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Article ; Online: Chromatin region binning of gene expression for improving embryo cell subtype identification.

Liang, Pengfei / Li, Hanshuang / Long, Chunshen / Liu, Mingzhu / Zhou, Jian / Zuo, Yongchun

2024 Volume 170, Page(s) 108049

Abstract: Mammalian embryonic development is a complex process, characterized by intricate spatiotemporal dynamics and distinct chromatin preferences. However, the quick diversification in early embryogenesis leads to significant cellular diversity and the ... ...

Abstract	Mammalian embryonic development is a complex process, characterized by intricate spatiotemporal dynamics and distinct chromatin preferences. However, the quick diversification in early embryogenesis leads to significant cellular diversity and the sparsity of scRNA-seq data, posing challenges in accurately determining cell fate decisions. In this study, we introduce a chromatin region binning method using scChrBin, designed to identify chromatin regions that elucidate the dynamics of embryonic development and lineage differentiation. This method transforms scRNA-seq data into a chromatin-based matrix, leveraging genomic annotations. Our results showed that the scChrBin method achieves high accuracy, with 98.0% and 89.2% on two single-cell embryonic datasets, demonstrating its effectiveness in analyzing complex developmental processes. We also systematically and comprehensively analysis of these key chromatin binning regions and their associated genes, focusing on their roles in lineage and stage development. The perspective of chromatin region binning method enables a comprehensive analysis of transcriptome data at the chromatin level, allowing us to unveil the dynamic expression of chromatin regions across temporal and spatial development. The tool is available as an application at https://github.com/liameihao/scChrBin.
MeSH term(s)	Animals ; Female ; Pregnancy ; Chromatin/genetics ; Embryonic Development/genetics ; Cell Differentiation/genetics ; Transcriptome ; Genome ; Gene Expression Profiling ; Sequence Analysis, RNA ; Mammals/genetics
Chemical Substances	Chromatin
Language	English
Publishing date	2024-01-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2024.108049
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Article ; Online: Characterizing Cellular Differentiation Potency and Waddington Landscape via Energy Indicator.

Li, Hanshuang / Long, Chunshen / Hong, Yan / Luo, Liaofu / Zuo, Yongchun

Research (Washington, D.C.)

2023 Volume 6, Page(s) 118

Abstract: The precise characterization of cellular differentiation potency remains an open question, which is fundamentally important for deciphering the dynamics mechanism related to cell fate transition. We quantitatively evaluated the differentiation potency of ...

Abstract	The precise characterization of cellular differentiation potency remains an open question, which is fundamentally important for deciphering the dynamics mechanism related to cell fate transition. We quantitatively evaluated the differentiation potency of different stem cells based on the Hopfield neural network (HNN). The results emphasized that cellular differentiation potency can be approximated by Hopfield energy values. We then profiled the Waddington energy landscape of embryogenesis and cell reprogramming processes. The energy landscape at single-cell resolution further confirmed that cell fate decision is progressively specified in a continuous process. Moreover, the transition of cells from one steady state to another in embryogenesis and cell reprogramming processes was dynamically simulated on the energy ladder. These two processes can be metaphorized as the motion of descending and ascending ladders, respectively. We further deciphered the dynamics of the gene regulatory network (GRN) for driving cell fate transition. Our study proposes a new energy indicator to quantitatively characterize cellular differentiation potency without prior knowledge, facilitating the further exploration of the potential mechanism of cellular plasticity.
Language	English
Publishing date	2023-04-11
Publishing country	United States
Document type	Journal Article
ISSN	2639-5274
ISSN (online)	2639-5274
DOI	10.34133/research.0118
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Article ; Online: Design of a Prism-Grating Wide Spectral Range Transmittance Imaging Spectrometer.

