bluuebunny/crossref_metadata_2025 huggingface dataset:
Session duration affects the magnitude of post-exercise hypervolemia but not the erythropoietin response to acute high-intensity interval exercise
Authors: Tripp Thomas R. , Caswell Allison M. , Edgett Brittany A. , MacInnis Martin J.
Published: September 2024

The increase in plasma volume ∼24 hours post-exercise may act as an erythropoietic signal, but this mechanism’s responsiveness to different exercise prescription variables is poorly understood. The purpose of this study was to determine the impact of high-intensity interval exercise duration on plasma volume and related responses. On separate days, 16 healthy, recreationally active participants (n=8 males; n=8 females) performed four (4×4) or eight intervals (8×4) consisting of 4 min at 105% critical power with 3 min recovery. Venous blood samples collected before, immediately after, and 24 hours after each HIIT session were used to measure hemoglobin concentration and hematocrit to calculate plasma volume changes. Erythropoietic and plasma volume regulating hormone concentrations were measured using ELISA kits. Plasma volume decreased immediately after both protocols (4×4: −4.4±3.5%, p<0.05; 8×4: −4.4±3.6%, p<0.05) but was only significantly elevated above baseline 24 hours after the 8×4 protocol (4×4: +1.0±7.1%, p>0.05; 8×4: +5.6±4.6%, p<0.05). Erythropoietin concentration ([EPO]) was higher than baseline 24 hours after the HIIT protocols (4×4: Pre vs 24 h post: 6.5±3.1 vs. 7.1±3.3 mIU/mL; 8×4: 6.9±3.7 vs. 7.3±3.7 mIU/mL; main effect of time, p<0.05) with no difference between protocols (p>0.05). [Aldosterone] was elevated immediately post-exercise after both protocols (4×4: Pre vs 0 h post: 295±151 vs. 544±259 pg/mL; 8×4: 335±235 vs. 821±553 pg/mL), but the 8×4 protocol caused a larger increase (interaction effect, p<0.05). That post-exercise hypervolemia may be exercise duration-dependent but is not required for increases in circulating EPO has important implications for endurance training aiming to increase oxygen delivery to active tissues.

NEWS AND NOTEWORTHY

This study is the first to show that both a common HIIT protocol length (4 x 4 min) and an extended HIIT protocol (8 x 4 min) similarly increased [erythropoietin] 24 h after exercise, despite only the extended protocol transiently increasing plasma volume. Previous works have investigated plasma volume regulation following different HIIT durations, but not explored links to erythropoietic signalling. This study’s findings have relevance for understanding the physiology of exercise-induced erythropoiesis.
Mouse Brain Extractor: Brain segmentation of mouse MRI using global positional encoding and SwinUNETR
Authors: Kim Yeun , Hrncir Haley , Meyer Cassandra E. , Tabbaa Manal , Moats Rex A. , Levitt Pat , Harris Neil G. , MacKenzie-Graham Allan , Shattuck David W.
Published: September 2024

In spite of the great progress that has been made towards automating brain extraction in human magnetic resonance imaging (MRI), challenges remain in the automation of this task for mouse models of brain disorders. Researchers often resort to editing brain segmentation results manually when automated methods fail to produce accurate delineations. However, manual corrections can be labor-intensive and introduce interrater variability. This motivated our development of a new deep-learning-based method for brain segmentation of mouse MRI, which we call Mouse Brain Extractor. We adapted the existing SwinUNETR architecture (Hatamizadeh et al., 2021) with the goal of making it more robust to scale variance. Our approach is to supply the network model with supplementary spatial information in the form of absolute positional encoding. We use a new scheme for positional encoding, which we call Global Positional Encoding (GPE). GPE is based on a shared coordinate frame that is relative to the entire input image. This differs from the positional encoding used in SwinUNETR, which solely employs relative pairwise image patch positions. GPE also differs from the conventional absolute positional encoding approach, which encodes position relative to a subimage rather than the entire image. We trained and tested our method on a heterogeneous dataset of N=223 mouse MRI, for which we generated a corresponding set of manually-edited brain masks. These data were acquired previously in other studies using several different scanners and imaging protocols and includedin vivoandex vivoimages of mice with heterogeneous brain structure due to different genotypes, strains, diseases, ages, and sexes. We evaluated our method’s results against those of seven existing rodent brain extraction methods and two state-of-the art deep-learning approaches, nnU-Net (Isensee et al., 2018) and SwinUNETR. Overall, our proposed method achieved average Dice scores on the order of 0.98 and average HD95 measures on the order of 100 µm when compared to the manually-labeled brain masks. In statistical analyses, our method significantly outperformed the conventional approaches and performed as well as or significantly better than the nnU-Net and SwinUNETR methods. These results suggest that Global Positional Encoding provides additional contextual information that enables our Mouse Brain Extractor to perform competitively on datasets containing multiple resolutions.
Natural Language Processing-like Deep Learning Aided in Identification and Validation of Thiosulfinate Tolerance Clusters in Diverse Bacteria
Authors: Myers Brendon K. , Lamichhane Anuj , Kvitko Brian H. , Dutta Bhabesh
Published: September 2024

