Single-cell and spatial omics:exploring hypothalamic heterogeneity

Elucidating the complex dynamic cellular organization in the hypothalamus is critical for understanding its role in coordinating fundamental body functions. Over the past decade, single-cell and spatial omics technologies have significantly evolved, overcoming initial technical challenges in capturing and analyzing individual cells. These high-throughput omics technologies now offer a remarkable opportunity to comprehend the complex spatiotemporal patterns of transcriptional diversity and cell-type characteristics across the entire hypothalamus. Current single-cell and single-nucleus RNA sequencing methods comprehensively quantify gene expression by exploring distinct phenotypes across various subregions of the hypothalamus. However, single-cell/single-nucleus RNA sequencing requires isolating the cell/nuclei from the tissue, potentially resulting in the loss of spatial information concerning neuronal networks. Spatial transcriptomics methods, by bypassing the cell dissociation, can elucidate the intricate spatial organization of neural networks through their imaging and sequencing technologies. In this review, we highlight the applicative value of single-cell and spatial transcriptomics in exploring the complex molecular-genetic diversity of hypothalamic cell types, driven by recent high-throughput achievements.

Single-cell transcriptomic profiling reveals ZEB1-mediated regulation in microglial subtypes and the impact of exercise on neuroinflammatory responses

Background:This study aims to identify distinct cellular subtypes within brain tissue using single-cell transcriptomic analysis,focusing on specific biomarkers that differentiate cell types and the effects of traditional and exercise therapy.Methods:Four samples were analyzed:older control(OC),older exercise(OE),younger control(YC),and younger exercise(YE).Single-cell RNA sequencing was used to distinguish cellular subtypes through their biomarker profiles.Data visualization included violin and t-SNE plots to illustrate biomarker expression across cell clusters such as oligodendrocytes,microglia,and astrocytes.Additionally,BV2 cells were exposed to amyloid-beta fragments to simulate Alzheimer’s disease,assessing the impact of exercise-induced cellular responses.Results:Distinct cellular subtypes were identified:oligodendrocytes(MBP,St18),microglia(Dock8),and astrocytes(Aqp4,Gpc5).Sample OE was predominantly oligodendrocytes,while YE had more astrocytes,inhibitory neurons,and Canal-Retzius cells.YC showed a significant presence of Olfm3+ganglion neurons.ZEB1 gene knockout revealed changes in SMAD family gene expression,which regulate ferroptosis.Oxidative stress levels were also evaluated.Conclusion:This profiling enhances our understanding of brain cellular functions and interactions,potentially informing targeted therapies in neurological research.Exercise may influence brain cell immune responses and cell death pathways by regulating specific gene expressions,offering new insights for treating neuroinflammation and degeneration.

Sulfolane‑Based Flame‑Retardant Electrolyte for High‑Voltage Sodium‑Ion Batteries

Sodium-ion batteries hold great promise as next-generation energy storage systems.However,the high instability of the electrode/electrolyte interphase during cycling has seriously hindered the development of SIBs.In particular,an unstable cathode–electrolyte interphase(CEI)leads to successive electrolyte side reactions,transition metal leaching and rapid capacity decay,which tends to be exacerbated under high-voltage conditions.Therefore,constructing dense and stable CEIs are crucial for high-performance SIBs.This work reports localized high-concentration electrolyte by incorporating a highly oxidation-resistant sulfolane solvent with non-solvent diluent 1H,1H,5H-octafluoropentyl-1,1,2,2-tetrafluoroethyl ether,which exhibited excellent oxidative stability and was able to form thin,dense and homogeneous CEI.The excellent CEI enabled the O3-type layered oxide cathode NaNi_(1/3)Mn_(1/3)Fe_(1/3)O_(2)(NaNMF)to achieve stable cycling,with a capacity retention of 79.48%after 300 cycles at 1 C and 81.15%after 400 cycles at 2 C with a high charging voltage of 4.2 V.In addition,its nonflammable nature enhances the safety of SIBs.This work provides a viable pathway for the application of sulfolane-based electrolytes on SIBs and the design of next-generation high-voltage electrolytes.

