bluuebunny/crossref_metadata_2025 huggingface dataset:
Lead (Pb) Inhibits-PMA Induced Microglia Multinucleation
Authors: Nicholson Stacia M. , Chen Karie , Schanne Francis A.X.
Published: April 2023

Multinucleated Microglia are formed in response to aging, inflammation, the presence of some pathogens, and are a histological feature of several CNS pathologies. Multinucleated microglia may be involved with increased clearance of CNS debris and whole cells. The present study has sought to determine the best model by which to study multinucleation in microgliain vitro, in order to investigate whether the known neurotoxicant metal lead (Pb) impacts the formation of multinucleated microglia. It was determined that isolated rat microglia (Sprague-Dawley), compared to murine (BV2) and human (HMC3) microglia cell-lines, when induced by Phorbol-myristate-acetate (PMA) results in the greatest amount of cell multinucleation and multinuclearity. In this model, it was shown that long-term exposure to Pb inhibited microglia cell proliferation, multinucleation, and multinuclearity in a dose-dependent manner. Pb appears to inhibit multinucleation in microglia by induction of multinuclear regression (karyolysis, pyknosis, or karyorrhexis) resulting in large mononuclear cells. The mechanism by which PMA induces multinucleation may involve p38/MAPK activity and Pb interferes with this activation.
Genomics to Notebook (g2nb): extending the electronic notebook to address the challenges of bioinformatics analysis
Authors: Reich Michael , Tabor Thorin , Liefeld John , Joshi Jayadev , Kim Forrest , Thorvaldsdottir Helga , Blankenberg Daniel , Mesirov Jill P.
Published: April 2023

We present Genomics to Notebook (g2nb), an environment that combines the JupyterLab notebook system with widely-used bioinformatics platforms. Galaxy, GenePattern, and the JavaScript versions of IGV and Cytoscape are currently available within g2nb. The analyses and visualizations within those platforms are presented as cells in a notebook, making thousands of genomics methods available within the notebook metaphor and allowing notebooks to contain workflows utilizing multiple software packages on remote servers, all without the need for programming. The g2nb environment is, to our knowledge, the only notebook-based system that incorporates multiple bioinformatics analysis platforms into a notebook interface.
Quantification of extracellular matrix components in immunolabeled tissue samples
Authors: Rubi-Sans Gerard , Cler Marina , Valls-Lacalle Laura , Nyga Agata , Pérez-Amodio Soledad , Mateos-Timoneda Miguel A. , Engel Elisabeth , Rebollo Elena
Published: April 2023

In recent years, the interaction between cells and the extracellular matrix (ECM) has become a new focus in understanding tissue morphogenesis, regeneration, and disease. However, the lack of specific techniques to study the ECM composition in preserved tissue structures remains a major obstacle to explaining ECM changes in response to extrinsic stimuli. To overcome this, we propose a novel strategy that uses multidimensional fluorescence microscopy and computational tools to quantify ECM composition in immunolabeled tissues and/or cell-derived matrices (CDM). This approach includes a detailed protocol for densitometric fluorescence calibration and procedures for image acquisition, processing, and automated quantification. Using this method, we present new data comparing collagen types I, III, and IV, and fibronectin contents in various tissues. These results emphasize the importance of studying ECM compositionin situunder both normal homeostatic and disease conditions.

Graphical abstract
Agent-Based Modelling shows that Operation of Fisher’s Principle does not explain Zero Heritability in Human Offspring Sex Ratio
Authors: Harper Kaitlyn T. , Sidari Morgan J. , Zietsch Brendan P.
Published: April 2023

The evolutionary basis of the ratio of male to female births has been a focus of research for over a century. Fisher’s principle suggests that offspring sex ratios remain roughly equal due to negative frequency-dependent balancing selection: individuals with alleles that produce the rarer sex have greater fitness, increasing these alleles’ frequency until the sex ratio is balanced. However, recent analysis of Swedish births since 1932 reveals that offspring sex ratio is not heritable, challenging Fisher’s principle’s application to humans. Here, we test the hypothesis that Fisher’s principle uniquely depletes offspring sex ratio heritability at equilibrium. We used agent-based modelling to simulate Fisher’s principle over 5000 generations and found that Fisher’s principle at equilibrium does not eliminate genetic variation. These findings, along with evidence of non-heritable offspring sex ratios in humans, suggest Fisher’s principle is not a suitable explanatory framework for human offspring sex ratio.
The purinergic receptor P2X7 and the NLRP3 inflammasome are druggable host factors required for SARS-CoV-2 infection
Authors: Lécuyer Déborah , Nardacci Roberta , Tannous Désirée , Gutierrez-Mateyron Emie , Deva-Nathan Aurélia , Subra Frédéric , Primio Cristina Di , Quaranta Paola , Petit Vanessa , Richetta Clémence , Mostefa-Kara Ali , Nonno Franca Del , Falasca Laura , Marlin Romain , Maisonnasse Pauline , Delahousse Julia , Pascaud Juliette , Deprez Eric , Naigeon Marie , Chaput Nathalie , Paci Angelo , Saada Véronique , Ghez David , Mariette Xavier , Costa Mario , Pistello Mauro , Allouch Awatef , Delelis Olivier , Piacentini Mauro , Le Grand Roger , Perfettini Jean-Luc
Published: April 2023

