres resembles hard-disk packing but with increased randomness; the stiffer cell nuclei act as the ‘hard disks’ surrounded by deformable cell bodies. Interestingly, we observe the emergence of topological packing order during alveolosphere growth, as a result of increasing nucleus-to-cell size ratio. Specifically, we find more hexagon-concentrated cellular packing with increasing bond orientational order, indicating a topological gas-to-liquid transition. Additionally, by osmotically changing the compactness of cells on alveolospheres, we observe that the variations in packing order align with the change of nucleus-to-cell size ratio. Together, our findings reveal the underlying rules of cell coordination and topological phases during human lung alveolosphere growth. These static packing characteristics are consistent with cell dynamics, together suggesting that better cellular packing stabilizes local cell neighborhoods and may regulate more complex biological functions such as organ development and cellular maturation.
Biosynthesis of Arcyriaflavin F fromStreptomyces venezuelaeATCC 10712
Authors: Lai Hung-En , Tanner Lewis , Kennedy Agata , Chee Soo Mei , Freemont Paul S , Moore Simon J
Published: April 2024

Indolocarbazoles are natural products with a broad spectrum of reported bioactivities. A distinct feature of indolocarbazole biosynthesis is the modification of the indole and maleimide rings by regioselective tailoring enzymes. Here, we study a new indolocarbazole variant, which is encoded by theacfXODCPgenes fromStreptomyces venezuelaeATCC 10712. First, we characterise this pathway by expressing theacfXODCPgenes inStreptomyces coelicolor, which led to the production of a C-5/C-5’-dihydroxylated indolocarbazole. We name this new product arcyriaflavin F. Second, we demonstrate the flavin-dependent monooxygenase AcfX catalyses the C-5/C-5’ dihydroxylation of the unsubstituted arcyriaflavin A into arcyriaflavin F. Interestingly, AcfX shares homology to EspX from erdasporine A biosynthesis, which instead catalyses a single C-6 indolocarbazole hydroxylation. In summary, we report a new indolocarbazole biosynthetic pathway and a regioselective C-5 indole ring tailoring enzyme AcfX.
Leptospiraseroprevalence in dogs, cats and horses: the effect of cross-reactivity between serovars and vaccination status on seroprevalence estimates
Authors: McCreight Kellie A. , Barbosa Liana N. , Agricola Odoi , Reed Porsha , Rajeev Sreekumari
Published: April 2024

In this study, we estimated theLeptospiraseroprevalence in dogs (n = 376), horses (n = 88), and cats (n = 169) using Microscopic Agglutination Test (MAT) against 12Leptospiraserovars. We observed aLeptospiraseroprevalence of 29.41%, 47.73%, and 12.35% in dogs, horses, and cats, respectively. The highest seroprevalence was observed for serovar Autumnalis (74.55%) in dogs, and Bratislava in horses (95.24%) and cats (42.86%). We found a significant level of potential cross-reactivity between multipleLeptospiraserovars tested, with highest cross-reactivity to serovar Autumnalis in dogs. The dogs that were vaccinated againstLeptospirahad a significantly higher seroprevalence (45.92%) compared to unvaccinated dogs (16.28%; p < 0.001). A significant difference in seroprevalence was observed in vaccinated and unvaccinated dogs to all four serovars included in the canine vaccine (p < 0.001). Among the diagnostic samples submitted from 2021-2023, 40% (103/252) of the canine serum samples were positive by MAT, with the highest positivity rate for the serovar Autumnalis. OnLeptospiraPCR, 10.7 % (35/325) urine samples and 5.8% (15/257) blood samples were positive. Our study findings show evidence ofLeptospiraexposure and potential disease in the study area. The cross-reactivity between theLeptospiraserovars used in the MAT and vaccination status may also overestimate the levels of exposure.
Mosquito Tissue Ultrastructure-Expansion Microscopy (MoTissU-ExM) enables ultrastructural and anatomical analysis of malaria parasites and their mosquito
Authors: Liffner Benjamin , Alves e Silva Thiago Luiz , Vega-Rodriguez Joel , Absalon Sabrina
Published: April 2024