Single-cell transcriptomic atlas of goat ovarian aging

Background The ovaries are one of the first organs that undergo degenerative changes earlier in the aging process,and ovarian aging is shown by a decrease in the number and quality of oocytes.However,little is known about the molecular mechanisms of female age-related fertility decline in different types of ovarian cells during aging,especially in goats.Therefore,the aim of this study was to reveal the mechanisms driving ovarian aging in goats at single-cell resolution.Results For the first time,we surveyed the single-cell transcriptomic landscape of over 27,000 ovarian cells from newborn,young and aging goats,and identified nine ovarian cell types with distinct gene-expression signatures.Functional enrichment analysis showed that ovarian cell types were involved in their own unique biological processes,such as Wnt beta-catenin signalling was enriched in germ cells,whereas ovarian steroidogenesis was enriched in granulosa cells(GCs).Further analysis showed that ovarian aging was linked to GCs-specific changes in the antioxidant system,oxidative phosphorylation,and apoptosis.Subsequently,we identified a series of dynamic genes,such as AMH,CRABP2,THBS1 and TIMP1,which determined the fate of GCs.Additionally,FOXO1,SOX4,and HIF1A were identified as significant regulons that instructed the differentiation of GCs in a distinct manner during ovarian aging.Conclusions This study revealed a comprehensive aging-associated transcriptomic atlas characterizing the cell typespecific mechanisms during ovarian aging at the single-cell level and offers new diagnostic biomarkers and potential therapeutic targets for age-related goat ovarian diseases.

An effective'salt in dimethyl sulfoxide/water'electrolyte enables high-voltage supercapacitor operated at-50℃

Compared with organic electrolytes,aqueous electrolytes exhibit significantly higher ionic conductivity and possess inherent safety features,showcasing unique advantages in supercapacitors.However,challenges remain for low-salt aqueous electrolytes operating at high voltage and low temperature.Herein,we report a low-salt(0.87 m,m means mol kg^(-1))'salt in dimethyl sulfoxide/water'hybrid electrolyte with non-flammability via hybridizing aqueous electrolyte with an organic co-solvent of dimethyl sulfoxide(hydrogen bond acceptor).As a result,the 0.87 m hybrid electrolyte exhibits enhanced electrochemical stability,a freezing temperature below-50℃,and an outstanding ionic conductivity of 0.52mS cm~(-1)at-50℃.Dimethyl sulfoxide can anchor water molecules through intermolecular hydrogen bond interaction,effectively reinforcing the stability of water in the hybrid electrolyte.Furthermore,the interaction between dimethyl sulfoxide and water molecules diminishes the involvement of water in the generation of ordered ice crystals,finally facilitating the low-temperature performance of the hybrid electrolyte.When paired with the 0.87 m'salt in dimethyl sulfoxide/water'hybrid electrolyte,the symmetric supercapacitor presents a 2.0 V high operating voltage at 25℃,and can operate stably at-50℃.Importantly,the suppressed electrochemical reaction of water at-50℃further leads to the symmetric supercapacitor operated at a higher voltage of 2.6 V.This modification strategy opens an effective avenue to develop low-salt electrolytes for high-voltage and low-temperature aqueous supercapacitors.

Deep neural network-enabled battery open-circuit voltage estimation based on partial charging data

Battery management systems(BMSs) play a vital role in ensuring efficient and reliable operations of lithium-ion batteries.The main function of the BMSs is to estimate battery states and diagnose battery health using battery open-circuit voltage(OCV).However,acquiring the complete OCV data online can be a challenging endeavor due to the time-consuming measurement process or the need for specific operating conditions required by OCV estimation models.In addressing these concerns,this study introduces a deep neural network-combined framework for accurate and robust OCV estimation,utilizing partial daily charging data.We incorporate a generative deep learning model to extract aging-related features from data and generate high-fidelity OCV curves.Correlation analysis is employed to identify the optimal partial charging data,optimizing the OCV estimation precision while preserving exceptional flexibility.The validation results,using data from nickel-cobalt-magnesium(NCM) batteries,illustrate the accurate estimation of the complete OCV-capacity curve,with an average root mean square errors(RMSE) of less than 3 mAh.Achieving this level of precision for OCV estimation requires only around 50 s collection of partial charging data.Further validations on diverse battery types operating under various conditions confirm the effectiveness of our proposed method.Additional cases of precise health diagnosis based on OCV highlight the significance of conducting online OCV estimation.Our method provides a flexible approach to achieve complete OCV estimation and holds promise for generalization to other tasks in BMSs.

