bluuebunny/crossref_metadata_2025 huggingface dataset:
Autophagy contributes to homeostasis in esophageal epithelium where high autophagic vesicle content marks basal cells with limited proliferation and enhanced self-renewal potential
Authors: Klochkova Alena , Karami Adam L. , Fuller Annie D. , Parham Louis R. , Panchani Surali R. , Natarajan Shruthi , Jackson Jazmyne L. , Mu Anbin , Tan Yinfei , Cai Kathy Q. , Klein-Szanto Andres J. , Muir Amanda B. , Tétreault Marie-Pier , Hamilton Kathryn E. , Whelan Kelly A.
Published: September 2023

Background & Aims

Autophagy has been demonstrated to play roles in esophageal pathologies both benign and malignant. Here, we aim to define the role of autophagy in esophageal epithelium under homeostatic conditions.

Methods

We generated tamoxifen-inducible, squamous epithelial-specificAtg7(autophagy related 7) conditional knockout mice to evaluate effects on esophageal homeostasis and response to the carcinogen 4-nitroquinoline 1-oxide (4NQO) using histological and biochemical analyses. We FACS sorted esophageal basal cells based upon fluorescence of the autophagic vesicle (AV)-identifying dye Cyto-ID, then subjected these cells to transmission electron microscopy, image flow cytometry, 3D organoid assays, RNA-Sequencing (RNA-Seq), and cell cycle analysis. 3D organoids were subjected to passaging, single cell (sc) RNA-Seq, cell cycle analysis, and immunostaining.

Results

Genetic autophagy inhibition in squamous epithelium resulted in increased proliferation of esophageal basal cells. Esophageal basal cells with high AV level (Cyto-IDHigh) displayed limited organoid formation capability upon initial plating but passaged more efficiently than their counterparts with low AV level (Cyto-IDLow). RNA-Seq suggested increased autophagy in Cyto- IDHighesophageal basal cells along with decreased cell cycle progression, the latter of which was confirmed by cell cycle analysis. scRNA-Seq of 3D organoids generated by Cyto-IDLowand Cyto- IDHighcells identified expansion of 3 cell populations, enrichment of G2/M-associated genes, and aberrant localization of cell cycle-associated genes beyond basal cell populations in the Cyto- IDHighgroup. Ki67 expression was also increased in organoids generated by Cyto-IDHighcells, including in cells beyond the basal cell layer. Squamous epithelial-specific autophagy inhibition induced significant weight loss in mice treated with 4NQO that further displayed perturbed epithelial tissue architecture.

Conclusions

High AV level identifies esophageal epithelium with limited proliferation and enhanced self-renewal capacity that contributes to maintenance of the esophageal proliferation- differentiation gradientin vivo.
Generalization of deep learning models for predicting spatial gene expression profiles using histology images: A breast cancer case study
Authors: Jiang Yuanhao , Xie Jacky , Tan Xiao , Ye Nan , Nguyen Quan
Published: September 2023

Spatial transcriptomics is a breakthrough technology that enables spatially-resolved measurement of molecular profiles in tissues, opening the opportunity for integrated analyses of morphology and transcriptional profiles through paired imaging and gene expression data. However, the high cost of generating data has limited its widespread adoption. Predicting gene expression profiles from histology images only can be an effective and cost-efficientin-silico spatial transcriptomicssolution but is computationally challenging and current methods are limited in model performance. To advance research in this emerging and important field, this study makes the following contributions. We first provide a systematic review of deep learning methods for predicting gene expression profiles from histology images, highlighting similarities and differences in algorithm, model architecture, and data processing pipelines. Second, we performed extensive experiments to evaluate the generalization performance of the reviewed methods on several spatial transcriptomics datasets for breast cancer, where the datasets are generated using different technologies. Lastly, we propose several ideas for model improvement and empirically investigate their effectiveness. Our results shed insight on key features in a neural network model that either improve or not the performance ofin-silico spatial transcriptomics, and we highlight challenges in developing algorithms with strong generalization performance.

Key Messages

We comprehensively compared the performance of existing methods for predicting spatial gene expression profiles from histology images

We assessed the roles of different algorithms, model architectures, and data processing pipelines to model performance

We performed extensive experiments to evaluate the generalization of the models on in-distribution and out-of-distribution spatial transcriptomics datasets

We proposed several strategies for improving existing models and empirically investigated their effectiveness
The precision of signals encoding active self-movement
Authors: Haynes Joshua D. , Gallagher Maria , Culling John F. , Freeman Tom C.A.
Published: September 2023

Everyday actions like moving the head, walking around and reaching out to grasp objects are typically self-controlled. This presents a problem when studying the signals encoding such actions because active self-movement is difficult to experimentally control. Available techniques demand repeatable trials, but each action is unique, making it difficult to measure fundamental properties like psychophysical thresholds. Here, we present a novel paradigm that can be used to recover both precision and bias of self-movement signals with minimal constraint on the participant. The paradigm takes care of a hidden source of external noise not previously accounted for in techniques that link display motion to self-movement in real time (e.g. virtual reality). We use head rotations as an example of self-movement, and show that the precision of the signals encoding head movement depends on whether they are being used to judge visual motion or auditory motion. We find perceived motion is slowed during head movement in both cases, indicating that the ‘non-image’ signals encoding active head rotation (motor commands, proprioception and vestibular cues) are biased to lower speeds and/or displacements. In a second experiment, we trained participants to rotate their heads at different rates and found that the precision of the head rotation signal rises proportionally with head speed (Weber’s Law). We discuss the findings in terms of the different motion cues used by vision and hearing, and the implications they have for Bayesian models of motion perception.

