bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-cell transcriptome unravels spermatogonial stem cells and dynamic heterogeneity of spermatogenesis in seasonal breeding teleost
Authors: Yang Yang , Zhou Yinan , Wessel Gary , Hu Weihua , Xu Dongdong
Published: June 2024

Seasonal spermatogenesis in fish is driven by spermatogonial stem cells (SSCs), which undergo a complex cellular process to differentiate into mature sperm. In this study, we characterized spermatogenesis in the large yellow croaker (Larimichthys crocea), a marine fish of significant commercial value, based on a high-resolution single-cell RNA-seq atlas of testicular cells from three distinct developmental stages- juvenile, adult differentiating and regressed testes. We detailed continuous developmental trajectory of spermatogenic cells, from spermatogonia to spermatids, elucidating the molecular events involved in spermatogenesis. We uncovered dynamic heterogeneity in cellular compositions throughout the annual reproductive cycle, accompanied by strong molecular signatures within specific testicular cells. Notably, we identified a distinct population of SSCs and observed a critical metabolic transition from glycolysis to oxidative phosphorylation, enhancing our understanding of the biochemical and molecular characteristics of SSCs. Additionally, we elucidated the interactions between somatic cells and spermatogonia, illuminating the mechanisms that regulate SSCs development. Overall, this work enhances our understanding of spermatogenesis in seasonal breeding teleost and provides essential insights for the further conservation and culture of SSCs.

Summary statement

Our study reveals new insights into the development of spermatogonial stem cells (SSCs), potentially impacting further conservation and culture of SSCs in teleost.
A tool for CRISPR-Cas9 gRNA evaluation based on computational models of gene expression
Authors: Cohen Shai , Bergman Shaked , Lynn Nicolas , Tuller Tamir
Published: June 2024

CRISPR based technologies have revolutionized all biomedical fields as it enables efficient genomic editing. These technologies are often used to silence genes by inducing mutations that are expected to nullify their expression. To this end, dozens of computational tools have been developed to design gRNAs, CRISPR’s gene-targeting molecular guide, with high cutting efficiency and no off-target effect. However, these tools do not consider the induced mutation’s effect on the gene’s expression, which is the actual objective that should be optimized. This fact can often lead to failures in the design, as an efficient cutting of the DNA does not ensure the desired effect in protein production. Therefore, we developed EXPosition, a computational tool for gRNA design. It is the first tool designed to improve the true objective of using CRISPR: the effect it has on gene expression. To this end, we used predictive deep-learning models for the relevant gene expression steps: transcription, splicing, and translation initiation. We validated our tool by demonstrating that it can classify sites as “silencing” or “non-silencing” better than models that consider only the cutting efficiency. We believe that this tool will significantly improve both the efficiency and accuracy of genome editing endeavors. EXPosition is available at http://www.cs.tau.ac.il/~tamirtul/EXPosition.
Single-Cell Transcriptomic Analysis Highlights Specific Cell Types of Wheat Manipulated byFusarium graminearumLeading to Susceptibility
Authors: Wei Wan-Qian , Li Shuang , Zhang Dong , Tang Wei-Hua
Published: June 2024

Phytopathogenic fungi can be recognized by the plant immune system and trigger host defenses, but adapted pathogens cause susceptibility. How different cell types cooperate and orchestrate biological processes in response to heterogeneous colonization of organs by adapted and non-adapted pathogens remains largely unknown. Here we employed single-cell RNA sequencing to dissect the responses of wheat coleoptiles to infection by the adapted fungal pathogenFusarium graminearum(Fgr) and the non-adapted fungal pathogenFusarium oxysporumf. sp.cubense(Foc) at 1-, 2-, and 3-days post-inoculation. We profiled the transcriptomes of over 90,000 cells and identified eight major cell types in coleoptiles: stomata, epidermis, chlorenchyma, parenchyma, outer sheath, inner sheath, phloem, and procambium. Differential expression analyses showed that the capacity of different cell types to respond to fungal infection varied. The upregulation of immune pathways was compartmentalized in nonhost resistance toFoc, but widespread in susceptible interaction withFgr. Pseudotime analyses revealed continuous cell state transitions in the disease progression of infected cell types. Our work indicates that the phloem and outer sheath are specific cell types that collaborate for the rapid onset of nonhost resistance.Fgrinduces a state of low transcriptional activity in the chlorenchyma. Cell trajectory analysis suggests that the competition between immune and susceptible processes in parenchyma results in specific cell states that are favored by the adapted pathogenFgr. Overall, this work explains how cell types collaborate and are manipulated during fungal infections, providing insight into the intercellular mechanisms of plant immunity.
Neural circuit-selective, multiplexed pharmacological targeting of prefrontal cortex-projecting locus coeruleus neurons drives antinociception
Authors: Kuo Chao-Cheng , McCall Jordan G.
Published: June 2024

