bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell analysis of lung epithelial cells reveals age and cell population-specific responses to SARS-CoV-2 infection in ciliated cells
Authors: Osborn Raven M. , Anderson Christopher S. , Leach Justin R. , Chu ChinYi , Dewhurst Stephen , Mariani Thomas J. , Thakar Juilee 
Published: April 2024

AbstractThe ability of SARS-CoV-2 to evade antiviral immune signaling in the airway contributes to the severity of COVID-19 disease. Additionally, COVID-19 is influenced by age and has more severe presentations in older individuals. This raises questions about innate immune signaling as a function of lung development and age. Therefore, we investigated the transcriptome of different cell populations of the airway epithelium using pediatric and adult lung tissue samples from the LungMAP Human Tissue Core Biorepository. Specifically, lung lobes were digested and cultured into a biomimetic model of the airway epithelium on an air-liquid interface. Cells were then infected with SARS-CoV-2 and subjected to single-cell RNA sequencing. Transcriptional profiling and differential expression analysis were carried out using Seurat.The clustering analysis identified several cell populations: club cells, proliferating epithelial cells, multiciliated precursor cells, ionocytes, and two biologically distinct clusters of ciliated cells (FOXJ1highand FOXJ1low). Interestingly, the two ciliated cell clusters showed different infection rates and enrichment of processes involved in ciliary biogenesis and function; we observed a cell-type-specific suppression of innate immunity in infected cells from the FOXJ1lowsubset. We also identified a significant number of genes that were differentially expressed in lung cells derived from children as compared to adults, suggesting the differential pathogenesis of SARS-CoV-2 infection in children versus adults. We discuss how this work can be used to identify drug targets to modulate molecular signaling cascades that mediate an innate immune response and begin to understand differences in COVID-19 outcomes for pediatric vs. adult populations.ImportanceViral innate immune evasion leads to uncontrolled viral spread in infected tissues and increased pathogenicity in COVID-19. Understanding the dynamic of the antiviral signaling in lung tissues may help us to understand which molecular signals lead to more severe disease in different populations, particularly considering the enhanced vulnerability of older populations. This study provides foundational insight into the age-related differences in innate immune responses to SARS-CoV-2, identifying distinct patterns of infection and molecular signaling in different cell populations of airway epithelial cells from pediatric and adult lung tissues. The findings provide a deeper understanding of age-related differences in COVID-19 pathology and pave the way for developing targeted therapies.
Data-driven simple agent-based model of scratch assays on healthy and keloid fibroblasts
Authors: Urcun Stéphane , Rolin Gwenaël , Eftimie Raluca , Lozinski Alexei , Bordas Stéphane P.A. 
Published: April 2024

AbstractIn this study we propose a novel agent-based model to reproduce and propose new hypotheses on the biological mechanisms of cell-cell interactions and cell migration from data obtained during scratch assay with healthy and keloid fibroblasts. The advantage of the agent-based model we propose in this paper lies in its simplicity: only three governing parameters. We conducted a parametric sensitivity analysis and we incorporated the evaluation of contact inhibition of locomotion, aligning with the observed loss during malignant invasion. To study invasion modalities, we conductedin vitrowound healing assays using healthy and pseudo-tumoral (keloid) fibroblasts under diverse conditions: control, macrophage type 1 secretome, and macrophage type 2 secretome. Mitomycin inhibition of proliferation isolated the contribution of migration to wound filling. Our agent-based mathematical model describes configurations based on our microscopy imaging and statistical data, which enables quantitative comparisons between our experimental and numerical results. Calibration and evaluation were performed on the same experiments, enriched by external datasets. With only three governing parameters, our model not only demonstrated good agreement (8.78% to 18.75% error) with external evaluation datasets for all experimental configurations but also provided us with a nuanced understanding of keloid fibroblast behavior during wound healing, especially regarding contact inhibition dynamics.
Polar confinement of a macromolecular machine by an SRP-type GTPase
Authors: Dornes Anita , Schmidt Lisa Marie , Mais Christopher-Nils , Hook John C. , Pané-Farré Jan , Kressler Dieter , Thormann Kai , Bange Gert 
Published: April 2024

