bluuebunny/crossref_metadata_2025 huggingface dataset:
Systemic injection of scopolamine increased the variability of temporal prediction in head-fixed mice
Authors: Ujihara Yusuke , Yamada Kota , Yamamoto Mizuki , Toda Koji
Published: September 2024

Several theories propose a close relationship between interval timing and the temporal properties of memory. Systemic administration of scopolamine, a muscarinic acetylcholine receptor antagonist, is known to induce memory deficits and impair temporal prediction. However, existing studies on timing using free-moving animals are challenging to interpret due to the confounding effects of movement on interval timing. In this study, we examined the effects of scopolamine on timing behavior in mice using a head-fixed experimental setup. Mice were trained on a fixed-time schedule task with a peak procedure, where a 10% sucrose solution was delivered every 10 seconds through a spout placed within the licking distance of the mice. Following training, the mice exhibited anticipatory licking behavior in response to the timing of sucrose delivery, indicating that they could predict the reward timing. Systemic administration of scopolamine increased the variability of temporal prediction in a dose-dependent manner but did not affect the mean temporal prediction. Single-trial bout analysis revealed that scopolamine impaired the duration of licking bouts without affecting the total number of licks in peak trials, suggesting that the mice were unable to sustain licking at the spout. Additionally, we assessed the effects of scopolamine on spontaneous locomotor activity and excretion in a free-moving open-field task. Scopolamine injections increased locomotor activity and decreased fecal output. Taken together, these findings suggest that the increased variability in timing behavior induced by scopolamine may be attributed to changes in transitions between behavioral states.
EyaHOST, a modular genetic system for investigation of intercellular and tumor-host interactionsin Drosophila melanogaster
Authors: Teles-Reis José , Jain Ashish , Liu Dan , Khezri Rojyar , Micheli Sofia , Gomez Alicia Alfonso , Dillard Caroline , Rusten Tor Erik
Published: September 2024

Cell biology and genetic analysis of intracellular, intercellular and inter-organ interaction studies in animal models are key for understanding development, physiology, and disease. The MARCM technique can emulate tumor development by simultaneous clonal tumor suppressor loss-of-function generation coupled with GAL4-UAS-driven oncogene and marker expression, but the utility is limited for studying tumor-host interactions due to genetic constraints. To overcome this, we introduce EyaHOST, a novel system that replaces MARCM with the QF2-QUAS binary gene expression system under theeyapromoter control, unleashing the fly community genome-wide GAL4-UAS driven tools to manipulate any host cells or tissue at scale. EyaHOST generates epithelial clones in the eye epithelium similar to MARCM. EyaHOST-driven RasV12oncogene overexpression coupled with scribble tumor suppressor knockdown recapitulates key cancer features, including systemic catabolic switching and organ wasting. We demonstrate effective tissue-specific manipulation of host compartments such as neighbouring epithelial cells, immune cells, fat body, and muscle using fly avatars with tissue-specific GAL4 drivers. Organ-specific inhibition of autophagy or stimulation of growth-signaling through PTEN knockdown in fat body or muscle prevents cachexia-like wasting. Additionally, we show thatRasV12, scribRNAitumors induce caspase-driven apoptosis in the epithelial microenvironment. Inhibition of apoptosis by p35 expression in the microenvironment promotes tumor growth. EyaHOST offers a versatile modular platform for dissecting tumor-host interactions and other mechanisms involving intercellular and inter-organ communication inDrosophila.

Highlights

*eyes absent, eye disc-specific enhancer drives clonal KD recombinase flip-out activated QF2 expression in the larval eye epithelium for simultaneous QUAS-driven gain and loss-of-function analysis of gene function.

*Clones are visualized by QUAS-tagBFP or QUAS-eGFP facilitating analysis of existing fluorescent reporters.

*The GAL4-UAS system and existing genome-wide genetic tools are released to independently manipulate any cell population in the animal for cell biology, intercellular or inter-organ analysis for developmental, physiological, or disease model analysis.

*Fly avatars for tumor-host interaction studies with multiple organs allow live monitoring and manipulation of tumors and organs in translucent larva.
Targeting CXCR4 with [212Pb/203Pb]-Pentixather Significantly Increases Overall Survival in Small Cell Lung Cancer
Authors: Christensen Keegan A. , Fath Melissa A. , Ewald Jordan T. , Robles-Planells Claudia , Graves Stephen A. , Johnson Spenser S. , Zacharias Zeb R. , Houtman Jon C.D. , O’Dorisio M Sue , Schultz Michael K. , Allen Bryan G. , Furqan Muhammad , Menda Yusuf , Liu Dijie , Spitz Douglas R.
Published: September 2024

Introduction

Small cell lung cancer (SCLC) has a 7% 5-year overall survival. C-X-C chemokine receptor 4 (CXCR4), an attractive target for theranostic agents, is highly expressed in SCLCs, and can be targeted with pentixather using the theranostic pair212Pb/203Pb. The hypothesis that [212Pb/203Pb]-pentixather can be used safely and effectively for imaging and therapy in SCLC in xenograft models was tested.