Selective manipulation of neural circuits using optogenetics and chemogenetics holds great translational potential but requires genetic access to neurons. Here, we demonstrate a general framework for identifying genetic tool-independent, pharmacological strategies for neural circuit-selective modulation. We developed an economically accessible calcium imaging-based approach for large-scale pharmacological scans of endogenous receptor-mediated neural activity. As a testbed for this approach, we used the mouse locus coeruleus due to the combination of its widespread, modular efferent neural circuitry and its wide variety of endogenously expressed GPCRs. Using machine learning-based action potential deconvolution and retrograde tracing, we identified an agonist cocktail that selectively inhibits medial prefrontal cortex-projecting locus coeruleus neurons.In vivo, this cocktail produces synergistic antinociception, consistent with selective pharmacological blunting of this neural circuit. This framework has broad utility for selective targeting of other neural circuits under different physiological and pathological states, facilitating non-genetic translational applications arising from cell type-selective discoveries.
DnaA modulates the gene expression and morphology of the Lyme disease spirochete
Authors: Krusenstjerna Andrew C. , Jusufovic Nerina , Saylor Timothy C. , Stevenson Brian
Published: June 2024

All bacteria encode a multifunctional DNA-binding protein, DnaA, which initiates chromosomal replication. Despite having the most complex, segmented bacterial genome, little is known aboutBorrelia burgdorferiDnaA and its role in maintaining the spirochete’s physiology. In this work we utilized inducible CRISPR-interference and overexpression to modulate cellular levels of DnaA to better understand this essential protein. Dysregulation of DnaA, either up or down, increased or decreased cell lengths, respectively, while also significantly slowing replication rates. Using fluorescent microscopy, we found the DnaA CRISPRi mutants had increased numbers of chromosomes with irregular spacing patterns. DnaA-depleted spirochetes also exhibited a significant defect in helical morphology. RNA-seq of the conditional mutants showed significant changes in the levels of transcripts involved with flagellar synthesis, elongation, cell division, virulence, and other functions. These findings demonstrate that the DnaA plays a commanding role in maintaining borrelial growth dynamics and protein expression, which are essential for the survival of the Lyme disease spirochete.

IMPORTANCE

Lyme disease is the most prevalent tick-borne infection in the Northern Hemisphere.Borrelia burgdorferi, the causative spirochete bacteria, has been maintained in nature for millennia in a consistent enzootic cycle betweenIxodesticks and various small vertebrate hosts. During the tick’s blood meal,B. burgdorferisubstantially increases its replication rate, alters its repertoire of outer surface proteins, and disseminates into the new vertebrate host. Across eubacteria, DnaA is the master regulatory protein that initiates chromosomal replication and acts as a transcription factor to regulate specific pathways. Here, we describe the roles thatB. burgdorferiDnaA has on the physiology and gene expression of this medically important pathogen.
Predicting RNA Structure and Dynamics with Deep Learning and Solution Scattering
Authors: Patt Edan , Classen Scott , Hammel Michal , Schneidman-Duhovny Dina
Published: June 2024

Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle X-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the absence of cations essential for stability and charge neutralization in predicted structures and the inadequacy of a single structure to represent RNA’s conformational plasticity. We introduce Solution Conformation Predictor for RNA (SCOPER) to address these challenges. This pipeline integrates kinematics-based conformational sampling with the innovative deep-learning model, IonNet, designed for predicting Mg2+ion binding sites. Validated through benchmarking against fourteen experimental datasets, SCOPER significantly improved the quality of SAXS profile fits by including Mg2+ions and sampling of conformational plasticity. We observe that an increased content of monovalent and bivalent ions leads to decreased RNA plasticity. Therefore, carefully adjusting the plasticity and ion density is crucial to avoid overfitting experimental SAXS data. SCOPER is an efficient tool for accurately validating the solution state of RNAs given an initial, sufficiently accurate structure and provides the corrected atomistic model, including ions.

The method is available from:https://github.com/dina-lab3d/IonNet

Our pipeline is available for use as a web server:https://bilbomd.bl1231.als.lbl.gov/

Statement of Significance

Understanding the behavior of RNA in solution is critical for deciphering its biological functions, yet predicting its macromolecular conformation remains challenging. While advanced computational methods can predict RNA structures, their accuracy in solution is often limited by the absence of stabilizing ions and the failure to account for RNA’s conformational flexibility. This study presents SCOPER, an innovative tool that addresses these challenges by integrating deep-learning-based ion binding site prediction with conformational sampling, offering a more reliable approach to validate and refine RNA structures against experimental SAXS data. We provide our source code and a web server that runs the pipeline.
Characterization of β-Hydroxybutyrate as a Cell Autonomous Fuel for Active Excitatory and Inhibitory Neurons
Authors: Bredvik Kirsten , Liu Charmaine , Ryan Timothy A.
Published: June 2024

The ketogenic diet is an effective treatment for drug-resistant epilepsy, but the therapeutic mechanisms are poorly understood. Although ketones are able to fuel the brain, it is not known whether ketones are directly metabolized by neurons on a time scale sufficiently rapid to fuel the bioenergetic demands of sustained synaptic transmission. Here, we show that nerve terminals can use the ketone β-hydroxybutyrate in a cell- autonomous fashion to support neurotransmission in both excitatory and inhibitory nerve terminals and that this flexibility relies on Ca2+dependent upregulation of mitochondrial metabolism. Using a genetically encoded ATP sensor, we show that inhibitory axons fueled by ketones sustain much higher ATP levels under steady state conditions than excitatory axons, but that the kinetics of ATP production following activity are slower when using ketones as fuel compared to lactate/pyruvate for both excitatory and inhibitory neurons.

