bluuebunny/crossref_metadata_2025 huggingface dataset:
Golgi retention and oncogenic KIT signaling via PLCγ2-PKD2-PI4KIIIβ activation in GIST cells
Authors: Obata Yuuki , Kurokawa Kazuo , Tojima Takuro , Natsume Miyuki , Shiina Isamu , Takahashi Tsuyoshi , Abe Ryo , Nakano Akihiko , Nishida Toshirou
Published: December 2022

Most gastrointestinal stromal tumors (GISTs) develop due to gain-of-function mutations in the tyrosine kinase,KIT. We recently showed that mutant KIT mislocalizes to the Golgi area and initiates uncontrolled signaling. However, the molecular mechanisms underlying its Golgi retention remain unknown. Here, we show that protein kinase D2 (PKD2) is activated by the mutant, which causes KIT’s Golgi retention. In PKD2-inhibited cells, KIT migrates from the Golgi region to lysosomes and subsequently undergoes degradation. Importantly, delocalized KIT is unable to trigger downstream activation. In the Golgi area, KIT activates the PKD2-phosphatidylinositol 4-kinaseIIIβ (PKD2-PI4KIIIβ) pathway through phospholipase γ2 (PLCγ2) to generate a PI4P-rich membrane domain, where the AP1-GGA1 complex is aberrantly recruited. Disruption of any factors in this cascade results in KIT release from the Golgi region, indicating that these PKD2-related pathways are responsible for the Golgi retention of KIT. Our findings unveil the molecular mechanisms underlying KIT mislocalization and provide evidence for a new strategy for inhibition of oncogenic signaling.
Probing the evolutionary dynamics of whole-body regeneration within planarian flatworms
Authors: Vila-Farré Miquel , Rozanski Andrei , Ivanković Mario , Cleland James , Brand Jeremias N. , Thalen Felix , Grohme Markus , von Kannen Stephanie , Grosbusch Alexandra , Vu Han T-K , Prieto Carlos E. , Carbayo Fernando , Egger Bernhard , Bleidorn Christoph , Rasko John E. J. , Rink Jochen C.
Published: December 2022

Why some animals can regenerate while many others cannot remains a fascinating question. Even amongst planarian flatworms, well-known for their ability to regenerate complete animals from small body fragments, species exist that have restricted regeneration abilities or are entirely regeneration incompetent. Towards the goal of probing the evolutionary dynamics of regeneration, we have assembled a diverse live collection of planarian species from around the world. The combined quantification of species-specific head regeneration abilities and comprehensive transcriptome-based phylogeny reconstructions reveals multiple independent transitions between robust whole-body regeneration and restricted regeneration in the freshwater species. Our demonstration that theRNAi-mediated inhibition of canonical Wnt signalling can nevertheless bypass all experimentally tractable head regeneration defects in the current collection indicates that the pathway may represent a hot spot in the evolution of planarian regeneration defects. Combined with our finding that Wnt signalling has multiple roles in the reproductive system of the model speciesS. mediterranea, this raises the possibility of a trade-off between egg-laying and asexual reproduction by fission/regeneration as a driver of regenerative trait evolution. Although initial quantitative comparisons of Wnt signalling levels, reproductive investment, and regenerative abilities across the collection confirm some of the model’s predictions, they also highlight the diversification of molecular mechanisms amongst the divergent planarian lineages. Overall, our study establishes a framework for the mechanistic evolution of regenerative abilities and planarians as model taxon for comparative regeneration research.
Diclofenac and other Non-Steroidal Anti-Inflammatory Drugs (NSAIDs) are Competitive Antagonists of the human P2X3 Receptor
Authors: Grohs Laura , Cheng Linhan , Cönen Saskia , Haddad Bassam G. , Obrecht Astrid , Toklucu Idil , Ernst Lisa , Körner Jannis , Schmalzing Günther , Lampert Angelika , Machtens Jan-Philipp , Hausmann Ralf
Published: December 2022

The P2X3 receptor (P2X3R), an ATP-gated non-selective cation channel of the P2X receptor family, is expressed in sensory neurons and involved in nociception. P2X3R inhibition was shown to reduce chronic and neuropathic pain. In a previous screening of 2000 approved drugs, natural products and bioactive substances, various non-steroidal anti-inflammatory drugs (NSAIDs) were found to inhibit P2X3R-mediated currents. To investigate whether the inhibition of P2X receptors contributes to the analgesic effect of NSAIDs, we characterized the potency and selectivity of various NSAIDs at P2X3R and other P2XR subtypes using two-electrode voltage clamp electrophysiology. We identified diclofenac as a hP2X3R and hP2X2/3R antagonist with micromolar potency (with IC50values of 138.2 µM and 76.7 µM, respectively). A weaker inhibition of hP2X1R, hP2X4R and hP2X7R by diclofenac was determined. Flufenamic acid (FFA) proved to inhibit hP2X3R, rP2X3R and hP2X7R (IC50values of 221µM, 264.1µM and ∼ 900µM, respectively), questioning its widespread use as a nonselective ion channel blocker, when P2XR-mediated currents are under study.

