bluuebunny/crossref_metadata_2025 huggingface dataset:
Neural Correlates of Self-Referential Belief Processes
Authors: Bruns Emily , Scholz Immanuel , Koppe Georgia , Kirsch Peter , Gerchen Martin Fungisai
Published: October 2023

Background

Belief processing as well as self-referential processing have both been consistently associated with cortical midline structures. In addition, seminal neuroimaging papers have implicated cortical regions such as the vmPFC ingeneralbelief processing. However, the neural correlates ofself-referentialbelief are yet to be investigated in functional magnetic resonance imaging (fMRI).

Methods

In this fMRI study, we presented 120 statements with trait adjectives as target words to N=27 young healthy participants and asked them to judge whether they believed that these trait adjectives applied to themselves, a self-chosen close person, or a public person (the German chancellor at that time). Participants subsequently rated how certain (0-100%) they were in their judgment.

Results

As expected, self-referential processing evoked a large cluster in the vmPFC, ACC and dmPFC. For belief, we found an activated cluster in the vmPFC during statement presentation, which partly overlapped with the cluster for self-referential processing. The cluster for self-belief vs. disbelief was similar in location and size to the cluster for general belief processing and distinct from the cluster for self-referential processing. We also found dmPFC activation for uncertainty in belief evaluations.

Discussion

We successfully replicated vmPFC involvement in belief processing and found a common neural correlate for belief and self-belief in the vmPFC. The activation clusters for self-belief versus self-referential processing were distinct, implying distinct neural processes. This insight will prove relevant for investigations in clinical populations with aberrant (self-)belief processing. Furthermore, we replicated the role of the dmPFC in uncertainty, supporting a dual neural process model of belief and certainty.
High-resolution label-free transcranial imaging ofin vivoneural activity via interferometric measurement of tissue deformation
Authors: Lefebvre Austen T. , Rodriguez Carissa L. , Bar-Kochba Eyal , Steiner Nicole E. , Mirski Marek , Blodgett David W.
Published: October 2023

Rapid sub-nanometer neuronal deformations have been shown to occur as a consequence of action potentialsin vitro, allowing for registration of discrete axonal and synaptic depolarizations and thus providing a novel signature for recording neural activity (1–3). We demonstrate that this signature can be extended toin vivomeasurements through recording of rapid neuronal deformations on the population level with optical phase-based recordings. Complicating these measurements is the optical phase noise due to microvascular flow as well as the presence of significant tissue clutter (deformation) associated with physiologic processes (e.g., heart and respiratory rate). These recordings were acquired using a full-field holographic imaging system with spatiotemporal resolutions of less than 1 ms and 0.1 mm3over a 3 mm diameter field of view (FOV). Our system demonstrates, for the first time, the ability to non-invasively recordin vivotissue deformation associated with population level neuronal activity. We confirmed this technique across a range of neural activation models, including direct epidural focal electrical stimulation (FES), activation of primary somatosensory cortex via whisker barrel stimulation, and pharmacologically-induced seizures. Calibrated displacement measurements of the associated tissue deformations provided additional insight into the underlying neural activation mechanisms. Collectively, we show that holographic imaging provides a pathway for high-resolution, label-free, non-invasive recording of transcranialin vivoneural activity at depth, making it highly advantageous for studying neural function and signaling.
CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer
Authors: Khwaja Emaad , Song Yun S. , Agarunov Aaron , Huang Bo
Published: October 2023

We present CELL-E 2, a novel bidirectional transformer that can generate images depicting protein subcellular localization from the amino acid sequences (andvice versa). Protein localization is a challenging problem that requires integrating sequence and image information, which most existing methods ignore. CELL-E 2 extends the work of CELL-E, not only capturing the spatial complexity of protein localization and produce probability estimates of localization atop a nucleus image, but also being able to generate sequences from images, enablingde novoprotein design. We train and finetune CELL-E 2 on two large-scale datasets of human proteins. We also demonstrate how to use CELL-E 2 to create hundreds of novel nuclear localization signals (NLS). Results and interactive demos are featured athttps://bohuanglab.github.io/CELL-E_2/.
Cryo-EM structures of Aβ40 filaments from the leptomeninges of individuals with Alzheimer’s disease and cerebral amyloid angiopathy
Authors: Yang Yang , Murzin Alexey G. , Peak-Chew Sew , Franco Catarina , Newell Kathy L. , Ghetti Bernardino , Goedert Michel , Scheres Sjors H.W.
Published: October 2023

We used electron cryo-microscopy (cryo-EM) to determine the structures of Aβ40 filaments from the leptomeninges of individuals with Alzheimer’s disease and cerebral amyloid angiopathy. In agreement with previously reported structures, which were solved to a resolution of 4.4 Å, we found three types of filaments. However, our new structures, solved to a resolution of 2.4 Å resolution, revealed differences in the sequence assignment that redefine the fold of Aβ40 peptides and their interactions. Filaments are made of pairs of protofilaments, the ordered core of which comprises D1-G38. The different filament types comprise one, two or three protofilament pairs. In each pair, residues H14-G37 of both protofilaments adopt an extended conformation and pack against each other in an anti-parallel fashion, held together by hydrophobic interactions and hydrogen bonds between main chains and side chains. Residues D1-H13 fold back on the adjacent parts of their own chains through both polar and non-polar interactions. There are also several additional densities of unknown identity. Sarkosyl extraction and aqueous extraction gave the same structures. By cryo-EM, parenchymal deposits of Aβ42 and blood vessel deposits of Aβ40 have distinct structures, supporting the view that Alzheimer’s disease and cerebral amyloid angiopathy are different Aβ proteinopathies.
Early nuclear phenotypes and reactive transformation in human iPSC-derived astrocytes from ALS patients withSOD1mutations
Authors: Soubannier Vincent , Chaineau Mathilde , Gursu Lale , Lepine Sarah , Kalaydjian David , Haghi Ghazal , Rouleau Guy , Durcan Thomas M. , Stifani Stefano
Published: October 2023