Significance Statement

The ketogenic diet is a standard treatment for drug resistant epilepsy, but the mechanism of treatment efficacy is largely unknown. Changes to excitatory and inhibitory balance is one hypothesized mechanism. Here, we determine that ATP levels are differentially higher in inhibitory neurons compared to excitatory neurons, suggesting that greater mitochondrial ATP production in inhibitory neurons could be one mechanism mediating therapeutic benefit. Further, our studies of ketone metabolism by synaptic mitochondria should inform management of side effects and risks associated with ketogenic diet treatments. These results provide novel insights that clarify the role of ketones at the cellular level in ketogenic diet treatment for intractable epilepsy and inform the use of ketogenic diets for neurologic and psychiatric conditions more broadly.
A Mechanistic Understanding of the Activity-Stability Trade-off in PETase
Authors: Chen Shuang , Akram Ekram , Qiao Weili , Zhang Yifei , Haider Shozeb , Cao Yufei
Published: June 2024

Enzymatic degradation of poly(ethylene terephthalate) (PET) has garnered considerable interest in plastic recycling efforts. Despite numerous descriptions of both natural and engineered enzymes, the fundamental mechanism underlying PETase-catalyzed PET depolymerization at the solid-liquid interface remains elusive. This lack of understanding hampers the rational design of highly efficient depolymerases. Here, we employ multiscale simulations and experiments to elucidate the complete catalytic pathway ofIsPETase, from enzyme adsorption at the interface to PET fragment capture, conformational refinement, and ester bond cleavage. Both endo- and exo-cleavage modes of the enzyme are identified, indicating its capacity for endo- and exo-lytic activities. We discover that the trade-off between the activity and stability ofIsPETase’s PET-capturing pliers brings compromises to its PET depolymerization performance. Reshaping the loop dynamics of the enzyme can break this trade-off and enhance its stability and activity simultaneously, as demonstrated by the evolved variant HotPETase. Overall, our study offers comprehensive details into how PETase functions at the interface and provides valuable insights for engineering efficient plastic-degrading enzymes.
Multi-modal Spatial-modality Attentive Fusion for Studying Neuropsychiatric Disorders
Authors: Rahaman Md Abdur , Garg Yash , Iraji Armin , Fu Zening , Kochunov Peter , Hong L. Elliot , Van Erp Theo G. M. , Preda Adrian , Chen Jiayu , Calhoun Vince
Published: June 2024

Multi-modal learning has emerged as a powerful technique that leverages diverse data sources to enhance learning and decision-making processes. Adapting this approach to analyzing data collected from different biological domains is intuitive, especially for studying neuropsychiatric disorders. A complex neuropsychiatric disorder like schizophrenia (SZ) can affect multiple aspects of the brain and biologies. These biological sources each present distinct yet correlated expressions of subjects’ underlying physiological processes. Joint learning from these data sources can improve our understanding of the disorder. However, combining these biological sources is challenging for several reasons: (i) observations are domains-specific, leading to data being represented in dissimilar subspaces, and (ii) fused data is often noisy and high-dimensional, making it challenging to identify relevant information. To address these challenges, we propose a multi-modal artificial intelligence (AI) model with a novel fusion module inspired by a bottleneck attention module (BAM). We use deep neural networks (DNN) to learn latent space representations of the input streams. Next, we introduce a two-dimensional (spatio-modality) attention module to regulate the intermediate fusion for SZ classification. We implement spatial attention via a dilated convolutional neural network that creates large receptive fields for extracting significant contextual patterns. The resulting joint learning framework maximizes complementarity allowing us to explore the correspondence among the modalities. We test our model on a multi-modal imaging-genetic dataset and achieve an SZ prediction accuracy of 94.10% (P < 0.0001), outperforming state-of-the-art unimodal and multi-modal models for the task. Moreover, the model provides inherent interpretability that helps identify concepts significant for the neural network’s decision and explains the underlying physiopathology of the disorder. Results also show that functional connectivity among subcortical, sensorimotor, and cognitive control domains plays an important role in characterizing SZ. Analysis of the spatio-modality attention scores suggests that structural components like the supplementary motor area, caudate, and insula play a significant role in SZ. Biclustering the attention scores discover a multi-modal cluster that includes genes CSMD1, ATK3, MOB4, and HSPE1, all of which have been identified as relevant to schizophrenia. In summary, feature attribution appears to be especially useful for probing the transient and confined but decisive patterns of complex disorders, and it shows promise for extensive applicability in future studies.
Protein fusion strategies for a multi-component Rieske oxygenase
Authors: Runda Michael E. , Miao Hui , Schmidt Sandy
Published: June 2024

