bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanosensitive PIEZO2 channels shape coronary artery development
Authors: Pampols-Perez Mireia , Fürst Carina , Sánchez-Carranza Oscar , Cano Elena , Raimundo Sandra , Lindberg Eric L. , Taube Martin , Heuser Arnd , Sporbert Anje , Hübner Norbert , Gerhardt Holger , Lewin Gary R. , Hammes Annette 
Published: July 2024

AbstractThe coronary arteries develop under substantial mechanical loads. However, the role of mechanosensitive ion channels has barely been addressed in this system. Here we demonstrate the expression of the mechanosensitive ion channel PIEZO2 in specific coronary endothelial cell populations during a crucial phase of vascular modeling.Piezo2positive coronary endothelial cells display distinct transcriptional profiles and have mechanically activated ionic currents. Strikingly,Piezo2-/-mouse embryos and mice with human pathogenic variants ofPIEZO2display coronary vessel malformations and left ventricular hyperplasia. We conclude that an optimal balance of PIEZO2 channel function is indispensable for coronary vessel formation, integrity, and remodeling and likely for proper cardiac function.
Disentangling the Roles of Distinct Cell Classes with Cell-Type Dynamical Systems
Authors: Jha Aditi , Gupta Diksha , Brody Carlos D. , Pillow Jonathan W. 
Published: July 2024

AbstractLatent dynamical systems have been widely used to characterize the dynamics of neural population activity in the brain. However, these models typically ignore the fact that the brain contains multiple cell types. This limits their ability to capture the functional roles of distinct cell classes, and to predict the effects of cell-specific perturbations on neural activity or behavior. To overcome these limitations, we introduce the “cell-type dynamical systems” (CTDS) model. This model extends latent linear dynamical systems to contain distinct latent variables for each cell class, with biologically inspired constraints on both dynamics and emissions. To illustrate our approach, we consider neural recordings with distinct excitatory (E) and inhibitory (I) populations. The CTDS model defines separate latents for both cell types, and constrains the dynamics so that E (I) latents have a strictly positive (negative) effects on other latents. We applied CTDS to recordings from rat frontal orienting fields (FOF) and anterior dorsal striatum (ADS) during an auditory decision-making task. The model achieved higher accuracy than a standard linear dynamical system (LDS), and revealed that the animal’s choice can be decoded from both E and I latents and thus is not restricted to a single cell-class. We also performed in-silico optogenetic perturbation experiments in the FOF and ADS, and found that CTDS was able to replicate the experimentally observed effects of different perturbations on behavior, whereas a standard LDS model—which does not differentiate between cell types—did not. Crucially, our model allowed us to understand the effects of these perturbations by revealing the dynamics of different cell-specific latents. Finally, CTDS can also be used to identify cell types for neurons whose class labels are unknown in electrophysiological recordings. These results illustrate the power of the CTDS model to provide more accurate and more biologically interpretable descriptions of neural population dynamics and their relationship to behavior.
Optimizing murine sample sizes for RNA-seq studies revealed from large-scale comparative analysis
Authors: Halasz Gabor , Schmahl Jennifer , Negron Nicole , Ni Min , Atwal Gurinder S. , Glass David J. 
Published: July 2024

ABSTRACTDetermining the appropriate sample size (N) for comparative biological experiments is critical for obtaining reliable results. In order to determine the N, the usual approach is to perform a power calculation, which involves understanding the variability between samples and the expected effect size. Here, we focused on bulk RNA-seq experiments, which have become ubiquitous in biology, but which have many unknown or difficult to estimate parameters, and so the required analyses to determine the minimum N is typically lacking. We therefore performed two N=30 profiling studies between wild-type mice and mice in which one copy of a gene had been deleted, to determine how many mice would be required to minimize false positives and to maximize true discoveries found in the N of 30 experiment. Results from experiments with N=4 or less are shown to be highly misleading, given the substantial false positive rate, and the lack of discovery of genes later found with higher N. For a cut-off of 2-fold expression differences, we found that an N of 6-7 mice was required to consistently decrease the false positive rate to below 50%, and that “more is always better” when it came to discovery rates - an N of 8-12 is significantly better in lowering the false positive rate.A common method to reduce false discovery rate in underpowered experiments is to raise the fold cutoff or increase the stringency of the P-value and include only highly perturbed, highly significant genes. We show that while this strategy is no substitute for increasing the N of the experiment, because it results in consistently inflated effect sizes and a substantial drop in sensitivity. These data should be helpful to others in choosing their Ns, since it’s often not practical to do such large studies for every mouse model.
The impact of Library Size and Scale of Testing on Virtual Screening
Authors: Liu Fangyu , Mailhot Olivier , Glenn Isabella S. , Vigneron Seth F. , Bassim Violla , Xu Xinyu , Fonseca-Valencia Karla , Smith Matthew S. , Radchenko Dmytro S. , Fraser James S. , Moroz Yurii S. , Irwin John J. , Shoichet Brian K. 
Published: July 2024

