bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic and machine learning-based screening of aquaculture associated introgression into at-risk wild North American Atlantic salmon (Salmo salar) populations
Authors: Nugent Cameron M. , Kess Tony , Brachmann Matthew K. , Langille Barbara L. , Holborn Melissa K. , Beck Samantha V. , Smith Nicole , Duffy Steven J. , Lehnert Sarah J. , Wringe Brendan F. , Bentzen Paul , Bradbury Ian R.
Published: November 2022

The negative genetic impacts of gene flow from domestic to wild populations can be dependent on the degree of domestication and exacerbated by the magnitude of pre-existing genetic differences between wild populations and the domestication source. Recent evidence of European ancestry within North American aquaculture Atlantic salmon (Salmo salar) has elevated the potential impact of escaped farmed salmon on often at-risk wild North American salmon populations. Here we compare the ability of single nucleotide polymorphism (SNP) and microsatellite (SSR) marker panels of different sizes (7-SSR, 100-SSR, and 220K-SNP) to detect introgression of European genetic information into North American wild and aquaculture populations. Linear regression comparing admixture predictions for a set of individuals common to the three data sets showed that the 100-SSR panel and 7-SSR panels replicated the full 220K-SNP-based admixture estimates with low accuracy (r2of 0.64 and 0.49 respectively). Additional tests explored the effects of individual sample size and marker number, which revealed that ~300 randomly selected SNPs could replicate the 220K-SNP admixture predictions with greater than 95% fidelity. We designed a custom SNP panel (301-SNP) for European admixture detection in future monitoring work and then developed and tested a Python package, SalmonEuAdmix (https://github.com/CNuge/SalmonEuAdmix), that uses a deep neural network to makede novoestimates of individuals’ European admixture proportion without the need to conduct complete admixture analysis utilizing baseline samples. The results demonstrate the mobilization of targeted SNP panels and machine learning in support of at-risk species conservation and management.
An open-access dataset of naturalistic viewing using simultaneous EEG-fMRI
Authors: Telesford Qawi K , Gonzalez-Moreira Eduardo , Xu Ting , Tian Yiwen , Colcombe Stanley , Cloud Jessica , Russ Brian Edward , Falchier Arnaud , Nentwich Maximilian , Madsen Jens , Parra Lucas , Schroeder Charles , Milham Michael , Franco Alexandre Rosa
Published: November 2022

In this work, we present a dataset that combines functional magnetic imaging (fMRI) and electroencephalography (EEG) to use as a resource for understanding human brain function in these two imaging modalities. The dataset can also be used for optimizing preprocessing methods for simultaneously collected imaging data. The dataset includes simultaneously collected recordings from 22 individuals (ages: 23-51) across various visual and naturalistic stimuli. In addition, physiological, eye tracking, electrocardiography, and cognitive and behavioral data were collected along with this neuroimaging data. Visual tasks include a flickering checkerboard collected outside and inside the MRI scanner (EEG-only) and simultaneous EEG-fMRI recordings. Simultaneous recordings include rest, the visual paradigm Inscapes, and several short video movies representing naturalistic stimuli. Raw and preprocessed data are openly available to download. We present this dataset as part of an effort to provide open-access data to increase the opportunity for discoveries and understanding of the human brain and evaluate the correlation between electrical brain activity and blood oxygen level-dependent (BOLD) signals.
Activity-regulated gene expression across cell types of the mouse hippocampus
Authors: Nelson Erik D. , Maynard Kristen R. , Nicholas Kyndall R. , Tran Matthew N. , Divecha Heena R. , Collado-Torres Leonardo , Hicks Stephanie C. , Martinowich Keri
Published: November 2022

Activity-regulated gene (ARG) expression patterns in the hippocampus (HPC) regulate synaptic plasticity, learning, and memory, and are linked to both risk and treatment response for many neuropsychiatric disorders. The HPC contains discrete classes of neurons with specialized functions, but cell type-specific activity-regulated transcriptional programs are not well characterized. Here, we used single-nucleus RNA-sequencing (snRNA-seq) in a mouse model of acute electroconvulsive seizures (ECS) to identify cell type-specific molecular signatures associated with induced activity in HPC neurons. We used unsupervised clustering anda priorimarker genes to computationally annotate 15,990 high-quality HPC neuronal nuclei fromN=4 mice across all major HPC subregions and neuron types. Activity-induced transcriptomic responses were divergent across neuron populations, with dentate granule cells being particularly responsive to activity. Differential expression analysis identified both upregulated and downregulated cell type-specific gene sets in neurons following ECS. Within these gene sets, we identified enrichment of pathways associated with varying biological processes such as synapse organization, cellular signaling, and transcriptional regulation. Finally, we used matrix factorization to reveal continuous gene expression patterns differentially associated with cell type, ECS, and biological processes. This work provides a rich resource for interrogating activity-regulated transcriptional responses in HPC neurons at single-nuclei resolution in the context of ECS, which can provide biological insight into the roles of defined neuronal subtypes in HPC function.
Lipid bicelles in the study of biomembrane characteristics
Authors: Pöhnl Matthias , Kluge Christoph , Böckmann Rainer A.
Published: November 2022

Simulations of lipid membranes typically make use of periodic boundary conditions to mimic macroscopically sized membranes and allow for comparison to experiments performed e.g. on planar lipid membranes or on unilamellar lipid vesicles. However, the lateral periodicity partly suppresses membrane fluctuations or membrane remodeling, processes that are of particular importance in the study of asymmetric membranes – i.e. membranes with integral or associated proteins and/or asymmetric lipid compositions.