Zhang, Xu / Li, Bo / Jiang, Xue / Gu, Guochao / Li, Hanshuang / Wang, Xiaoxu / Lin, Guanyu

Sensors (Basel, Switzerland)

2023 Volume 23, Issue 11

Abstract: As spectroscopic detection technology rapidly advances, back-illuminated InGaAs detectors with a wider spectral range have emerged. Compared to traditional detectors such as HgCdTe, CCD, and CMOS, InGaAs detectors offer a working range of 400-1800 nm and ...

Abstract	As spectroscopic detection technology rapidly advances, back-illuminated InGaAs detectors with a wider spectral range have emerged. Compared to traditional detectors such as HgCdTe, CCD, and CMOS, InGaAs detectors offer a working range of 400-1800 nm and exhibit a quantum efficiency of over 60% in both the visible and near-infrared bands. This is leading to the demand for innovative designs of imaging spectrometers with wider spectral ranges. However, the widening of the spectral range has led to the presence of significant axial chromatic aberration and secondary spectrum in imaging spectrometers. Additionally, there is difficulty in aligning the system optical axis perpendicular to the detector image plane, resulting in increased challenges during post-installation adjustment. Based on chromatic aberration correction theory, this paper presents the design of a wide spectral range transmission prism-grating imaging spectrometer with a working range of 400-1750 nm using Code V. The spectral range of this spectrometer covers both the visible and near-infrared regions, which is beyond the capability of traditional PG spectrometers. In the past, the working spectral range of transmission-type PG imaging spectrometers has been limited to 400-1000 nm. This study's proposed chromatic aberration correction process involves selecting optical glass materials that match the design requirements and correcting the axial chromatic aberration and secondary spectrum, ensuring that the system axis is perpendicular to the detector plane and easy to adjust during installation. The results show that the spectrometer has a spectral resolution of 5 nm, a root-mean-square spot diagram less than 8 μm over the full field of view, and an optical transfer function MTF greater than 0.6 at a Nyquist frequency of 30 lp/mm. The system size is less than 90 mm. Spherical lenses are employed in the system design to reduce manufacturing costs and complexity while meeting the requirements of wide spectral range, miniaturization, and easy installation.
MeSH term(s)	Diagnostic Imaging ; Commerce ; Fabaceae ; Glass ; Lenses
Language	English
Publishing date	2023-05-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s23115050
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Article ; Online: Identification of Key lncRNAs Associated with Immune Infiltration and Prognosis in Gastric Cancer.

Jin, Wen / Jia, Jianchao / Si, Yangming / Liu, Jianli / Li, Hanshuang / Zhu, Hao / Wu, Zhouying / Zuo, Yongchun / Yu, Lan

Biochemical genetics

2024

Abstract: Long non-coding RNAs (lncRNAs), as promising novel biomarkers for cancer treatment and prognosis, can function as tumor suppressors and oncogenes in the occurrence and development of many types of cancer, including gastric cancer (GC). However, little is ...

Abstract	Long non-coding RNAs (lncRNAs), as promising novel biomarkers for cancer treatment and prognosis, can function as tumor suppressors and oncogenes in the occurrence and development of many types of cancer, including gastric cancer (GC). However, little is known about the complex regulatory system of lncRNAs in GC. In this study, we systematically analyzed lncRNA and miRNA transcriptomic profiles of GC based on bioinformatics methods and experimental validation. An lncRNA-miRNA interaction network related to GC was constructed, and the nine crucial lncRNAs were identified. These 9 lncRNAs were found to be associated with the prognosis of GC patients by Cox proportional hazards regression analysis. Among them, the expression of lncRNA SNHG14 can affect the survival of GC patients as a potential prognostic marker. Moreover, it was shown that SNHG14 was involved in immune-related pathways and significantly correlated with immune cell infiltration in GC. Meanwhile, we found that SNHG14 affected immune function in many cancers, such as breast cancer and esophageal carcinoma. Such information revealed that SNHG14 may serve as a potential target for cancer immunotherapy. As well, our study could provide practical and theoretical guiding significance for clinical application of non-coding RNAs.
Language	English
Publishing date	2024-04-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2168-4
ISSN	1573-4927 ; 0006-2928
ISSN (online)	1573-4927
ISSN	0006-2928
DOI	10.1007/s10528-024-10801-w
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Article: Characterization of DNA Methylation Patterns and Mining of Epigenetic Markers During Genomic Reprogramming in SCNT Embryos.