Inhibition of the hP2X3R or hP2X2/3R by diclofenac could be overcome by prolonged ATP-application or increasing concentrations of the agonist α,β-meATP, respectively, indicating competition of diclofenac and the agonists. Molecular dynamics simulation showed that diclofenac largely overlaps with ATP bound to the open state of the hP2X3R. Our results strongly support a competitive antagonism through which diclofenac, by interacting with residues of the ATP-binding site, left flipper, and dorsal fin domains inhibits gating of P2X3R by conformational fixation of the left flipper and dorsal fin domains.

In summary, we demonstrate the inhibition of the human P2X3 receptor by various NSAIDs. Diclofenac proved to be the most effective antagonist with a strong inhibition of hP2X3R and hP2X2/3R and a weaker inhibition of hP2X1R, hP2X4R and hP2X7R. Considering their involvement in nociception, inhibition of hP2X3R and hP2X2/3R by micromolar concentrations of diclofenac may contribute to the analgesic effect as well as the side effect of taste disturbances of diclofenac and represent an additional mode of action besides the well-known high potency COX inhibition.
Constriction forces imposed by basement membranes regulate developmental cell migration
Authors: López Ester Molina , Kabanova Anna , Martín-Bermudo Maria D.
Published: December 2022

The basement membrane (BM) is a specialized extracellular matrix, which underlies or encase developing tissues. Mechanical properties of encasing BMs have been shown to profoundly influence the shaping of associated tissues. Here, we use the migration of the border cells (BCs) of theDrosophilaegg chamber to unravel a new role of encasing BMs in developmental cell migration. BCs move between a group of cells, the nurse cells (NCs), that are enclosed by a monolayer of follicle cells (FCs), enveloped in turn by a BM, the follicle BM. We show that increasing or reducing the stiffness of the follicle BM, by altering laminins or Coll IV levels, conversely affects BC migration speed and alters migration mode and dynamics. Follicle BM stiffness also controls pairwise NC and FC cortical tension. We propose that constriction forces imposed by the follicle BM influence NC and FC cortical tension, which, in turn, regulate BC migration. Encasing BMs emerge as key players in the regulation of collective cell migration during morphogenesis.
Regulation of excitatory presynaptic activity by Ambra1 protein determines neuronal networks in sex-dimorphic manner
Authors: Ju Anes , Altas Bekir , Rhee Hong Jun , Schwark Manuela , Hassouna Imam , Sigler Albrecht , Kawabe Hiroshi , Chowdhury Kamal , Ehrenreich Hannelore , Brose Nils , Rhee JeongSeop
Published: December 2022

Heterozygous mutation ofAmbra1, known as a positive autophagy regulator, produces autismlike behavior in mice and autistic phenotypes in humans in a female-specific manner. However, the substantial roles of theAmbra1mutation in neurons are still unknown. We find thatAmbra1heterozygotes display a moderate decrease in excitatory synaptic releasein-vitroandex-vivoexclusively in females without autophagy activity, resulting in significant alterations in γ-oscillation power and seizure susceptibility by excitatory/inhibitory (E/I) imbalance. Specifically,Ambra1deficiency has no effect on neurogenesis and morphogenesis, but selectively decreases excitatory synaptic activity without changes in synapse number, quantal size, synaptic release probability, and synaptic plasticity. Therefore, the limited excitatory synaptopathy by Ambra1 expression levels ultimately determines E/I imbalance in global neural networks leading to the female-specific ASD.
Blood flow diverts extracellular vesicles from endothelial degradative compartments to promote angiogenesis
Authors: Mary B. , Asokan N. , Jerabkova-Roda K. , Larnicol A. , Busnelli I. , Stemmelen T. , Pichot A. , Molitor A. , Carapito R. , Lefebvre O. , Goetz J.G. , Hyenne V.
Published: December 2022

Extracellular vesicles released by tumors (tEVs) disseminate via circulatory networks and promote microenvironmental changes in distant organs favoring metastatic seeding. Despite their abundance in the bloodstream, how hemodynamics affect the function of circulating tEVs remains unsolved. We experimentally tuned flow profiles in vitro (microfluidics) and in vivo (zebrafish) and demonstrated that efficient uptake of tEVs occurs in endothelial cells subjected to capillary-like hemodynamics. Such flow profiles partially reroute internalized tEVs towards non-acidic and non-degradative Rab14-positive endosomes, at the expense of lysosomes, suggesting that endothelial mechanosensing diverts tEVs from degradation. Subsequently, tEVs promote the expression of pro-angiogenic transcription factors in flow-stimulated endothelial cells and favor vessel sprouting in zebrafish. Altogether, we demonstrate that capillary-like flow profiles potentiate the pro-tumoral function of circulating tEVs by promoting their uptake and rerouting their trafficking. We propose that tEVs contribute to pre-metastatic niche formation by exploiting endothelial mechanosensing in specific vascular regions with permissive hemodynamics.
SGCI (Smartwatch Gait Coordination Index): New Measure for Human Gait Utilizing Smartwatch Sensor
Authors: Han Sumin , Paul Robert
Published: December 2022

