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Ribosome Engineering for Enhanced Butenyl-Spinosyn Production in Saccharopolyspora pogona

Current microbiology 2025年第8期82卷 337页

作者： Chao Guo Yuchun Liu Bo Lv Xinying Li Qingrong Wang Wei Han Chao Wang Academy of National Food and Strategic Reserves Administration 11 Baiwanzhuang Street Xicheng District Beijing 100037 China. Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering Ministry of Industry and Information Technology Institute of Biochemical Engineering School of Chemistry and Chemical Engineering Beijing Institute of Technology Beijing 100081 China. Academy of National Food and Strategic Reserves Administration 11 Baiwanzhuang Street Xicheng District Beijing 100037 China. wc@***.

Ribosome engineering, a strategy that utilizes antibiotic resistance mutations to modulate ribosomal function, has emerged as a powerful approach for enhancing microbial metabolite production. In this study, ribosome engineering was applied to Saccharopolyspora pogona ASAGF2-G4 under streptomycin selection to improve butenyl-spinosyn production. Screening for streptomycin-resistant mutants at concentrations ranging from 2 to 20 µg/mL resulted in the isolation of 58 mutants, of which 27.6% exhibited increased butenyl-spinosyn production. Among these, 22 mutants harbored six distinct mutations in the rpsL gene, resulting in five amino acid substitutions in the ribosomal protein S12: Lys43 to Arg, Lys43 to Thr, Lys43 to Asn, Lys88 to Glu, and Lys88 to Arg. The highest frequency of rpsL mutant isolation was observed at a streptomycin concentration of 15 µg/mL. Phenotypic characterization revealed altered growth dynamics, pH shifts, and glucose utilization among the mutants, with the K88R and K43R variants exhibiting significantly increased butenyl-spinosyn production-1.78-fold and 1.64-fold higher than that of the parental strain, respectively. Quantitative PCR analysis showed significant upregulation of translation-related genes (rpsL and frr), growth-related genes (whiA and bldD), and key butenyl-spinosyn biosynthetic genes (busA, busF, and busI) in the K88R mutant, suggesting that the K88R substitution enhances target compound biosynthesis by modulating ribosomal function and associated metabolic networks. Future research should explore combinatorial approaches, including the development of multi-antibiotic-resistant mutants and elevated expression of ribosomal genes, to maximize butenyl-spinosyn yields. This study underscores the potential of ribosome engineering as a platform for improving butenyl-spinosyn production and provides a foundation for subsequent industrial-scale applications.

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Article Diversity Monitoring of Coexisting Birds in Urban Forests by Integrating Spectrograms and Object-Based Image analysis

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Forests 2022年第2期13卷

作者： Zhao, Yilin Yan, Jingli Jin, Jiali Sun, Zhenkai Yin, Luqin Bai, Zitong Wang, Cheng Research Institute of Forestry Chinese Academy of Forestry Beijing100091 China Key Laboratory of Tree Breeding and Cultivation National Forestry and Grassland Administration Beijing100091 China Urban Forest Research Center National Forestry and Grassland Administration Beijing100091 China School of Agriculture and Biology Shanghai Jiao Tong University Shanghai200240 China Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station Ministry of Science and Technology Shanghai200240 China Beijing Institute of Landscape and Traditional Architecture Design and Research Co. Ltd Beijing100005 China

In the context of rapid urbanization, urban foresters are actively seeking management monitoring programs that address the challenges of urban biodiversity loss. Passive acoustic monitoring (PAM) has attracted attention because it allows for the collection of data passively, objectively, and continuously across large areas and for extended periods. However, it continues to be a difficult subject due to the massive amount of information that audio recordings contain. Most existing automated analysis methods have limitations in their application in urban areas, with unclear ecological relevance and efficacy. To better support urban forest biodiversity monitoring, we present a novel methodology for automatically extracting bird vocalizations from spectrograms of field audio recordings, integrating object-based classification. We applied this approach to acoustic data from an urban forest in beijing and achieved an accuracy of 93.55% (±4.78%) in vocalization recognition while requiring less than 1/8 of the time needed for traditional inspection. The difference in efficiency would become more significant as the data size increases because object-based classification allows for batch processing of spectrograms. Using the extracted vocalizations, a series of acoustic and morphological features of bird-vocalization syllables (syllable feature metrics, SFMs) could be calculated to better quantify acoustic events and describe the soundscape. A significant correlation between the SFMs and biodiversity indices was found, with 57% of the variance in species richness, 41% in Shannon’s diversity index and 38% in Simpson’s diversity index being explained by SFMs. Therefore, our proposed method provides an effective complementary tool to existing automated methods for long-term urban forest biodiversity monitoring and conservation. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

