bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatial and network principles behind neural generation of locomotion
Authors: Komi Salif , Winther August , Houser Grace A. , Topilko Thomas , Sørensen R.J.F. , Larsen Silas Dalum , Adamsson Bonfils Madelaine C. , Li Guanghui , Berg Rune W.
Published: October 2024

Generation of locomotion is a fundamental function of the spinal cord, yet the underlying principles remain unclear. In particular, the relationship between neuronal cell types, networks and functions has been difficult to establish1,2. Here, we propose principles by which functions arise primarily from spatial features of the cord. First, we suggest that projections of distinct cell types constitute an asymmetrical “Mexican hat” topology, i.e. local excitation and surrounding inhibition with dissimilar length of projection along the rostro-caudal axis. Second, this projection topology constitutes the mechanism of rhythm- and pattern generation of mammalian locomotion. Third, the role of segregation of cell types in the transversal plane is for descending fibers to find appropriate targets. Modulation of these targets allows control of motor activity by adjusting the symmetry of the projection topology. We extract these principles via a model of the mouse spinal cord, where networks are constructed by probabilistic sampling of synaptic connections from cell-specific projection patterns, which are based on previous studies3, 4. The cell-type distributions are derived from single-cell RNA sequencing combined with spatial transcriptomics5. We find that essential aspects of locomotion are readily reproduced and controlled without requiring parameter optimization, and several experimental observations can now be explained mechanistically. Further, two main features are predicted: propagating bumps of neural activity during rhythmical activity and formation of static bumps during arrest and posture. Besides linking cell types, structure and function, we propose our approach as a new theoretical framework for motor control.
Lung CD4+resident memory T cells use airway secretory cells to stimulate and regulate neutrophilic allergic airways disease
Authors: Ravi Vijay Raaj , Korkmaz Filiz T. , De Ana Carolina Lyon , Lu Lu , Shao Feng-Zhi , Odom Christine V. , Barker Kimberly A. , Ramanujan Aditya , Niszczak Emma N. , Goltry Wesley N. , Martin Ian M.C. , Ha Catherine T. , Quinton Lee J. , Jones Matthew R. , Fine Alan , Welch Joshua D. , Chen Felicia , Belkina Anna C. , Mizgerd Joseph P. , Shenoy Anukul T.
Published: October 2024

Neutrophilic asthma is a vexing disease, but mechanistic and therapeutic advancement will require better models of allergy-induced airway neutrophilia. Here, we find that periodic ovalbumin (OVA) inhalation in sensitized mice elicits allergic airway inflammation and pathophysiology mimicking neutrophilic asthma. OVA-experienced murine lungs harbor diverse clusters of CD4+resident memory TRMcells, including unconventional RORγtnegative/lowTH17 cells. Acute OVA challenge instigates IL-17A secretion from these TRMcells, driving CXCL5 production from Muc5achighairway secretory cells, leading to destructive airway neutrophilia. The TRM- and epithelial-cell signals discovered herein are also observed in adult human asthmatic airways. Epithelial antigen presentation regulates this biology by skewing TRMcells towards TH2 and TH1 fates, so that the TH1-related IFN-γ suppresses IL-17A-driven, CXCL5-mediated airway neutrophilia. Concordantly,in vivoIFN-γ supplementation improves disease outcomes. Thus, using our model of neutrophilic asthma we identify lung epithelial-CD4+TRMcell crosstalk as a key rheostat of allergic airway neutrophilia.

Highlights

Recurrent OVA inhalation experience predisposes mice to allergic airways neutrophilia

Neutrophil-prone lungs harbor CD4+TRMcells including RORγtnegative/lowTH17 cells

Muc5achighsecretory cells instruct CD4+TRMfates and neutrophilia via MHC-II and CXCL5, respectively

Prophylactic or therapeutic delivery of IFN-γ curbs allergic airway neutrophilia
Data-driven model discovery and model selection for noisy biological systems
Authors: Wu Xiaojun , McDermott MeiLu , MacLean Adam L.
Published: October 2024

Biological systems exhibit complex dynamics that differential equations can often adeptly represent. Ordinary differential equation models are widespread; until recently their construction has required extensive prior knowledge of the system. Machine learning methods offer alternative means of model construction: differential equation models can be learnt from data via model discovery using sparse identification of nonlinear dynamics (SINDy). However, SINDy struggles with realistic levels of biological noise and does not incorporate prior knowledge of the system. We propose a data-driven framework for model discovery and model selection using hybrid dynamical systems: partial models containing missing terms. Neural networks are used to approximate the unknown dynamics of a system, enabling the denoising the data while simultaneously learning the latent dynamics. Simulations from the fitted neural network are then used to infer models using SINDy. We show, via model selection, that model discovery in SINDy with hybrid dynamical systems outperforms alternative approaches. We find it possible to infer models correctly up to high levels of biological noise of different types. We demonstrate the potential to learn models from sparse, noisy data in application to a canonical cell state transition using data derived from single-cell transcriptomics. Overall, this approach provides a practical framework for model discovery in biology in cases where data are noisy and sparse, of particular utility when the underlying biological mechanisms are partially but incompletely known.
Aging at scale: Younger dogs and larger breeds from the Dog Aging Project show accelerated epigenetic aging
Authors: McCoy Brianah M. , Mariner Blaise L. , Cheng Claire F. , Slikas Elizabeth , Adjangba Christine , Greenier Ashlee , Brassington Layla , Marye Abbey , Harrison Benjamin R. , Partida-Aguilar Maria , Bamberger Tal , Algavi Yadid , Muller Efrat , Harris Adam , Rout Emily ,   The Dog Aging Project Consortium, Avery Anne , Borenstein Elhanan , Promislow Daniel , Snyder-Mackler Noah
Published: October 2024

