bluuebunny/crossref_metadata_2025 huggingface dataset:
The HRA Organ Gallery Affords Immersive Superpowers for Building and Exploring the Human Reference Atlas with Virtual Reality
Authors: Bueckle Andreas , Qing Catherine , Luley Shefali , Kumar Yash , Pandey Naval , Börner Katy
Published: February 2023

The Human Reference Atlas (HRA,https://humanatlas.io) funded by the NIH Human Biomolecular Atlas Program (HuBMAP,https://commonfund.nih.gov/hubmap) and other projects engages 17 international consortia to create a spatial reference of the healthy adult human body at single-cell resolution. The specimen, biological structure, and spatial data that define the HRA are disparate in nature and benefit from a visually explicit method of data integration. Virtual reality (VR) offers unique means to enable users to explore complex data structures in a threedimensional (3D) immersive environment. On a 2D desktop application, the 3D spatiality and real-world size of the 3D reference organs of the atlas is hard to understand. If viewed in VR, the spatiality of the organs and tissue blocks mapped to the HRA can be explored in their true size and in a way that goes beyond traditional 2D user interfaces. Added 2D and 3D visualizations can then provide data-rich context. In this paper, we present the HRA Organ Gallery, a VR application to explore the atlas in an integrated VR environment. Presently, the HRA Organ Gallery features 55 3D reference organs,1,203 mapped tissue blocks from 292 demographically diverse donors and 15 providers that link to 5,000+ datasets; it also features prototype visualizations of cell type distributions and 3D protein structures. We outline our plans to support two biological use cases:on-ramping novice and expert users to HuBMAP data available via the Data Portal(https://portal.hubmapconsortium.org), andquality assurance/quality control (QA/QC) for HRA data providers. Code and onboarding materials are available athttps://github.com/cns-iu/ccf-organ-vr-gallery#readme.
P-Selectin promotes SARS-CoV-2 interactions with platelets and the endothelium
Authors: Moreno Cesar L. , Castanheira Fernanda V. S. , Stella Alberto Ospina , Chung Felicity , Aggarwal Anupriya , Cole Alexander J. , Loo Lipin , Dupuy Alexander , Kong Yvonne , Hagimola Lejla , Fenwick Jemma , Coleman Paul , Willson Michelle , Bui-Marinos Maxwell , Hesselson Daniel , Gamble Jennifer , Passam Freda , Turville Stuart , Kubes Paul , Neely G. Gregory
Published: February 2023

COVID-19 causes a clinical spectrum of acute and chronic illness and host / virus interactions are not completely understood1,2. To identify host factors that can influence SARS-CoV-2 infection, we screened the human genome for genes that, when upregulated, alter the outcome of authentic SARS-CoV-2 infection. From this, we identify 34 new genes that can alter the course of infection, including the innate immune receptor P-selectin, which we show is a novel SARS-CoV-2 spike receptor. At the cellular level expression of P-selectin does not confer tropism for SARS-CoV-2, instead it acts to suppress infection. More broadly, P-selectin can also promote binding to SARS-CoV-2 variants, SARS-CoV-1 and MERS, acting as a general spike receptor for highly pathogenic coronaviruses. P-selectin is expressed on platelets and endothelium3, and we confirm SARS-CoV-2 spike interactions with these cells are P-selectin-dependent and can occur under shear flow conditions.In vivo, authentic SARS-CoV-2 uses P-selectin to home to airway capillary beds where the virus interacts with the endothelium and platelets, and blocking this interaction can clear vascular-associated SARS-CoV-2 from the lung. Together we show for the first time that coronaviruses can use the leukocyte recruitment system to control tissue localization, and this fundamental insight may help us understand and control highly pathogenic coronavirus disease progression.
Optimal evaluation of energy yield and driving force in microbial metabolic pathway variants
Authors: Taha Ahmed , Penas David R , Patón Mauricio , Banga Julio R , Rodríguez Jorge
Published: February 2023

This work presents a methodology to evaluate the bioenergetic feasibility of alternative metabolic pathways for a given microbial conversion, optimising their energy yield and driving forces as a function of the concentration of metabolic intermediates. The tool, based on thermodynamic principles and multi-objective optimisation, accounts for pathway variants in terms of different electron carriers, as well as energy conservation (proton translocating) reactions within the pathway. The method also accommodates other constraints, some of them non-linear, such as the balance of conserved moieties. The approach involves the transformation of the maximum energy yield problem into a multi-objective linear optimisation problem which is then subsequently solved using the epsilon-constraint method, highlighting the trade-off between yield and rate in metabolic reactions. The methodology is applied to analyse several pathway alternatives occurring during propionate oxidation in anaerobic fermentation processes, as well as to the reverse TCA cycle pathway occurring during autotrophic microbial CO2fixation. The results obtained using the developed methodology match previously reported literature, and bring about insights into the studied pathways.
Quantitative classification of energy landscapes inferred from single nanoparticle tracking of membrane receptors inside nanodomains reveals confinement functional and molecular features
Authors: Yu Chao , Richly Maximilian , Hoang Thi Thuy , El Beheiry Mohammed , Türkcan Silvan , Masson Jean-Baptiste , Alexandrou Antigoni , Bouzigues Cedric I.
Published: February 2023

The cell membrane organization has been hypothesized for a long time to have an essential functional role, through the control of membrane receptor confinement in micro- or nanodomains. Several mechanisms have been proposed to account for these properties, though some features of the resulting organization have remained controversial, notably the nature, size, and stability of cholesterol- and sphingolipid-rich domains called rafts.