Purinergic receptors and NOD-like receptor protein 3 (NLRP3) inflammasome regulate inflammation and viral infection, but their effects on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remain poorly understood. Here, we report that the purinergic receptor P2X7 and NLRP3 inflammasome are cellular host factors required for SARS-CoV-2 infection. Lung autopsies from patients with severe coronavirus disease 2019 (COVID-19) reveal that NLRP3 expression is increased in host cellular targets of SARS-CoV-2 including alveolar macrophages, type II pneumocytes and syncytia arising from the fusion of infected macrophages, thus suggesting a potential role of NLRP3 and associated signaling pathways to both inflammation and viral replication. In vitro studies demonstrate that NLRP3-dependent inflammasome activation is detected upon macrophage abortive infection. More importantly, a weak activation of NLRP3 inflammasome is also detected during the early steps of SARS-CoV-2 infection of epithelial cells and promotes the viral replication in these cells. Interestingly, the purinergic receptor P2X7, which is known to control NLRP3 inflammasome activation, also favors the replication of D614G and alpha SARS-CoV-2 variants. Altogether, our results reveal an unexpected relationship between the purinergic receptor P2X7, the NLRP3 inflammasome and the permissiveness to SARS-CoV-2 infection that offers novel opportunities for COVID-19 treatment.
Early consequences of the phospholamban mutation PLN-R14del+/-in a transgenic mouse model
Authors: Maniezzi Claudia , Eskandr Marem , Florindi Chiara , Ferrandi Mara , Barassi Paolo , Sacco Elena , Pasquale Valentina , Maione Angela S. , Pompilio Giulio , Oliveira Nunes Teixeira Vivian , de Boer Rudolf A , Silljé Herman H W , Lodola Francesco , Zaza Antonio
Published: April 2023

Aims

The heterozygous phospholamban (PLN) mutation R14del (PLN R14del+/-) is associated with a severe arrhythmogenic cardiomyopathy (ACM) developing in the adult. “Superinhibition” of SERCA2a by PLN R14del is widely assumed to underlie the pathogenesis, but alternative mechanisms such abnormal energy metabolism have also been reported. This work aims to 1) to evaluate Ca2+dynamics and energy metabolism in a transgenic (TG) mouse model of the mutation prior to cardiomyopathy development; 2) to test whether they are causally connected.

Methods and Results

Ca2+dynamics, energy metabolism parameters, reporters of mitochondrial integrity, energy and redox homeostasis were measured in ventricular myocytes of 8-12 weeks-old, phenotypically silent, TG mice. Mutation effects were compared to pharmacological PLN antagonism and analysed during modulation of sarcoplasmic reticulum (SR) and cytosolic Ca2+compartments. Transcripts and proteins of relevant signalling pathways were evaluated. The mutation was characterized by hyperdynamic Ca2+handling, similar to that induced by PLN antagonism. Albeit all components of energy metabolism were depressed at rest, functional signs of mitochondrial damage or energy starvation were absent and cell energy charge was preserved. The response of mitochondrial O2consumption to SERCA2a blockade was lost in mutant myocytes (SR-mitochondrial uncoupling) and ER-stress signalling was activated.

Conclusions

1) PLN R14del+/-loses its ability to inhibit SERCA2a, which argues against SERCA2a superinhibition as a mechanism of ACM; 2) depression of resting energy metabolism may at least partly reflect impairment of SR-mitochondrial coupling; 3) ER-stress may be an early factor in the pathogenesis.
N-linked glycosylation of the M-protein variable region: Glycoproteogenomics reveals a new layer of personalized complexity in multiple myeloma
Authors: Langerhorst Pieter , Baerenfaenger Melissa , Kulkarni Purva , Nadal Simon , Wijnands Charissa , Post Merel A. , Noori Somayya , vanDuijn Martijn M. , Joosten Irma , Dejoie Thomas , van Gool Alain J. , Gloerich Jolein , Lefeber Dirk J. , Wessels Hans J.C.T. , Jacobs Joannes F.M.
Published: April 2023

Multiple Myeloma (MM) is a plasma cell malignancy characterized by a monoclonal expansion of plasma cells that secrete a characteristic M-protein. This M-protein is crucial for diagnosis and monitoring of MM in the blood of patients. Recent evidence has emerged suggesting that N-glycosylation of the M-protein variable (Fab) region contributes to M-protein pathogenicity, and that it is a risk factor for disease progression of plasma cell disorders. Current methodologies lack the specificity to provide a site-specific glycoprofile of the Fab regions of M-proteins. Here, we introduce a novel glycoproteogenomics method that allows detailed M-protein glycoprofiling by integrating patient specific Fab region sequences (genomics) with glycoprofiling by glycoproteomics. Genomic analysis uncovered a more than two-fold increase in the Fab Light Chain N-glycosylation of M-proteins of patients with Multiple Myeloma compared to Fab Light Chain N-glycosylation of polyclonal antibodies from healthy individuals. Subsequent glycoproteogenomics analysis of 41 patients enrolled in the IFM 2009 clinical trial revealed that the majority of the Fab N-glycosylation sites were fully occupied with complex type glycans, distinguishable from Fc region glycans due to high levels of sialylation, fucosylation and bisecting structures. Together, glycoproteogenomics is a powerful tool to studyde novoFab N-glycosylation in plasma cell dyscrasias.
The super-enhancer landscape reflects molecular subgroups of adrenocortical carcinoma
Authors: Gunz Samuel , Kerdivel Gwenneg , Meirer Jonas , Shapiro Igor , Ragazzon Bruno , Amrouche Floriane , Calmejane Marie-Ange , Hamroune Juliette , Sigala Sandra , Berruti Alfredo , Bertherat Jérôme , Assié Guillaume , Hantel Constanze , Boeva Valentina
Published: April 2023

