bluuebunny/crossref_metadata_2025 huggingface dataset:
Ceftriaxone-resistantNeisseria gonorrhoeaedetected in England, 2015 to 2024; an observational study
Authors: Fifer Helen , Doumith Michel , Rubinstein Luciana , Mitchell Laura , Wallis Mark , Singh Selena , Singh Gurmit Jagjit , Rayment Michael , Evans-Jones John , Blume Alison , Dosekun Olamide , Poon Kenny , Nori Achyuta , Day Michaela , Pitt Rachel , Sun Suzy , Narayanan Prarthana , Callan Emma , Vickers Anna , Minshull Jack , Bennet Kirsty , Johnson James E.C. , Saunders John , Alexander Sarah , Mohammed Hamish , Woodford Neil , Sinka Katy , Cole Michelle
Published: August 2024

Background

Since June 2022, there has been a rise in the number of ceftriaxone resistantNeisseria gonorrhoeaecases detected in England (n = 15), of which one third were extensively-drug resistant (XDR). We describe the demographic and clinical details of the recent cases and investigate the phenotypic and molecular characteristics of the isolates. For a comprehensive overview, we also reviewed 16 ceftriaxone-resistant cases previously identified in England since December 2015 and performed a global genomic comparison of all publicly available ceftriaxone-resistantN. gonorrhoeaestrains with mosaicpenAalleles.

Methods

AllN. gonorrhoeaeisolates resistant to ceftriaxone (MIC >0.125 mg/L) were whole-genome sequenced and compared with 142 global sequences of ceftriaxone-resistantN. gonorrhoeae. Demographic, behavioural, and clinical data were collected, including treatment and outcomes.

Results

All cases were heterosexuals, and most infections were associated with travel to or from the Asia-Pacific region. However, some had not travelled outside England within the previous few months. There were no ceftriaxone genital treatment failures, but 3/5 pharyngeal infections and the only rectal infection failed treatment. The isolates represented 13 different multi-locus sequence types (MLSTs), and most had the mosaicpenA-60.001 allele. The global genomes clustered into eight major phylogroups, with regional associations. All XDR isolates belonged to the same phylogroup, represented by MLST 16406.

Conclusion

Ceftriaxone resistance inN. gonorrhoeaecontinues to be associated with thepenA-60.001 allele within multiple genetic backgrounds and with widespread dissemination in the Asia-Pacific region. Heightened surveillance activities have been initiated to detect further cases with the aim of interrupting further transmission.
FEDKEA: Enzyme function prediction with a large pretrained protein language model and distance-weighted k-nearest neighbor
Authors: Zheng Lei , Li Bowen , Xu Siqi , Chen Junnan , Liang Guanxiang
Published: August 2024

Recent advancements in sequencing technologies have led to the identification of a vast number of hypothetical proteins, surpassing current experimental capabilities for annotation. Enzymes, crucial for diverse biological functions, have garnered significant attention; however, accurately predicting enzyme EC numbers for proteins with unknown functions remains challenging. Here, we introduce FEDKEA, a novel computational method that integrates ESM-2 and distance-weighted KNN (k-nearest neighbor) to enhance enzyme function annotation. FEDKEA first employs a fine-tuned ESM-2 model with four fully connected layers to distinguish from other proteins. For predicting EC numbers, it adopts a hierarchical approach, utilizing distinct models and training strategies across the four EC number levels. Specifically, the classification of the first EC number level utilizes a fine-tuned ESM-2 model with three fully connected layers, while transfer learning with embeddings from this model supports the second and third-level tasks. The fourth-level classification employs a distance-weighted KNN model. Compared to existing tools such as CLEAN and ECRECer, two state-of-the-art computational methods, FEDKEA demonstrates superior performance. We anticipate that FEDKEA will significantly advance the prediction of enzyme functions for uncharacterized proteins, thereby impacting fields such as genomics, physiology and medicine. FEDKEA is easy to install and currently available at:https://github.com/Stevenleizheng/FEDKEA
Co-release of GABA and ACh from medial olivocochlear neurons fine tunes cochlear efferent inhibition
Authors: Castagnola Tais , Castagna Valeria C , Kitcher Siân R. , Torres Cadenas Lester , Di Guilmi Mariano N , Gomez Casati Maria Eugenia , Buonfiglio Paula I , Dalamón Viviana , Katz Eleonora , Elgoyhen Ana Belén , Weisz Catherine J.C. , Goutman Juan D , Wedemeyer Carolina
Published: August 2024

