Averrhoa carambola is commonly known as star fruit because of its peculiar shape,and its fruit is a rich source of minerals and vitamins.It is also used in traditional medicines in countries such as India,China,the Ph...Averrhoa carambola is commonly known as star fruit because of its peculiar shape,and its fruit is a rich source of minerals and vitamins.It is also used in traditional medicines in countries such as India,China,the Philippines,and Brazil for treating various ailments,including fever,diarrhea,vomiting,and skin disease.Here,we present the first draft genome of the Oxalidaceae family,with an assembled genome size of 470.51 Mb.In total,24,726 protein-coding genes were identified,and 16,490 genes were annotated using various well-known databases.The phylogenomic analysis confirmed the evolutionary position of the Oxalidaceae family.Based on the gene functional annotations,we also identified enzymes that may be involved in important nutritional pathways in the star fruit genome.Overall,the data from this first sequenced genome in the Oxalidaceae family provide an essential resource for nutritional,medicinal,and cultivational studies of the economically important star-fruit plant.展开更多
Extant giant pandas are divided into Sichuan and Qinling subspecies.The giant panda has many speciesspecific characteristics,including comparatively small organs for body size,small genitalia of male individuals,and l...Extant giant pandas are divided into Sichuan and Qinling subspecies.The giant panda has many speciesspecific characteristics,including comparatively small organs for body size,small genitalia of male individuals,and low reproduction.Here,we report the most contiguous,high-quality chromosomelevel genomes of two extant giant panda subspecies to date,with the first genome assembly of the Qinling subspecies.Compared with the previously assembled giant panda genomes based on short reads,our two assembled genomes increased contiguity over 200-fold at the contig level.Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago.Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2(DACH2)gene and specific changes in the synaptotagmin 6(SYT6)gene,which may be responsible for the reduced fertility of the giant panda.Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D(IQCD)gene may at least partly explain the different reproduction rates of the two subspecies.Furthermore,several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements,which may contribute to the reduced inner organ sizes of the giant panda.展开更多
The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology,from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing,by which the s...The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology,from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing,by which the scientific community has been able to visualize life at an unprecedented resolution.Most recently,the Spatially Resolved Transcriptomics(SRT)technologies have filled the gap in probing the spatial or even three-dimensional organization of the molecular foundation behind the molecular mysteries of life,including the origin of different cellular populations developed from totipotent cells and human diseases.In this review,we introduce recent progresses and challenges on SRT from the perspectives of technologies and bioinformatic tools,as well as the representative SRT applications.With the currently fast-moving progress of the SRT technologies and promising results from early adopted research projects,we can foresee the bright future of such new tools in understanding life at the most profound analytical level.展开更多
The fall armyworm(FAW),Spodoptera frugiperda,is a destructive pest native to America and has recently become an invasive insect pest in China.Because of its rapid spread and great risks in China,understanding of FAW g...The fall armyworm(FAW),Spodoptera frugiperda,is a destructive pest native to America and has recently become an invasive insect pest in China.Because of its rapid spread and great risks in China,understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies.Here,we assembled a chromosome-level genome of a male FAW(SFynMstLFR)and compared re-sequencing results of the populations from America,Africa,and China.Strain identification of 163 individuals collected from America,Africa and China showed that both C and R strains were found in the American pop-ulations,while only C strain was found in the Chinese and African populations.Moreover,population geno-mics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations.Taken toge-ther,FAWs invaded into China were most likely origi-nated from Africa.Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW,of which 283 genes are specific to FAW.Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles,and several detoxification genes such as AOX,UGT and GST spe-cially responded to the pesticides.These findings will be useful in developing effective strategies for manage-ment of FAW in China and other invaded areas.展开更多