Here, we devised a simple albeit powerful lipid bicelle model system that (i) displays similar structural, dynamical and mechanical properties compared to infinite periodic lipid membrane systems, and allows (ii) for the study of asymmetric lipid bilayer systems, and (iii) the unperturbed formation of local spontaneous curvature induced by lipids or proteins in coarse-grained and all-atom molecular dynamics simulations. In addition, the system is characterized by largely unbiased thermal fluctuations as opposed to standard bilayer systems. Application of the bicelle system for an asymmetric lipid composition resembling the plasma membrane reveals that the cholesterol density for a tension-free plasma membrane with a vanishing spontaneous curvature is larger by 28% within the extracellular leaflet compared to the cytosolic leaflet.

Graphical TOC Entry
Platelet pannexin-1 channels modulate inflammation during abdominal aortic aneurysm formation
Authors: Metz Lisa Maria , Feige Tobias , de Biasi Larissa , Ehrenberg Agnes , Mulorz Joscha , Toska Laura Mara , Reusswig Friedrich , Quast Christine , Gerdes Norbert , Kelm Malte , Schelzig Hubert , Elvers Margitta
Published: November 2022

Abdominal aortic aneurysm (AAA) is a common disease and highly lethal if untreated. The progressive dilatation of the abdominal aorta is accompanied by degradation and remodeling of the vessel wall due to chronic inflammation. Pannexins represent anion-selective channels and play a crucial role in non-vesicular ATP release to amplify paracrine signaling in cells. Thus, pannexins are involved in many (patho-) physiological processes. Recently, Panx1 channels were identified to be significantly involved in AAA formation through endothelial derived Panx1 regulated inflammation and aortic remodeling. In platelets, Panx1 becomes activated following activation of glycoprotein (GP)VI. Since platelets play a role in cardiovascular diseases including AAA, we analyzed the contribution of platelet Panx1 in the progression of AAA. We detected enhanced Panx1 plasma levels in AAA patients. In experimental AAA using the pancreatic porcine elastase (PPE) mouse model, a major contribution of platelet Panx1 channels in platelet activation, pro-coagulant activity of platelets and platelet-mediated inflammation has been detected. In detail, platelets are important for the migration of neutrophils into the aortic wall induced by direct cell interaction and by activation of endothelial cells. Decreased platelet activation and inflammation did not affect ECM remodeling or wall thickness in platelet-specific Panx1 knock-out mice following PPE surgery. Thus, aortic diameter expansion at different time points after elastase infusion of the aortic wall was unaltered in platelet-specific Panx1 deficient mice suggesting that the modulation of inflammation alone does not affect AAA formation and progression. In conclusion, our data strongly supports the role of platelets in inflammatory responses in AAA via Panx1 channels and adds important knowledge about the significance of platelets in AAA pathology important for the establishment of an anti-platelet therapy for AAA patients.
Model-free decision making resists improved instructions and is enhanced by stimulus-response associations
Authors: Luna Raúl , Vadillo Miguel A. , Luque David
Published: November 2022

Human behaviour may be thought of as supported by two different computational-learning mechanisms, model-free and model-based respectively. In model-free strategies, stimulus-response associations are strengthened when actions are followed by a reward and weakened otherwise. In model-based learning, previous to selecting an action, the current values of the different possible actions are computed based on a detailed model of the environment. Previous research with the two-stage task suggests that participants’ behaviour usually shows a mixture of both strategies. But, interestingly, a recent study by da Silva and Hare (2020) found that participants primarily deploy model-based behaviour when they are given detailed instructions about the structure of the task. In the present study, we reproduce this essential experiment. Our results confirm that improved instructions give rise to a stronger model-based component. Crucially, we also found a significant effect of reward that became stronger under conditions that favoured the development of strong stimulus-response associations. This suggests that the effect of reward, often taken as indicator of a model-free component, is related to stimulus-response learning.
Completing the TRB family: newly characterized members show ancient evolutionary origins and distinct localization, yet similar interactions
Authors: Kusová Alžbeta , Steinbachová Lenka , Přerovská Tereza , Drábková Lenka Záveská , Paleček Jan , Khan Ahmed , Rigóová Gabriela , Gadiou Zuzana , Jourdain Claire , Stricker Tino , Schubert Daniel , Honys David , Schrumpfová Petra Procházková
Published: November 2022