Allicin tolerance (alt) clusters in phytopathogenic bacteria, which provide resistance to thiosulfinates like allicin, are challenging to find using conventional approaches due to their varied architecture and the paradox of being vertically maintained within genera despite likely being horizontally transferred. This results in significant sequential diversity that further complicates their identification. Natural language processing (NLP) - like techniques, such as those used in DeepBGC, offers a promising solution by treating gene clusters like a language, allowing for identifying and collecting gene clusters based on patterns and relationships within the sequences. We curated and validatedalt-like clusters inPantoea ananatis97-1R (PA),Burkholderia gladiolipv.gladioliFDAARGOS 389 (BG), andPseudomonas syringaepv. tomato DC3000 –(PTO). Leveraging sequences from the RefSeq bacterial database, we conducted comparative analyses of gene synteny, gene/protein sequences, protein structures, and predicted protein interactions. This approach enabled the discovery of several novelalt-like clusters previously undetectable by other methods, which were further validated experimentally. Our work highlights the effectiveness of NLP-like techniques for identifying underrepresented gene clusters and expands our understanding of the diversity and utility ofalt-like clusters in diverse bacterial genera. This work demonstrates the potential of these techniques to simplify the identification process and enhance the applicability of biological data in real-world scenarios.

Significance Statement

Thiosulfinates, like allicin, are potent antifeedants and antimicrobials produced byAlliumspecies and pose a challenge for phytopathogenic bacteria. Phytopathogenic bacteria have been shown to utilize an allicin tolerance (alt) gene cluster to circumvent this host response, leading to economically significant yield losses. Due to the complexity of mining these clusters, we applied techniques akin to natural language processing to analyze Pfam domains and gene proximity. This approach led to the identification of novelalt-like gene clusters, showcasing the potential of artificial intelligence to reveal elusive and underrepresented genetic clusters and enhance our understanding of their diversity and role across various bacterial genera.
Predicting the effect of non-coding mutations on single-cell DNA methylation using deep learning
Authors: Liu Zhe , Gu An , Bao Yihang , Lin Guan Ning
Published: September 2024

Predicting the effects of non-coding mutations on DNA methylation is crucial for advancing our understanding of gene expression, epigenetic inheritance, and its role in disease mechanisms. Current methods lack the capability to predict the impact of non-coding mutations on DNA methylation at single-cell resolution and long range, while remain challenges in tracking SNP influences throughout disease progression. Here, we introduce Methven, a deep learning-based framework designed to predict the effects of non-coding mutations on DNA methylation at single-cell resolution, to overcome the challenges. Methven integrates DNA sequences and ATAC-seq data, employing a divide-and-conquer approach to handle varying scales of SNP-CpG interactions. By leveraging a pretrained DNA language model, Methven accurately predicts both the direction and magnitude of methylation changes across a 100kbp range with a lightweight architecture. The evaluation results demonstrate the superior performance of Methven in prioritizing functional non-coding mutation, model interpretability, and its potential for revealing personalized mutation-disease associations.
Gradients of Recognition Molecules Shape Synaptic Specificity of Visuomotor Transformation
Authors: Dombrovski Mark , Zang Yixin , Frighetto Giovanni , Vaccari Andrea , Jang Hyojong , Mirshahidi Parmis S. , Xie Fangming , Sanfilippo Piero , Hina Bryce W. , Rehan Aadil , Hussein Roni H. , Mirshahidi Pegah S. , Lee Catherine , Morris Aileen , Frye Mark A. , von Reyn Catherine R. , Kurmangaliyev Yerbol Z. , Card Gwyneth M. , Zipursky S. Lawrence
Published: September 2024

Converting sensory information into motor commands is fundamental to most of our actions1,2. InDrosophila, visuomotor transformations are mediated by Visual Projection Neurons (VPNs)3,4. These neurons encode object location and motion to drive directional behaviors through a synaptic gradient mechanism5. However, the molecular origins of such graded connectivity remain unknown. We addressed this question in a VPN cell type called LPLC26, which integrates looming motion and transforms it into an escape response through two separate dorsoventral synaptic gradients at its inputs and outputs. We identified two corresponding dorsoventral expression gradients of cell recognition molecules within the LPLC2 population that regulate this synaptic connectivity. Dpr13 determines synaptic outputs of LPLC2 axons by interacting with its binding partner, DIP-ε, expressed in the Giant Fiber – a neuron that mediates escape7. Similarly, Beat-VI regulates synaptic inputs onto LPLC2 dendrites by interacting with Side-II expressed in upstream motion-detecting neurons. Behavioral, physiological, and molecular experiments demonstrate that these coordinated molecular gradients regulate synaptic connectivity, enabling the accurate transformation of visual features into motor commands. As continuous variation in gene expression within a neuronal type is also observed in the mammalian brain8, graded expression of cell recognition molecules may represent a common mechanism underlying synaptic specificity.
Surface-Based vs. Voxel-Based Finite Element Head Models: Comparative Analyses of Strain Responses
Authors: Zhou Zhou , Li Xiaogai , Kleiven Svein
Published: September 2024