NEW AND NOTEWORTHY

We present a psychophysical technique for measuring the precision of signals encoding active self-movements. Using head movements, we show that: (1) precision declines when active head rotation is combined with auditory as opposed to visual motion; (2) precision rises with head speed (Weber’s Law); (3) perceived speed is lower during head movement. The findings may reflect the steps needed to convert different cues into common currencies, and challenge standard Bayesian models of motion perception.
Corticofugal oscillatory modulation of the cochlear receptor during auditory and visual attention in tinnitus
Authors: Martín Rodrigo Donoso-San , Leiva Alexis , Dragicevic Constantino D. , Medel Vicente , Delano Paul H.
Published: September 2023

The mechanisms underlying tinnitus perception are still under research. One of the proposed hypotheses involves an alteration in top-down processing of auditory activity. Low-frequency oscillations in the delta and theta bands have been recently described in brain and cochlear infrasonic signals during selective attention paradigms in normal hearing controls. Here, we propose that the top-down oscillatory activity observed in brain and cochlear signals during auditory and visual selective attention in normal subjects, is altered in tinnitus patients, reflecting an abnormal functioning of the corticofugal pathways that connect brain circuits with the cochlear receptor.Methods:To test this hypothesis, we used a behavioral task that alternates between auditory and visual top-down attention while we simultaneously measured electroencephalogram (EEG) and distortion-product otoacoustic emissions (DPOAE) signals in 14 tinnitus and 14 control subjects.Results:We found oscillatory activity in the delta and theta bands in cortical and cochlear channels in control and tinnitus patients. There were significant decreases in the DPOAE oscillatory amplitude during the visual attention period as compared to the auditory attention period in tinnitus and control groups, while frontal EEG oscillatory activity (Fz) was increased during the visual attention task only in the tinnitus group. The difference between auditory and visual DPOAE oscillatory power in the delta band was stronger in tinnitus individuals as compared to controls.Conclusions:These results confirm the presence of top-down infrasonic low-frequency cochlear oscillatory activity in the delta and theta bands in tinnitus patients. Our results show an increase in the EEG theta oscillatory power in frontal regions of tinnitus sufferers concomitant with a stronger corticofugal suppression of cochlear oscillations in the delta band during visual attention in tinnitus. These findings suggest an increased compensatory corticofugal inhibitory mechanism to the cochlear receptor in tinnitus.
Preictal dysfunctions of inhibitory interneurons paradoxically lead to their rebound hyperactivity and to Low-Voltage-Fast onset seizures in Dravet syndrome
Authors: Capitano Fabrizio , Kuchenbuch Mathieu , Lavigne Jennifer , Nabbout Rima , Mantegazza Massimo
Published: September 2023

Epilepsies have numerous specific mechanisms. Understanding neural dynamics leading to seizures is important for disclosing pathological mechanisms and developing targeted therapeutic approaches. We investigated electrographic activities and neural dynamics leading to convulsive seizures in patients and mouse models of Dravet syndrome (DS), a developmental and epileptic encephalopathy in which hypoexcitability of GABAergic neurons is considered to be the main dysfunction.

We analyzed EEGs from DS patients carrying aSCN1Apathogenic variant, as well as epidural electrocorticograms, hippocampal local field potentials and hippocampal single-unit neuronal activities inScn1a+/-knock-out andScn1aRH/+knock-in DS mice.

Strikingly, most seizures had low-voltage-fast onset in both patients and mice, which is thought to be generated by hyperactivity of GABAergic interneurons, the opposite of the main pathological mechanism of DS. Analyzing single unit recordings, we observed that temporal disorganization of the firing of putative interneurons in the period immediately before the seizure (preictal period) precedes the increase of their activity at seizure onset, together with the entire neuronal network. Moreover, we found early signatures of the preictal period in the spectral features of hippocampal and cortical field potential ofScn1amice and of patients’ EEG, which are consistent with the dysfunctions that we observed in single neurons.

Therefore, the perturbed preictal activity of interneurons leads to their hyperactivity at the onset of generalized seizures, which have low-voltage-fast features that are similar to those observed in other epilepsies and are triggered by hyperactivity of GABAergic neurons. Spectral features may be used as predictive seizure biomarker.