Telomere repeat binding proteins (TRBs) belong to a family of proteins possessing a Myb-like domain which binds to telomeric repeats. Three members of this family (TRB1, TRB2, TRB3) fromArabidopsis thalianahave already been described as associated with terminal telomeric repeats (telomeres) or short interstitial telomeric repeats in gene promoters (telo-boxes). They are also known to interact with several protein complexes: telomerase, Polycomb repressive complex 2 (PRC2) E(z) subunits and the PEAT complex (PWOs-EPCRs-ARIDs-TRBs). Here we characterize two novel members of the TRB family (TRB4 and TRB5). Our wide phylogenetic analyses have shown that TRB proteins evolved in the plant kingdom after the transition to a terrestrial habitat in Streptophyta, and consequently TRBs diversified in seed plants. TRB4-5 share common TRB motifs while differing in several others and seem to have an earlier phylogenetic origin than TRB1-3. Their common Myb-like domains bind long arrays of telomeric repeats in vitro, and we have determined the minimal recognition motif of all TRBs as onetelo-box. Our data indicate that despite the distinct localization patterns of TRB1-3 and TRB4-5 in situ, all members of TRB family mutually interact and also bind to telomerase/PRC2/PEAT complexes. Additionally, we have detected novel interactions between TRB4-5 and EMF2 and VRN2, which are Su(z)12 subunits of PRC2.
Oxidative stress-induced MMP- and γ-secretase-dependent VE-cadherin processing is modulated by the proteasome and BMP9/10
Authors: Ivaldo Caterina , Passalacqua Mario , Furfaro Anna Lisa , d’Abramo Cristina , Ruiz Santiago , Chatterjee Prodyot K. , Metz Christine N. , Nitti Mariapaola , Marambaud Philippe
Published: November 2022

Classical cadherins, including vascular endothelial (VE)-cadherin, are targeted by matrix metalloproteinases (MMPs) and γ-secretase during adherens junction (AJ) disassembly, a mechanism that might have relevance for endothelial cell (EC) integrity and vascular homeostasis. Here, we show that oxidative stress triggered by H2O2exposure induced efficient VE-cadherin proteolysis by MMPs and γ-secretase in human umbilical endothelial cells (HUVECs). The cytoplasmic domain of VE-cadherin produced by γ-secretase, VE-Cad/CTF2 - a fragment that has eluded identification so far - could readily be detected after H2O2treatment. VE-Cad/CTF2, released into the cytosol, was tightly regulated by proteasomal degradation and was sequentially produced from an ADAM10/17-generated C-terminal fragment, VE-Cad/CTF1. Interestingly, BMP9 and BMP10, two circulating ligands critically involved in vascular maintenance, significantly reduced VE-Cad/CTF2 levels during H2O2challenge, as well as mitigated H2O2-mediated actin cytoskeleton disassembly during VE-cadherin processing. Notably, BMP9/10 pretreatments efficiently reduced apoptosis induced by H2O2, favoring endothelial cell recovery. Thus, oxidative stress is a trigger of MMP- and γ-secretase-mediated endoproteolysis of VE-cadherin and AJ disassembly from the cytoskeleton in ECs, a mechanism that is negatively controlled by the EC quiescence factors, BMP9 and BMP10.
The RNA Binding proteome of axonal mRNAs in sympathetic neurons
Authors: Luisier Raphaëlle , Andreassi Catia , Riccio Antonella
Published: November 2022

Background

Neurons are morphologically complex cells that rely on the compartmentalization of protein expression to develop and maintain their cytoarchitecture. Targeting of RNA transcripts to axons is one of the mechanisms that allows rapid local translation of proteins in response to extracellular signals. 3’ untranslated regions (UTRs) of mRNA are non-coding sequences that play a critical role in determining transcript localisation and translation by interacting with specific RNA binding proteins (RBPs). However, how 3’UTRs contribute to mRNA metabolism and the nature of RBP complexes responsible for these functions remain elusive.

Results

We performed 3’ end sequencing of RNA isolated from axons and cell bodies of sympathetic neurons exposed to either Nerve Growth factor (NGF) or Neurotrophin 3 (NT3). NGF and NT3 are growth factors essential for sympathetic neuron development that act through distinct signalling mechanisms. Whereas NT3 is thought to act only locally, NGF signals back from axons to the cell bodies. We discovered that both NGF and NT3 affect transcription and alternative polyadenylation and induce the localisation of specific 3’UTR isoforms to axons. The finding that many transcripts with short 3’UTR were detected only in axons suggest that these may undergo local post-transcriptional remodelling. The integration of our data with CLIP-sequencing data revealed that long 3’UTR isoforms associate with RBP complexes in the nucleus, and once in axons, regulate cytoplasmic 3’ UTR isoform cleavage into shorter isoform.

Conclusions

Our findings shed new light on the complex interplay between nuclear polyadenylation, mRNA localisation and local 3’UTR remodelling in developing neurons.

Graphical abstract
Gamma-Protocadherins regulate filopodia self-recognition and dynamics to drive dendrite self-avoidance
Authors: Ing-Esteves Samantha , Lefebvre Julie L.
Published: November 2022