Rieske oxygenases (ROs) are enzyme systems involved in microbial biodegradation or late-stage modifications during natural product biosynthesis. A major obstacle to working with ROs is their dependence on multi-component electron transfer chains (ETCs). Thereby, electrons from NAD(P)H are shuttled directly via a reductase (Red) or indirectly via an additional ferredoxin (Fd) to a terminal oxygenase (Oxy) for oxygen activation and subsequent substrate conversion. The present work evaluates potential fusion strategies to simplify the ETC of the three-component cumene dioxygenase (CDO) fromPseudomonas fluorescence. Inin vitroreactions, the fusion of CDO-Red to CDO-Fd is the most suitable for activation of CDO-Oxy with product formation of approximately 22 mM (72 % conversion). Furthermore, protein fusion to CDO-Oxy was found to be feasible, highlighting the versatility of the redox partner fusion approach. Overall, this study aims to contribute to the research field of ROs by providing a promising strategy to simplify their multi-component nature.
Gangliosides in neural stem cell fate determination and nerve cell specification--preparation and administration
Authors: Itokazu Yutaka , Ariga Toshio , Fuchigami Takahiro , Li Dongpei
Published: June 2024

Gangliosides are sialylated glycosphingolipids with essential but enigmatic functions in healthy and disease brains. GD3 is the predominant species in neural stem cells (NSCs) and GD3-synthase (sialyltransferase II;St8Sia1) knockout (GD3S-KO) revealed reduction of postnatal NSC pools with severe behavioral deficits including cognitive impairment, depression-like phenotypes, and olfactory dysfunction. Exogenous administration of GD3 significantly restored the NSC pools and enhanced the stemness of NSCs with multipotency and self-renewal, followed by restored neuronal functions. Our group discovered that GD3 is involved in the maintenance of NSC fate determination by interacting with epidermal growth factor receptors (EGFRs), by modulating expression of cyclin-dependent kinase (CDK) inhibitors p27 and p21, and by regulating mitochondrial dynamics via associating a mitochondrial fission protein, the dynamin-related protein-1 (Drp1). Furthermore, we discovered that nuclear GM1 promotes neuronal differentiation by an epigenetic regulatory mechanism. GM1 binds with acetylated histones on the promoter ofN-acetylgalactosaminyltransferase (GalNAcT; GM2 synthase (GM2S); B4galnt1)as well as on theNeuroD1in differentiated neurons. In addition, epigenetic activation of the GM2S gene was detected as accompanied by an apparent induction of neuronal differentiation in NSCs responding to an exogenous supplement of GM1. Interestingly, GM1 induced epigenetic activation of thetyrosine hydroxylase (TH)gene, with recruitment of Nurr1 and PITX3, dopaminergic neuron-associated transcription factors, to theTHpromoter region. In this way, GM1 epigenetically regulates dopaminergic neuron specific gene expression, and it would modify Parkinson’s disease. Multifunctional gangliosides significantly modulate lipid microdomains to regulate functions of important molecules on multiple sites: the plasma membrane, mitochondrial membrane, and nuclear membrane. Versatile gangliosides regulate functional neurons as well as sustain NSC functions via modulating protein and gene activities on ganglioside microdomains. Maintaining proper ganglioside microdomains benefits healthy neuronal development and millions of senior citizens with neurodegenerative diseases.

Here, we introduce how to isolate GD3 and GM1 and how to administer them into the mouse brain to investigate their functions on NSC fate determination and nerve cell specification.
Interplay of kinetochores and catalysts drives rapid assembly of the mitotic checkpoint complex
Authors: Sethi Suruchi , Piano Valentina , Ghetti Sabrina , Cmentowski Verena , Stege Patricia , Musacchio Andrea
Published: June 2024

The spindle assembly checkpoint (SAC) makes mitotic exit contingent on completion of sister chromatid biorientation, but how this coordination is achieved in practice remains poorly understood. Kinetochores, megadalton chromosome attachment sites to spindle microtubules, contribute to SAC signaling. However, it is unclear whether kinetochores are mere docking sites for SAC proteins, or further contribute to co-orientation of SAC catalysts, including MAD1:MAD2 and BUB1:BUB3, to facilitate SAC signaling. Here, we combined biochemical reconstitutions of kinetochores and the SAC to address this questionin vitro. We engineered recombinant kinetochore particles that recruit most SAC components and activate SAC signaling after induction with Rapamycin, and challenged them with a battery of impairing mutants. At approximately physiological concentrations of SAC catalysts, kinetochores were crucially required for rapid assembly of the mitotic checkpoint complex (MCC), the SAC effector. Our observations depict kinetochores as a cradle that catalyzes rapid MCC assembly by concentrating and co-orienting distinct SAC catalysts.
Germline prediction of immune checkpoint inhibitor discontinuation for immune-related adverse events
Authors: Middha Pooja , Thummalapalli Rohit , Quandt Zoe , Balaratnam Karmugi , Cardenas Eduardo , Falcon Christina J. ,   Princess Margaret Lung Group, Gubens Matthew A. , Huntsman Scott , Khan Khaleeq , Li Min , Lovly Christine M. , Patel Devalben , Zhan Luna Jia , Liu Geoffrey , Aldrich Melinda C. , Schoenfeld Adam J. , Ziv Elad
Published: June 2024

Introduction

Immune checkpoint inhibitors (ICIs) can yield remarkable clinical responses in subsets of patients with solid tumors but can also often lead to immune-related adverse events (irAEs). Predictive features of clinically severe irAEs leading to cessation of ICIs have yet to be established. Using data from 1,327 patients with lung cancer treated with ICIs between 2009 and 2022 at four academic medical centers, we evaluated the association of a germline polygenic risk score for autoimmune disease and discontinuation of ICIs due to irAEs.