Amyotrophic Lateral Sclerosis (ALS) is a neurodegenerative disease characterized by the progressive death of motor neurons (MNs). MN degeneration in ALS involves both cell-autonomous and non-cell autonomous mechanisms, with glial cells playing important roles in the latter. More specifically, astrocytes with mutations in the ALS-associated geneCu/Zn superoxide dismutase 1(SOD1) promote MN death. The mechanisms by whichSOD1-mutated astrocytes reduce MN survival are incompletely understood. In order to characterize the impact ofSOD1mutations on astrocyte physiology, we generated astrocytes from human induced pluripotent stem cell (iPSC) derived from ALS patients carryingSOD1mutations, together with control isogenic iPSCs. We report that astrocytes harbouringSOD1(A4V) andSOD1(D90A) mutations exhibit molecular and morphological changes indicative of reactive astrogliosis when compared to matching isogenic astrocytes. We show further that a number of nuclear phenotypes precede, or coincide with, reactive transformation. These include increased nuclear oxidative stress and DNA damage, and accumulation of the SOD1 protein in the nucleus. These findings reveal early cell-autonomous phenotypes inSOD1-mutated astrocytes that may contribute to the acquisition of a reactive phenotype involved in alterations of astrocyte-MN communication in ALS.
An integrated transcriptomic cell atlas of human neural organoids
Authors: He Zhisong , Dony Leander , Fleck Jonas Simon , Szałata Artur , Li Katelyn X. , Slišković Irena , Lin Hsiu-Chuan , Santel Malgorzata , Atamian Alexander , Quadrato Giorgia , Sun Jieran , Paşca Sergiu P. , Camp J. Gray , Theis Fabian , Treutlein Barbara
Published: October 2023

Neural tissues generated from human pluripotent stem cells in vitro (known as neural organoids) are becoming useful tools to study human brain development, evolution and disease. The characterization of neural organoids using single-cell genomic methods has revealed a large diversity of neural cell types with molecular signatures similar to those observed in primary human brain tissue. However, it is unclear which domains of the human nervous system are covered by existing protocols. It is also difficult to quantitatively assess variation between protocols and the specific cell states in organoids as compared to primary counterparts. Single-cell transcriptome data from primary tissue and neural organoids derived with guided or un-guided approaches and under diverse conditions combined with large-scale integrative analyses make it now possible to address these challenges. Recent advances in computational methodology enable the generation of integrated atlases across many data sets. Here, we integrated 36 single-cell transcriptomics data sets spanning 26 protocols into one integrated human neural organoid cell atlas (HNOCA) totaling over 1.7 million cells. We harmonize cell type annotations by incorporating reference data sets from the developing human brain. By mapping to the developing human brain reference, we reveal which primary cell states have been generated in vitro, and which are under-represented. We further compare transcriptomic profiles of neuronal populations in organoids to their counterparts in the developing human brain. To support rapid organoid phenotyping and quantitative assessment of new protocols, we provide a programmatic interface to browse the atlas and query new data sets, and showcase the power of the atlas to annotate new query data sets and evaluate new organoid protocols. Taken together, the HNOCA will be useful to assess the fidelity of organoids, characterize perturbed and diseased states and facilitate protocol development in the future.
Structural Insights into the Unexpected Agonism of Tetracyclic Antidepressants at Serotonin Receptors 5-HT1eR and 5-HT1FR
Authors: Zilberg Gregory , Parpounas Alexandra K. , Warren Audrey L. , Fiorillo Bianca , Provasi Davide , Filizola Marta , Wacker Daniel
Published: October 2023

Serotonin (5-hydroxytryptamine, 5-HT) acts via 13 different receptors in humans. Of these receptor subtypes, all but 5-HT1eR have confirmed roles in native tissue and are validated drug targets. Despite 5-HT1eR’s therapeutic potential and plausible druggability, the mechanisms of its activation remain elusive. To illuminate 5-HT1eR’s pharmacology in relation to the highly homologous 5-HT1FR, we screened a library of aminergic receptor ligands at both receptors and observe 5-HT1e/1FR agonism by multicyclic drugs described as pan-antagonists at 5-HT receptors. Potent agonism by tetracyclic antidepressants mianserin, setiptiline, and mirtazapine suggests a mechanism for their clinically observed anti-migraine properties. Using cryoEM and mutagenesis studies, we uncover and characterize unique agonist-like binding poses of mianserin and setiptiline at 5-HT1eR distinct from similar drug scaffolds in inactive-state 5-HTR structures. Together with computational studies, our data suggest that these binding poses alongside receptor-specific allosteric coupling in 5-HT1eR and 5-HT1FR contribute to the agonist activity of these antidepressants.
Trehalose-based coacervates for local bioactive protein delivery to the central nervous system
Authors: Hassan Laboni F , Sen Riya , O’Shea Timothy M
Published: October 2023

