Nature Protocols
·
2024
·
IF 13.1
Chen Feng,Li Xinyin,Bai Min,Zhao Yongxi
Epigenetic modifications and spatial proximities of nucleic acids and proteins play important roles in regulating physiological processes and disease progression. Currently available cell imaging methods, such as fluorescence in situ hybridization (FISH) and immunofluorescence, struggle to detect low-abundance modifications and their spatial proximities. Here we describe a step-by-step protocol for three DNA-encoded amplifying FISH-based imaging strategies to overcome these challenges for varying applications: base-encoded amplifying FISH (BEA-FISH), pairwise proximity-differentiated amplifying FISH (PPDA-FISH) and cellular macromolecules-tethered DNA walking indexing (Cell-TALKING). They all use the similar core principle of DNA-encoded amplification, which transforms different nonsequence molecular features into unique DNA barcodes for in situ rolling circle amplification and FISH analysis. This involves three key reactions in fixed cell samples: target labeling, DNA encoding and rolling circle amplification imaging. Using this protocol, these three imaging strategies achieve in situ counting of low-abundance modifications alone, the pairwise proximity-differentiated visualization of two modifications and the exploration of multiple modifications around one protein (one-to-many proximity), respectively. Low-abundance modifications, including 5-hydroxymethylcytosine, 5-formylcytosine, 5-hydroxymethyluracil and 5-formyluracil, are clearly visualized in single cells. Various combinatorial patterns of nucleic acid modifications and/or histone modifications are found. The whole protocol takes ~2–4 d to complete, depending on different imaging applications.
研究领域:
分子生物学
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细胞生物学
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基因组学
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表观遗传学
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DOI
PubMed
高影响因子
Biomolecules
·
2024
·Vol. 14
·期 5
·581
·
IF 4.8
Jiaming Cao,Boyuan Xiang,Baojie Dou,Jingfei Hu,Lei Zhang,Xinxin Kang,Mingsheng Lyu,Shujun Wang
Peptides possessing antihypertensive attributes via inhibiting the angiotensin-converting enzyme (ACE) were derived through the enzymatic degradation ofTrichiurus lepturus(ribbonfish) using alkaline protease. The resulting mixture underwent filtration using centrifugation, ultrafiltration tubes, and Sephadex G-25 gels. Peptides exhibiting ACE-inhibitory properties and DPPH free-radical-scavenging abilities were isolated and subsequently purified via LC/MS-MS, leading to the identification of over 100 peptide components. In silico screening yielded five ACE inhibitory peptides: FAGDDAPR, QGPIGPR, IFPRNPP, AGFAGDDAPR, and GPTGPAGPR. Among these, IFPRNPP and AGFAGDDAPR were found to be allergenic, while FAGDDAPRR, QGPIGPR, and GPTGPAGP showed good ACE-inhibitory effects. IC50values for the latter peptides were obtained from HUVEC cells: FAGDDAPRR (IC50= 262.98 μM), QGPIGPR (IC50= 81.09 μM), and GPTGPAGP (IC50= 168.11 μM). Peptide constituents derived from ribbonfish proteins effectively modulated ACE activity, thus underscoring their therapeutic potential. Molecular docking and modeling corroborated these findings, emphasizing the utility of functional foods as a promising avenue for the treatment and prevention of hypertension, with potential ancillary health benefits and applications as substitutes for synthetic drugs.
