bluuebunny/crossref_metadata_2025 huggingface dataset:
Statistical method accounts for microscopic electric field distortions around neurons when simulating activation thresholds
Authors: Weise Konstantin , Makaroff Sergey N. , Numssen Ole , Bikson Marom , Knösche Thomas R.
Published: October 2024

Introduction

Notwithstanding advances in computational models of neuromodulation, there are mismatches between simulated and experimental activation thresholds. Transcranial Magnetic Stimulation (TMS) of the primary motor cortex generates motor evoked potentials (MEPs). At the threshold of MEP generation, whole-head models predict macroscopic (at millimeter scale) electric fields (50-70 V/m) which are considerably below conventionally simulated cortical neuron thresholds (175-350 V/m).

Methods

We hypothesize that this apparent contradiction is in part a consequence of electrical field warping by brain microstructure. Classical neuronal models ignore the physical presence of neighboring neurons and microstructure and assume that the macroscopic field directly acts on the neurons. In previous work, we performed advanced numerical calculations considering realistic microscopic compartments (e.g., cells, blood vessels), resulting in locally inhomogeneous (micrometer scale) electric field and altered neuronal activation thresholds. Here we combine detailed neural threshold simulations under homogeneous field assumptions with microscopic field calculations, leveraging a novel statistical approach.

Results

We show that, provided brain-region specific microstructure metrics, a single statistically derived scaling factor between microscopic and macroscopic electric fields can be applied in predicting neuronal thresholds. For the cortical sample considered, the statistical methods match TMS experimental thresholds.

Conclusions

Our approach can be broadly applied to neuromodulation models, where fully coupled microstructure scale simulations may not be computationally tractable.
Snapshots of Mitochondrial Fission Imaged by Cryo-Scanning Transmission Electron Tomography
Authors: Kirchweger Peter , Wolf Sharon Grayer , Varsano Neta , Dadosh Tali , Resch Guenter P. , Elbaum Michael
Published: October 2024

Mitochondria undergo constant remodeling via fission, fusion, extension, and degradation. Fission, in particular, depends on the accumulation of the mitochondrial fission factor (MFF) and subsequent recruitment of the dynamin-related protein Drp1. We used cryo-scanning transmission electron tomography (cryo-STET) to investigate mitochondrial morphologies in MFF mutant cells (MFF-/-) in ATP-depleting conditions that normally induce fission. The capability of cryo-STET to image through the cytoplasmic volume to a depth of 1 µm provides visualization of mitochondria and their surroundings intact. We imaged changes in mitochondrial morphology and cristae structure and contacts with endoplasmic reticulum, degradative organelles, and cytoskeleton at stalled fission sites. We found disruption of the outer membrane at contact sites with endoplasmic reticulum and degradative organelles at sites of mitophagy. We identified fission sites where the inner mitochondrial membrane is already separated while the outer is still continuous. While MFF is a general fission factor, these observations demonstrate that mitochondrial fission can proceed to the final stage in its absence. The use of cryo-STET allays concerns about the loss of structures due to sample thinning required for cryo-TEM tomography.

Summary Statement

Imaging the whole cytosol in three dimensions greatly aids in understanding cellular processes. Here, we applied cryo-scanning transmission electron tomography to study stages of mitochondrial fission in the absence of the mitochondrial fusion factor protein.
Ybx1guides C/EBPα and cBAF chromatin-remodeling complex to promote adipogenic gene expression in steatotic hepatocytes
Authors: Jordan James M. , Qiao Jixuan , Zou Chenhui , Steensels Sandra , Haczeyni Fahrettin , Fraim Alessandra , Mendoza Arturro , de Jong Ype P. , Ersoy Baran A.
Published: October 2024

Excessive lipid accumulation by hepatocytes underlies the pathogenesis of metabolic-dysfunction associated steatotic liver disease (MASLD) and metabolic-dysfunction associated steatohepatitis (MASH) from the earliest stages of the disease. How liver cells regulate the commitment to storing large volumes of fat despite resulting tissue damage is not well understood. Here, we showY box-binding protein 1(Ybx1) is necessary for ectopic activation of an adipocyte-specific gene expression module that potentiates lipid accumulation in hepatocytes. Diet-induced obese (DIO) mice, with liver-specific depletion ofYbx1(Ybx1LKO), are resistant to MASLD without becoming hyperlipidemic.Ybx1LKOlivers exhibit upregulation of hepatocyte markers, like urea processing enzyme carbamoyl phosphate synthetase I (Cps1), and downregulation of adipocyte markers known to be transcriptionally regulated by peroxisome proliferator-activated receptor gamma (PPARγ). In nuclei of DIO mice, YBX1 interacts with CCAAT-enhancer-binding proteins alpha (C/EBPα) and the canonical BRG1/BRM-associated factor complex (cBAF); andC/EBPαis required forYbx1-dependentPPARγexpression in cultured liver cells. The chromatin binding pattern of YBX1 from DIO mouse liver overlaps with those of C/EBPα and cBAF at key adipogenic loci includingPpargandCfd. However, most YBX1-DNA binding occurs on C/EBPα-cBAF-depleted stretches located on chromosomes 16, 18, and 19, spanning up to five Mb, and overlapping regions which are inaccessible in differentiating preadipocytes, thereby bounding activational C/EBPα-cBAF complex-DNA interactions. Moreover, YBX1 expression is increased up to nine-fold in the livers of obese patients with MASLD-MASH compared to healthy obese controls; and adipocyte-specific genes, upregulated byYbx1, are also upregulated in human MASLD-MASH. Overall, our study uncoversYbx1as a critical epigenetic regulator in liver and potential therapeutic target for treatment of MASLD and MASH.
OLIGONUCLEOTIDES TARGETING THE 3’ SPLICE SITE DOWNSTREAM OF A MICROEXON AS AN INNOVATIVE THERAPY FOR AUTISM
Authors: Martinez-Pizarro Ainhoa , Picó Sara , Holm Lise Lolle , Doktor Thomas K , Andresen Brage S , Lucas José J , Desviat Lourdes R
Published: October 2024