Dear Editor,The axolotl,Ambystoma mexicanum,has extraordinary capability to fully recover multiple tissues after lost,whereas such capability has disappeared in mammals.Thus,deci-phering detailed mechanisms underlying...Dear Editor,The axolotl,Ambystoma mexicanum,has extraordinary capability to fully recover multiple tissues after lost,whereas such capability has disappeared in mammals.Thus,deci-phering detailed mechanisms underlying axolotl regenera-tion could provide valuable lessons for regenerative medicine.However,many questions,such as the origin of essential progenitor cells and key responses of individual types of cells for regeneration remain elusive(Haas and Whited,2017).Newly developed single-cell RNA sequenc-ing(scRNA-seq)method enables researchers to observe cellular and molecular dynamics in axolotl regeneration at the single-cell resolution(Gerber et al.,2018;Leigh et al.,2018),but the reported transcriptome landscapes are only for certain cell types or in certain regenerative stages.A complete overview of the regeneration process for all cell types is still lacking.展开更多
The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic wri...The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects.展开更多
Microbial production of monoterpenoid indole alkaloids(MIAs)provides a sustainable and eco-friendly means to obtain compounds with high pharmaceutical values.However,efficient biosynthesis of MIAs in heterologous micr...Microbial production of monoterpenoid indole alkaloids(MIAs)provides a sustainable and eco-friendly means to obtain compounds with high pharmaceutical values.However,efficient biosynthesis of MIAs in heterologous microorganisms is hindered due to low supply of key precursors such as geraniol and its derivative 8-hydroxygeraniol catalyzed by geraniol 8-hydroxylase(G8H).In this study,we developed a facile evolution platform to screen strains with improved yield of geraniol by using the SCRaMbLE system embedded in the Sc2.0 synthetic yeast and confirmed the causal role of relevant genomic targets.Through genome mining,we identified several G8H enzymes that perform much better than the commonly used CrG8H for 8-hydroxygeraniol production in vivo.We further showed that the N-terminus of these G8H enzymes plays an important role in cellular activity by swapping experiments.Finally,the combination of the engineered chassis,optimized biosynthesis pathway,and utilization of G8H led to the final strain with more than 30-fold improvement in producing 8-hydroxygeraniol compared with the starting strain.Overall,this study will provide insights into the construction and optimization of yeast cells for efficient biosynthesis of 8-hydroxygeraniol and its derivatives.展开更多
The site-specific incorporation of the noncanonical amino acid(ncAA)into proteins via genetic code expansion(GCE)has enabled the development of new and powerful ways to learn,regulate,and evolve biological functions i...The site-specific incorporation of the noncanonical amino acid(ncAA)into proteins via genetic code expansion(GCE)has enabled the development of new and powerful ways to learn,regulate,and evolve biological functions in vivo.However,cellular biosynthesis of ncAA-containing proteins with high efficiency and fidelity is a formidable challenge.In this review,we summarize up-to-date progress towards improving the efficiency and orthogonality of GCE and enhancing intracellular compatibility of introduced translation machinery in the living cells by creation and optimization of orthogonal translation components,constructing genomically recoded organism(GRO),utilization of unnatural base pairs(UBP)and quadruplet codons(four-base codons),and spatial separation of orthogonal translation.展开更多
The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement.This developmental process incorporates a series of cell fate transitions and ...The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement.This developmental process incorporates a series of cell fate transitions and reprogramming.However,our understanding of cell heterogeneity and mechanisms of cell fate transition during callus induction remains quite limited.Here,we report a time-series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0,1,and 4 days,and the construction of a detailed single-cell transcriptional atlas of the callus induction process.We identify the cell types responsible for initiating the early callus:lateral root primordium-initiating(LRPI)-like cells and quiescent center(QC)-like cells.LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia.We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells.QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration.We also identify the transcription factors that regulate QC-like cells and the gene expression signatures that are related to cell fate decisions.Overall,our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transitions during callus formation,significantly improving our understanding of callus formation.展开更多