Cao, Pengbo / Li, Hanshuang / Zuo, Yongchun / Nashun, Buhe

Frontiers in cell and developmental biology

2020 Volume 8, Page(s) 570107

Abstract: Somatic cell nuclear transfer (SCNT), also known as somatic cell cloning, is a commonly used technique to study epigenetic reprogramming. Although SCNT has the advantages of being safe and able to obtain pluripotent cells, early developmental arrest ... ...

Abstract	Somatic cell nuclear transfer (SCNT), also known as somatic cell cloning, is a commonly used technique to study epigenetic reprogramming. Although SCNT has the advantages of being safe and able to obtain pluripotent cells, early developmental arrest happens in most SCNT embryos. Overcoming epigenetic barriers is currently the primary strategy for improving reprogramming efficiency and improving developmental rate in SCNT embryos. In this study, we analyzed DNA methylation profiles of
Language	English
Publishing date	2020-09-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2737824-X
ISSN	2296-634X
ISSN	2296-634X
DOI	10.3389/fcell.2020.570107
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Article ; Online: Nuclear Transfer Arrest Embryos Show Massive Dysregulation of Genes Involved in Transcription Pathways.

Long, Chunshen / Li, Hanshuang / Li, Xinru / Yang, Wuritu / Zuo, Yongchun

International journal of molecular sciences

2021 Volume 22, Issue 15

Abstract: Somatic cell nuclear transfer (SCNT) technology can reprogram terminally differentiated cell nuclei into a totipotent state. However, the underlying molecular barriers of SCNT embryo development remain incompletely elucidated. Here, we observed that ... ...

Abstract	Somatic cell nuclear transfer (SCNT) technology can reprogram terminally differentiated cell nuclei into a totipotent state. However, the underlying molecular barriers of SCNT embryo development remain incompletely elucidated. Here, we observed that transcription-related pathways were incompletely activated in nuclear transfer arrest (NTA) embryos compared to normal SCNT embryos and in vivo fertilized (WT) embryos, which hinders the development of SCNT embryos. We further revealed the transcription pathway associated gene regulatory networks (GRNs) and found the aberrant transcription pathways can lead to the massive dysregulation of genes in NTA embryos. The predicted target genes of transcription pathways contain a series of crucial factors in WT embryos, which play an important role in catabolic process, pluripotency regulation, epigenetic modification and signal transduction. In NTA embryos, however, these genes were varying degrees of inhibition and show a defect in synergy. Overall, our research found that the incomplete activation of transcription pathways is another potential molecular barrier for SCNT embryos besides the incomplete reprogramming of epigenetic modifications, broadening the understanding of molecular mechanism of SCNT embryonic development.
MeSH term(s)	Animals ; Blastocyst/metabolism ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Mice ; Nuclear Transfer Techniques/adverse effects ; RNA-Seq ; Single-Cell Analysis ; Transcription, Genetic ; Transcriptome
Language	English
Publishing date	2021-07-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22158187
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Article ; Online: The Cumulative Formation of R-loop Interacts with Histone Modifications to Shape Cell Reprogramming.

Li, Hanshuang / Long, Chunshen / Hong, Yan / Chao, Lemuge / Peng, Yong / Zuo, Yongchun

International journal of molecular sciences

2022 Volume 23, Issue 3

Abstract: R-loop, a three-stranded RNA/DNA structure, plays important roles in modulating genome stability and gene expression, but the molecular mechanism of R-loops in cell reprogramming remains elusive. Here, we comprehensively profiled the genome-wide ... ...