Therapeutic outcomes of local biomolecule delivery to the central nervous system (CNS) using bulk biomaterials are limited by inadequate drug loading, neuropil disruption, and severe foreign body responses. Effective CNS delivery requires addressing these issues and developing well-tolerated, highly-loaded carriers that are dispersible within local neural parenchyma. Here, we synthesized biodegradable trehalose-based polyelectrolyte oligomers using facile A2:B3:AR thiol-ene Michael addition reactions that form complex coacervates upon mixing of oppositely charged oligomers. Coacervates permit high concentration loading and controlled release of bioactive growth factors, enzymes, and antibodies, with modular formulation parameters that confer tunable release kinetics. Coacervates are cytocompatible with cultured neural cellsin vitroand can be formulated to either direct intracellular protein delivery or sequester media containing proteins and remain extracellular. Coacervates serve as effective vehicles for precisely delivering biomolecules, including bioactive neurotrophins, to the mouse striatum following intraparenchymal injection. These results support the use of trehalose-based coacervates as part of therapeutic protein delivery strategies for CNS disorders.
Collagen Tubular Airway-on-Chip for Extended Epithelial Culture and Investigation of Ventilation Dynamics
Authors: Gao Wuyang , Kanagarajah Kayshani R. , Graham Emma , Soon Kayla , Veres Teodor , Moraes Theo J. , Bear Christine E. , Veldhuizen Ruud A. , Wong Amy P. , Günther Axel
Published: October 2023

The lower respiratory tract is a hierarchical network of compliant tubular structures that are made from extracellular matrix proteins with a wall lined by an epithelium. While microfluidic airway-on-a-chip models incorporate the effects of shear and stretch on the epithelium, week-long air-liquid-interface (ALI) culture remains limited to static conditions. The circular cross-section and substrate compliance associated with intact airways have yet to be recapitulated to allow studies of epithelial injuries under physiological and ventilation conditions. To overcome these limitations, we present a collagen tube-based airway model. Sustaining a functional human bronchial epithelium during two-week perfusion is accomplished by continuously supplying warm, humid air at the apical side and culture medium at the basal side. The model faithfully recapitulates human airways in size, composition, and mechanical microenvironment, allowing for the first time dynamic studies of elastocapillary phenomena associated with regular breathing as well as mechanical ventilation, along with the impact on epithelial cells. Findings reveal the epithelium to become increasingly damaged when subjected to repetitive collapse and reopening as opposed to overdistension and suggest expiratory flow resistance to reduce atelectasis. We expect the model to find broad potential applications in organ-on-a-chip applications for various tubular tissues.
Genome-wide impact of codon usage bias on translation optimization inDrosophila melanogaster
Authors: Wu Xinkai , Yang Jian-Rong , Lu Jian
Published: October 2023

Accuracy and efficiency are fundamental characteristics of the translational process. Codon usage bias is widespread across species. Despite the long-standing association between codon optimization and improved translation, our understanding of the evolutionary basis and functional effects of codon optimization is limited.Drosophilahas been widely used to study codon usage bias, but genome-scale experimental data on codon optimization and translation are scarce. We examined high-resolution mass spectrometry datasets fromD. melanogasterdevelopment and employed different strategies to reduce bias when comparing translation error rates. We demonstrated that optimal codons have lower translation errors than nonoptimal codons after accounting for these biases. Our findings also shed light on codon-anticodon mismatches in translation errors. Through genomic-scale analysis of ribosome profiling data, we showed that optimal codons are translated more rapidly than nonoptimal codons inD. melanogaster. While we did not find conclusive evidence that natural selection favored synonymous mutations during the long-term evolution of theD. melanogaster lineage after its divergence fromD. simulans, we did find that positive selection drives codon optimization-related mutations in theD. melanogasterpopulation. This study expands our understanding of the functional consequences of codon optimization, and serves as a foundation for future investigations into the molecular mechanisms governing gene expression evolution at the translation level.
Regional specialization, polyploidy, and seminal fluid transcripts in the Drosophila female reproductive tract
Authors: Thayer Rachel C. , Polston Elizabeth S. , Xu Jixiang , Begun David J.
Published: October 2023

Internal fertilization requires the choreographed interaction of female cells and molecules with seminal fluid and sperm. In many animals, including insects, the female reproductive tract is physically subdivided into sections that carry out specialized functions. For example, females of many species have specialized organs for sperm storage.Drosophila melanogasteris a premier model system for investigating many aspects of animal reproduction. Nevertheless, in contrast to males, much of the basic biology of theD. melanogasterfemale reproductive tract remains poorly understood or completely unknown. Here we use single-cell RNA-seq data and in situ hybridization to reveal a rich and previously unknown female reproductive tract cell diversity, including widespread variation in ploidy levels. We find that many so-called seminal fluid protein genes appear to be transcribed in specialized cells of the female reproductive tract, motivating a re-evaluation of the functional and evolutionary biology of this major class of proteins.
Benchmarking AlphaMissense Pathogenicity Predictions Against Cystic Fibrosis Variants
Authors: McDonald Eli Fritz , Oliver Kathryn E. , Schlebach Jonathan P. , Meiler Jens , Plate Lars
Published: October 2023