Finite element (FE) models of the human head are important injury assessment tools but developing a high-quality, hexahedral-meshed FE head model without compromising geometric accuracy is a challenging task. Important brain features, such as the cortical folds and ventricles, were captured only in a handful of FE head models that were primarily developed from two meshing techniques, i.e., surface-based meshing with conforming elements to capture the interfacial boundaries and voxel-based meshing by converting the segmented voxels into elements with and without mesh smoothing. Despite these advancements, little knowledge existed of how similar the strain responses were between surface- and voxel-based FE head models. This study uniquely addressed this gap by presenting three anatomically detailed models - a surface-based model with conforming meshes to capture the cortical folds-subarachnoid cerebrospinal fluid and brain-ventricle interfaces, and two voxel-based models (with and without mesh smoothing) - derived from the same imaging dataset. These three models were employed to simulate head impacts. The results showed that, when calculating commonly used injury metrics, including the percentile strains below the maximum (e.g., 99 percentile strain) and the volume of brain element with the strain over certain thresholds, the responses of the three models were virtually identical. Different strain patterns existed between the surface- and the voxel-based models at the interfacial boundary (e.g., sulci and gyri in the cortex, regions adjacent to the falx and tentorium) with strain differences exceeding 0.1, but remarkable similarities were noted at the non-interfacial region. The mesh smoothing procedure marginally reduced the strain discrepancies between the voxel- and surface-based model. This study yielded new quantitative insights into the general similarity in the strain responses between the surface- and voxel-based FE head models and underscored that caution should be exercised when using the strain at the interface to predict injury.
Mitochondrial Hyperactivity and Reactive Oxygen Species Drive Innate Immunity to the Yellow Fever Virus-17D Live-Attenuated Vaccine
Authors: Muccilli Samantha G. , Schwarz Benjamin , Jessop Forrest , Shannon Jeffrey G. , Bohrnsen Eric , Shue Byron , Hong Seon-Hui , Hsu Thomas , Ashbrook Alison W. , Guarnieri Joseph W. , Lack Justin , Wallace Douglas C. , Bosio Catharine M. , MacDonald Margaret R. , Rice Charles M. , Yewdell Jonathan W. , Best Sonja M.
Published: September 2024

The yellow fever virus 17D (YFV-17D) live attenuated vaccine is considered one of the successful vaccines ever generated associated with high antiviral immunity, yet the signaling mechanisms that drive the response in infected cells are not understood. Here, we provide a molecular understanding of how metabolic stress and innate immune responses are linked to drive type I IFN expression in response to YFV-17D infection. Comparison of YFV-17D replication with its parental virus, YFV-Asibi, and a related dengue virus revealed that IFN expression requires RIG-I-like Receptor signaling through MAVS, as expected. However, YFV-17D uniquely induces mitochondrial respiration and major metabolic perturbations, including hyperactivation of electron transport to fuel ATP synthase. Mitochondrial hyperactivity generates reactive oxygen species (mROS) and peroxynitrite, blocking of which abrogated IFN expression in non-immune cells without reducing YFV-17D replication. Scavenging ROS in YFV-17D-infected human dendritic cells increased cell viability yet globally prevented expression of IFN signaling pathways. Thus, adaptation of YFV-17D for high growth uniquely imparts mitochondrial hyperactivity generating mROS and peroxynitrite as the critical messengers that convert a blunted IFN response into maximal activation of innate immunity essential for vaccine effectiveness.
Understanding therapeutic tolerance through a mathematical model of drug-induced resistance
Authors: Sontag Eduardo D. , Gevertz Jana L. , Greene James , Comandante-Lou Natacha , Prosperi Samantha
Published: September 2024

There is growing recognition that phenotypic plasticity enables cancer cells to adapt to various environmental conditions. An example of this adaptability is the persistence of an initially sensitive population of cancer cells in the presence of therapeutic agents. Understanding the implications of this drug-induced resistance is essential for predicting transient and long-term tumor tumor dynamics subject to treatment. This paper introduces a mathematical model of this phenomenon of drug-induced resistance which provides excellent fits to time-resolvedin vitroexperimental data. From observational data of total numbers of cells, the model unravels the relative proportions of sensitive and resistance subpopulations, and quantifies their dynamics as a function of drug dose. The predictions are then validated using data on drug doses which were not used when fitting parameters. The model is then used, in conjunction with optimal control techniques, in order to discover dosing strategies that might lead to better outcomes as quantified by lower total cell volume.
Harmonizing terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) with multiplexed iterative immunofluorescence enriches spatial contextualization of cell death
Authors: Sherman Marc S , McMahon-Skates Thomas , Gaston Lindsey S. , Majzoub Joseph A , Goessling Wolfram
Published: September 2024