研究领域:
食品科学
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生物化学
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药理学
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DOI
PubMed
高影响因子
The Innovation
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2025
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IF 25.7
Xiaoyan Jing,Yanhai Gong,Zhidian Diao,Yan Ma,Yu Meng,Jie Chen,Yishang Ren,Yuting Liang,Yinchao Li,Weihan Sun,Jia Zhang,Yuetong Ji,Zhiqi Cong,Shengying Li,Bo Ma,Zhisong Cui,Li Ma,Jian Xu
Microbiome-wide association studies (MWASs) have uncovered microbial markers linked to ecosystem traits, but the mechanisms underlying their functions can remain elusive. This is largely due to challenges in validating their in situ metabolic activities and tracing such activities to individual genomes. Here, we introduced a phylogeny-metabolism dual-directed single-cell genomics approach called fluorescence- in situ -hybridization-guided single-cell Raman-activated sorting and sequencing (FISH-scRACS-seq). It directly localizes individual cells from target taxon via an FISH probe for marker organism, profiles their in situ metabolic functions via single-cell Raman spectra, sorts cells of target taxonomy and target metabolism, and produces indexed, high-coverage, and precisely-one-cell genomes. From cyclohexane-contaminated seawater, cells representing the MWAS-derived marker taxon of γ-Proteobacteria and that are actively degrading cyclohexane in situ were directly identified via FISH and Raman, respectively, then sorted and sequenced for one-cell full genomes. In such a Pseudoalteromonas fuliginea cell, we discovered a three-component cytochrome P450 system that can convert cyclohexane to cyclohexanol in vitro , representing a previously unknown group of cyclohexane-degrading enzymes and organisms. Therefore, by unveiling enzymes, pathways, genomes, and their in situ cellular functions specifically for those organisms with ecological relevance at one-cell resolution, FISH-scRACS-seq is a rational and generally applicable approach to dissecting and mining microbiota functions.
研究领域:
微生物学
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基因组学
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环境科学
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生物信息学
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DOI
PubMed
高影响因子
Nanoscale
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2018
·Vol. 10
·期 23
·11079-11090
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IF 7.233
Jingpu Zhang,Yanlei Liu,Xiao Zhi,Chunlei Zhang,Tie Fu Liu,Daxiang Cui
Dysregulation of microRNAs (miRNAs) is correlated with cancer progression. In vitro detection methods using extracts from cell lysis cannot provide information about the spatial distribution of miRNAs. Due to the development of miRNA fluorescence in situ hybridization (FISH), increasing amounts of intracellular expression information are being obtained. However, miRNA FISH suffers from weak signals and complex steps and thus remains very challenging. Herein, a strategy based on DNA-templated silver nanoclusters (AgNCs/DNAs) and their G-rich fluorescence enhancement effect was developed for FISH detection of miRNAs in gastric cancer cells. The method combines hybridization and signal amplification into one step, which allows imaging of intracellular miRNAs immediately after hybridization. Most importantly, using the method based on our design, miR-101-3p, miR-16-5p and miR-19b-3p were found to be located in the nuclei of MGC803 cells with granulated shapes, indicating an unanticipated distribution pattern. In addition, before the final miRNA FISH, we performed an optimization of AgNCs/DNAs and their G-rich fluorescence enhancement effect; we found that the effect occurred at shorter wavelengths emitting green fluorescence, with weakened red fluorescence at longer wavelengths. However, the components involved in the FISH process impacted the fluorescence properties so greatly that the probes finally exhibited slightly strengthened red fluorescence signals. Our method enables facile visualization of miRNAs at the subcellular level, which may benefit the precise localization of miRNAs in single cells in the future.
研究领域:
癌症生物学
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分子生物学
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纳米技术
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生物医学工程
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产品关联
DOI
PubMed
高影响因子
Small
·
2022
·Vol. 18
·期 10
·2107232
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IF 15.153
Xingling Wang,Yuxiang Shi,Peng Yang,Xinglin Tao,Shuyao Li,Rui Lei,Zhaoqi Liu,Zhong Lin Wang,Xiangyu Chen
Conventional approaches to studying fish kinematics pose a great challenge for the real-time monitoring of fish motion kinematics. Here, a multifunctional fish-wearable data snooping platform (FDSP) for studying fish kinematics is demonstrated based on an air sac triboelectric nanogenerator (AS-TENG) with antibacterial coating. The AS-TENG not only can harvest energy from fish swimming but also serves as the self-powered sensory module to monitor the swimming behavior of the fish. The peak output power generated from each swing of the fishtail can reach 0.74 mW, while its output voltage can reflect the real-time behavior of the fishtail. The antibacterial coating on the FDSP can improve its biocompatibility and the elastic texture of the FDSP allows it to be tightly attached to fish. The wireless communication system is designed to transmit the sensory data to a cell phone, where the detailed parameters of fish motion can be obtained, including swing angle, swing frequency, and even the typical swing gestures. This FDSP has broad application prospects in underwater self-powered sensors, wearable tracking devices, and soft robots.