AbstractVirtual libraries for ligand discovery have recently increased 10,000-fold, and this is thought to have improved hit rates and potencies from library docking. This idea has not, however, been experimentally tested in direct comparisons of larger-vs-smaller libraries. Meanwhile, though libraries have exploded, the scale of experimental testing has little changed, with often only dozens of high-ranked molecules investigated, making interpretation of hit rates and affinities uncertain. Accordingly, we docked a 1.7 billion molecule virtual library against the model enzyme AmpC β-lactamase, testing 1,521 new molecules and comparing the results to the same screen with a library of 99 million molecules, where only 44 molecules were tested. Encouragingly, the larger screen outperformed the smaller one: hit rates improved by two-fold, more new scaffolds were discovered, and potency improved. Overall, 50-fold more inhibitors were found, supporting the idea that there are many more compounds to be discovered than are being tested. With so many compounds evaluated, we could ask how the results vary with number tested, sampling smaller sets at random from the 1521. Hit rates and affinities were highly variable when we only sampled dozens of molecules, and it was only when we included several hundred molecules that results converged. As docking scores improved, so too did the likelihood of a molecule binding; hit rates improved steadily with docking score, as did affinities. This also appeared true on re-analysis of large-scale results against the σ2 and dopamine D4 receptors. It may be that as the scale of both the virtual libraries and their testing grows, not only are better ligands found but so too does our ability to rank them.
Hypersensitivity of the vimentin cytoskeleton to net-charge states and Coulomb repulsion
Authors: Unger Bret A. , Wu Chun Ying , Choi Alexander A. , He Changdong , Xu Ke 
Published: July 2024

AbstractAs with most intermediate filament systems, the hierarchical self-assembly of vimentin into nonpolar filaments requires no nucleators or energy input. Utilizing a set of live-cell, single-molecule, and super-resolution microscopy tools, here we show that in mammalian cells, the assembly and disassembly of the vimentin cytoskeleton is highly sensitive to the protein net charge state. Starting with the intriguing observation that the vimentin cytoskeleton fully disassembles under hypotonic stress yet reassembles within seconds upon osmotic pressure recovery, we pinpoint ionic strength as its underlying driving factor. Further modulating the pH and expressing differently charged constructs, we converge on a model in which the vimentin cytoskeleton is destabilized by Coulomb repulsion when its mass-accumulated negative charges (-18 per vimentin protein) along the filament are less screened or otherwise intensified, and stabilized when the charges are better screened or otherwise reduced. Generalizing this model to other intermediate filaments, we further show that whereas the negatively charged GFAP cytoskeleton is similarly subject to fast disassembly under hypotonic stress, the cytokeratin, as a copolymer of negatively and positively charged subunits, does not exhibit this behavior. Thus, in cells containing both vimentin and keratin cytoskeletons, hypotonic stress disassembles the former but not the latter. Together, our results both provide new handles for modulating cell behavior and call for new attention to the effects of net charges in intracellular protein interactions.
Development of a DSM test battery to determine depression-like marmoset
Authors: Yamanaka Hajime , Ishibashi Hidetoshi , Nakamura Katsuki 
Published: July 2024

AbstractDepression is a serious and high-incidence mental disorder that can lead to suicide. Despite much depression research using humans and rodents to date, it has been difficult to completely overcome depression and elucidate its etiology. Marmoset monkeys have been utilized to study neuropsychiatric disorders in recent years. Since the clinical diagnostic criteria for psychiatric disorders are mainly based on multiple behavioral changes, test battery systems, a multifaceted and comprehensive strategy, are applied to depression research. Here, we devised a test battery with six tests to investigate depression-like symptoms corresponding to clinical criteria and set criteria for a test indicator-based judgment. We did a usability confirmation experiment using a drug and judged three of nine marmosets as depression-like. This rate is comparable with the incidence rate of human patients; i.e., 10-30% of patients who received reserpine treatment suffer from depression. Thus, we propose the test battery we constructed in this study will contribute to the study of depression.
L-type calcium channel blockade with verapamil prevents noise induced neuronal dys-synchrony
Authors: Yalcinoglu Selin , Braun Rod D. , Wattoo Ammaar , Apawu Aaron K. , Alrayashi Rasheed , Holt Avril Genene 
Published: July 2024