Human walking reflects the state of human health. Numerous medical studies have been conducted to analyze walking patterns and to diagnose disease progression. However, this process requires expensive equipment and considerable time and manpower. Smartwatches are equipped with gyro sensors to detect human movements and graph-walking patterns. To measure the abnormality in walking using this graph, we developed a smartwatch gait coordination index (SGCI) and examined its usefulness. The phase coordination index was applied to analyze arm movements. Based on previous studies, the PCI formula was applied to graphs obtained from arm movements, showing that arm and leg movements during walking are correlated with each other. To prove this, a smartwatch was worn on the arms and legs of eight healthy adults and the difference in arm movements was measured. The SGCI values with abnormal walking patterns were compared with the SGCI values obtained during normal walking. The SCGI can be automatically and continuously measured with the gyro sensor of the smartwatch and can be used as an indirect indicator of human walking conditions.
A characterization of cardiac-induced noise in R2* maps of the brain
Authors: Raynaud Quentin , Di Domenicantonio Giulia , Yerly Jérôme , Dardano Thomas , van Heeswijk Ruud B. , Lutti Antoine
Published: December 2022

Purpose

Cardiac pulsation increases the noise level in brain maps of the transverse relaxation rate R2*. Cardiac-induced noise is challenging to mitigate during the acquisition of R2* mapping data because its characteristics are unknown. In this work, we therefore aim to characterize cardiac-induced noise in brain maps of the MRI parameter R2*.

Methods

We designed a sampling strategy to acquire multi-echo 3D data in 12 intervals of the cardiac cycle, monitored with a fingertip pulse-oximeter. We measured the amplitude of cardiac-induced noise in this data and assessed the effect of cardiac pulsation on R2* maps computed across echoes. The area of k-space that contains most of the cardiac-induced noise in R2* maps was then identified. Based on these characteristics, we introduced a tentative sampling strategy that aims to mitigate cardiac-induced noise in R2* maps of the brain.

Results

In inferior brain regions, cardiac pulsation accounts for R2* variations of up to 3s-1across the cardiac cycle, i.e. ∼35% of the overall variability. Cardiac-induced fluctuations occur throughout the cardiac cycle, with a reduced intensity during the first quarter of the cycle. 50-60% of the overall cardiac-induced noise is localized near the k-space centre (k < 0.074 mm-1). The tentative cardiac noise mitigation strategy reduced the variability of R2* maps across repetitions by 11% in the brainstem and 6% across the whole brain.

Conclusion

We provide a characterisation of cardiac-induced noise in brain R2* maps that can be used as a basis for the design of mitigation strategies during data acquisition.
The arms race in noncoding regions of transposable element: the evolution of anti-silencing and RNAi
Authors: Sasaki Taku , Kato Kae , Hosaka Aoi , Fu Yu , Toyoda Atsushi , Fujiyama Asao , Tarutani Yoshiaki , Kakutani Tetsuji
Published: December 2022

Transposable elements (TEs) are among the most dynamic parts of genomes. Since TEs are potentially deleterious, eukaryotes silence them through epigenetic mechanisms such as DNA methylation and RNAi. We have previously reported that Arabidopsis TEs, calledVANDALs, counteract epigenetic silencing through a group of sequence-specific anti-silencing proteins, VANCs. VANC proteins bind to noncoding regions of specificVANDALcopies and induce a loss of silent chromatin marks. Sequence-specific anti-silencing allows these TEs to proliferate with minimum host damage. Here, we show that RNAi efficiently targets noncoding regions ofVANDALTEs to silence themde novo. Target motifs of VANC, in turn, evolved to escape RNAi. Escaping RNAi could be the primary event leading to the differentiation of sequence-specific anti-silencing systems. We propose that this selfish behaviour of TEs paradoxically could make them less harmful to the host.
Rewarding capacity of optogenetically activating a giant GABAergic central-brain interneuron in larvalDrosophila
Authors: Mancini Nino , Thoener Juliane , Tafani Esmeralda , Pauls Dennis , Mayseless Oded , Strauch Martin , Eichler Katharina , Champion Andrew , Kobler Oliver , Weber Denise , Sen Edanur , Weiglein Aliće , Hartenstein Volker , Thum Andreas S. , Rohwedder Astrid , Schleyer Michael , Gerber Bertram
Published: December 2022

Larvae of the fruit flyDrosophila melanogasterare a powerful study case for understanding the neural circuits underlying behavior. Indeed, the numerical simplicity of the larval brain has permitted the reconstruction of its synaptic connectome, and genetic tools for manipulating single, identified neurons allow neural circuit function to be investigated with relative ease and precision. We focus on one of the most complex neurons in the brain of the larva (of either sex), the GABAergic anterior paired lateral neuron (APL). Using behavioral and connectomic analyses, optogenetics, Ca2+imaging and pharmacology, we study how APL affects associative olfactory memory. We first provide a detailed account of the structure, regional polarity, connectivity, and metamorphic development of APL, and further confirm that optogenetic activation of APL has an inhibiting effect on its main targets, the mushroom body Kenyon cells. All these findings are consistent with the previously identified function of APL in the sparsening of sensory representations. To our surprise, however, we found that optogenetically activating APL can also have a strong rewarding effect. Specifically, APL activation together with odor presentation establishes an odor-specific, appetitive, associative short-term memory, whereas naïve olfactory behavior remains unaffected. An acute, systemic inhibition of dopamine synthesis as well as an ablation of the dopaminergic pPAM neurons impair reward learning through APL activation. Our findings provide a study case of complex circuit function in a numerically simple brain, and suggest a previously unrecognized capacity of central-brain GABAergic neurons to engage in dopaminergic reinforcement.