Results

SPECT/CT imaging and biodistribution studies of tumor bearing mice injected with [203Pb]-pentixather demonstrated CXCR4-dependent uptake in tumors and accumulation of radioligand in kidneys and livers. Dosimetry calculations estimated [212Pb]-pentixather uptake in tumor and normal tissue. [212Pb]-pentixather treatment (37-111 kBq/g) of SCLC xenografts (DMS273 and H69AR) significantly prolonged survival and delayed tumor growth. When NSG mice grafted with human hCD34+ bone marrow were treated with [212Pb]-pentixather (37-111 kBq/g), significant cytopenias were observed in peripheral blood complete blood counts (CBCs) at 13-18 days post treatment which resolved by day 28-31. Flow cytometry of bone marrow hematopeotic stem cells in these animals at day 28-31 demonstrated a significantly reduced frequency of the human hematopoietic marker CD45 (hCD45+) and reconstitution of the bone marrow with murine CD45+ (mCD45+) lineages.

Conclusions

[203Pb]-pentixather can be used to image CXCR4 expressing SCLC xenografts and treatment with alpha emitter [212Pb]-pentixather significantly prolongs SCLC xenograft median overall survival. Significantly greater mCD45+ bone marrow repopulation was detected in NSG mice engrafted with human bone marrow 28-31 days following [212Pb]-pentixather treatment, relative to hCD45+ bone marrow.
Brain-wide projections of mouse dopaminergic zona incerta neurons
Authors: Bono Bianca S , Negishi Kenichiro , Dumiaty Yasmina , Ponce Monica S , Akinbode Titilayo C , Baker Kayla S , Spencer C. Duncan P , Mejia Elizabeth , Guirguis Marina , Hebert Alex J , Khan Arshad M. , Chee Melissa J
Published: September 2024

The zona incerta (ZI) supports diverse behaviors including binge feeding, sleep/wake cycles, nociception, and hunting. This diversity of functions can be attributed to the heterogenous neurochemicals, cytoarchitecture, and efferent connections that characterize the ZI. The ZI is predominantly GABAergic, but we recently identified a subset of medial ZI GABA cells that co-express dopamine (DA), as marked by the enzyme tyrosine hydroxylase (TH). While the role of GABA within the ZI is well studied, little is understood about the function of ZI DA cells. To identify potential roles of ZI DA cells we mapped the efferent fiber projections from Th-cre ZI cells. We first validated a Th-cre;L10-Egfp mouse line and found that medial Egfp ZI cells were more likely to co-express TH-immunoreactivity (TH-ir). We thus delivered a cre-dependent virus into the medial ZI of Th-cre or Th-cre;L10-Egfp mice and selected two injection cases for full brain mapping. We selected the cases with the lowest (17%) and highest (53%) percentage of colocalization between TH-ir and virus transfected cells labelled with DsRed. Overall, DsRed-labelled fibers were observed throughout the brain and were most prominent within motor-related regions of the midbrain (MBmot), notably the periaqueductal grey area and superior colliculus. We also observed considerable DsRed-labelled fibers within the polymodal cortex associated regions of the thalamus (DORpm), including the paraventricular thalamic nucleus and nucleus of reunions. Overall, ZI DA cells displayed a similar connectivity profile to ZI GABA cells, suggesting that ZI DA cells may perform synergistic or opposing functions at the same target sites.
EpipwR: Efficient Power Analysis for EWAS with Continuous Outcomes
Authors: Barth Jackson , Reynolds Austin W.
Published: September 2024

Motivation

Epigenome-wide association studies (EWAS) have emerged as a popular way to investigate the pathophysiology of complex diseases and to assist in bridging the gap between genotypes and phenotypes. Despite the increasing popularity of EWAS, very few tools exist to aid researchers in power estimation and those are limited to case-control studies. The existence of user-friendly tools, expanding power calculation functionality to additional study designs would be a significant aid to researchers planning EWAS.

Results

We introduce EpipwR, an open-source R package that can efficiently estimate power for EWAS with continuous outcomes. EpipwR uses a quasi-simulated approach, meaning that data is generated only for CpG sites with methylation associated with the outcome, while p-values are generated directly for those with no association (when necessary). Like existing EWAS power calculators, reference datasets of empirical EWAS are used to guide the data generation process. Two simulation studies show the effect of the selected empirical dataset on the generated correlations and the relative speed of EpipwR compared to similar approaches.

Availability and Implementation

The EpipwR R-package is currently available for download atgithub.com/jbarth216/EpipwR.
Neurotransmitters Contribute Structure-Function Coupling: Evidence from Grey Matter Volume (GMV) and Brain Entropy (BEN)
Authors: Song Donghui , Wang Ze
Published: September 2024

The emergence of human brain function from macroscopic anatomical structures and its relationship with the coupling of structure and function have long been pivotal questions in neuroscience. Neurotransmitter receptors are critical in signal transmission, regulating brain function, and potentially enhancing the coupling between brain structure and function. Recent research suggests that neurotransmitter systems facilitate this coupling between structural and functional networks. However, the mechanisms of how neurotransmitters adapt to local anatomical structures and drive functional emergence are not yet fully understood. This study explores these mechanisms using gray matter volume (GMV) and brain entropy (BEN). BEN reflects the irregularity, unpredictability, and complexity of brain activity, and functional MRI (fMRI)-based BEN has identified its distribution in the normal human brain. BEN is correlated to cognitive and task performance, and aberrant BEN patterns link to various brain disorders. Notably, BEN can indicate neuroplasticity through non-invasive brain stimulation, and pharmacological intervention. We analyzed structural imaging data, as well as 7T resting-state and movie-watching fMRI data from 176 participants in the Human Connectome Project (HCP), to calculate GMV, resting-state BEN (rsBEN), and movie-watching BEN (mvBEN). By integrating data from the publicly available neurotransmitter receptors database, we evaluated the role of neurotransmitters in the coupling between GMV and rsBEN, GMV and mvBEN, and rsBEN and mvBEN. Our findings reveal that neurotransmitters significantly contribute to structural and functional coupling and influence the transition from task-free to movie-watching conditions.
Multi-epitope immunocapture of huntingtin reveals striatum-selective molecular signatures
Authors: Justice Joshua L. , Greco Todd M. , Hutton Josiah E. , Reed Tavis J. , Mair Megan L. , Botas Juan , Cristea Ileana M.
Published: September 2024

