bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cnidarian pharyngeal nervous system illustrates prebilaterian neurosecretory regulation of feeding
Authors: Nakamura Ryo , Nakamura Ryotaro , Watanabe Hiroshi 
Published: April 2023

AbstractNeurosecretory 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

AbstractBackgroundThe 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.ResultsHere, 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.ConclusionsIn 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

ABSTRACTDietary 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

AbstractThe 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

ABSTRACTBackgroundA 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.MethodsMale 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).ResultsPKA 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.ConclusionsThis 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

AbstractBiomolecular 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

AbstractPangenome 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

AbstractInterphase 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

AbstractKey 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

AbstractThe 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

SummaryStem 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

AbstractThe 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

SummaryDevelopment 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.