Dogs exhibit striking within-species variability in lifespan, with smaller breeds often living more than twice as long as larger breeds. This longevity discrepancy also extends to health and aging–larger dogs show higher rates of age-related diseases. Despite this well-established phenomenon, we still know little about the biomarkers and molecular mechanisms that might underlie breed differences in aging and survival. To address this gap, we generated an epigenetic clock using DNA methylation from over 3 million CpG sites in a deeply phenotyped cohort of 864 companion dogs from the Dog Aging Project, including some dogs sampled annually for 2-3 years. We found that the largest breed size tends to have epigenomes that are, on average, 0.37 years older per chronological year compared to the smallest breed size. We also found that higher residual epigenetic age was significantly associated with increased mortality risk, with dogs experiencing a 34% higher risk of death for each year increase in residual epigenetic age. These findings not only broaden our understanding of how aging manifests within a diverse species but also highlight the significant role that demographic factors play in modulating the biological mechanisms underlying aging. Additionally, they highlight the utility of DNA methylation as both a biomarker for healthspan-extending interventions, a mortality predictor, and a mechanism for understanding inter-individual variation in aging in dogs.
TheC. eleganshomolog of Sjögren’s Syndrome Nuclear Antigen 1 is required for the structural integrity of the centriole and bipolar mitotic spindle assembly
Authors: Pfister Jason A. , Agostini Lorenzo , Bournonville Lorène , Sankaralingam Prabhu , Bell Zachary G. , Hamel Virginie , Guichard Paul , Biertümpfel Christian , Mizuno Naoko , O’Connell Kevin F.
Published: October 2024

Centrioles play central roles in ciliogenesis and mitotic spindle assembly. Once assembled, centrioles exhibit long-term stability, a property essential for maintaining numerical control. How centriole stability is achieved and how it is lost in certain biological contexts are still not completely understood. In this study we show that SSNA-1, theCaenorhabditis elegansortholog of Sjogren’s Syndrome Nuclear Antigen 1, is a centriole constituent that localizes close to the microtubule outer wall, while also exhibiting a developmentally regulated association with centriole satellite-like structures. A complete deletion of thessna-1gene results in an embryonic lethal phenotype marked by the appearance of extra centrioles and spindle poles. We show that SSNA-1 genetically interacts with the centriole stability factor SAS-1 and is required post assembly for centriole structural integrity. In SSNA-1’s absence, centrioles assemble but fracture leading to extra spindle poles. However, if the efficiency of cartwheel assembly is reduced, the absence of SSNA-1 results in daughter centriole loss and monopolar spindle formation, indicating that the cartwheel and SSNA-1 cooperate to stabilize the centriole during assembly. Our work thus shows that SSNA-1 contributes to centriole stability during and after assembly, thereby ensuring proper centriole number.
Dissecting autonomous enzyme variability in single cells
Authors: Gnann Christian , Cesnik Anthony , Sigaeva Alina , Le Trang , Sariyar Sanem , Mahdessian Diana , Schutten Rutger , Raghavan Preethi , Leonetti Manuel D. , Lindskog Cecilia , Uhlén Mathias , Axelsson Ulrika , Lundberg Emma
Published: October 2024

Metabolic enzymes perform life-sustaining functions in various cellular compartments. Anecdotally, metabolic activity is observed to vary between genetically identical cells, which impacts drug resistance, differentiation, and immune cell activation. However, no large-scale resource systematically reporting metabolic cellular heterogeneity exists. Here, we leverage imaging-based single-cell spatial proteomics to reveal the extent of non-genetic variability of the human enzymatic proteome, as a proxy for metabolic states. Nearly two fifths of enzymes exhibit cell-to-cell variable expression, and half localize to multiple cellular compartments. Metabolic heterogeneity arises largely autonomously of cell cycling, and individual cells reestablish these myriad metabolic phenotypes over several cell divisions. These results establish that cell-to-cell enzymatic heterogeneity is an organizing principle of cell biology and one that may rewire our understanding of drug resistance, treatment design, and other aspects of medicine.
Beyond planar: fish schools adopt ladder formations in 3D
Authors: Ko Hungtang , Girma Abigail , Zhang Yangfan , Pan Yu , Lauder George V , Nagpal Radhika
Published: October 2024