Significance statement

Dravet syndrome (DS) is caused by mutations of the NaV1.1 sodium channel (SCN1Agene) leading to hypoexcitability of GABAergic interneurons. We found that most of the seizures in both DS patients and mouse models have low-voltage-fast onset, which is instead thought to be generated by hyperactivity of GABAergic neurons. We disclosed a disorganization in the temporal pattern of the firing of single interneurons before the seizure (preictal period), and a rebound hyperactivity at seizure onset. Consistently, the electrographic signal showed a decrease of fast oscillations in the preictal period. Thus, perturbed interneurons’ preictal activity, consistent with the main mechanism of DS, leads to their hyperactivity at seizure onset and induces specific electrographic signatures that may be exploited for seizure prediction.
Enhanced Diffusion through Multivalency
Authors: Bartoš Ladislav , Lund Mikael , Vácha Robert
Published: September 2023

In multivalent systems, multiple ligands from one entity simultaneously bind to multiple receptors on another entity. These interactions are of crucial significance in a wide range of biological and technological mechanisms, encompassing selectivity, host recognition, viral penetration, therapeutic delivery, as well as the adhesion phenomena found in cells, polymers, and nanoparticles. In this study, we used computer simulations to investigate 1D and 2D diffusion of adsorbed particles with varying valency but with the same overall affinity to the host. We demonstrate a remarkable diffusion acceleration for particles with increasing valency. Non-diffusing monovalent particle can attain almost unrestricted diffusion when becoming multivalent while retaining its affinity for the host tether or surface. Moreover, diffusion of multivalent particles with rigid ligand distribution can be controlled by patterned host receptors. Our results have practical implications for the design of fast-diffusing particles that maintain a strong affinity for target surfaces or molecules.

TOC Graphic

Significance

We investigated how the number of binding sites (referred to as valency) on particles or entities impacts their movement when attached to surfaces or filaments. Valency can be understood as how many “hands” a particle has to grip the surface. Surprisingly, particles with more “hands” move faster if they hold onto the surface with the same strength. Furthermore, the motion of these particles can be controlled by designing surfaces with specific patterns that the “hands” can grasp. This means that we can design particles that move rapidly while remaining attached to the desired locations. These findings hold promise for applications like drug delivery and materials technology, and for understanding biological processes.
DJ-1 products glycolic acid and D-lactate restore deficient axonal trafficking and DNA damage response in FUS and SOD1-associated amyotrophic lateral sclerosis
Authors: Pal Arun , Grossmann Dajana , Glaß Hannes , Zimyanin Vitaly , Günther René , Catinozzi Marica , Boeckers Tobias M. , Sterneckert Jared , Storkebaum Erik , Petri Susanne , Wegner Florian , Grill Stefan , Pan-Montojo Francisco , Hermann Andreas
Published: September 2023

Amyotrophic Lateral Sclerosis (ALS) is the most common motor neuron disease leading to death within 2-5 years. Currently available drugs can only slightly prolong survival. Despite the progress that has been achieved in unravelling the molecular mechanisms of the disease so far, the underlying pathophysiology is not fully understood. We present novel insights into the pathophysiology ofSuperoxide Dismutase 1(SOD1)- and in particularFused In Sarcoma(FUS)-ALS by revealing a putatively central role of the Parkinson’s disease (PD) associated glyoxylase DJ-1 and its products glycolic acid (GA) and D-lactic acid (DL). Combined, but not single, treatment with GA and DL restored axonal trafficking deficits of mitochondria and lysosomes in FUS- and SOD1-ALS patient-derived motoneurons (MNs). This was accompanied by restoration of mitochondrial membrane potential as well as mitochondrial fragmentation (FUS-ALS) or elongation (SOD1-ALS). Furthermore, GA and DL restored cytoplasmic mislocalization of FUS and FUS recruitment to DNA damage sites. We further show that despite presenting an early axonal transport deficiency as well, TDP-43 patient-derived MNs did not share this mechanism. While this points towards the necessity of individualized (gene-) specific therapy stratification, it also suggests common therapeutic targets across different gene variants of ALS. Thus, we introduce a putative novel treatment for ALS based on a combination of the two substances GA and DL which might be not only an interesting novel drug candidate in subsets of ALS cases but also in other neurodegenerative diseases characterized by mitochondrial depolarization.
Label-free, real-time monitoring of membrane binding events at zeptomolar concentrations using frequency-locked optical microresonators
Authors: Gin Adley , Nguyen Phuong-Diem , Melzer Jeffrey E. , Li Cheng , Strzelinski Hannah , Liggett Stephen B. , Su Judith
Published: September 2023

