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Article ; Online: Interplay of dynamic genome organization and biomolecular condensates.

Chung, Yu-Chieh / Tu, Li-Chun

2023 Volume 85, Page(s) 102252

Abstract: After 60 years of chromatin investigation, our understanding of chromatin organization has evolved from static chromatin fibers to dynamic nuclear compartmentalization. Chromatin is embedded in a heterogeneous nucleoplasm in which molecules are grouped ... ...

Abstract	After 60 years of chromatin investigation, our understanding of chromatin organization has evolved from static chromatin fibers to dynamic nuclear compartmentalization. Chromatin is embedded in a heterogeneous nucleoplasm in which molecules are grouped into distinct compartments, partitioning nuclear space through phase separation. Human genome organization affects transcription which controls euchromatin formation by excluding inactive chromatin. Chromatin condensates have been described as either liquid-like or solid-like. In this short review, we discuss the dynamic nature of chromatin from the perspective of biomolecular condensates and highlight new live-cell synthetic tools to probe and manipulate chromatin organization and associated condensates.
MeSH term(s)	Humans ; Biomolecular Condensates ; Cell Nucleus/genetics ; Chromatin/genetics
Chemical Substances	Chromatin
Language	English
Publishing date	2023-10-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1026381-0
ISSN	1879-0410 ; 0955-0674
ISSN (online)	1879-0410
ISSN	0955-0674
DOI	10.1016/j.ceb.2023.102252
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Article: Advances and challenges in CRISPR-based real-time imaging of dynamic genome organization.

Thuma, Jenna / Chung, Yu-Chieh / Tu, Li-Chun

Frontiers in molecular biosciences

2023 Volume 10, Page(s) 1173545

Abstract: Nuclear chromosome compaction is non-random and dynamic. The spatial distance among genomic elements instantly modulates transcription. Visualization of the genome organization in the cell nucleus is essential to understand nuclear function. In addition ... ...

Abstract	Nuclear chromosome compaction is non-random and dynamic. The spatial distance among genomic elements instantly modulates transcription. Visualization of the genome organization in the cell nucleus is essential to understand nuclear function. In addition to cell type-dependent organization, high-resolution 3D imaging shows heterogeneous compaction of chromatin organization among the same cell type. Questions remain to be answered if these structural variations were the snapshots of dynamic organization at different time points and if they are functionally different. Live-cell imaging has provided unique insights into dynamic genome organization at short (milliseconds) and long (hours) time scales. The recent development of CRISPR-based imaging opened windows for studying dynamic chromatin organization in single cells in real time. Here we highlight these CRISPR-based imaging techniques and discuss their advances and challenges as a powerful live-cell imaging method that poses high potential to generate paradigm-shifting discoveries and reveal functional implications of dynamic chromatin organization.
Language	English
Publishing date	2023-03-31
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2814330-9
ISSN	2296-889X
ISSN	2296-889X
DOI	10.3389/fmolb.2023.1173545
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Article: More attention should be paid to atrial-esophageal fistula, and not all atrial-esophageal fistulas are iatrogenic.

Xie, Hong / Tu, Li / Li, Xuejun / Du, Xiaojun / Zhou, Shi

Annals of translational medicine

2023 Volume 11, Issue 10, Page(s) 372

Language	English
Publishing date	2023-08-03
Publishing country	China
Document type	Journal Article ; Comment
ZDB-ID	2893931-1
ISSN	2305-5847 ; 2305-5839
ISSN (online)	2305-5847
ISSN	2305-5839
DOI	10.21037/atm-23-1275
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Article ; Online: Single-chromosome dynamics reveals locus-dependent dynamics and chromosome territory orientation.

Chung, Yu-Chieh / Bisht, Madhoolika / Thuma, Jenna / Tu, Li-Chun

Journal of cell science

2023 Volume 136, Issue 4

Abstract: Dynamic chromatin organization instantly influences DNA accessibility through modulating local macromolecular density and interactions, driving changes in transcription activities. Chromatin dynamics have been reported to be locally confined but ... ...

Abstract	Dynamic chromatin organization instantly influences DNA accessibility through modulating local macromolecular density and interactions, driving changes in transcription activities. Chromatin dynamics have been reported to be locally confined but contribute to coherent chromatin motion across the entire nucleus. However, the regulation of dynamics, nuclear orientation and compaction of subregions along a single chromosome are not well-understood. We used CRISPR-based real-time single-particle tracking and polymer models to characterize the dynamics of specific genomic loci and determine compaction levels of large human chromosomal domains. Our studies showed that chromosome compaction changed during interphase and that compactions of two arms on chromosome 19 were different. The dynamics of genomic loci were subdiffusive and dependent on chromosome regions and transcription states. Surprisingly, the correlation between locus-dependent nuclear localization and mobility was negligible. Strong tethering interactions detected at the pericentromeric region implies local condensation or associations with organelles within local nuclear microenvironments, such as chromatin-nuclear body association. Based on our findings, we propose a 'guided radial model' for the nuclear orientation of the long arm of chromosome 19.
MeSH term(s)	Humans ; Chromatin ; Cell Nucleus/physiology ; Chromosomes, Human ; Interphase
Chemical Substances	Chromatin
Language	English
Publishing date	2023-02-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.260137
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Article ; Online: Perianal abscess complicating a high complex-type anal fistula.

