bluuebunny/crossref_metadata_2025 huggingface dataset:
Deciphering interplay between biology and physics: finite element method-implemented vertex organoid model raises the challenge
Authors: Laussu J. , Michel D. , Magne L. , Segonds S. , Marguet S. , Hamel D. , Quaranta-Nicaise M. , Barreau F. , Mas E. , Velay V. , Bugarin F. , Ferrand A.
Published: May 2023

Understanding the intertwining of biology and mechanics in tissue architecture is a challenging issue, especially when it comes to the 3D tissue organization. Addressing this challenge requires both a biological model allowing multiscale observations from the cell to the tissue, and theoretical and computational approaches allowing the generation of a synthetic model, relevant to the biological model, and allowing access to the mechanical constraints experienced by the tissue.

Here, using human colon epithelium monolayer organoid as biological model, and combining vertex and FEM approaches, we generated a comprehensive elastic finite element model of the human colon organoid and demonstrated its flexibility. This FEM model provides a basis for relating cell shape, tissue deformation, and strain at the cellular level due to imposed stresses.

In conclusion, we demonstrated that the combination of vertex and FEM approaches allows for better modeling of the alteration of organoid morphology over time and better assessment of the mechanical cues involved in establishing the architecture of the human colon epithelium.
Synthetic Cooling Agent and Candy Flavors in California-marketed “non-Menthol” Cigarettes
Authors: Jabba Sairam V. , Erythropel Hanno C. , Anastas Paul T. , Zimmerman Julie B. , Jordt Sven E.
Published: May 2023

RATIONALE

The ban of menthol cigarettes is one of the key strategies to promote smoking cessation in the United States. Menthol cigarettes are preferred by young beginning smokers for smoking initiation. Almost 90% of African American smokers use menthol cigarettes, a result of decades-long targeted industry marketing. Several states and municipalities already banned menthol cigarettes, most recently California, effective on December 21, 2022. In the weeks before California’s ban took effect, the tobacco industry introduced several “non-menthol” cigarette products in California, replacing previously mentholated brands. Here, we hypothesize that tobacco companies replaced menthol with synthetic cooling agents to create a cooling effect without using menthol. Similar to menthol, these agents activate the TRPM8 cold-menthol receptor in sensory neurons innervating the upper and lower airways.

METHODS

Calcium microfluorimetry in HEK293t cells expressing the TRPM8 cold/menthol receptors was used to determine sensory cooling activity of extracts prepared from these “non-menthol” cigarette brands, and compared to standard menthol cigarette extracts of the same brands. Specificity of receptor activity was validated using TRPM8-selective inhibitor, AMTB. Gas chromatography mass spectrometry (GCMS) was used to determine presence and amounts of any flavoring chemicals, including synthetic cooling agents, in the tobacco rods, wrapping paper, filters and crushable capsule (if present) of these “non-menthol” cigarettes.

RESULTS

Compared to equivalent menthol cigarette extracts, several California-marketed “non-menthol” cigarette extracts activated cold/menthol receptor TRPM8 at higher dilutions and with stronger efficacies, indicating substantial pharmacological activity to elicit robust cooling sensations. Synthetic cooling agent, WS-3, was detected in tobacco rods of several of these “non-menthol” cigarette brands. Crushable capsules added to certain “non-menthol” crush varieties contained neither WS-3 nor menthol but included several “sweet” flavorant chemicals, including vanillin, ethyl vanillin and anethole.

CONCLUSION

Tobacco companies have replaced menthol with the synthetic cooling agent, WS-3, in California-marketed “non-menthol” cigarettes. WS-3 creates a cooling sensation similar to menthol, but lacks menthol’s characteristic “minty” odor. The measured WS-3 content is sufficient to elicit cooling sensations in smokers, similar to menthol, that facilitate smoking initiation and act as a reinforcing cue. Regulators need to act quickly to prevent the tobacco industry from bypassing menthol bans by substituting menthol with synthetic cooling agents, and thereby thwarting smoking cessation efforts.
Minimal effective dose of oral bedaquiline and activity of a long acting formulation of bedaquiline in the murine model of leprosy Bedaquiline for the treatment of leprosy
Authors: Chauffour Aurélie , Lounis Nacer , Andries Koen , Jarlier Vincent , Veziris Nicolas , Aubry Alexandra
Published: May 2023

Background

Bedaquiline (BDQ), by targeting the electron transport chain and having a long half-life, is a good candidate to simplify leprosy treatment. Our objectives were to (i) determine the minimal effective dose (MED) of oral BDQ, (ii) evaluate the benefit of adding another inhibitor of the respiratory chain to oral BDQ (i.e.clofazimine (CFZ)) and (iii) evaluate the benefit of an intramuscular injectable long-acting formulation of BDQ (intramuscular BDQ; BDQ-LA IM), in a murine model of leprosy.

Methodology/ Principal Findings

To determine the MED of oral BDQ and the benefit of adding CFZ, 100 four-week-old female nude mice were inoculated in the footpads with 5.103bacilli ofM. lepraestrain THAI53. Mice were randomly allocated into: 1 untreated group, 5 groups treated with oral BDQ (0.10 to 25 mg/kg), 3 groups treated with CFZ 20 mg/kg alone or combined with oral BDQ 0.10 or 0.33 mg/kg, and 1 group treated with rifampicin (RIF) 10 mg/kg. Mice were treated 5 days a week during 24 weeks.