Binding events to elements of the cell membrane act as receptors which regulate cellular function and communication and are the targets of many small molecule drug discovery efforts for agonists and antagonists. Conventional techniques to probe these interactions generally require labels and large amounts of receptor to achieve satisfactory sensitivity. Whispering gallery mode microtoroid optical resonators have demonstrated sensitivity to detect single-molecule binding events. Here, we demonstrate the use of frequency-locked optical microtoroids for characterization of membrane interactionsin vitroat zeptomolar concentrations using a supported biomimetic membrane. Arrays of microtoroids were produced using photolithography and subsequently modified with a biomimetic membrane, providing high quality (Q) factors (>106) in aqueous environments. Fluorescent recovery after photobleaching (FRAP) experiments confirmed the retained fluidity of the microtoroid supported-lipid membrane with a diffusion coefficient of 3.38 ± 0.26 μm2·s-1. Utilizing this frequency-locked membrane-on-a-chip model combined with auto-balanced detection and non-linear post-processing techniques, we demonstrate zeptomolar detection levels The binding of Cholera Toxin B-monosialotetrahexosyl ganglioside (GM1) was monitored in real-time, with an apparent equilibrium dissociation constant (kd) = 1.53 nM. The measured affiny of the agonist dynorphin A 1-13 to the κ-opioid receptor revealed a kd= 3.1 nM using the same approach. Radioligand binding competition with dynorphin A 1-13 revealed a Kdin agreement (1.1 nM) with the unlabeled method. The biosensing platform reported herein provides a highly sensitive real-time characterization of membrane embedded protein binding kinetics, that is rapid and label-free, for toxin screening and drug discovery, among other applications.
No support for the effect of tDCS on frontal alpha asymmetry and behavioral and brain activity indices of inhibitory control
Authors: Akil Atakan M. , Cserjési Renáta , Nagy Tamás , Demetrovics Zsolt , Németh Dezső , Logemann H.N. Alexander
Published: September 2023

Prior research links self-regulation failure to psychiatric disorders. While the left and right dorsolateral prefrontal cortices are associated with distinct components of self-regulation—approach and inhibitory systems, respectively—existing measures are considered indirect. Our preregistered study explored frontal alpha asymmetry (FAA) as a potential biomarker for self-regulation. We explored whether the assumed effects of transcranial direct current stimulation (tDCS) on behavioral and brain activity indices of inhibitory control are mediated through changes in FAA. We used a randomized controlled sham-feedback design with 65 healthy humans (46 females). Before and after 2 mA anodal tDCS on the right frontal site, we collected resting-state EEG data to assess FAA scores, and participants also completed a stop signal task with neutral and intrinsic reward (food) conditions. The tDCS had no impact on FAA or any behavioral or neural indices of inhibitory control. However, event-related potential analyses revealed a correlation between inhibitory brain activity in the reward condition and trait FAA. Higher right relative to left frontal brain activity was linked to lower early-onset inhibitory activity, possibly originating from the inferior Frontal Gyrus, but correlated with higher late-onset inhibitory control, presumably originating from the superior Frontal Gyrus. While tDCS yielded unexpected outcomes in FAA and inhibitory control metrics, we found an interesting dissociation regarding the lateralization of frontal brain activity and early and late onset inhibitory brain activity.
Insight into differing decision-making strategies that underlie cognitively effort-based decision making using computational modeling in rats
Authors: Hales Claire A. , Silveira Mason M. , Calderhead Lucas , Mortazavi Leili , Hathaway Brett A. , Winstanley Catharine A.
Published: September 2023

Rationale

The rat Cognitive Effort Task (rCET), a rodent model of cognitive rather than physical effort, requires animals to choose between an easy or hard visuospatial discrimination, with a correct hard choice more highly rewarded. Like in humans, there is stable individual variation in choice behavior. In previous reports, animals were divided into two groups - workers and slackers - based on their mean preference for the harder option. Although these groups differed in their response to pharmacological challenges, the rationale for using this criterion for grouping was not robust.

Methods

We collated experimental data from multiple cohorts of male and female rats performing the rCET, and used a model-based framework combining drift diffusion modeling with cluster analysis to identify the decision-making processes underlying variation in choice behavior.

Results

We verified that workers and slackers are statistically different groups, but also found distinct intra-group profiles. These subgroups exhibited dissociable performance during the attentional phase, linked to distinct decision-making profiles during choice. Reanalysis of previous pharmacology data using this model-based framework showed that serotonergic drug effects were explained by changes in decision boundaries and non-decision times, whilst scopolamine’s effects were driven by changes in decision starting points and rates of evidence accumulation.

Conclusions

Modeling revealed the decision-making processes that are associated with cognitive effort costs, and how these differ across individuals. Reanalysis of drug data provided insight into the mechanisms through which different neurotransmitter systems impact cognitively effortful attention and decision-making processes, with relevance to multiple psychiatric disorders.
Epithelial zonation along the mouse and human small intestine defines five discrete metabolic domains
Authors: Zwick Rachel K. , Kasparek Petr , Palikuqi Brisa , Viragova Sara , Weichselbaum Laura , McGinnis Christopher S. , McKinley Kara L. , Rathnayake Asoka , Vaka Dedeepya , Nguyen Vinh , Trentesaux Coralie , Reyes Efren , Gupta Alexander R. , Gartner Zev J. , Locksley Richard M. , Gardner James M. , Itzkovitz Shalev , Boffelli Dario , Klein Ophir D.
Published: September 2023