Wang, ChangXin / Zhao, ShuFeng / Tu, LiWen / Zeng, XiangFu

Asian journal of surgery

2023 Volume 47, Issue 3, Page(s) 1644–1645

MeSH term(s)	Humans ; Abscess/complications ; Abscess/diagnostic imaging ; Anus Diseases/surgery ; Anus Diseases/complications ; Rectal Fistula/surgery ; Rectal Fistula/complications
Language	English
Publishing date	2023-12-23
Publishing country	Netherlands
Document type	Letter
ZDB-ID	1068461-x
ISSN	0219-3108 ; 1015-9584
ISSN (online)	0219-3108
ISSN	1015-9584
DOI	10.1016/j.asjsur.2023.12.071
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Article ; Online: Neutrophil extracellular traps involved in the pathogenesis of IgA vasculitis: Confirmed in two IgAV rat models.

Chen, Xiu-Qi / Zou, Jia-Sen / Tu, Li / Yun, Xiang / Qin, Yuan-Han

PloS one

2023 Volume 18, Issue 7, Page(s) e0288538

Abstract: Background: Neutrophil extracellular traps (NETs) have been found to play a role in the development of autoimmune diseases. In the past two years, studies have demonstrated a significantly increase of NETs in skin tissues during the early stages of IgAV, ...

Abstract	Background: Neutrophil extracellular traps (NETs) have been found to play a role in the development of autoimmune diseases. In the past two years, studies have demonstrated a significantly increase of NETs in skin tissues during the early stages of IgAV, indicating their involvement in disease activity among children with IgAV. However, the presence of NETs in IgAV animal models has not yet been reported. The objective of this study is to investigate whether NETs are involved in the pathogenesis of IgA vasculitis (IgAV) rats. Methods: Twenty-four SD rats were randomly divided into three groups: the ovalbumin group, the gliadin group, and the control group. The IgAV rat models were established administering Indian ink with ovalbumin (ovalbumin group) or gliadin (gliadin group) with Freund's complete adjuvant. The cell-free DNA (cf-DNA) was quantified by using dsDNA quantification kit, while the levels of Immunoglobulins, complement C3 and myeloperoxidase-DNA (MPO-DNA) in serum were tested using enzyme linked immunosorbent assay (ELISA). The IgA, complement C3 and NETs in tissues were detected through multiple immunofluorescences. Results: Both the ovalbumin group and gliadin group showed IgA and C3 deposition in various tissues, including the glomerular mesangial region, skin, and digestive tract, while the control group showed no such deposition. The levels of circulatory cf-DNA and MPO-DNA, which are components of NETs, were significantly elevated in both ovalbumin and gliadin groups compared with the control group. Furthermore, the presence of NETs were found in gastrointestinal and renal tissues of the ovalbumin and gliadin groups, but not in the control group. Conclusions: IgAV model rat can be established through the combination of ovalbumin and gliadin with Indian ink and Freund's complete adjuvant. This study provides the first confirmation that NETs are involved in the pathogenesis of IgAV rat.
MeSH term(s)	Child ; Humans ; Rats ; Animals ; IgA Vasculitis ; Extracellular Traps ; Complement C3 ; Ovalbumin ; Gliadin ; Rats, Sprague-Dawley ; Immunoglobulin A ; DNA
Chemical Substances	Complement C3 ; Ovalbumin (9006-59-1) ; Gliadin (9007-90-3) ; Immunoglobulin A ; DNA (9007-49-2)
Language	English
Publishing date	2023-07-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0288538
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Article ; Online: DNase I targeted degradation of neutrophil extracellular traps to reduce the damage on IgAV rat.

Chen, Xiu-Qi / Tu, Li / Tang, Qing / Zou, Jia-Sen / Yun, Xiang / Qin, Yuan-Han

PloS one

2023 Volume 18, Issue 10, Page(s) e0291592

Abstract: Background: In the past two years, studies have found a significant increase in neutrophil extracellular traps (NETs) in patients with IgA vasculitis (IgAV), which is correlated with the severity of the disease. NETs have been reported as an ... ...

