Subtraction of liposome signals in cryo-EM structural determination of protein-liposome complexes

Reconstituting membrane proteins in liposomes and determining their structure is a common method for determining membrane protein structures using single-particle cryo-electron microscopy(cryo-EM).However,the strong signal of liposomes under cryo-EM imaging conditions often interferes with the structural determination of the embedded membrane proteins.Here,we propose a liposome signal subtraction method based on single-particle two-dimensional(2D)classification average images,aimed at enhancing the reconstruction resolution of membrane proteins.We analyzed the signal distribution characteristics of liposomes and proteins within the 2D classification average images of protein–liposome complexes in the frequency domain.Based on this analysis,we designed a method to subtract the liposome signals from the original particle images.After the subtraction,the accuracy of single-particle three-dimensional(3D)alignment was improved,enhancing the resolution of the final 3D reconstruction.We demonstrated this method using a PIEZO1-proteoliposome dataset by improving the resolution of the PIEZO1 protein.

Maternal Eomesodermin regulates zygotic nodal gene expression for mesendoderm induction in zebrafish embryos

Development of animal embryos before zygotic genome activation at the mid blastula transition （MBT） is essentially supported by eggderived maternal products. Nodal proteins are crucial signals for mesoderm and endoderm induction after the MBT. It remains unclear which maternal factors activate zygotic expression of nodal genes in the ventrotateral blastodermal margin of the zebrafish blastulas. In this study, we show that loss of maternal Eomesodermin a （Eomesa）, a T-box transcription factor, impairs zygotic expression of the nodal genes ndr1 and ndr2 as well as mesodermal and endodermal markers, indicating an involvement in mesendoderm induction. Maternal Eomesa is also required for timely zygotic expression of the transcription factor gene mxtx2, a regulator of nodal gene expression. Eomesa directly binds to the Eomes-binding sites in the promoter or enhancer of ndr1, ndr2, and rnxtx2 to activate their transcrip- tion. Furthermore, human and mouse Nodal genes are also regulated by Eomes. Transfection of zebrafish eomesa into murine embryonic stem cells promotes mesendodermal differentiation with constant higher levels of endogenous Nodal expression, suggesting a conserved function of Eomes. Taken together, our findings reveal a conserved rote of maternal T-box transcription factors in regulating nodal gene expression and mesendoderm induction in vertebrate embryos.

Cell mediated ECM-degradation as an emerging tool for anti-fibrotic strategy

Investigation into the role of cells with respect to extracellular matrix(ECM)remodeling is still in its infancy.Particularly,ECM degradation is an indispensable process during the recovery from fibrosis.Cells with ECM degradation ability due to the secretion of various matrix metalloproteinases(MMPs)have emerged as novel contributors to the treatment of fibrotic diseases.In this review,we focus on the ECM degradation ability of cells associated with the repertoire of MMPs that facilitate the attenuation of fibrosis through the inhibition of ECM deposition.Besides,innovative approaches to engineering and characterizing cells with degradation ability,as well as elucidating the mechanism of the ECM degradation,are also illustrated.Studies conducted to date on the use of cell-based degradation for therapeutic purposes to combat fibrosis are summarized.Finally,we discuss the therapeutic potential of cells with high degradation ability,hoping to bridge the gap between benchside research and bedside applications in treating fibrotic diseases.

Development of a 32-gene signature using machine learning for accurate prediction of inflammatory bowel disease

Inflammatory bowel disease(IBD)is a chronic inflammatory condition caused by multiple genetic and environmental factors.Numerous genes are implicated in the etiology of IBD,but the diagnosis of IBD is challenging.Here,XGBoost,a machine learning prediction model,has been used to distinguish IBD from healthy cases following elaborative feature selection.Using combined unsupervised clustering analysis and the XGBoost feature selection method,we successfully identified a 32-gene signature that can predict IBD occurrence in new cohorts with 0.8651 accuracy.The signature shows enrichment in neutrophil extracellular trap formation and cytokine signaling in the immune system.The probability threshold of the XGBoost-based classification model can be adjusted to fit personalized lifestyle and health status.Therefore,this study reveals potential IBD-related biomarkers that facilitate an effective personalized diagnosis of IBD.