Background

Microexons are highly conserved and mostly neuronal-specific 3-27 nucleotide exons, enriched in genes linked to autism spectrum disorders (ASD). We have previously shown decreased inclusion of a neuronal specific 24 bp microexon (exon 4) of the translational regulatorCPEB4in brains of idiopathic ASD cases and that this leads to CPEB4 aggregation and subsequent under-expression of multiple high confidence ASD-risk genes. Furthermore, enhanced skipping of theCPEB4microexon is also a novel etiological mechanism in schizophrenia (SCZ).

Methods

In this work we designed and tested in neuroblastoma cells a series of splice switching antisense oligonucleotides (SSO) targeting theCPEB4genomic region surrounding the microexon.

Results

SSOs targeting candidate intronic regions near the microexon resulted in a decrease in microexon inclusion by blocking hnRNPC/PTPB1 binding, thus mimicking the isoform imbalance observed in ASD. However, based on the kinetic coupling model correlating transcriptional elongation with splicing regulation, we identified SSOs targeting downstream 3’ splice site of exon 5 that favoured microexon inclusion in a dose-dependent manner and resulted in increased protein levels ofFOXP1andAUTS2,two high-confidence ASD risk genes that are known targets of CPEB4 and whose protein levels are reduced in ASD.

Conclusions

These results deepen our understanding of the complex splicing regulation of microexons and open new applications of SSOs to treat diseases such as ASD and SCZ that are characterized by altered microexon inclusion.
The Interaction ofUBR4, LRP1, andOPHN1in Refractory Epilepsy:DrosophilaModel to Investigate the Oligogenic Effect on Epilepsy
Authors: Huang Rui-Na , Luo Si-Yuan , Huang Tao , Li Xiong-Sheng , Zhou Fan-Chao , Li Ling-Ying , Chen Ze-Ru , Chen Sheng-Qiang , Tang Bin , Qiao Jing-Da
Published: October 2024

Refractory epilepsy is an intractable neurological disorder that is currently difficult to achieve effective pharmacological control in clinical practice and can result in poor quality of life as well as increased mortality. Genetic factors are important causes of epilepsy, especially idiopathic epilepsy. In the clinical gene sequencing work, we identified one refractory epileptic patient who carried three epileptogenic candidate genes:UBR4, LRP1, andOPHN1variants. To clarify the epileptogenicity and interactions ofUBR4, LRP1, andOPHN1variants, as well as explore the role of each mutant gene in eliciting epilepsy, we established single-knockdown, double-knockdown, and triple-knockdownDrosophilamodels by suppressing the gene expression of these three epileptogenic candidate genes. After conducting behavioral testing for epilepsy in the sevenDrosophilaknockdown models, regression equations illustrating the causal connection between genotype and phenotype were developed. The mutations of the three epileptogenic candidate genes:UBR4, LRP1, andOPHN1, were proved to be epileptogenic at the animal level both in seizure rates and logistic regression results. Moreover, significant negative interactions inUBR4-OPHN1KD andLRP1-OPHN1KD were found in the trigenic KD system as well as theUBR4-OPHN1andLRP1-OPHN1digenic KD system according to the logistic regression analysis result. However, despite the existence of negative interaction, three groups of digenic KD flies and one group of trigenic KD flies presented higher seizure rates than that of the corresponding monogenic KD flies.LRP1-OPHN1KD together with its negative interaction was regarded as the main causative factors for seizure in theUBR4-LRP1-OPHN1KD.
Saccade onset, not fixation onset, best explains early responses across the human visual cortex during naturalistic vision
Authors: Amme Carmen , Sulewski Philip , Spaak Eelke , Hebart Martin N. , König Peter , Kietzmann Tim C.
Published: October 2024

Visual processing has traditionally been investigated using static viewing paradigms, where participants are presented with streams of randomized stimuli. Observations from such experiments have been generalized to naturalistic vision, which is based on active sampling via eye movements. In studies of naturalistic vision, visual processing stages are thought to be initiated at the onset of fixations, equivalent to a stimulus onset. Here we test whether findings from static visual paradigms translate to active, naturalistic vision. Utilizing head-stabilized magnetoencephalography (MEG) and eye tracking data of 5 participants who freely explored thousands of natural images, we show that saccade onset, not fixation onset, explains most variance in latency and amplitude of the early sensory component M100. Source-projected MEG topographies of image and saccade onset were anticorrelated, demonstrating neural dynamics that share similar topographies but produce oppositely oriented fields. Our findings challenge the prevailing approach for studying natural vision and highlight the role of internally generated signals in the dynamics of sensory processing.
Principles of nutrition-dependent root-microbiome engineering for regulating crop yield via live microbial inoculants
Authors: Huang Yuxiao , Tang Shengyue , Liu Rumeng , Liu Ju , Xiao Ting , Ni Bin
Published: October 2024