Methods

Using Cox proportional hazards model, we assessed the association between a polygenic risk score for autoimmune disease (PRSAD) and cessation of ICI therapy due to irAEs. All models were adjusted for age at diagnosis, sex, lung cancer histology, type of therapy, recruiting center, and the first 5 principal components. To further understand the differential effects of type of therapy and disease stage on the association between PRSADand cessation of ICI due to irAEs, we conducted stratified logistic regression analysis by type of ICI therapy and disease stage.

Results

We found an association between PRSADand ICI cessation due to irAEs (HR per SD = 1.18, 95% CI = 1.02 – 1.37, P = 0.03). This association was particularly strong in patients who had ICI cessation due to irAEs within three months of therapy initiation (HR per SD = 1.38, 95% CI = 1.08 - 1.78, P = 0.01). Individuals in the top 20th percentile of PRSADhad 7.2% ICI discontinuation for irAEs by three months, compared to 3.9% discontinuation by three months among patients in the bottom 80th percentile (log-rank P = 0.02). In addition, among patients who received combination PD-1/PD-L1 and CTLA-4 inhibitor therapy, PRSADhad an OR per SD of 1.86 (95% CI = 1.08 - 3.51, P = 0.04).

Conclusions

We demonstrate an association between a polygenic risk score for autoimmune disease and early ICI discontinuation for irAEs, particularly among patients treated with combination ICI therapy. Our results suggest that germline genetics may be used as an adjunctive tool for risk stratification around ICI clinical decision-making in solid tumor oncology.
Optimization of an adult immunization program in Canada
Authors: Locke Nathan , Paulden Mike , MacDonald Shannon E. , Montesanti Stephanie , Tuite Ashleigh , Hempel Karsten , McDonald Wade , Rafferty Ellen
Published: June 2024

Background

Provincial decisions to fund a new immunization program are generally made on a case-by-case basis, without systematic consideration of how the new immunization program may fit within the larger provincial immunization portfolio.

Aim

The goal of this study was to develop evidence and tools to guide policy-makers in making fiscally and ethically responsible decisions on which adult immunization programs to include in their portfolio under various constrained budgetary scenarios.

Methods

Using previously published infectious disease models, cost-utility data was estimated for adult pneumococcal, influenza, pertussis, and shingles immunization programs. This data was then inputted into a newly developed constrained optimization model to determine portfolios of immunization programs that maximize either population health or incremental net monetary benefit, subject to a budget constraint. Sensitivity analyses were conducted on model parameters such as vaccine costs, cost-effectiveness thresholds, and the budget constraint.

Results

Optimized solutions changed dramatically based on the number of immunization programs included, total budget, what was optimized for (i.e., population health or incremental net monetary benefit), the cost-effectiveness threshold and the assumed vaccine prices. Maximal health gains and budget spending was achieved when optimizing based on population health. Reductions in health gains and budget spending were observed at a CAN$50,000 cost-effectiveness threshold, and at a CAN$30,000 threshold, the budget was significantly underutilized and health gains were noticeably reduced.

Conclusion

If budgets for the adult immunization portfolio are fixed, then shifting to more expensive programs that offer large health benefits may be preferable. However, if budgets can be spread across various public health programs (i.e., childhood immunization, well-baby programs), it may make more sense to optimize based on cost-effectiveness. Constrained optimization tools could improve goals-based decision-making and allow for transparent and effective methods to make allocation decisions.

Highlights

Optimized solutions changed dramatically based on the number of immunization programs available, total budget, and the cost-effectiveness threshold.

If budgets for the adult immunization portfolio are fixed, then shifting to more expensive programs that offer large health benefits may be preferable.

If budgets can be spread across various public health programs, it may make more sense to optimize based on cost-effectiveness.

Constrained optimization tools could improve goals-based decision-making and allow for transparent and effective methods to make allocation decisions.
Differential effects of theta-gamma tACS on motor skill acquisition in young individuals and stroke survivors: a double-blind, randomized, sham-controlled study
Authors: Grigutsch L.S. , Haverland B. , Timmsen L. S. , Asmussen L. , Braaß H. , Wolf S. , Luu T. V. , Stagg C.J. , Schulz R. , Quandt F. , Schwab B.C.
Published: June 2024

Background

Theta-gamma transcranial alternating current stimulation (tACS) was recently found to enhance thumb acceleration in young, healthy participants, suggesting a potential role in facilitating motor skill acquisition. Given the relevance of motor skill acquisition in stroke rehabilitation, theta-gamma tACS may hold potential for treating stroke survivors.

Objective

We aimed to examine the effects of theta-gamma tACS on motor skill acquisition in young, healthy participants and stroke survivors.

Methods

In a pre-registered, double-blind, randomized, sham-controlled study, 78 young, healthy participants received either theta-gamma peak-coupled (TGP) tACS, theta-gamma trough-coupled (TGT) tACS or sham stimulation. 20 individuals with a chronic stroke received either TGP or sham. TACS was applied over motor cortical areas while participants performed an acceleration-dependent thumb movement task. Stroke survivors were characterized using standardized testing, with a subgroup receiving additional anatomical brain imaging.