Neurons form cell type-specific morphologies that are shaped by molecular cues and their cellular events governing dendrite growth. One growth rule is distributing dendrites uniformly within a neuron’s territory by avoiding sibling or ‘self’ branches. In mammalian neurons, dendrite self-avoidance is regulated by the clustered Protocadherins (cPcdhs), a large family of recognition molecules. Genetic and molecular studies suggest that the cPcdhs mediate homophilic recognition and repulsion between self-dendrites but this model has not been tested through direct investigation of self-avoidance during development. Here we performed live imaging and 4D quantifications of dendrite morphogenesis to define the cPcdh-dependent mechanisms of self-avoidance. We focused on the mouse retinal starburst amacrine cell (SAC), which requires the gamma-Pcdhs (Pcdhgs) and self/non-self recognition to establish a stereotypic radial morphology while permitting dendritic interactions with neighboring SACs. Through morphogenesis, SACs extend a transient population of dynamic filopodia that fill the growing arbor and contact nearby self-dendrites. Compared to non-self-contacting filopodia, self-contacting events have longer lifetimes and a subset persists as filopodia bridges. In the absence of thePcdhgs, non-self-contacting filopodia dynamics are unaffected but self-contact-induced retractions are significantly diminished. Filopodia bridges accumulate, leading to the bundling of dendritic processes and disruption to the arbor shape. By tracking dendrite self-avoidance in real-time, our findings demonstrate that the γ-Pcdhs selectively mediate contact-induced retractions upon filopodia self-recognition. Our results also illustrate how self-avoidance shapes the stochastic and space-filling behaviors of filopodia for robust dendritic pattern formation in mammalian neurons.

HIGHLIGHTS

Dendrite self-avoidance proceeds through interstitial filopodia and contact-induced retractions between sibling processes.

Self-contacting filopodia exhibit longer lifetimes and a subset of contacts persist.

Pcdhgs selectively regulate self-contact-induced retractions.

Loss ofPcdhgsand filopodia self-avoidance disrupts dendritic arbor shape.
The Neural Correlates of Arousal: The Ventral Posterolateral Nucleus-Global Transient Co-Activation
Authors: Han Junrong , Xie Qiuyou , Wu Xuehai , Huang Zirui , Tanabe Sean , Fogel Stuart , Hudetz Anthony G. , Wu Hang , Northoff Georg , Mao Ying , He Sheng , Qin Pengmin
Published: November 2022

Arousal and awareness are two components of consciousness whose the neural mechanisms remain unclear. Spontaneous increases of global (brain-wide) blood-oxygenation-level-dependent (BOLD) signal has been found to be sensitive to changes in arousal. By contrasting BOLD datasets with altered arousal levels, we found that the activation of ventral posterolateral nucleus (VPL) decreased during transient increase in the global signal (top 17% data) in low arousal and awareness states (non-rapid eye movement sleep and anesthesia) as compared to wakefulness, and even in eye-closed (compared with eyes-open) in healthy awake-states, while this activation remained unchanged in patients with unresponsive wakefulness syndrome characterized by high arousal without awareness. These results demonstrate that co-activation of the VPL and global activity is critical to arousal, but not to awareness.

One-Sentence Summary

The VPL nucleus-global brain transient co-activation is related to physiological arousal but not to perceptual awareness.
Hepatic WDR23 proteostasis mediates insulin clearance by regulating insulin-degrading enzyme
Authors: Duangjan Chatrawee , Arpawong Thalida Em , Spatola Brett N. , Curran Sean P.
Published: November 2022

Clearance of circulating insulin is critical for metabolic homeostasis. In the liver, insulin is degraded by the activity of the insulin-degrading enzyme (IDE). Here we establish a hepatic regulatory axis for IDE through WDR23-proteostasis.Wdr23KOmice have increased IDE expression, reduced circulating insulin, and defective insulin responses. Genetically engineered human cell models lackingWDR23also increase IDE expression and display dysregulated phosphorylation of insulin signaling cascade proteins, IRS-1, AKT2, MAPK, FoxO, and mTOR, similar to cells treated with insulin, which can be mitigated by chemical inhibition of IDE. Mechanistically, the cytoprotective transcription factor NRF2, a direct target of WDR23-Cul4 proteostasis, mediates the enhanced transcriptional expression of IDE whenWDR23is ablated. Moreover, an analysis of human genetic variation inWDR23across a large naturally aging human cohort in the US Health and Retirement Study reveals a significant association ofWDR23with altered hemoglobin A1C (HbA1c) levels in older adults, supporting the use ofWDR23as new molecular determinant of metabolic health in humans.
Gasdermin D is the only Gasdermin that provides non-redundant protection against acuteSalmonellagut infection
Authors: Fattinger Stefan A. , Maurer Luca , Geiser Petra , Enz Ursina , Ganguillet Suwannee , Gül Ersin , Kroon Sanne , Demarco Benjamin , Furter Markus , Barthel Manja , Pelczar Pawel , Shao Feng , Broz Petr , Sellin Mikael E. , Hardt Wolf-Dietrich
Published: November 2022

Gasdermins (GSDMs) share a common functional domain structure and are best known for their capacity to form membrane pores. These pores are hallmarks of a specific form of cell death called pyroptosis and mediate the secretion of pro-inflammatory cytokines such as interleukin 1β (IL1β) and interleukin 18 (IL18). Thereby, Gasdermins have been implicated in various immune responses against cancer and infectious diseases such as acuteSalmonellaTyphimurium (S.Tm) gut infection. However, to date, we lack a comprehensive functional assessment of the different Gasdermins (GSDMA-E) duringS.Tm infectionin vivo. Here, we have performed littermate-controlled oralS.Tm infections to investigate the impact of all murine Gasdermins. While GSDMA, -C and -E appear dispensable, we show that GSDMD (i) restrictsS.Tm loads in the gut tissue and systemic organs, (ii) controls gut inflammation kinetics, and (iii) prevents epithelium disruption by 72h of the infection. Full protection requires GSDMD expression by both bone-marrow-derived lamina propria cells and intestinal epithelial cells (IECs).In vivoexperiments, 3D- and 2D-enteroid infections further show that infected IEC extrusion proceeds also without GSDMD, but that GSDMD controls the permeabilization and morphology of the extruding cells and affects extrusion kinetics. As such, this work identifies a non-redundant multipronged role of GSDMD in mucosal tissue defence against a common enteric pathogen.