Abstract	Background: In the past two years, studies have found a significant increase in neutrophil extracellular traps (NETs) in patients with IgA vasculitis (IgAV), which is correlated with the severity of the disease. NETs have been reported as an intervention target in inflammatory and autoimmune diseases. This study aimed to investigate the effect of targeted degradation of NETs using DNase I in IgAV rat model. Methods: Twenty-four Sprague-Dawley rats were randomly divided into three groups: the IgAV model group, the DNase I intervention group and the normal control group, with an average of 8 rats in each group. The model group was established by using Indian ink, ovalbumin, and Freund's complete adjuvant. In the intervention group, DNase I was injected through tail vein 3 days before the end of established model. The circulating cell free-DNA (cf-DNA) and myeloperoxidase-DNA (MPO-DNA) were analyzed. The presence of NETs in the kidney, gastric antrum and descending duodenum were detected using multiple fluorescences immunohistochemistry and Western blots. Morphological changes of the tissues were observed. Results: After the intervention of DNase I, there was a significant reduction in cf-DNA and MPO-DNA levels in the intervention group compared to the IgAV model group (all P<0.001). The presence of NETs in renal, gastric, and duodenal tissues of the intervention group exhibited a significant decrease compared to the IgAV model group (P < 0.01). Moreover, the intervention group demonstrated significantly lower levels of renal MPO and citrullinated histone H3 (citH3) protein expression when compared to the IgAV model group (all P < 0.05). The HE staining results of intervention group demonstrated a significant reduction in congestion within glomerular and interstitial capillaries. Moreover, there was a notable improvement in gastric and intestinal mucosa necrosis, congestion and bleeding. Additionally, there was a substantial decrease in inflammatory cells infiltration. Conclusion: The degradation of NETs can be targeted by DNase I to mitigate tissue damage in IgAV rat models. Targeted regulation of NETs holds potential as a therapeutic approach for IgAV.
MeSH term(s)	Humans ; Rats ; Animals ; Extracellular Traps/metabolism ; Neutrophils/metabolism ; Deoxyribonuclease I/metabolism ; IgA Vasculitis ; Rats, Sprague-Dawley ; Intestinal Diseases/metabolism ; DNA/metabolism
Chemical Substances	Deoxyribonuclease I (EC 3.1.21.1) ; DNA (9007-49-2)
Language	English
Publishing date	2023-10-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0291592
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Article ; Online: Prevention of exacerbation in patients with moderate-to-very severe COPD with the intent to modulate respiratory microbiome

Jian-lan Hua / Zi-feng Yang / Qi-jian Cheng / Yao-pin Han / Zheng-tu Li / Ran-ran Dai / Bin-feng He / Yi-xing Wu / Jing Zhang

Frontiers in Medicine, Vol

a pilot prospective, multi-center, randomized controlled trial

2024 Volume 10

Abstract: IntroductionConsidering the role of bacteria in the onset of acute exacerbation of COPD (AECOPD), we hypothesized that the use of influenza-Streptococcus pneumoniae vaccination, oral probiotics or inhaled amikacin could prevent AECOPD.MethodsIn this ... ...

Abstract	IntroductionConsidering the role of bacteria in the onset of acute exacerbation of COPD (AECOPD), we hypothesized that the use of influenza-Streptococcus pneumoniae vaccination, oral probiotics or inhaled amikacin could prevent AECOPD.MethodsIn this pilot prospective, muti-central, randomized trial, moderate-to-very severe COPD subjects with a history of moderate-to-severe exacerbations in the previous year were enrolled and assigned in a ratio of 1:1:1:1 into 4 groups. All participants were managed based on the conventional treatment recommended by GOLD 2019 report for 3 months, with three groups receiving additional treatment of inhaled amikacin (0.4 g twice daily, 5–7 days monthly for 3 months), oral probiotic Lactobacillus rhamnosus GG (1 tablet daily for 3 months), or influenza-S. pneumoniae vaccination. The primary endpoint was time to the next onset of moderate-to-severe AECOPD from enrollment. Secondary endpoints included CAT score, mMRC score, adverse events, and survival in 12 months.ResultsAmong all 112 analyzed subjects (101 males, 96 smokers or ex-smokers, mean ± SD age 67.19 ± 7.39 years, FEV1 41.06 ± 16.09% predicted), those who were given dual vaccination (239.7 vs. 198.2 days, p = 0.044, 95%CI [0.85, 82.13]) and oral probiotics (248.8 vs. 198.2 days, p = 0.017, 95%CI [7.49, 93.59]) had significantly delayed onset of next moderate-to-severe AECOPD than those received conventional treatment only. For subjects with high symptom burden, the exacerbations were significantly delayed in inhaled amikacin group as compared to the conventional treatment group (237.3 vs. 179.1 days, p = 0.009, 95%CI [12.40,104.04]). The three interventions seemed to be safe and well tolerated for patient with stable COPD.ConclusionThe influenza-S. pneumoniae vaccine and long-term oral probiotic LGG can significantly delay the next moderate-to-severe AECOPD. Periodically amikacin inhalation seems to work in symptomatic patients. The findings in the current study warrants validation in future studies with microbiome ...
Keywords	chronic obstructive pulmonary disease ; vaccination ; inhaled antibiotics ; probiotic ; amikacin ; Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2024-01-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article: [Seed morphology and germination characteristics of Tripterygium wilfordii].

