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Article ; Online: Deconstructing transcriptional variations and their effects on immunomodulatory function among human mesenchymal stromal cells.

Sun, Changbin / Zhang, Kehua / Yue, Jianhui / Meng, Shufang / Zhang, Xi

2021 Volume 12, Issue 1, Page(s) 53

Abstract: Background: Mesenchymal stromal cell (MSC)-based therapies are being actively investigated in various inflammatory disorders. However, functional variability among MSCs cultured in vitro will lead to distinct therapeutic efficacies. Until now, the ... ...

Abstract	Background: Mesenchymal stromal cell (MSC)-based therapies are being actively investigated in various inflammatory disorders. However, functional variability among MSCs cultured in vitro will lead to distinct therapeutic efficacies. Until now, the mechanisms behind immunomodulatory functional variability in MSCs are still unclear. Methods: We systemically investigated transcriptomic variations among MSC samples derived from multiple tissues to reveal their effects on immunomodulatory functions of MSCs. We then analyzed transcriptomic changes of MSCs licensed with INFγ to identify potential molecular mechanisms that result in distinct MSC samples with different immunomodulatory potency. Results: MSCs were clustered into distinct groups showing different functional enrichment according to transcriptomic patterns. Differential expression analysis indicated that different groups of MSCs deploy common regulation networks in response to inflammatory stimulation, while expression variation of genes in the networks could lead to different immunosuppressive capability. These different responsive genes also showed high expression variability among unlicensed MSC samples. Finally, a gene panel was derived from these different responsive genes and was able to regroup unlicensed MSCs with different immunosuppressive potencies. Conclusion: This study revealed genes with expression variation that contribute to immunomodulatory functional variability of MSCs and provided us a strategy to identify candidate markers for functional variability assessment of MSCs.
MeSH term(s)	Cell Differentiation ; Cells, Cultured ; Humans ; Immunomodulation ; Mesenchymal Stem Cells ; Signal Transduction
Language	English
Publishing date	2021-01-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2548671-8
ISSN	1757-6512 ; 1757-6512
ISSN (online)	1757-6512
ISSN	1757-6512
DOI	10.1186/s13287-020-02121-8
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Article ; Online: Effects of plant growth regulators and sucrose on proliferation and quality of embryogenic tissue in Picea pungens.

Gao, Fang / Cao, Xi / Qin, Caiyun / Chen, Shigang / Cai, Jufeng / Sun, Changbin / Kong, Lisheng / Tao, Jing

Scientific reports

2023 Volume 13, Issue 1, Page(s) 13194

Abstract: Embryogenic tissue (ET) is important for genetic modification and plant re-generation. The proliferation ability and vigor of ET are crucial for plant propagation via somatic embryogenesis. In this study, ET was induced from mature zygotic embryos in ... ...

Abstract	Embryogenic tissue (ET) is important for genetic modification and plant re-generation. The proliferation ability and vigor of ET are crucial for plant propagation via somatic embryogenesis. In this study, ET was induced from mature zygotic embryos in blue spruce (Picea pungens Engelm.). There were significant differences in ET induction between two provenances, i.e. 78.8 ± 12.5% and 62.50 ± 12.8% respectively. Effects of 2,4-Dichlorophenoxy acetic acid (2,4-D), 6-Benzyl amino-purine (6-BA) and/or sucrose on ET proliferation and somatic embryo (SE) maturation were further investigated with four cell lines. The highest ET proliferation rate reached 1473.7 ± 556.0% biweekly. Concentrations of 2,4-D or 6-BA applied at tissue proliferation stage impacted SE maturation among the cell lines, whereas sucrose showed less effects. The highest rate, 408 ± 230 mature SEs/g FW, was achieved in SE maturation cultures. This research demonstrated that the culture conditions, i.e. the specific concentrations of 2,4-D and BA, at ET proliferation stage affected not only ET growth, but also the quality of ET for SE maturation. This study revealed the necessity and benefit in developing both the general and the genotype-specific protocols for efficient production of mature SEs, or somatic plants in blue spruce.
MeSH term(s)	Plant Growth Regulators/pharmacology ; Plant Growth Regulators/metabolism ; Picea/genetics ; Sucrose/pharmacology ; Sucrose/metabolism ; Cell Proliferation ; 2,4-Dichlorophenoxyacetic Acid/pharmacology ; Seeds ; Plant Somatic Embryogenesis Techniques/methods
Chemical Substances	Plant Growth Regulators ; Sucrose (57-50-1) ; 2,4-Dichlorophenoxyacetic Acid (2577AQ9262)
Language	English
Publishing date	2023-08-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-39389-8
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Article ; Online: DEtail-seq is an ultra-efficient and convenient method for meiotic DNA break profiling in multiple organisms.

