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Wu S, Li X, Zhou M, Cui Y, Wu W, Ping J, Guo X, Hu Q. pH-triggered hydrophility-adjustable fluorescent probes for simultaneously imaging lipid droplets and lysosomes and the application in fatty liver detection. Biosens Bioelectron 2024; 251:116084. [PMID: 38330775 DOI: 10.1016/j.bios.2024.116084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024]
Abstract
To study the collaboration between lipid droplets (LDs) and lysosomes, and the lipid change in nonalcoholic fatty liver disease (NAFLD), herein two pH-triggered hydrophility-adjustable fluorescent probes (LD-Lyso and LD-Lyso 1) are designed. The mechanism is based on cyclization and ring-opening with thorough consideration of pH and hydrophilic differences between LDs and lysosomes. Both of the two probes exist in ring-opening form and emit red fluorescence in acidic environment, while they exist in cyclized form and the emission is blueshifted in alkaline environment due to reduced conjugate planes. Moreover, LD-Lyso exhibits near infrared fluorescence at 740 nm under ring-opening form, which facilitates further cell, tissue, and in vivo imaging. The cell imaging results show that LD-Lyso can simultaneously target LDs and lysosomes by two different colors. Impressively, LD-Lyso cannot only detect NAFLD tissues from the normal tissue, but also distinguish different degrees of NAFLD tissues and mice, which provides a very promising tool for timely diagnosis of early NAFLD.
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Affiliation(s)
- Shining Wu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, PR China
| | - Xuechen Li
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, PR China.
| | - Mingyang Zhou
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, PR China
| | - Yuezhi Cui
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, PR China
| | - Wenli Wu
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, PR China
| | - Jiantao Ping
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, PR China
| | - Xuezu Guo
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, PR China
| | - Qiongzheng Hu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250100, PR China; School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, PR China.
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Chandel N, Somvanshi PR, Thakur V. Characterisation of Indian gut microbiome for B-vitamin production and its comparison with Chinese cohort. Br J Nutr 2024; 131:686-697. [PMID: 37781761 PMCID: PMC10803823 DOI: 10.1017/s0007114523002179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023]
Abstract
The human gut microbiota can biosynthesize essential micronutrients such as B-vitamins and is also known for its metabolic cooperative behaviour. The present study characterises such B-vitamin biosynthesizers, their biosynthetic pathways, explores their prevalence and abundance, examines how lifestyle or diet affects them in multiple Indian cohorts and compares it with the Chinese cohort. To achieve this, publicly available faecal metagenome data of healthy individuals from multiple Indian (two urban and three tribal populations) and a Chinese cohort were analysed. The distribution of prevalence and abundance of B-vitamin biosynthesizers showed similar profiles to that of the entire gut community of the Indian cohort, and there were 28 B-vitamin biosynthesizers that had modest or higher prevalence and abundance. The omnivorous diet affected only the prevalence of a few B-vitamin biosynthesizers; however, lifestyle and/or location affected both prevalence and abundance. A comparison with the Chinese cohort showed that fourteen B-vitamin biosynthesizers were significantly more prevalent and abundant in Chinese as compared with Indian samples (False Discovery Rate (FDR) <= 0·05). The metabolic potential of the entire gut community for B-vitamin production showed that within India, the tribal cohort has a higher abundance of B-vitamin biosynthesis pathways as compared with two urban cohorts namely, Bhopal and Kasargod, and comparison with the Chinese cohort revealed a higher abundance in the latter group. Potential metabolic cooperative behaviour of the Indian gut microbiome for biosynthesis of the B-vitamins showed multiple pairs of species showed theoretical complementarity for complete biosynthetic pathways genes of thiamine, riboflavin, niacin and pantothenate.
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Affiliation(s)
- Nisha Chandel
- Department of Systems and Computational Biology, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Pramod R. Somvanshi
- Department of Systems and Computational Biology, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - Vivek Thakur
- Department of Systems and Computational Biology, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
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Zhang X, Luo M, Deng S, Long T, Sun L, Yu R. Field study of microbial community structure and dechlorination activity in a multi-solvents co-contaminated site undergoing natural attenuation. J Hazard Mater 2022; 423:127010. [PMID: 34474368 DOI: 10.1016/j.jhazmat.2021.127010] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
BTEX and chlorinated aliphatic hydrocarbons (CAHs) are the common pollutants found at contaminated sites, and natural attenuation (NA) of CAHs was widely observed where they coexist. In this work, the groundwater in a site co-contaminated with BTEX and CAHs was monitored for 1 year. The compositions and activities of the microfloras, especially dechlorinators and their relationships with the contaminants, geochemical properties, seasons and depth were evaluated. The results are consistent with the well-known NA conceptual model where CAHs are not able to stimulate the enrichment of dechlorinators alone, but BTEX does promote dechlorination. The higher temperature, rather than ORP in the deeper groundwater of the wet season became a key factor to promote the abundance of dechlorinators, but only when BTEX was available, indicating that the substrates from the BTEX biodegradation played an important role in the dechlorinator enrichment. The elevated ORP in the shallower groundwater exceeded the optimum conditions for reductive dechlorination and no significant seasonal variation of dechlorinators was found. The co-occurrence network revealed the cooperative interactions among the functional microfloras in which dechlorinators, BTEX degraders, and fermentative bacteria jointly promoted the dechlorination. These findings provided us a further understanding of the NA processes in a commingled plume.