Tu, Li-Chan / Cai, Xin-Bo / Gao, Jie / Tu, Yu-He / Liu, San-Bo / Gao, Wei

Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica

2022 Volume 47, Issue 11, Page(s) 2909–2914

Abstract: The seeds of Tripterygium wilfordii are characterized by dormancy and a long germination cycle under natural sowing conditions. In this study, we developed a method for rapid germination of T. wilfordii seeds by analyzing the size, morphology, thousand- ... ...

Abstract	The seeds of Tripterygium wilfordii are characterized by dormancy and a long germination cycle under natural sowing conditions. In this study, we developed a method for rapid germination of T. wilfordii seeds by analyzing the size, morphology, thousand-grain weight, viability, moisture content, physicochemical properties, and seed germination rates under different germination conditions. The seeds of T. wilfordii were fine columnar with a thick and hard outer seed coat. They had the length of 6.69 mm, the width of 2.14 mm, the thickness of 1.68 mm, the thousand-grain weight of 8.99 g, the moisture content of 8.86%, the soluble sugar content of 21.3 mg·g~(-1), the starch content of 28.9 mg·g~(-1), the soluble protein content of 44.2 mg·g~(-1), and the seed viability of only 54.0%. The seeds were respectively treated with distilled water, ultrasonication, low-temperature storage, 50 ℃ water, 100 mg·L~(-1) 6-BA, 0.6% KMnO_4, 1% KNO_3, 50 mg·L~(-1) NAA, and 100 mg·L~(-1) GA_3 solution. The results showed that soaking the seeds in 100 mg·L~(-1) GA_3 solution significantly promoted the germination. Further, the seeds were soaked in 50, 100, 250, 500, and 1 000 mg·L~(-1) GA_3 solutions, which demonstrated that high concentration(500 mg·L~(-1), 1 000 mg·L~(-1)) of GA_3 solutions increased the germination rate and speed and shortened the germination cycle from more than 3 months to less than 15 days. The findings of this study are of great significance to the breeding of T. wilfordii and lay a foundation for the large-scale propagation of T. wilfordii seeds and the excavation of T. wilfordii germplasm resources.
MeSH term(s)	Germination ; Plant Breeding ; Seeds/chemistry ; Tripterygium ; Water/analysis
Chemical Substances	Water (059QF0KO0R)
Language	Chinese
Publishing date	2022-02-26
Publishing country	China
Document type	Journal Article
ZDB-ID	1004649-5
ISSN	1001-5302 ; 0254-0029
ISSN	1001-5302 ; 0254-0029
DOI	10.19540/j.cnki.cjcmm.20220215.101
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Article ; Online: An Emerging Role for Neutrophil Extracellular Traps in IgA Vasculitis: A Mini-Review.

Chen, Xiu-Qi / Tu, Li / Tang, Qing / Huang, Li / Qin, Yuan-Han

Frontiers in immunology

2022 Volume 13, Page(s) 912929

Abstract: Immunoglobulin A vasculitis (IgAV) is the most common systemic small vessel vasculitis in childhood. Its clinical manifestations are non-thrombocytopenic purpura, accompanied by gastrointestinal tract, joint, kidney and other organ system involvement. ... ...

Abstract	Immunoglobulin A vasculitis (IgAV) is the most common systemic small vessel vasculitis in childhood. Its clinical manifestations are non-thrombocytopenic purpura, accompanied by gastrointestinal tract, joint, kidney and other organ system involvement. The pathogenesis of IgAV has not been fully elucidated. It may be related to many factors including genetics, infection, environmental factors, and drugs. The most commonly accepted view is that galactose-deficient IgA1 and the deposition of IgA and complement C3 in small blood vessel walls are key contributors to the IgAV pathogenesis. Extensive neutrophil extracellular traps (NETs) in the peripheral circulation and skin, kidney, and gastrointestinal tissue of patients with IgAV has been identified in the past two years and is associated with disease activity. This mini-review provides a possible mechanism for NETs involvement in the pathogenesis of IgAV.
MeSH term(s)	Extracellular Traps ; Humans ; IgA Vasculitis ; Immunoglobulin A ; Kidney ; Vasculitis
Chemical Substances	Immunoglobulin A
Language	English
Publishing date	2022-06-21
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2022.912929
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