During development, inner hair cells (IHCs) in the mammalian cochlea are unresponsive to acoustic stimuli but instead exhibit spontaneous activity. During this same period, neurons originating from the medial olivocochlear complex (MOC) transiently innervate IHCs, regulating their firing pattern which is crucial for the correct development of the auditory pathway. Although the MOC-IHC is a cholinergic synapse, previous evidence indicates the widespread presence of gamma-aminobutyric acid (GABA) signaling markers, including presynaptic GABABreceptors (GABABR). In this study, we explore the source of GABA by optogenetically activating either cholinergic or GABAergic fibers. The optogenetic stimulation of MOC terminals from GAD;ChR2-eYFP and ChAT;ChR2-eYFP mice evoked synaptic currents in IHCs that were blocked by α-bungarotoxin. This suggests that GABAergic fibers release ACh and activate α9α10 nicotinic acetylcholine receptors (nAChRs). Additionally, MOC cholinergic fibers release not only ACh but also GABA, as the effect of GABA on ACh response amplitude was prevented by applying the GABAB-R blocker (CGP 36216). Using optical neurotransmitter detection and calcium imaging techniques, we examined the extent of GABAergic modulation at the single synapse level. Our findings suggest heterogeneity in GABA modulation, as only 15 out of 31 recorded synaptic sites were modulated by applying the GABABR specific antagonist, CGP (100-200 µM). In conclusion, we provide compelling evidence that GABA and ACh are co-released from at least a subset of MOC terminals. In this circuit, GABA functions as a negative feedback mechanism, locally regulating the extent of cholinergic inhibition at certain efferent-IHC synapses during an immature stage.

Significance statement

Before hearing onset, the medial olivocochlear (MOC) efferent system of the mammalian cochlea regulates the pattern of IHC spontaneous firing rate through the activation of α9α10 nAChRs. However, GABA is also known to have a modulatory role at the MOC-IHC synapse. Our results show that GABA is co-released from at least a subset of MOC terminals, working as a precise regulatory mechanism for ACh release. Furthermore, we demonstrate that not all synaptic contacts within a single IHC are equally modulated by GABA.
Parvalbumin expression identifies subicular principal cells with high projection specificity
Authors: Baccini Gilda , Foggetti Angelica , Wernet Natalie , Engelhardt Karl-Alexander , Kronenbitter Kerstin , Michels Jan , Kulik Akos , Wozny Christian , Wulff Peer
Published: August 2024

The calcium-binding protein parvalbumin is an established marker for a subset of cortical inhibitory interneurons with similar biophysical features and connectivity. However, parvalbumin is also expressed in a small population of excitatory cells in layer 5 of the neocortex with specific sub-cortical projection targets. Parvalbumin may thus also in principal cells identify particular subclasses with distinct connectivity and function. Here we investigated whether parvalbumin is expressed in excitatory neurons of the hippocampal formation and if so, whether it delineated neurons with specific features. We report parvalbumin-expressing glutamatergic cells in the distal subiculum, which -based on location, connectivity and gene expression - separated into two subclasses: neurons in deep layers, which specifically project to the antero-ventral thalamus and neurons in superficial layers, which project to the mamillary bodies. Contrary to most adjacent pyramidal cells parvalbumin-positive neurons were non-bursting and displayed straight apical dendrites devoid of oblique dendrites. Functionally, the projections diverged from classical driver/modulator subdivisions. Parvalbumin expression thus marks two sub-types of subicular projection neurons with high target specificity and unique functional features.
Muscular expression of pezo-1 differentially contributes to swimming and crawling production in the nematode C. elegans.
Authors: Fazyl Adina , Sawilchik Erin , Stein Wolfgang , Vidal-Gadea Andres G
Published: August 2024

Mechanosensitive PIEZO ion channels are evolutionarily conserved proteins that are widely expressed in neuronal and muscular tissues. This study explores the role of the mechanoreceptor PEZO-1 in the body wall muscles of Caenorhabditis elegans, focusing on its influence on two locomotor behaviors, swimming and crawling. Using confocal imaging, we reveal that PEZO-1 localizes to the sarcolemma and plays a crucial role in modulating calcium dynamics that are important for muscle contraction. When we knocked down pezo-1 expression in striated muscles with RNA interference, calcium levels in head and tail muscles increased. While heightened, the overall trajectory of the calcium signal during the crawl cycle remained the same. While downregulation of pezo-1 led to an increase in crawling speed, it caused a reduction in swimming speed. Reduction in pezo-1 expression also resulted in the increased activation of the ventral tail muscles, and a disruption of dorsoventral movement asymmetry, a critical feature that enables propulsion in water. These alterations were correlated with impaired swimming posture and path curvature, suggesting that PEZO-1 has different functions during swimming and crawling.
Automated microinjection for zebrafish xenograft models
Authors: Ding Yi , van der Kolk Kees-Jan , van der Ent Wietske , Scotto di Mase Michele , Kowald Saskia , Huizing Jenny , Vidal Teuton Jana M , Mishra Gunja , Kempers Maxime , Almter Rusul , Kunz Sandra , Munier Laurine , Koschmann Carl , Waszak Sebastian M. , Di Donato Vincenzo , Dyballa Sylvia , Ten Dijke Peter , Esguerra Camila Vicencio , Jensen Lasse D. , de Sonneville Jan
Published: August 2024