As the second genome, host-associated microbiota can enhance the functions of host immune systems, improve host nutrient availability and acquisition capacity, and increase host resistance to abiotic stress. Constructing host-associated microbiomes by applying various bioinoculants has become an attractive tool for promoting human health and increasing food production. However, despite their promising properties, the efficacy of bioinoculants vary significantly in actual field and clinical practices. Understanding the global design principles that shape the outcomes of interactions between bioinoculants and target host–microbiome symbionts remains a considerable challenge. In this study, we used a wheat production system as a case study to quantitatively understand how soil nutrient status impacts the establishment of host–microbiome interaction networks and their subsequent interactions with external bioinoculants. We found that soil organic carbon, one of the most general soil properties for global crop productivity and resilience, could affect the outcome of bioinoculant applications in wheat production systems, which led to functional instability in bioinoculant application outcomes. The results of this study significantly improved our understanding of the global design principles of nutrition-dependent root-microbiome engineering for regulating crop yield via the application of live microbial inoculants and provide theoretical guidance for bioinoculant applications in agricultural practice.
The impact of dwell time on the contextual effect of visual and passive lead-in movements
Authors: Alvarez-Hidalgo Laura , Franklin David W. , Howard Ian S.
Published: October 2024

Contextual cues arising from distinct movements are crucial in shaping control strategies for human movement. Here, we examine the impact of visual and passive lead-in movement cues on unimanual motor learning, focusing on the influence of “dwell time”, in which two-part movements are separated by the interval between the end of the first movement and the start of the second. We used a robotic manipulandum to implement a point-to-point interference task with switching opposing viscous curl-fields in male and female human participants. Consistent with prior research, in both visual and passive lead-in conditions, participants showed significant adaptation to opposing dynamics with short dwell times. As dwell time increased for both visual and passive signals, past movement information had less contextual influence. However, the efficacy of visual movement cues declined faster as dwell times increased. At dwell times greater than 800ms, the contextual influence of prior visual movement was small, whereas the effectiveness of passive lead-in movement was found to be significantly greater. This indicates that the effectiveness of sensory movement cues in motor learning is modality-dependent. We hypothesize that such differences may arise because proprioceptive signals directly relate to arm movements, whereas visual inputs can relate to many aspects of movement in the environment and not just to our own arm movements. Therefore, the motor system may not always find them as relevant for predictive control of dynamics.

Significance Statement

This study reveals the critical role of contextual cues from distinct movements in shaping motor learning. Here, we examined the influence of “dwell time”, the interval between the end of the first and the start of the second movement. Notably, visual lead-in movement cues lose their effectiveness sooner than passive lead-in movement cues as dwell time increases. This is possibly due to their lesser relevance to self-generated movements and the longer processing delays in visual information. This finding underscores the modality-dependent nature of sensory cues in motor learning. Understanding these effects can inform the development of more effective rehabilitation and training programs by leveraging the strengths of different sensory modalities to optimize motor learning.

News & Noteworthy

This research uncovers, for the first time, how visual and proprioceptive sensory cues affect motor learning as a function of the pause or “dwell time” in two-part movements. The study has shown that visual lead-in movement cues lose their effectiveness sooner than passive lead-in movement cues as dwell time increases. By revealing the modality-dependent nature of sensory information, this study enhances our understanding of motor control and opens new possibilities for improving therapeutic interventions.
Prevalence of Key Spike Protein Mutations and Their Limited Effect on COVID-19 Clinical Manifestations in Sylhet, Bangladesh
Authors: Akter Shahina , Zeba Zebunnesa , Hossain Md. Anwar , Ofori Michael Arthur , Shahab Muhammad , Rolim Silva Gabriel Vinícius , Nobre Oliveira Jonas Ivan , Akash Shopnil , Banu Tanjina Akhtar , Islam Mousona , Sarkar Murshed Hasan , Goswami Barna , Chowdhury Sanjana Fatema , Habib Md. Ahashan , Khan Md. Salim
Published: October 2024

SARS-CoV-2 is the virus responsible for the COVID-19 pandemic, which has spread rapidly around the world and had a significant impact on public health and the economy worldwide. This study investigated the correlation between SARS-CoV-2 spike protein mutations, clinical outcomes and patient demographics in the Sylhet region of Bangladesh. We looked at the full genome sequences of 37 SARS-CoV-2 samples that were collected between January and June 2020. Specifically, we looked at five major spike protein mutations: D614G, A570D, D1118H, A222V, and P681R. The D614G mutation was the most prevalent (94.6%), followed by A570D and D1118H (both 32.4%), A222V (29.7%), and P681R (13.5%). Despite their high prevalence, we found no statistically significant associations between these mutations and clinical outcomes or demographic variables, except for possible trends for the P681R mutation. We found that age played a decisive role in recovery from COVID-19, with older patients exhibiting slower recovery rates. In terms of predictors of outcome, gender differences were observed: clinical symptoms and viral genetic mutations were more influential for men, while age and disease progression were more important for women. Common nucleotide substitutions (A23403G, C3037T, and C14408T) associated with European strains were identified, suggesting possible routes of transmission. This study contributes to our understanding of the genetics, clinical manifestations and epidemiology of SARS-CoV-2 in the Sylhet region and emphasizes the need for continuous genomic surveillance and adaptive public health strategies.
Simulated microgravity accelerates alpha-synuclein aggregation and induces oxidative stress in anin vitroParkinson’s disease model
Authors: Lentini Veronica , Uras Giuseppe , Manca Alessia , El Faqir Mohammed Amine , Lucas-Del-Pozo Sara , Deiana Nicola , Cao Giacomo , Schapira Anthony HV , Pantaleo Antonella
Published: October 2024

Parkinson’s disease (PD) is a neurodegenerative disorder characterized by the accumulation of alpha-synuclein aggregates and progressive neuronal loss in the substantia nigra, with aging being its primary risk factor. The current available models to study PD mechanisms are largely relying on genetic mutations to recapitulate PD typical hallmarks, such as increased alpha-synuclein aggregation. However, they do not model the aging features associated with the disease.