Xu, Wei / Liu, Chao / Zhang, Zhe / Sun, Changbin / Li, Qin / Li, Kuan / Jiang, Hui / Li, Wei / Sun, Qianwen

Science China. Life sciences

2023 Volume 66, Issue 6, Page(s) 1392–1407

Abstract: Programmed DNA double-strand break (DSB) formation is a crucial step in meiotic recombination, yet techniques for high-efficiency and precise mapping of the 3' ends of DSBs are still in their infancy. Here, we report a novel technique, named DNA End ... ...

Abstract	Programmed DNA double-strand break (DSB) formation is a crucial step in meiotic recombination, yet techniques for high-efficiency and precise mapping of the 3' ends of DSBs are still in their infancy. Here, we report a novel technique, named DNA End tailing and sequencing (DEtail-seq), which can directly and ultra-efficiently characterize the 3' ends of meiotic DSBs with near single-nucleotide resolution in a variety of species, including yeast, mouse, and human. We find that the 3' ends of meiotic DSBs are stable without significant resection in budding yeast. Meiotic DSBs are strongly enriched in de novo H3K4me3 peaks in the mouse genome at leptotene stage. We also profile meiotic DSBs in human and find DSB hotspots are enriched near the common fragile sites during human meiosis, especially at CCCTC-binding factor (CTCF)-associated enhancers. Therefore, DEtail-seq provides a powerful method to detect DSB ends in various species, and our results provide new insights into the distribution and regulation of meiotic DSB hotspots.
MeSH term(s)	Mice ; Humans ; Animals ; DNA Breaks, Double-Stranded ; Saccharomyces cerevisiae/genetics ; Homologous Recombination ; Saccharomyces cerevisiae Proteins/genetics ; Meiosis/genetics
Chemical Substances	Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2023-01-19
Publishing country	China
Document type	Journal Article
ZDB-ID	2546732-3
ISSN	1869-1889 ; 1674-7305
ISSN (online)	1869-1889
ISSN	1674-7305
DOI	10.1007/s11427-022-2277-y
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Article ; Online: Optimizing Somatic Embryogenesis Initiation, Maturation and Preculturing for Cryopreservation in Picea pungens

Cao, Xi / Gao, Fang / Qin, Caiyun / Chen, Shigang / Cai, Jufeng / Sun, Changbin / Weng, Yuhui / Tao, Jing

Forests. 2022 Dec. 08, v. 13, no. 12

2022

Abstract: Picea pungens (Engelm.), known for its blue-green needles, has become a likable ornamental species in northeast China since 2000. Nonetheless, a lack of propagation methods that can maintain genetic fidelity and develop seedlings at a large scale ... ...