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DOI
PubMed
高影响因子
FOOD HYDROCOLLOIDS
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2020
·
IF 7.053
Ting Zhang,Mengzhen Ding,Lina Tao,Lijie Liu,Ningping Tao,Xichang Wang,Jian Zhong
Molecular modification of emulsifiers has attracted many attentions in the field of emulsions. In this work, an octenyl succinic anhydride (OSA) modification method is developed to modify bovine bone gelatins and fish skin gelatins, and then the effect of OSA modification on the gelatins and their application for fish oil-loaded emulsions are explored and compared. The results demonstrate that OSA can be successfully applied to modify gelatins and change their isoelectric points. Moreover, the degree of succinylation (DS) logarithmically increases with OSA-gelatin mass ratios in the chemical reaction process. Further, the OSA modification has no obvious effects on the initial emulsion droplet sizes of fish oil-loaded emulsions. Finally, the emulsion storage experiments suggest that the DS increase of OSA-modified bovine bone gelatins increases the droplet stability, phase transition time, and creaming index of fish oil-loaded emulsions, whereas the DS increase of OSA-modified fish skin gelatins only increases the droplet stability and has no obvious effects on the phase transition and creaming index of fish oil-loaded emulsions. This work will provide useful information to understand the relationship among molecular modification, molecular structure, and function of protein. It also will provide a potential route to optimize the preparation and application of fish oil-loaded emulsions in the field of food and drug industries.
研究领域:
食品科学
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化学工程
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材料科学
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DOI
高影响因子
ACS Food Science & Technology
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2024
·
IF 2.6
Lijia Chen,Huan Gong,Wenjie Zhang,Qiqi Bian,Li Li,Ye Zi,Cuiping Shi,Xichang Wang,Jian Zhong
The development of food-grade hydrogels is an important topic for the encapsulation of bioactive substances. Herein, a dual gelation method of cold-setting with ion-alginate (ALG) cross-linking was developed to fabricate fish oil-loaded fish gelatin (FG)/ion-ALG dual hydrogels with five types of ions (H+, Ca2+, Ba2+, Fe2+, and Fe3+). The fish oil-loaded fish gelatin/ion-ALG mono hydrogels were also developed with Na+ and Mg2+. Four dual hydrogels had quicker diffusion and ion-cross-linking (H+, Ca2+, Ba2+, and Fe2+) than the FG/Fe3+-ALG dual hydrogel. All of the hydrogels showed similar water activity (0.94). The dual hydrogels had lower water contents than the mono hydrogels. Fe3+ induced the highest hydrogel hardness (28.6 ± 0.4 N) and Ba2+ induced the highest chewiness (6.3 ± 0.3 N) and gumminess (6.9 ± 0.3 N). The dual hydrogels showed lower peroxide values than the mono hydrogels. Compared with Na+, all other ions induced higher free fatty acid release percentages in the small intestinal phase. All results suggested that the cold-setting gelation and ion-ALG gelation method could be combined to prepare nutrient-loaded hydrogels. The obtained hydrogels could be applied to prepare hydrogel foods with good encapsulation of lipophilic nutrients.
研究领域:
食品科学
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材料科学
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生物技术
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产品关联
DOI
高影响因子
Engineering
·
2024
·
IF 10.1
Jialiang Zhang,Qing Yang,Qingyun Ma,Fangzheng Ren,Yang Cheng,Xiaodan Gou,Jie Liang,Feng Chen
Hard scales in scaly fish species ensure the structural and functional integrity of the inner skin and body, even when subjected to various types of external forces. Mucus and oil secreted from the inner layer of the fish skin to the surface exhibit resistance to a wide range of liquids, maintaining the antifouling properties of the fish skin surface. Inspired by these biological structures, ultra-sturdy and durable scale-armored-sliding surfaces (SASS) were fabricated in this study using femtosecond laser electrodeposition (FED). In the FED method, a scaly structure is grown from the substrate across a sliding layer to form an SASS. The unique scale-armored structure offers protection against impact and abrasion while maintaining the performance and integrity of the structure. The mechanical sturdiness of the SASS improved by four orders of magnitude compared to that of the conventional antifouling surface. In addition, the SASS exhibited remarkable chemical durability, excellent hydraulic pressure resistance, liquid repellency, and good corrosion resistance based on characterization using various methods. FED enables the preparation of SASS on several materials, including Cu and Al and more. SASS fabricated using FED has great potential for the application of antifouling surfaces in extremely harsh environments.