Here, we quantitatively probed the energy landscape experienced by single nanoparticle-labeled membrane receptors - epidermal growth factor receptors (EGFR), transferrin receptors (TfR), and receptors of ε-toxin produced byC. perfringensand α-toxin ofC.Septicum(CPεTR and CSαTR, respectively) - through the development of new computational methods. By establishing a new analysis pipeline combining Bayesian inference, decision trees and clustering approaches, we indeed systematically classified single protein trajectories according to the type of confining energy landscape. This revealed the existence of only two distinct organization modalities: (A) confinement in a quadratic energy landscape for EGF, CPεT and CSαT receptors and (B) free diffusion in confinement domains resulting from the steric hindrance due to F-actin barriers for transferrin receptors.

The characterization of confinement energy landscapes by Bayesian inference furthermore revealed the role of interactions with the domain environment in cholesterol- and sphingolipid-rich domains with (in the case of EGFR) or without (for CPεT and CSαT receptors) parallel interactions with F-actin, to regulate the confinement energy depth. Strikingly, these two distinct mechanisms result in the same organization type (A). We furthermore revealed that the apparent domain sizes for these receptor trajectories resulted from Brownian exploration of the energy landscape in a steady-state like regime at a common effective temperature, independently of the underlying molecular mechanisms. These results highlight that the membrane organization in confinement domains may be more adequately described as interaction hotspots rather than rafts with abrupt domain boundaries.

Altogether, these results establish a new computational approach, which paves the way to the constitution of an atlas of energy landscape of membrane proteins and of their control mechanisms, and support a new general model for functional receptor confinement in membrane nanodomains.
Modelling Phenomenological Differences in Aetiologically Distinct Visual Hallucinations Using Deep Neural Networks
Authors: Suzuki Keisuke , Seth Anil K. , Schwartzman David J.
Published: February 2023

Visual hallucinations (VHs) are perceptions of objects or events in the absence of the sensory stimulation that would normally support such perceptions. Although all VHs share this core characteristic, there are substantial phenomenological differences between VHs that have different aetiologies, such as those arising from neurological conditions, visual loss, or psychedelic compounds. Here, we examine the potential mechanistic basis of these differences by leveraging recent advances in visualising the learned representations of a coupled classifier and generative deep neural network – an approach we call ‘computational (neuro)phenomenology’. Examining three aetiologically distinct populations in which VHs occur - neurological conditions (Parkinson’s Disease and Lewy Body Dementia), visual loss (Charles Bonnet Syndrome, CBS), and psychedelics - we identify three dimensions relevant to distinguishing these classes of VHs: realism (veridicality), dependence on sensory input (spontaneity), and complexity. By selectively tuning the parameters of the visualisation algorithm to reflect influence along each of these phenomenological dimensions we were able to generate ‘synthetic VHs’ that were characteristic of the VHs experienced by each aetiology. We verified the validity of this approach experimentally in two studies that examined the phenomenology of VHs in neurological and CBS patients, and in people with recent psychedelic experience. These studies confirmed the existence of phenomenological differences across these three dimensions between groups, and crucially, found that the appropriate synthetic VHs were representative of each group’s hallucinatory phenomenology. Together, our findings highlight the phenomenological diversity of VHs associated with distinct causal factors and demonstrate how a neural network model of visual phenomenology can successfully capture the distinctive visual characteristics of hallucinatory experience.
Orthogonal outlier detection and dimension estimation for improved MDS embedding of biological datasets
Authors: Li Wanxin , Mirone Jules , Prasad Ashok , Miolane Nina , Legrand Carine , Duc Khanh Dao
Published: February 2023

Conventional dimensionality reduction methods like Multidimensional Scaling (MDS) are sensitive to the presence of orthogonal outliers, leading to significant defects in the embedding. We introduce a robust MDS method, called DeCOr-MDS (Detection and Correction of Orthogonal outliers using MDS), based on the geometry and statistics of simplices formed by data points, that allows to detect orthogonal outliers and subsequently reduce dimensionality. We validate our methods using synthetic datasets, and further show how it can be applied to a variety of large real biological datasets, including cancer image cell data and human microbiome project data.
NeoTCR: an immunoinformatic database of experimentally-supported functional neoantigen-specific TCR sequences
Authors: Zhou Weijun , Xiang Wenting , Yu Jinyi , Ruan Zhihan , Pan Yichen , Wang Kankan , Liu Jian
Published: February 2023

Neoantigen-based immunotherapy has demonstrated of long-lasting antitumor activity. Recognition of neoantigens by T cell receptors (TCRs) is considered a trigger for antitumor responses. Due to the overwhelming number of TCR repertoires in the human genome, it is challenging to computationally pinpoint neoantigen-specific TCRs. Recent studies have identified a number of functional neoantigen-specific TCRs, but the corresponding information is scattered across published literature and is difficult to retrieve. To improve access to these data, we developed the NeoTCR, an immunoinformatic database containing a unified description of publicly available neoantigen-specific TCR sequences, as well as relevant information on targeted neoantigens, from experimentally supported studies across 18 cancer subtypes. A user-friendly web interface allows interactive browsing and running of complex database queries based on numerous criteria. To facilitate rapid identification of neoantigen-specific TCRs from raw sequencing data, NeoTCR offers a one-stop analysis for annotation and visualization of TCR clonotypes, discovery of existing neoantigen-specific TCRs, and exclusion of bystander viral-associated TCRs. NeoTCR will serve as a valuable platform to study the biological functions of neoantigen-associated T-cells in anti-tumor immunity to better apply neoantigen-specific TCRs in clinics. NeoTCR is available athttp://www.neotcrdb.com/.
Mitochondrial Pyruvate Carrier Inhibition Attenuates Hepatic Stellate Cell Activation and Liver Injury in a Mouse Model of Metabolic Dysfunction-associated Steatotic Liver Disease
Authors: Habibi Mohammad , Ferguson Daniel , Eichler Sophie J. , Chan Mandy M. , LaPoint Andrew , Shew Trevor M. , He Mai , Lutkewitte Andrew J. , Schilling Joel D. , Cho Kevin Y. , Patti Gary J. , Finck Brian N.
Published: February 2023