Huntington’s disease (HD) is a debilitating neurodegenerative disorder affecting an individual’s cognitive and motor abilities. HD is caused by mutation in the huntingtin gene producing a toxic polyglutamine-expanded protein (mHTT) and leading to degeneration in the striatum and cortex. Yet, the molecular signatures that underlie tissue-specific vulnerabilities remain unclear. Here, we investigate this aspect by leveraging multi-epitope protein interaction assays, subcellular fractionation, thermal proteome profiling, and genetic modifier assays. Use of human cell, mouse, and fly models afforded capture of distinct subcellular pools of epitope-enriched and tissue-dependent interactions linked to dysregulated cellular pathways and disease relevance. We established an HTT association with nearly all subunits of the transcriptional regulatory Mediator complex (20/26), with preferential enrichment of MED15 in the tail domain. Using HD and KO models, we find HTT modulates the subcellular localization and assembly of Mediator. We demonstrated striatal enriched and functional interactions with regulators of calcium homeostasis and chromatin remodeling, whose disease relevance was supported by HD fly genetic modifiers assays. Altogether, we offer insights into tissue- and localization-dependent (m)HTT functions and pathobiology.
Early eukaryogenesis by host-initiated obligate ectosymbiosis and metabolic inhibition
Authors: Krishnan Nandakishor , Kun Ádám , Gokhale Chaitanya S. , Garay József
Published: September 2024

The evolution of cellular-level symbiosis in microbes is a significant phenomenon to understand the origin of ancestral eukaryotic cells from prokaryotes. Though syntrophy is considered to be the initial interaction mechanism between the involved individuals, the process of internalization (endosymbiosis) and integration to form a symbiotic consortium requires better clarity. This work deals with a theoretical model based on the hypothesis that an intermediate ectosymbiosis might have evolved before complete endosymbiosis. Assuming an already syntrophic environment of free-living hosts and symbionts, we investigate how obligate ectosymbiosis can evolve between the individuals of different species. An asymmetric multilevel selection approach is considered to mechanistically analyze the driving factors in the formation and fixation of the symbiotic consortia. A metabolite-based growth rate and growth inhibition are utilized to effectively model the ecological selection dynamics between the host and the symbiont species. We observed that reduced metabolic growth inhibition due to the effective reduction in exposure to toxic metabolites by the common surface area of contact might be an incentive to stabilize the ectosymbiotic consortia. Furthermore, robust syntrophy between the host and their ectosymbionts might have facilitated obligacy in their association. The model gives insights into the critical elements in the evolution of endosymbiotic features.
Progress in Developing a Bark Beetle Identification Tool
Authors: Marais G. Christopher , Stratton Isabelle C. , Johnson Andrew J. , Hulcr Jiri
Published: September 2024

This study presents an initial model for bark beetle identification, serving as a foundational step toward developing a fully functional and practical identification tool. Bark beetles are known for extensive damage to forests globally, as well as for uniform and homoplastic morphology which poses identification challenges. Utilizing a MaxViT-based deep learning backbone which utilizes blocked local and dilated global attention to classify bark beetles down to the genus level from images containing multiple beetles. The methodology involves a comprehensive process of image collection, preparation, and model training, leveraging pre-classified beetle species to ensure accuracy and reliability. The model’s F1 score estimates of 0.99 and 1.0 indicates a strong ability to accurately classify genera in the collected data, including those previously unknown to the model. This makes it a valuable first step towards building a tool for applications in forest management and ecological research. While the current model distinguishes among 12 genera, further refinement and additional data will be necessary to achieve reliable species-level identification, which is particularly important for detecting new invasive species. Despite the controlled conditions of image collection and potential challenges in real-world application, this study provides the first model capable of identifying the bark beetle genera, and by far the largest training set of images for any comparable insect group. We also designed a function that reports if a species appears to be unknown. Further research is suggested to enhance the model’s generalization capabilities and scalability, emphasizing the integration of advanced machine learning techniques for improved species classification and the detection of invasive or undescribed species.
Characterising global risk profiles of Mpox clade Ib importation
Authors: Asakura Toshiaki R. , Jung Sung-mok , Jin Shihui , Hu Gang , Endo Akira , Dickens Borame Lee
Published: September 2024

The novel mpox clade Ib initially identified in the Domestic Republic of Congo has spread to its multiple neighbouring countries as well as countries beyond the African continent. We characterised the global risk of importation of mpox clade Ib, highlighting the need to ramp up surveillance capacity for early detection.
Associations of Insomnia Symptoms and Trajectories with Incident Cardiovascular Disease: A Population-Based Cohort Study
Authors: Huang Qing-Mei , Yan Hao-Yu , Chen Huan , Xie Jia-Hao , Gao Jian , Li Zhi-Hao , Mao Chen
Published: September 2024