AbstractThe SRP-type GTPase FlhF, along with its regulator FlhG, orchestrates the localization and quantity of flagella in bacteria. Our study reveals that FlhF anchors developing flagellar structures to the polar landmark protein HubP/FimV, thereby restricting their formation to the cell pole. Specifically, the GTPase domain of FlhF interacts with HubP, while an as-yet-uncharacterized structured domain at the N-terminus of FlhF binds to FliG. This FlhF-bound FliG subsequently engages with the MS-ring protein FliF, but not with the C-ring proteins FliM/FliN. Consequently, FlhF’s interaction with HubP/FliG recruits a functional FliF/FliG complex to the pole, while FlhG’s modulation of FlhF controls FliG’s interaction with FliM/FliN, thereby regulating the progression of flagellar assembly at the pole.Significance statementFlagella serve as bacterial locomotion organelles, with their number and location, known as the flagellation pattern, being species-specific and among the earliest taxonomic criteria in microbiology. Bacteria replicate their flagellation pattern with each cell division. Flagella localization and abundance depends on the SRP-type GTPase FlhF, together with its regulator FlhG. Our study clarifies the mechanism through which FlhF coordinates the polar positioning of the flagellum, working in tandem with the polar landmark protein HubP and aiding in the assembly of flagellar MS-ring/C-ring components at the cellular pole.
Characterization and classification of fine-resolution soil profile for precision agriculture using random forest and self-organizing map
Authors: Elias Ani A. , Sharma Megha , Goel Shailendra 
Published: April 2024

AbstractThe availability of high throughput soil profile information is an important component in precision agriculture to perform efficient soil management for sustainable production. We collected 14 soil physiochemical features from Nagpur, Pune, and Haveri, representing target environments of safflower cultivation and also from our experiment station at Delhi, at fine resolution and created graphical maps to depict the variability. Additionally, we evaluated the predictive ability of two statistical learning models, random forest (RF) and self-organizing maps (SOM) against multinomial regression models for correctly classifying the soil profile. Clustering was performed around the medoids produced from the dissimilarity matrices of these models using partitioning around medoids (PAM) model. The robustness, versatility, and predictive ability of models in correctly classifying the soil profile to clusters were then tested using cross-validation which was repeated 100 times. This study was performed using training data with proportionate size varying from 60 to 95%, and increasing the unit area of observation up to nine times (or decreasing the total number of observations up to a ninth). RF model was found to be the best performing with average prediction accuracy above 85% in all settings which reached close to 100% in some settings. The predictive ability of all the models was maintained even when only the most influencing six variables were used for classification. The optimal training population size for prediction was found to be 70 – 80%. Based on our study, it is recommended to i) collect fine resolution edaphic features from a marginal farm before crop season, ii) use RF or SOM model to identify the most influencing features distinguishing the soil samples iii) expand the area of sample collection, find values for the most influencing features, and use RF model to correctly predict the class to which the new set of the soil belongs to.Graphical abstract
Interaction between ciliary component proteins fromChlamydomonasrevealed by CRISPR/CAS9, cryo-electron tomography and mass spectrometry
Authors: Luo Leo , Zimmermann Noemi , Noga Akira , Leitner Alexander , Ishikawa Takashi 
Published: April 2024

AbstractTo understand molecular mechanism of ciliary beating motion, knowledge of location, interaction and dynamics of >400 component proteins are indispensable. While recent progress of structural biology revealed conformation and localization of >100 proteins, we still need to investigate their networking, art of their interaction and assembly mechanism. We applied CRISPR/CAS9 genome editing technique to the green algaeChlamydomonasto engineer a deletion mutant of a ciliary component, FAP263, located at the distal protrusion, and examined it structurally by cryo-electron tomography (cryo-ET) and mass spectrometry (MS). Cryo-ET and atomic model fitting demonstrated that the FAP263 deletion mutant lacks additional components, FAP78, and FAP184. Unassigned density near FAP263 in the cryo-ET map of WT cilia is likely FAP151, as suggested by cross-linking mass spectrometry. Based on the structure, we modeled how these four proteins might form a complex. Furthermore, it was shown that dynein f phosphorylation is inhibited in the FAP263 mutant, indicating an important role of this protein complex for dynein f phosphorylation. Our study demonstrates a novel approach to investigate protein networking inside cilia.
Experience-induced drift in the neural coding of individual differences in perception
Authors: Maigler Kathleen C. , Crouse Ethan , Stone Bradly T. , Svedberg Daniel , Katz Donald B. 
Published: April 2024