A key aspect of nutrient absorption is the exquisite division of labor across the length of the small intestine, with individual classes of micronutrients taken up at different positions. For millennia, the small intestine was thought to comprise three segments with indefinite borders: the duodenum, jejunum, and ileum. By examining fine-scale longitudinal segmentation of the mouse and human small intestines, we identified transcriptional signatures and upstream regulatory factors that define five domains of nutrient absorption, distinct from the three traditional sections. Spatially restricted expression programs were most prominent in nutrient-absorbing enterocytes but initially arose in intestinal stem cells residing in three regional populations. While a core signature was maintained across mice and humans with different diets and environments, domain properties were influenced by dietary changes. We established the functions ofPpar-ẟandCdx1in patterning lipid metabolism in distal domains and generated a predictive model of additional transcription factors that direct domain identity. Molecular domain identity can be detected with machine learning, representing the first systematic method to computationally identify specific intestinal regions in mice. These findings provide a foundational framework for the identity and control of longitudinal zonation of absorption along the proximal:distal small intestinal axis.
Impact of operational conditions on drinking water biofilm dynamics and coliform invasion potential
Authors: Waegenaar Fien , García-Timermans Cristina , Van Landuyt Josefien , De Gusseme Bart , Boon Nico
Published: September 2023

Biofilms within drinking water distribution systems serve as a habitat for drinking water microorganisms. However, biofilms can negatively impact drinking water quality by causing water discoloration and deterioration and can be a reservoir for unwanted microorganisms. In this study, we investigated whether indicator organisms for drinking water quality, such as coliforms, can settle in mature drinking water biofilms. Therefore, a biofilm monitor consisting of glass rings was used to grow and sample drinking water biofilms. Two mature drinking water biofilms were characterized by flow cytometry, ATP measurements, confocal laser scanning microscopy and 16S rRNA sequencing. Biofilms developed under treated chlorinated surface water supply exhibited lower cell densities in comparison with biofilms resulting from treated groundwater. Overall, the phenotypic as well as the genotypic characteristics were significantly different between both biofilms. In addition, the response of the biofilm microbiome and possible biofilm detachment after minor water quality changes were investigated. Limited changes in pH and free chlorine addition, to simulate operational changes that are relevant for practice, were evaluated. It was shown that both biofilms remained resilient. Finally, mature biofilms were prone to invasion of the coliform,Serratia fonticola. After spiking low concentrations (i.e. ± 100 cells/100 mL) of the coliform to the corresponding bulk water samples, the coliforms were able to attach and get established within the mature biofilms. These outcomes are emphasizing the need for continued research on biofilm detachment and its implications for water contamination in distribution networks.

Importance

The revelation that even low concentrations of coliforms can infiltrate into mature drinking water biofilms highlights a potential public health concern. Nowadays, the measurement of coliform bacteria is used as an indicator for fecal contamination and to control the effectiveness of disinfection processes and the cleanliness and integrity of distribution systems. In Flanders (Belgium), 533 out of 18840 measurements exceeded the established norm for the coliform indicator parameter in 2021, however, the source of microbial contamination is mostly unknown. Here, we showed that mature biofilms, are susceptible to invasion ofSerratia fonticola. These findings emphasize the importance of understanding and managing biofilms in drinking water distribution systems, not only for their potential to influence water quality, but also for their role in harboring and potentially disseminating pathogens. Further research into biofilm detachment, long-term responses to operational changes, and pathogen persistence within biofilms is crucial to inform strategies for safeguarding drinking water quality.
4D Mesoscale liquid model of nucleus resolves chromatin’s radial organization
Authors: Laghmach Rabia , Di Pierro Michele , Potoyan Davit A.
Published: September 2023

Recent chromatin capture, imaging techniques, and polymer modeling advancements have dramatically enhanced our quantitative understanding of chromosomal folding. However, the dynamism inherent in genome architectures due to physical and biochemical forces and their impact on nuclear architecture and cellular functions remains elusive. While imaging techniques capable of probing the physical properties of chromatin in 4D are growing, there is a conspicuous lack of physics-based computational tools appropriate for revealing the underlying forces that shape nuclear architecture and dynamics. To this end, we have developed a multi-phase liquid model of the nucleus, which can resolve chromosomal territories, compartments, and nuclear lamina using a physics-based and data-informed free energy function. The model enables rapid hypothesis-driven prototyping of nuclear dynamics in 4D, thereby facilitating comparison with whole nucleus imaging experiments. As an application, we model theDrosophilanucleus spanning the interphase and map phase diagram of nuclear morphologies. We shed light on the interplay of adhesive and cohesive interactions within the nucleus, giving rise to distinct radial organization seen in conventional, inverted, and senescent nuclear architectures. The results also show the highly dynamic nature of the radial organization, the disruption of which leads to significant variability in domain coarsening dynamics and, consequently, variability of chromatin architecture. The model also highlights the impact of oblate nuclear geometry and heterochromatin sub-type interactions on the global chromatin architecture and local asymmetry of chromatin compartments.
Exploring Neural Dynamics in Self-Voice Processing and Perception: Implications for Hallucination Proneness
Authors: Duggirala Suvarnalata Xanthate , Honcamp Hanna , Schwartze Michael , van Amelsvoort Therese , Pinheiro Ana P. , Linden David E. J. , Kotz Sonja A.
Published: September 2023