Microgravity, a condition experience by astronauts during space missions, is known to induce ageing-like modifications on both systemic and cellular physiology.

To replicate the aging-related stress observed in PD patients, we exposed SH-SY5Y and 3K-SNCA mutant cell lines to simulated microgravity.

Our findings revealed that simulated microgravity enhanced PD alterations, with a significant increase in misfolded and phosphorylated a-syn. This was accompanied by heightened oxidative stress, as evidenced by increased levels of reactive oxygen species, without a sufficient antioxidant response. These results suggest that simulated microgravity effectively mimics and accelerate the stress associated with aging in PD cell models, regardless of the presence of PD mutation. This study highlights the potential of simulated microgravity as a tool for investigating aging processes in neurodegenerative diseases.
Culture of pluripotent stem cells in microscale droplets modulates differentiation and tissue patterning towards organoids on chip
Authors: Vertti-Quintero Nadia , Delahousse Clara , Aristov Andrey , Traboulsi Tatiana , Cossec Jack-Christophe , Baroud Charles N. , Sart Sébastien
Published: October 2024

1

The differentiation of pluripotent stem cells (PSCs) and their self-organization into organoids are influenced by cell-cell interactions mediated by contacts and secreted molecules. These interactions are enhanced in microfluidic droplets due to confinement and small culture volumes. However, a comprehensive study on the culture of PSCs within droplets and the impact of this microenvironment has yet to be conducted. In this study, we present a droplet platform for the 3D culture of PSCs at various stages of cellular commitment. We demonstrate PSC differentiation into the three germ layers and the feasibility of organoid formation within droplets. Our findings reveal that culturing PSCs in confined volumes regulates cell fate decisions, promoting tissue patterning in gastruloids through the sequential induction of growth and migration of distinct differentiated cell populations, and facilitating the self-organization of cardiac organoids. This technological approach provides unique insights into the intrinsic factors regulating tissue self-patterningin vitro.

2

Highlights and eTOC blurb

Highlights

Droplet microfluidics allows expansion and supports the pluripotency of 3D aggregates of PSCs.

Droplet microfluidics supports and regulates spontaneous differentiation into embryoid bodies.

Droplet promotes tissue patterning in gastruloids through the sequential induction of growth and migration of mesoderm followed by ectoderm.

Perfused microfluidic droplets support long term culture and derivation of organoids on chip.

Vertti-Quinteroet al. introduces a microfluidic droplet platform for the 3D culture of pluripotent stem cells (PSCs) at various differentiation stages. The format supports the long term 3D culture and the differentiation of PSCs -either spontaneous or directed-. This “microscale culture” can regulate PSCs fate decision, while promoting tissue pattering -as demonstrated in gastruloids polarization- and allowing self-organization towards cardioids formation.
The Mag-Click-Capture-Release Technology for Selective Capture and Release of Hepatocyte-Derived Extracellular Vesicles as Biomarkers for Liver Disease
Authors: Booijink Richell , Mentink Anouk , Jansen Larissa , Mentink Sven , van Rein Bo , Geraets Lieke , Scholten Jorinde , Brusse Maureen , Fu Siyu , Boonstra Andre , Bansal Ruchi
Published: October 2024

Chronic liver diseases, such as liver cirrhosis and hepatocellular carcinoma (HCC), present major global health challenges, often diagnosed late. Circulating extracellular vesicles (EVs), which carry disease-specific biomolecular cargo, is emerging as an early diagnostic and prognostic biomarker for several diseases including cancer. However, current EV purification methods including ultracentrifugation and size exclusion chromatography present several limitations. Here, we present the Mag-Click-Capture-Release Technology for selective capture and release of EVs that combinesmagnetic beads, trans-cyclooctene (TCO) and tetrazine (Tz)clickchemistry, immuno(antibody)-basedcaptureand disulfide-drivenreleaseof EVs. Importantly, the Mag-Click-Capture-Release Technology is customizable, whereby using specific antibodies conjugated to TCO antibodies, different EV subtypes can be selectively captured and released for further analysis. With our Mag-Click-Capture-Release Technology, we successfully isolated hepatocyte-derived EVs from human serum with good recovery, high specificity and purity when compared with standard ultracentrifugation. Validation in serum samples obtained from cirrhosis and HCC patients with alcohol-associated liver disease evidenced an increasing trend in hepatocyte-EV levels correlating with disease severity, suggesting potential for early diagnosis and prognosis. In conclusion, we present here the Mag-Click-Capture-Release Technology, a customizable and efficient approach for selective isolation of organ-, cell-specific, and disease-relevant EVs from biological samples that can be subsequently released for downstream molecular EV analysis and EV-related functional assays.
Single-cell transcriptomics reveal diverging pathobiology and opportunities for precision targeting in scleroderma-associated versus idiopathic pulmonary arterial hypertension
Authors: Tuhy Tijana , Coursen Julie C. , Graves Tammy , Patatanian Michael , Cherry Christopher , Niedermeyer Shannon E. , Khan Sarah L. , Rosen Darin T. , Croglio Michael P. , Elnashar Mohab , Kolb Todd M. , Mathai Stephen C. , Damico Rachel L. , Hassoun Paul M. , Shimoda Larissa A. , Suresh Karthik , Aldred Micheala A. , Simpson Catherine E.
Published: October 2024