The coordinated movement of fish schools has long captivated researchers studying animal collective behavior. Classical literature from Weihs and Lighthill suggests that fish schools should favor planar diamond formations to increase hydrodynamic efficiency, inspiring a large body of work ranging from fluid simulations to hydrofoil experiments. However, whether fish schools actually adopt and maintain this idealized formation remains debated and unresolved. When fish schools are free to self-organize in three dimensions, what formations do they prefer? By tracking polarized schools of giant danios (Devario aequipinnatus) swimming continuously for ten hours, we demonstrate that fish rarely stay in a horizontal plane, and even more rarely, in the classical diamond formation. Of all fish pairs within four body-lengths from each other, only 25.2% are in the same plane. Of these, 54.6% are inline, 30.0% are staggered, and 15.4% are side-by-side. The diamond formation was observed in less than 0.1% of all frames. Notably, a “ladder formation” emerged as the most probable formation for schooling giant danios, appearing in 79% of all fish pairs and fish schools elongate at higher swimming speeds. These findings highlight the dynamic and three-dimensional nature of fish schools and suggest that hydrodynamic benefits may be obtained without requiring fixed positions. This research provides a foundation for future studies that examine the hydrodynamics and control of underwater collectives in 3D formations.
Autophagy, the Ubiquitin proteasome system, and the MAPK pathway control the temperature dependence of synaptic growth
Authors: De Leon Kevin , Marie Bruno
Published: October 2024

There is clear evidence that Earth’s temperature is rising at an unprecedented rate. While consequences on ecosystems are being extensively studied, little is known about the consequences of temperature on the nervous system of ectothermic animals. Here we used theDrosophilamodel NMJ to assess the effect of temperature on the synaptic growth of a phasic, and a tonic, motoneuron. We find that the tonic neuron’s synaptic size is not affected by temperature, however we do observe a temperature-dependent synaptic growth in the phasic neuron, which might be related to the increased motility observed previously at higher temperatures. We find that the level of autophagy activity changes with temperature and that autophagy genes are responsible for the temperature dependence of synaptic growth. We present evidence that this regulation could occur through the major synaptic growth regulator and ubiquitin ligase Highwire, and a pathway involving the Mitogen-Activated Protein Kinases. We present a new function for the MAPKKK, Wallenda and the MAPK P38b in directing the additional synaptic growth that takes place between 25°C and 29°C. This illustrates that temperature has different effects on a diverse population of neurons and that distinct genetic pathways are involved in regulating temperature driven changes.
A Putative Binding Model of Nitazene Derivatives at the mu-Opioid Receptor
Authors: Clayton Joseph , Shi Lei , Skiniotis Georgios , Robertson Michael J , Michaelides Michael , Stavitskaya Lidiya , Shen Jana
Published: October 2024

Nitazenes are a class of novel synthetic opioids with exceptionally high potency. Currently, an experimental structure of mu-OR-opioid receptor (muOR) in complex with a nitazene is lacking. Here we used a suite of computational tools, including consensus docking, conventional molecular dynamics (MD) and metadynamics simulations, to investigate the muOR binding modes of nitro-containing meto-, eto-, proto-, buto-, and isotonitazenes and nitro-less analogs, metodes-, etodes-, and protodesnitazenes. Docking generated three binding modes, whereby the nitro-substituted or unsubstituted benzimidazole group extends into SP1 (subpocket 1 between transmembrane helix or TM 2 and 3), SP2 (subpocket 2 between TM1, TM2, and TM7) or SP3 (subpocket 3 between TM5 and TM6). Simulations suggest that etonitazene and likely also other nitazenes favor the SP2-binding mode. Comparison to the experimental structures of muOR in complex with BU72, fentanyl, and mitragynine pseudoindoxyl (MP) allows us to propose a putative model for muOR-ligand recognition in which ligand can access hydrophobic SP1 or hydrophilic SP2, mediated by the conformational change of Gln1242.60. Interestingly, in addition to water-mediated hydrogen bonds, the nitro group in nitazenes forms a pi-hole interaction with the conserved Tyr75. Our computational analysis provides new insights into the mechanism of muOR-opioid recognition, paving the way for investigations of the structure-activity relationships of nitazenes.
Contextual Neural Dynamics During Time Perception in Primate Ventral Premotor Cortex
Authors: Díaz Héctor , Bayones Lucas , Alvarez Manuel , Andrade-Ortega Bernardo , Valero Sebastián , Zainos Antonio , Romo Ranulfo , Rossi-Pool Román
Published: October 2024

Understanding how time perception adapts to cognitive demands remains a significant challenge. In some contexts, the brain encodes time categorically (as “long” or “short”), while in others, it encodes precise time intervals on a continuous scale. Although the ventral premotor cortex (VPC) is known for its role in complex temporal processes, such as speech, its specific involvement in time estimation remains underexplored. In this study, we investigated how the VPC processes temporal information during a time interval comparison task (TICT) and a time interval categorization task (TCT) in primates. We found a notable heterogeneity in neuronal responses associated with time perception across both tasks. While most neurons responded during time interval presentation, a smaller subset retained this information during the working memory periods. Population-level analysis revealed distinct dynamics between tasks: in TICT, population activity exhibited a linear and parametric relationship with interval duration, whereas in TCT, neuronal activity diverged into two distinct dynamics corresponding to the interval categories. During delay periods, these categorical or parametric representations remained consistent within each task context. This contextual shift underscores the VPC’s adaptive role in interval estimation and highlights how temporal representations are modulated by cognitive demands.