Zebrafish xenograft models have been increasingly recognized for their ability to predict patient responses to cancer therapeutics, suggesting their potential as diagnostic tools in clinical settings. However, these models require the precise microinjection of cancer cell suspensions in many small and fragile zebrafish larvae. Manual injections are so challenging that, even after months of training, variability in experimental results persists among researchers. This limits the uptake and deployment of zebrafish xenograft models for clinical use and drug discovery. To address this challenge, we have designed, built, and validated an automated microinjection robot. Combined results of injections into the vasculature, perivitelline space, and hindbrain ventricle demonstrated an average injection success rate of approximately 60%, with a larvae survival rate exceeding 70%, comparable to manual injections using a traditional micromanipulator. Notably, the full automated mode was twice as fast as manual injections. This automation of the microinjection process significantly reduces the need for extensive personnel training while it enhances reproducibility, efficiency, and accuracy, paving the way for more extensive use of zebrafish xenograft models in drug discovery and patient diagnostics.
Neuronal progenitors suffer genotoxic stress in theDrosophilaclock mutantper0
Authors: Romano Nunzia Colonna , Marchetti Marcella , Marangoni Anna , Leo Laura , Retrosi Diletta , Rosato Ezio , Fanti Laura
Published: August 2024

The physiological role and the molecular architecture of the circadian clock in fully developed organisms are well established. Yet, we have a limited understanding about the function of the clock during ontogenesis. We have used a null mutant (per0) of the clock geneperiod(per) inDrosophila melanogasterto ask whether PER may play a role during normal brain development. In 3rdinstar larvae, we have observed that absence of functionalperresults in increased genotoxic stress compared to wild type controls. We have detected increased double strand DNA breaks in the central nervous system and chromosome aberrations in dividing neuronal precursor cells. We have demonstrated that reactive oxygen species (ROS) are causal to the genotoxic effect and that expression of PER in glia is necessary and sufficient to suppress such a phenotype. Finally, preliminary evidence indicates that absence of PER may result in less condensed chromatin, which may contribute to DNA damage.
Silver nanoparticle induced immunogenic cell death can improve immunotherapy
Authors: Sargsian Ara , Koutsoumpou Xanthippi , Girmatsion Hermon , Buttiens Kiana , Rios Luci Carla , Soenen Stefaan J. , Manshian Bella B.
Published: August 2024

Cancer immunotherapy is often hindered by an immunosuppressive tumor microenvironment (TME). Various strategies are being evaluated to shift the TME from an immunologically ‘cold’ to ‘hot’ tumor and hereby improve current immune checkpoint blockades (ICB). One particular hot topic is the use of combination therapies. Here, we set out to screen a variety of metallic nanoparticles and explored their in-vitro toxicity against a series of tumor and non-tumor cell lines. For silver nanoparticles, we also explored the effects of core size and surface chemistry on cytotoxicity. Ag-citrate-5nm nanoparticles were found to induce high cytotoxicity in Renca cells through excessive generation of reactive oxygen species (ROS) and significantly increased cytokine production. The induced toxicity resulted in a shift of the immunogenic cell death (ICD) marker calreticulin to the cell surface in-vitro and in-vivo. Subcutaneous Renca tumors were treated with anti-PD1 or in combination with Ag-citrate-5nm. The combination group resulted in significant reduction in tumor size, increased necrosis, and immune cell infiltration at the tumor site. Inhibition of cytotoxic CD8+ T cells confirmed the involvement of these cells in the observed therapeutic effects. Our results suggest that Ag-citrate-5nm is able to promote immune cell influx and increase tumor responsiveness to ICB therapies.
High-fat diet exacerbates the loss of bone fracture toughness in aging for C57BL/6JN mice
Authors: Brown Kenna , Vahidi Ghazal , Hislop Brady D. , Moody Maya , Watson Steven , Welhaven Hope D. , Behzad Ramina , Paton Kat O. , Karim Lamya , June Ronald K. , Martin Stephen A. , Heveran Chelsea M.
Published: August 2024

The elderly are at increased risk of bone fracture and more often consume poor quality diets, such as high-fat diet (HFD). We hypothesized that HFD would exacerbate the loss of bone fracture resistance in aging. To test this hypothesis, we fed 5-month and 22-month C57BL/6JN mice of both sexes HFD or low-fat diet for 8 weeks. Aging and HFD lowered bone fracture toughness, while only aging reduced bone strength. At the tissue-scale, aging increased bone mineral maturity, while HFD altered bone mineralization and maturity as well as collagen structure. Cortical bone metabolism was also dysregulated with aging and HFD. Dysregulated pathways in aging and HFD were related to cellular function and viability, or glucose regulation, respectively. Aging with HFD also impacted osteoclast and adipocyte abundance and osteocyte viability. Together, these data demonstrate that HFD may exacerbate the loss of bone matrix quality and fracture resistance in aging.
Rhizosphere Microbiome Influence on Tomato Growth under Low-Nutrient Settings
Authors: Mejia Gerardo , Jara-Servin Angélica , Romero-Chora Luis , Hernández-Álvarez Cristóbal , Peimbert Mariana , Cruz-Ortega Rocío , Alcaraz Luis D.
Published: August 2024