Hepatic stellate cells (HSC) are non-parenchymal liver cells that produce extracellular matrix comprising fibrotic lesions in chronic liver diseases. Prior work demonstrated that mitochondrial pyruvate carrier (MPC) inhibitors suppress HSC activation and fibrosis in a mouse model of metabolic dysfunction-associated steatohepatitis (MASH). In the present study, pharmacologic or genetic inhibition of the MPC in HSC decreased expression of markers of activationin vitro. MPC knockdown also reduced the abundance of several intermediates of the TCA cycle, and diminished α-ketoglutarate played a key role in attenuating HSC activation by suppressing hypoxia inducible factor-1α signaling. On high fat diets, mice with HSC-specific MPC deletion exhibited reduced circulating transaminases, numbers of HSC, and hepatic expression of markers of HSC activation and inflammation compared to wild-type mice. These data suggest that MPC inhibition modulates HSC metabolism to attenuate activation and illuminate mechanisms by which MPC inhibitors could prove therapeutically beneficial for treating MASH.
DeepTAP: an RNN-based method of TAP-binding peptide prediction in the selection of tumor neoantigens
Authors: Zhang Xue , Wu Jingcheng , Baeza Joseph , Gu Katie , Zhou Zhan
Published: February 2023

The transport of antigenic peptides from cytoplasm to the endoplasmic reticulum (ER) via transporter associated with antigen processing (TAP) is a critical step during the presentation of tumor neoantigens. The application of computational approaches significantly speed up the analysis of this biological process. Here, we present a tool named DeepTAP for TAP-binding peptide prediction, which employs a sequence-based multilayered recurrent neural network (RNN). Compared with traditional machine learning and other available prediction tools, DeepTAP achieves state-of-the-art performance on the benchmark datasets. The source code and dataset of DeepTAP are available freely via GitHub athttps://github.com/zjupgx/DeepTAP.
kakapo: Easy extraction and annotation of genes from raw RNA-seq reads
Authors: Ramanauskas Karolis , Igić Boris
Published: February 2023

kakapo(kākāpō) is a python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing assembly of entire transcriptomes. The pipeline identifies open reading frames in the assembled gene transcripts and annotates them. It optionally filters raw reads for ribosomal, plastid, and mitochondrial reads, or reads belonging to non-target organisms (e.g., viral, bacterial, human).kakapocan be employed to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics or candidate genes and gene families in phylogenomic and metagenomic studies. We provide example applications and discuss how its use can offset the declining value of the GenBank’s single-gene databases and help assemble datasets for a variety of phylogenetic analyses.
Transmembrane protein CD69 acts as an S1PR1 agonist
Authors: Chen Hongwen , Qin Yu , Chou Marissa , Cyster Jason G. , Li Xiaochun
Published: February 2023

The activation of Sphingosine-1-phosphate receptor 1 (S1PR1) by S1P promotes lymphocyte egress from lymphoid organs, a process critical for immune surveillance and T cell effector activity1-4. Multiple drugs that inhibit S1PR1 function are in use clinically for the treatment of autoimmune diseases. Cluster of Differentiation 69 (CD69) is an endogenous negative regulator of lymphocyte egress that interacts with S1PR1 incisto facilitate internalization and degradation of the receptor5,6. The mechanism by which CD69 causes S1PR1 internalization has been unclear. Moreover, although there are numerous class A GPCR structures determined with different small molecule agonists bound, it remains unknown whether a transmembrane protein per se can act as a class A GPCR agonist. Here, we present the cryo-EM structure of CD69-bound S1PR1 coupled to the heterotrimeric Gicomplex. The transmembrane helix (TM) of one protomer of CD69 homodimer contacts the S1PR1-TM4. This interaction allosterically induces the movement of S1PR1-TMs 5-6, directly activating the receptor to engage the heterotrimeric Gi. Mutations in key residues at the interface affect the interactions between CD69 and S1PR1, as well as reduce the receptor internalization. Thus, our structural findings along with functional analyses demonstrate that CD69 acts incisas a protein agonist of S1PR1, thereby promoting Gi-dependent S1PR1 internalization, loss of S1P gradient sensing, and inhibition of lymphocyte egress.
The SapM phosphatase arrests phagosome maturation in an ESX-1 independent manner inMycobacterium tuberculosisand BCG
Authors: Xander Christian , Rajagopalan Saranathan , Jacobs William R , Braunstein Miriam
Published: February 2023