AbstractLike humans, no two rodents like precisely the same tastes. Here, we ask whether these individual differences determine cortical taste responses, late epochs of which “code” palatability. We show that rats’ individual preferences match late-epoch responses with a fidelity significantly higher than that expected on the basis of canonical palatability rankings. A single tasting session, however, induces “neural drift,” such that previously-assessed preferences are no longer reflected in cortical activity.
Modulation of endogenous opioid signaling by inhibitors of puromycin sensitive aminopeptidase
Authors: Singh Rohit , Jiang Rongrong , Williams Jessica , Dobariya Prakashkumar , Hanak Filip , Xie Jiashu , Rothwell Patrick E. , Vince Robert , More Swati S. 
Published: April 2024

ABSTRACTThe endogenous opioid system regulates pain through local release of neuropeptides and modulation of their action on opioid receptors. However, the effect of opioid peptides, the enkephalins, is short-lived due to their rapid hydrolysis by enkephalin-degrading enzymes. In turn, an innovative approach to the management of pain would be to increase the local concentration and prolong the stability of enkephalins by preventing their inactivation by neural enkephalinases such as puromycin sensitive aminopeptidase (PSA). Our previous structure-activity relationship studies offered the S-diphenylmethyl cysteinyl derivative of puromycin (20) as a nanomolar inhibitor of PSA. This chemical class, however, suffered from undesirable metabolism to nephrotoxic puromycin aminonucleoside (PAN). To prevent such toxicity, we designed and synthesized 5′-chloro substituted derivatives. The compounds retained the PSA inhibitory potency of the corresponding 5′-hydroxy analogs and had improved selectivity toward PSA. In vivo treatment with the lead compound19caused significantly reduced pain response in antinociception assays, alone and in combination with Met-enkephalin. The analgesic effect was reversed by the opioid antagonist naloxone, suggesting the involvement of opioid receptors. Further, PSA inhibition by compound19in brain slices caused local increase in endogenous enkephalin levels, corroborating our rationale. Pharmacokinetic assessment of compound19showed desirable plasma stability and identified the cysteinyl sulfur as the principal site of metabolic liability. We gained additional insight into inhibitor-PSA interactions by molecular modeling, which underscored the importance of bulky aromatic amino acid in puromycin scaffold. The results of this study strongly support our rationale for the development of PSA inhibitors for effective pain management.
Orbitofrontal high-gamma reflects spike-dissociable value and decision mechanisms
Authors: Sharma Dixit , Lupkin Shira M. , McGinty Vincent B. 
Published: April 2024