AbstractPrevious studies have established the protective effects of calcium channel blockade on the peripheral auditory system in response to noise exposure. While these studies implicate L-type calcium channels (LTCCs) in noise generated dysfunction in the auditory periphery, contributions of LTCCs to noise-induced central dysfunction remains unclear. To begin to elucidate the roles of LTCCs in hearing, peripheral and central auditory function were assessed longitudinally after LTCC blockade. Neuronal synchrony and activity were assessed by analyzing wave I (peripheral) and wave V (central) auditory brainstem responses (ABRs). Just prior to a noise exposure resulting in a temporary shift in hearing thresholds, rats were administered verapamil (LTCC blocker) or saline. Verapamil administration prevented the noise-induced decrease in ABR wave I and V amplitudes. Interestingly, when non-noise exposed animals were administered verapamil, wave V amplitude decreased, suggesting that LTCCs are critical for neuronal synchrony in the inferior colliculus. The inferior colliculus mediates inhibition of the acoustic startle reflex (giASR). Following noise exposure giASR was enhanced, but the enhancement was not prevented by LTCC blockade. These results suggest that while LTCCs are necessary for auditory-related synchronous activity, these channels do not contribute to noise-induced hyperactivity in the inferior colliculus.
Translatome analysis reveals cellular network in DLK-dependent hippocampal glutamatergic neuron degeneration
Authors: Ritchie Erin M , Acar Dilan , Zhong Siming , Pu Qianyi , Li Yunbo , Zheng Binhai , Jin Yishi 
Published: July 2024

AbstractThe conserved MAP3K12/Dual Leucine Zipper Kinase (DLK) plays versatile roles in neuronal development, axon injury and stress responses, and neurodegeneration, depending on cell-type and cellular contexts. Emerging evidence implicates abnormal DLK signaling in several neurodegenerative diseases. However, our understanding of the DLK-dependent gene network in the central nervous system remains limited. Here, we investigated the roles of DLK in hippocampal glutamatergic neurons using conditional knockout and induced overexpression mice. We found that dorsal CA1 and dentate gyrus neurons are vulnerable to elevated expression of DLK, while CA3 neurons appear less vulnerable. We identified the DLK-dependent translatome that includes conserved molecular signatures and displays cell-type specificity. Increasing DLK signaling is associated with disruptions to microtubules, potentially involving STMN4. Additionally, primary cultured hippocampal neurons expressing different levels of DLK show altered neurite outgrowth, axon specification, and synapse formation. The identification of translational targets of DLK in hippocampal glutamatergic neurons has relevance to our understanding of selective neuron vulnerability under stress and pathological conditions.
Sleep induced by mechanosensory stimulation provides cognitive and health benefits inDrosophila
Authors: Inami Sho , Koh Kyunghee 
Published: July 2024