HIGHLIGHTS

Gasdermin D restrictsSalmonellaTyphimurium (S.Tm) translocation across the gut tissue, controls gut inflammation kinetics, and prevents epithelium disruption by 72h of the infection.

Gasdermins A, C and E appear dispensable for protection against acuteS.Tm gut infection.

Gasdermin D in bone-marrow-derived lamina propria cells and intestinal epithelial cells complement each other to suppress gut tissueS.Tm loads.

Gasdermin D is not required for extrusion of infected intestinal epithelial cells but drives their permeabilization and affects qualitative features of the extrusion process.
A multi-layer mean-field model for the cerebellar cortex: design, validation, and prediction
Authors: Lorenzi Roberta M. , Geminiani Alice , Zerlaut Yann , Destexhe Alain , Gandini Wheeler-Kingshott Claudia A.M. , Palesi Fulvia , Casellato Claudia , D’Angelo Egidio
Published: November 2022

Mean-field (MF) models can be used to summarize in a few statistical parameters the salient properties of an inter-wired neuronal network incorporating different types of neurons and synapses along with their topological organization. MF are crucial to efficiently implement the modules of large-scale brain models maintaining the specificity of local microcircuits. While MFs have been generated for the isocortex, they are still missing for other parts of the brain. Here we have designed and simulated a multi-layer MF of the cerebellar network (including Granule Cells, Golgi Cells, Molecular Layer Interneurons, and Purkinje Cells) and validated it against experimental data and the corresponding spiking neural network (SNN) microcircuit model. The cerebellar MF was built using a system of equations, where properties of neuronal populations and topological parameters are embedded in inter-dependent transfer functions. The model time constant was optimised using local field potentials recorded experimentally from acute mouse cerebellar slices as a template. The MF satisfactorily reproduced the average dynamics of the different neuronal populations in response to various input patterns and predicted the modulation of Purkinje Cells firing depending on cortical plasticity, which drives learning in associative tasks, and the level of feedforward inhibition. The cerebellar MF provides a computationally efficient tool that will allow to investigate the causal relationship between microscopic neuronal properties and ensemble brain activity in virtual brain models addressing both physiological and pathological conditions.
Precision RNAi using synthetic shRNAmir target sites
Authors: Hoffmann Thomas , Hörmann Alexandra , Corcokovic Maja , Zmajkovic Jakub , Hinterndorfer Matthias , Salkanovic Jasko , Spreitzer Fiona , Köferle Anna , Gitschtaler Katrin , Popa Alexandra , Oberndorfer Sarah , Andersch Florian , Schäfer Markus , Fellner Michaela , Budano Nicole , Ruppert Jan G. , Chetta Paolo , Wurm Melanie , Zuber Johannes , Neumüller Ralph A.
Published: November 2022

Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient and inducible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.
Structural modelling of human complement FHR1 and two of its synthetic derivatives provides insight into theirin-vivofunctions
Authors: Ruiz-Molina Natalia , Parsons Juliana , Decker Eva L. , Reski Ralf
Published: November 2022

Human complement is the first line of defence against invading pathogens and is involved in tissue homeostasis. Complement-targeted therapies to treat several diseases caused by a dysregulated complement are highly desirable. Despite huge efforts invested in their development, only very few are currently available, and a deeper understanding of the numerous interactions and complement regulation mechanisms is indispensable. Two important complement regulators are human Factor H (FH) and Factor H-related protein 1 (FHR1). MFHR1 and MFHR13, two promising therapeutic candidates based on these regulators, combine the dimerization and C5-regulatory domains of FHR1 with the central C3-regulatory and cell surface-recognition domains of FH. Here, we used AlphaFold2 to model the structure of these two synthetic regulators. Moreover, we used AlphaFold-Multimer (AFM) to study possible interactions of C3 fragments and membrane attack complex (MAC) components C5, C7 and C9 in complex with FHR1, MFHR1, MFHR13 as well as the best-known MAC regulators vitronectin (Vn), clusterin and CD59, whose experimental structures remain undetermined. AFM successfully predicted the binding interfaces of FHR1 and the synthetic regulators with C3 fragments and suggested binding to C3. The models revealed structural differences in binding to these ligands through different interfaces. Additionally, AFM predictions of Vn, clusterin or CD59 with C7 or C9 agreed with previously published experimental results. Because the role of FHR1 as a MAC regulator has been controversial, we analysed possible interactions with C5, C7 and C9. AFM predicted interactions of FHR1 with proteins of the terminal complement complex (TCC) as indicated by experimental observations, and located the interfaces in FHR11-2and FHR4-5. According to AFM predictions, FHR1 might partially block the C3b binding site in C5, inhibiting C5 activation, and block C5b-7 complex formation and C9 polymerization, with similar mechanisms of action as clusterin and vitronectin. Here, we generate hypotheses and provide the basis for the design of rational approaches to understand the molecular mechanism of MAC inhibition, which will facilitate the development of further complement therapeutics.
A bacterial ribosome hibernation factor with evolutionary connections to eukaryotic protein synthesis
Authors: Helena-Bueno Karla , Ekemezie Chinenye L. , Brown Charlotte R. , Baslé Arnaud , Blaza James N. , Hill Chris H. , Melnikov Sergey V.
Published: November 2022