To evaluate the benefit of the BDQ-LA IM, 340 four-week-old female Swiss mice were inoculated in the footpads with 5.103to 5.101bacilli (or 5.100for the untreated control group) ofM. lepraestrain THAI53. Mice were randomly allocated into the following 11 groups treated with a single dose (SD) or 3 doses (3D) 24h after the inoculation: 1 untreated group, 2 treated with RIF 10 mg/kg SD or 3D, 8 treated with oral BDQ or BDQ-LA IM 2 or 20 mg/kg, SD or 3D.

Twelve months later, mice were sacrificed andM. lepraebacilli enumerated in the footpad. All the footpads became negative with BDQ at 3.3 mg/kg. The MED of oral BDQ againstM. lepraein this model is therefore 3.3 mg/kg. The addition of CFZ to a dose of BDQ 10-fold lower than this MED increased the bactericidal activity of BDQ suggesting synergies between both drugs. The BDQ-LA IM displayed similar or lower bactericidal activity than the oral BDQ.

Conclusion

We demonstrated that the MED of oral BDQ againstM. lepraewas 3.3 mg/kg in mice and the addition of CFZ to oral BDQ may improve the efficacy of BDQ. BDQ-LA IM was similar or less active than oral BDQ at equivalent dosing and frequency but should be tested at higher dosing in order to reach equivalent exposure in further experiments.
Investigating mitochondrial gene expression patterns inDrosophila melanogasterusing network analysis to understand aging mechanisms
Authors: Mangoni Manuel , Petrizzelli Francesco , Liorni Niccolò , Bianco Salvatore Daniele , Biagini Tommaso , Napoli Alessandro , Adinolfi Marta , Guzzi Pietro Hiram , Novelli Antonio , Caputo Viviana , Mazza Tommaso
Published: May 2023

The process of aging is a complex phenomenon that involves a progressive decline in physiological functions required for survival and fertility. To better understand the mechanisms underlying this process, the scientific community has utilized several tools. Among them, mitochondrial DNA has emerged as a crucial factor in biological aging, given that mitochondrial dysfunction is thought to significantly contribute to this phenomenon. Additionally,Drosophila melanogasterhas proven to be a valuable model organism for studying aging due to its low cost, capacity to generate large populations, and ease of genetic manipulation and tissue dissection. Moreover, graph theory has been employed to understand the dynamic changes in gene expression patterns associated with aging and to investigate the interactions between aging and aging-related diseases. In this study, we have integrated these approaches to examine the patterns of gene co-expression inDrosophila melanogasterat various stages of development. By applying graph-theory techniques, we have identified modules of co-expressing genes, highlighting those that contain a significantly high number of mitochondrial genes. We found important mitochondrial genes involved in aging and age-related diseases inDrosophila melanogaster, including UQCR-C1, ND-B17.2, ND-20, and Pdhb. Our findings shed light on the role of mitochondrial genes in the aging process and demonstrate the utility ofDrosophila melanogasteras a model organism and graph theory in aging research.
Benchmarking of Hi-C tools for scaffolding de novo genome assemblies
Authors: Obinu Lia , Trivedi Urmi , Porceddu Andrea
Published: May 2023

The implementation of Hi-C reads in thede novogenome assembly allows to order large regions of the genome in scaffolds, obtaining chromosome-level assemblies. Several bioinformatics tools have been developed for genome scaffolding with Hi-C, and all have pros and cons which need to be carefully evaluated before adoption.

We developed assemblyQC, a bash pipeline that combines QUAST, BUSCO, Merqury and, optionally, Liftoff, plus a gene positioning validation script to evaluate and benchmark the performance of three scaffolders, 3d-dna, SALSA2, and YaHS, on two de novo assembly of Arabidopsis thaliana obtained from the same raw PacBio HiFi and ONT data.

In our analysis, YaHS proved to be the best-performing bioinformatic tool for scaffolding ofde novogenome assembly.
ExMove: An open-source toolkit for processing and exploring animal tracking data in R
Authors: Langley Liam Patrick , Lang Stephen , Ozsanlav-Harris Luke , Trevail Alice
Published: May 2023

Ongoing technological advances have led to a rapid increase in the number, type, and scope of animal tracking studies. In response, many software tools have been developed to analyse animal movement data. These tools generally focus on movement modelling, but the steps required to clean raw data files from different tracking devices have been largely ignored. Such pre-processing steps are often time-consuming and involve a steep learning curve but are crucial for the creation of high quality, standardised, and shareable data. Moreover, decisions made at this early stage can substantially influence subsequent analyses, and in the current age of reproducibility crisis, the transparency of this process is vital.

Here we present an open-access, reproducible toolkit written in the programming language R for processing raw data files into a single cleaned data set for analyses and upload to online tracking databases (found here:https://github.com/ExMove/ExMove). The toolkit comprises well documented and flexible code to facilitate data processing and user understanding, both of which can increase user confidence and improve the uptake of sharing open and reproducible code. Additionally, we provide an overview website (found here:https://exmove.github.io/) and a Shiny app to help users visualise tracking data and assist with parameter determination during data cleaning.

The toolkit is generalisable to different data formats and device types, uses modern ‘tidy coding’ practices, and relies on few well-maintained packages. Amongst these, we perform spatial manipulations using the packagesf, providing a timely resource for movement ecologists following the recent deprecation of the widely-usedsppackage.