Abstract	Picea pungens (Engelm.), known for its blue-green needles, has become a likable ornamental species in northeast China since 2000. Nonetheless, a lack of propagation methods that can maintain genetic fidelity and develop seedlings at a large scale prevents the further expansion of the species. Somatic embryogenesis (SE), paired with cryopreservation technologies, may provide a valid alternative. Picea pungens SE is not new, but its practical application has been limited due to low efficiencies in SE initiation and maturation as well as a lack of effective cryopreservation technology. In this study, experiments were carried out to overcome the limitations by modifying culture media. For initiation, the efficiency was enhanced by adjusting concentrations of 2.4-dichlorophenoxy acetic acid (2,4-D), 6-benzyl amino–purine (6-BA) or sucrose supplemented to the induction medium. The concentrations of 4.0 mg/L 2,4-D, 2 mg/L 6-BA, and 5 to 10 g/L sucrose were found optimal in maximizing initiation efficiency. For maturation, the efficiency, expressed as the number of mature somatic embryos per gram of fresh mass cultured (E/gFM), varied greatly with the choices of the basal medium and concentration of abscisic acid (ABA) of the maturation medium. Based on our results, the judicial choices were using the DCR medium as the basal medium and 10 mg/L ABA. The maturation efficiency could also be improved by adjusting the maturation medium’s osmotic pressure by manipulating the concentrations of carbohydrate and Gelrite and culture density. While the maturation medium, using sucrose as carbohydrate source or supplemented with a low (<8 g/L) Gelrite concentration, facilitated maturation, optimal selections were truly genotype-dependent. Our results also suggest that, while the optimal culture density varied with genotype, in general it is needless to culture more than 100 mg embryogenesis tissues per dish (size: 10 × 1.5 cm). Based on this study, the optimum pretreatment for embryogenesis tissue cryopreservation was culturing the tissues on the proliferation medium with 0.4 mol/L sorbitol for 24 h, followed by treatment with 5% Dimethyl sulfoxide. This study significantly improved the initiation (achieved a frequency of 0.56) and embryo maturation efficiencies (achieved 1030 E/gFM) and established an effective preculturing protocol for cryopreservation (recovered 1354 E/gFM) for the species. The protocols developed here, paired with the available ones for other SE steps in the literature, form a well-refined SE technology intended for commercial application to Picea pungens.
Keywords	2,4-D ; Picea pungens ; abscisic acid ; acetic acid ; cryopreservation ; culture media ; dimethyl sulfoxide ; genotype ; osmotic pressure ; somatic embryogenesis ; sorbitol ; sucrose ; China
Language	English
Dates of publication	2022-1208
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article ; Online
ZDB-ID	2527081-3
ISSN	1999-4907
ISSN	1999-4907
DOI	10.3390/f13122097
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Article: Advance in the research on super-enhancer.

Sun, Chang-bin / Zhang, Xi

Yi chuan = Hereditas

2016 Volume 38, Issue 12, Page(s) 1056–1068

Abstract: Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive expression of genes controlling cell identity. They play important roles in development, disease initiation and progression such as tumorigenesis. Compared to typical ... ...

Abstract	Super-enhancers (SEs) are large clusters of transcriptional enhancers that drive expression of genes controlling cell identity. They play important roles in development, disease initiation and progression such as tumorigenesis. Compared to typical enhancers (TEs), most key oncogenes in tumor cells are driven by SEs, and common diseases such as Alzheimer's disease related variations are enriched in SEs. SEs hold great promising in key oncogenes identification and diseases-associated variants discovery. In this review, we first summarize how to identify enhancers on a genome-wide scale, and then introduce the concept of SEs and the methodology for SEs identification. Lastly, we describe SEs' main structural and functional properties and discuss its application in the future research.
MeSH term(s)	Animals ; Humans ; Regulatory Sequences, Nucleic Acid/genetics ; Regulatory Sequences, Nucleic Acid/physiology ; Transcription, Genetic/genetics
Language	English
Publishing date	2016--20
Publishing country	China
Document type	Journal Article ; Review
ISSN	0253-9772
ISSN	0253-9772
DOI	10.16288/j.yczz.16-158
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Article: Time-course single-cell RNA sequencing reveals transcriptional dynamics and heterogeneity of limbal stem cells derived from human pluripotent stem cells.

Sun, Changbin / Wang, Hailun / Ma, Qiwang / Chen, Chao / Yue, Jianhui / Li, Bo / Zhang, Xi

Cell & bioscience

2021 Volume 11, Issue 1, Page(s) 24

Abstract: Background: Human pluripotent stem cell-derived limbal stem cells (hPSC-derived LSCs) provide a promising cell source for corneal transplants and ocular surface reconstruction. Although recent efforts in the identification of LSC markers have increased ... ...