Significance Statement

The neural representation of time has long intrigued neuroscientists, particularly how it adapts to cognitive demands. Depending on the task, the brain encodes time either categorically (“long” or “short”) or as precise intervals. While the ventral premotor cortex (VPC) is known for its role in temporal processes, its role in time estimation remains underexplored. Here, we examined how the VPC processes temporal information in primates during a time interval comparison task (TICT) and a categorization task (TCT). The VPC exhibited heterogeneous neuronal responses with distinct dynamics: a linear, parametric relationship in TICT and bifurcated dynamics in TCT. These representations remained consistent during delay periods, underscoring the VPC’s adaptive role in time interval estimation.
Warming treatments shift the temporal dynamics of diversity and composition of bacteria in wild blueberry soils
Authors: Alaba Oluwafemi A. , Ishaq Suzanne L. , Chen Yu-Ying , Calderwood Lily , Hao Jianjun , Zhang Yong-Jiang
Published: October 2024

Soil bacterial communities are a crucial biological indicator of soil health and crop performance; however, their response to climate change remains poorly understood. In Maine, wild blueberry farms are experiencing unprecedented temperature changes, which may exacerbate microbial responses and potentially harm the crop. To elucidate the response of bacterial communities to warming during the growing season, we employed passive and active open-top chambers to simulate climate warming scenarios in wild blueberry fields. Warming treatments elevated atmospheric temperatures by 1.2 and 3.3 °C (passive and active warming), respectively, but did not affect soil temperatures. Nevertheless, soils in the active warming treatment exhibited significantly lower water content than ambient conditions. Overall, soil bacterial diversity and richness (June, July, and August data combined) under the warming (passive and active) treatments and ambient controls did not demonstrate significant differences after two years of experimental warming. However, significantly higher bacterial evenness and diversity under warming treatments were observed in the early growing season (June). Our study also reveals pronounced seasonal shifts in the evenness and diversity of bacteria in wild blueberry soil, suggesting that the variation in bacterial community structure may be more influenced by seasonal changes in temperature and plant activity during the growing season than by warming treatments. The increased bacterial evenness and diversity under warming treatments in June may be attributed to advanced plant phenology, indicating a potential future shift in seasonal dynamics of bacterial activity under global warming.
Analyzing Biodiversity in Protected vs. Unprotected Tide Pools
Authors: Chen Vicki , Campbell Rowan , Chirputkar Arohi , Tran Emma , Chaturvedi Parnika , Han Sally , Lu Amber , Chu Zoe , Erb Melody , Mehta Tejin , Bindal Vidya , Lee Isaac , Benson Andrew , Adams Connor T.
Published: October 2024

This study assessed the efficacy of marine protected areas (MPAs) by comparing tide pool biodiversity in Half Moon Bay, California between a protected site (Fitzgerald Marine Reserve) and an unprotected site (Maverick’s Beach). Samples were collected through random quadrat surveys. ImageJ and RStudio were used to analyze data through three methods utilizing the Simpson’s Diversity Index along with three metrics. The unprotected Maverick’s Beach displayed greater biodiversity through two metrics while the third did not find significant difference in biodiversity between sites. 30 unique species were present at each site with 43 species between both. These mixed findings prevent us from drawing definitive conclusions on the effectiveness of Half Moon Bay’s tide pool MPAs but suggest the MPA is less biodiverse. Potential explanations include the Intermediate Disturbance Hypothesis, lack of sample size, or that the MPA is not effective in maintaining biodiversity.
Cell cycle regulation of polymerase theta mediated end-joining underlies its sensitivity to loss of BLM-DNA2
Authors: McBrine Connor P. , Jensen Ryan B. , King Megan C.
Published: October 2024

DNA double-strand breaks (DSBs) are predominantly resolved by the error-prone non-homologous end-joining (NHEJ) or high-fidelity homologous recombination (HR) DNA repair pathways. NHEJ involves minimal end-processing and drives direct ligation of the broken ends, while HR first requires a DSB resection step that degrades 5’ strands to generate 3’ ssDNA tails necessary for homology search. When HR fails, an alternative end-joining pathway involving polymerase theta can serve as a backup repair mechanism by annealing and ligating microhomologies present in ssDNA tails on either side of a resected DSB. Resection is the early step that commits a DSB to repair by HR, and is therefore considered a prerequisite for TMEJ as well. It has been proposed that the exonuclease EXO1 and the helicase/nuclease complex of BLM-DNA2 have redundant roles in resection, and therefore may both contribute to TMEJ. Here, we use a sensitive deep-sequencing approach to identify DSB repair outcomes at an endogenous locus in response to genetic and chemical perturbation of the resection machinery. While we observe that both EXO1 and BLM-DNA2 contribute to resection, our findings highlight a predominant role for BLM-DNA2 in facilitating TMEJ. However, careful cell cycle analysis revealed that BLM-DNA primarily contributes to TMEJ by ensuring normal progression to the G2/M transition, required for TMEJ to become activated. We propose that rather than direct, mechanistic roles in resection, the critical functions of BLM and DNA2 in genome replication largely account for their genetic contribution to efficient TMEJ.
Synergy betweencis-regulatory elements can render cohesin dispensable for distal enhancer function
Authors: Hansen Karissa L. , Adachi Annie S. , Braccioli Luca , Kadvani Smit , Boileau Ryan M. , Pokorny Bozhena , Shah Rini , Anderson Erika C. , Martinovic Moreno , Zhang Kaite , Carel Irié , Bonitto Kenya , Blelloch Robert , Fudenberg Geoffrey , de Wit Elzo , Nora Elphège P.
Published: October 2024