Deer antlers constitute a unique mammalian model for the study of both organ formation in postnatal life and annual full regeneration.Previous studies revealed that these events are achieved through the proliferation ...Deer antlers constitute a unique mammalian model for the study of both organ formation in postnatal life and annual full regeneration.Previous studies revealed that these events are achieved through the proliferation and differentiation of antlerogenic periosteum(AP)cells and pedicle periosteum(PP)cells,respectively.As the cells resident in the AP and the PP possess stem cell attributes,both antler generation and regeneration are stem cell-based processes.However,the cell composition of each tissue type and molecular events underlying antler development remain poorly characterized.Here,we took the approach of single-cell RNA sequencing(scRNA-Seq)and identified eight cell types(mainly THY1^(+)cells,progenitor cells,and osteochondroblasts)and three core subclusters of the THY1^(+)cells(SC2,SC3,and SC4).Endothelial and mural cells each are heterogeneous at transcriptional level.It was the proliferation of progenitor,mural,and endothelial cells in the activated antler-lineage-specific tissues that drove the rapid formation of the antler.We detected the differences in the initial differentiation process between antler generation and regeneration using pseudotime trajectory analysis.These may be due to the difference in the degree of stemness of the AP-THY1+and PP-THY1^(+)cells.We further found that androgen-RXFP2 axis may be involved in triggering initial antler full regeneration.Fully deciphering the cell composition for these antler tissue types will open up new avenues for elucidating the mechanism underlying antler full renewal in specific and regenerative medicine in general.展开更多
Traditional silicon-based storage media will soon be unable to meet the exponentially increasing data archiving demands,and efforts must be made to find alternatives.As an ancient and efficient information carrier in ...Traditional silicon-based storage media will soon be unable to meet the exponentially increasing data archiving demands,and efforts must be made to find alternatives.As an ancient and efficient information carrier in living organisms,DNA has been believed to have great potential as a novel storage medium.It holds numerous advantages,such as remarkably high storage density,extremely long durability,and the costefficiency of information replication.展开更多
The preexistence of immune cells in the tumor microenvironment substantiates the efficacy of immunotherapy in cancer patients.Although the complex intratumoral immune heterogeneity has been extensively studied in sing...The preexistence of immune cells in the tumor microenvironment substantiates the efficacy of immunotherapy in cancer patients.Although the complex intratumoral immune heterogeneity has been extensively studied in single cell resolution,hi-res spatial investigations are limited.In this study,we performed a spatial transcriptome analysis of 4 colorectal adenocarcinoma specimens and 2 paired distant normal specimens to identify the molecular pattern involved in a discontinuous inflammatory response in pathologically annotated cancer regions.Based on the location of spatially varied gene expression,we unmasked the spatially-varied immune ecosystem and identified the locoregional“warmed-up”immune response in predefined“cold”tumor with substantial infiltration of immune components.This“warmed-up”immune profile was found to be associated with the in-situ copy number variance and the tissue remodeling process.Further,“warmed-up”signature genes indicated improved overall survival in CRC patients obtained from TCGA database.展开更多
基金supported by funding from the National Key R&D Program of China(No.2019YFC1711000)the Shenzhen Municipal Government of China(grants JCYJ20170817145512476 and JCYJ20160510141910129)+1 种基金the Guangdong Provincial Key Laboratory of Genome Read and Write(grant 2017B030301011)the NMPA Key Laboratory for the Rapid Testing Technology of Drugs.
文摘Averrhoa carambola is commonly known as star fruit because of its peculiar shape,and its fruit is a rich source of minerals and vitamins.It is also used in traditional medicines in countries such as India,China,the Philippines,and Brazil for treating various ailments,including fever,diarrhea,vomiting,and skin disease.Here,we present the first draft genome of the Oxalidaceae family,with an assembled genome size of 470.51 Mb.In total,24,726 protein-coding genes were identified,and 16,490 genes were annotated using various well-known databases.The phylogenomic analysis confirmed the evolutionary position of the Oxalidaceae family.Based on the gene functional annotations,we also identified enzymes that may be involved in important nutritional pathways in the star fruit genome.Overall,the data from this first sequenced genome in the Oxalidaceae family provide an essential resource for nutritional,medicinal,and cultivational studies of the economically important star-fruit plant.