Terminal deoxynucleotidyl transferase dUTP Nick End Labeling (TUNEL) is an essential tool for the detection of cell death in tissues. Although TUNEL is not known to be compatible with multiplexed spatial proteomic methods, harmonizing TUNEL with such methods offers the opportunity to delineate cell-type specific cell death labeling and precise spatial contextualization of cell death in complex tissues. Here we evaluated variations of the TUNEL assay for their compatibility with a multiplexed immunofluorescence method, multiple iterative labeling by antibody neodeposition (MILAN), in two different tissues and injury models for cell death, acetaminophen-induced hepatocyte necrosis and dexamethasone-induced adrenocortical apoptosis. Using a commercial Click-iT-based assay as a standard, TUNEL signal could be reliably produced independent of antigen-retrieval method, with tissue-specific minor differences in signal-to-noise. In contrast, proteinase K treatment consistently reduced or even abrogated protein antigenicity, while pressure cooker treatment consistently enhanced protein antigenicity for the targets tested. Antibody-based TUNEL protocols using pressure-cooker antigen retrieval were MILAN erasure-compatible thus enabling harmonization of TUNEL with MILAN. As many as four staining cycles could be performed without loss of subsequent TUNEL signal, while first-round TUNEL did not influence protein antigenicity in subsequent rounds. We conclude this harmonized assay performs comparably to an established commercial assay, but preserves protein antigenicity, thus enabling versatile integration with multiplexed immunofluorescence using MILAN. We anticipate this harmonized protocol will enable broad and flexible integration of TUNEL into multiplexed spatial proteomic assays, thus vastly enhancing the spatial contextualization of cell death in complex tissues.
Differential Effectiveness of Poloxamer 188 in Dystrophic Cardiomyopathy Reveals Complex Pathophysiology
Authors: Stevens Jackie , Banyard F. Parker , Millner Balagtas Danielle , Williams Derek , Townsend DeWayne
Published: September 2024

Synthetic membrane stabilizers, such as poloxamer 188 (P188), have great promise in the treatment of Duchenne muscular dystrophy and other diseases associated with disrupted membranes. The aim of this study was to assess the efficacy of P188 to limit myocardial damage in models of muscular dystrophy subjected to highly injurious stress. These studies use male and female mdx and β-sarcoglycan null (β-SG-/-) mice subjected to an isoproterenol stress protocol in the presence or absence of P188. We show that P188 provides a significant level of protection to male mdx hearts from the isoproterenol induced injury. Surprisingly, we find that P188 has no protective actions in female mdx mice or in β-SG-/-mice of either sex. These results suggest that the mechanism of action of P188 is more complicated than previously thought. The presence of sex differences in the absence of dystrophin is not consistent with a model of P188 working by biophysical restoration of membrane integrity. Furthermore, the absence of protective effects of P188 in β-SG-/-myocardium indicates that there are important differences in the mechanisms of membrane damage in hearts lacking dystrophin and hearts lacking the sarcoglycan complex. Developing a better understanding of these differences will be important in the development of therapies for dystrophic cardiomyopathy and other forms of heart disease.
Limited O-specific polysaccharide (OSP)-specific functional antibody responses in young children with Shigella infection in Bangladesh
Authors: Bernshtein Biana , Zhiteneva Julia A. , Janardhanan Jeshina , Wagh Chanchal , Kelly Meagan , Verma Smriti , Jung Wonyeong , Basher Salima Raiyan , Amin Mohammad Ashraful , Mahamud Shakil , Rajib Nazmul Hasan , Chowdhury Fahima , Khan Ashraful Islam , Charles Richelle C. , Xu Peng , Kováč Pavol , Chakraborty Subhra , Kaminski Robert W. , Alter Galit , Bhuiyan Taufiqur R. , Qadri Firdausi , Ryan Edward T.
Published: September 2024

Shigellosis is the second leading cause of diarrheal death in children younger than five years of age globally. At present, there is no broadly licensed vaccine against shigella infection. Previous vaccine candidates have failed at providing protection for young children in endemic settings. Improved understanding of correlates of protection against Shigella infection and severe shigellosis in young children living in endemic settings is needed. Here, we applied a functional antibody profiling approach to define Shigella-specific antibody responses in young children versus older individuals with culture-confirmed shigellosis in Bangladesh, a Shigella endemic area. We analyzed Shigella-specific antibody isotypes, FcR binding and antibody-mediated innate immune cell activation in longitudinal serum samples collected at clinical presentation and up to 1 year later. We found that higher initial Shigella O-specific polysaccharide (OSP)-specific and protein-specific IgG and FcγR binding levels correlated with less severe disease regardless of patient age, but that individuals under 5 years of age developed a less prominent class switched, FcR-binding, functional and durable antibody response against both OSP and protein Shigella antigens than older individuals. Focusing on the largest cohort, we found that functionalS. flexneri2a OSP-specific responses were significantly induced only in individuals over age 5 years, and that these responses promoted monocyte phagocytosis and activation. Our findings suggest that in a Shigella endemic region, young children with shigellosis harbor a functional antibody response that fails to maximally activate monocytes; such a response may be important in facilitating subsequent innate cell clearance of Shigella, especially via recruitment and activation of polymorphonuclear cells capable of directly killing Shigella.
Direct contact of bacterial surface induces phase separation of the host phagosome membrane
Authors: Bhausaheb Aher Jayesh , Aniruddha N , Koiri Debraj , Shaikh Jafarulla , Choubey Sandeep , Saleem Mohammed
Published: September 2024

