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Article ; Online: Dynamic monitoring of an enzymatically driven dissipative toehold-mediated strand displacement reaction.

Li, Shuang / Zhao, Disong / Yang, Fangfang / Liu, Shufeng

Chemical communications (Cambridge, England)

2024 Volume 60, Issue 5, Page(s) 570–573

Abstract: A general strategy to program self-resettable and dissipative toehold-mediated strand displacement reactions was proposed, using DNA strands as the fuel and lambda exonuclease as the fuel-consuming unit. This non-equilibrium system is reversible and ... ...

Abstract	A general strategy to program self-resettable and dissipative toehold-mediated strand displacement reactions was proposed, using DNA strands as the fuel and lambda exonuclease as the fuel-consuming unit. This non-equilibrium system is reversible and temporally controllable. Furthermore, it can be well integrated into a DNA network to temporally control its cascade reaction or dynamic behaviour.
MeSH term(s)	DNA/genetics ; Recombination, Genetic
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2024-01-11
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/d3cc05061k
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Article ; Online: 2-Aminopurine-based quencher-free DNA tweezers with fluorescence properties well tuned by surrounding bases.

Yang, Fangfang / Li, Shuang / Wu, Jialiang / Liu, Shufeng

Analytical methods : advancing methods and applications

2024 Volume 16, Issue 4, Page(s) 576–582

Abstract: Reversible structural changes in DNA nanomachines have great potential in the field of bioanalysis. Here, we demonstrate an assembly strategy for quencher-free and tunable DNA tweezers based on 2-aminopurine (2-AP), avoiding the tedious fluorescence ... ...

Abstract	Reversible structural changes in DNA nanomachines have great potential in the field of bioanalysis. Here, we demonstrate an assembly strategy for quencher-free and tunable DNA tweezers based on 2-aminopurine (2-AP), avoiding the tedious fluorescence labelling step. The conformational state of the tweezers could be controlled by specific oligonucleotides (fuel or anti-fuel). Taking advantage of the local environmental sensitivity of 2-AP, the structural changes of the tweezers were easily tracked, and multiple cyclic switching of the tweezers between the open and closed states was achieved. In addition, the influence of oligonucleotide structure on the fluorescence properties of 2-AP was deeply explored. We figured out that the fluorescence of 2-AP was highly quenched by the base-stacking of natural bases in DNA oligonucleotides. Moreover, by comprehensively regulating the type of bases surrounding the inserted 2-AP site, a sensitive fluorescence response towards dynamic change can be obtained. This principle of quencher-free nanodevices based on 2-AP provides a convenient method for monitoring the structural changes of DNA nanomachines.
MeSH term(s)	2-Aminopurine/chemistry ; Fluorescence ; DNA/chemistry ; Oligonucleotides/chemistry ; Base Sequence
Chemical Substances	2-Aminopurine (452-06-2) ; DNA (9007-49-2) ; Oligonucleotides
Language	English
Publishing date	2024-01-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2515210-5
ISSN	1759-9679 ; 1759-9660
ISSN (online)	1759-9679
ISSN	1759-9660
DOI	10.1039/d3ay01973j
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Article ; Online: CPT1A mediates the succinylation of SP5 which activates transcription of PDPK1 to promote the viability and glycolysis of prostate cancer cells.

Liu, Shufeng / Chen, Xiaoguang / Zhang, Liqi / Lu, Bo

Cancer biology & therapy

2024 Volume 25, Issue 1, Page(s) 2329372

Abstract: Succinylation modification involves in the progression of human cancers. The present study aimed to investigate the role of CPT1A, which is a succinyltransferase in the progression of prostate cancer (PCa). CCK-8 was used to detect the cell viability. ... ...

Abstract	Succinylation modification involves in the progression of human cancers. The present study aimed to investigate the role of CPT1A, which is a succinyltransferase in the progression of prostate cancer (PCa). CCK-8 was used to detect the cell viability. Seahorse was performed to evaluate the cell glycolysis. Luciferase assay was used to detect the transcriptional regulation. ChIP was performed to assess the binding between transcriptional factors with the promoters. Co-IP was used to assess the binding between proteins. We found that CPT1A was highly expressed in PCa tissues and cell lines. Silencing of CPT1A inhibited the viability and glycolysis of PCa cells. Mechanistically, CPT1A promoted the succinylation of SP5, which strengthened the binding between SP5 and the promoter of PDPK1. SP5 activated PDPK1 transcription and PDPK1 activated the AKT/mTOR signal pathway. These findings might provide novel targets for the diagnosis or therapy of prostate cancer.
MeSH term(s)	Male ; Humans ; Transcription Factors/metabolism ; Cell Line ; Signal Transduction ; Prostatic Neoplasms/genetics ; Glycolysis ; 3-Phosphoinositide-Dependent Protein Kinases/metabolism
Chemical Substances	Transcription Factors ; PDPK1 protein, human (EC 2.7.11.1) ; 3-Phosphoinositide-Dependent Protein Kinases (EC 2.7.11.1)
Language	English
Publishing date	2024-03-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2146305-0
ISSN	1555-8576 ; 1538-4047
ISSN (online)	1555-8576
ISSN	1538-4047
DOI	10.1080/15384047.2024.2329372
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Article ; Online: CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater.