Mycobacterium tuberculosis(Mtb) is an intracellular pathogen that survives and grows in macrophages. A mechanism used byMtbto achieve intracellular survival is to secrete effector molecules that arrest the normal process of phagosome maturation. Through phagosome maturation arrest (PMA),Mtbremains in an early phagosome and avoids delivery to degradative phagolysosomes. One PMA effector ofMtbis the secreted SapM phosphatase. Because the host target of SapM, phosphatidylinositol-3-phosphate (PI3P), is located on the cytosolic face of the phagosome, SapM needs to be both released by the mycobacteria and escape the phagosome to carry out its function. To date, the only mechanism known forMtbmolecules to escape the phagosome is phagosome permeabilization by the ESX-1 secretion system. To understand this step of SapM function in PMA, we generated identical in-framesapMmutants in both the attenuatedMycobacterium bovisbacille Calmette-Guérin (BCG) vaccine strain, which lacks the ESX-1 system, andMtb. Characterization of these mutants demonstrated that SapM is required for PMA in both BCG andMtb. Further, by establishing a role for SapM in PMA in BCG, and subsequently in aMtbmutant lacking the ESX-1 system, we demonstrated that the role of SapM is ESX-1-independent. We further determined that ESX-2 or ESX-4 are also not required for SapM to function in PMA. These results indicate that SapM is a secreted effector of PMA in both BCG andMtband that it functions independent of the known mechanism forMtbmolecules to escape the phagosome.
Dysregulated miR-3959-3p in response to Lumpy skin disease virus
Authors: Pandita Sakshi , Singh Davinder , Kumar Naveen , Chander Yogesh
Published: February 2023

Lumpy skin disease virus (LSDV), a member of theCapripoxvirusgenus, causes substantial economic losses in the livestock industry and is rapidly spreading among various LSDV-free countries across the globe. Viral infections are known to alter the cellular miRNA expression profile of the host significantly.Besides being important biomarker candidates, circulating miRNAs have a significant role in controlling viral infection and antiviral immune responses, including several molecular mechanisms. miR-3959-3p, a significantly downregulated miRNA revealed in RNA-sequencing results of LSDV-infected LT cells, was selected to bedetected in the serum of LSDV-infected and uninfected cattle sera (40 LSDV-infected and 40 LSDV-uninfected). We optimized quantitative real-time PCR (qRT-PCR) for quantitative determination of miR-3959-3p in the bovine sera samples. The level of miR-3959-3p appears to be towards lower side in the LSDV-infected as compared to the uninfected animals. However, no significant correlation could be established between the two groups due to fluctuations in the miRNA levels in both groups. This is the first report on the detection of circulating miRNA in LSDV-infected cattle sera.The dysregulation pattern of miR-3959-3p appears to suggest that several other miRNAs need to be explored and may serve as biomarkers for LSDV infection. However, this needs further investigation by screening several other miRNAs and on large number of LSDV positive and negative animals.

Author summary

MicroRNAs are the key regulators of viral infections. However, in LSDVinfection the miRNA response is greatly unknown.

In this study, miRNA expression in Vero cell linepost LSDV infection was studied for the first time.

One of the miRNAs identified in the RNA-sequencing results i.emiR-3959-3p, was shown to be downregulated LSDV infection. We detected the levels of mir-3959-3p in sera of LSDV-infected and uninfected cattle to explore its potential as a biomarker.
Design, EHR Integration and Evaluation of Clinical Decision Support Workflows Driven by a Mortality Prediction Model to Promote Goal Concordant Care*
Authors: Roberts Laura M. , Rossi Lorenzo A. , Zachariah Finly
Published: February 2023

We present a clinical decision support (CDS) framework to promote goal-concordant care for cancer patients nearing end of life, enabled by a 90-day mortality prediction model. Design, workflow, and deployment for four model driven CDS tools are described alongside utilization patterns and detailed performance analysis of the first of such tools integrated into clinical practice: an alert promoting advance directive completion. The alert achieved a precision of 44.1% (95% CI: 39.6 - 48.8%) and a recall of 34% (95% CI: 30.3 - 37.4%) with 9.8% 90-day mortality prevalence over a period of 8 months. Our analysis shows that both precision and recall of the alert were significantly impacted by the underlying clinical workflows. Based on feedback, clinicians have accepted model-driven CDS as a legitimate means to prioritize patients for advance care planning interventions.
Disease-causing Slack potassium channel mutations produce opposite effects on excitability of excitatory and inhibitory neurons
Authors: Wu Jing , Quraishi Imran H , Zhang Yalan , Bromwich Mark , Kaczmarek Leonard K
Published: February 2023

KCNT1encodes the sodium-activated potassium channel Slack (KCNT1, KNa1.1), an important mediator of neuronal membrane excitability. Gain-of-function (GOF) mutations in humans lead cortical network hyperexcitability and seizures, as well as very severe intellectual disability. Using a mouse model of Slack GOF-associated epilepsy, we found that both excitatory and inhibitory neurons of the cerebral cortex have increased Na+-dependent K+(KNa) currents and voltage-dependent sodium (NaV) currents. The characteristics of the increased KNacurrents were, however, different in the two cell types such that the intrinsic excitability of excitatory neurons was enhanced but that of inhibitory neurons was suppressed. We further showed that the expression of NaVchannel subunits, particularly that of NaV1.6, is upregulated and that the length of the axon initial segment (AIS) and of axonal NaVimmunostaining is increased in both neuron types. We found that the proximity of the AIS to the soma is shorter in excitatory neurons than in inhibitory neurons of the mutant animals, potentially contributing to the different effects on membrane excitability. Our study on the coordinate regulation of KNacurrents and the expression of NaVchannels may provide a new avenue for understanding and treating epilepsies and other neurological disorders.