Background There is limited understanding regarding associations between insomnia symptoms, particularly the trajectories of insomnia symptoms, and cardiovascular disease (CVD). We aimed to investigate the associations of insomnia symptoms and trajectories with the risk of incident CVD. Methods This study used data from the Health and Retirement Study. Insomnia symptoms included non-restorative sleep, difficulty initiating sleep, early morning awakening, and difficulty maintaining sleep, classified on a scale ranging from 0 to 8. We also identified four distinct trajectories of insomnia symptoms: low, decreasing, increasing, and high insomnia symptoms. Examined outcomes included incident heart disease, stroke, and the combination of the two referred as CVD in the present study. Cox proportional hazard models were used to calculate the hazard ratio (HR) and 95% confidence interval (95% CI) after adjusting for potential confounders. Results A total of 12 102 participants aged 50 years or over without CVD at baseline were included. During a median follow-up of 10.2 years, 3 962 first CVD events occurred (3 372 heart disease and 1 200 stroke). Participants experiencing one (HR, 1.16 [95% CI, 1.05-1.27]), two (HR, 1.16 [ 95% CI, 1.05-1.28]), or three to four (HR, 1.26 [95% CI, 1.15-1.38]) insomnia symptoms had a higher risk of incident CVD compared to those not experiencing any insomnia symptoms. After a median follow-up of 8.4 years after the visit 2, 2 375 first CVD events occurred (1 981 heart disease and 705 stroke). Using the trajectory with low insomnia symptoms as the reference, increasing insomnia symptoms (HR, 1.28 [95% CI, 1.10-1.50]) and high insomnia symptoms (HR, 1.32 [95% CI, 1.15-1.50]) were associated with an increased risk of incident CVD. Conclusions Higher insomnia symptoms and increasing insomnia symptoms over time are associated with a higher risk of CVD in the community. Public health awareness and screening for insomnia symptoms in the middle-aged and elderly population should be encouraged to reduce CVD. Keywords Cardiovascular disease; Insomnia symptoms; Trajectory; Cohort study
Plasma proteome-based test (PROphetNSCLC) predicts response to immune checkpoint inhibitors (ICI) independent of tumor programmed death-ligand 1(PD-L1) expression and tumor mutational burden (TMB)
Authors: Brody Yehuda , Yellin Ben , Sela Itamar , Elon Yehonatan , Puzanov Igor , Nechushtan Hovav , Zerkuch Alona , Gottfried Maya , Katzenelson Rivka , Moskovitz Mor , Levy-Barda Adva , Lotem Michal , Leibowitz Raya , Lou Yanyan , Dicker Adam P. , Gandara David R. , McGregor Kimberly
Published: September 2024

Despite the approval of PD-(L)1 inhibitors for the first-line treatment of all metastatic, driver-negative, non-small cell lung cancer patients (mNSCLC) in the United States since 2018, there still is a lack discerning biomarkers to predict which patients will derive significant benefit. Tumor expression of programmed-death ligand 1 (PD-L1), measured as the tumor proportion score (TPS), is a standard biomarker approved for the selection of initial therapy. Tumor mutational burden (TMB), a promising biomarker, thought to represent the tumors’ ability to engage the host’s immune system, has demonstrated clinical utility primarily in the context of immunotherapy monotherapy. PROphetNSCLC, a test developed through proteomic analysis and machine learning, provides a novel approach by capturing biological processes from both tumor and host. In a previously published study, PROphetNSCLC, was validated to correlate with the probability of clinical benefit, independent of but also complementary to PD-L1 expression levels predicting specific treatment-related survival outcomes. Utilizing available tumor TMB measurements from this investigation, we sought to assess the correlation between the PROphetNSCLC clinical benefit probability score and TMB measurement. PROphetNSCLC demonstrated a correlation with various outcomes from PD-(L)1 inhibitor treatment independent of TMB status, whereas TMB did not exhibit an association with outcomes. This finding emphasizes the significance in of novel systemic biomarkers in refining personalized treatment strategies for mNSCLC.
Reconciling heterogeneous dengue virus infection risk estimates from different study designs
Authors: Huang Angkana T. , Buddhari Darunee , Kaewhiran Surachai , Iamsirithaworn Sopon , Khampaen Direk , Farmer Aaron , Fernandez Stefan , Thomas Stephen J. , Rodriguez Barraquer Isabel , Hunsawong Taweewun , Srikiatkhachorn Anon , Ribeiro dos Santos Gabriel , O’Driscoll Megan , Hamins-Puertolas Marco , Endy Timothy , Rothman Alan L. , Cummings Derek A. T. , Anderson Kathryn , Salje Henrik
Published: September 2024

Uncovering rates at which susceptible individuals become infected with a pathogen, i.e. the force of infection (FOI), is essential for assessing transmission risk and reconstructing distribution of immunity in a population. For dengue, reconstructing exposure and susceptibility statuses from the measured FOI is of particular significance as prior exposure is a strong risk factor for severe disease. FOI can be measured via many study designs. Longitudinal serology are considered gold standard measurements, as they directly track the transition of seronegative individuals to seropositive due to incident infections (seroincidence). Cross-sectional serology can provide estimates of FOI by contrasting seroprevalence across ages. Age of reported cases can also be used to infer FOI. Agreement of these measurements, however, have not been assessed. Using 26 years of data from cohort studies and hospital-attended cases from Kamphaeng Phet province, Thailand, we found FOI estimates from the three sources to be highly inconsistent. Annual FOI estimates from seroincidence was 2.46 to 4.33-times higher than case-derived FOI. Correlation between seroprevalence-derived and case-derived FOI was moderate (correlation coefficient=0.46) and no systematic bias. Through extensive simulations and theoretical analysis, we show that incongruences between methods can result from failing to account for dengue antibody kinetics, assay noise, and heterogeneity in FOI across ages. Extending standard inference models to include these processes reconciled the FOI and susceptibility estimates. Our results highlight the importance of comparing inferences across multiple data types to uncover additional insights not attainable through a single data type/analysis.