Introduction

Pulmonary arterial hypertension (PAH) involves progressive cellular and molecular change within the pulmonary vasculature, leading to increased vascular resistance. Current therapies targeting nitric oxide (NO), endothelin, and prostacyclin pathways yield variable treatment responses. Patients with systemic sclerosis-associated PAH (SSc-PAH) often experience worse outcomes than those with idiopathic PAH (IPAH).

Methods

Lung tissue samples from four SSc-PAH, four IPAH, and four failed donor specimens were obtained from the Pulmonary Hypertension Breakthrough Initiative (PHBI) lung tissue bank. Single-cell RNA sequencing (scRNAseq) was performed using the 10X Genomics Chromium Flex platform. Data normalization, clustering, and differential expression analysis were conducted using Seurat. Additional analyses included gene set enrichment analysis (GSEA), transcription factor activity analysis, and ligand-receptor signaling. Pharmacotranscriptomic screening was performed using the Connectivity Map.

Results

SSc-PAH samples showed a higher proportion of fibroblasts and dendritic cells/macrophages compared to IPAH and donor samples. GSEA revealed enriched pathways related to epithelial-to-mesenchymal transition (EMT), apoptosis, and vascular remodeling in SSc-PAH samples. There was pronounced differential gene expression across diverse pulmonary vascular cell types and in various epithelial cell types in both IPAH and SSc-PAH, with epithelial to endothelial cell signaling observed. Macrophage to endothelial cell signaling was particularly pronounced in SSc-PAH. Pharmacotranscriptomic screening identified TIE2, GSK-3, and PKC inhibitors, among other compounds, as potential drug candidates for reversing SSc-PAH gene expression signatures.

Discussion

Overlapping and distinct gene expression patterns exist in SSc-PAH versus IPAH, with significant molecular differences suggesting unique pathogenic mechanisms in SSc-PAH. These findings highlight the potential for precision-targeted therapies to improve SSc-PAH patient outcomes. Future studies should validate these targets clinically and explore their therapeutic efficacy.
Temporal dynamics of inflammatory and transcriptome changes in the myocardium in a murine model of cardiac arrest
Authors: Panigrahi Soumya , Jiang Alice , Enriquez Angela , Tummala Sanjana , Rempinski Donald , Remy Kenneth E. , Rutledge Cody A.
Published: October 2024

Background

It is increasingly recognized that inflammatory changes play a significant role in myocardial injury following cardiac arrest. However, the pathophysiological mechanisms responsible for functional changes in the myocardium following the event remain incompletely understood. Here, we characterize the transcriptomic and immunological changes in a mouse model of cardiac arrest to explore the roles of epinephrine and ischemia/reperfusion on myocardial inflammation.

Methods and Results

Male and female mice (C57BL/6J) were divided into three groups: (1) Naïve (anesthesia only), (2) Sham (anesthesia + saline injection + epinephrine), and (3) Arrest (8-minute cardiac arrest followed by resuscitation (anesthesia + potassium chloride + epinephrine). We monitored the animals over 0.5, 1, 3, and 7 days with serial echocardiography. Hearts were harvested for transcriptomic analysis and inflammatory changes as assessed by flow cytometry and immunohistochemistry. Plasma samples were collected for cytokine signaling analysis by multiplex ELISA. Our data indicate that the cardiac arrest group have increased infiltrating neutrophils in the myocardium and elevated plasma levels of pro-inflammatory cytokines, peaking at 0.5 days after the initial insult and subsequently resolving. In contrast, Sham mice displayed less pronounced inflammatory changes, which peaked at 1 day after the procedure. Notably, these inflammatory alterations coincided with cardiac stunning, as demonstrated by echocardiography.

Conclusions

In our murine model of cardiac arrest, epinephrine exposure and ischemia/reperfusion induce significant inflammatory changes in the myocardium with increased infiltrating neutrophils and elevated circulating cytokines which subsequently resolve in a time-dependent manner. These changes correlate with improving cardiac function by echocardiography.
Flagellar motility and the mucus environment influence aggregation mediated antibiotic tolerance ofPseudomonas aeruginosain chronic lung infection
Authors: Higgs Matthew G. , Greenwald Matthew A. , Roca Cristian , Macdonald Jade K. , Sidders Ashelyn E. , Conlon Brian P. , Wolfgang Matthew C.
Published: October 2024

Pseudomonas aeruginosafrequently causes chronic lung infection in individuals with muco-obstructive airway diseases (MADs). ChronicP. aeruginosainfections are difficult to treat, primarily owing to antibiotic treatment failure, which is often observed in the absence of antimicrobial resistance. In MADs,P. aeruginosaforms biofilm-like aggregates within the luminal mucus. While the contribution of mucin hyperconcentration towards antibiotic tolerance has been described, the mechanism for mucin driven antibiotic tolerance and the influence of aggregates have not been fully elucidated. In this study, we investigated the contribution of flagellar motility towards aggregate formation as it relates to the diseased mucus environment. We found that loss of flagellar motility resulted in increasedP. aeruginosaaggregation and tolerance to multiple classes of antibiotics. Further, we observed differential roles in antimicrobial tolerance of themotABandmotCDstators, which power the flagellum. Additionally, we found that control offliCexpression was important for aggregate formation and antibiotic tolerance as a strain constitutively expressingfliCwas unable to form aggregates and was highly susceptible to treatment. Lastly, we demonstrate that neutrophil elastase, an abundant immune mediator and biomarker of chronic lung infection, promotes aggregation and antibiotic tolerance by impairing flagellar motility. Collectively, these results highlight the key role of flagellar motility in aggregate formation and antibiotic tolerance and deepens our understanding of how the MADs lung environment promotes antibiotic tolerance ofP. aeruginosa.