Overall, by collating all required steps from data collection to archiving on open access databases into a single, robust pipeline, our toolkit provides a valuable resource for anyone conducting animal movement analyses and represents an important step towards increased standardisation and reproducibility in animal movement ecology.
Distinct Local and Global Functions of Aβ Low-Threshold Mechanoreceptors in Mechanical Pain Transmission
Authors: Gautam Mayank , Yamada Akihiro , Yamada Ayaka I , Wu Qinxue , Kridsada Kim , Ling Jennifer , Yu Huasheng , Dong Peter , Ma Minghong , Gu Jianguo , Luo Wenqin
Published: May 2023

The roles of Aβ low-threshold mechanoreceptors (LTMRs) in transmitting mechanical hyperalgesia and in alleviating chronic pain have been of great interest but remain contentious. Here we utilized intersectional genetic tools, optogenetics, and high-speed imaging to specifically examine functions ofSplitCrelabeled Aβ-LTMRs in this regard. Genetic ablation of SplitCre-Aβ-LTMRs increased mechanical pain but not thermosensation in both acute and chronic inflammatory pain conditions, indicating their modality-specific role in gating mechanical pain transmission. Local optogenetic activation of SplitCre-Aβ-LTMRs triggered nociception after tissue inflammation, whereas their broad activation at the dorsal column still alleviated mechanical hypersensitivity of chronic inflammation. Taking all data into consideration, we propose a new model, in which Aβ-LTMRs play distinctive local and global roles in transmitting and alleviating mechanical hyperalgesia of chronic pain, respectively. Our model suggests a new strategy of global activation plus local inhibition of Aβ-LTMRs for treating mechanical hyperalgesia.
Effects of junk-food on food-motivated behavior and NAc glutamate plasticity; insights into the mechanism of NAc calcium-permeable AMPA receptor recruitment
Authors: Fetterly Tracy L. , Catalfio Amanda M. , Ferrario Carrie R.
Published: May 2023

In rats, eating obesogenic diets increase calcium-permeable AMPA receptor (CP-AMPAR) transmission in the nucleus accumbens (NAc) core, and enhances food-motivated behavior. Interestingly these diet-induced alterations in NAc transmission are pronounced in obesity-prone (OP) rats and absent in obesity-resistant (OR) populations. However, effects of diet manipulation on food motivation, and the mechanisms underlying NAc plasticity in OPs is unknown. Using male selectively-bred OP and OR rats, we assessed food-motivated behavior following ad lib access to chow (CH), junk-food (JF), or 10d of JF followed by a return to chow diet (JF-Dep). Behavioral tests included conditioned reinforcement, instrumental responding, and free consumption. Additionally, optogenetic, chemogenetic, and pharmacological approaches were used to examine NAc CP-AMPAR recruitment following diet manipulation and ex vivo treatment of brain slices. Motivation for food was greater in OP than OR rats, as expected. However, JF-Dep only produced enhancements in food-seeking in OP groups, while continuous JF access reduced food-seeking in both OPs and ORs. Reducing excitatory transmission in the NAc was sufficient to recruit CP-AMPARs to synapses in OPs, but not ORs. In OPs, JF-induced increases in CP-AMPARs occurred in mPFC-, but not BLA-to-NAc inputs. Diet differentially affects behavioral and neural plasticity in obesity susceptible populations. We also identify conditions for acute recruitment of NAc CP-AMPARs; these results suggest that synaptic scaling mechanisms contribute to NAc CP-AMPAR recruitment. Overall, this work improves our understanding of how sugary, fatty food consumption interacts with obesity susceptibility to influence food-motivated behavior. It also extends our fundamental understanding of NAc CP-AMPAR recruitment; this has important implications for motivation in the context of obesity as well as drug addiction.
VirB, a key transcriptional regulator ofShigellavirulence, requires a CTP ligand for its regulatory activities
Authors: Gerson Taylor M. , Ott Audrey M. , Karney Monika MA. , Socea Jillian N. , Ginete Daren R. , Iyer Lakshminarayan M. , Aravind L. , Gary Ronald K. , Wing Helen J.
Published: May 2023

The VirB protein, encoded by the large virulence plasmid ofShigellaspp., is a key transcriptional regulator of virulence genes. Without a functionalvirBgene,Shigellacells are avirulent. On the virulence plasmid, VirB functions to offset transcriptional silencing mediated by the nucleoid structuring protein, H-NS, which binds and sequesters AT-rich DNA, making it inaccessible for gene expression. Thus, gaining a mechanistic understanding of how VirB counters H-NS-mediated silencing is of considerable interest. VirB is unusual in that it does not resemble classic transcription factors. Instead, its closest relatives are found in the ParB superfamily, where the best-characterized members function in faithful DNA segregation before cell division. Here, we show that VirB is a fast-evolving member of this superfamily and report for the first time that the VirB protein binds a highly unusual ligand, CTP. VirB binds this nucleoside triphosphate preferentially and with specificity. Based on alignments with the best-characterized members of the ParB family, we identify amino acids of VirB likely to bind CTP. Substitutions in these residues disrupt several well-documented activities of VirB, including its anti-silencing activity at a VirB-dependent promoter, its role in generating a Congo red positive phenotype inShigella, and the ability of the VirB protein to form foci in the bacterial cytoplasm when fused to GFP. Thus, this work is the first to show that VirB is a bona fide CTP-binding protein and linksShigellavirulence phenotypes to the nucleoside triphosphate, CTP.