Studies have shown that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates the role of Plant Growth-Promoting Rhizobacteria (PGPR) in enhancing the growth ofSolanum lycopersicumunder hydroponic conditions. We hypothesised that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. Our hydroponic system, with treatments consisting of 50% reduced fertiliser application supplemented with a soil-derived inoculum, exhibited greater bacterial diversity and biomass than controls, suggesting a successful enrichment of PGPR that compensates for nutrient deficiencies. Using 16S rRNA gene sequencing, we found a significant enrichment (p≤ 0.001) and correlation with beneficial plant traits (p≤ 0.05) of bacterial genera such asLuteolibacter,Sphingopyxis, andKaistia. Shotgun metagenomics identified the critical role ofMethyloversatilisin nitrogen fixation and other key taxa bacterial proteins in plant-bacteria interactions. Additionally, our findings identify core taxa across different cultivation systems. These results support the potential for microbiome engineering to enhance microbial diversity and plant productivity, offering a path to reduce fertiliser use in agriculture and improve sustainability.
The ageing stopping network: Regional and network changes in the IFG, preSMA, and STN across the adult lifespan
Authors: Kemp Sarah A , Bazin Pierre-Louis , Miletic Steven , Boag Russell J , Keuken Max , Hinder Mark R , Forstmann Birte
Published: August 2024

Response inhibition, the cancellation of planned movement, is essential for everyday motor control. Extensive fMRI and brain stimulation research provides evidence for the crucial role of a number of cortical and subcortical regions in response inhibition, including the subthalamic nucleus (STN), pre-supplementary motor area (preSMA), and the inferior frontal gyrus (IFG). Current models assume that these regions operate as a network, with action cancellation originating in the cortical areas and then executed rapidly via the subcortex. Response inhibition slows in older age, a change that has been attributed to deterioration or changes in the connectivity and integrity of this network. However, previous research has mainly used whole-brain approaches when investigating changes in structural connectivity across the lifespan, or have used simpler measures to investigate structural ageing. Here, we used high-resolution quantitative and diffusion MRI to extensively examine the anatomical changes that occur in this network across the lifespan. We found substantial changes in iron concentration in these tracts, increases in the apparent diffusion coefficient, and some evidence for demyelination. Conversely, we found very little evidence for age-related anatomical changes in the regions themselves. We propose that some of the functional changes observed in these regions in older adult populations (e.g., increased BOLD recruitment) are a reflection of alterations to the connectivity between the regions, rather than localised regional change.
SynDRep: A Knowledge Graph-Enhanced Tool based on Synergistic Partner Prediction for Drug Repurposing
Authors: Shalaby Karim S. , Rao Sathvik Guru , Schultz Bruce , Hofmann-Apitius Martin , Tom Kodamullil Alpha , Bharadhwaj Vinay Srinivas
Published: August 2024

Motivation

Drug repurposing is gaining interest due to its high cost-effectiveness, low risks, and improved patient outcomes. However, most drug repurposing methods depend on drug-disease-target semantic connections of a single drug rather than insights from drug combination data. In this study, we propose SynDRep, a novel drug repurposing tool based on enriching knowledge graphs (KG) with drug combination effects. It predicts the synergistic drug partner with a commonly prescribed drug for the target disease, leveraging graph embedding and machine learning techniques. This partner drug is then repurposed as a single agent for this disease by exploring pathways between them in KG.

Results

HolE was the best-performing embedding model (with 84.58% of true predictions for all relations), and random forest emerged as the best ML model with an ROC-AUC value of 0.796. Some of our selected candidates, such as miconazole and albendazole for Alzheimer’s disease, have been validated through literature, while others lack either a clear pathway or literature evidence for their use for the disease of interest. Therefore, complementing SynDRep with more specialized KG, and additional training data, would enhance its efficacy and offer cost-effective and timely solutions for patients.

Availability and Implementation

SynDRep is available as an open-source Python package athttps://github.com/SynDRep/SynDRepunder the Apache 2.0 License.
Self-assembly of mycolic acid in water: monolayer or bilayer
Authors: Kumar Yogendra , Basu Subhadip , Maiti Prabal Kumar
Published: August 2024

The enduring pathogenicity of Mycobacterium tuberculosis can be attributed to its lipid-rich cell wall, with mycolic acids (MAs) being a significant constituent. Different MAs’ fluidity and structural adaptability within the bacterial cell envelope significantly influence their physicochemical properties, operational capabilities, and pathogenic potential. Therefore, an accurate conformational representation of various MAs in aqueous media can provide insights into their potential role within the intricate structure of the bacterial cell wall. We have carried out the MD simulations of MAs in an aqueous solution and shed light on the various structural properties such as thickness, order parameters, area-per-MAs, conformational changes, and principle component (PC) in the single component and mixed MAs monolayer. The different conformational populations in the monolayer have been estimated using the distance-based analysis between the function groups represented as W, U, and Z-conformations that lead to the fold of the MAs chain in the monolayer. Additionally, we have also simulated the mixture of alpha-MA (α-MA or AMA), methoxy-MA (MMA), and keto-MA (KMA) with 56% AMA, 40 % MMA, and 14 % KMA composition. The thickness of the MAs monolayer was observed to range from 5 nm to 7 nm with an average 820 kg/m3density for α-MA, MMA, and KMA quantitative agreement with experimental results. The mero-chain (long chain), consisting of a functional group at the proximal and distal positions, tends to fold and exhibit a more disordered phase than the short chain. The keto-MA showed the greatest WUZ total conformations (35.32 %) with decreasing trend of eZ > eU > aU > aZ folds in both single component and mixture. Our results are in quantitative agreement with the experimental observations. The most minor population of sZ folds (0.75 % in a single component and 1.1 % in a mixture). However, eU and aU folds are most probable for the AMA and MMA. One striking observation is the abundance of MA conformers beyond the known WUZ convention because of the wide range distribution of intramolecular distances and change in dihedral angles. From the thermodynamic viewpoint, all monolayers were found to be stable in nature. The results from enhanced simulation revealed that changes in the magnitude of minimum free energy of the MAs are in order of KMA > AMA > MMA, and keto-MA exhibits more resistance (based on free energy values) for the drug molecules to permeate through the monolayer.
Audiomotor prediction errors drive speech adaptation even in the absence of overt movement
Authors: Parrell Benjamin , Naber Chris , Kim Olivia A. , Nizolek Caroline A. , McDougle Samuel D.
Published: August 2024