In brief

In a genetic mouse model of Na+-activated K+potassium channel geneSlack-related childhood epilepsy, Wuet al. show that a disease-causing gain-of-function (GOF) mutationR455Hin Slack channel causes opposite effects on excitability of cortical excitatory and inhibitory neurons. In contrast to heterologous expression systems, they find that the increase in potassium current substantially alters the expression of sodium channel subunits, resulting in increased lengths of axonal initial segments.

Highlights

GOF mutations in Slack potassium channel cause elevated outward K+currents and inward voltage-dependent Na+(NaV) currents in cortical neurons

Slack GOF does not alter the expression of Slack channel but upregulates the expression of NaVchannel

Slack GOF enhances the excitability of excitatory neurons but suppresses the firing of inhibitory interneurons

Slack GOF alters the length of AIS in both excitatory and inhibitory neurons

Proximity of AIS to the soma is different between excitatory neuron and inhibitory neuron
Plasticity of the binding pocket in peptide transporters underpins promiscuous substrate recognition
Authors: Kotov Vadim , Killer Maxime , Jungnickel Katharina E. J. , Lei Jian , Finocchio Giada , Steinke Josi , Bartels Kim , Strauss Jan , Dupeux Florine , Humm Anne-Sophie , Cornaciu Irina , Márquez José A. , Pardon Els , Steyaert Jan , Löw Christian
Published: February 2023

Proton-coupled oligopeptide transporters (POTs) are promiscuous transporters of the Major Facilitator Superfamily, that constitute the main route of entry for a wide range of dietary peptides and orally administrated peptidomimetic drugs. Given their clinical and pathophysiological relevance, several bacterial and mammalian POT homologs have been extensively studied on a structural and molecular level. However, the molecular basis of recognition and transport of the wide range of peptide substrates has remained elusive. Here we present 14 X-ray structures of the bacterial POT DtpB in complex with chemically diverse di- and tripeptides, providing novel insights into the plasticity of the conserved central binding cavity. We analyzed binding affinities for more than 80 peptides and monitored uptake by a fluorescence-based transport assay. To probe if all natural 8400 di- and tripeptides can bind to DtpB, we employed state-of-the-art molecular docking and machine learning and conclude that peptides of a specific subset with compact hydrophobic residues are the best DtpB binders.
LPD-3 as a megaprotein brake for aging and insulin-mTOR signaling inC. elegans
Authors: Pandey Taruna , Wang Bingying , Wang Changnan , Zu Jenny , Deng Huichao , Shen Kang , Dias do Vale Goncalo , McDonald Jeffrey G. , Ma Dengke K.
Published: February 2023

Insulin-mTOR signaling drives anabolic growth during organismal development, while its late-life dysregulation may detrimentally contribute to aging and limit lifespans. Age-related regulatory mechanisms and functional consequences of insulin-mTOR remain incompletely understood. Here we identify LPD-3 as a megaprotein that orchestrates the tempo of insulin-mTOR signaling duringC. elegansaging. We find that an agonist insulin INS-7 is drastically over-produced in early life and shortens lifespan inlpd-3mutants, aC. elegansmodel of human Alkuraya-Kučinskas syndrome. LPD-3 forms a bridge-like tunnel megaprotein to facilitate phospholipid trafficking to plasma membranes. Lipidomic profiling reveals increased abundance of hexaceramide species inlpd-3mutants, accompanied by up-regulation of hexaceramide biosynthetic enzymes, including HYL-1 (Homolog of Yeast Longevity). Reducing HYL-1 activity decreases INS-7 levels and rescues the lifespan oflpd-3mutants through insulin receptor/DAF-2 and mTOR/LET-363. LPD-3 antagonizes SINH-1, a key mTORC2 component, and decreases expression with age in wild type animals. We propose that LPD-3 acts as a megaprotein brake for aging and its age-dependent decline restricts lifespan through the sphingolipid-hexaceramide and insulin-mTOR pathways.
Exploring the ageing methylome in the model insect,Nasonia vitripennis
Authors: Brink K. , Thomas C.L. , Jones A. , Chan T.W. , Mallon E. B.
Published: February 2023

Background

The ageing process is a multifaceted phenomenon marked by the gradual deterioration of cellular and organismal functions, accompanied by an elevated susceptibility to diseases. The intricate interplay between genetic and environmental factors complicates research, particularly in complex mammalian models. In this context, simple invertebrate organisms have been pivotal, but the current models lack detectable DNA methylation limiting the exploration of this critical epigenetic ageing mechanism.

This study introduces Nasonia vitripennis, the jewel wasp, as an innovative invertebrate model for investigating the epigenetics of ageing. Leveraging its advantages as a model organism and possessing a functional DNA methylation system, Nasonia emerges as a valuable addition to ageing research.

Results

Whole-genome bisulfite sequencing unveiled dynamic alterations in DNA methylation, with differentially methylated CpGs between distinct time points in both male and female wasps. These changes were associated with numerous genes, enriching for functions related to telomere maintenance, histone methylation, and mRNA catabolic processes. Additionally, other CpGs were found to be variably methylated at each timepoint. Sex-specific effects on epigenetic entropy were observed, indicating differential patterns in the loss of epigenetic stability over time. Constructing an epigenetic clock containing 19 CpGs revealed a robust correlation between epigenetic age and chronological age.