IMPORTANCE

Antibiotic recalcitrance of chronicPseudomonas aeruginosainfections in muco-obstructive airway diseases is a primary driver of mortality. Mechanisms that drive antibiotic tolerance are poorly understood. We investigated motility phenotypes related toP. aeruginosaadaptation and antibiotic tolerance in the diseased mucus environment. Loss of flagellar motility drives antibiotic tolerance by promoting aggregate formation. Regulation of flagellar motility appears to be a key step in aggregate formation as the inability to turn off flagellin expression resulted in poor aggregate formation and increased antibiotic susceptibility. These results deepen our understanding of the formation of antibiotic tolerant aggregates within the MADs airway and opens novel avenues and targets for treatment of chronicP. aeruginosainfections.
Differential Responses of Lung and Intestinal Microbiota to SARS-CoV-2 Infection: A Comparative Study of the Wuhan and Omicron Strains in K18-hACE2 tg Mice
Authors: Kim Chae Won , Ku Keun Bon , Hwang Insu , Jung Hi Eun , Kim Kyun-Do , Lee Heung Kyu
Published: October 2024

The COVID-19 pandemic, caused by SARS-CoV-2, has led to the emergence of viral variants with distinct characteristics. We investigated the differential effects of the original Wuhan strain and the emergent Omicron variant of SARS-CoV-2 using a K18-hACE2 transgenic mouse model. We compared the mortality rates, viral loads, and histopathological changes in lung and tracheal tissues, as well as alterations in the lung and intestinal microbiota following infection. We observed significant differences in disease severity, with the Wuhan strain causing higher mortality and more severe lung damage than the Omicron variant. Furthermore, microbiome analyses revealed distinct shifts in microbiota associated with infection by each variant, suggesting that microbiome-related mechanisms might influence disease outcomes. This comprehensive comparison enhances our understanding of COVID-19 pathogenesis and highlights the importance of microbiome dynamics in viral infections, providing insights for future therapeutic and preventive strategies.

Importance

Understanding the differential impacts of SARS-CoV-2 variants is crucial for effective public health response and treatment development. This study provides insights into the pathogenesis of the original Wuhan strain and the Omicron variant of SARS-CoV-2, revealing significant differences in host mortality, viral load, and lung pathology. The use of the K18-hACE2 transgenic mouse model enables detailed examination of these differences in a controlled setting. Furthermore, this study highlights the importance of the microbiome in modulating disease severity and host responses to viral infections. By uncovering distinct microbial shifts associated with infection by different SARS-CoV-2 variants, this study suggests potential microbiome-related mechanisms that might be targeted to mitigate disease outcomes.
The PUF RNA-binding protein, FBF-2, maintains stem cells without binding to RNA
Authors: Carrick Brian H. , Crittenden Sarah L. , Linsley MaryGrace , Dos Santos Stephany J. Costa , Wickens Marvin , Kimble Judith
Published: October 2024

Like all canonical PUF proteins,C. elegansFBF-2 binds to specific RNAs via tripartite recognition motifs (TRMs). Here we report that an FBF-2 mutant protein that cannot bind to RNA, is nonetheless biologically active and maintains stem cells. This unexpected result challenges the conventional wisdom that RBPs must bind to RNAs to achieve biological activity. Also unexpectedly, FBF-2 interactions with partner proteins can compensate for loss of RNA-binding. FBF-2 only loses biological activity when its RNA-binding and partner interactions are both defective. These findings highlight the complementary contributions of RNA-binding and protein partner interactions to activity of an RNA-binding protein.
Impaired erythroid maturation in murine embryos upon loss of the preeclampsia-associated serine protease prostasin
Authors: Di Carlo Sara , Salas-Bastos Adrian , Castelblanco Mariela Castelblanco , Auberson Muriel , Rumpler Marie , Tournier Malaury , Sommer Lukas , Naveiras Olaia , Hummler Edith
Published: October 2024

In humans, the membrane-bound serine protease prostasin encoded byPrss8is associated with preeclampsia, a gestational hypertension disorder affecting blood supply of the placenta. Mice deficient inPrss8resulted in the death of embryos at embryonic day (E) 14.5 and it was characterized by impaired placental labyrinth maturation and vascularization. A pale phenotype was observed in these embryos, suggesting ineffective erythropoiesis. Thus, in this study we analyzed this phenotype further inPrss8-/-embryos at E11.5 and E12.5. We found a reduced number of fetal erythroblasts in placenta, yolk sac and fetal liver ofPrss8-/-embryos, while the reticulocyte number was increased, suggesting a defective terminal erythroid differentiation. Further, single-cell RNA sequencing (scRNA-seq) analyses of aorta-gonad-mesonephros (AGM) revealed an upregulation of several ribosomal genes associated with Diamond-Blackfan anemia in erythroid cells ofPrss8-/-(KO) embryos. These cells showed a lower capacity to maturate into erythrocytesin vivoand invitro,despite hematopoietic cells (HSCs) being produced normally. We suggested prostasin influenced erythropoiesis in a cell-extrinsic manner, sincePrss8expression was not detected in erythroid cells but highly expressed in ectoderm-like cells within the AGM. Congruently, while yolk sac-derived cells displayed no erythroid maturation defectin vitro, the yolk sac vascular remodeling in KO embryos was impaired as evidenced by reduced secondary branching likely as a consequence of the reduced blood flow. Our findings unveiled a novel role for this serine protease in terminal maturation of erythrocytes in the fetal liver and open new research avenues for understanding the physiological mechanism of prostasin and its pathological implications.