Adrenocortical carcinoma (ACC) is a rare cancer of the adrenal gland with generally very unfavourable outcome. Two molecular subgroups, C1A and C1B, have been previously identified with a significant association with patient survival. In this work, we study chromatin state organization characterized by histone modifications using ChIP-sequencing in adult ACC. We describe the super-enhancer landscape of ACC, characterized by H3K27ac, and identify super-enhancer regulated genes that play a significant role in tumorigenesis. We show that the super-enhancer landscape reflects differences between the molecular sub-groups C1A and C1B and identify networks of master transcription factors mirroring these differences. Additionally, we study the effects of molecules THZ1 and JQ1 previously reported to affect super-enhancer-driven gene expression in ACC cell lines. Our results reveal that the landscape of histone modifications in ACC is linked to its molecular subgroups and thus provide the groundwork for future analysis of epigenetic reprogramming in ACC.
A supervised data-driven spatial filter denoising method for speech artifacts in intracranial electrophysiological recordings
Authors: Peterson Victoria , Vissani Matteo , Luo Shiyu , Rabbani Qinwan , Crone Nathan E. , Bush Alan , Richardson R. Mark
Published: April 2023

Neurosurgical procedures that enable direct brain recordings in awake patients offer unique opportunities to explore the neurophysiology of human speech. The scarcity of these opportunities and the altruism of participating patients compel us to apply the highest rigor to signal analysis. Intracranial electroencephalography (iEEG) signals recorded during overt speech can contain a speech artifact that tracks the fundamental frequency (F0) of the participant’s voice, involving the same high-gamma frequencies that are modulated during speech production and perception. To address this artifact, we developed a spatial-filtering approach to identify and remove acoustic-induced contaminations of the recorded signal. We found that traditional reference schemes jeopardized signal quality, whereas our data-driven method denoised the recordings while preserving underlying neural activity.
Neutral Drift and Threshold Selection Promote Phenotypic Variation
Authors: Erdoğan Ayşe N. , Dasmeh Pouria , Socha Raymond D. , Chen John Z. , Life Ben , Jun Rachel , Kiritchkov Linda , Kehila Dan , Serohijos Adrian W.R. , Tokuriki Nobuhiko
Published: April 2023

Phenotypic variations within a population exist on different scales of biological organization and play a central role in evolution by providing adaptive capacity at the population-level. Thus, the question of how evolution generates phenotypic variation within an evolving population is fundamental in evolutionary biology. Here we address this question by performing experimental evolution of an antibiotic resistance gene, VIM-2 β-lactamase, combined with diverse biochemical assays and population genetics. We found that neutral drift,i.e., evolution under a static environment, with a low antibiotic concentration can promote and maintain significant phenotypic variation within the population with >100-fold differences in resistance strength. We developed a model based on the phenotype-environment-fitness landscape generated with >5,000 VIM-2 variants, and demonstrated that the combination of “mutation-selection balance” and “threshold-like fitness-phenotype relationship” is sufficient to explain the generation of large phenotypic variation within the evolving population. Importantly, high-resistance conferring variants can emerge during neutral drift, without being a product of adaptation. Our findings provide a novel and simple mechanistic explanation for why most genes in nature, and by extension, systems and organisms, inherently exhibit phenotypic variation, and thus, population-level evolvability.
A cell atlas of the developing human outflow tract of the heart and its adult derivatives
Authors: Leshem Rotem , Baker Syed Murtuza , Mallen Joshua , Wang Lu , Dark John , Sharrocks Andrew D , Hanley Karen Piper , Hanley Neil A , Rattray Magnus , Bamforth Simon D , Bobola Nicoletta
Published: April 2023

The outflow tract (OFT) of the heart carries blood away from the heart into the great arteries. During embryogenesis, the OFT divides to form the aorta and pulmonary trunk, creating the double circulation present in mammals. Defects in this area account for one-third of all congenital heart disease cases. Here, we present comprehensive transcriptomic data on the developing OFT at two distinct timepoints (embryonic and fetal) and its adult derivatives, the aortic valves, and use spatial transcriptomics to define the distribution of cell populations. We uncover that distinctive embryonic signatures persist in adult cells and can be used as labels to retrospectively attribute relationships between cells separated by a large time scale. Our findings define the cellular and molecular signatures of the OFT and its distinct cell lineages, which is critical for understanding congenital heart defects and developing cardiac tissue for regenerative medicine.
Evaluating drought tolerance stability in soybean by the response of irrigation change captured from time-series multispectral data
Authors: Sakurai Kengo , Toda Yusuke , Hamazaki Kosuke , Ohmori Yoshihiro , Yamasaki Yuji , Takahashi Hirokazu , Takanashi Hideki , Tsuda Mai , Tsujimoto Hisashi , Kaga Akito , Nakazono Mikio , Fujiwara Toru , Iwata Hiroyoshi
Published: April 2023