Tang, Moran / Chen, Qian / Zhong, Haohui / Liu, Shufeng / Sun, Weiling

Water research

2024 Volume 251, Page(s) 121137

Abstract: The accumulation of antibiotics in the natural environment can disrupt microbial population dynamics. However, our understanding of how microbial communities adapt to the antibiotic stress in groundwater ecosystems remains limited. By recovering 2675 ... ...

Abstract	The accumulation of antibiotics in the natural environment can disrupt microbial population dynamics. However, our understanding of how microbial communities adapt to the antibiotic stress in groundwater ecosystems remains limited. By recovering 2675 metagenome-assembled genomes (MAGs) from 66 groundwater samples, we explored the effect of antibiotics on bacterial, archaeal, and fungal communities, and revealed the pivotal microbes and their mechanisms in coping with antibiotic stress. The results indicated that antibiotics had the most significant influence on bacterial and archaeal communities, while the impact on the fungal community was minimal. Analysis of co-occurrence networks between antibiotics and microbes revealed the critical roles of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea, two representative microbial groups in groundwater ecosystem, in coping with antibiotic resistance and enhancing network connectivity and complexity. Further genomic analysis demonstrated that CPR bacteria carried approximately 6 % of the identified antibiotic resistance genes (ARGs), indicating their potential to withstand antibiotics on their own. Meanwhile, the genomes of CPR bacteria and DPANN archaea were found to encode diverse biosynthetic gene clusters (BGCs) responsible for producing antimicrobial metabolites, which could not only assist CPR and DPANN organisms but also benefit the surrounding microbes in combating antibiotic stress. These findings underscore the significant impact of antibiotics on prokaryotic microbial communities in groundwater, and highlight the importance of CPR bacteria and DPANN archaea in enhancing the overall resilience and functionality of the microbial community in the face of antibiotic stress.
MeSH term(s)	Archaea/genetics ; Archaea/metabolism ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/metabolism ; Bacteria/genetics ; Bacteria/metabolism ; Microbiota ; Groundwater/microbiology ; Phylogeny
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-01-13
Publishing country	England
Document type	Journal Article
ZDB-ID	202613-2
ISSN	1879-2448 ; 0043-1354
ISSN (online)	1879-2448
ISSN	0043-1354
DOI	10.1016/j.watres.2024.121137
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Article ; Online: Immobilization-free and label-free electrochemical DNA biosensing based on target-stimulated release of redox reporter and its catalytic redox recycling.

Yang, Fangfang / Zhang, Xiaolin / Li, Shuang / Yu, Xiaoxiao / Liu, Shufeng

Bioelectrochemistry (Amsterdam, Netherlands)

2024 Volume 158, Page(s) 108727

Abstract: Herein, we demonstrate a simple, homogenous and label-free electrochemical biosensing system for sensitive nucleic acid detection based on target-responsive porous materials and nuclease-triggered target recycling amplification. The Fe(CN) ...

Abstract	Herein, we demonstrate a simple, homogenous and label-free electrochemical biosensing system for sensitive nucleic acid detection based on target-responsive porous materials and nuclease-triggered target recycling amplification. The Fe(CN)
Language	English
Publishing date	2024-05-08
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2010650-6
ISSN	1878-562X ; 0302-4598 ; 1567-5394
ISSN (online)	1878-562X
ISSN	0302-4598 ; 1567-5394
DOI	10.1016/j.bioelechem.2024.108727
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Article ; Online: DNA Polymerase-Steered Self-Propelled and Self-Enhanced DNA Walker for Rapid and Distinctly Amplified Electrochemical Sensing.

Liu, Shufeng / Wu, Jialiang / Li, Shuang / Wang, Li

Analytical chemistry

2023 Volume 96, Issue 2, Page(s) 828–838

Abstract: The development of a simple, rapid, easy-to-operate, and ultrasensitive DNA walker-based sensing system is challenging but would be very intriguing for the enormous applications in biological analysis and disease monitoring. Herein, a new self-propelled ... ...