Key Points

Prss8deficiency causes transcriptional changes in erythroid progenitor cells in the AGM leading to impaired embryonic erythropoiesis

Overexpression of Rpl and Rps genes by erythroid cells lackingPrss8leads to defective erythropoiesis and embryonic lethality
In VivoExpression of an SCA27A-linkedFGF14Mutation Results in Haploinsufficiency and Impaired Firing of Cerebellar Purkinje Neurons
Authors: Ransdell Joseph L. , Brown Samuel P. , Xiao Maolei , Ornitz David M. , Nerbonne Jeanne M.
Published: October 2024

Autosomal dominant mutations inFGF14, which encodes intracellular fibroblast growth factor 14 (iFGF14), underlie spinocerebellar ataxia type 27A (SCA27A), a devastating multisystem disorder resulting in progressive deficits in motor coordination and cognitive function. Mice lacking iFGF14 (Fgf14-/-) exhibit similar phenotypes, which have been linked to iFGF14-mediated modulation of the voltage-gated sodium (Nav) channels that control the high frequency repetitive firing of Purkinje neurons, the main output neurons of the cerebellar cortex. To investigate the pathophysiological mechanisms underlying SCA27A, we developed a targeted knock-in strategy to introduce the first point mutation identified inFGF14into the mouseFgf14locus (Fgf14F145S), we determined the impact ofin vivoexpression of the mutantFgf14F145Sallele on the motor performance of adult animals and on the firing properties of mature Purkinje neurons in acute cerebellar slices. Electrophysiological experiments revealed that repetitive firing rates are attenuated in adultFgf14F145S/+cerebellar Purkinje neurons, attributed to a hyperpolarizing shift in the voltage-dependence of steady-state inactivation of Nav channels. More severe effects on firing properties and Nav channel inactivation were observed in homozygousFgf14F145S/F145SPurkinje neurons. Interestingly, the electrophysiological phenotypes identified in adultFgf14F145S/+andFgf14F145S/F145Scerebellar Purkinje neurons mirror those observed in heterozygousFgf14+/-and homozygousFgf14-/-Purkinje neurons, respectively, suggesting that the mutation results in the loss of the iFGF14 protein. Western blot analysis of lysates from adult heterozygousFgf14F145S/+and homozygousFgf14F145S/F145Sanimals revealed reduced or undetectable, respectively, iFGF14 expression, supporting the hypothesis that the mutant allele results in loss of the iFGF14 protein and that haploinsufficiency underlies SCA27A neurological phenotypes.
Determining zygosity with multiplex Kompetitive Allele-Specific PCR (mxKASP) genotyping
Authors: de Visser Manon C. , Meilink Willem R.M. , Theodoropoulos Anagnostis , Fahrbach Michael , Wielstra Ben
Published: October 2024

We introduce multiplex Kompetitive Allele-Specific PCR (mxKASP): a modification of ‘classical’ KASP genotyping that allows zygosity to be determined in diploid organisms. Rather than targeting a SNP associated with a single marker, mxKASP targets two non-homologous markers. We show proof of concept by applying mxKASP to the balanced lethal system inTriturusnewts, in which individuals are known to possess either: (1) zero copies of the 1A version of chromosome 1 and two copies of the 1B version; (2) one copy of 1A and one copy of 1B; or (3) two copies of 1A and zero copies of 1B. mxKASP is successful in amplifying both a 1A and a 1B marker in a single reaction (if present), allowing the zygosity of individuals to be inferred. We independently confirm our mxKASP results with a multiplex PCR approach. We argue that mxKASP can be applied to rapidly and economically determine zygostity in diploid organisms, for a large number of samples at once.
EEG-VLM Toolbox: Extending voxel-based lesion mapping to multi-dimensional EEG data
Authors: Hardstone Richard , Ostrowski Lauren , Dusang Aliceson N. , López-Larraz Eduardo , Jesser Jessica , Cash Sydney S. , Cramer Steven C. , Hochberg Leigh R. , Ramos-Murguialday Ander , Lin David J.
Published: October 2024

Focal brain lesions (such as with stroke) cause functional changes in local and distributed neural systems. While there is a long history of post-stroke neurophysiological assessment using electroencephalography (EEG), the observed neurophysiological changes have rarely been related to specific lesion locations. Therefore, the relationships between anatomical injury and physiological changes after stroke remain unclear. Voxel-based lesion symptom mapping (VLSM) is a tool for statistically relating stroke lesion locations to “symptoms”, but current VLSM methods are restricted to symptoms that can be defined by a single value. Therefore, current VLSM techniques are unable to map the relationships between anatomical injury and multidimensional neurophysiological data such as EEG, which contains rich spatio-temporal information across different channels and frequency bands.