基金supported by the National Key Program(2016YFC0503200)from the Ministry of Science and Technology of Chinaa special grant for the giant panda from the State Forestry Administration of the People’s Republic of China+2 种基金the Fundamental Research Funds for the Central Universities of the People’s Republic of Chinathe Foundation of Key Laboratory of State Forestry and Grassland Administration(State Park Administration)on Conservation Biology of Rare Animals in the Giant Panda National Park(KLSFGAGP2020.002)the Guangdong Provincial Key Laboratory of Genome Read and Write(2017B030301011)。
文摘Extant giant pandas are divided into Sichuan and Qinling subspecies.The giant panda has many speciesspecific characteristics,including comparatively small organs for body size,small genitalia of male individuals,and low reproduction.Here,we report the most contiguous,high-quality chromosomelevel genomes of two extant giant panda subspecies to date,with the first genome assembly of the Qinling subspecies.Compared with the previously assembled giant panda genomes based on short reads,our two assembled genomes increased contiguity over 200-fold at the contig level.Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago.Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2(DACH2)gene and specific changes in the synaptotagmin 6(SYT6)gene,which may be responsible for the reduced fertility of the giant panda.Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D(IQCD)gene may at least partly explain the different reproduction rates of the two subspecies.Furthermore,several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements,which may contribute to the reduced inner organ sizes of the giant panda.
基金supported by the Shenzhen Key Laboratory of Single-Cell Omics(ZDSYS20190902093613831)the Guangdong Provincial Key Laboratory of Genome Read and Write(2017B030301011)Longqi Liu was supported by the National Natural Science Foundation of China(31900466).
文摘The ability to explore life kingdoms is largely driven by innovations and breakthroughs in technology,from the invention of the microscope 350 years ago to the recent emergence of single-cell sequencing,by which the scientific community has been able to visualize life at an unprecedented resolution.Most recently,the Spatially Resolved Transcriptomics(SRT)technologies have filled the gap in probing the spatial or even three-dimensional organization of the molecular foundation behind the molecular mysteries of life,including the origin of different cellular populations developed from totipotent cells and human diseases.In this review,we introduce recent progresses and challenges on SRT from the perspectives of technologies and bioinformatic tools,as well as the representative SRT applications.With the currently fast-moving progress of the SRT technologies and promising results from early adopted research projects,we can foresee the bright future of such new tools in understanding life at the most profound analytical level.
基金This study was financially supported by the Yunnan Eco-friendly Food International Cooperation Research Center(YEFICRC)Project of Yunnan Provincial Key Programs(Grant No.2019ZG009)the National Key R&D Program of China(Grant No.2019YFD0300101)+3 种基金the Guangdong Provincial Key Laboratory of Genome Read and Write(Grant No.2017B030301011)the Key Research Program of the Chinese Academy of Sciences(KJZD-SW-L07)the Youth Innovation Promotion Association,CAS(No.2016080)Key-Area Research and Development Program of Guangdong Province(No.2020B020224002)。
文摘The fall armyworm(FAW),Spodoptera frugiperda,is a destructive pest native to America and has recently become an invasive insect pest in China.Because of its rapid spread and great risks in China,understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies.Here,we assembled a chromosome-level genome of a male FAW(SFynMstLFR)and compared re-sequencing results of the populations from America,Africa,and China.Strain identification of 163 individuals collected from America,Africa and China showed that both C and R strains were found in the American pop-ulations,while only C strain was found in the Chinese and African populations.Moreover,population geno-mics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations.Taken toge-ther,FAWs invaded into China were most likely origi-nated from Africa.Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW,of which 283 genes are specific to FAW.Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles,and several detoxification genes such as AOX,UGT and GST spe-cially responded to the pesticides.These findings will be useful in developing effective strategies for manage-ment of FAW in China and other invaded areas.
文摘Dear Editor,The axolotl,Ambystoma mexicanum,has extraordinary capability to fully recover multiple tissues after lost,whereas such capability has disappeared in mammals.Thus,deci-phering detailed mechanisms underlying axolotl regenera-tion could provide valuable lessons for regenerative medicine.However,many questions,such as the origin of essential progenitor cells and key responses of individual types of cells for regeneration remain elusive(Haas and Whited,2017).Newly developed single-cell RNA sequenc-ing(scRNA-seq)method enables researchers to observe cellular and molecular dynamics in axolotl regeneration at the single-cell resolution(Gerber et al.,2018;Leigh et al.,2018),but the reported transcriptome landscapes are only for certain cell types or in certain regenerative stages.A complete overview of the regeneration process for all cell types is still lacking.