During starvation and stress, virtually all organisms arrest protein synthesis to conserve energy. Inactive ribosomes are converted into a dormant state, in which they are protected from damage by hibernation factor proteins. In bacteria, two major families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats, and environmental stressors has confounded their discovery. In this study, using proteomics and cryo-EM, we identify a new dormancy factor from the psychrophilic bacteriumPsychrobacter urativorans. By isolating ribosomes under cold-shock conditions, we observe a previously unknown protein bound to the ribosomal A site, protecting critical elements of both the decoding and peptidyl transferase centers. We show that this new factor, which we term Balon, is a homolog of the archaeo-eukaryotic translation factor aeRF1, providing a long-predicted evolutionary “missing link” between the eukaryotic and bacterial translation machinery. Our structures reveal that Balon is delivered to both vacant and actively translating ribosomes by EF-Tu, highlighting an unexpected and previously unknown role for this elongation factor in the bacterial stress response. We describe several unique structural motifs that allow Balon to bind ribosomes in an mRNA-independent manner, initiating a new mode of ribosome dormancy that can commence while ribosomes are still engaged in protein synthesis. Our bioinformatic analysis shows that putative Balon-encoding genes can be found within stress-response operons in nearly 20 % of all known bacterial species, including many human pathogens. Taken together, our work suggests that Balon/EF-Tu regulated ribosome dormancy is likely to be a ubiquitous stress-response mechanism throughout the bacterial kingdom. These findings call for a revision of our model of bacterial translation inferred from common model organisms and hold numerous implications for how we understand and study ribosome dormancy.
Epigenomic tomography for probing spatially-defined molecular state in the brain
Authors: Liu Zhengzhi , Deng Chengyu , Zhou Zirui , Xiao Ya , Jiang Shan , Zhu Bohan , Naler Lynette B. , Jia Xiaoting , Yao Danfeng (Daphne) , Lu Chang
Published: November 2022

Spatially-resolved genomic profiling is critical for understanding biology in a spatially ordered organ such as mammalian brain. Single-cell spatial genomic assays were developed recently for this purpose but they remain costly and labor-intensive for examining brain tissues across substantial dimensions and surveying a collection of brain samples. Here we demonstrate a new approach, brain epigenomic tomography, that maps spatial epigenomic variations at the scale of centimeters. We profiled neuronal and glial fractions of mouse neocortex slices with 0.5 mm thickness using a low-input technology. H3K27me3 or H3K27ac features across these slices were grouped into clusters based on their spatial variation patterns. Our approach reveals striking dynamics in frontal and caudal cortex due to kainic acid-induced seizure, linked with transmembrane ion transporter, exocytosis of synaptic vesicles, and secretion of neurotransmitter. Epigenomic tomography provides a powerful and cost-effective tool for profiling and discerning brain samples based on their spatial epigenomes.
Efficient Gene Transduction in Pigs and Macaques with the Engineered AAV Vector AAV.GT5 for Hemophilia B Gene Therapy
Authors: Kashiwakura Yuji , Endo Kazuhiro , Ugajin Atsushi , Kikuchi Tomohiro , Hishikawa Shuji , Nakamura Hitoyasu , Katakai Yuko , Baatartsogt Nemekhbayar , Hiramoto Takafumi , Hayakawa Morisada , Kamoshita Nobuhiko , Yamazaki Shoji , Kume Akihiro , Mori Harushi , Sata Naohiro , Sakata Yoichi , Muramatsu Shin-ichi , Ohmori Tsukasa
Published: November 2022

Gene therapy for hemophilia using adeno-associated virus (AAV) vectors allows long-term coagulation factor expression. We examined the potential of a novel engineered liver-tropic AAV3B-based vector AAV.GT5 for hemophilia B gene therapy.In vitrotransduction with AAV.GT5 in human hepatocytes was more than 100 times higher than with AAV-Spark100, whilein vivotransduction efficacy into the liver and the increase in coagulation factor IX (FIX) antigen following intravenous injection of these vectors were similar in PXB mice (chimeric mice with a humanized liver) and macaques. The discrepancy was due to the low recovery and short half-life of AAV.GT5 in blood, depending on the positive charge of the heparin-binding site in the original AAV3B. The intra-hepatic vascular administration of AAV.GT5, but not AAV-Spark100, enhanced vector transduction into the liver and reduced vector distribution to the kidney in pigs. In macaques, the intra-hepatic artery injection of AAV.GT5 yielded a comparable increase in FIX antigen with a one-third dosage of peripheral venous administration. Two of four macaques who received AAV.GT5 intravenously did not develop neutralizing antibodies (NAbs) against AAV.GT5, while AAV-Spark100 induced serotype-specific NAbs in all four macaques. The NAb produced after the administration was relatively specific to the serotype and less responsive to the other serotype. As a result, the administration of AAV.GT5 successfully boosted FIX expression in one animal previously given AAV-Spark100. Thus, AAV.GT5 has different biodistribution and immunogenic characteristics compared with AAV-Spark100, and the intra-hepatic vascular administration may lessen the vector dose and avoid vector distribution to other organs.