研究领域:
材料科学
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仿生学
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表面工程
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产品关联
DOI
高影响因子
FOOD HYDROCOLLOIDS
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2025
·
IF 12.4
Kemeng Qin,Xinyu Sun,Ruican Wang,Jingmin Liu,Haitao Wang,Yi Wang,Shuo Wang
The development of sustainable and high-performance food packaging materials is crucial for addressing global food waste and environmental pollution issues. An innovative approach was proposed by using fish skin protein (FSP) from Channa argus as a natural carrier to promote the self-assembly of rosmarinic acid (RA) and curcumin (CUR) into stable nanospheres (FSP/CUR/RA) through non-covalent interactions such as hydrogen bonds, π-alkyl/π-anion interactions, and electrostatic interactions in this study. Compared with binary systems, the self-assembled FSP/CUR/RA ternary nanospheres exhibited significant advantages in colloidal stability and functionality: the optimized RA6 nanospheres have the smallest particle size (508 ± 19.30 nm), the highest ζ-potential (13.04 mV), and excellent antioxidant activity (ABTS + scavenging rate of 87.91 % at 20 μL), effectively overcoming the limitations of poor solubility and instability of CUR and RA. Upon incorporating the nanospheres into the active film, its overall performance was significantly enhanced. Specifically: Barrier properties were improved, with the water vapor transmission rate reduced to 4.06 × 10 −13 g m −1 ·Pa −1 ·s −1 , representing a 27.6 % decrease compared to the pure FSP film. Mechanical properties were optimized due to RA's effective inhibition of CUR aggregation, achieving a well-balanced tensile strength (TS) and elongation at break (EAB). The film demonstrated outstanding antioxidant capacity, with a free radical scavenging rate of 86.39 %, significantly higher than the control groups. Multifunctional characteristics were evident, including ultraviolet shielding capability, controlled release of CUR/RA, and complete biocompatibility (cell viability 100 %). In practical applications, FSP/CUR/RA films significantly extended the shelf life of fresh shrimp by reducing weight loss (3 % compared to 4.44 % in the control group), maintaining a low TVB-N level (11.84 mg/100 g after 3 days), and inhibiting lipid oxidation (TBARS < 1 mg MDA/100 g). This study not only provided a sustainable strategy for the value-added utilization of fish processing by-products but also promoted the design of multifunctional food packaging materials with enhanced preservation capability.
研究领域:
食品包装
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可持续材料
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生物高分子
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功能性薄膜
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产品关联
DOI
高影响因子
Current Research in Food Science
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2024
·
IF 6.2
Weibo Lu,Yunyan Li,Lijun Ge,Honghai Wang,Ting Liu,Qiaoling Zhao,Zhujun Mao,Jingjing Liang,Pingya Wang,Kang Chen,Jing Xue,Qing Shen
The authenticity of fish products has become a widespread issue in markets due to substitution and false labeling. Lipidomics combined with chemometrics enables the fraudulence identification of food through the analysis of a large amount of data. This study utilized ultra-high-performance liquid chromatography (UHPLC)-QE Orbitrap MS technology to comprehensively analyze the lipidomics of commercially available basa catfish and sole fish. In positive and negative ion modes, a total of 779 lipid molecules from 21 lipid subclasses were detected, with phospholipid molecules being the most abundant, followed by glycerides molecules. Significant differences in the lipidome fingerprinting between the two fish species were observed. A total of 165 lipid molecules were screened out as discriminative features to distinguish between basa catfish and sole fish, such as TAG(16:0/16:0/18:1), PC(14:0/22:3), and TAG(16:1/18:1/18:1), etc. This study could provide valuable insights into authenticating aquatic products through comprehensive lipidomics analysis, contributing to quality control and consumer protection in the food industry.