Abstract	Background: Human pluripotent stem cell-derived limbal stem cells (hPSC-derived LSCs) provide a promising cell source for corneal transplants and ocular surface reconstruction. Although recent efforts in the identification of LSC markers have increased our understanding of the biology of LSCs, much more remains to be characterized in the developmental origin, cell fate determination, and identity of human LSCs. The lack of knowledge hindered the establishment of efficient differentiation protocols for generating hPSC-derived LSCs and held back their clinical application. Results: Here, we performed a time-course single-cell RNA-seq to investigate transcriptional heterogeneity and expression changes of LSCs derived from human embryonic stem cells (hESCs). Based on current protocol, expression heterogeneity of reported LSC markers were identified in subpopulations of differentiated cells. EMT has been shown to occur during differentiation process, which could possibly result in generation of untargeted cells. Pseudotime trajectory analysis revealed transcriptional changes and signatures of commitment of hESCs-derived LSCs and their progeny-the transit amplifying cells. Conclusion: Single-cell RNA-seq revealed time-course expression changes and significant transcriptional heterogeneity during hESC-derived LSC differentiation in vitro. Our results demonstrated candidate developmental trajectory and several new candidate markers for LSCs, which could facilitate elucidating the identity and developmental origin of human LSCs in vivo.
Language	English
Publishing date	2021-01-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2593367-X
ISSN	2045-3701
ISSN	2045-3701
DOI	10.1186/s13578-021-00541-4
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Article: Cobalt sulfides constructed heterogeneous interfaces decorated on N,S-codoped carbon nanosheets as a highly efficient bifunctional oxygen electrocatalyst

Sun, Changbin / Ding, Jia / Wang, Haozhi / Liu, Jie / Han, Xiaopeng / Deng, Yida / Zhong, Cheng / Hu, Wenbin

Journal of materials chemistry A. 2021 June 22, v. 9, no. 24

2021

Abstract: The rational design and controllable synthesis of excellent bifunctional oxygen reduction and evolution reaction (ORR/OER) electrocatalysts are of vital importance for zinc–air battery applications. Herein, we report nitrogen/sulfur-codoped carbon ... ...

Abstract	The rational design and controllable synthesis of excellent bifunctional oxygen reduction and evolution reaction (ORR/OER) electrocatalysts are of vital importance for zinc–air battery applications. Herein, we report nitrogen/sulfur-codoped carbon nanosheets (NSC) decorated with dense Co₉S₈/Co₁₋ₓS heterostructures (Co₉S₈/Co₁₋ₓS@NSC), prepared by a one-pot salt template-assisted pyrolysis procedure. The population of the Co₉S₈/Co₁₋ₓS heterostructure can be effectively controlled by tuning the precursor components. Salt templates constructed hierarchical porosity for the wide-open carbon nanosheets, which maximized the N functional groups to anchor highly dispersive Co₉S₈/Co₁₋ₓS species. Experiments and theoretical simulations revealed notable electronic interactions within Co₉S₈/Co₁₋ₓS interfaces, which can effectively optimize the adsorption/desorption behaviors of intermediates in ORR/OER, thus promoting the bifunctional electrocatalytic performance. The half-wave potential for the ORR of 0.86 V and the OER electrocatalytic potential of 1.52 V at 10 mA cm⁻² were obtained. Benefiting from the strong coupling effect between the Co₉S₈/Co₁₋ₓS species and the carbon substrate, superior durability was obtained for 2000 ORR/OER cycles. The practical zinc–air battery based on the Co₉S₈/Co₁₋ₓS@NSC cathode manifested a high open-circuit voltage, small voltage gap and robust reversibility. Our study revealed the great potential of the bi-elemental (Co and S) heterostructure in enhancing the ORR/OER activity, which suggests a logical extension to other electrocatalysis systems.
Keywords	adsorption ; batteries ; carbon ; cathodes ; cobalt ; desorption ; durability ; electric potential difference ; nanosheets ; oxygen ; porosity ; pyrolysis
Language	English
Dates of publication	2021-0622
Size	p. 13926-13935.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	2702232-8
ISSN	2050-7496 ; 2050-7488
ISSN (online)	2050-7496
ISSN	2050-7488
DOI	10.1039/d1ta02330f
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Article: Graphitic Carbon Nitride Doped Copper-Manganese Alloy as High-Performance Electrode Material in Supercapacitor for Energy Storage.

Siwal, Samarjeet Singh / Zhang, Qibo / Sun, Changbin / Thakur, Vijay Kumar

Nanomaterials (Basel, Switzerland)

2019 Volume 10, Issue 1

Abstract: Here, we report the synthesis of copper-manganese alloy ( ... ...

Abstract	Here, we report the synthesis of copper-manganese alloy (CuMnO
Language	English
Publishing date	2019-12-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano10010002
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Article ; Online: Single-cell RNA-seq highlights heterogeneity in human primary Wharton's jelly mesenchymal stem/stromal cells cultured in vitro.