Variants in the cystic fibrosis transmembrane conductance regulator gene (CFTR) result in cystic fibrosis – a lethal autosomal recessive disorder. Missense variants that alter a single amino acid in the CFTR protein are among the most common cystic fibrosis variants, yet tools for accurately predicting molecular consequences of missense variants have been limited to date. AlphaMissense (AM) is a new technology that predicts the pathogenicity of missense variants based on dual learned protein structure and evolutionary features. Here, we evaluated the ability of AM to predict the pathogenicity of CFTR missense variants. AM predicted a high pathogenicity for CFTR residues overall, resulting in a high false positive rate and fair classification performance on CF variants from theCFTR2.orgdatabase. AM pathogenicity score correlated modestly with pathogenicity metrics from persons with CF including sweat chloride level, pancreatic insufficiency rate, andPseudomonas aeruginosainfection rate. Correlation was also modest with CFTR trafficking and folding competencyin vitro. By contrast, the AM score correlated well with CFTR channel functionin vitro– demonstrating the dual structure and evolutionary training approach learns important functional information despite lacking such data during training. Different performance across metrics indicated AM may determine if polymorphisms in CFTR are recessive CF variants yet cannot differentiate mechanistic effects or the nature of pathophysiology. Finally, AM predictions offered limited utility to inform on the pharmacological response of CF variants i.e.,theratype. Development of new approaches to differentiate the biochemical and pharmacological properties of CFTR variants is therefore still needed to refine the targeting of emerging precision CF therapeutics.
Generating complex explanations from machine learning models using class-contrastive reasoning
Authors: Yang Yujia , Banerjee Soumya
Published: October 2023

Objective

One of the major limitations of most black-box machine learning models is the lack of explainability. In healthcare, explainability is important. Furthermore, most healthcare professionals do not have technical knowledge of machine learning. Consequently, it is necessary to translate the predictions of the machine learning model into an explainable narrative.

Our research focuses on the healthcare domain. The goal of this study is to generate complex explanations from a black-box machine learning model applied to heaalthcare.

Results

Class-contrastive techniques can be used to generate explanations. In this method, class-contrastive counterfactual reasoning is applied to a machine learning model on tabular data (in health-care). The model predictions are explained by observing the changes in prediction by altering the inputs. This is visualized using heatmaps (class-contrastive heatmaps). This approach displays prediction results as visualizations (heatmaps).

Our contribution is to extend class-contrastive analysis of black-box machine learning models to numeric features. Our work also allows machine learning scientists to visually inspect class-contrastive heatmaps and generate complex explanations for models. The resulting explanations (visual and text) are easier for non-technical people to follow.

We show how machine learning scientists can extract complex explanations from machine learning models which can be interpreted by nontechnical audiences. Our work may be broadly applicable in domains where explainability is important.
Assessing health equity in wastewater monitoring programs: Differences in the demographics and social vulnerability of sewered and unsewered populations across North Carolina
Authors: Hu Xindi C. , Reckling Stacie K. , Keshaviah Aparna
Published: October 2023

Background

Wastewater monitoring is a valuable tool to track community-level disease trends. However, the extent to which vulnerable populations have been included in statewide wastewater monitoring programs remains unstudied.

Objectives

We conducted a geospatial analysis to examine (1) the representativeness of wastewater data collected through the North Carolina Wastewater Monitoring Network as of June 2022, and (2) the potential of wastewater data to generalize to unsewered populations in the county.

Methods

After intersecting wastewater treatment plant (WWTP) service areas (sewersheds) with census block and tract boundaries for 38 WWTPs across 18 counties, we compared the demographics and social vulnerability of (1) people residing in sewersheds of monitored WWTPs with countywide and statewide populations, and (2) people connected to any sewer system—regardless of inclusion in wastewater monitoring—with unsewered populations. We flagged differences greater than +/-5 percentage points or percent (for categorical and continuous variables, respectively) and noted which were statistically significant (i.e., greater than twice the margin of error).

Results

As a whole, populations in monitored sewersheds resembled the statewide population on most demographics analyzed, with a few exceptions. When multiple WWTPs were monitored within a county, their combined service populations resembled the countywide population, although populations in individually monitored sewersheds sometimes differed from the countywide population. In nine counties for which we had comprehensive sewershed maps, we found that sewered residents had higher social vulnerability, a greater share of Hispanics and African Americans, lower income, and lower educational attainment than unsewered residents.

Discussion

Our results suggest that wastewater monitoring in North Carolina well represents the larger community. Ongoing analyses will be needed as sites are added or removed. The approach we present here can be used to ensure that wastewater surveillance programs nationwide are implemented in a manner that informs equitable public health decision-making.
Risk Factors for Sudden Cardiac Arrest and Ventricular Arrhythmias in Arrhythmogenic Mitral Valve Prolapse Syndrome
Authors: Chakrabarti Apurba , Giudicessi John R. , Ezzeddine Fatima M. , Delling Francesca N. , Dixit Shalini , Lee Yoo Jin , Muser Daniele , Magnani Silvia , Van Wijngaarden Aniek , Ajmone Marsan Nina , Miller Marc A. , Gandhi Jonathan , Trivieri Maria G. , Font Jonaz , Martins Raphael , McCaffrey James A. , Santangeli Pasquale , Marchlinski Francis E. , Chapagain Himal , Mathew Don , Kancharla Krishna , Syed Faisal F. , Abid Ahad , Cerbin Lukasz , Tzou Wendy S. , Garg Lohit , Della Rocca Domenico G. , Natale Andrea , Mohanty Sanghamitra , Sheldon Seth H. , Kuo Ling , Haugaa Kristina H. , Aabel Eivind W. , Enriquez Andres , Maeda Shingo , Deshmukh Amrish , Ghannam Michael , Bogun Frank M. , Ackerman Michael J. , Liang Jackson J.
Published: October 2023