Enhancers are critical genetic elements controlling transcription from promoters, but the mechanisms by which they convey regulatory information across large genomic distances remain elusive. Here, we engineered pluripotent stem cells in which cohesin loop extrusion can be inducibly disrupted without causing confounding cell cycle defects. While evident, transcriptional dysregulation was cell-type specific, and not all loci with distal enhancers depend equally on cohesin extrusion. Using comparative genome editing, we demonstrate that enhancer-promoter communication across as little as 20 kilobases can rely on cohesin. However, promoter-proximal regulatory elements can support long-range, cohesin-independent enhancer action – either upon disabling extrusion or across strong CTCF insulators. Finally, transcriptional dynamics and the emergence of new embryonic cell types in response to differentiation cues remained largely robust to disrupting cohesin extrusion. Beyond establishing novel experimental strategies to study cohesin functions in enhancer biology, our work provides mechanistic insight accounting for both cell type- and genomic context-specificity.
An Expanded Substrate Scope for Cross-Chiral Ligation Enables Efficient Synthesis of Long L-RNAs
Authors: Han Xuan , Sczepanski Jonathan T.
Published: October 2024

Despite the growing interest in mirror-image L-oligonucleotides, both as a robust nucleic acid analogue and as an artificial genetic polymer, their broader adoption in research and medicine remains hindered by challenges associated with the synthesis of long sequences, especially for L-RNA. Herein, we present a novel strategy for assembling long L-RNAs via the joining of two or more shorter fragments using cross-chiral ligase ribozymes together with new substrate activation chemistry. We show that 5′-monophosphorylated L-RNA, which is readily prepared by solid phase synthesis, can be activated by chemical attachment of a 5′-adenosine monophosphate (AMP) or diphosphate (ADP), yielding 5′-adenosyl (di-or tri-) phosphate L-RNA. The activation reaction is performed in mild aqueous conditions, proceeds efficiently with short or large L-RNA, and, yielding few biproducts, requires little or no further purification after activation. Importantly, both groups, when added to L-RNA, are compatible with ribozyme-mediated ligation, with the 5′-adenosyl triphosphate permitting rapid and efficient joining of multiple, long L-RNA strands. This is exemplified by the assembly of a 129-nt L-RNA molecule via a single cross-chiral ligation event. Overall, by relying on ribozymes that can be readily prepared byin vitrotranscription and L-RNA substrates that can be activated through simple chemistry, these methods are expected to make long L-RNAs more accessible to a wider range of researchers and facilitate the expansion of L-ON-based technologies.
APOE Protects Against Severe Infection withMycobacterium tuberculosisby Restraining Production of Neutrophil Extracellular Traps
Authors: Liu Dong , Mai Dat , Jahn Ana N. , Murray Tara A. , Aitchison John D. , Gern Benjamin H. , Urdahl Kevin B. , Aderem Alan , Diercks Alan H. , Gold Elizabeth S.
Published: October 2024

While neutrophils are the predominant cell type in the lungs of humans with active tuberculosis (TB), they are relatively scarce in the lungs of most strains of mice that are used to study the disease. However, similar to humans, neutrophils account for approximately 45% of CD45+ cells in the lungs ofApoe-/-mice on a high-cholesterol (HC) diet following infection withMycobacterium tuberculosis(Mtb). We hypothesized that the susceptibility ofApoe-/-HC mice might arise from an unrestrained feed-forward loop in which production of neutrophil extracellular traps (NETs) stimulates production of type I interferons by pDCs which in turn leads to the recruitment and activation of more neutrophils, and demonstrated that depleting neutrophils, depleting plasmacytoid dendritic cells (pDCs), or blocking type I interferon signaling, improved the outcome of infection. In concordance with these results, we found that Mtb-infected inApoe-/-HC mice produce high levels of LTB4 and 12-HETE, two eicosanoids known to act as neutrophil chemoattractants and showed that blocking leukotriene B4 (LTB4) receptor signaling also improved the outcome of tuberculosis. While production of NETs has been associated with severe tuberculosis in other mouse models and in humans, a causative role for NETs in the pathology has not been directly established. We demonstrate that blocking the activation of peptidylarginine deiminase 4 (PAD4), an enzyme critical to NET formation, leads to fewer NETs in the lungs and, strikingly, completely reverses the hypersusceptibility ofApoe-/-HC mice to tuberculosis.
Early Postnatal Dysfunction of mPFC PV Interneurons in Shank3B−/−Mice
Authors: Shih Yi-Chun , Nelson Lars , Janeček Michael , Matarazzo Michael , Peixoto Rui T.
Published: October 2024