Results

Neither TGP nor TGT tACS significantly modified general motor skill acquisition in the young, healthy cohort. In contrast, in the stroke cohort, TGP diminished motor skill acquisition compared to sham. Exploratory analyses revealed that, independent of general motor skill acquisition, healthy participants receiving TGP or TGT exhibited greater peak thumb acceleration than those receiving sham.

Conclusion

Although theta-gamma tACS increased thumb acceleration in young, healthy participants, consistent with previous reports, it did not enhance overall motor skill acquisition in a more complex motor task. Furthermore, it even had detrimental effects on motor skill acquisition in stroke survivors.
The Microbiome and Metatranscriptome of a Panel from theSarraceniaMapping Population Reveal Complex Assembly and Function Involving Host Influence
Authors: Cai Jiazhang , Mohsin Iqra , Rogers Willie , Zhang Mengrui , Jiang Lin , Malmberg Russell , Alabady Magdy
Published: June 2024

Sarraceniaprovide an optimal system for deciphering the host-microbiome interactions at various levels. We analyzed the pitcher microbiomes and metatranscriptomes of the parental species, and F1 and F2 generations from the mapping population (Sarracenia purpureaXSarracenia psittacina) utilizing high-throughput sequencing methods. This study aimed to examine the host influences on the microbiome structure and function and to identify the key microbiome traits. Our quality datasets included 8,892,553 full-length bacterial 16s rRNA gene sequences and 65,578 assembled metatranscripts with microbial protein annotations. The correlation network of the bacterial microbiome revealed the presence of 3-7 distinct community clusters, with 8 hub and 19 connector genera. The entire microbiome consisted of viruses, bacterial, archaea, and fungi. The richness and diversity of the microbiome varied among the parental species and offspring genotypes despite being under the same greenhouse environmental conditions. We have discovered certain microbial taxa that are genotype-enriched, including the community hub and connector genera. Nevertheless, there were no significant differences observed in the functional enrichment analysis of the metatranscriptomes across the different genotypes, suggesting a functional convergence of the microbiome. Our results revealed that the pitcher microcosm harbors both rhizosphere and phyllosphere microbiomes within its boundaries, resulting in a structurally diverse and functionally complex microbiome community. A total of 50,424 microbial metatranscripts were linked to plant growth-promoting microbial proteins. We show that this complex pitcher microbiome possesses various functions that contribute to plant growth promotion, such as biofertilization, bioremediation, phytohormone signaling, stress regulation, and immune response stimulation. Additionally, the pitcher microbiome exhibits traits related to microbe-microbe interactions, such as colonization of plant systems, biofilm formation, and microbial competitive exclusion. In summary, the demonstrated taxonomical divergence and functionally convergence of the pitcher microbiome are impacted by the host genetics, making it an excellent system for discovering novel beneficial microbiome traits.
Retinoid X Receptor as a Novel Drug Target to Treat Neurological Disorders Associated with α- Synucleinopathies
Authors: Zhylkibayev Assylbek , Starr Christopher R. , Atigadda Venkatram , Grant Maria B. , Gorbatyuk Marina S. , Gorbatyuk Oleg S.
Published: June 2024

The pathology of Parkinson’s Disease (PD) is multifaceted, with chronic neuroinflammation associated with glial cell activation standing out as a hallmark of PD pathophysiology. While a few treatments exist to interfere with inflammation, a breakthrough therapy based on innovative molecular mechanisms and targets is still awaited. The nuclear retinoid X receptor (RXR) is of particular interest for therapeutic intervention due to its ability to bind and activate permissive partners, NURR1 and PPARs, which have been shown to be dysfunctional in PD brains. Therefore, the goal of this study was to validate RXR-based therapy to slow down PD pathogenesis. Adult C57BL6 male mice were used in the study. PD-like pathology was triggered by co-delivery of AAV expressing α-Syn and PFF (AAV/PFF) to the substantia nigra pars compacta. The therapeutic potential of RXR activation was evaluated using AAV-mediated gene transport. Unbiased stereology, immunohistochemical analysis, LC/MS, and western blotting were employed to assess the therapeutic effect. At 8 weeks post-injection—elevated GFAP and Iba1 levels, associated with accumulated LB-like aggregates, pronounced loss of TH neuronal cells, and diminished dopamine (DA) levels—were observed in affected brains. Moreover, PPAR and NURR1 protein levels were also reduced in these brains. Conversely, RXR overexpression resulted in an increase in PPAR and NURR1 levels, a reduction in GFAP and Iba1 levels, and a decrease in the number and distribution of LB-like aggregates. These phenomena were also accompanied by the prevention of tyrosine hydroxylase (TH)+cell loss and the DA deficit in the treated brains. Therefore, our data provide direct evidence of the therapeutic potential of RXR-based therapy and highlight RXR as a novel drug target for PD.
Endogenous opioids facilitate stress‐induced binge eating via an insular cortex‐claustrum pathway
Authors: Chen Jingyi , Mangieri Leandra , Mar Sophia , Piantadosi Sean , Marcus David , Davis Phoenix , Land Benjamin B , Bruchas Michael
Published: June 2024