Challenges in Li-ion battery high-voltage technology and recent advances in high-voltage electrolytes

The electrolyte directly contacts the essential parts of a lithium-ion battery,and as a result,the electrochemical properties of the electrolyte have a significant impact on the voltage platform,charge discharge capacity,energy density,service life,and rate discharge performance.By raising the voltage at the charge/discharge plateau,the energy density of the battery is increased.However,this causes transition metal dissolution,irreversible phase changes of the cathode active material,and parasitic electrolyte oxidation reactions.This article presents an overview of these concerns to provide a clear explanation of the issues involved in the development of electrolytes for high-voltage lithium-ion batteries.Additionally,solidstate electrolytes enable various applications and will likely have an impact on the development of batteries with high energy densities.It is necessary to improve the high-voltage performance of electrolytes by creating solvents with high thermal stabilities and high voltage resistance and additives with superior film forming performance,multifunctional capabilities,and stable lithium salts.To offer suggestions for the future development of high-energy lithium-ion batteries,we conclude by offering our own opinions and insights on the current development of lithium-ion batteries.

Identification and validation of a pyroptosis-related prognostic model for colorectal cancer based on bulk and single-cell RNA sequencing data

BACKGROUND Pyroptosis impacts the development of malignant tumors,yet its role in colorectal cancer(CRC)prognosis remains uncertain.AIM To assess the prognostic significance of pyroptosis-related genes and their association with CRC immune infiltration.METHODS Gene expression data were obtained from The Cancer Genome Atlas(TCGA)and single-cell RNA sequencing dataset GSE178341 from the Gene Expression Omnibus(GEO).Pyroptosis-related gene expression in cell clusters was analyzed,and enrichment analysis was conducted.A pyroptosis-related risk model was developed using the LASSO regression algorithm,with prediction accuracy assessed through K-M and receiver operating characteristic analyses.A nomo-gram predicting survival was created,and the correlation between the risk model and immune infiltration was analyzed using CIBERSORTx calculations.Finally,the differential expression of the 8 prognostic genes between CRC and normal samples was verified by analyzing TCGA-COADREAD data from the UCSC database.RESULTS An effective pyroptosis-related risk model was constructed using 8 genes-CHMP2B,SDHB,BST2,UBE2D2,GJA1,AIM2,PDCD6IP,and SEZ6L2(P<0.05).Seven of these genes exhibited differential expression between CRC and normal samples based on TCGA database analysis(P<0.05).Patients with higher risk scores demonstrated increased death risk and reduced overall survival(P<0.05).Significant differences in immune infiltration were observed between low-and high-risk groups,correlating with pyroptosis-related gene expression.CONCLUSION We developed a pyroptosis-related prognostic model for CRC,affirming its correlation with immune infiltration.This model may prove useful for CRC prognostic evaluation.

The early life immune dynamics and cellular drivers at single-cell resolution in lamb forestomachs and abomasum

Background Four-chambered stomach including the forestomachs(rumen,reticulum,and omasum)and abomasum allows ruminants convert plant fiber into high-quality animal products.The early development of this four-chambered stomach is crucial for the health and well-being of young ruminants,especially the immune development.However,the dynamics of immune development are poorly understood.Results We investigated the early gene expression patterns across the four-chambered stomach in Hu sheep,at 5,10,15,and 25 days of age.We found that forestomachs share similar gene expression patterns,all four stomachs underwent widespread activation of both innate and adaptive immune responses from d 5 to 25,whereas the metabolic function were significantly downregulated with age.We constructed a cell landscape of the four-chambered stomach using single-cell sequencing.Integrating transcriptomic and single-cell transcriptomic analyses revealed that the immune-associated module hub genes were highly expressed in T cells,monocytes and macrophages,as well as the defense-associated module hub genes were highly expressed in endothelial cells in the four-stomach tissues.Moreover,the non-immune cells such as epithelial cells play key roles in immune maturation.Cell communication analysis predicted that in addition to immune cells,non-immune cells recruit immune cells through macrophage migration inhibitory factor signaling in the forestomachs.Conclusions Our results demonstrate that the immune and defense responses of four stomachs are quickly developing with age in lamb's early life.We also identified the gene expression patterns and functional cells associated with immune development.Additionally,we identified some key receptors and signaling involved in immune regulation.These results help to understand the early life immune development at single-cell resolution,which has implications to develop nutritional manipulation and health management strategies based on specific targets including key receptors and signaling pathways.

Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ morphogenesis.Here,the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17,a popular Chinese indica rice cultivar.Of 15 cell clusters,13 were assigned to cell types using marker genes and cluster-specific genes.Marker genes of multiple cell types were expressed in several clusters,suggesting a complex developmental system.Some genes for signaling by phytohormones such as abscisic acid were highly expressed in specific clusters.Various cis-elements in the promoters of genes specifically expressed in cell clusters were calculated,and some key hormone-related motifs were frequent in certain clusters.Spatial expression patterns of genes involved in rapid seed germination,seedling growth,and development were identified.These findings enhanced our understanding of cellular diversity and specialization within plumules of rice,a monocotyledonous model crop.

Understanding the correlation between energy-state mismatching and open-circuit voltage loss in bulk heterojunction solar cells

Photoinduced intermolecular charge transfer(PICT)determines the voltage loss in bulk heterojunction(BHJ)organic photovoltaics(OPVs),and this voltage loss can be minimized by inducing efficient PICT,which requires energy-state matching between the donor and acceptor at the BHJ interfaces.Thus,both geometrically and energetically accessible delocalized state matching at the hot energy level is crucial for achieving efficient PICT.In this study,an effective method for quantifying the hot state matching of OPVs was developed.The degree of energy-state matching between the electron donor and acceptor at BHJ interfaces was quantified using a mismatching factor(MF)calculated from the modified optical density of the BHJ.Furthermore,the correlation between the open-circuit voltage(Voc)of the OPV device and energy-state matching at the BHJ interface was investigated using the calculated MF.The OPVs with small absolute MF values exhibited high Voc values.This result clearly indicates that the energy-state matching between the donor and acceptor is crucial for achieving a high Voc in OPVs.Because the MF indicates the degree of energy-state matching,which is a critical factor for suppressing energy loss,it can be used to estimate the Voc loss in OPVs.

Dynamic Write-Voltage Design and Read-Voltage Optimization for MLC NAND Flash Memory

To mitigate the impact of noise and inter-ference on multi-level-cell(MLC)flash memory with the use of low-density parity-check(LDPC)codes,we propose a dynamic write-voltage design scheme con-sidering the asymmetric property of raw bit error rate(RBER),which can obtain the optimal write voltage by minimizing a cost function.In order to further improve the decoding performance of flash memory,we put forward a low-complexity entropy-based read-voltage optimization scheme,which derives the read voltages by searching for the optimal entropy value via a log-likelihood ratio(LLR)-aware cost function.Simulation results demonstrate the superiority of our proposed dynamic write-voltage design scheme and read-voltage optimization scheme with respect to the existing counterparts.

Applications of single-cell RNA sequencing in spermatogenesis and molecular evolution

Spermatogenic cell heterogeneity is determined by the complex process of spermatogenesis differentiation.However,effectively revealing the regulatory mechanisms underlying mammalian spermatogenic cell development and differentiation via traditional methods is difficult.Advances in technology have led to the emergence of many single-cell transcriptome sequencing protocols,which have partially addressed these challenges.In this review,we detail the principles of 10x Genomics technology and summarize the methods for downstream analysis of single-cell transcriptome sequencing data.Furthermore,we explore the role of single-cell transcriptome sequencing in revealing the heterogeneity of testicular ecological niche cells,delineating the establishment and disruption of testicular immune homeostasis during human spermatogenesis,investigating abnormal spermatogenesis in humans,and,ultimately,elucidating the molecular evolution of mammalian spermatogenesis.