Light-stabilized GIL1 suppresses PIN3 activity to inhibit hypocotyl gravitropism

Light and gravity coordinately regulate the directional growth of plants.Arabidopsis Gravitropic in the Light 1(GIL1)inhibits the negative gravitropism of hypocotyls in red and far-red light,but the underlying molecular mechanisms remain elusive.Our study found that GIL1 is a plasma membrane-localized protein.In endodermal cells of the upper part of hypocotyls,GIL1 controls the negative gravitropism of hypocotyls.GIL1 directly interacts with PIN3 and inhibits the auxin transport activity of PIN3.Mutation of PIN3 suppresses the abnormal gravitropic response of gil1 mutant.The GIL1 protein is unstable in darkness but it is stabilized by red and far-red light.Together,our data suggest that light-stabilized GIL1 inhibits the negative gravitropism of hypocotyls by suppressing the activity of the auxin transporter PIN3,thereby enhancing the emergence of young seedlings from the soil.

Mouse knockout models reveal largely dispensable but context-dependent functions of IncRNAs during development

Dear Editor, In mammalian genomes, pervasive transcription produces thousands of long non-coding RNA （IncRNA） transcripts （Olebali et al., 2012; Hon et al., 2017）. Compared to protein-coding mRNAs, IncRNAs are less conserved, and often exhibit low-level, developmental stage-and tissue-specific expression （Pauli et al., 2011; Hu et al., 2012; Lee, 2012; Ulitsky and Bartel, 2013; Cech and Steitz, 2014; Hon et al., 2017）. Many IncRNAs are strongly correlated with their neighboring mRNA genes in terms of expression and function, and tend to regulate nearby transcription （Orom et al., 2010; Engreitz et al., 2016; Luo etal., 2016）. It has been implicated that IncRNAs play versatile roles in regulating diverse aspects of cell biology through mechanisms at multiple levels （Pauli et al., 2011; Lee.

Arabidopsis DET1 Represses Photomorphogenesis in Part by Negatively Regulating DELLA Protein Abundance in Darkness

Arabidopsis De-etiolated 1 （DET1） is one of the key repressors that maintain the etiolated state of seedlings in darkness. The plant hormone gibberellic acid （GA） also participates in this process, and plants deficient in GA synthesis or signaling show a partially de.etiolated phenotype in darkness. However, how DET1 and the GA pathway work in concert in repressing photomorphogenesis remains largely unknown. In this study, we found that the abundance of DELLA proteins in detl-1 was increased in comparison with that in the wildtype plants. Mutation in DET1 changed the sensitivity of hypocotyl elongation of mutant seedlings to GA and paclobutrazol （PAC）, an inhibitor of GA synthesis. However, we did not find obvious differences between detl-1 and wild-type plants with regard to the bioactive GA content or the GA signaling upstream of DELLAs. Genetic data showed that removal of several DELLA proteins suppressed the detl-1 mutant phenotype more obviously than GA treatment, indicating that DET1 can regulate DELLA proteins via some other mechanisms. In addition, a large-scale transcriptomic analysis revealed that DET1 and DELLAs play antagonistic roles in regulating expression of photosynthetic and cell elongation-related genes in etiolated seedlings. Taken together, our results show that DET1 represses photomorphogenesis in darkness in part by reducing the abundance of DELLA proteins.

Standard:Human intestinal organoids

Organoids have attracted great interest for disease modelling,drug discovery and development,and tissue growth and homeostasis investigations.However,lack of standards for quality control has become a prominent obstacle to limit their translation into clinic and other applications.“Human intestinal organoids”is the first guideline on human intestinal organoids in China,jointly drafted and agreed by the experts from the Chinese Society for Cell Biology and its branch society:the Chinese Society for Stem Cell Research.This standard specifies terms and definitions,technical requirements,test methods,inspection rules for human intestinal organoids,which is applicable to quality control during the process of manufacturing and testing of human intestinal organoids.It was originally released by the Chinese Society for Cell Biology on 24 September 2022.We hope that the publication of this standard will guide institutional establishment,acceptance and execution of proper practical protocols and accelerate the international standardization of human intestinal organoids for applications.