Importance

Shigellaspecies cause bacillary dysentery (shigellosis), the second leading cause of diarrheal deaths worldwide. With growing antibiotic resistance, there is a pressing need to identify novel molecular drug targets.Shigellavirulence phenotypes are controlled by the transcriptional regulator, VirB. We show that VirB belongs to a fast-evolving, primarily plasmid-borne clade of the ParB superfamily, which has diverged from versions that have a distinct cellular role – DNA partitioning. We are the first to report that, like classic members of the ParB family, VirB binds a highly unusual ligand, CTP. Mutants predicted to be defective in CTP binding are compromised in a variety of virulence attributes controlled by VirB. This study i) reveals that VirB binds CTP, ii) provides a link between VirB-CTP interactions andShigellavirulence phenotypes, and iii) broadens our understanding of the ParB superfamily, a group of bacterial proteins that play critical roles in many different bacteria.
Interpretable modeling of time-resolved single-cell gene-protein expression using CrossmodalNet
Authors: Yang Yongjian , Lin Yu-Te , Li Guanxun , Zhong Yan , Xu Qian , Cai James J.
Published: May 2023

Cell-surface proteins play a critical role in cell function and are primary targets for therapeutics. CITE-seq is a single-cell technique that enables simultaneous measurement of gene and surface protein expression. It is powerful but costly and technically challenging. Computational methods have been developed to predict surface protein expression using gene expression information such as from single-cell RNA sequencing (scRNA-seq) data. Existing methods however are computationally demanding and lack the interpretability to reveal underlying biological processes. We propose CrossmodalNet, an interpretable machine learning model, to predict surface protein expression from scRNA-seq data. Our model with a customized adaptive loss accurately predicts surface protein abundances. When samples from multiple time points are given, our model encodes temporal information into an easy-to-interpret time embedding to make prediction in a time point-specific manner able to uncover noise-free causal gene-protein relationships. Using two publicly available time-resolved CITE-seq data sets, we validate the performance of our model by comparing it to benchmarking methods and evaluate its interpretability. Together, we show our method accurately and interpretably profiles surface protein expression using scRNA-seq data, thereby expanding the capacity of CITE-seq experiments for investigating molecular mechanisms involving surface proteins.
Chronic stress triggers seeking of a starvation-like state in anxiety-prone female mice
Authors: Kucukdereli Hakan , Amsalem Oren , Pottala Trent , Lim Michelle , Potgieter Leilani , Hasbrouck Amanda , Lutas Andrew , Andermann Mark L.
Published: May 2023

Elevated anxiety often precedes anorexia nervosa and persists after weight restoration. Patients with anorexia nervosa often describe hunger as pleasant, potentially because food restriction can be anxiolytic. Here, we tested whether chronic stress can cause animals to prefer a starvation-like state. We developed a virtual reality place preference paradigm in which head-fixed mice can voluntarily seek a starvation-like state induced by optogenetic stimulation of hypothalamic agouti-related peptide (AgRP) neurons. Prior to stress induction, male but not female mice showed mild aversion to AgRP stimulation. Strikingly, following chronic stress, a subset of females developed a strong preference for AgRP stimulation that was predicted by high baseline anxiety. Such stress-induced changes in preference were reflected in changes in facial expressions during AgRP stimulation. Our study suggests that stress may cause females predisposed to anxiety to seek a starvation state, and provides a powerful experimental framework for investigating the underlying neural mechanisms.
Pathological Tau transmission initiated by binding lymphocyte-activation gene 3
Authors: Chen Chan , Kumbhar Ramhari , Wang Hu , Yang Xiuli , Gadhave Kundlik , Rastegar Cyrus , Kimura Yasuyoshi , Behensky Adam , Katakam Sruthi , Jeong Deok , Wang Liang , Wang Anthony , Chen Rong , Zhang Shu , Jin Lingtao , Workman Creg J. , Vignali Dario A.A. , Pletinkova Olga , Nauen David W. , Wong Philip C. , Troncoso Juan C. , Ying Mingyao , Dawson Valina L. , Dawson Ted M. , Mao Xiaobo
Published: May 2023

The spread of prion-like protein aggregates is believed to be a common driver of pathogenesis in many neurodegenerative diseases. Accumulated tangles of filamentous Tau protein are considered pathogenic lesions of Alzheimer’s disease (AD) and related Tauopathies, including progressive supranuclear palsy, and corticobasal degeneration. Tau pathologies in these illnesses exhibits a clear progressive and hierarchical spreading pattern that correlates with disease severity1, 2. Clinical observation combined with complementary experimental studies3, 4have shown that Tau preformed fibrils (PFF) are prion-like seeds that propagate pathology by entering cells and templating misfolding and aggregation of endogenous Tau. While several receptors of Tau are known, they are not specific to the fibrillar form of Tau. Moreover, the underlying cellular mechanisms of Tau PFF spreading remains poorly understood. Here, we show that the lymphocyte-activation gene 3 (Lag3) is a cell surface receptor that binds to PFF, but not monomer, of Tau. Deletion ofLag3or inhibition of Lag3 in primary cortical neurons significantly reduces the internalization of Tau PFF and subsequent Tau propagation and neuron-to-neuron transmission. Propagation of Tau pathology and behavioral deficits induced by injection of Tau PFF in the hippocampus and overlying cortex are attenuated in mice lackingLag3selectively in neurons. Our results identify neuronal Lag3 as a receptor of pathologic Tau in the brain, and for AD and related Tauopathies a therapeutic target.