Pathogenic bacteria evade host defense by rupturing the phagosomal compartment, enabling their escape into the host cytosol. The bacteria is known to establish direct physical contact with the host compartment prior to phagosome disruption. However, the impact of direct-physical contact on the phagosome remodeling and deformation remains elusive. To probe this, we first developed a method wherein we reconstitute a phagosome-like giant compartment encapsulatingMycobacterium smegmatis, a non-motile opportunistic bacterium. We discover that the direct contact between the bacteria and the encapsulating host membrane induces membrane bending, lipid wrapping, and local lipid phase separation at the contact site. The degree of phase separation is driven by the bacterial load leading to fluidization of the membrane, as evident from the decreased area stretch and bending modulus, making the host compartment more deformable. Surprisingly, for saturating bacterial load the fluid host membrane transforms into a scaffold-like rigid layer. We also find that the direct contact of the bacteria enhances the membranolytic potential of ESAT-6 thus contributing to its virulence. Together our findings provide mechanistic insights into the role of direct physical contact of the bacteria during phagosome disruption.
Structural stability determines evolutionary stability in mutualistic model ecosystems
Authors: Lurgi Miguel , Pascual-García Alberto
Published: September 2024

Understanding the factors that influence the persistence and stability of complex ecological networks is a central focus of ecological research. Recent research into these factors has predominantly attempted to unveil the ecological processes and structural constraints that influence network stability. Comparatively little attention has been given to the consequences of evolutionary events, despite the fact that the interplay between ecology and evolution has been recognised as fundamental to understand the formation of ecological communities and predict their reaction to change. In light of current environmental challenges, there is a compelling need for a quantitative framework to predict biodiversity loss under environmental perturbations while accounting for evolutionary processes.

We extend existing mutualistic population dynamical models by incorporating evolutionary adaptation events to address this critical gap. We relate ecological aspects of mutualistic community stability to the stability of persistent evolutionary pathways. Our findings highlight the significance of the structural stability of ecological systems in predicting biodiversity loss under both evolutionary and environmental changes, particularly in relation to species-level selection. Notably, our simulations reveal that the evolution of mutualistic networks tends to increase a network-dependent parameter termed critical competition, which places systems in a regime in which mutualistic interactions enhance structural stability and, consequently, biodiversity.

This research emphasizes the pivotal role of natural selection in shaping ecological networks, steering them towards reduced effective competition below a critical threshold where mutualistic interactions foster stability. The outcomes of our study contribute to the development of a predictive framework for eco-evolutionary dynamics, offering insights into the interplay between ecological and evolutionary processes in the face of environmental change.
How can interspecific pollen transfer affect the coevolution and coexistence of two closely related plant species?
Authors: Morita Keiichi , Sasaki Akira , Iritani Ryosuke
Published: September 2024

Interspecific pollen transfer (IPT), the movement of pollen grains between different plant species by sharing pollinators, incurs costs (fitness reduction) for seed production. IPT thereby reduces the reproductive success of co-flowering plants sharing pollinators, thus preventing their coexistence. However, the impact of IPT on the evolutionary dynamics and evolution-mediated ecological dynamics of sex allocation resource investment to pollen versus ovules) is poorly understood. Here, we investigate the consequences of the female costs incurred by IPT for the co-evolution and coexistence of two plants, by using a mathematical model where two plant species interact with each other via resource competition, pollen movements within and between species, and reduced fertilization due to IPT. The ecological situation we consider here is that an invasive species with female-biased sex allocation immigrates into a habitat of a resident species whose sex allocation is evolutionarily maintained at Fisherian sex allocation (FSA). By using adaptive dynamics theory, we found that regardless of the strength of IPT, natural selection favours the equal allocation to pollen grains and ovules (FSA) for both species. If the mutual impact of IPT on two species is similar in magnitude, we find that the eco-evolutionary dynamics can lead to their stable coexistence. In contrast, when only the invasive species negatively impacts the resident species through IPT, the evolution in invasive species from female-biased sex allocation to FSA causes the extinction of the resident species. Given that local mate competition in small populations is expected to result in female-based sex allocation, our finding suggests that if invasive species are relaxed from local mate competition, they may drive the resident species to extinction. Our study highlights the importance and complexity of the evolution of biased sex allocation driven by IPT to understand the coexistence of closely related plant species.
Sarcolemmal and mitochondrial membrane potentials measuredex vivoandin vivoin the heart by pharmacokinetic modelling of [99mTc]sestamibi
Authors: Waters Edward CT. , Baark Friedrich , Orton Matthew R. , Shattock Michael J. , Southworth Richard , Eykyn Thomas R.
Published: September 2024

We present a compartmental modelling approach to analyse radioactive time activity curves for first pass kinetics of [99mTc]sestamibi in the heart. Reparametrizing the kinetic equations using the Nernst membrane-potential equation provides a novel means of non-invasively estimating the sarcolemmal (Em) and mitochondrial (ΔΨm) membrane potentials in the heart. A Markov Chain Monte Carlo (MCMC) fitting approach was applied to data derived from established interventions in Langendorff perfused rat hearts where the sarcolemmal membrane was depolarised using hyperkalaemic Krebs Henseleit buffers; the mitochondrial membrane was depolarised using carbonylcyanide-3-chlorophenylhydrazone (CCCP); or both membranes were depolarised using their combination. Translating this approach to single photon emission planar scintigraphy kinetics from healthy rats allowed an estimate of these membrane potentials (voltages)in vivofor the first time; the values wereEm= –62 ± 5 mV and ΔΨm= –151 ± 5 mV (n = 4, mean ± SD).
Temperature Sensitive Glutamate Gating of AMPA-subtype iGluRs
Authors: Kumar Mondal Anish , Carrillo Elisa , Jayaraman Vasanthi , Twomey Edward C.
Published: September 2024

Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that mediate the majority of excitatory neurotransmission1. iGluRs are gated by glutamate, where upon glutamate binding, they open their ion channels to enable cation influx into post-synaptic neurons, initiating signal transduction2. The structural mechanism of iGluR gating by glutamate has been extensively studied in the context of positive allosteric modulators (PAMs)3–15. A fundamental question has remained – are the PAM activated states of iGluRs representative of glutamate gating in the absence of PAMs? Here, using the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid subtype iGluR (AMPAR) we show that glutamate gating is unique from gating in the presence of PAMs. We demonstrate that glutamate gating is temperature sensitive, and through temperature-resolved cryo-electron microscopy (cryo-EM), capture all major glutamate gating states. Physiological temperatures augment channel activation and conductance. Activation by glutamate initiates ion channel opening that involves all ion channel helices hinging away from the pores axis in a motif that is conserved across all iGluRs. Desensitization occurs when the local dimer pairs decouple and enables closure of the ion channel below through restoring the channel hinges and refolding the channel gate. Our findings define how glutamate gates iGluRs, provide foundations for therapeutic design, and point to iGluR gating being temperature sensitive.
Membrane-assisted Aβ40 aggregation pathways
Authors: Muhammedkutty Fidha Nazreen Kunnath , Zhou Huan-Xiang
Published: September 2024

Alzheimer’s disease (AD) is caused by the assembly of amyloid-beta (Aβ) peptides into oligomers and fibrils. Endogenous Aβ aggregation may be assisted by cell membranes, which can accelerate the nucleation step enormously, but knowledge of membrane-assisted aggregation is still very limited. Here we used extensive MD simulations to structurally and energetically characterize key intermediates along the membrane-assisted aggregation pathways of Aβ40. Reinforcing experimental observations, the simulations reveal unique roles of GM1 ganglioside and cholesterol in stabilizing membrane-embedded β-sheets and of Y10 and K28 in the ordered release of a small oligomeric seed into solution. The same seed leads to either an open-shaped or R-shaped fibril, with significant stabilization provided by inter- or intra-subunit interfaces between a straight β- sheet (residues Q15-D23) and a bent β-sheet (residues A30-V36). This work presents the first comprehensive picture of membrane-assisted aggregation of Aβ40, with broad implications for developing AD therapies and rationalizing disease-specific polymorphisms of amyloidogenic proteins.
Distinct evolution at TCRα and TCRβ loci in the genusMus
Authors: Peters Moritz , Soltys Volker , Su Dingwen , Chan Yingguang Frank
Published: September 2024

T cells recognize an immense spectrum of pathogens to initiate immune responses by means of a large repertoire of T cell receptors (TCRs) that arise from somatic rearrangements ofvariable,diversityandjoininggene segments at the TCR loci. These gene segments have emerged from a limited number of ancestral genes through a series of gene duplication events, resulting in a greatly variable number of such genes across different species. Apart from the complete V(D)J gene annotations in the human and mouse reference assemblies, little is known about the structure of TCR loci in other species.

Here, we performed a comprehensive comparison of the TCRα and TCRβ gene segment clusters in mice and three of its closely related sister species. We show that the TCRαvariablegene cluster is frequently rearranged, leading to deletions and sequence inversions in this region. The resulting complexity of TCR loci severely complicates the assembly of these loci and the annotation of gene segments. By jointly utilizing genomic and transcriptomic data, we show that inMus musculus castaneusthe variable gene cluster at the α locus has undergone a recent major locus contraction, leading to the loss of 74variablegene segments. Additionally, we validated the expression of functional variable genes, including atypical ones with inverted orientation relative to other such segments. Disentangling the fine-scale structure of TCR loci in different species can provide valuable insights in the evolution and diversity of TCR repertoires.
Wildlife provisioning selects for higher pathogen virulence in hosts with incomplete immunity
Authors: Walsman Jason Cosens , Fleming-Davies Arietta E , Hall Richard , Hawley Dana
Published: September 2024

Anthropogenic food provisioning provides massive inputs of food to wildlife, with profound ecological and evolutionary consequences. By altering wildlife condition, density, and behavior, provisioning can influence transmission of infectious diseases and thus may impose strong selection pressure on wildlife pathogens. But surprisingly, we lack theory on the eco-evolutionary consequences of provisioning for host-pathogen dynamics. Here we develop a mathematical model of the eco-evolutionary dynamics of a wildlife pathogen under provisioning, motivated byMycoplasma gallisepticum, a bacterial pathogen that emerged, spread, and changed its virulence in provisioned house finches. We model how provisioning influences the evolution of pathogen virulence, defined here as mortality associated with infection. Consistent with past empirical work, house finches recover from infection and acquire incomplete immunity; this incomplete immunity is stronger if their initial infection was with a more virulent pathogen strain. We find that, even though provisioning improves body condition, it should still select for higher virulence, and thus may actually lead to declines in host populations. These negative effects arise because provisioning magnifies the impact of incomplete immunity, selecting for higher virulence and driving host populations down. Our results highlight that food provisioning can select for more virulent pathogens, with potentially far-reaching implications for conservation.
Feature-specific divisive normalization improves natural image encoding for depth perception
Authors: Ni Long , Burge Johannes
Published: September 2024