Abstract	R-loop, a three-stranded RNA/DNA structure, plays important roles in modulating genome stability and gene expression, but the molecular mechanism of R-loops in cell reprogramming remains elusive. Here, we comprehensively profiled the genome-wide landscape of R-loops during cell reprogramming. The results showed that the R-loop formation on most different types of repetitive elements is stage-specific in cell reprogramming. We unveiled that the cumulative deposition of an R-loop subset is positively correlated with gene expression during reprogramming. More importantly, the dynamic turnover of this R-loop subset is accompanied by the activation of the pluripotent transcriptional regulatory network (TRN). Moreover, the large accumulation of the active histone marker H3K4me3 and the reduction in H3K27me3 were also observed in these R-loop regions. Finally, we characterized the dynamic network of R-loops that facilitates cell fate transitions in reprogramming. Together, our study provides a new clue for deciphering the interplay mechanism between R-loops and HMs to control cell reprogramming.
MeSH term(s)	Animals ; Cellular Reprogramming/genetics ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Genome ; Histone Code/genetics ; Mice ; Pluripotent Stem Cells/metabolism ; R-Loop Structures/genetics
Language	English
Publishing date	2022-01-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms23031567
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Article ; Online: Competitive binding of TET1 and DNMT3A/B cooperates the DNA methylation pattern in human embryonic stem cells.

Chao, Lemuge / Yang, Siqi / Li, Hanshuang / Long, Chunshen / Xi, Qilemuge / Zuo, Yongchun

Biochimica et biophysica acta. Gene regulatory mechanisms

2022 Volume 1865, Issue 7, Page(s) 194861

Abstract: DNMT3A/B and TET1 play indispensable roles in regulating DNA methylation that undergoes extensive reprogramming during mammalian embryogenesis. Yet the competitive and cooperative relationships between TET1 and DNMT3A/B remain largely unknown in the ... ...

Abstract	DNMT3A/B and TET1 play indispensable roles in regulating DNA methylation that undergoes extensive reprogramming during mammalian embryogenesis. Yet the competitive and cooperative relationships between TET1 and DNMT3A/B remain largely unknown in the human embryonic stem cells. Here, we revealed that the main DNA-binding domain of TET1 contains more positive charges by using charge reduction of amino acid alphabet, followed by DNMT3A and DNMT3B. The genome-wide binding profiles showed that TET1 prefers binding to the proximal promoters and CpG islands compared with DNMT3A/B. Moreover, the binding regions of these three transcription factors can be divided into specific and co-binding regions. And a stronger inhibitory effect of DNMT3A on TET1 demethylation was observed in co-binding regions. Furthermore, we integrated TET1 knockout data to further discuss the competitive binding patterns of TET1 and DNMT3A/B. The lack of TET1 increased the occupation of DNMT3A/B at the specific binding regions of TET1 causing focal hypermethylation. The knockout of TET1 was also accompanied by a reduction of DNMT3A/B binding in the co-binding regions, further confirming the cooperative binding function between TET1 and DNMT3A/B. In conclusion, our studies found that the competitive binding of TET1 and DNMT3A/B cooperatively shapes the global DNA methylation pattern in human embryonic stem cells.
MeSH term(s)	Amino Acids/metabolism ; Binding, Competitive ; DNA/metabolism ; DNA (Cytosine-5-)-Methyltransferases/genetics ; DNA (Cytosine-5-)-Methyltransferases/metabolism ; DNA Methylation ; DNA Methyltransferase 3A/genetics ; DNA Methyltransferase 3A/metabolism ; Human Embryonic Stem Cells/metabolism ; Humans ; Mixed Function Oxygenases/genetics ; Mixed Function Oxygenases/metabolism ; Proto-Oncogene Proteins/genetics ; Proto-Oncogene Proteins/metabolism ; Transcription Factors/metabolism ; DNA Methyltransferase 3B
Chemical Substances	Amino Acids ; DNMT3A protein, human ; Proto-Oncogene Proteins ; Transcription Factors ; DNA (9007-49-2) ; Mixed Function Oxygenases (EC 1.-) ; TET1 protein, human (EC 1.-) ; DNA (Cytosine-5-)-Methyltransferases (EC 2.1.1.37) ; DNA Methyltransferase 3A (EC 2.1.1.37)
Language	English
Publishing date	2022-08-20
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2918786-2
ISSN	1876-4320 ; 1874-9399
ISSN (online)	1876-4320
ISSN	1874-9399
DOI	10.1016/j.bbagrm.2022.194861
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Article: Deciphering the decisive factors driving fate bifurcations in somatic cell reprogramming.