Here we present a novel algorithm, EEG Voxel-based Lesion Mapping (EEG-VLM), that produces the set of significant relationships between precise neuroanatomical injury locations and neurophysiology (defined by a cluster of adjacent EEG channels and frequency bands). Further, the algorithm provides statistical analyses to define the overall significance of each neural structure-function relationship by correcting for multiple comparisons using a permutation test. Applying EEG-VLM to a dataset of recordings from chronic stroke patients performing a cued upper extremity movement task, we found that subjects with lesions in frontal subcortical white matter have reduced ipsilesional parietal cue-evoked EEG responses. These results are consistent with damage to a frontal-parietal network that has been associated with impairments in attention. EEG-VLM is a novel and unbiased method for relating neurophysiologic changes after stroke with neuroanatomic lesions. In the context of focal brain lesions associated with neurological impairments, we propose that this method will enable improved mechanistic understanding, facilitate biomarker development, and guide neurorehabilitation strategies.
Dissociable Default Mode Network Connectivity Patterns Underlie Distinct Symptoms in Psychosis Risk
Authors: Ajunwa Chelsea C. , Zhang Jiahe , Collin Guusje , Keshavan Matcheri S. , Tang Yingying , Zhang Tianhong , Li Huijun , Shenton Martha E. , Stone William S. , Wang Jijun , Niznikiewicz Margaret , Whitfield-Gabrieli Susan
Published: October 2024

The Clinical High Risk (CHR) stage of psychosis is characterized by subthreshold symptoms of schizophrenia including negative symptoms, dysphoric mood, and functional deterioration. Hyperconnectivity of the default-mode network (DMN) has been observed in early schizophrenia, but the extent to which hyperconnectivity is present in CHR, and the extent to which such hyperconnectivity may underlie transdiagnostic symptoms, is not clear. As part of the Shanghai At-Risk for Psychosis (SHARP) program, resting-state fMRI data were collected from 251 young adults (158 CHR and 93 controls, M = 18.72, SD = 4.68, 129 male). We examined functional connectivity of the DMN by performing a whole-brain seed-to-voxel analysis with the MPFC as the seed. Symptom severity across a number of dimensions, including negative symptoms, positive symptoms, and affective symptoms were assessed. Compared to controls, CHRs exhibited significantly greater functional connectivity (p < 0.001 uncorrected) between the MPFC and 1) other DMN nodes including the posterior cingulate cortex (PCC), and 2) auditory cortices (superior and middle temporal gyri, STG/MTG). Furthermore, these two patterns of hyperconnectivity were differentially associated with distinct symptom clusters. Within CHR, MPFC-PCC connectivity was significantly correlated with anxiety (r= 0.23, p=0.006), while MPFC-STG/MTG connectivity was significantly correlated with negative symptom severity (r=0.26, p=0.001). Secondary analyses using item-level symptom scores confirmed a similar dissociation. These results demonstrate that two dissociable patterns of DMN hyperconnectivity found in the CHR stage may underlie distinct dimensions of symptomatology.
Brain-like learning with exponentiated gradients
Authors: Cornford Jonathan , Pogodin Roman , Ghosh Arna , Sheng Kaiwen , Bicknell Brendan A. , Codol Olivier , Clark Beverley A. , Lajoie Guillaume , Richards Blake A.
Published: October 2024

Computational neuroscience relies on gradient descent (GD) for training artificial neural network (ANN) models of the brain. The advantage of GD is that it is effective at learning difficult tasks. However, it produces ANNs that are a poor phenomenological fit to biology, making them less relevant as models of the brain. Specifically, it violates Dale’s law, by allowing synapses to change from excitatory to inhibitory, and leads to synaptic weights that are not log-normally distributed, contradicting experimental data. Here, starting from first principles of optimisation theory, we present an alternative learning algorithm, exponentiated gradient (EG), that respects Dale’s Law and produces log-normal weights, without losing the power of learning with gradients. We also show that in biologically relevant settings EG outperforms GD, including learning from sparsely relevant signals and dealing with synaptic pruning. Altogether, our results show that EG is a superior learning algorithm for modelling the brain with ANNs.
Conserved gene content and unique phylogenetic history characterize the ‘bloopergene’ underlyingTriturus’balanced lethal system
Authors: de Visser Manon Chantal , France James , Paulouskaya Olga , Brown Thomas , Fahrbach Michael , van der Ploeg Chris , Wielstra Ben
Published: October 2024

In a balanced lethal system, half the reproductive output succumbs.Triturusnewts are the best-known example. Their chromosome 1 comes in two distinct versions and embryos carrying the same version twice experience developmental arrest. Those possessing two different versions survive, suggesting that each version carries something uniquely vital. With target capture we obtain over 7,000 nuclear DNA markers across the genusTriturusand all main lineages of Salamandridae (the family to whichTriturusbelongs) to investigate the evolutionary history ofTriturus’chromosome 1 versus other chromosomes. Dozens of genes are completely missing from either one or the other version of chromosome 1 inTriturus. Furthermore, the unique gene content of 1A versus 1B is remarkably similar acrossTriturusspecies, suggesting that the balanced lethal system evolved beforeTriturusradiated. The tree topology of chromosome 1 differs from the rest of the genome, presumably due to pervasive, ancient hybridization betweenTriturus’ancestor and other newt lineages. Our findings accentuate the complex nature ofTriturus’chromosome 1 – the ‘bloopergene’ driving the evolutionarily enigmatic balanced lethal system.