DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, t...DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing （BS-seq） data. With that, we optimized a computational pipeline for estimating the heterogeneity in DNA methylation from bulk BS-seq data. We further built HeteroMeth, a database for searching, browsing, visualizing, and downloading the data for heterogeneity in DNA methylation for a total of 141 samples in humans, mice, Arabidopsis, and rice. Three genes are used as examples to illustrate the power of HeteroMeth in the identification of unique features in DNA methylation. The optimization of the computational strategy and the construction of the database in this study complement the recent experimental attempts on single-cell DNA methylomes and will facilitate the understanding of epigenetic mechanisms underlying cell differentiation and embryonic development. HeteroMeth is publicly available at http：//qianlab.genetics.ac.cn/HeteroMeth.展开更多
Two-photon excitation fluorescence microscopy(TPM),owing to its capacity for subcellular resolution,intrinsic optical sectioning,and superior penetration depth in turbid samples,has revolutionized biomedical research....Two-photon excitation fluorescence microscopy(TPM),owing to its capacity for subcellular resolution,intrinsic optical sectioning,and superior penetration depth in turbid samples,has revolutionized biomedical research.However,its layer-by-layer scanning to form a three-dimensional image inherently limits the volumetric imaging speed and increases phototoxicity significantly.In this study,we develop a gradient excitation technique to accelerate TPM volumetric imaging.The axial positions of the fluorophores can be decoded from the intensity ratio of the paired images obtained by sequentially exciting the specimen with two axially elongated two-photon beams of complementary gradient intensities.We achieved a 0.63μm axial localization precision and demonstrate the flexibility of the gradient TPM on various sparsely labeled samples,including bead phantoms,mouse brain tissues,and live macrophages.Compared with traditional TPM,our technique improves volumetric imaging speed(by at least sixfold),decreases photobleaching(i.e.,less than 2.07±2.89%in 25 min),and minimizes photodamages.展开更多
Allergen immunotherapy is executed by the repeated administration of specific allergens to patients with allergic disorders to protect against allergic reactions.It is the only disease-modifying therapy for allergic r...Allergen immunotherapy is executed by the repeated administration of specific allergens to patients with allergic disorders to protect against allergic reactions.It is the only disease-modifying therapy for allergic rhinitis and asthma,and many clinical trials and meta-analyses have demonstrated its beneficial effects.[1]Immunologic changes associated with immunotherapy are complicated,and the underlying mechanism needs further elucidation.Cluster immunotherapy is an improved immunotherapy with an accelerated build-up schedule that achieves symprom improvement earlier than the conventional way.展开更多
Background： The shortage of available organs for transplantation is the major obstacle hindering the application of regenerative medicine, and has also become the desperate problem faced by more and more patients now...Background： The shortage of available organs for transplantation is the major obstacle hindering the application of regenerative medicine, and has also become the desperate problem faced by more and more patients nowadays. The recent development and application of 3D printing technique in biological research （bioprinting） has revolutionized the tissue engineering methods, and become a promising solution for tissue regeneration. Results： In this review, we summarize the current application of bioprinting in producing tissues and organoids, and discuss the future directions and challenges of 3D bioprinting. Conclusions： Currently, 3D bioprinting is capable to generate patient-specialized bone, cartilage, blood vascular network, hepatic unit and other simple components/tissues, yet pure cell-based functional organs are still desired.展开更多
Coronaviruses,members of the family Coronaviridae and sub-family Coronavirinae,are enveloped positive-strand RNA viruses which have spikes of glycoproteins projecting from their viral envelopes,thus exhibit a corona o...Coronaviruses,members of the family Coronaviridae and sub-family Coronavirinae,are enveloped positive-strand RNA viruses which have spikes of glycoproteins projecting from their viral envelopes,thus exhibit a corona or halo-like appearance(Masters and Perlman,2013;Cui et al..2019).Coronaviruses are the causal path-ogens for a wide spectrum of respiratory and gastrointestinal diseases in both wild and domestic animals,including birds,pigs,rodents,etc(Dhama et al,2014).Previous studies have found that six strains of coronaviruses are capable to infect humans,including four strains circulating yearly to cause common cold,and other two strains which are the source for severe acute respiratory syndrome(SARS)and Middle East respiratory syndrome(MERS-CoV),respectively(Dhama et al,2014;Cui et al..2019).展开更多
Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasio...Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica （93-11 ） and japonica （Nipponbare） inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By con- trast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-of- origin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9acJH3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells.展开更多
基金supported by the Strategic Priority Research Program of Chinese Academy of Sciences, China awarded to WQ (Grant No. XDA08020303)
文摘DNA methylation is an important epigenetic mark that plays a vital role in gene expression and cell differentiation. The average DNA methylation level among a group of cells has been extensively documented. However, the cell-to-cell heterogeneity in DNA methylation, which reflects the differentiation of epigenetic status among cells, remains less investigated. Here we established a gold standard of the cell-to-cell heterogeneity in DNA methylation based on single-cell bisulfite sequencing （BS-seq） data. With that, we optimized a computational pipeline for estimating the heterogeneity in DNA methylation from bulk BS-seq data. We further built HeteroMeth, a database for searching, browsing, visualizing, and downloading the data for heterogeneity in DNA methylation for a total of 141 samples in humans, mice, Arabidopsis, and rice. Three genes are used as examples to illustrate the power of HeteroMeth in the identification of unique features in DNA methylation. The optimization of the computational strategy and the construction of the database in this study complement the recent experimental attempts on single-cell DNA methylomes and will facilitate the understanding of epigenetic mechanisms underlying cell differentiation and embryonic development. HeteroMeth is publicly available at http：//qianlab.genetics.ac.cn/HeteroMeth.