Vision science and visual neuroscience seek to understand how stimulus and sensor properties limit the precision with which behaviorally-relevant latent variables are encoded and decoded. In the primate visual system, binocular disparity—the canonical cue for stereo-depth perception—is initially encoded by a set of binocular receptive fields with a range of spatial frequency preferences. Here, with a stereo-image database having ground-truth disparity information at each pixel, we examine how response normalization and receptive field properties determine the fidelity with which binocular disparity is encoded in natural scenes. We quantify encoding fidelity by computing the Fisher information carried by the normalized receptive field responses. Several findings emerge from an analysis of the response statistics. First, broadband (or feature-unspecific) normalization yields Laplace-distributed receptive field responses, and narrowband (or feature-specific) normalization yields Gaussian-distributed receptive field responses. Second, the Fisher information in narrowband-normalized responses is larger than in broadband-normalized responses by a scale factor that grows with population size. Third, the most useful spatial frequency decreases with stimulus size and the range of spatial frequencies that is useful for encoding a given disparity decreases with disparity magnitude, consistent with neurophysiological findings. Fourth, the predicted patterns of psychophysical performance, and absolute detection threshold, match human performance with natural and artificial stimuli. The current computational efforts establish a new functional role for response normalization, and bring us closer to understanding the principles that should govern the design of neural systems that support perception in natural scenes.
NetMedPy: A Python package for Large-Scale Network Medicine Screening
Authors: Aldana Andrés , Sebek Michael , Ispirova Gordana , Dorantes-Gilardi Rodrigo , Barabási Albert-László , Loscalzo Joseph , Menichetti Giulia
Published: September 2024

Network medicine leverages the quantification of information flow within sub-cellular networks to elucidate disease etiology and comorbidity, as well as to predict drug efficacy and identify potential therapeutic targets. However, current Network Medicine toolsets often lack computationally efficient data processing pipelines that support diverse scoring functions, network distance metrics, and null models. These limitations hamper their application in large-scale molecular screening, hypothesis testing, and ensemble modeling. To address these challenges, we introduce NetMedPy, a highly efficient and versatile computational package designed for comprehensive Network Medicine analyses.

Availability

NetMedPy is an open-source Python package under an MIT license. Source code, documentation, and installation instructions can be downloaded fromhttps://github.com/menicgiulia/NetMedPyandhttps://pypi.org/project/NetMedPy. The package can run on any standard desktop computer or computing cluster.
Allosteric modulation of proton binding confers Cl-activation and glutamate selectivity to vesicular glutamate transporters
Authors: Borghans Bart , Kortzak Daniel , Longo Piersilvio , Machtens Jan-Philipp , Fahlke Christoph
Published: September 2024

Vesicular glutamate transporters (VGLUTs) fill synaptic vesicles with glutamate and remove luminal Cl-via an additional anion channel mode. Both of these transport functions are stimulated by luminal acidification, luminal-positive membrane potential, and luminal Cl-. We studied VGLUT1 transporter/channel activation using a combination of heterologous expression, cellular electrophysiology, fast solution exchange, and mathematical modeling. Cl-channel gating can be described with a kinetic scheme that includes two protonation sites and distinct opening, closing, and Cl--binding rates for each protonation state. Cl-binding promotes channel opening by modifying the pKavalues of the protonation sites and rates of pore opening and closure. VGLUT1 transports glutamate and aspartate at distinct stoichiometries: H+-glutamate exchange at 1:1 stoichiometry and aspartate uniport. Neurotransmitter transport with variable stoichiometry can be described with an alternating access model that assumes that transporters without substrate translocate in the doubly protonated state to the inward-facing conformation and return with the bound amino acid substrate as either singly or doubly protonated. Glutamate, but not aspartate, promotes the release of one proton from inward-facing VGLUT1, resulting in preferential H+-coupled glutamate exchange. Cl-stimulates glutamate transport by making the glutamate-binding site accessible to cytoplasmic glutamate and by facilitating transitions to the inward-facing conformation after outward substrate release. We conclude that allosteric modification of transporter protonation by Cl-is crucial for both VGLUT1 transport functions.
Rhopilema nomadicain the Mediterranean: molecular evidence for migration and ecological hypothesis regarding its proliferation
Authors: Kuplik Zafrir , Dror Hila , Tamar Karin , Sutton Alan , Lusana James , Lugendo Blandina , Angel Dror
Published: September 2024

Since it was first observed in Israel in the 1970s, the ‘nomad jellyfish’Rhopilema nomadicahas established a reputation as one of the worst invasive species in the Mediterranean Sea. It was assumed to originate in the Red Sea, or in the Indo-Pacific region, but in the absence of additional reports of live specimens outside the Mediterranean, its origins remained a mystery. Here, via molecular analysis, we present the first verified results of the existence ofR. nomadicain the Western Indian Ocean. Moreover, using additional evidence fromCassiopea andromedaandR. nomadica, we propose that the construction of the Aswan High Dam may have led to the proliferation ofR. nomadicain the Levantine Basin.
Exploring cellular changes in ruptured human quadriceps tendons at single-cell resolution
Authors: Mimpen Jolet Y. , Baldwin Mathew J. , Paul Claudia , Ramos-Mucci Lorenzo , Kurjan Alina , Cohen Carla J. , Sharma Shreeya , Chevalier Florquin Marie S.N. , Hulley Philippa A. , McMaster John , Titchener Andrew , Martin Alexander , Costa Matthew L. , Gwilym Stephen E. , Cribbs Adam P. , Snelling Sarah J.B.
Published: September 2024