One Sentence Summary

Lag3 is a neuronal receptor specific for Tau PFF, and is required for uptake, propagation and transmission of Tau pathology.
The AMP deaminase of the molluskHelix pomatiais an unexpected member of the adenosine deaminase-related growth factor (ADGF) family
Authors: Tzertzinis George , Ganatra Mehul B. , Ruse Cristian , Taron Christopher H. , Causey Bryce , Wang Liang , Schildkraut Ira
Published: May 2023

We report here the first occurrence of an adenosine deaminase-related growth factor (ADGF) that deaminates adenosine 5’ monophosphate (AMP) in preference to adenosine. The ADGFs are a group of secreted deaminases found throughout the animal kingdom that affect the extracellular concentration of adenosine by converting it to inosine. The AMP deaminase studied here was first isolated and biochemically characterized from the roman snailHelix pomatiain 1983. Determination of the amino acid sequence of the AMP deaminase enabled sequence comparisons to protein databases and revealed it as a member of the ADGF family. Cloning and expression of its cDNA inPichia pastorisallowed the comparison of the biochemical characteristics of the native and recombinant forms of the enzyme and confirmed they correspond to the previously reported activity. Uncharacteristically, theH. pomatiaAMP deaminase was determined to be dissimilar to the AMP deaminase family by sequence comparison while demonstrating similarity to the ADGFs despite having AMP as its preferred substrate rather than adenosine.
Visible-Light Optical Coherence Tomography Fibergraphy of the Tree Shrew Retinal Ganglion Cell Axon Bundles
Authors: Miller David A. , Grannonico Marta , Liu Mingna , Savier Elise , McHaney Kara , Erisir Alev , Netland Peter A. , Cang Jianhua , Liu Xiaorong , Zhang Hao F.
Published: May 2023

We seek to develop techniques for high-resolution imaging of the tree shrew retina for visualizing and parameterizing retinal ganglion cell (RGC) axon bundles in vivo. We applied visible-light optical coherence tomography fibergraphy (vis-OCTF) and temporal speckle averaging (TSA) to visualize individual RGC axon bundles in the tree shrew retina. For the first time, we quantified individual RGC bundle width, height, and cross-sectional area and applied vis-OCT angiography (vis-OCTA) to visualize the retinal microvasculature in tree shrews. Throughout the retina, as the distance from the optic nerve head (ONH) increased from 0.5 mm to 2.5 mm, bundle width increased by 30%, height decreased by 67%, and cross-sectional area decreased by 36%. We also showed that axon bundles become vertically elongated as they converge toward the ONH. Ex vivo confocal microscopy of retinal flat-mounts immunostained with Tuj1 confirmed our in vivo vis-OCTF findings.
Infection-induced epilepsy is caused by increased expression of chondroitin sulfate proteoglycans in hippocampus and amygdala
Authors: Patel Dipan C. , Swift Nathaniel , Tewari Bhanu P. , Browning Jack L. , Prim Courtney , Chaunsali Lata , Kimbrough Ian , Olsen Michelle L. , Sontheimer Harald
Published: May 2023

Alterations in the extracellular matrix (ECM) are common in epilepsy, yet whether they are cause or consequence of disease is unknow. Using Theiler’s virus infection model of acquired epilepsy we findde novoexpression of chondroitin sulfate proteoglycans (CSPGs), a major ECM component, in dentate gyrus (DG) and amygdala exclusively in mice with seizures. Preventing synthesis of CSPGs specifically in DG and amygdala by deletion of major CSPG aggrecan reduced seizure burden. Patch-clamp recordings from dentate granule cells (DGCs) revealed enhanced intrinsic and synaptic excitability in seizing mice that was normalized by aggrecan deletion.In situexperiments suggest that DGCs hyperexcitability results from negatively charged CSPGs increasing stationary cations (K+, Ca2+) on the membrane thereby depolarizing neurons, increasing their intrinsic and synaptic excitability. We show similar changes in CSPGs in pilocarpine-induced epilepsy suggesting enhanced CSPGs in the DG and amygdala may be a common ictogenic factor and novel therapeutic potential.
Curiosity satisfaction increases event-related potentials sensitive to reward
Authors: Rueterbories Tim , Mecklinger Axel , Eschmann Kathrin C. J. , Crivelli-Decker Jordan , Ranganath Charan , Gruber Matthias J.
Published: May 2023

Successful learning depends on various factors such as depth of processing, motivation, or curiosity about information. A strong drive to learn something or the expectation of receiving a reward can be crucial to enhance learning. However, the influence of curiosity on the processing of new information and its similarity with reward processing is not well understood. This study examined whether states of curiosity influence specific event-related-potentials (ERPs) associated with reward processing and whether these ERPs are related with later memory benefits. In an initial screening phase, participants indicated their curiosity and confidence in prior knowledge about answers to various trivia questions. In a subsequent study phase, we targeted different time windows related to reward processing during the presentation of trivia answers containing the Reward-Positivity (RewP; 250 - 350 ms), the P3 (250 - 500 ms), and the Late-Positive-Potential (LPP; 600 - 1000 ms). In a following surprise memory test, we found that participants recalled more high- than low-curiosity answers. The RewP, P3 and LPP showed greater positive mean amplitudes for high compared to low curiosity, reflecting increased reward processing. In addition, we found that the RewP and the P3 showed more positive mean amplitudes for later recalled compared to later forgotten answers, but curiosity did not modulate this encoding-related results. These findings support the view that the satisfaction of curiosity resembles reward processing, indicated by event-related-potentials.
Genomic surveillance of antimicrobial-resistantEscherichia coliin fecal sludge and sewage in Uganda
Authors: Gomi Ryota , Matsumura Yasufumi , Yamamoto Masaki , Tanaka Mai , Komakech Allan John , Matsuda Tomonari , Harada Hidenori
Published: May 2023