Observed outcomes of our movements sometimes differ from our expectations. These sensory prediction errors recalibrate the brain’s internal models for motor control, reflected in alterations to subsequent movements that counteract these errors (motor adaptation). While leading theories suggest that all forms of motor adaptation are driven by learning from sensory prediction errors, dominant models of speech adaptation argue that adaptation results from integrating time-advanced copies of corrective feedback commands into feedforward motor programs. Here, we tested these competing theories of speech adaptation by inducing planned, but not executed, speech. Human speakers (male and female) were prompted to speak a word and, on a subset of trials, were rapidly cued to withhold the prompted speech. On standard trials, speakers were exposed to real-time playback of their own speech with an auditory perturbation of the first formant to induce single-trial speech adaptation. Speakers experienced a similar sensory error on movement cancelation trials, hearing a perturbation applied to a recording of their speech from a previous trial at the time they would have spoken. Speakers adapted to auditory prediction errors in both contexts, altering the spectral content of spoken vowels to counteract formant perturbations even when no actual movement coincided with the perturbed feedback. These results build upon recent findings in reaching, and suggest that prediction errors, rather than corrective motor commands, drive adaptation in speech.
Deep graph convolutional neural network for one-dimensional hepatic vascular haemodynamic prediction
Authors: Zhang Weiqng , Shi Shuaifeng , Qi Quan
Published: August 2024

Hepatic vascular hemodynamics is an important reference indicator in the diagnosis and treatment of hepatic diseases. However, Method based on Computational Fluid Dynamics(CFD) are difficult to promote in clinical applications due to their computational complexity. To this end, this study proposed a deep graph neural network model to simulate the one-dimensional hemodynamic results of hepatic vessels. By connecting residuals between edges and nodes, this framework effectively enhances network prediction accuracy and efficiently avoids over-smoothing phenomena. The graph structure constructed from the centerline and boundary conditions of the hepatic vasculature can serve as the network input, yielding velocity and pressure information corresponding to the centerline. Experimental results indicate that our proposed method achieves higher accuracy on a hepatic vasculature dataset with significant individual variations and can be extended to applications involving other blood vessels. Following training, errors in both the velocity and pressure fields are maintained below 1.5%. The trained network model can be easily deployed on low-performance devices and, compared to CFD-based methods, can output velocity and pressure along the hepatic vessel centerline at a speed three orders of magnitude faster.

Author summary

When using deep learning methods for hemodynamic analysis, simple point cloud data cannot express the real geometric structure of the blood vessels, and it is necessary for the network to have additional geometric information extraction capability. In this paper, we use graph structure to express the structure of hepatic blood vessels, and deep graph neural network to predict the corresponding hemodynamic parameters. The graph structure can effectively express the geometric information of hepatic blood vessels and the topology of branch blood vessels, which can effectively improve the prediction accuracy with strong geometric generalisation ability. The results show that the method achieves the highest prediction accuracy in the one-dimensional hepatic vessel blood flow simulation dataset, and the experimental results on the human aorta also show that our method can be effectively applied to the blood flow simulation of other vascular organs.
Borrelia burgdorferiSecretes c-di-AMP as an Extracellular Pathogen-Associated Molecular Pattern to Elicit Type I Interferon Responses in Mammalian Hosts
Authors: Priya Raj , Ye Meiping , Raghunanadanan Sajith , Liu Qiang , Li Wei , Yu Qigui , Lou Yongliang , Sintim Herman O. , Yang X. Frank
Published: August 2024

Borrelia burgdorferi(B. burgdorferi), an extracellular spirochetal pathogen, elicits a type-I interferon (IFN-I) response that contributes to the pathology of Lyme disease, including the development and severity of Lyme arthritis. However, the specific Pathogen-Associated Molecular Patterns (PAMPs) ofB. burgdorferiresponsible for triggering the IFN-I response are not well understood. Previous studies have identified an unknown, nuclease-resistant component inB. burgdorfericulture supernatants that significantly stimulates the IFN-I response, but its identity remains unknown. In this study, we reveal thatB. burgdorferisecretes cyclic-di-adenosine monophosphate (c-di-AMP) as a key extracellular PAMP, inducing the host IFN-I response in macrophages. Using genetically manipulatedB. burgdorferistrains, we demonstrate a requirement of c-di-AMP for stimulating IFN-I response by macrophagesex vivo. Additionally, infecting mice withB. burgdorferialongside exogenous c-di-AMP resulted in a markedly increased IFN-I response in mouse tissues. Furthermore, inactivation or inhibition of the host STING signaling pathway significantly reduced the IFN-I response, indicating that c-di-AMP-induced IFN-I production is STING-dependent. Our findings identify c-di-AMP as a crucial PAMP secreted byB. burgdorferito elicit the host IFN-I response via activation of STING signaling pathway, suggesting that targeting c-di-AMP production could represent a novel therapeutic strategy against Lyme arthritis.