Significance statement

Dengue virus infections are surging globally. Knowing who, where, and how many people are at risk of infection is crucial in determining means to protect them. Here, we compare three current approaches in measuring risk (two involving blood samples and one involving case counts) to estimate the risk of infection. Estimates derived from each method differed greatly. By accounting for rise and falls of antibodies following infections, noise in the antibody titer measurements, and heterogeneity in infection risk across ages, we reconciled the measurements. As measurements from blood samples and case counts are pillars in uncovering risk of most infectious diseases, our results signifies integrating these processes into risk measurements of pathogens beyond dengue virus.
Investigation of hemodynamic bulk flow patterns caused by aortic stenosis using a combined 4D Flow MRI-CFD framework
Authors: Wang Tianai , Quast Christine , Bönner Florian , Kelm Malte , Zeus Tobias , Lemainque Teresa , Steinseifer Ulrich , Neidlin Michael
Published: September 2024

Aortic stenosis (AS) leads to alterations of supra-valvular flow patterns. These patterns might lead to, inter alia, increased damage of red blood cell (RBC) membranes. We investigated these patient specific patterns of a severe AS patient and their reversal in healthy flow through a 4D Flow MRI-based CFD methodology. Computational models of subject-specific aortic geometries were created using in-vivo medical imaging data. Temporally and spatially resolved boundary conditions derived from 4D Flow MRI were implemented for an AS patient and a healthy subject. After validation of the in-silico results with in-vivo data, a healthy inflow profile was set for the AS patient in the CFD model. Pathological versus healthy flow fields were compared regarding their blood flow characteristics, i.e. shear stresses on RBCs and helicity. The accuracy of the 4D Flow MRI-based CFD model was proven with excellent agreement between in-vivo and in-silico velocity fields and R² = 0.9. A pathological high shear stress region in the bulk flow was present during late systole with an increase of 125 % compared to both healthy flow. The physiological bihelical structure with predominantly right-handed helices vanished for the pathological state. Instead, a left-handed helix appeared, accompanied by an overall increase in turbulent kinetic energy in areas of accumulated left-handed helicity.

The validated 4D Flow MRI-based CFD model identified marked differences between AS and healthy flow. It suggests that altered turbulent and helical structures in the bulk flow are the cause for increased, potentially damaging forces acting upon RBCs in AS.

Author Summary

Aortic stenosis (AS) is a condition that alters the flow of blood through the aorta, potentially increasing damage to red blood cells (RBCs). It is therefore crucial to understand the precise nature of these changes, especially in the bulk region where the RBCs are mainly circulating. To investigate this, we developed a computational model based on patient-specific 4D Flow MRI data to simulate blood flow in a patient with severe AS and a healthy individual. Our high-fidelity models show high agreement with real-world data. We then imposed synthetically generated healthy flow conditions in the AS patient to eliminate age- and geometry-related uncertainties. Our results revealed significantly higher shear stresses and changes in helical flow patterns in the AS patient compared to healthy flow, suggesting that these alterations could increase the risk of RBC membrane damage. These findings underscore the importance of deepening our understanding about the interplay between bulk flow alterations and their impact on RBCs, as previous studies were mostly focused on near wall regions. This methodology could also be extended to other cardiovascular conditions, aiding in the development of patient-specific treatment strategies.
Aversion encoding and behavioral state modulation of lateral habenula neurons
Authors: Zouridis Ioannis S , Schmors Lisa , Lecca Salvatore , Congiu Mauro , Mameli Manuel , Berens Philipp , Burgalossi Andrea
Published: September 2024

The lateral habenula (LHb) integrates aversive information to regulate motivated behaviors. Despite recent advances in identifying neuronal diversity at the molecular level,in vivoelectrophysiological diversity of LHb neurons remains poorly understood. Understanding this diversity is essential for deciphering how information is processed in the LHb. To address this gap, we conductedin vivoelectrophysiological recordings in mice and applied unsupervised clustering algorithm to analyze firing patterns. This analysis identified four distinct spontaneous firing patterns of LHb neurons, which were consistent across both anesthetized and awake states. To determine whether these firing patterns correlate with function, we recorded neuronal responses to foot shock stimulation in anesthetized mice and monitored spontaneous behavior in awake mice. We found that low-firing, bursting neurons were preferentially modulated by foot shocks in anesthetized mice and also tracked behavioral states in awake mice. Collectively, our findings indicate significant electrophysiological diversity among LHb neurons, which is associated with their modulation by aversive stimuli and behavioral state.
Early development and co-evolution of microstructural and functional brain connectomes: A multi-modal MRI study in preterm and full-term infants
Authors: Andrea Gondová , Sara Neumane , Tomoki Arichi , Jessica Dubois
Published: September 2024

Introduction

Functional networks characterised by coherent neural activity across distributed brain regions have been observed to emerge early in neurodevelopment. Synchronized maturation across regions that relate to functional connectivity (FC) could be partially reflected in the developmental changes in underlying microstructure. Nevertheless, covariation of regional microstructural properties, termed ‘microstructural connectivity’ (MC), and its relationship to the emergence of functional specialization during the early neurodevelopmental period remains poorly understood.