This study investigated a method to evaluate the drought tolerance stability of a genotype in a single environmental trial by capturing the plant response to irrigation changes. Genotypes that exhibit stable phenotypes under various drought stress conditions are required for stable crop production. However, considerable time and money are required to evaluate the environmental stability of a genotype through multiple environmental trials. As an index of drought tolerance stability, we calculated the coefficient of variation (CV) of shoot fresh weight of 178 soybean (Glycine max(L.) Merr.) accessions in a total of nine types of drought treatments, including changing irrigation treatments (every five or ten days) over 3-year trials. To capture the plant responses to irrigation changes, time-series multispectral (MS) data were collected, including the timings of the irrigation/non-irrigation switch in the changing irrigation treatments. We built a random regression model (RRM) for each of the nine treatments using the time-series MS data. We built a genomic prediction model (MTRRMmodel) using the genetic random regression coefficients of RRM as secondary traits and evaluated the accuracy of each model for predicting CV. In two out of the three years, the prediction accuracy of MTRRMmodels built in the changing irrigation treatment was higher than that in the continuous drought treatment in the same year. When the CV was predicted using the MTRRMmodel across years in the changing irrigation treatment, the prediction accuracy was 61% higher than that of the simple genomic prediction model. These results suggest that drought tolerance stability can be evaluated in a single environmental trial, which may reduce the time and cost of selecting genotypes with high drought tolerance stability.
Cnidarian pharyngeal nervous system illustrates prebilaterian neurosecretory regulation of feeding
Authors: Nakamura Ryo , Nakamura Ryotaro , Watanabe Hiroshi
Published: April 2023

Neurosecretory brain centers exist as part of the central nervous system of many bilaterian animals and play pivotal roles in the control of feeding and metabolism. In the animal evolution, the nutrition regulation appears to have been essential for the early heterotrophic metazoan ancestor, but the underlying evolutionary processes remain unclear. We found that the cnidarianNematostella vectensisdevelops an oral/pharyngeal nervous system that shares a core signature with bilaterian neurosecretory brain centers comprisingOrthopediaand neuropeptide RFamide-positive neurons, and that is essential for feeding regulation. Our data suggest that prior to the bilaterian evolution, theOrthopedia/RFamide-positive neural assembly was already functioning as a prototype of the neurosecretory brain center for the feeding regulation that could be the driving force of neural centralization.
GEGVIC: A workflow to analyze Gene Expression, Genetic Variations and Immune cell Composition of tumor samples using Next Generation Sequencing data
Authors: Arqués Oriol , Bassaganyas Laia
Published: April 2023

Background

The application of next-generation sequencing techniques for genome and transcriptome profiling is to build the main source of data for cancer research. Hundreds of bioinformatic pipelines have been developed to handle the data generated by these technologies, but their use often requires specialized expertise in data wrangling and analysis that limit many biomedical researchers. Providing easy-to-use, yet comprehensive and integrative open-source tools is essential to help wet-lab and clinical scientists feel more autonomous in performing common omics data analysis in cancer research.

Results

Here, we present GEGVIC, an R tool to easily perform a set of frequently used analyses in cancer research, including differential gene expression, genomic mutations exploration and immune cell deconvolution using minimally processed human/mouse genomic and transcriptomic sequencing data. GEGVIC is designed as a modular pipeline that combines a variety of widely used available methods distributed in three principal modules (Gene Expression,Genomic VariationandImmune Composition), which run independently and include several visualization tools. This open-source software is also presented as a graphical user interface (GUI) using the Shiny framework (GEGVICShine) to eliminate the coding barrier for non-R users and enable comprehensive analyses of tumor samples via one-click features.

Conclusions

In summary, GEGVIC provides a simple, powerful and highly flexible workflow for researchers to process and interpret tumor transcriptomic and genomic data while decreasing or eliminating coding burden and facilitating efficiency for inexperienced bioinformatics users. GEGVIC R package instructions and source code are published on Github (https://github.com/oriolarques/GEGVIC), whereas GEGVICShine is hosted athttps://gegvic.vhio.net/.
Increased response to immune checkpoint inhibitors with dietary methionine restriction
Authors: Morehead Lauren C. , Garg Sarita , Wallis Katherine F. , Siegel Eric R. , Tackett Alan J. , Miousse Isabelle R.
Published: April 2023

Dietary methionine restriction, defined as reduction of methionine intake by around 80%, reproducibly decreases tumor growth and synergizes with cancer therapies. Here, we combined dietary methionine restriction with immune checkpoint inhibitors in a model of colon adenocarcinoma.In vitro, we observed that methionine restriction increased the expression of MHC-I and PD-L1 in both mouse and human colorectal cancer cells. We also saw an increase in the gene expression of STING, a known inducer of type I interferon signaling. Inhibition of the cGAS-STING pathway, pharmacologically or with siRNA, blunted the increase in MHC-I and PD-L1 surface and gene expression following methionine restriction. PD-L1 expression was also This indicated that the cGAS-STING pathway in particular, and interferon in general, is playing a role in the immune response to methionine restriction. We then combined dietary methionine restriction with immune checkpoint inhibitors targeted against CTLA-4 and PD-1 in a MC38 colorectal cancer tumor model in C57BL/6 mice. The combination treatment was five times more effective at reducing tumor size than immune checkpoint inhibition alone in males. We noted sex differences in the response to dietary methionine restriction for the MC38 tumor model in C57BL/6 mice. Finally, we observed an increase in PD-L1 protein expression in MC38 tumors from animals who were fed a methionine-restricted diet. Furthermore, the distribution of CD8 staining changed from mostly peripheric in the controls, to intratumoral in the methionine-restricted tumors. MHC-I, which has a high basal expression in MC38 cells, was highly expressed in all tumors. These results indicate that methionine restriction improves the response to immune checkpoint inhibitors in mice, and that this improvement is associated with the cGAS-STING pathway and interferon signaling.
Free energy landscapes of KcsA inactivation
Authors: Pérez-Conesa Sergio , Delemotte Lucie
Published: April 2023