Borrelia burgdorferi, the bacteria that causes Lyme disease, induces a robust host immune response, including the production of type-I interferon (IFN-I). While this response helps combat the infection, it also contributes to complications such as Lyme arthritis. Our research aimed to identify the specific bacterial component that triggers the IFN-I response. We discovered thatBorrelia burgdorferireleases a second messenger molecule, cyclic-di-adenosine monophosphate (c-di-AMP), which is recognized by host immune cells and subsequently triggers IFN-I production. This finding is significant as it advances our understanding of Lyme disease pathogenesis and offers a new strategy to tackle Lyme disease by targeting the production of c-di-AMP, in which we may be able to reduce the severity of the disease and mitigate long-term tissue damage.

One sentence summary

Borrelia burgdorferic-di-AMP induces Type I IFN response
Orexin population activity precisely reflects net body movement across behavioral and metabolic states
Authors: Tesmer Alexander L. , Viskaitis Paulius , Donegan Dane , Bracey Eva F. , Grujic Nikola , Patriarchi Tommaso , Peleg-Raibstein Daria , Burdakov Denis
Published: August 2024

Tracking net body movement in real time may enable the brain to estimate ongoing demands and thus better orchestrate muscle tone, energy balance, and arousal. To identify neural populations specializing in tracking net body movement, here we compared self-initiated movement-related activity across genetically-defined subcortical neurons in the mouse brain, including dopaminergic, glutamatergic, noradrenergic, and key peptidergic neurons. We show that hypothalamic orexin/hypocretin-producing neurons (HONs) are exceptionally precise movement-trackers, encoding net body movement across multiple classified behaviors with a high degree of precision, independent of head acceleration. This tracking was so precise, that video analysis of the mouse body movement reliably served as a low-cost biometric for HON population activity. The movement tracking was independent of internal nutritional states, and occurred in a communication bandwidth distinct from HON encoding of blood glucose. At key projection targets, orexin/hypocretin peptide outputs correlated with self-initiated movement in a projection-specific manner, indicating functional heterogeneity in HON outputs. Finally, we found that body movement was not encoded to the same extent in other key neural populations related to arousal or energy. These findings indicate that subcortical orchestrators of arousal and metabolism are finely tuned to encode net body movement, constituting a bridge multiplexing ongoing motor activity with internal energy resources.
VIPER-TACs leverage viral E3 ligases for disease-specific targeted protein degradation
Authors: Mangano Kyle , Guenette Robert G. , Hill Spencer , Li Shiqian , Yang Seung Wook , Ashton Kate S. , Potts Patrick Ryan
Published: August 2024

In targeted protein degradation (TPD) a protein of interest is degraded by chemically induced proximity to an E3 ubiquitin ligase. One limitation of using TPD therapeutically is that most E3 ligases have broad tissue expression, which can contribute to toxicity via target degradation in healthy cells. Many pathogenic and oncogenic viruses encode E3 ligases (vE3s), which de facto have strictly limited expression to diseased cells. Here, we provide proof-of-concept forViral E3Pan-EssentialRemovingTargetingChimeras (VIPER-TACs) that are bi-functional molecules that utilize viral E3 ubiquitin ligases to selectively degrade pan-essential proteins and eliminate diseased cells. We find that the human papillomavirus (HPV) ligase E6 can degrade the SARS1 pan-essential target protein in a model of HPV-positive cervical cancer to selectively kill E6 expressing cancer cells. Thus, VIPER-TACs have the capacity to dramatically increase the therapeutic window, alleviate toxicity concerns, and ultimately expand the potential target space for TPD.
Circadian geneBmal1in the lateral habenula regulates alcohol drinking behavior in a sex specific manner
Authors: Goldfarb Cassandra , Hasenhundl Vanessa , Menasce Arianne , Amir Shimon , Schöttner Konrad
Published: August 2024

The circadian clock regulates most aspects of mammalian physiology and behaviour, including alcohol drinking behaviour. Disrupted circadian clock function via deletion of clock genes along the mesolimbic dopamine (DA) pathway has been linked to altered patterns of alcohol drinking behaviour. The lateral habenula (LHb), an epithalamic structure that house a semi-autonomous circadian clock, is a negative regulator of the mesolimbic DA system and of alcohol consumption. To study the role of the LHb circadian clock in alcohol consumption, we knocked out the core clock gene,Bmal1specifically in the LHb and examined the impact on various alcohol drinking paradigms and affective behaviours in male and female mice. Our findings demonstrate thatBmal1deletion in the LHb leads to sex-specific alterations in alcohol consumption. Male knockout mice exhibited increased voluntary alcohol intake, enhanced consumption of a bitter alcohol solution, and elevated alcohol binge drinking compared to controls. Conversely, female knockouts showed a marginal decrease in voluntary intake, significantly reduced consumption of an aversive alcohol solution, and lower post abstinence, relapse-like drinking. These results indicate thatBmal1in the LHb exerts a repressive effect on alcohol intake in males, while it facilitates intake under certain aversive conditions in females. Interestingly,Bmal1deletion did not significantly affect anxiety-like or depressive-like behaviours, suggesting that the habenular clock’s role in alcohol consumption is independent of affective state. These findings markBmal1in the LHb as a novel sexually dimorphic regulator of alcohol consumption in mice. Potential mechanisms involving the circadian modulation of DA and serotonin signaling pathways by the LHb clock is discussed.
Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition
Authors: Fahlberg Marissa D. , Forward Sarah , Assita Emane Rose , Mazzola Michael , Kiem Anna , Handley Maris , Yun Seok-Hyun , Kwok Sheldon J.J.
Published: August 2024