The global increase of antimicrobial resistance (AMR) is a major public health concern. An effective AMR surveillance tool is needed to track the emergence and spread of AMR. Wastewater surveillance has been proposed as a resource-efficient tool for monitoring AMR carriage in the community. Here, we performed genomic surveillance of antimicrobial-resistantEscherichia coliobtained from fecal sludge and sewage in Uganda to gain insights intoE. coliepidemiology and AMR burden in the underlying population. Selective media containing different antibiotic combinations (cefotaxime, ciprofloxacin, cefotaxime + ciprofloxacin + gentamicin) were used to obtain antimicrobial-resistantE. colifrom fecal sludge and sewage. Short-read sequencing was performed for the obtained isolates, and a subset of isolates (selected from predominant sequence types (STs)) was also subjected to long-read sequencing. Genomic analysis of the obtainedE. coliisolates (n = 181) revealed the prevalence of clonal complex 10, including ST167 (n = 43), ST10 (n = 28), ST1284 (n = 17), and ST617 (n = 4), in both fecal sludge and sewage, irrespective of antibiotics used for selection. We also detected global high-risk clones ST1193 (n = 10) and ST131 (n = 2 clade A, n = 3 subclade C1-M27, and n = 1 subclade C2). Diverse AMR determinants, including extended-spectrum β-lactamase genes (mostlyblaCTX-M-15) and mutations ingyrAandparC, were identified. Analysis of the completed genomes revealed that diverse IncF plasmids and chromosomal integration were the major contributors to the spread of AMR genes in the predominant STs. This study showed that a combination of sewage surveillance (or fecal sludge surveillance) and whole-genome sequencing can be a powerful tool for monitoring AMR carriage in the underlying population.
Unraveling cellular complexity with unlimited multiplexed super-resolution imaging
Authors: Schueder Florian , Rivera-Molina Felix , Su Maohan , Kidd Phylicia , Rothman James E. , Toomre Derek , Bewersdorf Joerg
Published: May 2023

Mapping the intricate spatial relationships between the many different molecules inside a cell is essential to understanding cellular functions in all their complexity. Super-resolution fluorescence microscopy offers the required spatial resolution but struggles to reveal more than four different targets simultaneously. Exchanging labels in subsequent imaging rounds for multiplexed imaging extends this number but is limited by its low throughput. Here we present a novel imaging method for rapid multiplexed super-resolution microscopy of a nearly unlimited number of molecular targets by leveraging fluorogenic labeling in conjunction with Transient Adapter-mediated switching for high-throughput DNA-PAINT (FLASH-PAINT). We demonstrate the cell biological versatility of FLASH-PAINT in mammalian cells in four applications: i) mapping nine proteins in a single mammalian cell, ii) elucidating the functional organization of primary cilia by nine-target imaging, iii) revealing the changes in proximity of twelve different targets in unperturbed and dissociated Golgi stacks and iv) investigating inter-organelle contacts at 3D super-resolution.
A novel mitochondrial regulon for Ferroptosis during fungal pathogenesis
Authors: Shen Qing , Yang Fan , Naqvi Naweed I.
Published: May 2023

Ferroptosis remains an underexamined iron- and lipid peroxides-driven cell death modality despite its importance to several human- and plant-diseases and to immunity thereof. Here, we utilized a range of chemical biological tools, genetic mutants and biochemical analyses to gain insights into how the fungal pathogenMagnaporthe oryzaeundergoes Ferroptosis strictly in the spore cells to successfully transit to infectious development. We reveal a functional dependency between such intrinsic Ferroptosis and autophagy-mediated mitochondrial degradation. Mechanistically, the requirement of mitophagy for ferroptotic cell death was attributed to its ability to maintain a pool of metabolically active mitochondria. Pharmacological disruption of the electron transport chain or membrane potential led to complete inhibition of ferroptosis, thus simulating the loss of mitophagy phenotypes. Conversely, increased mitochondrial membrane potential in a mitophagy-defective mutant alleviated the Ferroptosis defects therein. Graded inhibition of mitochondrial Coenzyme Q (CoQ) biosynthesis with or without ferroptosis inhibitor Liproxstation-1 distinguished its antioxidant function in such regulated cell death. Membrane potential-dependent regulation of ATP synthesis and iron homeostasis, as well as dynamics of Aconitase in the Tricarboxylic acid cycle in the presence or absence of mitophagy, mitochondrial poisoning or iron chelation further linked mitochondrial metabolism to Ferroptosis. Lastly, we present an important mitochondrial bioenergetics and redox-regulatory network regulon essential for intrinsic Ferroptosis and its precise role in fungal pathogenesis leading up to the establishment of the devastating rice blast disease.
Prolonged stalling of RNA Polymerase II at DNA damage explains phenotypical differences between Cockayne and UV-sensitive syndromes
Authors: Hansen Camila Gonzalo , Steurer Barbara , Janssens Roel C. , Zhou Di , van Sluis Marjolein , Lans Hannes , Marteijn Jurgen A.
Published: May 2023

Faithful transcription of eukaryotic genes by RNA polymerase II (Pol II) is essential for proper cell function. Nevertheless, the integrity of the DNA template of Pol II is continuously challenged by different sources of DNA damage, such as UV-light, that impede transcription. When unresolved, these transcription-blocking lesions (TBLs) can cause cellular dysfunction, senescence and apoptosis, eventually resulting in DNA damage-induced aging. Cells counteract these deleterious effects by Transcription-Coupled Nucleotide Excision Repair (TC-NER), which specifically removes TBLs, thereby safeguarding transcription. TC-NER initiation relies on the concerted actions of the CSB, CSA and UVSSA proteins, and loss of either of these factors results in a complete TC-NER deficiency. Although their TC-NER defect is similar, UVSSA loss results in UV-Sensitive Syndrome (UVSS), with only mild phenotypes like freckling and photosensitivity, while loss of CSA or CSB activity results in the severe Cockayne Syndrome (CS), characterized by premature aging, progressive neurodegeneration and mental retardation. Thus far the underlying mechanism for these striking differences in phenotypes remains unclear. Using live-cell imaging approaches, here we show that in TC-NER proficient cells lesion-stalled Pol II is swiftly resolved by repair of the TBL. However, in CSA and CSB knockout (KO) cells, elongating Pol II remains chromatin-bound. This lesion-stalled Pol II will obstruct other DNA transacting processes and will also shield the damage from repair by alternative pathways. In contrast, in UVSSA KO cells, Pol II is removed from the TBL by VCP-mediated proteasomal degradation, thereby, allowing alternative repair mechanisms to remove the TBL.
Single-cycle SARS-CoV-2 vaccine elicits high protection and sterilizing immunity in hamsters
Authors: Lett Martin Joseph , Otte Fabian , Hauser David , Schön Jacob , Kipfer Enja Tatjana , Hoffmann Donata , Halwe Nico J. , Ulrich Lorenz , Zhang Yuepeng , Cmiljanovic Vladimir , Wylezich Claudia , Urda Lorena , Lang Christopher , Beer Martin , Mittelholzer Christian , Klimkait Thomas
Published: May 2023