关键词： Birds

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Corrigendum to "Investigating the stability of chimeric murine polyomavirus VP1 Capsomeres via molecular dynamics simulations and experimental analysis" [Int. J. Biol. Macromol., volume 286, January 2025, 138372]

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International journal of biological macromolecules 2025年 303卷 140511页

作者： Hong Luo Yanyan Ma Zhiguo Su Yanhao Gu Songping Zhang Lukas Gerstweiler School of Chemical Engineering Faculty of Science Engineering and Technology University of Adelaide Adelaide 5005 Australia State Key Laboratory of Biochemical Engineering Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS) Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 PR China Institute of Pharmaceutical and Food Engineering Shanxi University of Chinese Medicine Jinzhong 030619 PR China. State Key Laboratory of Biochemical Engineering Key Laboratory of Biopharmaceutical Preparation and Delivery (CAS) Institute of Process Engineering Chinese Academy of Sciences Beijing 100190 PR China. School of Chemical Engineering Faculty of Science Engineering and Technology University of Adelaide Adelaide 5005 Australia. School of Chemical Engineering Faculty of Science Engineering and Technology University of Adelaide Adelaide 5005 Australia. Electronic address: lukas.gerstweiler@adelaide.edu.au.

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DNA-modulated Mo-Zn single-atom nanozymes: Insights from molecular dynamics simulations to smartphone-assisted biosensing

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Chinese Chemical Letters 2024年

作者： Zhimin Song Zhe Tang Yu Zhang Yanru Zhou Xiaozheng Duan Yan Du Chong-Bo Ma Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education National & Local United Engineering Laboratory for Power Batteries Key Laboratory of Nanobiosensing and Nanobioanalysis at Universities of Jilin Province Analysis and Testing Center Department of Chemistry Northeast Normal University Changchun 130024 China Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun 130022 China Department of Chemistry University of Science & Technology of China Hefei 230026 China School of Physics Science and Technology Yili Normal University Yining 835000 China School of Physics Northeast Normal University Changchun 130024 China State Key Laboratory of Molecular Engineering of Polymers Department of Macromolecular Science Fudan University Shanghai 200438 China

Recent advancements in nanotechnology have spotlighted the catalytic potential of nanozymes, particularly single-atom nanozymes (SANs), which are pivotal for innovations in biosensing and medical diagnostics. Among others, DNA stands out as an ideal biological regulator. Its inherent programmability and interaction capabilities allow it to significantly modulate nanozyme activity. This study delves into the dynamic interplay between DNA and molybdenum-zinc single-atom nanozymes (Mo-Zn SANs). Using molecular dynamics simulations, we uncover how DNA influences the peroxidase-like activities of Mo-Zn SANs, providing a foundational understanding that enhances the application scope of SANs in biosensing. With these insights as a foundation, we developed and demonstrated a model aptasensor for point-of-care testing (POCT), utilizing a label-free colorimetric approach that leverages DNA-nanozyme interactions to achieve high-sensitivity detection of lysozyme. Our work elucidates the nuanced control DNA exerts over nanozyme functionality and illustrates the application of this molecular mechanism through a smartphone-assisted biosensing platform. This study not only underscores the practical implications of DNA-regulated Mo-Zn SANs in enhancing biosensing platforms, but also highlights the potential of single-atom nanozyme technology to revolutionize diagnostic tools through its inherent versatility and sensitivity.