Altered sensory feedback processing and attention control are assumed to contribute to auditory verbal hallucinations, which are experienced by the general population and patients with psychosis, implying a continuum of hallucination proneness (HP). However, the interaction of altered sensory feedback processing and attention control along this HP continuum remains unclear. Manipulating the level of certainty of sensory feedback by changing self-voice quality (100% neutral, 60-40% neutral-angry, 50-50% neutral-angry, 40-60% neutral-angry, 100% angry) in individuals varying in HP, we tested this interaction using electroencephalography while participants self-generated or passively listened to their voices. Regardless of voice quality, HP modulated the N100 and P200 suppression effects. High HP individuals showed an increased N100 response to the self-generated voices and an increased P200 response for externally-generated voices. This may indicate increased error awareness and attention allocation in high HP individuals for self-voice generation stemming from altered sensory feedback processing, and/or attentional control. The current findings suggest that alterations of the sensory feedback processing in self-voice production are a fundamental characteristic of the continuum of HP, regardless of the clinical status of voice hearers.

Highlights

Altered N100 voice suppression in high HP, regardless of the clinical status.

High HP associated with altered sensory feedback processing and attentional control.

Current findings support a ‘neurophysiological’ continuum of HP.
Sparse and distributed cortical populations mediate sensorimotor integration
Authors: Pancholi Ravi , Sun-Yan Andrew , Laughton Maya , Peron Simon
Published: September 2023

Touch information is central to sensorimotor integration, yet little is known about how cortical touch and movement representations interact. Touch- and movement-related activity is present in both somatosensory and motor cortices, making both candidate sites for touch-motor interactions. We studied touch-motor interactions in layer 2/3 of the primary vibrissal somatosensory and motor cortices of behaving mice. Volumetric two-photon calcium imaging revealed robust responses to whisker touch, whisking, and licking in both areas. Touch activity was dominated by a sparse population of broadly tuned neurons responsive to multiple whiskers that exhibited longitudinal stability and disproportionately influenced interareal communication. Movement representations were similarly dominated by sparse, stable, reciprocally projecting populations. In both areas, many broadly tuned touch cells also produced robust licking or whisking responses. These touch-licking and touch-whisking neurons showed distinct dynamics suggestive of specific roles in shaping movement. Cortical touch-motor interactions are thus mediated by specialized populations of highly responsive, broadly tuned neurons.
Fusion-negative rhabdomyosarcoma orthotopic tongue xenografts for study of invasion, intravasation and metastasis in live animals
Authors: Hammoudeh Sarah M. , Ng Yeap , Wei Bih-Rong , Madsen Thomas D. , Simpson R. Mark , Weigert Roberto , Randazzo Paul A.
Published: September 2023

PAX3/7 Fusion-negative rhabdomyosarcoma (FN-RMS) is a childhood mesodermal lineage malignancy with a poor prognosis for metastatic or relapsed cases. Towards achieving a more complete understanding of advanced FN-RMS, we developed an orthotopic tongue xenograft model for studies of molecular basis of FN-RMS invasion and metastasis. The behavior of FN-RMS cells injected into murine tongue was examined using in vivo bioluminescence imaging, non-invasive intravital microscopy (IVM), and histopathology and compared to the prevailing hindlimb intramuscular and subcutaneous xenografts. FN-RMS cells were retained in the tongue and invaded locally into muscle mysial spaces and vascular lumen. While evidence of hematogenous dissemination to the lungs occurred in tongue and intramuscular xenografts, evidence of local invasion and lymphatic dissemination to lymph nodes only occurred in tongue xenografts. IVM and RNA-seq of tongue xenografts reveal shifts in cellular phenotype and differentiation state in tongue xenografts. IVM also shows homing to blood and lymphatic vessels, lymphatic intravasation, and dynamic membrane protrusions. Based on these findings, the tongue orthotopic xenograft of FN-RMS is a valuable model for tumor progression studies at the tissue, cellular and subcellular levels providing insight into kinetics and molecular bases of tumor invasion and metastasis and, hence, new therapeutic avenues for advanced FN-RMS.
Glutamate neurotransmission from leptin receptor cells is required for typical puberty and reproductive function in female mice
Authors: Sáenz de Miera Cristina , Bellefontaine Nicole , Allen Susan J. , Myers Martin G. , Elias Carol F.
Published: September 2023