Tendon ruptures in humans have regularly been studied during the chronic phase of injury. However, the early response to injury remains less investigated. Quadriceps tendons, which require prompt surgical treatment, offer a model to investigate this early response. Therefore, this study aimed to explore the early cellular changes in ruptured compared to healthy human quadriceps tendons. Quadriceps tendon samples were collected from patients undergoing tibial shaft fracture repair (healthy) or tendon repair surgery for complete rupture (collected 7-8 days post-injury). Nuclei were isolated for single-nucleus RNA sequencing, and comprehensive transcriptomic analysis was conducted to profile cellular changes. The transcriptomes of 12,808 nuclei were profiled, including 7,268 nuclei from healthy and 5,540 nuclei from ruptured quadriceps tendons, revealing 12 major cell types and several cell subtypes and states. Rupture samples showed increased expression of genes related to extracellular matrix organisation and cell cycle signalling, and a decrease in expression of genes in lipid metabolism pathways. These changes were driven predominantly by gene expression changes in the fibroblast, vascular endothelial cells (VECs), mural cell, and macrophage populations: fibroblasts shift to an activated phenotype upon rupture and there is an increase in proportion of capillary and dividing VECs, suggesting an angiogenic response. A diverse immune environment was observed, with a shift from homeostatic to activated macrophages following rupture. Cell-cell interactions increased in rupture, both in their number and diversity, and primarily involving fibroblast and endothelial cell populations. Collectively, this transcriptomic analysis suggests that fibroblasts and endothelial cells are key orchestrators of the early injury response within ruptured quadriceps tendon.
Multiscale topological analysis of kinetoplast DNA via high-resolution AFM
Authors: Diggines Bradley , Whittle Sylvia , Yadav Indresh , Holmes Elizabeth P. , Rollins Daniel E. , Catley Thomas E. , Doyle Patrick S. , Pyne Alice L.B.
Published: September 2024

Kinetoplast DNA is a complex nanoscale network, naturally assembled from thousands of interconnected DNA circles within the mitochondrion of certain parasites. Despite the relevance of this molecule to parasitology and the recent discovery of tuneable mechanics, its topology remains highly contested. Here we present a multiscale analysis into the structure of kDNA using a combination of high-resolution atomic force microscopy and custom-designed image analysis protocols. By capturing a notably large set of high-resolution images, we are able to look beyond individual kDNA variations and quantify population properties throughout several length scales. Within the sample, geometric fluctuations of area and mean curvature are observed, corresponding with previous in-vitro measurements. These translate to localised variations in density, with a sample-wide decrease in DNA density from the outer rim of the molecule to the centre and an increase in pore size. Nodes were investigated in a single molecule study, and their estimated connectivity significantly exceeded mean valence, with a high dependence on their position in the network. While node separation was approximately half the minicircle circumference, it followed a strong bimodal distribution, suggesting more complex underlying behaviour. Finally, upon selective digestion of the network, breakdown of the fibril-cap heterogeneity was observed, with molecules expanding less upon immobilisation on the mica surface. Additionally, selective digestion was seen in localised areas of the network, increasing pore size disproportionately. Overall, the combination of high-resolution AFM and single molecule image analysis provides a promising method to the continued investigation of complex nanoscale structures. These findings support the ongoing characterisation of kDNA topology to aid understanding of its biological and mechanical phenomena.
Integrating promiscuous enzyme activities in protein-constrained models pinpoints the role of underground metabolism in robustness of metabolic phenotypes
Authors: de Moura Ferreira Maurício Alexander , Menezes de Almeida Eduardo Luís , Batista da Silveira Wendel , Nikoloski Zoran
Published: September 2024

The integration of enzyme parameters in constraint-based models have significantly improved the prediction of physiological and molecular traits, including enzyme resource usage and distribution. However, current approaches largely neglect the set of promiscuous enzyme activities that jointly comprise the so-called underground metabolism. To allow enzyme-constrained study of underground metabolism, we developed the CORAL Toolbox. This toolbox reworks enzyme usage into subpools for each reaction catalysed by a promiscuous enzyme, increasing the resolution of modelled enzyme resource allocation. Applying CORAL with an enzyme-constrained genome-scale metabolic model ofEscherichia coli, we found that underground metabolism resulted in larger flexibility in metabolic fluxes and enzyme usage. Knocking out the main activity of a promiscuous enzyme led to small enzyme redistribution to the side activities. Further, knocking out pairs of main activities showed that non-promiscuous enzymes exhibited larger effect on growth. In addition, we demonstrated these findings are robust with respect to the parameterization of the models with catalytic rates from different prediction tools. Together, our results from modelling underground metabolism in enzyme-constrained models indicated that promiscuous enzyme activities are vital to maintain robust metabolic function and growth.