研究领域:
食品科学
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分析化学
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生物化学
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产品关联
DOI
PubMed
高影响因子
JOURNAL OF FISH BIOLOGY
·
2024
·Vol. 105
·期 4
·1086-1108
·
IF 1.7
Cao Thang Luong,Gilbert Audira,Kevin Adi Kurnia,Chih-Hsin Hung,Chung-Der Hsiao
This paper introduces the Fish 3D Locomotion app (F3LA), a Python-based, Graphical User Interface (GUI)-equipped tool designed to automate behavioral endpoint extraction in zebrafish locomotion assays. Building on our previous work, which utilized a specialized aquatic tank with a mirror and a single camera for fish movement tracking in three dimensions, F3LA significantly enhances data processing efficiency. Its accuracy was tested by reanalyzing and comprehensively comparing the calculated data with the previously published data from prior publications. From the comparison results, 90% of endpoints showed a similar statistical difference result. These minor differences were due to the different starting points for the dataset and updated calculation formulas that are implemented in F3LA. In addition, shoaling area or shoaling volume calculations are also included in F3LA as a new feature that can serve as sensitive indicators of social cohesion, group dynamics, or stress responses, offering insights into neuropsychological conditions or the effects of pharmacological interventions. Furthermore, F3LA offers a marked improvement over manual operations, being at least five times faster, while maintaining consistent accuracy as it reduces human-induced errors, ensuring a higher degree of reliability in the results. Finally, the potency of F3LA was tested to evaluate the toxicities of 14 rare earth elements (REEs) to the adult zebrafish behaviors. Based on the results, our findings suggested that each tested REE altered fish behaviors in different patterns and magnitudes to each other. However, among the tested light rare earth elements (LREEs), neodymium was demonstrated to cause more relatively severe behavior alterations than other LREEs, indicated by the statistically higher value of entropy (0.2695 ± 0.04977 (mean with a standard deviation)) than the control group (0.2352 ± 0.05896). Meanwhile, in terms of heavy rare earth elements (HREEs), erbium seemed to lead to more distinct behavior toxicities than other HREEs, which was shown by the statistically lower level of fractal dimension (2.022 ± 0.3412) than the untreated group (2.255 ± 0.1661). Taken together, F3LA's development marks a significant advance in high-throughput toxicological and pharmacological assessments in zebrafish, leveraging three-dimensional locomotion data for a more comprehensive analysis of fish behavior performance, providing a significant contribution to research in various fields.
研究领域:
生物学
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毒理学
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药理学
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神经科学
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产品关联
DOI
PubMed
高影响因子
ACS Applied Energy Materials
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2024
·
IF 5.4
Fancheng Meng,Peng Chen,Shulin Li,Na Cao,Sheng Cheng,Xiangfeng Wei,Jiangtao Di,Jiehua Liu
Compared with the rapidly developing lithium- and sodium-ion batteries, zinc-air batteries (ZABs) offer the advantages of safety and high energy density. Nevertheless, their applications in underwater conditions are currently limited due to the low oxygen levels in such environments. Drawing inspiration from fish gills, we have successfully constructed a self-breathing zinc-air battery (ZAB) that can extract dissolved oxygen from water and convert it to electrical energy. By utilizing a Co2Fe-NC catalyst and a large-window cathode, the ZAB demonstrates a continuous discharge duration of 68.6 h in the underwater condition, thanks to its well-engineered architecture, optimized catalyst, and gas diffusion layer. Meanwhile, the underwater ZAB outperforms fish gills as it also operates efficiently in air, exhibiting a high capacity of 740 mA h g–1 and a high power density of 320 mW cm–2. Additionally, prolonged cycling tests indicate the ZAB’s capability for stable charging and discharging with minimal potential variation. This study introduces an innovative approach to the development of breathable underwater metal–air batteries.
研究领域:
材料科学
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能源技术
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仿生学
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产品关联
DOI
高影响因子
危险品化学品经营许可证（带存储）