Stress has been shown to promote the development and persistence of binge eating behaviors. However, the neural circuit mechanisms for stress-induced binge-eating behaviors are largely unreported. The endogenous dynorphin (dyn)/kappa opioid receptor (KOR) opioid neuropeptide system has been well-established to be a crucial mediator of the anhedonic component of stress. Here, we aimed to dissect the basis of dynorphinergic control of stress-induced binge-like eating behavior. We first established a mouse behavioral model for stress-induced binge-like eating behaviors. We found that mice exposed to stress increased their food intake of familiar palatable food (high fat, high sugar, HPD) compared to non-stressed mice. Following a brain-wide analysis, we isolated robust cFos-positive cells in the Claustrum (CLA), a subcortical structure with highly abundant KOR expression, following stress-induced binge-eating behavior. We report that KOR signaling in CLA is necessary for this elevated stress-induced binge eating behavior using local pharmacology and local deletion of KOR. In vivo calcium recordings using fiber photometry revealed a disinhibition circuit structure in the CLA during the initiation of HPD feeding bouts. We further established the dynamics of endogenous dynorphinergic control of this behavior using a genetically encoded dynorphin biosensor, Klight. Combined with 1-photon single-cell calcium imaging, we report significant heterogeneity with the CLA population during stress-induced binge eating and such behavior attenuates local dynorphin tone. Furthermore, we isolate the anterior Insular cortex (aIC) as the potential source of endogenous dynorphin afferents in the CLA. By characterizing neural circuits and peptidergic mechanisms within the CLA, we uncover a pathway that implicates endogenous opioid regulation stress-induced binge eating.
Dye-based Fluorescent Organic Nanoparticles, New Promising Tools for Optogenetics
Authors: Lesas Jeremy , Bienvenu Thomas , Kurek Eleonore , Verlhac Jean-Baptiste , Girard Delphine , Lanore Frédéric , Blanchard-Desce Mireille , Herry Cyril , Daniel Jonathan , Dejean Cyril
Published: June 2024

Dye-based fluorescent organic nanoparticles are a specific class of nanoparticles obtained by nanoprecipitation in water of pure dyes only. While the photophysical and colloidal properties of the nanoparticles strongly depend on the nature of the aggregated dyes, their excellent brightness in the visible and in the near infrared make these nanoparticles a unique and versatile platform for in vivo application. This article examines the promising utilization of these nanoparticles for in vivo optogenetics applications. Their photophysical properties as well as their biocompatibility and their capacity to activate Chrimson opsin in vivo through fluorescence reabsorption process are demonstrated. Additionally, an illustrative example of employing these nanoparticles in fear reduction in mice through close-loop stimulation is presented. Through an optogenetic methodology, the nanoparticles demonstrate an ability to selectively manipulate neurons implicated in the fear response and diminish the latter. Dye-based fluorescent organic nanoparticles represent a promising and innovative strategy for optogenetic applications, holding substantial potential in the domain of translational neuroscience. This work paves the way for novel therapeutic modalities for neurological and neuropsychiatric disorders.
Systemic and targeted activation of Nrf2 reverses doxorubicin-induced cognitive impairments and sensorimotor deficits in mice
Authors: Singh Anand Kumar , Ruiz David , Ur Rasheed Mohd Sami , Avery Thomas D. , Turner Dion J. L. , Abell Andrew D. , Grace Peter M.
Published: June 2024

While cancer survivorship has increased due to advances in treatments, chemotherapy often carries long-lived neurotoxic side effects which reduce quality of life. Commonly affected domains include memory, executive function, attention, processing speed and sensorimotor function, colloquially known as chemotherapy-induced cognitive impairment (CICI) or “chemobrain”. Oxidative stress and neuroimmune signaling in the brain have been mechanistically linked to the deleterious effects of chemotherapy on cognition and sensorimotor function. With this in mind, we tested if activation of the master regulator of antioxidant response nuclear factor E2-related factor 2 (Nrf2) alleviates cognitive and sensorimotor impairments induced by doxorubicin. The FDA-approved systemic Nrf2 activator, diroximel fumarate (DRF) was used, along with our recently developed prodrug1cwhich has the advantage of specifically releasing monomethyl fumarate at sites of oxidative stress. DRF and1cboth reversed doxorubicin-induced deficits in executive function, spatial and working memory, as well as decrements in fine motor coordination and grip strength, across both male and female mice. Both treatments reversed doxorubicin-induced loss of synaptic proteins and microglia phenotypic transition in the hippocampus. Doxorubicin-induced myelin damage in the corpus callosum was reversed by both Nrf2 activators. These results demonstrate the therapeutic potential of Nrf2 activators to reverse doxorubicin-induced cognitive impairments, motor incoordination, and associated structural and phenotypic changes in the brain. The localized release of monomethyl fumarate by1chas the potential to diminish unwanted effects of fumarates while retaining efficacy.
Neural correlates of retrieval success and precision: an fMRI study
Authors: Hou Mingzhu , Hill Paul F. , Aktas Ayse N. Z. , Ekstrom Arne D. , Rugg Michael D.
Published: June 2024