Medial prefrontal cortex(mPFC)dysfunction is associated with cognitive and sensory abnormalities in individuals with autism spectrum disorder(ASD), yet the trajectory of mPFC circuit development in these conditions remains poorly understood. In this study, we investigated the postnatal maturation of glutamatergic connectivity and neuronal excitability in pyramidal neurons(PYR)and parvalbumin-positive interneurons(PVIN)in the mPFC of mice harboring deletions in SHANK3, a well-established genetic cause of autism associated with severe cognitive impairments and seizures. Our findings reveal early deficits in PVIN excitability that precede changes in the synaptic and intrinsic properties of PYR, resulting in impaired feedforward inhibition.In vivocalcium imaging demonstrated hypoactivity of PVIN in dorsal mPFC circuits during early postnatal development, characterized by reduced frequency of calcium transients. By adulthood, excitability phenotypes were reversed, with PVIN becoming hyperexcitable and PYR hypoexcitable. These results suggest that PVIN dysfunction in Shank3B−/−mice emerges during postnatal development and may represent a key pathogenic mechanism and potential therapeutic target in SHANK3-related disorders.
A browser-based platform for storage, visualization, and analysis of large-scale 3D images in HPC environments
Authors: Walker Logan A , Lee Wei Jie , Duan Bin , Weatherspoon Menelik , Li Ye , Shen Fred Y , Cheng Mou-Chi , Niu Xiaoman , Eggerd Jacob , Xie Bin , Cheng Jimmy Hon Pong , Xu Humphrey , Zhong Xiao-Xiang , Jiang Hehai , Cui Meng , Yan Yan , Cai Dawen
Published: October 2024

High-throughput microscopy necessitates 3D image storage, visualization, and analysis in terabyte to petabyte scales. Centralized high-performance computing (HPC) infrastructure provides the resources, but interfacing software is limited. We developed an extensible platform with a scalable image storage format (SISF) and content delivery network (CDN) to enable fast, random access to compressed data. Additionally, we built a cloud-based nTracer2 software to annotate neuron morphology from SISF images in a web browser.
EASI-ORC: A Pipeline for the Efficient Analysis and Segmentation of smFISH Images for Organelle-RNA Colocalization Measurements in Yeast
Authors: Garin Shahar , Levavi Liav , Gerst Jeffrey E.
Published: October 2024

Analysis of single-molecule fluorescentin situhybridization (smFISH) images is an arduous and time-consuming task that is important to perform accurately in order to translate image data into a quantifiable format. This task becomes increasingly more difficult greater the experimental scope and number of images captured. Although smFISH is the gold standard for RNA localization measurements, there are no freely available, user-friendly applications for assaying messenger RNA localization to sub-cellular structures, like the endoplasmic reticulum (ER) or mitochondria). We have developed a pipeline that allows for the automated analysis of multiple smFISH images in yeast cells: EASI-ORC (EfficientAnalysis andSegmentation of smFISH Images forOrganelle-RNAColocalization). The EASI-ORC pipeline automates the segmentation of cells and sub-cellular structures (e.g.organelles), identifiesbona fidesmFISH signals, and measures the level of colocalization between an organelle and mRNA signals. Importantly, EASI-ORC works in a fast, accurate, and unbiased manner that is difficult to replicate manually. It also allows for the visualization of data filtering and outputs graphical representations of the colocalization data along with statistical analysis. EASI-ORC is based on existing ImageJ plugins and original scripts, thus, allowing free access and a relative ease of use. To circumvent any technical literacy issues, a step-by-step user guide is provided. EASI-ORC offers a robust solution for smFISH image analysis for both new and experienced researchers - one that saves time and effort, as well as providing more consistent overall measurements of RNA-organelle colocalization in yeast.
A post-mitoticin vitromurine as a model of muscle damage and repair
Authors: Galluccio Angelo , Maurotti Samantha , Noto Francesca Rita , Scionti Francesca , Pujia Carmelo , Mazza Elisa , Ferro Yvelise , Mare Rosario , Geirola Nadia , Scopacasa Bernadette , Candeloro Patrizio , Tirinato Luca , Sciacqua Angela , Pujia Arturo , Romeo Stefano , Montalcini Tiziana
Published: October 2024

Sarcopenia is a degenerative condition characterized by the atrophy and functional decline of myofibers, resulting in disability. While the clinical risk factors are known, there is no validatedin vitromodel to understand the molecular mechanisms and identify therapeutics. To tackle this challenge, we generated anin vitropost-mitotic muscular system by differentiating mouse myoblast cells, namely C2C12. After 12 days of differentiation, cells were expressing physiological markers of myotubes and became self-contracting. Importantly, transcriptomic analyses demonstrated high similarity (r=0.70) when compared to primary human myotubes (HSkMC) providing evidence of resemblance to human cells. Next, we starved and incubated cells with dexamethasone and observed myotube shrinkage, oxidative stress, modification of anabolic, inflammatory, and catabolic markers recapitulating sarcopenia. Conversely, cell refeeding resulted in a recovery in the model with nutrient deprivation but not when incubated also with dexamethasone. In conclusion, we present a model of sarcopenia due to nutrient deprivation and corticosteroids. This model may allow more efficient and effective future research to identify therapeutics against sarcopenia in humans.
Generating brain-wide connectome using synthetic axonal morphologies
Authors: Petkantchin Remy , Berchet Adrien , Peng Hanchuan , Markram Henry , Kanari Lida
Published: October 2024