The bacterial ion channel KcsA has become a useful model of complex K+-ion channels thanks to its single pore domain structure whose sequence shares many similarities with eukaryotic channels. Like many physiologically-relevant ion channels, KcsA inactivates after prolonged exposure to stimuli (in this case, a lowered pH). The inactivation mechanism has been heavily investigated, using structural, functional and simulations methods, but the molecular basis underlying the energetics of the process remains actively debated. In this work, we use the “string method with swarms of trajectories” enhanced sampling technique to characterize the free energy landscape lining the KcsA inactivation process. After channel opening following a pH drop, KcsA presents metastable open states leading to an inactivated state. The final inactivation step consists of a constriction of the selectivty filter and entry of three water molecules into binding sites behind each selectivity filter subunit. Based our simulations, we propose a key role for residue L81 in opening a gateway for water molecules to enter their buried sites, rather than for Y82 which has previously been suggested to act as a lid. In addition, since we found the energetically favored inactivation mechanism to be dependent on the force field, our results also address the importance of parameter choice for this type of mechanism. In particular, inactivation involves passing through the fully-open state only when using the AMBER force field. In contrast, using CHARMM, selectivity filter constriction proceeds directly from the partially open state. Finally, our simulations suggest that removing the co-purifying lipids stabilizes the partially open states, rationalizing their importance for the proper inactivation of the channel.
Ser14-RPN6 Phosphorylation Mediates the Activation of 26S Proteasomes by cAMP and Protects against Cardiac Proteotoxic Stress in Mice
Authors: Yang Liuqing , Parajuli Nirmal , Wu Penglong , Liu Jinbao , Wang Xuejun
Published: April 2023

Background

A better understanding of the regulation of proteasome activities can facilitate the search for new therapeutic strategies. A cell culture study shows that cAMP-dependent protein kinase (PKA) activates the 26S proteasome by phosphorylating Ser14 of RPN6 (pS14-RPN6), but this discovery and its physiological significance remain to be establishedin vivo.

Methods

Male and female mice with Ser14 of Rpn6 mutated to Ala (S14A) or Asp (S14D) to respectively block or mimic pS14-Rpn6 were created and used along with cells derived from them. cAMP/PKA were manipulated pharmacologically. Ubiquitin-proteasome system (UPS) functioning was evaluated with the GFPdgn reporter mouse and proteasomal activity assays. Impact of S14A and S14D on proteotoxicity was tested in mice and cardiomyocytes overexpressing the misfolded protein R120G-CryAB (R120G).

Results

PKA activation increased pS14-Rpn6 and 26S proteasome activities in wild-type (WT) but not S14A embryonic fibroblasts (MEFs), adult cardiomyocytes (AMCMs), and mouse hearts. Basal 26S proteasome activities were significantly greater in S14D myocardium and AMCMs than in WT counterparts. S14D::GFPdgn mice displayed significantly lower myocardial GFPdgn protein but not mRNA levels than GFPdgn mice. In R120G mice, a classic model of cardiac proteotoxicity, basal myocardial pS14-Rpn6 was significantly lower compared with non- transgenic littermates, which was not always associated with reduction of other phosphorylated PKA substrates. Cultured S14D neonatal cardiomyocytes displayed significantly faster proteasomal degradation of R120G than WT neonatal cardiomyocytes. Compared with R120G mice, S14D/S14D::R120G mice showed significantly greater myocardial proteasome activities, lower levels of total and K48-linked ubiquitin conjugates and of aberrant CryAB protein aggregates, less reactivation of fetal genes and cardiac hypertrophy, and delays in cardiac malfunction.

Conclusions

This study establishes in animals that pS14-Rpn6 mediates the activation of 26S proteasomes by PKA and that the reduced pS14-Rpn6 is a key pathogenic factor in cardiac proteinopathy, thereby identifies a new therapeutic target to reduce cardiac proteotoxicity.
Membrane curvature sensing by model biomolecular condensates
Authors: Anila Midhun Mohan , Ghosh Rikhia , Różycki Bartosz
Published: April 2023

Biomolecular condensates (BCs) are fluid droplets that form in biological cells by liquid-liquid phase separation. Their major components are intrinsically disordered proteins. Vast attention has been given in recent years to BCs inside the cytosol and nucleus. BCs at the cell membrane have not been studied to the same extent so far. However, recent studies provide increasingly more examples of interfaces between BCs and membranes which function as platforms for diverse biomolecular processes. Galectin-3, for example, is known to mediate clathrin-independent endocytosis and has been recently shown to undergo liquid-liquid phase separation, but the function of BCs of galectin-3 in endocytic pit formation is unknown. Here, we use dissipative particle dynamics simulations to study a generic coarse-grained model for BCs interacting with lipid membranes. In analogy to galectin-3, we consider polymers comprising two segments – one of them mediates multivalent attractive interactions between the polymers, and the other one has affinity for association with specific lipid head groups. When these polymers are brought into contact with a multi-component membrane, they spontaneously assemble into droplets and, simultaneously, induce lateral separation of lipids within the membrane. Interestingly, we find that if the membrane is bent, the polymer droplets localize at membrane regions curved inward. Although the polymers have no particular shape or intrinsic curvature, they appear to sense membrane curvature when clustered at the membrane. Our results indicate toward a generic mechanism of membrane curvature sensing by BCs involved in such processes as endocytosis.
Building pangenome graphs
Authors: Garrison Erik , Guarracino Andrea , Heumos Simon , Villani Flavia , Bao Zhigui , Tattini Lorenzo , Hagmann Jörg , Vorbrugg Sebastian , Marco-Sola Santiago , Kubica Christian , Ashbrook David G. , Thorell Kaisa , Rusholme-Pilcher Rachel L. , Liti Gianni , Rudbeck Emilio , Golicz Agnieszka A. , Nahnsen Sven , Yang Zuyu , Mwaniki Moses Njagi , Nobrega Franklin L. , Wu Yi , Chen Hao , de Ligt Joep , Sudmant Peter H. , Huang Sanwen , Weigel Detlef , Soranzo Nicole , Colonna Vincenza , Williams Robert W. , Prins Pjotr
Published: April 2023

Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder (PGGB), a pipeline for constructing pangenome graphs without bias or exclusion. PGGB uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.
Cyclic-polymer grafted colloids in spherical confinement: insights for interphase chromosome organization
Authors: Paturej Jarosław , Erbaş Aykut
Published: April 2023

Interphase chromosome structures are known to remain segregated in the micron-sized eukaryotic cell nucleus and occupy a certain fraction of nuclear volume, often without mixing. Using extensive coarse-grained simulations, we model such chromosome structures as colloidal particles whose surfaces are grafted by cyclic polymers. This model system is known as Rosetta. The cyclic polymers, with varying polymerization degrees, mimic the functionality of structural protein complexes, while the rigid core models the chromocenter sections of chromosomes. Our simulations show that the colloidal chromosome model provides a well-segregated particle distribution without specific attraction between the chain monomers. Notably, linear-polymer grafted particles also provide the same segregation scheme. However, unlike linear chains, cyclic chains result in less contact between the polymer layers of neighboring chromosome particles, demonstrating the effect of DNA breaks in altering genome-wide contacts. As the polymerization degree of the chains decreases while maintaining the total chromosomal length (the total polymer length per particle), particles form quasi-crystalline order, reminiscent of a glassy state. This order weakens for polymer chains with a characteristic size on the order of the confinement radius. Our simulations demonstrate that polymer systems can help decipher 3D chromosomal architectures along with fractal globular and loop-extrusion models.
Uncovering and engineering the mechanical properties of the adhesion GPCR ADGRG1 GAIN domain
Authors: Dumas L. , Marfoglia M. , Yang B. , Hijazi M. , Larabi A.N. , Lau K. , Pojer F. , Nash M.A. , Barth P.
Published: April 2023

Key cellular functions depend on the transduction of extracellular mechanical signals by specialized membrane receptors including adhesion G-protein coupled receptors (aGPCRs). While recently solved structures support aGPCR activation through shedding of the extracellular GAIN domain, the molecular mechanisms underpinning receptor mechanosensing remain poorly understood. When probed using single-molecule atomic force spectroscopy and molecular simulations, ADGRG1 GAIN dissociated from its tethered agonist at forces significantly higher than other reported signaling mechanoreceptors. Strong mechanical resistance was achieved through specific structural deformations and force propagation pathways under mechanical load. ADGRG1 GAIN variants computationally designed to lock the alpha and beta subdomains and rewire mechanically-induced structural deformations were found to modulate the GPS-Stachel rupture forces. Our study provides unprecedented insights into the molecular underpinnings of GAIN mechanical stability and paves the way for engineering mechanosensors, better understanding aGPCR function, and informing drug-discovery efforts targeting this important receptor class.
A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup
Authors: Qiu Chengxiang , Martin Beth K. , Welsh Ian C. , Daza Riza M. , Le Truc-Mai , Huang Xingfan , Nichols Eva K. , Taylor Megan L. , Fulton Olivia , O’Day Diana R. , Gomes Anne Roshella , Ilcisin Saskia , Srivatsan Sanjay , Deng Xinxian , Disteche Christine M. , Noble William Stafford , Hamazaki Nobuhiko , Moens Cecilia B. , Kimelman David , Cao Junyue , Schier Alexander F. , Spielmann Malte , Murray Stephen A. , Trapnell Cole , Shendure Jay
Published: April 2023

The house mouse,Mus musculus, is an exceptional model system, combining genetic tractability with close homology to human biology. Gestation in mouse development lasts just under three weeks, a period during which its genome orchestrates the astonishing transformation of a single cell zygote into a free-living pup composed of >500 million cells. Towards a global framework for exploring mammalian development, we applied single cell combinatorial indexing (sci-*) to profile the transcriptional states of 12.4 million nuclei from 83 precisely staged embryos spanning late gastrulation (embryonic day 8 or E8) to birth (postnatal day 0 or P0), with 2-hr temporal resolution during somitogenesis, 6-hr resolution through to birth, and 20-min resolution during the immediate postpartum period. From these data (E8 to P0), we annotate dozens of trajectories and hundreds of cell types and perform deeper analyses of the unfolding of the posterior embryo during somitogenesis as well as the ontogenesis of the kidney, mesenchyme, retina, and early neurons. Finally, we leverage the depth and temporal resolution of these whole embryo snapshots, together with other published data, to construct and curate a rooted tree of cell type relationships that spans mouse development from zygote to pup. Throughout this tree, we systematically nominate sets of transcription factors (TFs) and other genes as candidate drivers of thein vivodifferentiation of hundreds of mammalian cell types. Remarkably, the most dramatic shifts in transcriptional state are observed in a restricted set of cell types in the hours immediately following birth, and presumably underlie the massive changes in physiology that must accompany the successful transition of a placental mammal to extrauterine life.
Truncated CD19 as a selection marker for the isolation of stem cell derived β-cells
Authors: Huang Luo Ting (Helen) , Zhang Dahai , Nian Cuilan , Francis C. Lynn
Published: April 2023