Methods

We investigated the evolution of MC and FC postnatally across a set of cortical and subcortical regions, focusing on 45 preterm infants scanned longitudinally, and compared to 45 matched full-term neonates as part of the developing Human Connectome Project (dHCP) using direct comparisons of grey-matter connectivity strengths as well as network-based analyses.

Results

Our findings revealed a global strengthening of both MC and FC with age, with connection-specific variability influenced by the connection maturational stage. Prematurity at term-equivalent age was associated to significant connectivity disruptions, particularly in FC. During the preterm period, direct comparisons of MC and FC strength showed positive linear relationship, which seemed to weaken with development. On the other hand, overlaps between MC-and FC-derived networks (estimated with Mutual Information) increased with age, suggesting a potential convergence towards a shared underlying network structure that may support the co-evolution of microstructural and functional systems.

Conclusion

Our study offers novel insights into the dynamic interplay between microstructural and functional brain development and highlights the potential of MC as a complementary descriptor for characterizing the brain network development and alterations due to perinatal insults such as premature birth.

Keypoints

Our study reveals a significant positive linear relationship between grey-matter functional connectivity and underlying microstructural connectivity during development, that decreases with age and varies across connection types.

Despite progressive maturational decoupling of microstructural and functional connectivity, a shared network structure may underlie changes in both properties.

Prematurity impacts the maturation of connectivity in both modalities, but with a higher reduction of functional than microstructural connectivity strengths.
The Conformational Space of the SARS-CoV-2 Main Protease Active Site Loops is Determined by Ligand Binding and Interprotomer Allostery
Authors: Lee Ethan , Rauscher Sarah
Published: September 2024

The main protease (Mpro) of SARS-CoV-2 is essential for viral replication and is, therefore, an important drug target. Here, we investigate two flexible loops in Mprothat play a role in catalysis. Using all-atom molecular dynamics simulations, we analyze the structural ensemble of Mproin an apo state and substrate-bound state. We find that the flexible loops can adopt open, intermediate (partly open) and closed conformations in solution, which differs from the partially closed state observed in crystal structures of Mpro. When the loops are in closed or intermediate states, the catalytic residues are more likely to be in close proximity, which is crucial for catalysis. Additionally, we find that substrate binding to one protomer of the homodimer increases the frequency of intermediate states in the bound protomer, while also affecting the structural propensity of the apo protomer’s flexible loops. Using dynamic network analysis, we identify multiple allosteric pathways connecting the two active sites of the homodimer. Common to these pathways is an allosteric hotspot involving the N-terminus, a critical region that comprises part of the binding pocket. Taken together, the results of our simulation study provide detailed insight into the relationships between the flexible loops and substrate binding in a prime drug target for COVID-19.
Antiviral Mechanisms and Preclinical Evaluation of Amantadine Analogs that Continue to Inhibit Influenza A Viruses with M2S31N-Based Drug Resistance
Authors: Tietjen Ian , Kwan Daniel C. , Petrich Annett , Zell Roland , Antoniadou Ivi Theodosia , Gavriilidou Agni , Tzitzoglaki Christina , Rallis Michail , Fedida David , Sureda Francesc X. , Mestdagh Cato , Naesens Lieve , Chiantia Salvatore , Johnson F. Brent , Kolocouris Antonios
Published: September 2024

To better manage seasonal and pandemic influenza infections, new drugs are needed with enhanced activity against contemporary amantadine- and rimantadine-resistant influenza A virus (IAV) strains containing the S31N variant of the viral M2 ion channel (M2S31N). Here we tested 36 amantadine analogs against a panel of viruses containing either M2S31Nor the parental, M2 S31 wild-type variant (M2WT). We found that several analogs, primarily those with sizeable lipophilic adducts, inhibited up to three M2S31N-containing viruses with activities at least 5-fold lower than rimantadine, without inhibiting M2S31Nproton currents or modulating endosomal pH. While M2WTviruses in passaging studies rapidly gained resistance to these analogs through the established M2 mutations V27A and/or A30T, resistance development was markedly slower for M2S31Nviruses and did not associate with additional M2 mutations. Instead, a subset of analogs, exemplified by 2-propyl-2-adamantanamine (38), but not 2-(1-adamantyl)piperidine (26), spiro[adamantane-2,2’-pyrrolidine] (49), or spiro[adamantane-2,2’-piperidine] (60), inhibited cellular entry of infectious IAV following pre-treatment and/or H1N1 pseudovirus entry. Conversely, an overlapping subset of the most lipophilic analogs including compounds26,49,60, and others, disrupted viral M2-M1 protein colocalization required for intracellular viral assembly and budding. Finally, a pilot toxicity study in mice demonstrated that38and49were tolerated at doses approaching those of amantadine. Together, these results indicate that amantadine analogs act on multiple, complementary mechanisms to inhibit replication of M2S31Nviruses.