Conclusions

Nasonia vitripennis emerges as a promising model for investigating the epigenetics of ageing, shedding light on the intricate dynamics of DNA methylation and their implications for age-related processes. This research not only expands the repertoire of ageing models but also opens avenues for deeper exploration of epigenetic mechanisms in the context of ageing.
Organic cation transporter 2 contributes to SSRI antidepressant efficacy by controlling tryptophan availability in the brain
Authors: Orrico-Sanchez Alejandro , Guiard Bruno P. , Manta Stella , Callebert Jacques , Launay Jean-Marie , Louis Franck , Paccard Antoine , Gruszczynski Carole , Betancur Catalina , Vialou Vincent , Gautron Sophie
Published: February 2023

Selective serotonin reuptake inhibitors (SSRI) are common first-line treatments for major depression. However, a significant number of depressed patients do not respond adequately to these pharmacological treatments. In the present preclinical study, we demonstrate that organic cation transporter 2 (OCT2), an atypical monoamine transporter, contributes to the effects of SSRI by regulating the routing of the essential amino acid tryptophan to the brain. Contrarily to wild-type mice, OCT2-invalidated mice failed to respond to prolonged fluoxetine treatment in a chronic depression model induced by corticosterone exposure recapitulating core symptoms of depression,i.e., anhedonia, social withdrawal, anxiety, and memory impairment. After corticosterone and fluoxetine treatment, the levels of tryptophan and its metabolites serotonin and kynurenine were decreased in the brain ofOCT2mutant mice compared to wild-type mice and reciprocally tryptophan and kynurenine levels were increased in mutants’ plasma. OCT2 was detected by immunofluorescence in several structures at the blood-cerebrospinal fluid (CSF) or brain-CSF interface. Tryptophan supplementation during fluoxetine treatment increased brain concentrations of tryptophan in wild-type and OCT2 mutant mice, yet more efficiently in WT than in mutants, while discretely increasing 5-HT concentrations. Importantly, tryptophan supplementation improved the sensitivity to fluoxetine treatment ofOCT2mutant mice, impacting chiefly anhedonia and short-term memory. Western blot analysis showed that glycogen synthase kinase-3β (GSK3β) and mammalian/mechanistic target of rapamycin (mTOR) intracellular signaling was impaired inOCT2mutant mice brain after corticosterone and fluoxetine treatment and, conversely, tryptophan supplementation recruited selectively the mTOR protein complex 2. This study provides the first evidence of the physiological relevance of OCT2-mediated tryptophan transport, and its biological consequences on serotonin homeostasis in the brain and SSRI efficacy.
The Energetics and Ion Coupling of Cholesterol Transport Through Patched1
Authors: Ansell T. Bertie , Corey Robin A. , Viti Lucrezia Vittoria , Kinnebrew Maia , Rohatgi Rajat , Siebold Christian , Sansom Mark S. P.
Published: February 2023

Patched1 (PTCH1) is the principal tumour suppressor protein of the mammalian Hedgehog (HH) signalling pathway, implicated in embryogenesis and tissue homeostasis. PTCH1 inhibits the Class F G protein-coupled receptor Smoothened (SMO) via a debated mechanism involving modulating accessible cholesterol levels within ciliary membranes. Using extensive molecular dynamics (MD) simulations and free energy calculations to evaluate cholesterol transport through PTCH1, we find an energetic barrier of ~15-20 kJ mol-1for cholesterol export. In simulations we identify cation binding sites within the PTCH1 transmembrane domain (TMD) which may provide the energetic impetus for cholesterol transport.In silicodata are coupled toin vivobiochemical assays of PTCH1 mutants to probe coupling between transmembrane motions and PTCH1 activity. Using complementary simulations of Dispatched1 (DISP1) we find that transition between ‘inward-open’ and solvent ‘occluded’ states is accompanied by Na+induced pinching of intracellular helical segments. Thus, our findings illuminate the energetics and ion-coupling stoichiometries of PTCH1 transport mechanisms, whereby 1-3 Na+or 2-3 K+couple to cholesterol export, and provide the first molecular description of transitions between distinct transport states.
GermanIxodes inopinatussamples may not actually represent this tick species
Authors: Rollins Robert E. , Margos Gabriele , Brachmann Andreas , Krebs Stefan , Mouchet Alexia , Dingemanse Niels J. , Laatamna AbdElkarim , Reghaissia Nassiba , Fingerle Volker , Metzler Dirk , Becker Noémie S. , Chitimia-Dobler Lidia
Published: February 2023

Ticks are important vectors of human and animal pathogens, but many questions remain unanswered regarding their taxonomy. Molecular sequencing methods have allowed research to start understanding the evolutionary history of even closely related tick species.Ixodes inopinatusis considered a sister species and highly similar toIxodes ricinus, an important vector of many tick-borne pathogens in Europe, but identification between these species remains ambiguous with disagreement on the geographic extent ofI. inopinatus. In 2018-2019, 1583 ticks were collected from breeding great tits (Parus major) in southern Germany, of which 45 were later morphologically identified asI. inopinatus. We aimed to confirm morphological identification using molecular tools. Utilizing two genetic markers (16S rRNA, TROSPA) (n=37) and whole genome sequencing of specific ticks (n=8), we were able to determine that German samples morphologically identified asI. inopinatus, genetically representI. ricinusregardless of previous morphological identification and most likely are notI. ricinus/I. inopinatushybrids. Further, our results showed that the entire mitochondrial genome, let alone singular mitochondrial genes (i.e., 16S), is unable to distinguish betweenI. ricinusandI. inopinatus. As most examples ofI. inopinatusin Germany were based on morphology and mitochondrial sequences, the results of the current study brings into question whetherI. inopinatuswas properly identified in previous research and if this species exists in Central Europe. Our results highlight the power of utilizing genomic data in answering questions regarding tick taxonomy even when closely related species are considered.