基金supported by the Guangdong Provincial Key Laboratory of Genome Read and Write (Grant No. 2017B030301011)Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics (Grant No. DRC-SZ[2016]884)
文摘The ultimate goal of synthetic biology is to build customized cells or organisms to meet specific industrial or medical needs. The most important part of the customized cell is a synthetic genome. Advanced genomic writing technologies are required to build such an artificial genome. Recently, the partially-completed synthetic yeast genome project represents a milestone in this field. In this mini review, we briefly introduce the techniques for de novo genome synthesis and genome editing. Furthermore, we summarize recent research progresses and highlight several applications in the synthetic genome field. Finally, we discuss current challenges and future prospects.
基金supported by grants from the National Key Research and Development Program of China (No.2021YFC2100800 to Y.Z.)the Science,Technology and Innovation Commission of Shenzhen Municipality under grant (No.JCYJ20180507183534578)the Tip-top Scientific and Technical Innovative Youth Talents of Guangdong Special Support Program (2019TQ05Y876 to Y.S.)。
文摘Microbial production of monoterpenoid indole alkaloids(MIAs)provides a sustainable and eco-friendly means to obtain compounds with high pharmaceutical values.However,efficient biosynthesis of MIAs in heterologous microorganisms is hindered due to low supply of key precursors such as geraniol and its derivative 8-hydroxygeraniol catalyzed by geraniol 8-hydroxylase(G8H).In this study,we developed a facile evolution platform to screen strains with improved yield of geraniol by using the SCRaMbLE system embedded in the Sc2.0 synthetic yeast and confirmed the causal role of relevant genomic targets.Through genome mining,we identified several G8H enzymes that perform much better than the commonly used CrG8H for 8-hydroxygeraniol production in vivo.We further showed that the N-terminus of these G8H enzymes plays an important role in cellular activity by swapping experiments.Finally,the combination of the engineered chassis,optimized biosynthesis pathway,and utilization of G8H led to the final strain with more than 30-fold improvement in producing 8-hydroxygeraniol compared with the starting strain.Overall,this study will provide insights into the construction and optimization of yeast cells for efficient biosynthesis of 8-hydroxygeraniol and its derivatives.
基金the National Key Research and Development Program of China(No.2018YFA0900100)National Natural Science Foundation of China(No.31901029 to X.F.and No.31800078 to Y.S.)+1 种基金Natural Science Foundation of Guangdong Province,China(No.2021A1515010995 to X.F.)Guangdong Provincial Key Laboratory of Genome Read and Write(No.2017B030301011).
文摘The site-specific incorporation of the noncanonical amino acid(ncAA)into proteins via genetic code expansion(GCE)has enabled the development of new and powerful ways to learn,regulate,and evolve biological functions in vivo.However,cellular biosynthesis of ncAA-containing proteins with high efficiency and fidelity is a formidable challenge.In this review,we summarize up-to-date progress towards improving the efficiency and orthogonality of GCE and enhancing intracellular compatibility of introduced translation machinery in the living cells by creation and optimization of orthogonal translation components,constructing genomically recoded organism(GRO),utilization of unnatural base pairs(UBP)and quadruplet codons(four-base codons),and spatial separation of orthogonal translation.
基金supported by the National Key R&D Program of China(2022YFC3400300)the Guangdong Provincial Key Laboratory of Genome Read and Write(no.2017B030301011)+2 种基金the Shenzhen Key Laboratory of Single-Cell Omics(no.ZDSYS20190902093613831)the Guangdong Genomics Data Center(2021B1212100001)the theme project of Shenzhen Institute of Synthetic Biology(no.ZTXM20190004).