AbstractStudy ObjectivesSleep is a complex phenomenon regulated by various factors, including sensory input. Anecdotal observations have suggested that gentle rocking helps babies fall asleep, and experimental studies have verified that rocking promotes sleep in both humans and mice. Recent studies have expanded this understanding, demonstrating that gentle vibration also induces sleep inDrosophila. Natural sleep serves multiple functions, including learning and memory, synaptic downscaling, and clearance of harmful substances associated with neurodegenerative diseases. Here, we investigated whether vibration-induced sleep provides similar cognitive and health benefits inDrosophila.MethodsWe administered gentle vibration to flies that slept very little due to a forced activation of wake-promoting neurons and investigated how the vibration influenced learning and memory in the courtship conditioning paradigm. Additionally, we examined the effects of VIS on synaptic downscaling by counting synapse numbers of select neurons. Finally, we determined whether vibration could induce sleep inDrosophilamodels of Alzheimer’s disease (AD) and promote the clearance of Amyloid β (Aβ) and Tubulin Associated Unit (TAU).ResultsVibration-induced sleep enhanced performance in a courtship conditioning paradigm and reduced the number of synapses in select neurons. Moreover, vibration improved sleep inDrosophilamodels of AD, promoting the clearance of Aβ and TAU.ConclusionsMechanosensory stimulation offers a promising non-invasive avenue for enhancing sleep, potentially providing associated cognitive and health benefits.Significance StatementSleep is critical for a healthy mind and body, and sleep disturbances are commonly associated with neurodegenerative diseases such as Alzheimer’s disease. Sleep is influenced by sensory input, and mechanical stimulation, such as gentle rocking and vibration, has been shown to promote sleep in various species, including humans, mice, and fruit flies. This study demonstrates that gentle vibration not only helps flies sleep better but also improves their performance in a learning and memory task and makes their brains more efficient in clearing harmful substances. Notably, vibration can facilitate the clearance of Amyloid β and the TAU proteins, which accumulate in Alzheimer’s disease. These results highlight the potential for gentle mechanosensory stimulation to promote sleep and cognitive health.
Single-cell RNA-sequencing identifies unique cell-specific gene expression profiles in high-grade cardiac allograft vasculopathy
Authors: Amancherla Kaushik , Schlendorf Kelly H. , Chow Nelson , Sheng Quanhu , Freedman Jane E. , Rathmell Jeffrey C. 
Published: July 2024

AbstractBackgroundCardiac allograft vasculopathy (CAV), a diffuse thickening of the intima of the coronary arteries and microvasculature, is the leading cause of late graft failure and mortality after heart transplantation (HT). Diagnosis involves invasive coronary angiography, which carries substantial risk, and minimally-invasive approaches to CAV diagnosis are urgently needed. Using single-cell RNA-sequencing in peripheral blood mononuclear cells (PBMCs), we sought to identify cell-specific gene expression profiles in CAV.MethodsWhole blood was collected from 22 HT recipients with angiographically-confirmed CAV and 18 HT recipients without CAV. PBMCs were isolated and subjected to single-cell RNA-sequencing using a 10X Genomics microfluidic platform. Downstream analyses focused on differential expression of genes, cell compositional changes, and T cell receptor repertoire analyses.ResultsAcross 40 PBMC samples, we isolated 134,984 cells spanning 8 major clusters and 31 subclusters of cell types. Compositional analyses showed subtle, but significant increases in CD4+ T central memory cells, and CD14+ and CD16+ monocytes in high-grade CAV (CAV-2 and CAV-3) as compared to low-grade or absent CAV. After adjusting for age, gender, and prednisone use, 745 genes were differentially expressed in a cell-specific manner in high-grade CAV. Weighted gene co-expression network analyses showed enrichment for putative pathways involved in inflammation and angiogenesis. There were no significant differences in T cell clonality or diversity with increasing CAV severity.ConclusionsUnbiased whole transcriptomic analyses at single-cell resolution identify unique, cell-specific gene expression patterns in CAV, suggesting the potential utility of peripheral gene expression biomarkers in diagnosing CAV.
Risk of Delayed Percutaneous Coronary Intervention for STEMI in the Southeast United States
Authors: Messinger Maxwell C. , Ashburn Nicklaus P. , Chait Joshua S. , Snavely Anna C. , Hapig-Ward Siena , Stopyra Jason P. , Mahler Simon A. 
Published: July 2024