Abstract	The development of a simple, rapid, easy-to-operate, and ultrasensitive DNA walker-based sensing system is challenging but would be very intriguing for the enormous applications in biological analysis and disease monitoring. Herein, a new self-propelled and self-enhanced DNA walking strategy was developed on the basis of a simple DNA polymerase-steered conversion from a typical alternate DNA assembly process. The sensing platform was fabricated easily by immobilizing only one hairpin probe (H1) and the sensing process was based on a simple one-step mixing with another hairpin-like DNA probe (H2) and DNA polymerase. The DNA polymerization could achieve target recycling and successive DNA walking steps. Interestingly, along with each DNA walking step, the new DNA walker sequence could be autonomously accumulated for a self-enhanced DNA walking effect. This provided a multilevel signal amplification ability for the ultrasensitive detection of the target with a low detection limit of 0.18 fM. Moreover, it could greatly reduce the reaction time with the sensing process finished within 1 h. The detection selectivity and the applicative potential in a complicated biological matrix were also demonstrated. Furthermore, the flexible control of sensing modes (self-enhanced DNA walking or the alternate DNA assembly) by using DNA polymerase or not offered a powerful means for sensing performance modulation. It thus opens a new avenue toward the development of a DNA walker-based sensing platform with both rapid and ultrasensitive features and might hold a huge potential for point-of-care diagnostic applications.
MeSH term(s)	Biosensing Techniques ; DNA/genetics ; DNA Probes ; DNA-Directed DNA Polymerase ; Polymerization ; Electrochemical Techniques ; Limit of Detection
Chemical Substances	DNA (9007-49-2) ; DNA Probes ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2023-12-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.3c04340
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Article: Electrochemical DNA Scaffold-Based Sensing Platform for Multiple Modes of Protein Assay and a Keypad Lock System

Wang, Li / Wang, Xu / Chen, Zhiqiang / Liu, Shufeng

Analytical chemistry. 2022 June 01, v. 94, no. 23

2022

Abstract: Development of a flexible, easy-to-use, and well-controllable DNA-based sensing platform would provide enormous opportunities to boost molecular diagnosis and signal transduction or information processing. Herein, a duplex DNA scaffold containing a bulge ...

Abstract	Development of a flexible, easy-to-use, and well-controllable DNA-based sensing platform would provide enormous opportunities to boost molecular diagnosis and signal transduction or information processing. Herein, a duplex DNA scaffold containing a bulge was deployed for the fabrication of a simple and general DNA-based electrochemical sensing platform. It could be harnessed for different signal output behaviors (one signal-off and two signal-on modes) toward a single-step analysis of the target protein. The detection limit toward the target protein could reach about 0.1 nM. Also, it could be used as a streamlined electrochemical workflow for the successive monitoring of protein binding. Furthermore, such an electrochemical sensing platform could be explored for the operation of the concatenated AND logic gates as a molecular keypad lock system. The current sensing platform based on only one duplex DNA scaffold presented features such as simple biosensor design and fabrication, flexible operation for different signal outputs, sensitive and selective protein detection, and expandable logic operation. It thus would pave a broad road toward the development of high-performance biosensors or logic devices to be applied for molecular diagnosis or computing.
Keywords	DNA ; analytical chemistry ; biosensors ; detection limit ; electrochemistry ; signal transduction
Language	English
Dates of publication	2022-0601
Size	p. 8317-8326.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c00800
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Article ; Online: Electrochemical DNA Scaffold-Based Sensing Platform for Multiple Modes of Protein Assay and a Keypad Lock System.

Wang, Li / Wang, Xu / Chen, Zhiqiang / Liu, Shufeng

Analytical chemistry

2022 Volume 94, Issue 23, Page(s) 8317–8326

Abstract	Development of a flexible, easy-to-use, and well-controllable DNA-based sensing platform would provide enormous opportunities to boost molecular diagnosis and signal transduction or information processing. Herein, a duplex DNA scaffold containing a bulge was deployed for the fabrication of a simple and general DNA-based electrochemical sensing platform. It could be harnessed for different signal output behaviors (one signal-off and two signal-on modes) toward a single-step analysis of the target protein. The detection limit toward the target protein could reach about 0.1 nM. Also, it could be used as a streamlined electrochemical workflow for the successive monitoring of protein binding. Furthermore, such an electrochemical sensing platform could be explored for the operation of the concatenated AND logic gates as a molecular keypad lock system. The current sensing platform based on only one duplex DNA scaffold presented features such as simple biosensor design and fabrication, flexible operation for different signal outputs, sensitive and selective protein detection, and expandable logic operation. It thus would pave a broad road toward the development of high-performance biosensors or logic devices to be applied for molecular diagnosis or computing.
MeSH term(s)	Biosensing Techniques ; DNA/chemistry ; Electrochemical Techniques ; Logic
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-06-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c00800
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Article: Simultaneous nitrogen and carbon removal in a single biological aerated filter by the bioaugmentation with heterotrophic-aerobic nitrogen removal bacteria

Wang, Haizhen / Gao, Qiang / Liu, Shufeng / Chen, Qian

Environmental technology. 2021 Oct. 28, v. 42, no. 24

2021

Abstract: Agrobacterium sp. LAD9 capable of heterotrophic-aerobic nitrogen removal was applied into a single biological aerated filter (BAF) for bioaugmented treatment of municipal wastewater. The achievement of simultaneous nitrogen and carbon removal in the ... ...