文摘The acquisition of pluripotent callus from somatic cells plays an important role in plant development studies and crop genetic improvement.This developmental process incorporates a series of cell fate transitions and reprogramming.However,our understanding of cell heterogeneity and mechanisms of cell fate transition during callus induction remains quite limited.Here,we report a time-series single-cell transcriptome experiment on Arabidopsis root explants that were induced in callus induction medium for 0,1,and 4 days,and the construction of a detailed single-cell transcriptional atlas of the callus induction process.We identify the cell types responsible for initiating the early callus:lateral root primordium-initiating(LRPI)-like cells and quiescent center(QC)-like cells.LRPI-like cells are derived from xylem pole pericycle cells and are similar to lateral root primordia.We delineate the developmental trajectory of the dedifferentiation of LRPI-like cells into QC-like cells.QC-like cells are undifferentiated pluripotent acquired cells that appear in the early stages of callus formation and play a critical role in later callus development and organ regeneration.We also identify the transcription factors that regulate QC-like cells and the gene expression signatures that are related to cell fate decisions.Overall,our cell-lineage transcriptome atlas for callus induction provides a distinct perspective on cell fate transitions during callus formation,significantly improving our understanding of callus formation.
基金This project was supported by National Natural Science Foundation of China(No.U20A20403 and No.31901058)the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDA16030305)+2 种基金Natural Science Foundation of Jilin Province(YDZJ202201ZYTS690)Jilin Province Education Department Support Program(No.JJKH20221324KJ)Changchun Science and Technology Development Funds(No.21ZY51).
文摘Deer antlers constitute a unique mammalian model for the study of both organ formation in postnatal life and annual full regeneration.Previous studies revealed that these events are achieved through the proliferation and differentiation of antlerogenic periosteum(AP)cells and pedicle periosteum(PP)cells,respectively.As the cells resident in the AP and the PP possess stem cell attributes,both antler generation and regeneration are stem cell-based processes.However,the cell composition of each tissue type and molecular events underlying antler development remain poorly characterized.Here,we took the approach of single-cell RNA sequencing(scRNA-Seq)and identified eight cell types(mainly THY1^(+)cells,progenitor cells,and osteochondroblasts)and three core subclusters of the THY1^(+)cells(SC2,SC3,and SC4).Endothelial and mural cells each are heterogeneous at transcriptional level.It was the proliferation of progenitor,mural,and endothelial cells in the activated antler-lineage-specific tissues that drove the rapid formation of the antler.We detected the differences in the initial differentiation process between antler generation and regeneration using pseudotime trajectory analysis.These may be due to the difference in the degree of stemness of the AP-THY1+and PP-THY1^(+)cells.We further found that androgen-RXFP2 axis may be involved in triggering initial antler full regeneration.Fully deciphering the cell composition for these antler tissue types will open up new avenues for elucidating the mechanism underlying antler full renewal in specific and regenerative medicine in general.
文摘Traditional silicon-based storage media will soon be unable to meet the exponentially increasing data archiving demands,and efforts must be made to find alternatives.As an ancient and efficient information carrier in living organisms,DNA has been believed to have great potential as a novel storage medium.It holds numerous advantages,such as remarkably high storage density,extremely long durability,and the costefficiency of information replication.
基金This work was supported by grants from the National Natural Science Foundation of China(82002628)Natural Science Foundation of Guangdong Province(2021A1515010096)+3 种基金China Postdoctoral Science Foundation(2019M660227)Chinese Society of Clinical Oncology Foundation(Y-HR2018-319,Y-L2017-002,and Y-JS2019-009)Sun Yat-sen University Basic Research Fund(19ykpy180)the open research funds from the Sixth Affiliated Hospital of Guangzhou Medical University,Qingyuan People’s Hospital(202011-103)。
文摘The preexistence of immune cells in the tumor microenvironment substantiates the efficacy of immunotherapy in cancer patients.Although the complex intratumoral immune heterogeneity has been extensively studied in single cell resolution,hi-res spatial investigations are limited.In this study,we performed a spatial transcriptome analysis of 4 colorectal adenocarcinoma specimens and 2 paired distant normal specimens to identify the molecular pattern involved in a discontinuous inflammatory response in pathologically annotated cancer regions.Based on the location of spatially varied gene expression,we unmasked the spatially-varied immune ecosystem and identified the locoregional“warmed-up”immune response in predefined“cold”tumor with substantial infiltration of immune components.This“warmed-up”immune profile was found to be associated with the in-situ copy number variance and the tissue remodeling process.Further,“warmed-up”signature genes indicated improved overall survival in CRC patients obtained from TCGA database.