Prior studies examining the neural mechanisms underlying retrieval success and precision have yielded inconsistent results. Here, their neural correlates were examined using a memory task that assessed precision for spatial location. A sample of healthy young adults underwent fMRI scanning during a single study-test cycle. At study, participants viewed a series of object images, each placed at a randomly selected location on an imaginary circle. At test, studied images were intermixed with new images and presented to the participants. The requirement was to move a cursor to the location of the studied image, guessing if necessary. Participants then signaled whether the presented image as having been studied. Memory precision was quantified as the angle between the studied location and the location selected by the participant. A precision effect was evident in the left angular gyrus, where BOLD activity covaried across trials with location accuracy. Multi-voxel pattern analysis also revealed a significant item-level reinstatement effect for high-precision trials. There was no evidence of a retrieval success effect in the angular gyrus. BOLD activity in the hippocampus was insensitive to both success and precision. These findings are partially consistent with prior evidence that success and precision are dissociable features of memory retrieval.
Biochemical characterization of extended-spectrum β-lactamases fromAkkermansiagenus
Authors: Lin Jiafu , Wang Tiantian , Zhou Yaliang , Sha Jingzhou , Chen Xueke , Wang Wenjie , Zhang Chuan , Xie Feng , Chu Yiwen , Wang Xinrong , Luo Dan , Song Tao
Published: June 2024

Akkermansia muciniphila, a member of theVerrucomicrobiotaphylum, is recognized as a key gut microbe and has emerged as a potential next-generation probiotic. Assessment of antibiotic resistance in probiotics is a prerequisite for their therapeutic application, while very few is known inAkkermansiaspecies. Firstly, we screened eight representative class A β-lactamases (36.90%-41.30% identity with known β-lactamases) from theAkkermansiaspecies, which could increase the minimum inhibitory concentration (MIC) ofEscherichia colitoβ-lactams. Secondly, fourβ-lactamases were purified and identified as extended-spectrum β-lactamase because they exhibited hydrolase activity against 19 β-lactam antibiotics from penicillin, cephalosporins, and monobactam classes. Based on sequence alignment, three-dimensional structure, and binding pocket information, we hypothesized and validated that serine at 51 position was catalytic amino acid. Thirdly, the genomic context analysis revealed the absence of mobile genetic elements or other antibiotic resistance genes surrounding β-lactamase genes, suggesting that the β-lactamases fromAkkermansiaspecies may not be transferable. The finding and biochemical characterization of β-lactamase fromAkkermansiaspecies provide a foundational basis for the safety evaluation ofAkkermansiaspecies as probiotics.
Leveraging Artificial Intelligence to Mitigate Adolescent Risky Behaviors: A Scoping Review Protocol
Authors: Sadeghsalehi Hamidreza , Joulaei Hassan
Published: June 2024

Adolescents are particularly vulnerable to engaging in risky behaviors such as violence, unprotected sex, and substance abuse, which have significant negative impacts on their health and development. Recent advancements in artificial intelligence (AI) offer innovative solutions to address these behaviors, yet the evidence regarding the efficacy and implementation of AI-based interventions remains fragmented. This scoping review aims to systematically explore and map the literature on AI-based interventions designed to reduce risky behaviors among adolescents.

This review will follow the methodological frameworks outlined by Arksey and O’Malley (2005) and improved by Levac, Colquhoun, and O’Brien (2010), in line with the Joanna Briggs Institute guidelines. The PRISMA Extension for Scoping Reviews (PRISMA-ScR) will guide the reporting. The search strategy will be executed across PubMed, Scopus, Web of Science Core Collection, CINAHL, PsycINFO, Cochrane Central Register of Controlled Trials, Embase, SID, and Magiran, focusing on articles published up to June 2024 in English and Farsi. Titles and abstracts will be screened by two independent reviewers using Rayyan, followed by full-text screening of relevant studies. Data will be charted using a standardized form, and discrepancies will be resolved through discussion or by consulting a third reviewer. Data will be synthesized descriptively and presented in tables, figures, and diagrams.
Correlative light and electron microscopy for human brain and other biological models
Authors: Shafiei Notash , Stahli Daniel , Burger Domenic , Di Fabrizio Marta , Van den Heuvel Lukas , Daraspe Jean , Boing Carolin , Shahmoradian Sarah H , van de Berg Wilma D.J. , Genoud Christel , Stahlberg Henning , Lewis Amanda
Published: June 2024

Correlative light and electron microscopy (CLEM) combines light microscopy, for identifying a target via genetic labels, dyes, antibodies, and morphological features, with electron microscopy, for analyzing high-resolution subcellular ultrastructures. Here, we describe the step-by-step instructions to perform a CLEM experiment, optimized for the investigation of ultrastructural features in human brain tissue. The procedure is carried out at room-temperature and can be also adapted to other human and animal tissue samples. The procedure requires 8-days to complete and includes the stages of sample fixation for optimal ultrastructural preservation, immunofluorescence staining, image acquisition, multi-modal image correlation, and is executable within standard EM laboratories. Serving as a critical tool for characterizing human tissue and disease models, room-temperature CLEM facilitates the identification and quantification of subcellular morphological features across brain regions.