Significance statement

The single, identified giant anterior paired lateral (APL) neuron is one of the most complex neurons in the insect brain. It is GABAergic and contributes to the sparsening of neuronal activity in the mushroom body, the memory center of insects. We provide the most detailed account yet of the structure of APL in larvalDrosophilaas a neurogenetically accessible study case. We further reveal that, contrary to expectations, the experimental activation of APL can exert a rewarding effect, likely via dopaminergic reward pathways. The present study both provides an example of unexpected circuit complexity in a numerically simple brain, and reports an unexpected effect of activity in central-brain GABAergic circuits.
Chemoproteomics yields a selective molecular host for acetyl-CoA
Authors: Lieberman Whitney K. , Brown Zachary A. , Jing Yihang , Evans Nya D. , Jhulki Isita , Grose Carissa , Jones Jane E. , Meier Jordan L.
Published: December 2022

Chemoproteomic profiling is a powerful approach to define the selectivity of small molecules and endogenous metabolites with the human proteome. In addition to mechanistic studies, proteome specificity profiling also has the potential to identify new scaffolds for biomolecular sensing. Here we report a chemoproteomics-inspired strategy for selective sensing of acetyl-CoA. First, we use chemoproteomic capture experiments to validate the N-terminal acetyltransferase NAA50 as a protein capable of differentiating acetyl-CoA and CoA. A Nanoluc-NAA50 fusion protein retains this specificity and can be used to generate a bioluminescence resonance energy transfer (BRET) signal in the presence of a CoA-linked fluorophore. This enables the development of a ligand displacement assay in which CoA metabolites are detected via their ability to bind the Nanoluc-NAA50 protein ‘host’ and compete binding of the CoA-linked fluorophore ‘guest.’ We demonstrate that the specificity of ligand displacement reflects the molecular recognition of the NAA50 host, while the window of dynamic sensing can be controlled by tuning the binding affinity of the CoA-linked fluorophore guest. Finally, we show the method’s specificity for acetyl-CoA can be harnessed for gain-of-signal optical detection of enzyme activity. Overall, our studies demonstrate the potential of harnessing insights from chemoproteomics for molecular sensing and provide a foundation for future applications in target engagement and selective metabolite detection.
Automated segmentation of fetal intracranial volume in 3D ultrasound using deep learning: identifying sex differences in prenatal brain development
Authors: de Zwarte Sonja MC , Teeuw Jalmar , He Jiaojiao , Bekker Mireille N , van Sloun Ruud JG , Hulshoff Pol Hilleke E
Published: December 2022

The human brain undergoes major developmental changes during pregnancy. Three-dimensional (3D) ultrasound images allow for the opportunity to investigate typical prenatal brain development on a large scale. Here, we developed a convolutional neural network (CNN) model for automated segmentation of fetal intracranial volume (ICV) from 3D ultrasound, and we applied the trained model in a large independent sample (N = 9795 ultrasounds; N=1763 participants) from the YOUth Baby and Child cohort measured at 20- and 30-week of gestational age to investigate sex differences in fetal ICV and ICV growth. 168 3D ultrasound images with ICV annotations were included to develop a 3D CNN model for automated fetal ICV segmentation. A data augmentation strategy provided physical variation and additional data to train the network. K-fold cross-validation and Bayesian optimization were used for network selection and the ensemble-based system combined multiple networks to form the final ensemble network. The final ensemble network produced consistent and high-quality segmentations of ICV. Our trained model successfully predicted ICV and ICV growth in a large independent longitudinal data set. Boys had significantly larger ICV at 20- (B=2.83;p=1.4e-13) and 30-weeks of pregnancy (B=12.01;p=2.0e-28), and more pronounced ICV growth than girls (t=-4.395;p=1.3e-5). Our approach provides us with the opportunity to investigate fetal brain development on a much larger scale and to answer fundamental questions related to prenatal brain development.
Purging due to self-fertilization does not prevent accumulation of expansion load
Authors: Zeitler Leo , Parisod Christian , Gilbert Kimberly J.
Published: December 2022

Species range expansions are a common demographic history presenting populations with multiple evolutionary challenges. It is not yet fully understood if self-fertilization, which is often observed at species range edges, may create an evolutionary advantage against these challenges. Selfing provides reproductive reassurance to counter Allee effects and selfing may purge accumulated mutational burden due to founder events (expansion load) by further increasing homozygosity. We study how selfing impacts the accumulation of genetic load during range expansion via purging and/or speed of colonization. Using simulations, we disentangle inbreeding effects due to demography versus due to selfing and find that selfers expand faster, but still accumulate load, regardless of mating system. The severity of variants contributing to this load, however, differs across mating system: higher selfing rates purge large-effect recessive variants leaving a burden of smaller-effect alleles. We compare these predictions to the mixedmating plantArabis alpina, using whole-genome sequences from refugial outcrossing populations versus expanded selfing populations. Empirical results indicate accumulation of expansion load along with evidence of purging in selfing populations, concordant with our simulations, and suggesting that while purging is a benefit of selfing evolving during range expansions, it is not sufficient to prevent load accumulation due to range expansion.