ABSTRACTBackgroundEmergent reperfusion by percutaneous coronary intervention (PCI) within 90 minutes of first medical contact (FMC) is indicated in patients with ST-segment elevation myocardial infarction (STEMI). However, long transport times in rural areas in the Southeast US make meeting this goal difficult. The objective of this study was to determine the number of Southeast US residents with prolonged transport times to the nearest 24/7 primary PCI (PPCI) center.MethodsA cross-sectional study of residents in the Southeastern US was conducted based on geographical and 2022 5-Year American Community Survey data. The geographic information system (GIS) ArcGIS Pro was used to estimate Emergency Medical Services (EMS) transport times for Southeast US residents to the nearest PPCI center. All 24/7 PPCI centers in North Carolina, South Carolina, Georgia, Florida, Mississippi, Alabama, and Tennessee were included in the analysis, as well as nearby PPCI centers in surrounding states. To identify those at risk of delayed FMC-to-device time, the primary outcome was defined as a >30-minute transport time, beyond which most patients would not have PCI within 90 minutes. A secondary outcome was defined as transport >60 minutes, the point at which FMC-to-device time would be >120 minutes most of the time. These cutoffs are based on national median EMS scene times and door-to-device times.ResultsWithin the Southeast US, we identified 62,880,528 residents and 350 PPCI centers. Nearly 11 million people living in the Southeast US reside greater than 30 minutes from a PPCI center (17.3%, 10,866,710, +/- 58,143), with 2% (1,271,522 +/- 51,858) living greater than 60 minutes from a PPCI hospital. However, most patients reside in short transport zones; 82.7% (52,013,818 +/- 98,741). Within the Southeast region, 8.4% (52/616) of counties have more than 50% of their population in a long transport zone and 42.3% (22/52) of those have more than 90% of their population in long transport areas.ConclusionsNearly 11 million people in the Southeast US do not have access to timely PCI for STEMI care. This disparity may contribute to increased morbidity and mortality.
Using breathing systems in anaesthesia for up to 7 days instead of 24 hours: a comparative microbial safety study
Authors: Haanappel Cynthia P. , Rieff Elisabeth A. , Pavkovic Lucija , van Holst-Raaphorst Merel N. , de Groot Woutrinus , van der Marel Caroline D. , Voor in ’t holt Anne F. , Severin Juliëtte A. 
Published: July 2024

SummaryThe replacement frequency of mechanical ventilator’s breathing systems used in operating rooms (ORs) currently varies between hospitals. In light of evidence-based decision-making and sustainability efforts, we aim to determine whether 7-day use of breathing systems instead of 24 hours is microbial safe. In this prospective single-centre explorative study, 30mm UniflowTM breathing systems used in eight ORs were included. In four ORs, breathing systems were replaced daily following standard practice. In the remaining four ORs, they were intended for a 7-day use. Breathing systems were sampled daily on three locations of the exterior surface and cultured for the presence of microorganisms. A total of 128 breathing systems were included, 99 from an OR with daily replacement and 29 from an OR with weekly replacement. A total of 604 samples were cultured, of which the majority, 549 (90.9%) cultures were negative. From the 55 (9.1%) positive cultures, the majority (n=49, 70%) were coagulase-negative staphylococci. None of the identified microorganisms were found in consecutive cultures. Cultures from day 2 to 7 did not show a statistically significant increased positivity rate compared to cultures from day 1, respectively 22.9% vs. 24.1%. The weekly replacement regimen, furthermore, decreased the number of breathing systems used with 71%.Our data indicates that use of breathing systems up to seven days remains microbial safe. Additionally, only a minimal number of pathogenic microorganisms were detected, and these were not persistent on the breathing systems. Transitioning from 24-hours to intended 7-day use could significantly reduce costs and CO2emissions.
Antagonistic Roles for MITF and TFE3 in Melanoma Plasticity
Authors: Chang Jeremy , Campbell-Hanson Katelyn R. , Vanneste Marion , Bartschat Nicholas I. , Nagel Ryan , Arnadottir Asdis K , Nhung Vu Hong , Montgomery Collin , Yevdash Julius , Jiang Jiarui , Bhinu Ardith , Helverson Annika , Henry Michael D. , Steingrímsson Eiríkur , Weigel Ronald J. , Cornell Robert A. , Kenny Colin 
Published: July 2024

SummaryMelanoma cells have the ability to switch from a melanocytic and proliferative state to a mesenchymal and invasive state and back again. This plasticity drives intra-tumoral heterogeneity, progression, and therapeutic resistance. Microphthalmia-associated Transcription Factor (MITF) promotes the melanocytic/proliferative phenotype, but factors that drive the mesenchymal/invasive phenotype and the mechanisms that effect the switch between cell states are unclear. Here, we identify the MITF paralog TFE3 and the non-canonical mTORC1 pathway as regulators of the mesenchymal state. We show that TFE3 expression drives the metastatic phenotype in melanoma cell lines and tumors. Deletion of TFE3 in MITF-low melanoma cell lines suppresses their ability to migrate and metastasize. Further, MITF suppresses the mesenchymal phenotype by directly or indirectly activating expression ofFNIP1, FNIP2,andFLCN, which encode components of the non-canonical mTORC1 pathway, thereby promoting cytoplasmic retention and lysosome-mediated degradation of TFE3. These findings highlight a molecular pathway controlling melanoma plasticity and invasiveness.