The hypothalamic ventral premammillary nucleus (PMv) is a glutamatergic nucleus essential for the metabolic control of reproduction. However, conditional deletion of leptin receptor (LepRb) in vesicular glutamate transporter 2 (Vglut2) expressing neurons results in virtually no reproductive deficits. In this study, we determine the role of glutamatergic signaling from leptin responsive PMv neurons on puberty and fertility. We first assessed if stimulation of PMv neurons induces LH release in fed adult females. We used the stimulatory form of designer receptor exclusively activated by designer drugs (DREADDs) in LepRb-Cre mice. We collected blood sequentially before and for 1h after iv. clozapine-N-oxide injection. LH level increased in animals correctly targeted to the PMv, and LH level was correlated to the number of cFos immunoreactive neurons in the PMv. Next, females with deletion ofVglut2in LepRb neurons (LepRΔVGlut2) showed delayed age of puberty, disrupted estrous cycles, increased GnRH concentration in the axon terminals and disrupted LH responses, suggesting impaired GnRH release. To assess if glutamate is required for PMv actions in pubertal development, we generated a Cre-induced reexpression of endogenous LepRb (LepRloxTB)with concomitant deletion of Vglut2 (Vglut2-floxed) mice. Rescue of Lepr and deletion of Vglut2 in the PMv was obtained by stereotaxic injection of an adeno-associated virus vector expressing Cre recombinase. Control LepRloxTBmice with PMv LepRb rescue showed vaginal opening, follicle maturation and became pregnant, while LepRloxTB;Vglut2floxmice showed no pubertal development. Our results indicate that glutamatergic signaling from leptin sensitive neurons regulates the reproductive axis, and that leptin action on pubertal development via PMv neurons requires Vglut2.

SIGNIFICANCE STATEMENT

Age of puberty and reproductive function are strongly influenced by energy balance. Leptin is the primary metabolic hormone in reproductive control, but the neural circuitry involved is not fully understood. Previous studies have suggested that GABAergic but not glutamatergic neurotransmission is required for leptin action on reproduction. However, the PMv, a nucleus essential for the metabolic control of the reproductive function, densely expressesLeprand is essentially glutamatergic. Here we show that remote activation of leptin-responsive neurons in the PMv induces LH secretion, while deletion of glutamatergic neurotransmission in LepR (or PMv) neurons disrupts pubertal development and impairs the reproductive function in female mice. Our findings indicate that glutamate in LepR, and specifically in PMv, neurons is required for reproductive maturation and function.
KRAS inhibition activates an actionable CD24 ‘don’t eat me’ signal in pancreas cancer
Authors: Wei Yongkun , Liu Minghui , Yen Er-Yen , Yao Jun , Nguyen Phuoc T , Wang Xiaofei , Yang Zecheng , Yousef Abdelrahman , Pan Dean , Jin Yanqing , Theady Madelaine S. , Park Jungho , Cai Yiming , Takeda Mitsunobu , Vasquez Matthew , Zhou Yong , Zhao Hong , Viale Andrea , Wang Huamin , Zhao Dan , DePinho Ronald A. , Yao Wantong , Ying Haoqiang
Published: September 2023

KRASG12Cinhibitor (G12Ci) has produced encouraging, albeit modest and transient, clinical benefit in pancreatic ductal adenocarcinoma (PDAC). Identifying and targeting resistance mechanisms to G12Ci treatment is therefore crucial. To better understand the tumor biology of the KRASG12Callele and possible bypass mechanisms, we developed a novel autochthonous KRASG12C-driven PDAC model. Compared to the classical KRASG12DPDAC model, the G12C model exhibit slower tumor growth, yet similar histopathological and molecular features. Aligned with clinical experience, G12Ci treatment of KRASG12Ctumors produced modest impact despite stimulating a ‘hot’ tumor immune microenvironment. Immunoprofiling revealed that CD24, a ‘do-not-eat-me’ signal, is significantly upregulated on cancer cells upon G12Ci treatment. Blocking CD24 enhanced macrophage phagocytosis of cancer cells and significantly sensitized tumors to G12Ci treatment. Similar findings were observed in KRASG12D-driven PDAC. Our study reveals common and distinct oncogenic KRAS allele-specific biology and identifies a clinically actionable adaptive mechanism that may improve the efficacy of oncogenic KRAS inhibitor therapy in PDAC.

Significance

Lack of faithful preclinical models limits the exploration of resistance mechanisms to KRASG12Cinhibitor in PDAC. We generated an autochthonous KRASG12C-driven PDAC model, which revealed allele-specific biology of the KRASG12Cduring PDAC development. We identified CD24 as an actionable adaptive mechanisms in cancer cells induced upon KRASG12Cinhibition and blocking CD24 sensitizes PDAC to KRAS inhibitors in preclinical models.
Inter-organellar nucleic acid communication by a mitochondrial tRNA regulates nuclear metabolic transcription
Authors: Rouya Christopher , Yambire King Faisal , Derbyshire Mark L. , Alwaseem Hanan , Tavazoie Sohail F.
Published: September 2023

Efficient communication between mitochondria and the nucleus underlies homoeostatic metabolic control, though the involved mitochondrial factors and their mechanisms are poorly defined. Here, we report the surprising detection of multiple mitochondrial-derived transfer RNAs (mito-tRNAs) within the nuclei of human cells. Focused studies of nuclear-transported mito-tRNA-asparagine (mtAsn) revealed that its cognate charging enzyme (NARS2) is also present in the nucleus. MtAsn promoted interaction of NARS2 with histone deacetylase 2 (HDAC2), and repressed HDAC2 association with specific chromatin loci. Perturbation of this axis using antisense oligonucleotides promoted nucleotide biogenesis and enhanced breast cancer growth, and RNA and nascent transcript sequencing demonstrated specific alterations in the transcription of nuclear genes. These findings uncover nucleic-acid mediated communication between two organelles and the existence of a machinery for nuclear gene regulation by a mito-tRNA that restricts tumor growth through metabolic control.