Author Summary

The geographic space that species occupy, i.e. the species range, is known to fluctuate over time due to changing environmental conditions. Since the most recent glaciation, many species have recolonized available habitat as the ice sheets melted, expanding their range. When populations at species range margins expand into newly available space, they suffer from an accumulation of deleterious alleles due to repeated founder effects. We study whether self-fertilization, which is considered an evolutionary deadend, can be favored under these expanding edge conditions. Selfing has two important effects: allowing for faster expansion due to reproductive assurance and purging recessive deleterious alleles by exposing them to selection as homozygotes. We use simulations to identify the impact of selfing on expanded populations and then compare these results to an empirical dataset to assess whether our predictions are met. We use the mixed-mating plant alpine rock-cress (Arabis alpina) since it has both expanded since the last glaciation and undergone a mating shift to selfing. We find that selfing does not prevent the accumulation of deleterious load, however purging does still act to remove the most severe variants, indicating that selfing provides this benefit during range expansions.
Similar neural pathways link psychological stress and brain health in health and multiple sclerosis
Authors: Schulz Marc-Andre , Hetzer Stefan , Eitel Fabian , Asseyer Susanna , Meyer-Arndt Lil , Schmitz-Hübsch Tanja , Bellmann-Strobl Judith , Cole James H. , Gold Stefan M. , Paul Friedemann , Ritter Kerstin , Weygandt Martin
Published: December 2022

Clinical and neuroscientific studies suggest a link between psychological stress and reduced brain health - in healthy humans and patients with neurological disorders. However, it is unclear which neural pathways mediate between stress and brain health and whether these pathways are similar in health and disease. Here, we applied an Arterial-Spin-Labeling MRI stress task in 42 healthy persons and 56 with multiple sclerosis. We tested whether brain-predicted age differences (“brain-PAD”), a highly sensitive structural brain health biomarker derived from machine learning, mirror functional connectivity between stress-responsive regions. We found that regional neural stress responsivity did not differ between groups. Although elevated brain-PAD indicated worse brain health in patients, anterior insula-occipital functional connectivity correlated with brain-PAD in both groups. Grey matter variations contributed similarly to brain-PAD in both groups. These findings suggest a generic connection between stress and brain health whose impact is amplified in multiple sclerosis by disease-specific vulnerability factors.
Small Molecule Properties Define Partitioning into Biomolecular Condensates
Authors: Thody Sabareesan Ambadi , Clements Hanna D. , Baniasadi Hamid , Lyon Andrew S. , Sigman Matthew S. , Rosen Michael K.
Published: December 2022

Biomolecular condensates regulate cellular function by compartmentalizing molecules without a surrounding membrane1,2. Condensate functions are believed to arise from the specific exclusion or enrichment of molecules3-5. Thus, understanding the principles governing condensate composition is critical to characterizing condensate function. The molecular bases of macromolecular composition have been studied in detail for several condensates6-9, but partitioning of small molecules into condensates remains poorly understood. Using mass spectrometry with validation by fluorescence microscopy, we quantified partitioning of ∼1700 metabolites and FDA-approved drugs into four condensates composed of different DNA and/or protein scaffolds. We found that partitioning spanned from ∼100-fold exclusion to ∼10,000-fold enrichment. Strong correlations between the different condensates suggest an underlying physical similarity despite disparate macromolecular components. Strongly partitioning molecules generally did not bind condensate-forming proteins with high affinity under conditions where condensates do not form, suggesting only a minor role for stereospecific interactions in partitioning. We developed a machine learning model that accurately predicts partitioning using only physicochemical properties of the compounds. The strongest predictors of partitioning were features related to aqueous solubility and hydrophobicity. Small molecule partitioning was similar for condensates in aqueous buffer and in concentrated cell extracts, suggesting analogous behaviors in vivo. Together, the data and model suggest that small molecule partitioning is not generally based on high-affinity, stereospecific interactions with scaffolds, but rather on physical properties of the compounds, and their compatibility with an emergent hydrophobic environment within the condensate. Our results will aid design of chemical compounds that target biomolecular condensates and reveal unexpected physical and functional similarities of distinct condensates.
Molecular insights into the gating mechanisms of voltage-gated calcium channel CaV2.3
Authors: Gao Yiwei , Xu Shuai , Cui Xiaoli , Xu Hao , Qiu Yunlong , Wei Yiqing , Dong Yanli , Zhu Boling , Peng Chao , Liu Shiqi , Zhang Xuejun Cai , Sun Jianyuan , Huang Zhuo , Zhao Yan
Published: December 2022

High-voltage-activated R-type CaV2.3 channel plays pivotal roles in many physiological activities and is implicated in epilepsy, convulsions, and other neurodevelopmental impairments. Here, we determine the high-resolution cryo-electron microscopy (cryo-EM) structure of human CaV2.3 in complex with the α2δ1 and β1 subunits. The VSDIIis stabilized in the resting state. Electrophysiological experiments elucidate that the conformational change of VSDIIin response to variation in membrane potential is not required for channel activation, whereas the other VSDs are essential for channel opening. The intracellular gate is blocked by the W-helix. A pre-W-helix adjacent to the W-helix can significantly regulate closed-state inactivation (CSI) by modulating the association and dissociation of the W-helix with the gate. Electrostatic interactions formed between the negatively charged domain on S6II, which is exclusively conserved in the CaV2 family, and nearby regions at the alpha-interacting domain (AID) and S4-S5IIhelix are identified. Further functional analyses indicate that these interactions are critical for the open-state inactivation (OSI) of CaV2 channels.
A superoxide reductase contributes toClostridioides difficileresistance to oxygen
Authors: Kochanowsky Rebecca , Carothers Katelyn , Roxas Bryan Angelo P. , Anwar Farhan , Viswanathan V.K. , Vedantam Gayatri
Published: December 2022