Stem cell-derived β-cells (SCβ-cell) are a renewable and scalable alternative to cadaveric islets as a cell replacement therapy for type 1 diabetes (T1D). However, heterogeneity within SCβ-cell cultures remains problematic for graft safety and function. Magnetic selection of SCβ-cells expressing a unique cell surface marker may help deplete undesirable cell types and facilitate functional maturation. Here, we explored CD19 as a potential cell surface marker for the enrichment of insulin-expressing SCβ-cells. Using CRISPR/Cas9 technology, we created a knock-in add-on of CD19-mScarlet downstream of the insulin coding sequence in human embryonic stem cells (hESCs). We established reproducible SCβ-cell surface expression of CD19-mScarlet. Importantly, we developed and optimized a magnetic sorting protocol for CD19-mScarlet-expressing cells, forming enriched SCβ-cell clusters with improved glucose-stimulated c-peptide secretion. This strategy holds promise to facilitate large-scale production of functional SCβ-cells for disease modeling and cell replacement therapy.
Functional connectivity in northern swamp deer (Rucervus duvaucelii duvaucelii) population across a fragmented, human-dominated landscape along Gangetic Plains of north India: Implications for conservation in non-protected areas
Authors: Paul Shrutarshi , Saha Sohini , Nigam Parag , Pandey Garima , Habib Bilal , Mohan Dhananjai , Pandav Bivash , Mondol Samrat
Published: April 2023

The Indian subcontinent has witnessed disproportionate declines in large mammalian herbivore communities. The northern swamp deer (Rucervus duvaucelii duvaucelii) exemplifies the conservation challenges of typical non-protected area species, where apart from distribution status other ecological information is limited for the upper Gangetic basin population. We combined elements of radio-telemetry and conservation genetics to evaluate dispersal patterns, population connectivity and assess genetic variation and inbreeding status of this population living across a highly human-dominated area. We genetically identified 266 unique swamp deer and further analyses revealed presence of two spatially-admixed genetic lineages with moderate heterozygosity (Ho=0.51, SD= 0.10) and low inbreeding (FIS=0.133) status. Multi- disciplinary evidence suggests that the small, isolated grassland patches between Jhilmil Jheel Conservation Reserve (JJCR) and Hastinapur Wildlife Sanctuary (HWLS) are highly preferred by swamp deer during migrations and are genetically connected. The southern part of the area in HWLS showed early signatures of genetic discontinuity that require immediate conservation attention. We hypothesized that the human settlement history of this landscape, river dynamics and species’ ability to negotiate various pressures and disperse has helped to maintain such connectivity. While these signatures are encouraging for this small, isolated cervid population, careful management interventions are required to ensure the integrity and functionality of this landscape. We recommend a scientifically robust population estimation approach across this landscape and a multi-stakeholder-driven strategies to augment population and habitat recovery, plantation and riverscape management to ensure long-term survival of this species.
Suppression of ferroptosis by vitamin A or antioxidants is essential for neuronal development
Authors: Tschuck Juliane , Nair Vidya Padmanabhan , Galhoz Ana , Ciceri Gabriele , Rothenaigner Ina , Tchieu Jason , Tai Hin-Man , Stockwell Brent R. , Studer Lorenz , Menden Michael P. , Vincendeau Michelle , Hadian Kamyar
Published: April 2023

Development of functional neurons is a complex orchestration of several signaling pathways controlling cell proliferation, differentiation, and homeostasis1. However, details about the involved factors are not fully understood. The balance of antioxidants and vitamins is important for neuronal survival, synaptic plasticity, and early neuronal development; thus, we hypothesized that ferroptosis—a lipid peroxidation dependent cell death modality that is inhibited by antioxidanats2,3—needs to be suppressed to gain neurons. Our study shows that removal of antioxidants diminishes neuronal development and laminar organization of cortical organoids. Intriguingly, impaired neuronal development in conditions lacking antioxidants can be fully restored when ferroptosis is specifically inhibited by ferrostatin-1, or neuronal differentiation occurs in the presence of sufficient amounts of vitamin A. Mechanistically, vitamin A activates the heterodimeric nuclear receptor complex Retinoic Acid Receptor (RAR)/Retinoid X Receptor (RXR)4, which upregulates expression of the ferroptosis regulators GPX4, FSP1, GCH1, and ACSL3, amongst others. Therefore, our study reveals that above a certain threshold, vitamin A increases expression of essential cellular gatekeepers of lipid peroxidation. This study uncovers a critical process during early neuronal development, where suppression of ferroptosis by radical-trapping antioxidants or vitamin A is required to obtain maturing neurons and proper laminar organization in cortical organoids.
Correlated signatures of social behavior in cerebellum and anterior cingulate cortex
Authors: Hur Sung Won , Safaryan Karen , Yang Long , Blair Hugh T , Masmanidis Sotiris C , Mathews Paul J , Aharoni Daniel , Golshani Peyman
Published: April 2023