Study of malaria parasite cell biology is challenged by their small size, which can make visualisation of individual organelles difficult or impossible using conventional light microscopy. In recent years, the ﬁeld has attempted to overcome this challenge through the application of ultrastructure expansion microscopy (U-ExM), which physically expands a biological sample approximately 4.5-fold. To date, U-ExM has mostly been used to visualise blood-stage parasites and used exclusively on parasitesin vitro. Here we developMosquitoTissueU-ExM(MoTissU-ExM), a method for preparing dissected mosquito salivary glands and midguts by U-ExM. MoTissU-ExM preserves both host and parasite ultrastructure, enabling visualisation of oocysts and sporozoitesin situ. We validate that MoTissU-ExM samples expand as expected, provide a direct comparison of the same dissected tissues before and after MoTissU-ExM, and highlight some of the key host and parasite structures that can be visualised following MoTissU-ExM. Finally, we provide a point-by-point protocol for how to perform MoTissU-ExM, along with details on how best to image the expanded tissues, and how to troubleshoot common issues.
Dynamic Formation of the Protein-Lipid Pre-fusion Complex
Authors: Bykhovskaia Maria
Published: April 2024

Synaptic vesicles (SVs) fuse with the presynaptic membrane (PM) to release neuronal transmitters. The SV protein Synaptotagmin 1 (Syt1) serves as a Ca2+sensor for evoked fusion. Syt1 is thought to trigger fusion by penetrating into PM upon Ca2+binding, however the mechanistic detail of this process is still debated. Syt1 interacts with the SNARE complex, a coiled-coil four-helical bundle that enables the SV-PM attachment. The SNARE-associated protein Complexin (Cpx) promotes the Ca2+-dependent fusion, possibly interacting with Syt1. We employed all-atom molecular dynamics (MD) to investigate the formation of the Syt1-SNARE-Cpx complex interacting with the lipid bilayers of PM and SV. Our simulations demonstrated that the PM-Syt1-SNARE-Cpx complex can transition to a “dead-end” state, wherein Syt1 attaches tightly to PM but does not immerse into it, as opposed to a pre-fusion state, which has the tips of the Ca2+-bound C2 domains of Syt1 inserted into PM. Our simulations unraveled the sequence of Syt1 conformational transitions, including the simultaneous Syt1 docking to the SNARE-Cpx bundle and PM, followed by the Ca2+chelation and the penetration of the tips of Syt1 domains into PM, leading to the pre-fusion state of the protein-lipid complex. Importantly, we found that the direct Syt1-Cpx interactions are required to promote these transitions. Thus, we developed the all-atom dynamic model of the conformational transitions that lead to the formation of the pre-fusion PM-Syt1-SNARE-Cpx complex. Our simulations also revealed an alternative “dead-end” state of the protein-lipid complex that can be formed if this pathway is disrupted.

Statement of Significance

Neurons communicate by releasing transmitter molecules. Transmitters are packed in synaptic vesicles (SVs) and released by the fusion of SVs with the presynaptic membrane (PM). This process is regulated by a dynamic complex of fusion proteins, including the coil-coiled SNARE bundle that attaches SV to PM, Synaptotagmin that serves as a Ca2+sensor for the release process, and Complexin that attaches to the SNARE bundle and promotes the Ca2+-dependent release. To understand how these proteins interact dynamically with the lipid bilayers of SV and PM, we employed molecular dynamics, a computational approach that enables simulating the behavior of proteins and lipids at the atomistic resolution. Our simulations enabled us to delineate the stages of the formation of prefusion protein-lipid complex.
Expected reward value and reward prediction errors reinforce but also interfere with human time perception
Authors: DiMarco Emily K. , Shipp Ashley Ratcliffe , Kishida Kenneth T.
Published: April 2024