Background

Patients with the arrhythmogenic mitral valve prolapse syndrome (AMVPS) are at increased risk for life-threatening ventricular arrhythmias (VAs), but studies have been limited by small sample sizes. We sought to assemble an international AMVPS registry to delineate clinical, imaging, treatment characteristics, and risk factors for sudden cardiac arrest (SCA).

Methods

We retrospectively identified two groups of subjects with AMVPS: 1) the MVP-SCA group with SCA, sustained ventricular tachycardia (VT), and ventricular fibrillation (VF); and 2) the MVP-PVC group with significant premature ventricular complexes (PVCs) only. Deidentified data was abstracted locally and combined centrally.

Results

We included 217 subjects with AMVPS: 148 (68%) had SCA or VT/VF (MVP-SCA group) and 69 (32%) had PVCs only (MVP-PVC group). Phenotypically, both groups were similar [mean age 44.2±16.7 years, 66% female, 76% with bileaflet prolapse, 55% with mitral annular disjunction (MAD)]. Syncope was more common in the MVP-SCA group than the MVP-PVC group (47% vs 22%, p=0.001) as were anterolateral T-wave inversions (TWIs, 22% vs 7%, p=0.011). Prior mitral valve surgery was less common in the MVP-SCA group (6% vs 20%, p=0.002). These differences remained significant after multivariable adjustment. An electrophysiology (EP) study was negative in 15/45 (33%) of the MVP-SCA subjects.

Conclusions

In this international registry, AMVPS subjects were young, female, and had bileaflet prolapse with MAD. A history of syncope and anterolateral TWIs were associated with SCA. Prior mitral valve surgery was less common in SCA subjects. A negative EP study had limited negative predictive value in high-risk patients.
Quantifying Adaptive Evolution of the Human Immune Cell Landscape
Authors: Salvador-Martínez Irepan , Murga-Moreno Jesus , Nieto Juan C. , Alsinet Clara , Enard David , Heyn Holger
Published: October 2023

The human immune system is under constant evolutionary pressure, primarily through its role as first line of defence against pathogens. Accordingly, population genomics studies have shown that immune-related genes have a high rate of adaptive evolution. These studies, however, are mainly based on protein-coding genes without cellular context, leaving the adaptive role of cell types and states uncharted. Inferring the rate of protein-coding genes adaptation in developing and adult immune cells at cellular resolution, we found cell types from both the lymphoid and myeloid compartments to harbour significantly increased adaptation rates. Specific cell states, such as foetal Pre-Pro B cells and adult T resident memory CD8+ cells show highly elevated rates of adaptation. We further analysed activated cell states, specifically, iPSC-derived macrophages responding to various challenges, including pro- and anti-inflammatory cytokines or bacterial and viral infections, the latter simulating the evolutionary arms race between humans and pathogens. Here, we found positive selection to be concentrated in early immune responses, suggesting benefits for the host to adapt to early stages of infection to control pathogen numbers and spread. Together, our study reveals spatio-temporal and functional biases in human immune populations with evidence of rapid adaptive evolution and provides a retrospect of forces that shaped the complexity, architecture, and function of the human body.
Reply to: Commentary on Pang et al. (2023) Nature
Authors: Pang James C. , Aquino Kevin M. , Oldehinkel Marianne , Robinson Peter A. , Fulcher Ben D. , Breakspear Michael , Fornito Alex
Published: October 2023

In Pang et al. (2023)1, we identified a close link between the geometry and function of the human brain by showing that: (1) eigenmodes derived from cortical geometry parsimoniously reconstruct activity patterns recorded with functional magnetic resonance imaging (fMRI); (2) task-evoked cortical activity results from excitations of brain-wide modes with long wavelengths; (3) wave dynamics, constrained by geometry and distance-dependent connectivity, can account for diverse aspects of spontaneous and evoked brain activity; and (4) geometry and function are strongly coupled in the subcortex. Faskowitz et al. (2023)2raise concerns about the framing of our paper and the specificity of the eigenmode reconstructions in result (1). Here, we address these concerns and show how specificity is established by using appropriate benchmarks.
Identification of secretory autophagy as a novel mechanism modulating activity-induced synaptic remodeling
Authors: Chang Yen-Ching , Gao Yuan , Lee Joo Yeun , Langen Jennifer , Chang Karen T.
Published: October 2023