Clostridioides difficilecauses a serious diarrheal disease and is a common healthcare-associated bacterial pathogen. Although it has a major impact on human health, mechanistic details ofC. difficileintestinal colonization remain undefined.C. difficileis highly sensitive to oxygen and requires anaerobic conditions forin vitrogrowth. However, the mammalian gut is not entirely devoid of oxygen, andC. difficiletolerates moderate oxidative stressin vivo. TheC. difficilegenome encodes several antioxidant proteins, including a predicted superoxide reductase (SOR) that is upregulated upon exposure to antimicrobial peptides. The goal of this study was to establish SOR enzymatic activity and assess its role in protectingC. difficileagainst oxygen exposure. Insertional inactivation ofsorrenderedC. difficilemore sensitive to superoxide indicating that SOR contributes to antioxidant defense. HeterologousC. difficile sorexpression inEscherichia coliconferred protection against superoxide-dependent growth inhibition, and the corresponding cell lysates showed superoxide scavenging activity. Finally, aC. difficileSOR mutant exhibited global proteome changes under oxygen stress when compared to its parent strain. Collectively, our data establish the enzymatic activity ofC. difficileSOR, confirm its role in protection against oxidative stress, and demonstrate its broader impacts on the vegetative cell proteome.

Importance

Clotridioides difficileis an important pathogen strongly associated with healthcare settings and capable of causing severe diarrheal disease. While considered a strict anaerobein vitro, C. difficilehas been shown to tolerate low levels of oxygen in its mammalian host. Among other well-characterized antioxidant proteins, theC. difficilegenome includes a predicted superoxide reductase (SOR), an understudied component of antioxidant defense in pathogens. The significance of the research reported herein is the characterization of the enzymatic activity of the putative SOR protein, including confirmation of its role in protection ofC. difficileagainst oxidative stress. This furthers our understanding ofC. difficilepathogenesis and presents a potential new avenue for targeted therapies.
The common oral parasitic protozoanEntamoeba gingivalisforms cysts in response to antibiotic treatment
Authors: Becker Christin , Adam Aysegül , Dommisch Henrik , Stach Thomas , Schaefer Arne S.
Published: December 2022

The eukaryotic protozoanEntamoeba gingivalis(E.g.) is strongly associated with inflamed periodontal pockets. Unlike other obligate anaerobicEntamoebaspecies, it is considered to not have a life cycle of actively dividing trophozoites and dormant cysts. Accordingly, it has been regarded as non-infectious. To investigate ifE.gis capable of encystation in response to adverse environmental conditions, we cultivated clinical isolates ofE.g. collected from inflamed periodontal pockets in antibiotics for 8 days. The cytomorphological and ultrastructure forms of the amoeba were investigated by transmission and scanning electron microscopy to reveal cyst formation. We observed exocysts and the encapsulated trophozoids separated by an intra-cystic space, a dense poorly vesiculated cytoplasma and polygonal surface areas of cysts. The cysts walls were composed of chitin. Cysts were conspicuously smaller compared to trophozoids and lacked pseudo- and filipodia. We did not observe multi-nucleated trophozoids after antibiotic induces encystation. Cyst formation inE.gmay explain why established treatment approaches often do not stop periodontal tissue destruction during periodontitis and periimplantitis.
The onset of late severe lung impairment in COVID-19 is associated with high inflammation markers at admission and metabolic syndrome markers
Authors: Epaulard Olivier , Le Gouellec Audrey , Le Marechal Marion , Nemoz Benjamin , Borel Anne-Laure , Dartevel Anaïs , Gheerbrant Hubert , Herault Marie-Christine , Bosseray Annick , Clavarino Giovanna , Lupo Julien , Viglino Damien , Quenard Fanny , Candille Clara , Camara Boubou , Durand Michel , Faure Patrice , Guergour Dorra , Chidlovski Elena , Jacob Marie-Christine , Larrat Sylvie , Froidure Marie , Terzi Nicolas , Quetant Sébastien , Payen Jean-François , Colombe Barbara , Raskovalova Tatiana , Morand Patrice , Pierre Isabelle , Schwebel Carole , Hamidfar Rebecca , Bouillet Laurence , Brion Jean-Paul , Trocme Candice , Berthier Sylvie , Chirica Carole , Mounayar Anne-Laure , Blanc Myriam , Pavese Patricia , Toussaint Bertrand
Published: December 2022

Background

COVID-19 severity is mainly related to lung impairment. However, preexisting patient characteristics and biomarkers at admission associated with this event are not precisely known.

Methods

We report 205 patients admitted for a proven COVID-19 in our institution between March 7 and April 22, 2020, particularly their comorbidities, respiratory severity, immune profile, and metabolic profile.