Recent experimental advancements, including electron microscopy reconstructions, have produced detailed connectivity data for local brain regions. On the other hand, for inter-regional connectivity, large-scale imaging techniques such as MRI are best suited to provide insights. However, understanding the relationship between local and long-range connectivity is essential for studying both healthy and pathological conditions of the brain. Leveraging a novel dataset of whole-brain axonal reconstructions, we present a technique to predict whole-brain connectivity at single cell level by generating detailed whole-brain axonal morphologies from sparse experimental data. The computationally generated axons accurately reproduce the local and global morphological properties of experimental reconstructions. Furthermore, the computationally synthesized axons generate large-scale inter-regional connectivity, defining the projectome and the connectome of the brain, thereby enabling the in silico experimentation of large brain regions.
Structural basis of Nipah virus replication
Authors: Sala Fernanda A. , Ditter Katja , Dybkov Olexandr , Urlaub Henning , Hillen Hauke S.
Published: October 2024

Nipah virus (NiV) is a non-segmented negative-strand RNA virus (nsNSV) with high pandemic potential, as it frequently causes zoonotic outbreaks and can be transmitted from human to human. Its RNA-dependent RNA polymerase (RdRp) complex carries out viral genome replication and transcription and is therefore an attractive drug target. However, to date no structural data is available on the NiV RdRp complex. Here, we report cryo-EM structures of NiV RdRp in the apo and in an early elongation state with RNA and incoming substrate bound. The structure of the apo enzyme reveals the architecture of the NiV RdRp complex, which shows a high degree of similarity to other nsNSV RdRps. The structure of the RNA-bound NiV RdRp shows how the enzyme interacts with template and product RNA during early replication and how nucleoside triphosphates are bound in the active site. Comparisons show that RNA binding leads to rearrangements of key elements in the RdRp core and to ordering of the flexible C-terminal domains of NiV L required for RNA capping. Taken together, these results reveal the first structural snapshots of an actively replicating nsNSV RdRp and provide insights into the mechanisms of genome replication and transcription by NiV and related viruses.
Soil pH influences the composition of bacteriophage communities infecting individual hosts
Authors: Lee Sungeun , Nicol Graeme W. , Hazard Christina
Published: October 2024

Bacteriophages (phages) can infect a range of hosts in highly diverse soil bacterial communities. However, selection of host communities across ecological gradients and co-evolutionary processes may influence both the distribution of phages and the susceptibility of individual hosts through virus interactions and local adaptation within distinct ecological niches. Metagenomic-based analyses have revealed that soil pH selects for distinct populations and community structures for both phage and hosts at local and global scales. However, whether contrasting soil pH represents a selective barrier for phages capable of infecting an individual host is unknown. To examine the influence of pH on individual host-virus interactions, two closely relatedBacillusstrains were isolated and characterized from pH 7.5 soil associated with a long-term contiguous pH gradient (pH 4.5 to 7.5). Phages infecting each strain were subsequently enriched from soils across the pH gradient (pH 4.5, 5.5, 6.5 and 7.5), enumerated using a plaque assay, and characterized via metagenomic analysis. Phages infecting each strain were cultivated from all soils but their community composition and abundance varied with pH. Phage populations infecting each of the two strains were distinct despite the close relatedness of the two hosts, indicating relatively narrow host ranges for each virus. These results suggest that while phage community structures vary substantially across an ecological gradient, soil pH alone does not represent a barrier for the distribution of phages capable of infecting an individual host.
Comparative Analysis of Lipid Nanoparticles in Pfizer-BioNTech and Moderna COVID-19 Vaccines: Insights from Molecular Dynamics Simulations
Authors: Biswal Malay Ranjan , Roy Sudip , Singh Jayant K
Published: October 2024

COVID-19 vaccines, such as Pfizer-BioNTech’s BNT162b and Moderna’s mRNA-1273, have demonstrated robust efficacy. However, direct comparisons of their delivery vehicles remain limited. Notably, BNT162b requires storage at -80°C, while mRNA-1273 is stored at -20°C. This discrepancy in storage temperatures may be influenced by differences in the structure and stability of the lipid nanoparticles (LNPs) used in these vaccines. Ionizable lipids, such as SM-102 in Moderna’s vaccine and ALC-0315 in Pfizer’s vaccine, play a crucial role in LNP stability and function, affecting endosomal escape, cellular uptake, and drug release. Understanding these variations is essential for optimizing vaccine delivery systems. In our study, we use molecular dynamics simulations with the coarse-grained Martini forcefield to compare the LNPs in Moderna and Pfizer’s COVID-19 vaccines, providing insights at an experimental scale. Our findings indicate that the ionizable lipid tail of BNT162b (ALC-0315) exhibits a higher degree of branching, resulting in a more bifurcated appearance compared to the structure of the ionizable lipids in mRNA-1273 (SM-102).
Discovering Temporally Compositional Neural Manifolds with Switching Infinite GPFA
Authors: Yu Changmin , Sahani Maneesh , Lengyel Máté
Published: October 2024