Highlights

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Current IAVs have M2 mutations that confer resistance to amantadine and rimantadine

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Several amantadine analogs inhibit these viruses without acting on M2 proton currents

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Alternative antiviral targets include IAV entry and M2-M1 protein colocalization

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Amantadine analogs are also tolerated in mice

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Future amantadine antivirals could simultaneously act on multiple IAV mechanisms
Desmoplakin mutations in cardiac fibroblasts cause TGFβ1-mediated pathological fibrogenesis in desmoplakin cardiomyopathy via beclin-1 regulation
Authors: Wei Chuanyu , Chan Shing-Fai , Saguner Ardan M. , Brunckhorst Corinna , Duru Firat , Marine Joseph E. , James Cynthia A. , Calkins Hugh , Judge Daniel P. , Shou Weinian , Chen Huei-Sheng Vincent
Published: September 2024

Background

Pathological fibrosis is a major finding in cardiovascular diseases and can result in arrhythmia and heart failure. Desmosome gene mutations can lead to arrhythmogenic cardiomyopathy (ACM). Among ACM, pathogenic desmoplakin (DSP) variants cause a distinctive cardiomyopathy with excessive cardiac fibrosis that could precede ventricular dysfunction.DSPvariants are also linked to other fibrotic diseases. Whether DSP plays any role in pathological fibrosis remain unknown.

Methods

Mesenchymal stromal cells (MSCs) are resident fibroblast-like cells that are responsible for fibrogenesis in most organs, including hearts. We first used unbiased genome-wide analyses to generate cardiac fibroblasts-like, induced pluripotent stem cell-derived MSCs from normal donors and ACM patients withDSPmutations. We then studied the fibrogenic responses of cardiac MSCs to transforming growth factor beta-1 (TGF-β1) using Western/Co-IP, autophagy assay, gene knockdowns/over-expressions, genomic analyses, mouse DSP knockdown models, immunostaining, and qPCR.

Results

TGFβ1 induced excessive accumulations of vimentin (VIM)/fibrillar collagens, and over-activated fibrotic genes inDSP-mutant MSCs when compared to normal MSCs. In normal MSCs, VIMs bind to wild-type DSP during normal fibrogenesis after TGFβ1.DSP-mutant MSCs exhibited a haplo-insufficient phenotype with increased DSP-unbound VIMs that sequestered beclin-1 (BECN1) from activating autophagy and caveolin-1 (CAV1)-mediated endocytosis. Decreased autophagy caused collagen accumulations and diminished CAV1 endocytosis resulted in abnormal CAV1 plaque formation that over-activated fibrotic genes [COL1A1, COL3A1,and fibronectin (FN)] via heightened p38 activities after TGFβ1. Genome-wide analysis and DSP knockdown in mouse fibroblasts confirmed this novel role ofDSPmutations in pathological fibrosis. Overexpression of VIM-binding domains of DSP could suppress pathological fibrosis by increasing collagen autophagic degradation and decreasing fibrotic gene expressions.

Conclusions

Our data reveal that DSP deficiency in MSCs/fibroblasts leads to exaggerated fibrogenesis in DSP-cardiomyopathy by decreasing BECN1 availability for autophagy and CAV1-endocytosis. Overexpression of VIM binding domains of DSP could be a new strategy to treat pathological fibrosis.
A male seminal fluid protein SFP-1 regulates hermaphrodite post-mating longevity and fat metabolism inCaenorhabditis elegans
Authors: Chen Mingqing , Gong Jianke
Published: September 2024

There are several causes of mating-induced physiological changes in hermaphrodites exposed to males, such as functional male sperms causing shrinking and the male pheromone mediating shortened lifespan, which utilize different molecular pathways and are shared across species. However, it is unclear whether the male seminal fluid protein contributes to this post-mating regulation. Here, we investigated the transmit way and the impacts of theCaenorhabditismale seminal fluid protein SFP-1 in mated hermaphrodite tissues. We find that SFP-1 is the key component in seminal fluid to induce post-mating physiological changes in mated hermaphrodites. It acts as a cargo packing into exophers which require the phospholipid scramblase ANOH-1 and ANOH-2 to develop in male seminal vesicle. Exophers carrying SFP-1 cross over the somatic gonad uterus and eventually the protein is uptaken by the intestinal cells via endocytosis. Within the intestine, the NTF2-like domain of SFP-1 assists the association and interaction with the transcription factors SKN-1 and DAF-16 to induce post-mating somatic fat depletion and a shortened lifespan. Our study reveals the elaborate strategies of the male seminal fluid protein on triggering mating-induced physiological changes elicited by sexual interactions that could exist in other species.
Development of a Conditional Plasmid for Gene Deletion in Non-ModelFusobacterium nucleatumstrains
Authors: Zhou Peng , Bibek G C , Wu Chenggang
Published: September 2024