Sun, Changbin / Wang, Lei / Wang, Hailun / Huang, Tingrun / Yao, Wenwen / Li, Jing / Zhang, Xi

Stem cell research & therapy

2020 Volume 11, Issue 1, Page(s) 149

Abstract: Background: Mesenchymal stem/stromal cells (MSCs) are multipotent cells with a promising application potential in regenerative medicine and immunomodulation. However, MSCs cultured in vitro exhibit functional heterogeneity. The underlying molecular ... ...

Abstract	Background: Mesenchymal stem/stromal cells (MSCs) are multipotent cells with a promising application potential in regenerative medicine and immunomodulation. However, MSCs cultured in vitro exhibit functional heterogeneity. The underlying molecular mechanisms that define MSC heterogeneity remain unclear. Methods: We investigated the gene expression profile via single-cell RNA sequencing (scRNA-seq) of human primary Wharton's jelly-derived MSCs (WJMSCs) cultured in vitro from three donors. We also isolated CD142 Results: GO enrichment analysis of highly variable genes (HVGs) obtained from WJMSCs revealed that these genes are significantly enriched in extracellular region with binding function, involved in developmental process, signal transduction, cell proliferation, etc. Pathway analysis showed that these HVGs are associated with functional characteristics of classic MSCs, such as inflammation mediated by chemokine and cytokine signaling, integrin signaling, and angiogenesis. After regressing out the batch and cell cycle effects, these HVGs were used for dimension reduction and clustering analysis to identify candidate subpopulations. Differentially expressed gene analysis revealed the existence of several distinct subpopulations of MSCs that exhibit diverse functional characteristics related to proliferation, development, and inflammation response. In line with our data, sorted CD142 Conclusion: HVGs identified in MSCs are associated with classic MSC function. Regarding therapeutic potential, these genes are associated with functional characteristics, on which the MSC clinical application were theoretically based, such as development and inflammation response. Altogether, these HVGs hold the potential to be used as candidate markers for further potency association studies.
MeSH term(s)	Cell Differentiation ; Cell Proliferation/genetics ; Cells, Cultured ; Humans ; Mesenchymal Stem Cells ; RNA-Seq ; Umbilical Cord ; Wharton Jelly
Language	English
Publishing date	2020-04-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2548671-8
ISSN	1757-6512 ; 1757-6512
ISSN (online)	1757-6512
ISSN	1757-6512
DOI	10.1186/s13287-020-01660-4
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Article ; Online: Somatic embryogenesis in mature zygotic embryos of Picea pungens.

Tao, Jing / Chen, Shigang / Qin, Caiyun / Li, Qingmei / Cai, Jufeng / Sun, Changbin / Wang, Weiming / Weng, Yuhui

Scientific reports

2021 Volume 11, Issue 1, Page(s) 19072

Abstract: This study developed somatic embryogenesis protocols for Picea pungens (Engelm), an important ornamental species, including initiation, proliferation, maturation, germination, and acclimation. Somatic embryogenic tissues were induced from mature zygotic ... ...

Abstract	This study developed somatic embryogenesis protocols for Picea pungens (Engelm), an important ornamental species, including initiation, proliferation, maturation, germination, and acclimation. Somatic embryogenic tissues were induced from mature zygotic embryos of five families, with a frequency of [Formula: see text] 22% for each. Embryogenic tissues (ET) from 13 clones of three families were proliferated for one week, achieving an average rate of 179.1%. The ET of 38 clones of three families were cultured in maturation medium for six weeks; 188 mature embryos on average were counted per gram ET cultured, of which [Formula: see text] 81.1% appeared normal, and each clone developed at least 28 normally matured embryos. A total of 69.9% or more of cotyledonary somatic embryos germinated normally and developed into normal emblings. The experiment of transplanting the emblings into a greenhouse had an average survival rate of 68.5%. Considerable variation among and within families during initiation and proliferation was observed, but this variation decreased in the maturation and germination. Changing the concentration of plant growth regulator of the initiation medium did not significantly change the initiation frequency. We recommend incorporating these protocols into the current Picea pungens practical programs, although further research is essential to increase efficiencies and reduce cost.
MeSH term(s)	Germination ; Picea/embryology ; Picea/physiology ; Seeds/growth & development
Language	English
Publishing date	2021-09-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-98511-w
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