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.

Deep eutectic solvents for separation and purification applications in critical metal metallurgy:Recent advances and perspectives

Solvent extraction,a separation and purification technology,is crucial in critical metal metallurgy.Organic solvents commonly used in solvent extraction exhibit disadvantages,such as high volatility,high toxicity,and flammability,causing a spectrum of hazards to human health and environmental safety.Neoteric solvents have been recognized as potential alternatives to these harmful organic solvents.In the past two decades,several neoteric solvents have been proposed,including ionic liquids(ILs)and deep eutectic solvents(DESs).DESs have gradually become the focus of green solvents owing to several advantages,namely,low toxicity,degradability,and low cost.In this critical review,their classification,formation mechanisms,preparation methods,characterization technologies,and special physicochemical properties based on the most recent advancements in research have been systematically described.Subsequently,the major separation and purification applications of DESs in critical metal metallurgy were comprehensively summarized.Finally,future opportunities and challenges of DESs were explored in the current research area.In conclusion,this review provides valuable insights for improving our overall understanding of DESs,and it holds important potential for expanding separation and purification applications in critical metal metallurgy.

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.

Role of tannin pretreatment in flotation separation of magnesite and dolomite

Flotation separation of magnesite and its calcium-containing carbonate minerals is a difficult problem.Recently,new regulat-ors have been proposed for magnesite flotation decalcification,although traditional regulators such as tannin,water glass,sodium carbon-ate,and sodium hexametaphosphate are more widely used in industry.However,they are rarely used as the main regulators in research because they perform poorly in magnesite and dolomite single-mineral flotation tests.Inspired by the limonite presedimentation method and the addition of a regulator to magnesite slurry mixing,we used a tannin pretreatment method for separating magnesite and dolomite.Microflotation experiments confirmed that the tannin pretreatment method selectively and largely reduces the flotation recovery rate of dolomite without affecting the flotation recovery rate of magnesite.Moreover,the contact angles of the tannin-pretreated magnesite and dolomite increased and decreased,respectively,in the presence of NaOl.Zeta potential and Fourier transform infrared analyses showed that the tannin pretreatment method efficiently hinders NaOl adsorption on the dolomite surface but does not affect NaOl adsorption on the magnesite surface.X-ray photoelectron spectroscopy and density functional theory calculations confirmed that tannin interacts more strongly with dolomite than with magnesite.

Direct capture and separation of CO_(2) from air

Direct air capture(DAC)has attracted increasing interest and investment over the past few years.There are a fast-growing number of companies that entered the field and demonstrated DAC carbon removal setups and potential.However,current DAC methods are still based on solid absorbents or alkali solutions approaches which have low capture efficiency and low energy efficiency.This highlight proposed a promising CO_(2) capture technology,an electric energy driven closed-loop system for the direct removal of CO_(2) from ambient air which are based on two individual technologies:Polyam-N-Cu hybrid system promoted CO_(2) capture with ocean as anthropogenic CO_(2) sink and a chloride-mediated electrochemical pH swing system to remove CO_(2) from oceanwater.

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.

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.

Phase separation and transcriptional regulation in cancer development

Liquid-liquid phase separation,a novel biochemical phenomenon,has been increasingly studied for its medical applications.It underlies the formation of membrane-less organelles and is involved in many cellular and biological processes.During transcriptional regulation,dynamic condensates are formed through interactions between transcriptional elements,such as transcription factors,coactivators,and mediators.Cancer is a disease characterized by uncontrolled cell proliferation,but the precise mechanisms underlying tumorigenesis often remain to be elucidated.Emerging evidence has linked abnormal transcriptional condensates to several diseases,especially cancer,implying that phase separation plays an important role in tumorigenesis.Condensates formed by phase separation may have an effect on gene transcription in tumors.In the present review,we focus on the correlation between phase separation and transcriptional regulation,as well as how this phenomenon contributes to cancer development.

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.

Advances in depressants for flotation separation of Cu–Fe sulfide minerals at low alkalinity:A critical review

The flotation separation of Cu–Fe sulfide minerals at low alkalinity can be achieved using selective depressants.In the flotation system of Cu–Fe sulfide minerals,depressants usually preferentially interact with the pyrite surface to render the mineral surface hydrophilic and hinder the adsorption of the collector.This review summarizes the advances in depressants for the flotation separation of Cu–Fe sulfide minerals at low alkalinity.These advances include use of inorganic depressants (oxidants and sulfur–oxygen compounds),natural polysaccharides (starch,dextrin,konjac glucomannan,and galactomannan),modified polymers (carboxymethyl cellulose,polyacrylamide,lignosulfonate,and tricarboxylate sodium starch),organic acids (polyglutamic acid,sodium humate,tannic acid,pyrogallic acid,salicylic acid,and lactic acid),sodium dimethyl dithiocarbamate,and diethylenetriamine.The potential application of specific inorganic and organic depressants in the flotation separation of Cu–Fe sulfide minerals at low alkalinity is reviewed.The advances in the use of organic depressants with respect to the flotation separation of Cu–Fe sulfide minerals are comprehensively detailed.Additionally,the depression performances and mechanisms of different types of organic depressants on mineral surfaces are summarized.Finally,several perspectives on depressants vis-à-vis flotation separation of Cu–Fe sulfide minerals at low alkalinity are proposed.