Highlights

GermanIxodes inopinatussamples representI. ricinusbased on genomic data

The mitochondrial genome is not sufficient for delineation ofI. inopinatusandI. ricinus

German samples most likely do not representI. ricinus/I. inopinatushybrids
A single-cell map of antisense oligonucleotide activity in the brain
Authors: Mortberg Meredith A , Gentile Juliana E , Nadaf Naeem , Vanderburg Charles , Simmons Sean , Dubinsky Dan , Slamin Adam , Maldonado Salome , Petersen Caroline L , Jones Nichole , Kordasiewicz Holly B , Zhao Hien T , Vallabh Sonia M , Minikel Eric Vallabh
Published: February 2023

Antisense oligonucleotides (ASOs) dosed into cerebrospinal fluid (CSF) distribute broadly throughout the brain and hold the promise of treating myriad brain diseases by modulating RNA. CNS tissue is not routinely biopsied in living individuals, leading to reliance on CSF biomarkers to inform on drug target engagement. Animal models can link CSF biomarkers to brain parenchyma, but our understanding of how individual cells contribute to bulk tissue signal is limited. Here we employed single nucleus transcriptomics on tissue from mice treated with RNase H1 ASOs againstPrnpandMalat1and macaques treated with an ASO againstPRNP. Activity was observed in every cell type, though sometimes with substantial differences in magnitude. Single cell RNA count distributions implied target suppression in every single sequenced cell, rather than intense knockdown in only some cells. Duration of action up to 12 weeks post-dose differed across cell types, being shorter in microglia than in neurons. Suppression in neurons was generally similar to, or more robust than, the bulk tissue. In macaques, PrP in CSF was lowered 40% in conjunction withPRNPknockdown across all cell types including neurons, arguing that a CSF biomarker readout is likely to reflect disease-relevant cells in a neuronal disorder.
Development of the branchial musculature of the Siberian sturgeon (Acipenser baerii) reveals a heterochronic shift during the evolution of acipenseriform cranial muscles
Authors: Naumann Benjamin , Warth Peter , Hammel Jörg U. , Moosmann Julian , Konstantinidis Peter , Olsson Lennart
Published: February 2023

Heterochronic shifts are regarded one of the major evolutionary changes acting on developmental modules and underlying the origin of morphological disparity. Conserved characters, rarely subject to heterochronic shifts during the curse of evolution, in contrast could indicate underlying developmental or functional constraints. Here we use the development of the cranial musculature Siberian sturgeon (Acipenser baerii) as a model to investigate the role of heterochrony during the evolution of the craniofacial system of Actinopterygii. Using histology, fluorescent antibody staining and fast propagation-based phase contrast imaging in combination with 3D-reconstruction we describe the development of the branchial and hypobranchial musculature. We show that the development of the first branchial arch is accelerated compared to other basal-branching actinopterygians leading to a more synchronous development with the hyoid arch. A pattern that could relate to the derived migratory behaviour of the neural crest cells in sturgeons. In contrast, the developmental timing of the more posterior branchial musculature, including thecucullarismuscle in the Siberian sturgeon, appears to be highly conserved compared to other Actinopterygii and even Osteognathostomata. This could indicate the presence of functional or developmental constraints underlying the evolution of the muscles at the head/trunk interface.
The composition of piRNA clusters inDrosophila melanogasterdeviates from expectations under the trap model
Authors: Wierzbicki Filip , Kofler Robert
Published: February 2023

It is widely assumed that the invasion of a transposable element (TE) in mammals and invertebrates is stopped when a copy of the TE jumps into a piRNA cluster (i.e. the trap model). However, recent works, which for example showed that deletion of three major piRNA clusters has no effect on TE activity, cast doubt on the trap model. Therefore, we aim to test the trap model. We show with population genetic simulations that the composition of regions that act as transposon traps (i.e. possible piRNA clusters) ought to deviate from regions that have no effect on TE activity. Next, we investigated TEs in fiveD. melanogasterstrains using three complementary approaches to test whether the composition of piRNA clusters matches these expectations. We found that the abundance of TE families inside and outside of piRNA clusters is highly correlated, although this is not expected under the trap model. Furthermore, we found that the distribution of the number of TE insertions in piRNA clusters is also much broader than expected, where some families have zero cluster insertions and others more than 14. One feasible explanation is that insertions in piRNA clusters have little effect on TE activity and that the trap model is therefore incorrect. Alternatively, dispersed piRNA producing TE insertions and temporal as well as spatial heterogeneity of piRNA clusters may explain some of our observations.
A hyper-quiescent chromatin state formed during aging is reversed by regeneration
Authors: Yang Na , Occean James R. , Melters Daniël P. , Shi Changyou , Wang Lin , Stransky Stephanie , Doyle Maire E. , Cui Chang-Yi , Delannoy Michael , Fan Jinshui , Slama Eliza , Egan Josephine M. , De Supriyo , Cunningham Steven C. , de Cabo Rafael , Sidoli Simone , Dalal Yamini , Sen Payel
Published: February 2023