The ability of neurons to rapidly remodel their synaptic structure and strength in response to neuronal activity is highly conserved across species and crucial for complex brain functions. However, mechanisms required to elicit and coordinate the acute, activity-dependent structural changes across synapses are not well understood. Here, using an RNAi screen inDrosophilaagainst genes affecting nervous system functions in humans, we uncouple cellular processes important for synaptic plasticity from synapse development. We find mutations associated with neurodegenerative and mental health disorders are 2-times more likely to affect activity-induced synaptic remodeling than synapse development. We further demonstrate that neuronal activity stimulates autophagy activation but diminishes degradative autophagy, thereby driving the pathway towards autophagy-based secretion. Presynaptic knockdown of Snap29, Sec22, or Rab8, proteins implicated in the secretory autophagy pathway, is sufficient to abolish activity-induced synaptic remodeling. This study uncovers secretory autophagy as a novel trans-synaptic signaling mechanism modulating structural plasticity.
Hybrid hydrogel-extracellular matrix scaffolds identify distinct ligand and mechanical signatures in cardiac aging
Authors: Sun Avery Rui , Ramli Md. Faris H. , Shen Xingyu , Chen Dixiao , Foo Roger S. , Zhu Jin , Ackers-Johnson Matthew , Young Jennifer L.
Published: October 2023

Extracellular matrix (ECM) remodeling of cardiac tissue is a key contributor to age-related cardiovascular disease and dysfunction. Aberrant secretion, structural perturbations, and degradation of specific ECM components lead to significant alterations in ECM properties that disrupt healthy cell and tissue homeostasis. These changes in ECM are multifaceted, as alterations in ligand presentation, including both biochemical and architectural aspects, are often accompanied by stiffness changes, clouding our understanding of how and which ECM properties contribute to a dysfunctional state. To identify the specific roles of these interconnected ECM cues and elucidate their mechanistic regulation in cellular function, we developed a material system that can independently present these two distinct matrix properties, i.e., ligand presentation and stiffness, to cultured cellsin vitro. We describe a decellularized ECM-synthetic hydrogel hybrid scaffold that maintains native matrix composition and organization of young or aged murine cardiac tissue with independently tunable scaffold mechanics that mimic young or aged tissue stiffness. Seeding these scaffolds with primary cardiac fibroblasts (CFs) from young or aged mice, we identify distinct age- and ECM-dependent mechanisms of CF activation. Importantly, we show that ligand presentation of young ECM can outweigh profibrotic stiffness cues typically present in aged ECM in maintaining or driving CF quiescence, thereby highlighting the unique roles of ECM in aging. Ultimately, these tunable scaffolds can enable the discovery of specific ECM targets to prevent aging dysfunction and promote rejuvenation.

DECIPHER:DECellularizedIn SituPolyacrylamideHydrogel-ECM hybRid
Modular RNA motifs for orthogonal phase separated compartments
Authors: Stewart Jaimie Marie , Li Shiyi , Tang Anli , Klocke Melissa Ann , Gobry Martin Vincent , Fabrini Giacomo , Di Michele Lorenzo , Rothemund Paul W.K. , Franco Elisa
Published: October 2023

Recent discoveries in biology have highlighted the importance of protein and RNA-based condensates as an alternative to classical membrane-bound organelles for the task of compartmentalizing molecules and biochemical reactions. Here, we demonstrate the rational design of pure RNA condensates from star-shaped RNA motifs. We generate condensates using two different RNA nanostar architectures: multi-stranded nanostars whose binding interactions are programmed via single-stranded overhangs, and single-stranded nanostars whose interactions are programmed via kissing loops. Through rational design of the nanostar interaction sequences, we demonstrate that both architectures can produce orthogonal (distinct and immiscible) condensates, which can be individually tracked via fluorogenic aptamers. We also show that aptamers make it possible to recruit peptides and proteins to the condensates with high specificity. Successful cotranscriptional formation of condensates from single-stranded nanostars suggests that they may be genetically encoded and produced in living cells. We provide a library of orthogonal RNA condensates that can be modularly customized and offer a route toward creating systems of functional artificial organelles.
Inhibition of the Eukaryotic Initiation Factor-2-α Kinase PERK Decreases Risk of Autoimmune Diabetes in Mice
Authors: Muralidharan Charanya , Huang Fei , Enriquez Jacob R. , Wang Jiayi E. , Nelson Jennifer B. , Nargis Titli , May Sarah C. , Chakraborty Advaita , Figatner Kayla T. , Navitskaya Svetlana , Anderson Cara M. , Calvo Veronica , Surguladze David , Mulvihill Mark J. , Yi Xiaoyan , Sarkar Soumyadeep , Oakes Scott A. , Webb-Robertson Bobbie-Jo M. , Sims Emily K. , Staschke Kirk A , Eizirik Decio L. , Nakayasu Ernesto S. , Stokes Michael E. , Tersey Sarah A. , Mirmira Raghavendra G.
Published: October 2023

Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress-responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eIF2α. In T1D, maladaptive unfolded protein response (UPR) in insulin-producing β cells renders these cells susceptible to autoimmunity. We show that inhibition of the eIF2α kinase PERK, a common component of the UPR and ISR, reverses the mRNA translation block in stressed human islets and delays the onset of diabetes, reduces islet inflammation, and preserves β cell mass in T1D-susceptible mice. Single-cell RNA sequencing of islets from PERK-inhibited mice shows reductions in the UPR and PERK signaling pathways and alterations in antigen processing and presentation pathways in β cells. Spatial proteomics of islets from these mice shows an increase in the immune checkpoint protein PD-L1 in β cells. Golgi membrane protein 1, whose levels increase following PERK inhibition in human islets and EndoC-βH1 human β cells, interacts with and stabilizes PD-L1. Collectively, our studies show that PERK activity enhances β cell immunogenicity, and inhibition of PERK may offer a strategy to prevent or delay the development of T1D.
Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals
Authors: Oh Jin Woo , Beer Michael A.
Published: October 2023