Fusobacterium nucleatumis an opportunistic pathogen with four subspecies:nucleatum(FNN),vincentii(FNV),polymorphum(FNP), andanimalis(FNA), each with distinct disease potentials. Research on fusobacterial pathogenesis has mainly focused on the model strain ATCC 23726 from FNN. However, this narrow focus may overlook significant behaviors of other FNN strains and those from other subspecies, given the genetic and phenotypic diversity withinF. nucleatum. While ATCC 23726 is highly transformable, most otherFusobacteriumstrains exhibit low transformation efficiency, complicating traditional gene deletion methods that rely on non-replicating plasmids. To address this, we developed a conditional plasmid system in which the RepA protein, essential for replication of a pCWU6-based shuttle plasmid, is controlled by an inducible system combining anfdxpromoter with a theophylline-responsive riboswitch. This system allows plasmid replication in host cells upon induction and plasmid loss when the inducer is removed, forcing chromosomal integration via homologous recombination in the presence of the antibiotic thiamphenicol. We validated this approach by targeting thegalKgene, successfully generating mutants in FNN (ATCC 23726, CTI-2), FNP (ATCC 10953), FNA (21_1A), and the closely related speciesFusobacterium periodonticum. Incorporating asacBcounterselection marker in this conditional plasmid enabled the deletion of theradDgene in non-model strains. Interestingly, whileradDdeletion in 23726, 10953, and 21_1A abolished coaggregation withActinomyces oris, the CTI-2 mutant retained this ability, suggesting the involvement of other unknown adhesins. This work significantly advances gene deletion in genetically recalcitrantF. nucleatumstrains, enhancing our understanding of this pathogen.

IMPORTANCE

Fusobacterium nucleatumis implicated in various human diseases, including periodontal disease, preterm birth, and colorectal cancer, often linked to specific strains and reflecting the species’ genetic and phenotypic diversity. Despite this diversity, most genetic research has centered on the model strain ATCC 23726, potentially missing key aspects of other strains’ pathogenic potential. This study addresses a critical gap by developing a novel conditional plasmid system that enables gene deletion in genetically recalcitrant strains ofF. nucleatum. We successfully deleted genes in the clinical strain CTI-2, the FNA strain 21_1A, andF. periodonticumfor the first time. Our findings, particularly the varying behavior of theradDgene production in coaggregation across strains, underscore the complexity ofF. nucleatumand the need for broader genetic studies. This work advances our understanding ofF. nucleatumvirulence at the strain level and provides a valuable tool for future bacterial genetics research.
The food–gut axis: the phyllosphere virome of fresh vegetables is diverse, abundant, and transmitted to the human gut virome
Authors: Park Ji-Woo , Yun Yeo-Eun , Cho Jin Ah , Yoon Su-In , In Su-A , Park Eun-Jin , Kim Min-Soo
Published: September 2024

Fresh vegetables harbor diverse microorganisms on leaf surfaces, yet their viral communities remain unexplored. We investigated the diversity and ecology of phyllosphere viromes of six leafy green vegetables using virus-like particle (VLP) enrichment and shotgun metagenome sequencing. On average, 9.2 × 107viruses were present per gram of leaf tissue. The majority (93.1 ± 6.2%) of these viruses were taxonomically unclassified. Virome compositions were distinct among vegetable types and exhibited temporal variations. Virulent phages with replication-enhancing auxiliary metabolic genes (AMGs) were more dominant than temperate phages with host fitness-benefiting AMGs. Analysis of 1,498 human fecal VLP metagenomes revealed that approximately 10% of vegetable viruses were present in the human gut virome, including viruses commonly observed in multiple studies. These gut-associated vegetable viruses were enriched with short-term vegetable intake, and depleted in individuals with metabolic and immunologic disorders. Overall, this study elucidates the ecological contribution of the fresh vegetable virome to human gut virome diversity.
Sleep inertia drives the association of evening chronotype with psychiatric disorders: epidemiological and genetic evidence
Authors: Burns Angus C , Zellers Stephanie , Windred Daniel P. , Daghlas Iyas , Sinnott-Armstrong Nasa , Rutter Martin , Hublin Christer , Friligkou Eleni , Polimanti Renato , Phillips Andrew J. K. , Cain Sean W. , Kaprio Jaakko , Ollila Hanna , Saxena Richa , Lane Jacqueline M.
Published: September 2024

Evening chronotypes (a.k.a. night-owls) are held to be at greater risk for psychiatric disorders. This is postulated to be due to delayed circadian timing increasing the likelihood of circadian misalignment in an early-oriented society. Circadian misalignment is known to heighten sleep inertia, the difficulty transitioning from sleep to wake characterized by low arousal and cognitive impairment, and evening chronotypes experience greater sleep inertia. Therefore, difficulty awakening may explain the relationship between evening chronotype and psychiatric disorders by acting as a biomarker of circadian misalignment. In analyzing the longitudinal incidence of psychiatric disorders in the UK Biobank (n = 496,820), we found that evening chronotype predicted increased incidence of major depressive disorder, schizophrenia, generalized anxiety disorder and bipolar disorder. Crucially, this effect was dependent on sleep inertia, which was a much stronger predictor of these disorders, such that evening types without sleep inertia were at no higher risk as compared to morning types. Longitudinal analyses of suicide and depressed mood (CES-D score) in the Older Finnish Twin Cohort (n = 23,854) replicated this pattern of results. Twin and genome-wide association analyses of difficulty awakening identified the trait to be heritable (Twin H2 = 0.40; SNP h2 = 0.08), enriched for circadian rhythms genes and have substantial shared genetic architecture with chronotype. Marginal and conditional Mendelian randomization analyses mirrored the epidemiological results, such that the causal effect of evening chronotype on psychiatric disorders was driven by shared genetic architecture with difficulty awakening. In contrast, difficult awakening was strongly causally associated with psychiatric disorders independently of chronotype. Psychiatric disorders were only weakly reverse causally linked to difficult awakening. Collectively, these results challenge the notion that evening chronotype is a risk factor for psychiatric disorders per se, suggesting instead that evening types are at greater risk for psychiatric disorders due to circadian misalignment, for which sleep inertia may be acting as a biomarker.