Epigenetic alterations are a key hallmark of aging but have been limitedly explored in tissues. Here, using naturally aged murine liver as a model and extending to other quiescent tissues, we find that aging is driven by temporal chromatin alterations that promote a refractory cellular state and compromise cellular identity. Using an integrated multi-omics approach, and the first direct visualization of aged chromatin we find that globally, old cells show H3K27me3-driven broad heterochromatinization and transcription suppression. At the local level, site-specific loss of H3K27me3 over promoters of genes encoding developmental transcription factors leads to expression of otherwise non-hepatocyte markers. Interestingly, liver regeneration reverses H3K27me3 patterns and rejuvenates multiple molecular and physiological aspects of the aged liver.
High-throughput quantitative screening of glucose-stimulated insulin secretion and insulin content using automated MALDI-TOF mass spectrometry
Authors: Delannoy Clément Philippe , Heuson Egon , Herledan Adrien , Oger Frederik , Thiroux Bryan , Chevalier Mickaël , Gromada Xavier , Rolland Laure , Froguel Philippe , Deprez Benoit , Paul Sebastien , Annicotte Jean-Sébastien
Published: February 2023

Type 2 diabetes (T2D) is a metabolic disorder characterized by loss of pancreatic β- cell function, decreased insulin secretion and increased insulin resistance, that affects more than 400 million people worldwide. Although several treatments are proposed to patients suffering from T2D, long-term control of glycemia remains a challenge. Therefore, identifying new potential drugs and targets that positively affect β-cell function and insulin secretion remains crucial. Here, we developed an automated approach to allow the identification of new compounds or genes potentially involved in β-cell function in a 384-well plate format, using the murine β-cell model Min6. Using MALDI-TOF mass spectrometry, we have implemented a high-throughput screening (HTS) strategy based on the automation of a cellular assay allowing to detect insulin secretion in response to glucose, quantitative detection of insulin, in a miniaturized system. As a proof of concept, we screened siRNA targeting well-know β-cell genes and 1600 chemical compounds and identified several molecules as potential regulators of insulin secretion and/or synthesis, demonstrating that our approach allows HTS of insulin secretionin vitro.
Odor representations from the two nostrils are temporally segregated in human piriform cortex
Authors: Dikecligil Gülce Nazlı , Yang Andrew I. , Sanghani Nisha , Lucas Timothy , Chen H. Isaac , Davis Kathryn A. , Gottfried Jay A.
Published: February 2023

The human olfactory system has two discrete channels of sensory input, arising from olfactory epithelia housed in the left and right nostrils. Here, we asked whether primary olfactory cortex (piriform cortex, PC) encodes odor information arising from the two nostrils as integrated or distinct stimuli. We recorded intracranial EEG signals directly from PC while human subjects participated in an odor identification task where odors were delivered to the left, right, or both nostrils. We analyzed the time-course of odor-identity coding using machine learning approaches, and found that uni-nostril odor inputs to the ipsilateral nostril are encoded ∼480 ms faster than odor inputs to the contralateral nostril on average. During naturalistic bi-nostril odor sampling, odor information emerged in two temporally segregated epochs with the first epoch corresponding to the ipsilateral and the second epoch corresponding to the contralateral odor representations. These findings reveal that PC maintains distinct representations of odor input from each nostril through temporal segregation, highlighting an olfactory coding scheme at the cortical level that can parse odor information across nostrils within the course of a single inhalation.
BLINK: Ultrafast tandem mass spectrometry cosine similarity scoring
Authors: Harwood Thomas , Treen Daniel G.C. , Wang Mingxun , de Jong Wibe , Northen Trent R. , Bowen Benjamin P.
Published: February 2023

Metabolomics has a long history of using cosine similarity to match experimental tandem mass spectra to databases for compound identification. Here we introduce the Blur-and-Link (BLINK) approach for scoring cosine similarity. BLINK calculates substantially equivalent cosine similarity scores (>99% identification agreement) over 1000 times faster than commonly used loop-based implementations by bypassing fragment alignment and simultaneously scoring all pairs of spectra using sparse matrix operations. This performance improvement can enable calculations to be performed that would typically be limited by time and available computational resources.

Availability and Implementation

BLINK is implemented in Python3 and is published under a modified open source license. Code and license are available on Github:https://github.com/biorack/blink
A Systematic Benchmark of Machine Learning Methods for Protein-RNA Interaction Prediction
Authors: Horlacher Marc , Cantini Giulia , Hesse Julian , Schinke Patrick , Goedert Nicolas , Londhe Shubhankar , Moyon Lambert , Marsico Annalisa
Published: February 2023

Abstract

RNA-binding proteins (RBPs) are central actors of RNA post-transcriptional regulation. Experiments to profile binding sites of RBPsin vivoare limited to transcripts expressed in the experimental cell type, creating the need for computational methods to infer missing binding information. While numerous machine-learning based methods have been developed for this task, their use of heterogeneous training and evaluation datasets across different sets of RBPs and CLIP-seq protocols makes a direct comparison of their performance difficult. Here, we compile a set of 37 machine learning (primarily deep learning) methods forin vivoRBP-RNA interaction prediction and systematically benchmark a subset of 11 representative methods across hundreds of CLIP-seq datasets and RBPs. Using homogenized sample pre-processing and two negative-class sample generation strategies, we evaluate methods in terms of predictive performance and assess the impact of neural network architectures and input modalities on model performance. We believe that this study will not only enable researchers to choose the optimal prediction method for their tasks at hand, but also aid method developers in developing novel, high-performing methods by introducing a standardized framework for their evaluation.