Recent progress in ternary mixed matrix membranes for CO_(2) separation

Mixed matrix membranes(MMMs)could combine the advantages of both polymeric membranes and porousfillers,making them an effective alternative to conventional polymer membranes.However,interfacial incompatibility issues,such as the presence of interfacial voids,hardening of polymer chains,and blockage of micropores by polymers between common MMMsfillers and the polymer matrix,currently limit the gas sep-aration performance of MMMs.Ternary phase MMMs(consisting of afiller,an additive,and a matrix)made by adding a third compound,usually functionalized additives,can overcome the structural problems of binary phase MMMs and positively impact membrane separation performance.This review introduces the structure and fabrication processes for ternary MMMs,categorizes various nanofillers and the third component,and summarizes and analyzes in detail the CO_(2) separation performance of newly developed ternary MMMs based on both rubbery and glassy polymers.Based on this separation data,the challenges of ternary MMMs are also discussed.Finally,future directions for ternary MMMs are proposed.

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.

The flow behavior of droplet adsorption on a liquid-liquid interface accompanied by cross-linking reaction and phase separation in a microchannel

The adsorption process of droplets on the liquid-liquid interface and phase separation process can regulate the spatial distribution of the fluid system,which are crucial for chemical engineering.However,the cross-linking reaction,which is widely used in the field of polymers,can change the physical properties of the fluids and affect the flow behavior accordingly.A configuration of microchannels is designed to conveniently generate uniform droplets in one phase of the parallel flow.The flow behavior of the adsorption process of sodium alginate droplets on the liquid-liquid interface is investigated,and the subsequent process of phase separation is studied.In the process of droplet adsorption,the crosslinking reaction occurs synchronously,which makes the droplet viscosity and the elasticity modules of the droplet surface increase,thus affecting the dynamics of the adsorption process and the equilibrium shape of the droplet.The variation of the adsorption length with time is divided into three stages,which all conform to power law relationship.The exponents of the second and third stages deviate from the results of the Tanner's law.The flow pattern maps of droplet adsorption and phase separation are drawn,and the operating ranges of complete adsorption and complete separation are provided.This study provides a theoretical basis for further studying the flow behavior of droplets with cross-linking reaction in a microchannel.

Environmental,economic and exergy analysis of separation of ternary azeotrope by variable pressure extractive distillation based on multi-objective optimization

In this work,the ternary azeotrope of tert-butyl alcohol/ethyl acetate/water is separated by extractive distillation(ED)to recover the available constituents and protect the environment.Based on the conductor like shielding model and relative volatility method,ethylene glycol was selected as the extractant in the separation process.In addition,in view of the characteristic that the relative volatility between components changes with pressure,the multi-objective optimization method based on nondominated sorting genetic algorithm II optimizes the pressure and the amount of solvent cooperatively to avoid falling into the optimal local solution.Based on the optimal process parameters,the proposed heat-integrated process can reduce the gas emissions by 29.30%.The heat-integrated ED,further coupled with the pervaporation process,can reduce gas emission by 42.36%and has the highest exergy efficiency of 47.56%.In addition,based on the heat-integrated process,the proposed two heat pump assisted heat-integrated ED processes show good economic and environmental performance.The double heat pump assisted heat-integrated ED can reduce the total annual cost by 28.78%and the gas emissions by 55.83%compared with the basis process,which has a good application prospect.This work provides a feasible approach for the separation of ternary azeotropes.

Flotation separation of scheelite from calcite using luteolin as a novel depressant

This paper proposes luteolin(LUT)as a novel depressant for the flotation-based separation of scheelite and calcite in a sodium oleate(NaOL)system.The suitability of LUT as a calcite depressant is confirmed through micro-flotation testing.At pH=9,with LUT concentration of 50 mg·L^(-1) and NaOL concentration of 50 mg·L^(-1),scheelite recovery reaches 80.3%.Calcite,on the other hand,exhibits a recovery rate of 17.6%,indicating a significant difference in floatability between the two minerals.Subsequently,the surface modifica-tions of scheelite and calcite following LUT treatment are characterized using adsorption capacity testing,Zeta potential analysis,Fourier transform infrared spectroscopy(FT-IR),X-ray photoelectron spectroscopy(XPS),and atomic force microscopy(AFM).The study in-vestigates the selective depressant mechanism of LUT on calcite.Adsorption capacity testing and Zeta potential analysis demonstrate sub-stantial absorption of LUT on the surface of calcite,impeding the further adsorption of sodium oleate,while its impact on scheelite is min-imal.FT-IR and XPS analyses reveal the selective adsorption of LUT onto the surface of calcite,forming strong chemisorption bonds between the hydroxyl group and calcium ions present.AFM directly illustrates the distinct adsorption densities of LUT on the two miner-al types.Consequently,LUT can effectively serve as a depressant for calcite,enabling the successful separation of scheelite and calcite.

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.

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.

Comment on:Recurrence after spontaneous separation of epiretinal membrane in a young woman:a case report

Dear Editor,Herein,we provide a commentary on the recently published article by Zeng QZ and Yu WZ[1].This case report provides interesting novel insights into the recurrence of epiretinal membrane(ERM)following self-separation in a young patient.In addition to the study,we have been investigating spontaneous ERM release for many years and have recently published a related paper[2].