Abstract

Gaussian Process Factor Analysis (GPFA) is a powerful latent variable model for extracting low-dimensional manifolds underlying population neural activities. However, one limitation of standard GPFA models is that the number of latent factors needs to be pre-specified or selected through heuristic-based processes, and that all factors contribute at all times. We propose the infinite GPFA model, a fully Bayesian non-parametric extension of the classical GPFA by incorporating an Indian Buffet Process (IBP) prior over the factor loading process, such that it is possible to infer a potentially infinite set of latent factors, and the identity of those factors that contribute to neural firings in a compositional manner ateachtime point. Learning and inference in the infinite GPFA model is performed through variational expectation-maximisation, and we additionally propose scalable extensions based on sparse variational Gaussian Process methods. We empirically demonstrate that the infinite GPFA model correctly infers dynamically changing activations of latent factors on a synthetic dataset. By fitting the infinite GPFA model to population activities of hippocampal place cells during spatial navigation, we identify non-trivial and behaviourally meaningful dynamics in the neural encoding process.
Rho/Rok-dependent regulation of actomyosin contractility at tricellular junctions controls epithelial permeability in Drosophila
Authors: Jacobs Thea , Isasti Sanchez Jone , Reger Steven , Luschnig Stefan
Published: October 2024

Cell contacts in epithelia are remodeled to regulate paracellular permeability and to control passage of migrating cells, but how barrier function is modulated while preserving epithelial integrity is not clear. In the follicular epithelium ofDrosophilaovaries, tricellular junctions (TCJs) open transiently in a process termed patency to allow passage of externally produced yolk proteins for uptake by the oocyte. Here we show that modulation of actomyosin contractility at cell vertices controls TCJ permeability. Before patency, circumferential actomyosin bundles are anchored at apical follicle cell vertices, where tension-sensing junctional proteins, Rho-associated kinase (Rok), and active Myosin II accumulate and maintain vertices closed. TCJ opening is initiated by redistribution of Myosin II from circumferential bundles to a medial pool, accompanied by decreasing tension on vertices. This transition requires activation of Cofilin-dependent F-actin disassembly by the phosphatase Slingshot and Myosin II inactivation by Myosin light chain phosphatase, and is counteracted by Rok. Accordingly, constitutive activation of Myosin or of Rho signaling prevent vertex opening, whereas reduced Myosin II or Rok activity cause excessive and premature vertex opening. Thus, opening of intercellular gaps in the follicular epithelium does not require actomyosin-based forces, but relies on a reduction of actomyosin contractility. Conversely, F-actin assembly is required for closing intercellular gaps after patency. Our findings are consistent with a force transduction model in which TCJ integrity is maintained by vertex-anchored contractile actomyosin. We propose that the cell-type-specific organization of actomyosin at cell vertices determines the mode of contractility-dependent regulation of epithelial permeability.
The A-C Linker controls centriole cohesion and duplication
Authors: Bournonville Lorène , Laporte Marine. H. , Borgers Susanne , Guichard Paul , Hamel Virginie
Published: October 2024

Centrioles are evolutionarily conserved barrel-shaped organelles playing crucial roles in cell division and ciliogenesis. These functions are underpinned by specific structural sub-elements whose functions have been under investigation since many years. The A- C linker structure, connecting adjacent microtubule triplets in the proximal region, has remained unexplored due to its unknown composition. Here, using ultrastructure expansion microscopy, we characterized two recently identified A-C linker proteins, CCDC77 and WDR67, along with a newly discovered protein, MIIP. Our findings reveal that these proteins localize between microtubule triplets at the A-C linker, forming a complex. Depletion of A-C linker components disrupt microtubule triplet cohesion, leading to breakage at the proximal end. Co-removal of the A-C linker and the inner scaffold demonstrates their joint role in maintaining centriole architecture. Moreover, we uncover an unexpected function of the A-C linker in centriole duplication through torus regulation, underscoring the interplay between these protein modules.
A remarkable psyllomorph family from Cretaceous Burmese amber, Miralidae stat. nov. (= Dinglidae syn. nov.; Hemiptera: Sternorrhyncha)
Authors: Ivanov Grigory A. , Vorontsov Dmitry D. , Shcherbakov Dmitry E.
Published: October 2024

Cretaceous resins have preserved a remarkable diversity of sternorrhynchans. Burmese amber, formed in the mid-Cretaceous tropics, contains more numerous and diverse Psyllomorpha than all other fossil localities of the period together. The genusDinglaSzwedo et Drohojowska, 2020, previously placed into a separate family and infraorder, turned out to be similar in all essential characters toMiralaBurckhardt et Poinar, 2019 andBurmalaLiu et al., 2021; therefore we synonymize Dinglidae Szwedo et Drohojowska, 2020 with Miralinae Shcherbakov, 2020 and raise the last subfamily to the full family status. A sister-group relationship between Dinglomorpha and Aleyrodomorpha in the cladistic analysis of Drohojowska et al. (2020a) was based on incorrect interpretation of characters.@@ala @@ioidesgen. et sp. nov. from Burmese amber differs from other miralid genera by spotted forewings without pterostigma and the structure of terminalia in both sexes. In Miralidae, we discovered a long annulated labium and compound wax pores on the ventral side of the abdomen—for the first time among Hemiptera. The compound wax pores may have helped prevent miralids from sticking to the honeydew excreted. The long, flexible second labial segment, reinforced by sclerotized rings, probably allowed the protrusible length of the stylet bundle to be increased by arching the labium, as in mosquitoes.