ABSTRACTThe orbitofrontal cortex (OFC) plays a crucial role in value-based decision-making. While previous research has focused on spiking activity in OFC neurons, the role of OFC local field potentials (LFPs) in decision-making remains unclear. LFPs are important because they can reflect synaptic and subthreshold activity not directly coupled to spiking, and because they are potential targets for less invasive forms of brain-machine interface (BMI). We recorded LFPs and spiking activity using multi-channel vertical probes while monkeys performed a two-option value-based decision-making task. We compared the value- and decision-coding properties of high-gamma range LFPs (HG, 50-150 Hz) to the coding properties of spiking multi-unit activity (MUA) recorded concurrently on the same electrodes. Results show that HG and MUA both represent the values of decision targets, and that their representations have similar temporal profiles in a trial. However, we also identified value-coding properties of HG that were dissociable from the concurrently-measured MUA. On average across channels, HG amplitude increased monotonically with value, whereas the average value encoding in MUA was net neutral. HG also encoded a signal consistent with a comparison between the values of the two targets, a signal which was much weaker in MUA. In individual channels, HG was better able to predict choice outcomes than MUA; however, when simultaneously recorded channels were combined in population-based decoder, MUA provided more accurate predictions than HG. Interestingly, HG value representations were accentuated in channels in or near shallow cortical layers, suggesting a dissociation between neuronal sources of HG and MUA. In summary, we find that HG signals are dissociable from MUA with respect to cognitive variables encoded in prefrontal cortex, evident in the monotonic encoding of value, stronger encoding of value comparisons, and more accurate predictions about behavior. High-frequency LFPs may therefore be a viable – or even preferable – target for BMIs to assist cognitive function, opening the possibility for less invasive access to mental contents that would otherwise be observable only with spike-based measures.
Limb loss and specialized leg dynamics in tiny water-walking insects
Authors: O’Neil Johnathan N. , Yung Kai Lauren , Difini Gaetano , Rohilla Pankaj , Bhamla M. Saad 
Published: April 2024

AbstractThe air-water of the planet’s water bodies, such as ponds, lakes and streams, presents an uncertain ecological niche with predatory threats from above and below. AsMicroveliamove across the water surface in small ponds, they face potential injury from attacks by birds, fish, and underwater invertebrates. Thus, our study investigates the effects of losing individual or pairs of tarsi on theMicrovelia’sability to walk on water. Removal of both hind tarsi causesMicrovelia spp. to rock their bodies (yaw) while running across the water surface at ±19°, compared to ±7° in non-ablated specimens. This increase in yaw, resulting from the removal of hind tarsi, indicates thatMicroveliause their hind legs as ‘rudders’ to regulate yaw, originating from the contralateral middle legs’ strokes on the water’s surface through an alternating tripod gait. Ablation of the ipsilateral middle and hind tarsi disrupts directionality, makingMicroveliaturn in the direction of their intact limbs. This loss of directionality does not occur with the removal of contralateral middle and hind tarsi. However,Microvelialose their ability to use the alternating tripod gait to walk for water walking on the day of contralateral ablation. Remarkably, by the next dayMicroveliaadapt and regain the ability to walk on water using the alternating tripod gait. Our findings elucidate the specialized leg dynamics within the alternating tripod gait ofMicrovelia spp., and their adaptability to tarsal loss. This research could guide the development and design strategies of small, adaptive, and resilient micro-robots that can adapt to controller malfunction or actuator damage for walking on water and terrestrial surfaces.
Stored Elastic Bending Tension as a Mediator of Embryonic Body Folding
Authors: Zaher Mira , Yelin Ronit , Arraf Alaa A. , Jadon Julian , Asleh Manar Abboud , Goltzman Sivan , Shaulov Lihi , Reinhardt Dieter P. , Schultheiss Thomas M. 
Published: April 2024

AbstractDuring development, amniote vertebrate embryos transform from a flat, multi-layered sheet into a three-dimensional cylindrical form, through ventral folding of the lateral sides of the sheet (the lateral plate, LP) and their fusion in the ventral midline. Although this basic aspect of vertebrate body plan formation has long been described, it is not understood at the mechanistic level. Each side of the LP is comprised of two tissue layers: a dorsal somatopleure (Sop) of pseudostratified coelomic epithelium, extracellular matrix (ECM) and ectoderm, and a ventral splanchnopleure (Spl) of similar construction except with endoderm instead of ectoderm. Using a chick embryo slice system we find that the flat stage is actually a poised balance of opposing elastic bending tensions, with dorsal bending tension in the Sop opposing ventral bending tension in the Spl. An intact extracellular matrix is required for generating the bending tensions, as localized enzymatic digestion of Sop or Spl ECM dissipates tension, while removal of the endodermal or ectodermal layers has no effect. As development proceeds, the Sop undergoes Epithelial-Mesenchymal Transition, ECM fragmentation and dissipation of dorsal bending tension, while the Spl ECM and ventral bending tension remain intact, thus changing the balance of bending forces in the LP to promote ventral folding. Consistent with these findings, interference with the elastic ECM component fibrillin in the Splin vivoreduces stored bending tension and perturbs ventral body folding. A generalizable conceptual model is presented in which embryonic growth, in the context of specific embryonic geometrical constraints, leads to accumulation of bending tension in the LP ECM, which is harnessed to drive body folding.
Development of BODIPY-based fluorescent probes for highly selective amino acid identification
Authors: Hendrick Nathaniel , Martin Andrew , Chan Andrew , Lenihan Jason , Reiter Harrison , Clough Mitchell , Jiang Lian , Whaley Eddie , Huh Yoo Jeong , McNeely James , Chen Anderson , Emili Andrew , Beeler Aaron 
Published: April 2024