Abstract	Agrobacterium sp. LAD9 capable of heterotrophic-aerobic nitrogen removal was applied into a single biological aerated filter (BAF) for bioaugmented treatment of municipal wastewater. The achievement of simultaneous nitrogen and carbon removal in the bioaugmented system was systematically evaluated by ratios of COD to nitrogen (COD/N), ranging from 1 to 20. The results showed that at an appropriate COD/N ratio of 10, the BAF exhibited excellent carbon and nutrients removal, the averaged removal efficiencies for COD, NH₄ ⁺-N and TN were 92.3%, 100% and 80.0%, respectively. Long-term operation of the bioaugmented system also confirmed the stability of the treatment efficiency. Further comparisons of SOUR and PCR-DGGE profiles between the bioaugmented and the control system revealed that the introduction of strain LAD9 greatly changed the structure of original microbial community and facilitated their capabilities of aerobic nutrients removal. The proposed bioaugmentation strategy is of particular importance to upgrading or retrofitting concurrent municipal wastewater treatment systems.
Keywords	Agrobacterium ; bioaugmentation ; biofilters ; carbon ; environmental technology ; microbial communities ; municipal wastewater ; nitrogen ; wastewater treatment
Language	English
Dates of publication	2021-1028
Size	p. 3716-3724.
Publishing place	Taylor & Francis
Document type	Article
ISSN	1479-487X
DOI	10.1080/09593330.2020.1739147
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Article ; Online: Long-term impact of self-compassion training with core stability exercise on patients with nonspecific chronic low back pain: A randomized controlled trial.

Zheng, Fuming / Liu, Shufeng / Yin, Qunhui / Zheng, Yiyi / Yang, Jiajia / Huang, Haoxuan / Chen, Lichang / Wang, Yuyin / Chen, Xi / Wang, Chuhuai

Journal of psychosomatic research

2024 Volume 181, Page(s) 111678

Abstract: Objective: To compare the long-term effectiveness of self-compassion therapy (SCT) combined with core stability exercise (CSE) versus CSE alone in managing nonspecific chronic low back pain (NCLBP).: Methods: The combined group received SCT and CSE, ... ...

Abstract	Objective: To compare the long-term effectiveness of self-compassion therapy (SCT) combined with core stability exercise (CSE) versus CSE alone in managing nonspecific chronic low back pain (NCLBP). Methods: The combined group received SCT and CSE, while the exercise group only received CSE. Treatment was administered once weekly for four weeks, followed by one year of follow-up. The primary outcomes were changes in functional limitations (measured by Roland and Morris Disability Questionnaire scores[RMDQ]) and self-reported back pain (measured by the Numeric Pain Rating Scale[NRS]) at 52 weeks, with assessments also conducted at 2, 4, and 16 weeks. Results: 52 (83.9%) completed the follow-up assessments and were included in the analysis (42 women [80.8%]; mean [SD] age,35.3 [10.0] years). In the combined group, the baseline mean (SD) RMDQ score was 9.3 (4.1),5.7 (5.8) at 2 weeks, 3.8 (3.4) at 4 weeks, 3.8 (3.7) at 16 weeks, and 2.4 (2.7) at 52 weeks. For the exercise group, the RMDQ scores were 8.2 (3.3) at baseline, 6.2 (4.2) at 2 weeks, 5.5 (4.7) at 4 weeks, 4.4 (4.5) at 16 weeks, and 5.2 (5.6) at 52 weeks. The estimated mean difference between the groups at 52 weeks was -3.356 points (95% CI, -5.835 to -0.878; P = 0.009), favoring the combined group. NRS scores showed similar changes. Conclusion: The addition of self-compassion therapy enhances the long-term efficacy of core stability training for NCLBP (Preregistered at chictr.org.cn:ChiCTR2100042810).
Language	English
Publishing date	2024-04-16
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	80166-5
ISSN	1879-1360 ; 0022-3999
ISSN (online)	1879-1360
ISSN	0022-3999
DOI	10.1016/j.jpsychores.2024.111678
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