Time perception is often investigated in animal models and in humans using instrumental paradigms where reinforcement learning (RL) and associated dopaminergic processes have modulatory effects. For example, interval timing, which includes the judgment of relatively short intervals of time (ranging from milliseconds to minutes), has been shown to be modulated by manipulations of striatal dopamine. The ‘expected value of reward’ (EV) and ‘reward prediction errors’ (RPEs) are key variables described in RL-theory that explain dopaminergic signals during reward processing during instrumental learning. Notably, the underlying connection between RL-processes and time perception in humans is relatively underexplored. Herein, we investigated the impact of EV and RPEs on interval timing in humans. We tested the hypotheses that EV and RPEs modulate the experience of short time intervals. We demonstrate that expectations of monetary gains or losses increases the initial performance error for 1000ms intervals. Temporal learning over repeated trials is observed with accelerated learning of non-reinforced 1000ms intervals; however, RPEs – specifically about rewards and not punishments – appear to reinforce performance errors, which effectively interferes with the rate at which (reinforced) 1000ms intervals were learned. These effects were not significant for 3000ms and 5000ms intervals. Our results demonstrate that EV and RPEs influence human behavior about 1000ms time intervals. We discuss our results considering model-free ‘temporal difference RL-theory’, which suggests the hypothesis that interval timing may be mediated by dopaminergic signals that reinforce the learning and prediction of dynamic state-transitions which could be encoded without an explicit reference to ‘time’ intervals.
CRISPR knockout genome-wide screens identify the HELQ-RAD52 axis in regulating the repair of cisplatin-induced single stranded DNA gaps
Authors: Pale Lindsey M. , Khatib Jude B. , Nicolae Claudia M. , Moldovan George-Lucian
Published: April 2024

Treatment with genotoxic agents, such as platinum compounds, is still the mainstay therapeutical approach for the majority of cancers. Our understanding of the mechanisms of action of these drugs is however imperfect, and continuously evolving. Recent advances in the field highlighted single stranded DNA (ssDNA) gap accumulation as a potential determinant underlying cisplatin chemosensitivity, at least in some genetic backgrounds, such as BRCA mutations. Cisplatin-induced ssDNA gaps form upon the arrest of replication forks at sites of cisplatin adducts, and restart of DNA synthesis downstream of the lesion through repriming catalyzed by the PRIMPOL enzyme. Here, we show that PRIMPOL overexpression in otherwise wildtype cells results in accumulation of cisplatin-induced ssDNA gaps without sensitizing cells to cisplatin, suggesting that ssDNA gap accumulation does not confer cisplatin sensitivity in BRCA-proficient cells. To understand how ssDNA gaps may cause cellular sensitivity, we employed CRISPR-mediated genome-wide genetic screening to identify factors which enable the cytotoxicity of cisplatin-induced ssDNA gaps. We found that the helicase HELQ specifically suppresses cisplatin sensitivity in PRIMPOL-overexpressing cells, and this is associated with reduced ssDNA accumulation. We moreover identify RAD52 as a mediator of this pathway, and show that RAD52 promotes ssDNA gap accumulation through a BRCA-mediated mechanism. Our work identified the HELQ-RAD52-BRCA axis as a regulator of ssDNA gap processing, shedding light on the mechanisms of cisplatin sensitization in cancer therapy.
Sickness behaviour within cleaning interactions
Authors: Marquês Tânia , Pereira Beatriz , Marques Mélanie , Repolho Tiago , Paula José Ricardo
Published: April 2024

When facing diseases, strategies such as social distancing have proven effective in preventing disease spread. Cleaning interactions are social interactions where cleaner organisms remove ectoparasites from clients. These interactions can be potential vectors of infectious diseases in reef fishes. Here, we aimed to determine if cleaner wrasses (Labroides dimidiatus) employ social distancing and other behavioural tactics to prevent disease spread within the context of cleaning interactions. To this end, we used bacterial lipopolysaccharides (LPS) immunostimulation to induce “sickness” behaviour in cleaners. After LPS injection, we performed four behavioural trials: social preference (from cleaner and client perspectives), social interaction, and bystander cooperativeness tests. In the social preference test, LPS-injected cleaners showed lower activity rates but no change in their social preference. However, some clients preferred “sick” cleaners. Contrarily, during the social interaction test, cleaners reduced the number of interactions, despite clients’ willingness to interact. For the bystander test, LPS-injected cleaners were unable to adjust their behaviour to be more cooperative. Reduced activity levels revealed lethargy, which may lead to passive self-isolation, allowing for some social distancing of healthy individuals. This suggests that immune-stimulated cleaners undergo changes in their behaviour which can be viewed as a passive social distancing preventing disease spread.