Gene regulatory elements drive many complex biological phenomena such as fetal development, and their mutations are linked to a multitude of common human diseases. The phenotypic impacts of regulatory variants are often tested using their conserved orthologous counterparts in model organisms such as mice. However, mapping human enhancers to conserved elements in mice remains a challenge, due to both rapid evolution of enhancers and limitations of current computational methods to detect conserved regulatory sequences. To improve upon existing computational methods and to better understand the sources of this apparent regulatory divergence, we comprehensively measured the evolutionary dynamics of distal enhancers across 45 matched human/mouse cell/tissue pairs from more than 1,000 DNase-seq experiments. Using this expansive dataset, we show that while cell-specific regulatory vocabulary is conserved, enhancers evolve more rapidly than other genomic elements such as promoters and CTCF binding sites. We observed surprisingly high levels of cell-specific variability in enhancer conservation rates, in part explainable by tissue specific transposable element activity. To improve orthologous enhancer mapping, we developed an improved genome alignment algorithm using gapped-kmer sequence features, and using the matched cell/tissue pairs, we show that this novel computational method,gkm-align, discovers 23,660 novel human/mouse conserved enhancers missed by standard alignment algorithms.
Pulsation waves along theCionaheart tube reverse by bimodal rhythms expressed by a remote pair of pacemakers
Authors: Fujikake Yuma , Fukuda Keita , Matsushita Katsuyoshi , Iwatani Yasushi , Fujimoto Koichi , Nishino Atsuo S.
Published: October 2023

The heart of ascidians, marine invertebrate chordates, exhibits a tubular structure, and heartbeats propagate from one end to the other. The direction of pulsation waves intermittently reverses in the heart of ascidians and their relatives; however, the underlying mechanisms remain unclear. We herein performed a series of experiments to characterize the pacemaker systems in isolated hearts and their fragments and applied a mathematical model to examine the conditions leading to heart reversals. The isolated heart ofCionasufficiently performed heart reversals, and experimental bisections of isolated hearts revealed that independent pacemakers resided on each side and also that their beating frequencies periodically changed as they expressed bimodal rhythms. Only fragments including 5% or shorter terminal regions of the heart tube maintained autonomous pulsation rhythms, whereas other regions did not. Our mathematical model, based on FitzHugh-Nagumo equations applied to a one-dimensional alignment of cells, demonstrated that the difference between frequencies expressed by the two independent terminal pacemakers determined the direction of propagated waves. Changes in the statuses of the terminal pacemakers between the excitatory and oscillatory modes as well as in their endogenous oscillation frequencies were sufficient to lead to heart reversals. These results suggest that the directions of pulsation waves in theCionaheart reverse according to the changing rhythms independently expressed by remotely coupled terminal pacemakers.

Summary statement

Pulsation waves traveling along the heart tube of the ascidianCionaintermittently reverse because of autonomous and periodical changes in beating frequencies at a pair of terminal pacemakers.
Sex-specific resilience of neocortex to food restriction
Authors: Padamsey Zahid , Katsanevaki Danai , Maeso Patricia , Rizzi Manuela , Osterweil Emily , Rochefort Nathalie L.
Published: October 2023

Mammals have evolved sex-specific adaptations to reduce energy usage in times of food scarcity. These adaptations are well described for peripheral tissue, though much less is known about how the energy-expensive brain adapts to food restriction, and how such adaptations differ across the sexes. Here, we examined how food restriction impacts energy usage and function in the primary visual cortex (V1) of adult male and female mice. Molecular analysis and RNA sequencing in V1 revealed that in males, but not in females, food restriction significantly modulated canonical, energy-regulating pathways, including pathways associated with AMP-activated protein kinase (AMPK), peroxisome proliferator-activated receptor alpha (PPARα), mammalian target of rapamycin (mTOR), and oxidative phosphorylation. Moreover, we found that in contrast to males, food restriction in females did not significantly affect V1 ATP usage or visual coding precision (assessed by orientation selectivity). Decreased serum leptin is known to be necessary for triggering energy-saving changes in V1 during food restriction. Consistent with this, we found significantly decreased serum leptin in food-restricted males but no significant change in food-restricted females. Collectively, our findings demonstrate that cortical function and energy usage in female mice are more resilient to food restriction than in males. The neocortex, therefore, contributes to sex-specific, energy-saving adaptations in response to metabolic challenge.
LRRK2 kinase inhibition reverses G2019S mutation-dependent effects on tau pathology spread
Authors: Lubben Noah , Brynildsen Julia K. , Webb Connor M. , Li Howard L. , Leyns Cheryl E. G. , Changolkar Lakshmi , Zhang Bin , Meymand Emily S. , O’Reilly Mia , Madaj Zach , DeWeerd Daniella , Fell Matthew J. , Lee Virginia M.Y. , Bassett Dani S. , Henderson Michael X.
Published: October 2023

Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson’s disease (PD). These mutations elevate LRRK2 kinase activity, making LRRK2 kinase inhibitors an attractive therapeutic target. LRRK2 kinase activity has been consistently linked to specific cell signaling pathways, mostly related to organelle trafficking and homeostasis, but its relationship to PD pathogenesis has been more difficult to define.LRRK2-PD patients consistently present with loss of dopaminergic neurons in the substantia nigra but show variable development of Lewy body or tau tangle pathology. Animal models carrying LRRK2 mutations do not develop robust PD-related phenotypes spontaneously, hampering the assessment of LRRK2 inhibitors’ efficacy against disease processes. We hypothesized that mutations in LRRK2 may not be directly related to a single disease pathway, but instead may elevate susceptibility to multiple disease processes, depending on the disease trigger. To test this hypothesis, we have previously evaluated progression of α-synuclein and tau pathologies following injection of proteopathic seeds. We demonstrated that transgenic mice overexpressing mutant LRRK2 show alterations in the brain-wide progression of pathology, especially at older ages. Here, we assess tau pathology progression in relation to long-term LRRK2 kinase inhibition. Wildtype or LRRK2G2019Sknock-in mice were injected with tau fibrils and treated with control diet or diet containing LRRK2 kinase inhibitor MLi-2 targeting the IC50 or IC90 of LRRK2 for 3 to 6 months. Mice were evaluated for tau pathology by brain-wide quantitative pathology in 665 brain regions and subsequent linear diffusion modeling of progression. Consistent with our previous work, we found systemic alterations in the progression of tau pathology in LRRK2G2019Smice that were most pronounced at 6 months. Importantly, LRRK2 kinase inhibition reversed these effects in LRRK2G2019Smice, but had minimal effect in wildtype mice, suggesting that LRRK2 kinase inhibition is likely to reverse specific disease processes in G2019S mutation carriers, but additional work may be necessary to determine the potential effect in non-carriers. This work supports a protective role of LRRK2 kinase inhibition in G2019S carriers and provides a rational workflow for systematic evaluation of brain-wide phenotypes in therapeutic development.
A metapopulation framework integrating landscape heterogeneity to model an airborne plant pathogen: the case of brown rot of peach in France
Authors: Radici Andrea , Martinetti Davide , Vanalli Chiara , Cunniffe Nik J. , Bevacqua Daniele
Published: October 2023

Plant disease dynamics are driven by the concurrent interplay of host susceptibility, pathogen presence, and environmental conditions. While host susceptibility and local environmental conditions can readily be characterised, the transmission of an airborne pathogen depends on the biotic and abiotic conditions of the surrounding environment.

Here, we propose an original metapopulation framework integrating landscape heterogeneity, in terms of climate and host density, where local populations of plant hosts are connected via air-masses which allow pathogen dispersal. We explicitly account for climatic drivers affecting pathogen release and survival while modelling aerial dispersal using Lagrangian simulations, as well as host phenology and infection. We calibrate the model parameters according to the literature and using Approximate Bayesian Computation against observations of brown rot incidence in French peach orchards from 2001-2020 across an area of 50,000km2. We used the model to produce maps of risk, distinguishing site dangerousness (risk of causing secondary infection in other sites) and vulnerability (risk of becoming infected) across the our study area.

We find that most dangerous and vulnerable sites are located along the Rhône Valley, due to the concurrence of high density of peach cultivation, a suitable climate and persistent airborne connections. Our work represents a first step to integrate metapopulation theory, epidemiology and air-mass movements to inform plant protection strategies, and could be adapted to optimize crop protection under future climate projections.
N-cadherin mechanosensing in ovarian follicles controls oocyte maturation and ovulation
Authors: Emery Alaknanda , Blaschuk Orest W. , Dinh Thao D. , McPhee Tim , Becker Rouven , Abell Andrew D. , Mrozik Krzysztof M. , Zannettino Andrew C.W. , Robker Rebecca L , Russell Darryl L
Published: October 2023

The cell adhesion molecule N-cadherin (CDH2) is a membrane component of adherens junctions which regulates tissue morphogenesis and architecture. In the follicles of mammalian ovaries, N-cadherin adherens junctions are present between granulosa cells, cumulus cells and at the interface of cumulus cell transzonal projections and the oocyte. We demonstrate a mechanosensory role of N-cadherin integrating tissue structure and hormonal regulation of follicular morphogenic events including expansion of the cumulus oocyte complex (COC) matrix, oocyte maturation and ovulation. Two small molecule N-cadherin antagonists inhibited COC maturationin vitro. Transcriptome profiling revealed that targets of β-catenin and YAP1 pathways were dysregulated by N-cadherin antagonists.In vivo, N-cadherin antagonist significantly reduced ovulation in mice compared to controls (11 vs 26 oocytes/ovary; p=5.8×10-6). Ovarian follicles exhibited structural dysgenesis with granulosa and cumulus cell layers becoming disorganised and the connection between cumulus cells and the oocyte disrupted and the transcriptome again indicated altered mechanical sensing causing dysregulation of the Hippo/YAP and β-catenin pathways and ECM reorganization. Granulosa specific N-cadherin depletion in Cdh2Fl/FL;Amhr2-Cre also showed significantly altered mechanosensitive gene expression and reduced ovulation. Our findings demonstrate a critical role for N-cadherin in ovarian follicular development and ovulation, and the potential to inhibit ovulation through targeting this signalling mechanism.