CAMSAP2 and CAMSAP3 localize at microtubule intersections to regulate the spatial distribution of microtubules

Microtubule networks support many cellular processes and exhibit a highly ordered architecture.However,due to the limited axial resolution of conventional light microscopy,the structural features of these networks cannot be resolved in three-dimensional(3D)space.Here,we used customized ultra-high-resolution interferometric single-molecule localization microscopy to characterize the microtubule networks in Caco2 cells.We found that the calmodulin-regulated spectrin-associated proteins(CAMSAPs)localize at a portion of microtubule intersections.Further investigation showed that depletion of CAMSAP2 and CAMSAP3 leads to the narrowing of the inter-microtubule distance.Mechanistically,CAMSAPs recognize microtubule defects,which often occur near microtubule intersections,and then recruit katanin to remove the damaged microtubules.Therefore,the CAMSAP–katanin complex is a regulatory module for the distance between microtubules.Taken together,our results characterize the architecture of cellular microtubule networks in high resolution and provide molecular insights into how the 3D structure of microtubule networks is controlled.

Standard:Human intestinal cancer organoids

Intestinal cancer is one of the most frequent and lethal types of cancer.Modeling intestinal cancer using organoids has emerged in the last decade.Human intestinal cancer organoids are physiologically relevant in vitro models,which provides an unprecedented opportunity for fundamental and applied research in colorectal cancer.“Human intestinal cancer organoids”is the first set of guidelines on human intestinal organoids in China,jointly drafted and agreed by the experts from the Chinese Society for Cell Biology and its branch society:the Chinese Society for Stem Cell Research.This standard specifies terms and definitions,technical requirements,test methods for human intestinal cancer organoids,which apply to the production and quality control during the process of manufacturing and testing of human intestinal cancer organoids.It was released by the Chinese Society for Cell Biology on 24 September 2022.We hope that the publication of this standard will guide institutional establishment,acceptance and execution of proper practocal protocols,and accelerate the international standardization of human intestinal cancer organoids for clinical development and therapeutic applications.

R-loop:The new genome regulatory element in plants

An R-loop is a three-stranded chromatin structure that consists of a displaced single strand of DNA and an RNA:DNA hybrid duplex,which was thought to be a rare by-product of transcription.However,recent genome-wide data have shown that R-loops are widespread and pervasive in a variety of genomes,and a growing body of experimental evidence indicates that R-loops have both beneficial and harmful effects on an organism.To maximize benefit and avoid harm,organisms have evolved several means by which they tightly regulate R-loop levels.Here,we summarize our current understanding of the biogenesis and effects of R-loops,the mechanisms that regulate them,and methods of R-loop profiling,reviewing recent research advances on R-loops in plants.Furthermore,we provide perspectives on future research directions for R-loop biology in plants,which might lead to a more comprehensive understanding of R-loop functions in plant genome regulation and contribute to future agricultural improvements.

BMP signaling in cancer stemness and differentiation

The BMP(Bone morphogenetic protein)signaling pathway plays a central role in metazoan biology,intricately shaping embryonic development,maintaining tissue homeostasis,and influencing disease progression.In the context of cancer,BMP signaling exhibits context-dependent dynamics,spanning from tumor suppression to promotion.Cancer stem cells(CSCs),a modest subset of neoplastic cells with stem-like attributes,exert substantial influence by steering tumor growth,orchestrating therapy resistance,and contributing to relapse.A comprehensive grasp of the intricate interplay between CSCs and their microenvironment is pivotal for effective therapeutic strategies.Among the web of signaling pathways orchestrating cellular dynamics within CSCs,BMP signaling emerges as a vital conductor,overseeing CSC self-renewal,differentiation dynamics,and the intricate symphony within the tumor microenvironment.Moreover,BMP signaling’s influence in cancer extends beyond CSCs,intricately regulating cellular migration,invasion,and metastasis.This multifaceted role underscores the imperative of comprehending BMP signaling’s contributions to cancer,serving as the foundation for crafting precise therapies to navigate multifaceted challenges posed not only by CSCs but also by various dimensions of cancer progression.This article succinctly encapsulates the diverse roles of the BMP signaling pathway across different cancers,spanning glioblastoma multiforme(GBM),diffuse intrinsic pontine glioma(DIPG),colorectal cancer,acute myeloid leukemia(AML),lung cancer,prostate cancer,and osteosarcoma.It underscores the necessity of unraveling underlying mechanisms and molecular interactions.By delving into the intricate tapestry of BMP signaling’s engagement in cancers,researchers pave the way for meticulously tailored therapies,adroitly leveraging its dualistic aspects-whether as a suppressor or promoter-to effectively counter the relentless march of tumor progression.