基金National Key Research and Development Program of China(2017YFC0110200)National Natural Science Foundation of China(81822023,81927803,91959121,92159104,82071972)+2 种基金Natural Science Foundation of Guangdong Province(2019A1515011746,2020B121201010)Scientific Instrument Innovation Team of Chinese Academy of Sciences(GJJSTD20180002)Shenzhen Basic Research Program(QCYJ20180507182432303,RCJC20200714114433058,ZDSY20130401165820357).
文摘Two-photon excitation fluorescence microscopy(TPM),owing to its capacity for subcellular resolution,intrinsic optical sectioning,and superior penetration depth in turbid samples,has revolutionized biomedical research.However,its layer-by-layer scanning to form a three-dimensional image inherently limits the volumetric imaging speed and increases phototoxicity significantly.In this study,we develop a gradient excitation technique to accelerate TPM volumetric imaging.The axial positions of the fluorophores can be decoded from the intensity ratio of the paired images obtained by sequentially exciting the specimen with two axially elongated two-photon beams of complementary gradient intensities.We achieved a 0.63μm axial localization precision and demonstrate the flexibility of the gradient TPM on various sparsely labeled samples,including bead phantoms,mouse brain tissues,and live macrophages.Compared with traditional TPM,our technique improves volumetric imaging speed(by at least sixfold),decreases photobleaching(i.e.,less than 2.07±2.89%in 25 min),and minimizes photodamages.
基金This work was supported by a grant of Natural Science Foundation of Beijing Municipality(No.7172179).
文摘Allergen immunotherapy is executed by the repeated administration of specific allergens to patients with allergic disorders to protect against allergic reactions.It is the only disease-modifying therapy for allergic rhinitis and asthma,and many clinical trials and meta-analyses have demonstrated its beneficial effects.[1]Immunologic changes associated with immunotherapy are complicated,and the underlying mechanism needs further elucidation.Cluster immunotherapy is an improved immunotherapy with an accelerated build-up schedule that achieves symprom improvement earlier than the conventional way.
文摘Background： The shortage of available organs for transplantation is the major obstacle hindering the application of regenerative medicine, and has also become the desperate problem faced by more and more patients nowadays. The recent development and application of 3D printing technique in biological research （bioprinting） has revolutionized the tissue engineering methods, and become a promising solution for tissue regeneration. Results： In this review, we summarize the current application of bioprinting in producing tissues and organoids, and discuss the future directions and challenges of 3D bioprinting. Conclusions： Currently, 3D bioprinting is capable to generate patient-specialized bone, cartilage, blood vascular network, hepatic unit and other simple components/tissues, yet pure cell-based functional organs are still desired.
基金This work is supported by grants from CAS Advance Research Programs(QYZDJ-SSW-SMC015)National Natural Science Foundation of China(91940304 and 81790622)to X.-J.W.
文摘Coronaviruses,members of the family Coronaviridae and sub-family Coronavirinae,are enveloped positive-strand RNA viruses which have spikes of glycoproteins projecting from their viral envelopes,thus exhibit a corona or halo-like appearance(Masters and Perlman,2013;Cui et al..2019).Coronaviruses are the causal path-ogens for a wide spectrum of respiratory and gastrointestinal diseases in both wild and domestic animals,including birds,pigs,rodents,etc(Dhama et al,2014).Previous studies have found that six strains of coronaviruses are capable to infect humans,including four strains circulating yearly to cause common cold,and other two strains which are the source for severe acute respiratory syndrome(SARS)and Middle East respiratory syndrome(MERS-CoV),respectively(Dhama et al,2014;Cui et al..2019).
基金supported by the National Basic Research Program of China (2014CB943500)the National Program for Support of Top-Notch Young Professionals+1 种基金the Recruitment Program of Global Youth Expertsthe State Key Laboratory of Plant Genomics (SKLPG2011B0103 and SKLPG2016C0219-01)
文摘Monoallelic gene expression refers to the phenomenon that all transcripts of a gene in a cell are expressed from only one of the two alleles in a diploid organism. Although monoallelic gene expression has been occasionally reported with bulk transcriptome analysis in plants, how prevalent it is in individual plant cells remains unknown. Here, we developed a single-cell RNA-seq protocol in rice and investigated allelic expression patterns in mesophyll cells of indica （93-11 ） and japonica （Nipponbare） inbred lines, as well as their F1 reciprocal hybrids. We observed pervasive monoallelic gene expression in individual mesophyll cells, which could be largely explained by stochastic and independent transcription of two alleles. By con- trast, two mechanisms that were proposed previously based on bulk transcriptome analyses, parent-of- origin effects and allelic repression, were not well supported by our data. Furthermore, monoallelically expressed genes exhibited a number of characteristics, such as lower expression levels, narrower H3K4me3/H3K9acJH3K27me3 peaks, and larger expression divergences between 93-11 and Nipponbare. Taken together, the development of a single-cell RNA-seq protocol in this study offers us an excellent opportunity to investigate the origins and prevalence of monoallelic gene expression in plant cells.