The fixation and permeabilization of cells are essential for labeling intracellular biomarkers in flow cytometry. However, these chemical treatments often alter fragile targets, such as cell surface and fluorescent proteins, and can destroy chemically-sensitive fluorescent labels. This reduces measurement accuracy and introduces compromises into sample workflows, leading to losses in data quality. Here, we demonstrate a novel multi-pass flow cytometry approach to address this long-standing problem. Our technique utilizes individual cell barcoding with laser particles, enabling sequential analysis of the same cells with single-cell resolution maintained. Chemically-fragile protein markers and their fluorochrome conjugates are measured prior to destructive sample processing and adjoined to subsequent measurements of intracellular markers after fixation and permeabilization. We demonstrate the effectiveness of our technique in accurately measuring intracellular fluorescent proteins and methanol-sensitive antigens and fluorophores, along with various surface and intracellular markers. This approach significantly enhances assay flexibility, enabling accurate and comprehensive cell analysis without the constraints of conventional one-time measurement flow cytometry. This innovation paves new avenues in flow cytometry for a wide range of applications in immuno-oncology, stem cell research, and cell biology.
Age-Dependent Cortical Overconnectivity in Shank3 Mice is Reversed by Anesthesia
Authors: Elena Montagni , Ambrosone Manuel , Martello Alessandra , Curti Lorenzo , Baroncelli Laura , Guido Mannaioni , Pavone Francesco Saverio , Masi Alessio , Allegra Mascaro Anna Letizia
Published: August 2024

Growing evidence points to brain network dysfunction as a central neurobiological basis for autism spectrum disorders (ASDs). As a result, studies on Functional Connectivity (FC) have become pivotal for understanding the large-scale network alterations associated with ASD. Despite ASD being a neurodevelopmental disorder, and FC being significantly influenced by the brain state, existing FC studies in mouse models predominantly focus on adult subjects under anesthesia. The differential impact of anesthesia and age on cortical functional networks in ASD subjects remains unexplored. To fill this gap, we conducted a longitudinal evaluation of FC across three brain states and three ages in the Shank3b mouse model of autism. We utilized wide-field calcium imaging to monitor cortical activity in Shank3b+/-and Shank3b+/+mice fromlate development (P45) through adulthood (P90), and isoflurane anesthesia to manipulate the brain state. Our findings reveal that network hyperconnectivity, emerging from the barrel-field cortices during the juvenile stage, progressively expands to encompass the entire dorsal cortex in adult Shank3b+/-mice. Notably, the severity of FC imbalance is highly dependent on the brain state: network alterations are more pronounced in the awake state and shift towards hypoconnectivity under anesthesia. These results underscore the crucial role of anesthesia in detecting autism-related FC alterations and identify a significant network of early cortical dysfunction associated with autism. This network represents a potential target for non-invasive translational treatments.
Experimental and Computational Methods for Allelic Imbalance Analysis from Single-Nucleus RNA-seq Data
Authors: Simmons Sean K , Adiconis Xian , Haywood Nathan , Parker Jacob , Lin Zechuan , Liao Zhixiang , Tuncali Idil , Al'Khafaji Aziz , Shin Asa , Jagadeesh Karthik , Gosik Kirk , Gatzen Michael , Smith Jonathan T , El Kodsi Daniel N , Kuras Yuliya , Baecher-Allan Clare , Serrano Geidy E , Beach Thomas G , Garimella Kiran , Rozenblatt-Rosen Orit , Regev Aviv , Dong Xianjun , Scherzer Clemens , Levin Joshua Z
Published: August 2024

Single-cell RNA-seq (scRNA-seq) is emerging as a powerful tool for understanding gene function across diverse cells. Recently, this has included the use of allele-specific expression (ASE) analysis to better understand how variation in the human genome affects RNA expression at the single-cell level. We reasoned that because intronic reads are more prevalent in single-nucleus RNA-Seq (snRNA-Seq), and introns are under lower purifying selection and thus enriched for genetic variants, that snRNA-seq should facilitate single-cell analysis of ASE. Here we demonstrate how experimental and computational choices can improve the results of allelic imbalance analysis. We explore how experimental choices, such as RNA source, read length, sequencing depth, genotyping, etc., impact the power of ASE-based methods. We developed a new suite of computational tools to process and analyze scRNA-seq and snRNA-seq for ASE. As hypothesized, we extracted more ASE information from reads in intronic regions than those in exonic regions and show how read length can be set to increase power. Additionally, hybrid selection improved our power to detect allelic imbalance in genes of interest. We also explored methods to recover allele-specific isoform expression levels from both long- and short-read snRNA-seq. To further investigate ASE in the context of human disease, we applied our methods to a Parkinson's disease cohort of 94 individuals and show that ASE analysis had more power than eQTL analysis to identify significant SNP/gene pairs in our direct comparison of the two methods. Overall, we provide an end-to-end experimental and computational approach for future studies.
Eomes directs the formation of spatially and functionally diverse extra-embryonic hematovascular tissues
Authors: Theeuwes Bart , Harland Luke TG , Bisia Alexandra , Costello Ita , Ton Mai-Linh , Lohoff Tim , Clark Stephen J , Argelaguet Ricard , Wilson Nicola K , Reik Wolf , Bikoff Elizabeth , Robertson Elizabeth J , Gottgens Berthold
Published: August 2024