Cross-species single-cell transcriptomic analysis of animal gastric antrum reveals intense porcine mucosal immunity

As an important part of the stomach,gastric antrum secretes gastrin which can regulate acid secretion and gastric emptying.Although most cell types in the gastric antrum are identified,the comparison of cell composition and gene expression in the gastric antrum among different species are not explored.In this study,we collected antrum epithelial tissues from human,pig,rat and mouse for scRNA-seq and compared cell types and gene expression among species.In pig antral epithelium,we identified a novel cell cluster,which is marked by high expression of AQP5,F3,CLCA1 and RRAD.We also discovered that the porcine antral epithelium has stronger immune function than the other species.Further analysis revealed that this may be due to the insufficient function of porcine immune cells.Together,our results replenish the information of multiple species of gastric antral epithelium at the single cell level and provide resources for understanding the homeostasis maintenance and regeneration of gastric antrum epithelium.

The cyclooxygenase-expressing mesenchyme resists intestinal epithelial injury by paracrine signaling

Paracrine signals play pivotal roles in organ homeostasis.Mesenchymal stromal cells(MSCs)play a key role in regulating epithelium homeostasis in the intestine while their paracrine effects are poorly characterized.Here,we identified prostaglandin E2(PGE2)secreted by cyclooxygenase(COX)-expressing MSCs as a vital factor to maintain the intestinal mucosal barrier.We found that MSCs-induced organoid swelling through paracrine effect in vitro,a process due to enhanced water adsorption and is mediated by the COX-PGE2-EP4 axis.To further explore the regulatory effect of this axis on the intestinal epithelial barrier in vivo,we established the conditional knockout mouse model to specifically delete COX in MSCs and found that PGE2 reduction downregulated the gene Muc2 and induced a gastric metaplasia-like phenotype.Moreover,PGE2 defects increased the susceptibility of intestinal epithelium to colitis.Our study uncovers the paracrine signaling of COX-expressing MSCs in intestinal mucosal barrier maintenance,providing a basis for understanding the role of mesenchymal cells in the pathophysiological function of the intestine.

T-cell immunity:a barrier to Omicron immune evasion

A recent study published in Cell by Naranbhai et al.disclosed that although the extent may vary,T-cell responses induced by infection by or vaccination against the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)are cross-reactive toward the Omicron variant in most individuals,highlighting the role T-cell immunity plays in preventing immune evasion by the Omicron and even future variants.

Old and new damage‐associated molecular patterns (DAMPs) in autoimmune diseases

All organisms living in complex environments have evolved effective mechanisms of dynamic responses to extracellular stimuli.The immune system activates when damaged or injured cells release damage‐associated molecular patterns(DAMPs).In addition to well‐characterized DAMPs such as high‐mobility group box 1 and adenosine triphosphate,studies on new classes of DAMPs have emerged.Here,we review recent reports of a new class of isoprenoid‐derived DAMPs,including farnesyl pyrophosphate and geranylgeranyl pyrophosphate,both of which are pivotal metabolic inter-mediates of the mevalonate pathway.We also explore the roles of old and new DAMPs in autoimmune diseases that result from dysregulated inflammation.The findings highlight that understanding the functional mechanisms of DAMPs is important to enrich the DAMP family and decipher their immunoregulatory mechanisms to provide new therapeutics for the prevention and treatment of autoimmune diseases.