Vaccines have been central in ending the COVID-19 pandemic, but newly emerging SARS-CoV-2 variants increasingly escape first-generation vaccine protection. To fill this gap, live particle-based vaccines mimicking natural infection aim at protecting against a broader spectrum of virus variants. We designed “single-cycle SARS-CoV-2 viruses” (SCVs) that lack essential viral genes, possess superior immune-modulatory features and provide an excellent safety profile in the Syrian hamster model. Full protection of all intranasally vaccinated animals was achieved against an autologous challenge with SARS-CoV-2 virus using an Envelope-gene-deleted vaccine candidate. By deleting key immune-downregulating genes, sterilizing immunity was achieved with an advanced candidate without virus spread to contact animals. Hence, SCVs have the potential to induce a broad and durable protection against COVID-19 superior to a natural infection.
“Ghost” fragment ions in structure and site-specific glycoproteomics analysis
Authors: Campos Diana , Girgis Michael , Yang Qiang , Zong Guanghui , Goldman Radoslav , Wang Lai-Xi , Sanda Miloslav
Published: May 2023

Mass spectrometry (MS) can unlock crucial insights into the intricate world of glycosylation analysis. Despite its immense potential, the qualitative and quantitative analysis of isobaric glycopeptide structures remains one of the most daunting hurdles in the field of glycoproteomics. The ability to distinguish between these complex glycan structures poses a significant challenge, hindering our ability to accurately measure and understand the role of glycoproteins in biological systems. A few recent publications described the use of collision energy (CE) modulation to improve structural elucidation, especially for qualitative purposes. Different linkages of glycan units usually demonstrate different stabilities under CID/HCD fragmentation conditions. Fragmentation of the glycan moiety produces low molecular weight ions (oxonium ions) that can serve as a structure-specific signature for specific glycan moieties, however, specificity of these fragments has never been examined closely. Here, we investigated fragmentation specificity using synthetic stable isotope-labelled glycopeptide standards. These standards were isotopically labelled at the reducing terminal GlcNAc, which allowed us to resolve fragments produced by oligomannose core moiety and fragments generated from outer antennary structures. Our research identified the potential for false positive structure assignments due to the occurrence of “Ghost” fragments resulting from single glyco unit rearrangement or mannose core fragmentation within the collision cell. To mitigate this issue, we have established a minimal intensity threshold for these fragments to prevent the misidentification of structure-specific fragments in glycoproteomics analysis. Our findings provide a crucial step forward in the quest for more accurate and reliable glycoproteomics measurements.

Graphical abstract
Epigenome Editing Durability Varies Widely Across Cardiovascular Disease Target Genes
Authors: Whittaker Madelynn N. , Testa Lauren C. , Quigley Aidan , Jindal Ishaan , Cortez-Alvarado Saúl V. , Qu Ping , Yang Yifan , Alameh Mohamad-Gabriel , Musunuru Kiran , Wang Xiao
Published: May 2023

Background

Hepatic knockdown of the proprotein convertase subtilisin/kexin type 9 (PCSK9) gene or the angiopoietin-like 3 (ANGPTL3) gene has been demonstrated to reduce blood low-density lipoprotein cholesterol (LDL-C) levels, and hepatic knockdown of the angiotensinogen (AGT) gene has been demonstrated to reduce blood pressure. Genome editing can productively target each of these three genes in hepatocytes in the liver, offering the possibility of durable “one-and-done” therapies for hypercholesterolemia and hypertension. However, concerns around making permanent gene sequence changes via DNA strand breaks might hinder acceptance of these therapies. Epigenome editing offers an alternative approach to gene inactivation, via silencing of gene expression by methylation of the promoter region, but the long-term durability of epigenome editing remains to be established.

Methods

We assessed the ability of epigenome editing to durably reduce the expression of the humanPCSK9, ANGPTL3, andAGTgenes in HuH-7 hepatoma cells. Using the CRISPRoff epigenome editor, we identified guide RNAs that produced efficient gene knockdown immediately after transfection. We assessed the durability of gene expression and methylation changes through serial cell passages.

Results

Cells treated with CRISPRoff andPCSK9guide RNAs were maintained for up to 124 cell doublings and demonstrated durable knockdown of gene expression and increased CpG dinucleotide methylation in the promoter, exon 1, and intron 1 regions. In contrast, cells treated with CRISPRoff andANGPTL3guide RNAs experienced only transient knockdown of gene expression. Cells treated with CRISPRoff andAGTguide RNAs also experienced transient knockdown of gene expression; although initially there was increased CpG methylation throughout the early part of the gene, this methylation was geographically heterogeneous—transient in the promoter, and stable in intron 1.