During mouse gastrulation, extraembryonic mesoderm (ExEM) contributes to the extraembryonic yolk sac (YS) and allantois, both of which are essential for successful gestation. Although the genetic networks coordinating intra-embryonic mesodermal subtype specification are well-studied, the mechanisms driving ExEM diversification are poorly understood. Here, we reveal that embryoid bodyin vitrodifferentiation generates two distinct lineages of mesodermal cells matching YS and allantois respectively. Combiningin vitromodels within vivochimeric embryo analysis, we discover that Eomesodermin (Eomes) regulates the formation of a subset of YS-fated ExEM but is dispensable for allantois formation. Furthermore, simultaneous disruption of Eomes and T impedes the specification of any YS or allantois mesoderm, indicating compensatory roles for T during allantois formation when Eomes is disrupted. Our study highlights previously unrecognized functional and mechanistic diversity in ExEM diversification and endothelial development and introduces a tractable EB model to dissect the signaling pathways and transcriptional networks driving the formation of key extraembryonic tissues.
The relationship between sleep and cognitive performance on tests of pattern separation
Authors: Roenningen Aina , Gill Devan , Kent Brianne A
Published: August 2024

Study objectives

Sleep disturbances are considered both a risk factor and symptom of dementia. The present research aimed to identify cognitive tests that are sensitive to sleep-dependent cognition, focusing on cognitive tests designed to evaluate the earliest cognitive changes in dementia.

Methods

In Experiment 1, we recruited younger (n=89) and older (n=40) adults and remotely monitored their sleep patterns for 7 consecutive days using actigraphy and sleep diaries. On day 7, participants completed a battery of cognitive tests, which included the Prodromal Alzheimer’s and MCI battery from the Cambridge Neuropsychological Test Automated Battery (CANTAB) and the Mnemonic Similarity Task (MST). In Experiment 2, we examined the effects of a night of total sleep deprivation on cognitive performance in young adults. We observed a sleep deprived group (n=16) overnight in the lab. The rested control group (n=32) slept normally at home.

Results

In Experiment 1, there was a significant relationship between performance on MST and total sleep time in the older adults. There were no relationships between cognitive performance and sleep quantity or quality in the younger adults. In the older adults, Montreal Cognitive Assessment (MoCA) scores were correlated with performance on the CANTAB and MST. In Experiment 2, the young adults who underwent 24-hour sleep deprivation performed worse than the rested participants on the MST task.

Conclusion

Performance on cognitive tests designed to assess pattern separation are sensitive to sleep patterns, particularly in older adults and should be evaluated for potential use as clinical trial outcome measures for sleep-promoting treatments.

Statement of Significance

There is growing emphasis on the importance of sleep as a potential therapeutic target for neurodegenerative diseases (e.g., Alzheimer’s disease). Finding cognitive measures sensitive to sleep are needed for use as outcome measures in clinical trials evaluating the effectiveness of sleep-promoting interventions. Our research addresses this need by investigating the relationship between sleep patterns and performance on a variety of cognitive tests. Our results suggest that cognitive tests designed to assess pattern separation are uniquely sensitive to sleep quality and quantity, particularly in older adults.
Contingency awareness shapes neural responses in fear conditioning
Authors: Pavlov Yuri G. , Menger Nick S. , Keil Andreas , Kotchoubey Boris
Published: August 2024

Contingency awareness refers to an observer’s ability to identify the association between a conditioned (CS) and an unconditioned stimulus (US). A widely held belief in human fear conditioning is that this form of associative learning may occur independently of contingency awareness. To test this hypothesis, in this preregistered study (https://osf.io/vywq7), we recorded electroencephalography (EEG) during a task, where participants were presented with compounds of words (from two semantic categories) and tactile stimulation, followed by either a neutral sound (US-) or a loud noise (US+). Based on interviews, participants were divided into an aware (N=50) and an unaware (N=31) group. Only the aware group showed signs of learning, as expressed in larger stimulus-preceding negativity developing before US+ and a stronger theta response to vibrations predicting US+. The aware group also showed stronger alpha and beta suppression around the vibrations and a weaker theta response to US+, possibly indicating heightened attention to the cue and the violation/confirmation of expectation. Personality tests showed that elevated anxiety, neuroticism, higher intolerance of uncertainty, or harm avoidance are not predictive to the acquisition of contingency awareness. Our findings support the notion that fear conditioning, as reflected in cortical measures, cannot occur without contingency awareness.