Single-cell transcriptomics reveals T-cell heterogeneity and immunomodulatory role of CD4^(+) T native cells in Candida albicans infection

Objective:Candida albicans is a common fungal pathogen that triggers complex host defense mechanisms,including coordinated innate and adaptive immune responses,to neutralize invading fungi effectively.Exploring the immune microenvironment has the potential to inform the development of therapeutic strategies for fungal infections.Methods:The study analyzed individual immune cell profiles in peripheral blood mononuclear cells from Candida albicans-infected mice and healthy control mice using single-cell transcriptomics,fluorescence quantitative PCR,and Western blotting.We investigated intergroup differences in the dynamics of immune cell subpopulation infiltration,pathway enrichment,and differentiation during Candida albicans infection.Results:Our findings indicate that infiltration of CD4^(+)naive cells,regulatory T(Treg)cells,and Microtubules(MT)-associated cells increased after infection,along with impaired T cell activity.Notably,CD4^(+) T cells and plasma cells were enhanced after infection,suggesting that antibody production is dependent on T cells.In addition,we screened 6 hub genes,transcription factor forkhead box protein 3(Foxp3),cytotoxic T-lymphocyte associated protein 4(CTLA4),Interleukin 2 Receptor Subunit Beta(Il2rb),Cd28,C-C Motif Chemokine Ligand 5(Ccl5),and Cd27 for alterations associated with CD4^(+) T cell differentiation.Conclusions:These results provide a comprehensive immunological landscape of the mechanisms of Candida albicans infection and greatly advance our understanding of adaptive immunity in fungal infections.

Single-cell profiling of the pig cecum at various developmental stages

The gastrointestinal tract is essential for food digestion,nutrient absorption,waste elimination,and microbial defense.Single-cell transcriptome profiling of the intestinal tract has greatly enriched our understanding of cellular diversity,functional heterogeneity,and their importance in intestinal tract development and disease.Although such profiling has been extensively conducted in humans and mice,the single-cell gene expression landscape of the pig cecum remains unexplored.Here,single-cell RNA sequencing was performed on 45572 cells obtained from seven cecal samples in pigs at four different developmental stages(days(D)30,42,150,and 730).Analysis revealed 12 major cell types and 38 subtypes,as well as their distinctive genes,transcription factors,and regulons,many of which were conserved in humans.An increase in the relative proportions of CD8^(+)T and Granzyme A(low expression)natural killer T cells(GZMA^(low)NKT)cells and a decrease in the relative proportions of epithelial stem cells,Tregs,RHEX^(+)T cells,and plasmacytoid dendritic cells(pDCs)were noted across the developmental stages.Moreover,the post-weaning period exhibited an up-regulation in mitochondrial genes,COX2 and ND2,as well as genes involved in immune activation in multiple cell types.Cell-cell crosstalk analysis indicated that IBP6^(+)fibroblasts were the main signal senders at D30,whereas IBP6^(−)fibroblasts assumed this role at the other stages.NKT cells established interactions with epithelial cells and IBP6^(+)fibroblasts in the D730 cecum through mediation of GZMA-F2RL1/F2RL2 pairs.This study provides valuable insights into cellular heterogeneity and function in the pig cecum at different development stages.

Influence of extraction voltage on electron and ion behavior characteristics

The characteristics of the extracted ion current have a significant impact on the design and testing of ion source performance.In this paper,a 2D in space and 3D in velocity space particle in cell(2D3V PIC)method is utilized to simulate plasma motion and ion extraction characteristics under various initial plasma velocity distributions and extraction voltages in a Cartesian coordinate system.The plasma density is of the order of 10^(15)m^(-3)-10^(16)m^(-3)and the extraction voltage is of the order of 100 V-1000 V.The study investigates the impact of various extraction voltages on the velocity and density distributions of electrons and positive ions,and analyzes the influence of different initial plasma velocity distributions on the extraction current.The simulation results reveal that the main reason for the variation of extraction current is the spacecharge force formed by the relative aggregation of positive and negative net charges.This lays the foundation for a deeper understanding of extraction beam characteristics.