Key Points

The AAV.GT5 vector has a strong transduction efficacy in human hepatocytes but has a faster clearance after systemic administration.

Intra-hepatic vascular administration of the AAV.GT5 vector is an effective liver transduction method for hemophilia gene therapy.
Multi-omics analyses of single cell-derived colorectal cancer organoids reveal intratumor heterogeneity and immune response diversity
Authors: Yue Jian-Hui , Li Jie , Xu Qu-Miao , Ma Qi-Wang , Chen Chao , Liu Song-Ming , Sun Hai-Xi , Sui Qiao-Qi , Mu Feng , Ding Pei-Rong , Liu Long-Qi , Perez-Moreno Mirna , Zhang Xi
Published: November 2022

Colorectal cancer (CRC) organoids have similar genomic and functional characteristics to the original specimens. They have become a novel and promising tumor model. However, systematic research of heterogeneity and evolution based on tumor organoids and unbiased evaluation of CD4+T cell-mediated tumor recognition is presently lacking. Here, we study the variability in genomic characterization and single-cell transcriptome between different tumor organoid clones derived from the same CRC patient. While clone-specific differences in driver gene mutations and cancer stem cell (CSC) subpopulations were observed, inter-clone heterogeneity was even more prevalent. Using single-cell RNA sequencing, we found that compared with bulk organoids, CRC organoid clones are mainly composed of cancer stem cells and transiently-amplifying cells (TACs), but no epithelial-mesenchymal transition (EMT)-like (S100A4+CDH1-) cells. In addition, we study the phenotypic characteristics and TCR properties of tumor-reactive CD4+T cells by coupling the organoid-TILs co-culture model, single-cell profiling, and recognition testing of candidate TCRs. We found that the proliferating CD4+T cells increased significantly from 7.1% to 35.4%, and the TCR clonotypes increased from 110 to 1043 after co-culture with organoids. Moreover, 4 of 10 (40%) candidate TCRs with a significant increase in clone abundance exhibited tumor recognition. These results provide evidence that the proliferating CD4+T cells with clonal expansion after co-culture with tumor organoids are the potential tumor-reactive T cells. Collectively, we reconstructed intra-patient heterogeneity in single cell-derived organoid models and characterized the phenotypic characteristics and functional properties of tumor-reactive CD4+T cells.
Brief temporal perturbations in somatosensory reafference disrupt perceptual and neural attenuation and increase supplementary motor-cerebellar connectivity
Authors: Kilteni Konstantina , Houborg Christian , Ehrsson H. Henrik
Published: November 2022

Intrinsic delays in sensory feedback can be detrimental for motor control. As a compensation strategy, the brain predicts the sensory consequences of movement via a forward model on the basis of a copy of the motor command. Using these predictions, the brain attenuates the somatosensory reafference to facilitate the processing of exafferent information. Theoretically, this predictive attenuation gets disrupted by (even minimal) temporal errors between the predicted and the actual reafference, but direct evidence for such disruption is lacking since previous neuroimaging studies contrasted conditions of nondelayed reafferent input with exafferent one. Here, we combined psychophysics with functional magnetic resonance imaging to test whether subtle perturbations in the timing of somatosensory reafference disrupt its predictive processing. Twenty-eight participants generated touches on their left index finger by tapping a sensor with their right index finger. The touches on the left index finger were delivered at the time of the two fingers’ contact or with a 100 ms delay. We found that such brief temporal perturbations disrupted the attenuation of the somatosensory reafference both at the perceptual and neural level, leading to greater somatosensory and cerebellar responses and weaker somatosensory connectivity with the cerebellum proportionally to perceptual changes. Moreover, we observed increased connectivity of the supplementary motor area with the cerebellum during the perturbations. We interpret these effects as the failure of the forward model to predictively attenuate the delayed somatosensory reafference and the return of the prediction error to the motor centers, respectively.

Significance statement

Our brain receives the somatosensory feedback of our movements with delay. To counteract these delays, motor control theories postulate that the brain predicts the timing of the somatosensory consequences of our movements and attenuates sensations received at that timing. This makes a self-generated touch feel weaker than an identical external touch. However, how subtle temporal errors between the predicted and the actual somatosensory feedback perturb this predictive attenuation remains unknown. We show that such errors make the otherwise attenuated touch feel stronger, elicit stronger somatosensory responses, weaken the cerebellar connectivity with somatosensory areas, and increase it with motor areas. These findings show that motor and cerebellar areas are fundamental in forming temporal predictions about the sensory consequences of our movements.
Deep Domain Adversarial Neural Network for the Deconvolution of Cell Type Mixtures in Tissue Proteome Profiling
Authors: Wang Fang , Yang Fan , Huang Longkai , Song Jiangning , Gasser Robin B. , Aebersold Ruedi , Wang Guohua , yao Jianhua
Published: November 2022