Findings

Median age was 70 years [interquartile range (IQR) 25-75: 60;79]; 115 (56·1%) patients were men. Oxygen supplementation of >2L/min was required in 107 patients (52·2%) after a median time of 8 days [IQR: 6;10] after the first symptoms; 67 (32·7%) patients were admitted to the intensive care unit (ICU), almost exclusively due to severe hypoxia. Patients requiring >2L/min oxygen therapy and/or ICU admission were older and more frequently males, with a significantly higher body mass index (BMI), a significantly higher total cholesterol (TC) / HDL cholesterol ratio, and higher triglycerides. They also had higher plasma levels of C-reactive protein (CRP) and interleukin 6 (IL-6); IL-6 >20 ng/L and CRP >70 mg/L were significantly associated with ICU admission and/or (for patients with a decision of limitation of life-support therapy) death. Higher BMI and TC/HDL-c ratio were associated with higher CRP and IL-6 levels. Steroid therapy was performed in 61 patients; while its clinical impact was inconclusive due to heterogeneous situations, IL-6 levels decreased significantly more in these patients.

Interpretation

Severe COVID-19 mostly relates to late-onset pneumonia associated with preexisting metabolic syndrome markers and a surge in inflammatory markers, allowing the early identification of at-risk patients.

Funding

This work was supported by Foundation University of Grenoble Alpes.
Machine Learning Classification Of Autism Spectrum Disorder Based On Reciprocity In Naturalistic Social Interactions
Authors: Koehler J.C. , Dong M.S. , Nelson A.M. , Fischer S. , Späth J. , Plank I.S. , Koutsouleris N. , Falter-Wagner C.M.
Published: December 2022

Autism spectrum disorder is characterized by impaired social communication and interaction. As a neurodevelopmental disorder typically diagnosed during childhood, diagnosis in adulthood is preceded by a resource-heavy clinical assessment period. The ongoing developments in digital phenotyping give rise to novel opportunities within the screening and diagnostic process. In this study, we investigated videos of naturalistic social interaction between autistic and non-autistic adults on their predictiveness for autistic behaviors. Non-autistic control participants were either paired with each other or an autistic participant to engage in two conversational tasks. We used existing computer vision algorithms to extract information based on the synchrony of movement and facial expression. These were subsequently used as features in a support vector machine learning model to predict interaction dyad membership. Results showed high predictive accuracy of synchrony in facial movements, underlining the distinctive nature of non-verbal behavior in autism and its feasibility for digitalized assessment.
Data-driven estimation of the instantaneous reproduction number and growth rates for the 2022 monkeypox outbreak in Europe
Authors: Saldaña Fernando , Daza-Torres Maria L. , Aguiar Maíra
Published: December 2022

Objective

To estimate the instantaneous reproduction numberRtand the epidemic growth rates for the 2022 monkeypox outbreaks in the European region.

Methods

We gathered daily laboratory-confirmed monkeypox cases in the most affected European countries from the beginning of the outbreak to September 23, 2022. A data-driven estimation of the instantaneous reproduction number is obtained using a novel filtering type Bayesian inference. A phenomenological growth model coupled with a Bayesian sequential approach to update forecasts over time is used to obtain time-dependent growth rates in several countries.

Results

The instantaneous reproduction numberRtfor the laboratory-confirmed MPX cases in Spain, France, Germany, the UK, the Netherlands, Portugal, and Italy. At the early phase of the outbreak, our estimation forRt, which can be used as a proxy for the basic reproduction numberR0, was 2.32 (95% CI 1.81−3.05) for Spain, 2.91 (95% CI 2.33−3.52) for France, 1.84 (95% CI 1.55−2.31) for UK, 3.16 (95% CI 2.55−3.64) for Germany, 2.97 (95% CI 2.01−4.32) for the Netherlands, 1.18 (95% CI 0.98−1.33) for Portugal, 3.74 (95% CI 2.91−4.49) for Italy. Cumulative cases for these countries present subexponential rather than exponential growth dynamics.

Conclusions

Our findings suggest that the current monkeypox outbreaks present limited transmission chains of human-to-human secondary infection so the possibility of a huge pandemic is very low. Confirmed monkeypox cases are decreasing significantly in the European region, the decline might be attributed to public health interventions and behavioral changes in the population due to increased risk perception. Nevertheless, further strategies toward elimination are essential to avoid the subsequent evolution of the monkeypox virus that can result in new outbreaks.
Modeling IP3induced Ca2+signaling based on its interspike interval statistics
Authors: Friedhoff Victor Nicolai , Falcke Martin
Published: December 2022