Voltage-modulated polymer nanopore field-effect transistor for multi-sized nanoparticle detection

Solid-state nanopores offer a range of distinct advantages over biological nanopores,such as structural diversity and greater stability and durability;this makes them highly promising for high-resolution nanoparticle sensing.Biological nanopores can exhibit gating characteristics with stress-responsive switches and can demonstrate specificity toward particular molecules.Drawing inspiration from biological nanopores,this paper introduces a novel polymer nanopore with field-effect characteristics,leveraging a conductive polymer in its construction to showcase intriguing gating behavior.Notably,in this device,the polymer layer serves as the gate,enabling precise control over the source–drain current response inside and outside the pore by simply adjusting the gate voltage.This unique feature allows fine-tuning of the nanopore’s sensitivity to nanoparticles of varying sizes and facilitates its operation in multiple modes.Experimental results reveal that the developed polymer nanopore field-effect transistor demonstrates remarkable selectivity in detecting nanoparticles of various sizes under different applied voltages.The proposed single device demonstrates the exceptional ability to detect multiple types of nanoparticle,showcasing its immense potential for a wide range of applications in biological-particle analysis and medical diagnostics.

Revolutionizing stem cell research:unbiased insights through single-cell sequencing

Stem cells have shown great application potential in wound repair,tissue regeneration,and disease treatment.Therefore,a full understanding of stem cells and their related regulatory mechanisms in disease treatment is conducive to improving the therapeutic effect of stem cells.However,thus far,there are still many unsolved mysteries in thefield of stem cells due to technical limitations,which hinder the in-depth exploration of stem cells and their wide clinical application.Single-cell sequencing(SCS)has provided very powerful and unbiased insights into cell gene expression profiles at the single-cell level,bringing exciting results to the stem cellfield.At present,SCS has been widely applied in thefield of stem cells,covering various aspects,including lineage tracing the development of stem cells,identifying new stem cell types,exploring cellular heterogeneity,and identifying internal functional subpopulations.In this paper,we focus on the latest research progress and discuss the application of SCS technology in stem cells.

Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer

Advances in chimeric antigen receptor(CAR)-T cell therapy have significantly improved clinical outcomes of patients with relapsed or refractory hematologic malignancies.However,progress is still hindered as clinical benefit is only available for a fraction of patients.A lack of understanding of CAR-T cell behaviors in vivo at the single-cell level impedes their more extensive application in clinical practice.Mounting evidence suggests that single-cell sequencing techniques can help perfect the receptor design,guide gene-based T cell modification,and optimize the CAR-T manufacturing conditions,and all of them are essential for long-term immunosurveillance and more favorable clinical outcomes.The information generated by employing these methods also potentially informs our understanding of the numerous complex factors that dictate therapeutic efficacy and toxicities.In this review,we discuss the reasons why CAR-T immunotherapy fails in clinical practice and what this field has learned since the milestone of single-cell sequencing technologies.We further outline recent advances in the application of single-cell analyses in CAR-T immunotherapy.Specifically,we provide an overview of single-cell studies focusing on target antigens,CAR-transgene integration,and preclinical research and clinical applications,and then discuss how it will affect the future of CAR-T cell therapy.

Food nutrition and toxicology targeting on specific organs in the era of single-cell sequencing

Due to the complex natures of dietary food components,it is difficult to elucidate how the compounds affect host health.Dietary food often selectively presents its mechanism of action on different cell types,and participates in the modulation of targeted cells and their microenvironments within organs.However,the limitations of traditional in vitro assays or in vivo animal experiments cannot comprehensively examine cellular heterogeneity and the tissue-biased influences.Single-cell RNA sequencing(sc RNA-seq)has emerged as an indispensable methodology to decompose tissues into different cell types for the demonstration of transcriptional profiles of individual cells.Sc RNA-seq applications has been summarized on three typical organs(brain,liver,kidney),and two representative immune-and tumor related health problems.The everincreasing role of sc RNA-seq in dietary food research with further improvement can provide sub-cellular information and the coupling between other cellular modalities.In this review,we propose utilizing sc RNAseq to more effectively capture the subtle and complex effects of food chemicals,and how they may lead to health problems at single-cell resolution.This novel technique will be valuable to elucidate the underlying mechanism of both the health benefits of food nutrients and the detrimental consequences food toxicants at the cellular level.