Cell type deconvolution is a computational method for the determination/resolution of cell type proportions from bulk sequencing data, frequently used for the analysis of divergent cell types in tumor tissue samples. However, deconvolution technology is still in its infancy for the analysis of cell types using proteomic data due to challenges with repeatability/reproducibility, variable reference standards and the lack of single-cell proteomic reference data. Here, we developed a novel deep learning-based deconvolution method (scpDeconv) tailored to proteomic data. scpDeconv uses an autoencoder to leverage the information from bulk proteomic data to improve the quality of single-cell proteomic data, and employs a domain adversarial architecture to bridge the single-cell and bulk data distributions and transfer labels from single-cell data to bulk data. Extensive experiments validated the performance of scpDeconv in the deconvolution of proteomic data produced from various species/sources and different proteomic technologies. This method should find broad applicability to areas including tumor microenvironment interpretation and clinical diagnosis/classification.
Transcriptional diversity in synaptic gene sets is sufficient to discriminate cortical neuronal identity
Authors: Adam Amparo Roig , López Jose Martínez , van der Spek Sophie ,   The SYNGO consortium, Sullivan Patrick F , Smit August B. , Verhage Matthijs , Hjerling-Leffler Jens
Published: November 2022

Synapse diversity has been described from different perspectives, ranging from the specific neurotransmitters released, to their diverse biophysical properties and proteome profiles. However, synapse diversity at the transcriptional level has not been systematically identified across all synapse populations in the brain. To quantify postsynaptic and identify specific synaptic features of neuronal cell types we combined the SynGO (Synaptic Gene Ontology) database with single-cell RNA sequencing data of the mouse neocortex. We show that cell types can be discriminated by synaptic genes alone with the same power as all genes. The cell type discriminatory power is not equally distributed across synaptic genes as we could identify functional categories and synaptic compartments with greater cell type specific expression. Synaptic genes, and specific SynGO categories, belonged to three different types of gene modules: gradient expression over all cell types, gradient expression in selected cell types and cell class- or type-specific profiles. This data provides a deeper understanding of synapse diversity in the neocortex and identifies potential markers to selectively identify synapses from specific neuronal populations.
Thermodynamic Parameters Contributions of Single Internal Mismatches In RNA/DNA Hybrid Duplexes
Authors: Xiang Tongjun , Feng Huibao , Xing Xin-hui , Zhang Chong
Published: November 2022

Nucleic acid is a fundamental component of life. The thermodynamic is a basic physical quantity for nucleic acid and has been adopted in varieties of biotechnological applications. However, the parameters predicting thermodynamic parameters of RNA/DNA hybrid duplexes is incomplete and thus lead to the inability to proper predicting the properties. To address this problem, we measured for 99 RNA/DNA hybrid duplexes with 11 nucleotide length in a 1 M NaCl buffer using UV absorbance thermal denaturation. Thermodynamic parameters were obtained by fitting absorbance versus temperature profiles using SciPy non-linear curve fit. A dataset of 228 duplexes were constructed combining with literature experimental thermodynamic parameters for fitting a full set of all 113 possible Watson-Crick and single internal mismatch involving nearest-neighbor parameters using singular value decomposition. The new nearest-neighbor parameters predict thermodynamic parameters of RNA/DNA hybrid duplexes within an average error of 0.26 kcal/mol (3.55%) in free energy at 37°C (ΔG°37), 5.05 kcal/mol (6.70%) in enthalpy (ΔH°), 16.3 cal/mol·K (7.50%) in entropy (ΔS°) and 1.14°C (2.91%) in melting temperature (Tm). The highest accuracy of all parameters reported. We observed a trend of increased stability for mismatch involving pairs of rG/dT >> rU/dG > rG/dA > rG/dG ≈ rA/dC ≈ rA/dG > rC/dA ≈ rC/dT > rU/dT ≈ rU/dC >> rA/dA >> rC/dC, which can be explained by different hydrogen bond conditions in mismatch pairs. We further compared the stability with RNA/RNA and DNA/DNA duplexes and found a backbone structure depended pattern in these three kinds of nucleic acid duplexes. This nearest-neighbor parameter set could enhance thermodynamical understanding of RNA/DNA combination and have potential usage in predicting on- and off-target RNA-DNA binding activity when applied to biotechnological applications such as CRISPR/Cas systems, RNAi and qPCR.
Leverage Edu: caught between novelty and efficiency
Authors: Kumari Deepa , Srivastava Ritu
Published: November 2022

Learning outcomes

The learning outcomes are as follows:

1. enable students to appreciate how a platform company can navigate through diminishing network effects;

2. enable students to foresee the downside of scaling up a platform business;

3. enable students to appreciate the trade-off between an efficiency-centric and a novelty-centric business model for platform businesses; and

4. enable students to create a platform business model canvas for a company.

Case overview/synopsis

The teaching case discusses the dilemma of Akshay Chaturvedi, the founder of Leverage Edu, an artificial intelligence-enabled platform for students seeking admission to foreign universities. It had received nearly US$9.6m in funding until December 2021.

Chaturvedi wanted to make the best use of his funds, but was torn between turning Leverage Edu into an “efficient platform” and transforming it into a “novelty-centric platform”. The teaching note attempts to resolve Chaturvedi’s dilemma by analyzing competitors using the platform canvas model and determining how Chaturvedi could create and use network effects to Leverage Edu’s advantage. The case is based on secondary data that is freely available in the public domain.

Complexity academic level

This case is intended for MBA Entrepreneurship students taking a platform business elective. It can also be used in faculty and management development programs under the banner “Technology and Platform Businesses”.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 3: Entrepreneurship.