Conclusions

This work demonstrates precise and durable gene regulation via methylation, supporting a new therapeutic approach for protection against cardiovascular disease via knockdown of genes such asPCSK9. However, the durability of knockdown with methylation changes is not generalizable across target genes, likely limiting the therapeutic potential of epigenome editing compared to other modalities.
Environmental Persistence and Disinfection of Lassa Virus
Authors: Shaffer Marlee , Fischer Robert J. , Gallogly Shane , Ginn Olivia , Munster Vincent , Bibby Kyle
Published: May 2023

Lassa Fever, caused by Lassa virus (LASV), is endemic to West Africa, where approximately 300,000 illnesses and 5,000 deaths occur annually. LASV is primarily spread by infected multimammate rats via urine and fomites, highlighting the importance of understanding the environmental fate of LASV. This study evaluated the persistence of LASV strains on surfaces in aqueous solutions and with sodium hypochlorite disinfection. LASV strains (Josiah and Sauerwald) were more stable in DI water (k = 0.23 and 0.34 days-1) than primary influent wastewater (k = 1.3 and 1.9 days-1). The decay rates of LASV on HDPE (k = 4.3 and 2.3 days-1) and Stainless Steel (k = 5.3 and 2.7 days-1) were not significantly different for either strain. Sodium hypochlorite was highly effective at inactivating both strains of LASV. This work presents data for the environmental persistence of LASV to inform future risk assessment and management efforts.
Community-based Reconstruction and Simulation of a Full-scale Model of Region CA1 of Rat Hippocampus
Authors: Romani Armando , Antonietti Alberto , Bella Davide , Budd Julian , Giacalone Elisabetta , Kurban Kerem , Sáray Sára , Abdellah Marwan , Arnaudon Alexis , Boci Elvis , Colangelo Cristina , Courcol Jean-Denis , Delemontex Thomas , Ecker András , Falck Joanne , Favreau Cyrille , Gevaert Michael , Hernando Juan B. , Herttuainen Joni , Ivaska Genrich , Kanari Lida , Kaufmann Anna-Kristin , King James Gonzalo , Kumbhar Pramod , Lange Sigrun , Lu Huanxiang , Lupascu Carmen Alina , Migliore Rosanna , Petitjean Fabien , Planas Judit , Rai Pranav , Ramaswamy Srikanth , Reimann Michael W. , Riquelme Juan Luis , Guerrero Nadir Román , Shi Ying , Sood Vishal , Sy Mohameth François , Van Geit Werner , Vanherpe Liesbeth , Freund Tamás F. , Mercer Audrey , Muller Eilif , Schürmann Felix , Thomson Alex M. , Migliore Michele , Káli Szabolcs , Markram Henry
Published: May 2023

The CA1 region of the hippocampus is one of the most studied regions of the rodent brain, thought to play an important role in cognitive functions such as memory and spatial navigation. Despite a wealth of experimental data on its structure and function, it has been challenging to reconcile information obtained from diverse experimental approaches. To address this challenge, we present a community-driven, full-scalein silicomodel of the rat CA1 that integrates a broad range of experimental data, from synapse to network, including the reconstruction of its principal afferents, the Schaffer collaterals, and a model of the effects that acetylcholine has on the system. We tested and validated each model component and the final network model, and made input data, assumptions, and strategies explicit and transparent. The unique flexibility of the model allows scientists to address a range of scientific questions. In this article, we describe the methods used to set up simulations that reproduce and extendin vitroandin vivoexperiments. Among several applications in the article, we focus on theta rhythm, a prominent hippocampal oscillation associated with various behavioral correlates and use our computer model to reproduce and reconcile experimental findings. Finally, we make data, code and model available through the hippocampushub.eu portal, which also provides an extensive set of analyses of the model and a user-friendly interface to facilitate adoption and usage. This neuroscience community-driven model represents a valuable tool for integrating diverse experimental data and provides a foundation for further research into the complex workings of the hippocampal CA1 region.
Bacteriophage populations mirror those of bacterial pathogens at sites of infection
Authors: Haddock NL , Barkal LJ , Bollyky PL
Published: May 2023

Bacteriophages, viruses that parasitize bacteria, are known to be abundant at sites of bacterial colonization but the relationship between phages and bacteria at sites of infection is unclear. Bacteriophage are highly specific to their bacterial host species and so we hypothesize that phage populations would mirror those of bacterial pathogens within infected tissues. To test this, here we study publicly-available cell-free DNA generated using next generation sequencing of infected bodily fluids, including urine, joint fluid, peritoneal fluid, bronchoalveolar lavage fluid, cerebrospinal fluid, and abscess fluid as well as uninfected control samples. These were analyzed using a computational pipeline for identifying bacteriophage sequences in cfDNA. We find that bacteriophage sequences are present in both infected and uninfected bodily fluids and represent a variety of bacteriophage morphologies and bacterial hosts. Additionally, phages fromE. coli, Streptococcus, andS. aureusare overrepresented both in terms of proportion and diversity in fluids infected with these same pathogens. These data indicate that phages reflect the relative abundance of their bacterial hosts at sites of infection. Bacteriophage sequences may help inform future investigative and diagnostic approaches that utilize cell-free DNA to study the microbiome within infected tissues.

Importance

Bacteriophages are an active area of investigation in microbiome research but most studies have focused on phage populations at sites of bacterial colonization. Little is known about bacteriophage ecology at sites of active infection. To address this gap in knowledge, we utilized a publicly available dataset to study bacteriophage populations in cell free DNA collected from sites of infection. We find that phages reflect the relative abundance of their bacterial hosts at sites of infection. These studies may lead to future investigative and diagnostic approaches that incorporate phages as well as bacterial cell free DNA.