The cerebellum has been implicated in the regulation of social behavior. Its influence is thought to arise from communication, via the thalamus, to forebrain regions integral in the expression of social interactions, including the anterior cingulate cortex (ACC). However, the signals encoded or the nature of the communication between the cerebellum and these brain regions is poorly understood. Here, we describe an approach that overcomes technical challenges in exploring the coordination of distant brain regions at high temporal and spatial resolution during social behavior. We developed the E-Scope, an electrophysiology-integrated miniature microscope, to synchronously measure extracellular electrical activity in the cerebellum along with calcium imaging of the ACC. This single coaxial cable device combined these data streams to provide a powerful tool to monitor the activity of distant brain regions in freely behaving animals. During social behavior, we recorded the spike timing of multiple single units in cerebellar right Crus I (RCrus I) Purkinje cells (PCs) or dentate nucleus (DN) neurons while synchronously imaging calcium transients in contralateral ACC neurons. We found that during social interactions a significant subpopulation of cerebellar PCs were robustly inhibited, while most modulated neurons in the DN were activated, and their activity was correlated with positively modulated ACC neurons. These distinctions largely disappeared when only non-social epochs were analyzed suggesting that cerebellar-cortical interactions were behaviorally specific. Our work provides new insights into the complexity of cerebellar activation and co-modulation of the ACC during social behavior and a valuable open-source tool for simultaneous, multimodal recordings in freely behaving mice.
Ziqi Dihuang decoction ameliorates thrombosis in septic rats by inhitbiting plasminogen activator inhibitor-1
Authors: Geng YanXia , Fei ShuYe , Pei YingHao , Chen QiuHua , Wang Jian , Jiang Hua
Published: April 2023

Background and Aim

Sepsis is now a global medical burden with high morbility and mortality. The focus of this study was to observe and elaborate the effect of Ziqi Dihuang (ZQDH) decoction on inflammatory and thrombosis-related parameters in septic rats.

Experimental procedure

A rat model of sepsis was established by cecal ligation and puncture (CLP). 24 male Sprague-Dawley (SD) rats were randomly divided into Sham group, CLP group, ZQDH-1ow group (0.735g/kg) and ZQDH-high group (1.47g/kg). Rats in ZQDH groups were given ZQDH decoction by gavage for 7 days before CLP, while rats in Sham and CLP groups were given the same amount of normal saline. Leukocytes and percentage of neutrophils (N %) in blood, and inflammatory cell infiltration of liver, kidney and lung were used to assess systemic inflammatory response. Coagulation and fibrinolytic indexes included platelet count, coagulation function, fibrin deposition, and levels of tissue plasminogen activator (tPA) and plasminogen activator inhibitor-1 (PAI-1) in serum, liver, kidney and lung.

Results

ZQDH decoctioninhibited N% growth in blood and inflammatory cell infiltration in the lung of CLP rats. Moreover, ZQDH decoctionalso ameliorated thrombocytopenia and prothrombin time, alleviated renal fibrin deposition, and improved tPA and PAI-1 levels in kidney.

Conclusion

These results suggest that ZQDH decoction can dose-dependently relieve systemic inflammatory injury and regulate coagulation-fibrinolysis system in septic rats, which may be mediated by PAI-1.

Highlights of the findings and novelties

ZQDH decoction relieves systemic inflammatory injury in sepsis;

ZQDH decoction regulates coagulation-fibrinolysis system in sepsis;

ZQDH decoction inhibits fibrinolysis by reducing inhibitor-1 (PAI-1) level in sepsis.
Metagenome mining and functional analysis reveal oxidized guanine DNA repair at the Lost City Hydrothermal Field
Authors: Utzman Payton H. , Mays Vincent P. , Miller Briggs C. , Fairbanks Mary C. , Brazelton William J. , Horvath Martin P.
Published: April 2023

The GO DNA repair system protects against GC → TA mutations by finding and removing oxidized guanine. The system is mechanistically well understood but its origins are unknown. We searched metagenomes and abundantly found the genes encoding GO DNA repair at the Lost City Hydrothermal Field (LCHF). We recombinantly expressed the final enzyme in the system to show MutY homologs function to suppress mutations. Microbes at the LCHF thrive without sunlight, fueled by the products of geochemical transformations of seafloor rocks, under conditions believed to resemble a young Earth. High levels of the reductant H2and low levels of O2in this environment raise the question, why are resident microbes equipped to repair damage caused by oxidative stress? MutY genes could be assigned to metagenome assembled genomes (MAGs), and thereby associate GO DNA repair with metabolic pathways that generate reactive oxygen, nitrogen and sulfur species. Our results indicate that cell-based life was under evolutionary pressure to cope with oxidized guanine well before O2levels rose following the great oxidation event.
Control of working memory maintenance by theta-gamma phase amplitude coupling of human hippocampal neurons
Authors: Daume Jonathan , Kaminski Jan , Schjetnan Andrea G. P. , Salimpour Yousef , Khan Umais , Reed Chrystal , Anderson William , Valiante Taufik A. , Mamelak Adam N. , Rutishauser Ueli
Published: April 2023

Retaining information in working memory (WM) is a demanding process that relies on cognitive control to protect memoranda-specific persistent activity from interference. How cognitive control regulates WM storage, however, remains unknown. We hypothesized that interactions of frontal control and hippocampal persistent activity are coordinated by theta-gamma phase amplitude coupling (TG-PAC). We recorded single neurons in the human medial temporal and frontal lobe while patients maintained multiple items in WM. In the hippocampus, TG-PAC was indicative of WM load and quality. We identified cells that selectively spiked during nonlinear interactions of theta phase and gamma amplitude. These PAC neurons were more strongly coordinated with frontal theta activity when cognitive control demand was high, and they introduced information-enhancing and behaviorally relevant noise correlations with persistently active neurons in the hippocampus. We show that TG-PAC integrates cognitive control and WM storage to improve the fidelity of WM representations and facilitate behavior.