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Affiliation(s)
- Xiaodong Zhang
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, China; State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, Jiangsu, China
| | - Moye Luo
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, China; State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, Jiangsu, China
| | - Shaopo Deng
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, Jiangsu, China
| | - Tao Long
- State Environmental Protection Key Laboratory of Soil Environmental Management and Pollution Control, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, Jiangsu, China
| | - Liwei Sun
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, China
| | - Ran Yu
- Department of Environmental Science and Engineering, School of Energy and Environment, Southeast University, Nanjing, Jiangsu, China.
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Anink-Groenen LCM, Maarleveld TR, Verschure PJ, Bruggeman FJ. Mechanistic stochastic model of histone modification pattern formation. Epigenetics Chromatin 2014; 7:30. [PMID: 25408711 PMCID: PMC4234852 DOI: 10.1186/1756-8935-7-30] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The activity of a single gene is influenced by the composition of the chromatin in which it is embedded. Nucleosome turnover, conformational dynamics, and covalent histone modifications each induce changes in the structure of chromatin and its affinity for regulatory proteins. The dynamics of histone modifications and the persistence of modification patterns for long periods are still largely unknown. RESULTS In this study, we present a stochastic mathematical model that describes the molecular mechanisms of histone modification pattern formation along a single gene, with non-phenomenological, physical parameters. We find that diffusion and recruitment properties of histone modifying enzymes together with chromatin connectivity allow for a rich repertoire of stochastic histone modification dynamics and pattern formation. We demonstrate that histone modification patterns at a single gene can be established or removed within a few minutes through diffusion and weak recruitment mechanisms of histone modification spreading. Moreover, we show that strong synergism between diffusion and weak recruitment mechanisms leads to nearly irreversible transitions in histone modification patterns providing stable patterns. In the absence of chromatin connectivity spontaneous and dynamic histone modification boundaries can be formed that are highly unstable, and spontaneous fluctuations cause them to diffuse randomly. Chromatin connectivity destabilizes this synergistic system and introduces bistability, illustrating state switching between opposing modification states of the model gene. The observed bistable long-range and localized pattern formation are critical effectors of gene expression regulation. CONCLUSION This study illustrates how the cooperative interactions between regulatory proteins and the chromatin state generate complex stochastic dynamics of gene expression regulation.
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Affiliation(s)
- Lisette C M Anink-Groenen
- Swammerdam Institute for Life Science (SILS), University of Amsterdam, Science Park 904, P.O. Box 94215, 1098 GE Amsterdam, The Netherlands
| | - Timo R Maarleveld
- Systems Bioinformatics, Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands ; Life Sciences, Centrum Wiskunde & Informatica, Amsterdam, The Netherlands ; BioSolar Cells, Wageningen, The Netherlands
| | - Pernette J Verschure
- Swammerdam Institute for Life Science (SILS), University of Amsterdam, Science Park 904, P.O. Box 94215, 1098 GE Amsterdam, The Netherlands
| | - Frank J Bruggeman
- Systems Bioinformatics, Amsterdam Institute for Molecules Medicines and Systems, VU University Amsterdam, Amsterdam, The Netherlands
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Villarreal LP, Witzany G. Rethinking quasispecies theory: From fittest type to cooperative consortia. World J Biol Chem 2013; 4:79-90. [PMID: 24340131 PMCID: PMC3856310 DOI: 10.4331/wjbc.v4.i4.79] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 08/20/2013] [Accepted: 09/04/2013] [Indexed: 02/05/2023] Open
Abstract
Recent investigations surprisingly indicate that single RNA “stem-loops” operate solely by chemical laws that act without selective forces, and in contrast, self-ligated consortia of RNA stem-loops operate by biological selection. To understand consortial RNA selection, the concept of single quasi-species and its mutant spectra as drivers of RNA variation and evolution is rethought here. Instead, we evaluate the current RNA world scenario in which consortia of cooperating RNA stem-loops (not individuals) are the basic players. We thus redefine quasispecies as RNA quasispecies consortia (qs-c) and argue that it has essential behavioral motifs that are relevant to the inherent variation, evolution and diversity in biology. We propose that qs-c is an especially innovative force. We apply qs-c thinking to RNA stem-loops and evaluate how it yields altered bulges and loops in the stem-loop regions, not as errors, but as a natural capability to generate diversity. This basic competence-not error-opens a variety of combinatorial possibilities which may alter and create new biological interactions, identities and newly emerged self identity (immunity) functions. Thus RNA stem-loops typically operate as cooperative modules, like members of social groups. From such qs-c of stem-loop groups we can trace a variety of RNA secondary structures such as ribozymes, viroids, viruses, mobile genetic elements as abundant infection derived agents that provide the stem-loop societies of small and long non-coding RNAs.
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