Inositol 1,4,5-trisphosphate (IP3) induced Ca2+signaling is a second messenger system used by almost all eukaryotic cells. Recent research identified 8 general properties of Ca2+spiking common to all cell types investigated and demonstrated randomness of Ca2+signaling on all structural levels. We suggest a theory of Ca2+spiking starting from the random behaviour of IP3receptor channel clusters mediating the release of Ca2+from the endoplasmic reticulum. Spike generation begins after the absolute refractory period of the previous spike. According to its hierarchical spreading from initiating channel openings to cell level, we describe it as a first passage process from none to all clusters open while the cell recovers from the inhibition which terminated the previous spike. Our theory reproduces quantitatively all general properties for different IP3pathways including the exponential stimulation response relation of the average interspike interval (ISI) Tavand its robustness properties, random spike timing with a linear moment relation between Tavand the ISI standard deviation and its robustness properties, sensitive dependency of Tavon diffusion properties, and non-oscillatory local dynamics. We explain large cell variability of Tavobserved in experiments by variability of channel cluster coupling by Ca2+induced Ca2+release, the number of clusters and IP3pathway components expression levels. We predict the relation between puff probability and agonist concentration, and [IP3] and agonist concentration. Differences of spike behaviour between cell types and stimulating agonists are explained by the different types of negative feedback terminating spikes. In summary, the hierarchical random character of spike generation explains all of the identified general properties.
Status and future perspectives for pikeperch (Sander lucioperca) stocks in Europe
Authors: Jakubavičiūtė Eglė , Arula Timo , Dainys Justas , Deweber J. Tyrell , Gorfine Harry , Härkönen Laura S. , Hyvärinen Pekka , Hommik Kristiina , Kubecka Jan , Ložys Linas , Mustamäki Noora , Naddafi Rahmat , Olin Mikko , Pūtys Žilvinas , Sepp Elor , Souza Allan T. , Šiaulys Andrius , Vaino Väino , Audzijonyte Asta
Published: December 2022

Pikeperch (Sander lucioperca) is a European fresh and brackish water piscivorous fish, important as both a key predator and a valuable commercial and recreational fisheries species. There are concerns that some stocks are depleted due to overfishing and environmental changes. We review data collection and population assessments currently used for nine pikeperch stocks across six European countries and apply a unified assessment framework to evaluate population status and trends. For this we first standardised commercial, scientific, and recreational catch-per-unit-effort (CPUE) and catch time series and then applied Bayesian surplus production models. Our results showed that three stocks (including two in the Baltic Sea) were strongly depleted, with estimated biomasses considerably lower than the biomass at maximum sustainable yield (Bmsy). Other stocks were either close or higher than their estimated Bmsy. Looking at the trends, we find that four stocks (Lake Oulujärvi, Kvädöfjärden, Lake Peipsi and Lipno) showed increasing biomass trends and two (Curonian Lagoon, Galtfjärden) had a strong decline in biomass. In most cases the stocks with clear signs of recovery were also those for which strong management strategies have been implemented. We find that, despite pikeperch being one of the most valuable inland fisheries, formalised stock assessments and regular surveys remain rare. Importantly, although most stocks are strongly targeted by recreational fishing, estimates of recreational catch are highly uncertain. We conclude that data limited stock assessment methods are useful for assessing fish population status and highlight an urgent need to improve pikeperch scientific monitoring and assessment of recreational catches.
Genetic load and adaptive potential of a recovered avian species that narrowly avoided extinction
Authors: Femerling Georgette , van Oosterhout Cock , Feng Shaohong , Bristol Rachel M. , Zhang Guojie , Groombridge Jim , Gilbert M. Thomas P. , Morales Hernán E.
Published: December 2022

High genetic diversity is often a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the IUCN Red List in 2020. By comparing historical, pre-bottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after the demographic recovery. We show that the proportion of severely deleterious mutations has reduced in modern individuals, but mildly deleterious mutations have remained unchanged. Computer simulations suggest that the Seychelles paradise flycatcher avoided extinction and recovered due to its long-term small Ne. This reduced the masked load and made the species more resilient to inbreeding. However, we also show that the chronically small Neand the severe bottleneck resulted in very low genetic diversity in the modern population. Our simulations show this is likely to reduce the species’ adaptive potential when faced with environmental change, thereby compromising its long-term population viability. In light of rapid global rates of population decline, our work highlights the importance of considering genomic erosion and computer modelling in conservation assessments
Professional shariah audit training via the e-learning approach during COVID-19: challenges and prospects
Authors: Kamaruddin Muhammad Iqmal Hisham , Hanefah Mustafa Mohd
Published: December 2022

Purpose

This study aims to explore and identify potential challenges and prospects for conducting the professional shariah audit training programme via an e-learning approach during coronavirus disease 2019 (COVID-19).

Design/methodology/approach

Questionnaires were administered to 296 participants who were enrolled in the professional shariah audit training programme via e-learning during the COVID-19 pandemic outbreak in 2020. These participants were final-year students from selected Malaysian public universities.

Findings

Findings show that several main challenges are faced in adopting an e-learning approach for conducting the professional shariah audit training programme such as the inability to do more hands-on, group and physical activities, different understandings based on academic backgrounds, difficulty in learning practical and technical topics, technical issues and problems during e-learning sessions. These lead to the unsuitability of conducting professional training via the e-learning approach. In terms of prospects of knowledge learnt via the e-learning approach, participants showed that they are able to master all six modules covered in the professional shariah audit training programme via the e-learning approach. These include (1) shariah principles; (2) shariah governance; (3) Islamic financial transactions; (4) shariah risk management; (5) shariah audit planning and programme; and (6) shariah audit fieldwork and communication.

Practical implications

Based on the findings, it is suggested to have more time spent and earlier preparation on the learning contents and sessions, more discussion on actual contents and practical exercises and competency of the trainers in delivering e-learning sessions.

Originality/value

This study is believed to be one among the pioneering studies on the potential challenges and prospects in adopting e-learning for conducting the professional shariah audit training programme due to COVID-19.