ABSTRACTAmino acid sensing is a powerful tool for intra- and extra-cellular assays. We report herein the generation and optimization of bioconjugatable fluorescent reporter for pan-amino acid sensing, the OMNI probe, that through inductive electronics produces a unique photophysical response upon coupling to the α-amino group of an amino acid depending on the identity of the adjacent side chain. Using an auto-photocatalyzed Meerwein arylation reaction, we created a library of bis-arylated 8-methylthio-BODIPY dye derivatives exhibiting improved spectral variation, brightness, dynamic range, robustness, water solubility, and reactivity. Aryl groups with optimal photophysical behaviors were combined to create asymmetric versions conferring high spectral range, brightness, and water solubility. Combining aryl group modifications yielded a set of engineered asymmetric probes that achieved complete spectral resolution in a multi-variable analysis (fluorescent emission, lifetime, brightness) for all twenty native amino acid-dye conjugates while increasing reactivity toward amino acids in aqueous buffer. With our robust OMNI probe design, pan-amino acid resolution and identification through high sensitivity fluorescence down to single molecules is now routinely possible for diverse potential applications including protein sequencing.
Opposing actions of JIP4 and RILPL1 provide antagonistic motor force to dynamically regulate membrane reformation during lysosomal tubulation/sorting driven by LRRK2
Authors: Bonet-Ponce Luis , Tegicho Tsion , Beilina Alexandra , Kluss Jillian H. , Li Yan , Cookson Mark R. 
Published: April 2024

ABSTRACTLysosomes are dynamic cellular structures that adaptively remodel their membrane in response to stimuli, including membrane damage. We previously uncovered a process we term LYTL (LYsosomal Tubulation/sorting driven by Leucine-Rich Repeat Kinase 2 [LRRK2]), wherein damaged lysosomes generate tubules sorted into mobile vesicles. LYTL is orchestrated by the Parkinson’s disease-associated kinase LRRK2 that recruits the motor adaptor protein and RHD family member JIP4 to lysosomes via phosphorylated RAB proteins. To identify new players involved in LYTL, we performed unbiased proteomics on isolated lysosomes after LRRK2 kinase inhibition. Our results demonstrate that there is recruitment of RILPL1 to ruptured lysosomes via LRRK2 activity to promote phosphorylation of RAB proteins at the lysosomal surface. RILPL1, which is also a member of the RHD family, enhances the clustering of LRRK2-positive lysosomes in the perinuclear area and causes retraction of LYTL tubules, in contrast to JIP4 which promotes LYTL tubule extension. Mechanistically, RILPL1 binds to p150Glued, a dynactin subunit, facilitating the transport of lysosomes and tubules to the minus end of microtubules. Further characterization of the tubulation process revealed that LYTL tubules move along tyrosinated microtubules, with tubulin tyrosination proving essential for tubule elongation. In summary, our findings emphasize the dynamic regulation of LYTL tubules by two distinct RHD proteins and pRAB effectors, serving as opposing motor adaptor proteins: JIP4, promoting tubulation via kinesin, and RILPL1, facilitating tubule retraction through dynein/dynactin. We infer that the two opposing processes generate a metastable lysosomal membrane deformation that facilitates dynamic tubulation events.