Highlights

Multiple mitochondrial-derived tRNAs are detected in human cell nuclei

MtAsn promotes binding between NARS2 and HDAC2

Metabolic alterations driven by mtAsn impact cell proliferation

MtAsn inhibition releases HDAC2 to bind and transcriptionally regulate multiple nuclear genes
Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes
Authors: Overgaard Christina Karmisholt , Jamy Mahwash , Radutoiu Simona , Burki Fabien , Dueholm Morten Kam Dahl
Published: September 2023

The use of short-read metabarcoding for classifying microeukaryotes is challenged by the lack of comprehensive 18S rRNA reference databases. While recent advances in high-throughput long-read sequencing provide the potential to greatly increase the phylogenetic coverage of these databases, the performance of different sequencing technologies and subsequent bioinformatics processing remain to be evaluated, primarily because of the absence of well-defined eukaryotic mock communities. To address this challenge, we created a eukaryotic rRNA operons clone-library and turned it into a precisely defined synthetic eukaryotic mock community. This mock community was then used to evaluate the performance of three long-read sequencing techniques (PacBio HiFi, and Nanopore UMI with/without clonal pre-amplification) and three tools for resolving amplicons sequence variants (ASVs) (Uchime3, Unoise3, and DADA2). We investigated the sensitivity of the sequencing techniques based on the number of detected mock taxa, and the accuracy of the different ASV-calling tools with a specific focus on the presence of chimera among the final rRNA operon ASVs. Based on our findings, we provide recommendations and best practice protocols for how to cost-effectively obtain essential error-free rRNA operons in high-throughput. An agricultural soil sample was used to demonstrate that the sequencing and bioinformatic results from the mock community also translates to highly diverse natural samples.
Targeted hypermutation of putative antigen sensors in multicellular bacteria
Authors: Doré H. , Eisenberg A. R. , Junkins E. N. , Leventhal G. E. , Ganesh Anakha , Cordero O. X. , Paul B. G. , Valentine D. , O’Malley M. A. , Wilbanks E. G.
Published: September 2023

Diversity-generating retroelements (DGRs) are used by bacteria, archaea and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remains elusive. We find that 85% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacteriumThiohalocapsasp. PB-PSB1 as an example, we characterized nine distinct DGR loci that cumulatively lead to more than 10294possible different combinations of target polypeptides. With environmental metagenomes from individualThiohalocapsaaggregates, we show that most of PB-PSB1’s DGR targets are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In PSB1 and other members of this lineage of cellular DGRs, diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified target genes act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia. These findings have implications for the emergence of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans.

Significance

To defend themselves against predators, bacteria employ a wide range of conflict systems, some of which are enriched in multicellular bacteria. Here, we show that numerous multicellular bacteria use related diversity-generating retroelements (DGRs) to diversify such conflict systems. Error-prone reverse transcription in DGRs introduces random, targeted mutations and rapid diversification. We usedThiohalocapsaPB-PSB1, a member of multicellular bacterial consortia, as a model to study this association between conflict systems and DGRs. We characterized the natural diversity of PB-PSB1 DGRs and propose they function as hypervariable antigen sensors. The accumulation of such DGR-diversified defense systems in multicellular bacteria emphasizes the fitness advantage of a rapidly diversifying immune system for the evolution of multicellularity.
Epileptic responses in marmosets induced by knockdown of CREB Regulated Transcription Coactivator 1 (CRTC1)
Authors: Nakagami Yuki , Komatsu Misako , Nakae Ken , Otsuka Masanari , Hata Junichi , Mizukami Hiroaki , Takemori Hiroshi , Ishii Shin , Okano Hideyuki , Watakabe Akiya , Yamamori Tetsuo
Published: September 2023

Animal models have contributed greatly to the development of anticonvulsant drugs. However, 20-30% of epilepsy patients still do not achieve adequate seizure control. It is important to understand the biological mechanisms of epilepsy in order to develop treatments and novel anticonvulsant drugs. Here we reportCRTC1knockdown (KD) induced abnormalcFOSexpression beyond the injection sites followed by epileptic response by three local injections of short hairpin RNA (shRNA) in marmoset V1. Longitudinal monitoring of cortical-wide neural activity revealed transient changes in high frequency oscillations by cortical electrocorticography throughout the cortex, and a lesion in the temporal lobe was observed by MRI and postmortem histology.shCRTC1KD marmosets showed severe lesions surrounding the injection site several months after injection. Glial cell activation may occur simultaneously or prior to IEG induction aftershCRTC1injection. Thus, the epileptic process from seizure onset to remission can be studied in this animal model.