Long, Chunshen / Li, Hanshuang / Liang, Pengfei / Chao, Lemuge / Hong, Yan / Zhang, Junping / Xi, Qilemuge / Zuo, Yongchun

Molecular therapy. Nucleic acids

2023 Volume 34, Page(s) 102044

Abstract: Single-cell studies have demonstrated that somatic cell reprogramming is a continuous process of cell fates transition. Only partial reprogramming intermediates can overcome the molecular bottlenecks to acquire pluripotency. To decipher the underlying ... ...

Abstract	Single-cell studies have demonstrated that somatic cell reprogramming is a continuous process of cell fates transition. Only partial reprogramming intermediates can overcome the molecular bottlenecks to acquire pluripotency. To decipher the underlying decisive factors driving cell fate, we identified induced pluripotent stem cells or stromal-like cells (iPSCs/SLCs) and iPSCs or trophoblast-like cells (iPSCs/TLCs) fate bifurcations by reconstructing cellular trajectory. The mesenchymal-epithelial transition and the activation of pluripotency networks are the main molecular series in successful reprogramming. Correspondingly, intermediates diverge into SLCs accompanied by the inhibition of cell cycle genes and the activation of extracellular matrix genes, whereas the TLCs fate is characterized by the up-regulation of placenta development genes. Combining putative gene regulatory networks, seven (
Language	English
Publishing date	2023-10-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	2662631-7
ISSN	2162-2531
ISSN	2162-2531
DOI	10.1016/j.omtn.2023.102044
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Article ; Online: Design method for a small F-number two-material uniform dispersion immersion grating imaging spectrometer.

Liu, Yang / Li, Jinhuan / Zhang, Pengfei / Zhou, Aiming / Wang, Xiaoxu / Wang, Junbo / Li, Bo / Lin, Guanyu / Gu, Guochao / Li, Hanshuang

Optics express

2023 Volume 31, Issue 21, Page(s) 35054–35067

Abstract: Immersion gratings have high dispersion efficiency and have important application value in miniaturized imaging spectrometers, but its serious dispersion nonlinearity causes difficulties in calibration and image processing, which limits its application ... ...

Abstract	Immersion gratings have high dispersion efficiency and have important application value in miniaturized imaging spectrometers, but its serious dispersion nonlinearity causes difficulties in calibration and image processing, which limits its application range. To solve this, this paper presents a design method for a two-material linear dispersion immersion grating device design method, and a compact small F-number immersion grating spectrometer based on it. First the vector form dispersion equation of the two-material immersion grating is derived and the linear spectral dispersion immersion grating design process is given, then a compact small F-number uniform dispersion imaging spectrometer is given as a design example using the proposed method. The results show that when the operating band of the system is 1590-1675 nm, the spectral resolution is better than 0.25 nm, and F-number can achieve better than 2. Compared with traditional single-material immersion grating imaging spectrometer, the designed imaging spectrometer dispersion linearity is significantly improved. Finally, the influence of prism materials, structure parameters and grating parameters on dispersion nonlinearity is analyzed. Design and analysis results show that the proposed two-material immersion grating device has much better spectral dispersion nonlinearity correction ability, and its design method can provide reference to the compact spectrometer design based on immersion gratings.
Language	English
Publishing date	2023-10-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	1491859-6
ISSN	1094-4087 ; 1094-4087
ISSN (online)	1094-4087
ISSN	1094-4087
DOI	10.1364/OE.502867
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