关键词： Single-atom nanozymes DNA-regulated biosensors Molecular dynamics simulations Colorimetric aptasensing Point-of-care diagnostics

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Nutrient value of wild fodder species and the implications for improving the diet of mithun (Bos frontalis) in Dulongjiang area, Yunnan Province, China

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Plant Diversity 2020年第6期42卷 455-463页

作者： Yanfei Geng Sailesh Ranjitkar Qiaoshun Yan Zhijun He Baqi Su Shengtao Gao Junli Niu Dengpan Bu Jianchu Xu College of Tea Science Guizhou UniversityGuiyang 550025China Key Laboratory of Economic Plants and Biotechnology Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China CAAS-ICRAF Joint Lab on Agroforestry and Sustainable Animal Husbandry World AgroforestryEast and Central AsiaBeijing 100193China NGene Solutions of Natural InnovationKathmanduGPO 44614Nepal Mid-Western University Faculty of Humanities and Social ScienceNaya BatoLalitpur 44600Nepal Agriculture Bureau of Gongshan Derung and Nu Autonomous County Nujiang 673500China State Key Laboratory of Animal Nutrition Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijing 100193China College of Animal Science and Technology Shihezi UniversityShihezi 832003China Hunan Co-Innovation Center of Animal Production Safety CICAPSChangsha 410128China World Agroforestry East and Central AsiaKunming 650201China

Wild fodder plants are valuable because they provide an important livestock feed resource globally,especially for smallholder farmers,and have important roles in natural resource ***-depth knowledge of wild forage plants can motivate local people for feed resource and habitat conservation of threatened herbivores such as Mithun(Bos frontalis).Mithun occur in small patches in the mountains of Dulongjiang,nearby villagers domesticated this animal but left animal to freely graze in the *** fodder plants occur in these mountains,however,little is known about their nutritional *** conducted an ethnobotanical survey to document important wild fodder plants consumed by mithun in the Dulongjiang *** nutritional content of 21 highly mentioned wild fodder plants in an ethnobotanical survey was *** analysis showed that Fagopyrum dibotrys were the fodder species with the highest crude protein(CP)content(26.89%),followed by Polygonum molle(21.88%)and Hydrangea longipes(21.12%).Synthesis of relative feed value index and grey relational grade,***,*** and Tetrastigma obtectum were ranked the top three nutritional *** was a significant difference between 21 species on their in vitro digestibility and the most highly digestible fodder species was Elatostema *** model analysis on relationship between frequency of citation of 21 wild forage plants by local farmers and their nutrient composition showed that the frequency was significantly positively correlated with the nutritional value of the feed(R2?0.28,P<0.05).We concluded that these species have high nutritional values to improve mithun production in integrated crop-livestock *** species or mixtures of species with useful nutritional characters could be cultivated to improve livestock productivity,habitat conservation including that of mithun and wild forage resource management.

关键词： Wild fodder species Nutritional value Mithun Nature conservation

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A lightweight privacy-preserving scheme using label-based pixel block mixing for image classification in deep learning

arXiv

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arXiv 2021年

作者： Xiang, Yuexin Li, Tiantian Ren, Wei Zhu, Tianqing Raymond Choo, Kim-Kwang School of Computer Science China University of Geosciences Wuhan China Henan Key Laboratory of Network Cryptography Technology Zhengzhou China Key Laboratory of Network Assessment Technology CAS Institute of Information Engineering Chinese Academy of Sciences Beijing100093 China Department of Information Systems and Cyber Security University of Texas at San Antonio San AntonioTX78249-0631 United States

To ensure the privacy of sensitive data used in the training of deep learning models, a number of privacy-preserving methods have been designed by the research community. However, existing schemes are generally designed to work with textual data, or are not efficient when a large number of images is used for training. Hence, in this paper we propose a lightweight and efficient approach to preserve image privacy while maintaining the availability of the training set. Specifically, we design the pixel block mixing algorithm for image classification privacy preservation in deep learning. To evaluate its utility, we use the mixed training set to train the ResNet50, VGG16, InceptionV3 and DenseNet121 models on the WIKI dataset and the CNBC face dataset. Experimental findings on the testing set show that our scheme preserves image privacy while maintaining the availability of the training set in the deep learning models. Additionally, the experimental results demonstrate that we achieve good performance for the VGG16 model on the WIKI dataset and both ResNet50 and DenseNet121 on the CNBC dataset. The pixel block algorithm achieves fairly high efficiency in the mixing of the images, and it is computationally challenging for the attackers to restore the mixed training set to the original training set. Moreover, data augmentation can be applied to the mixed training set to improve the training’s *** Codes 68T07 Copyright © 2021, The Authors. All rights reserved.

关键词： Image classification

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First-order liquid-liquid phase transition in nitrogen-oxygen mixtures

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Physical Review B 2021年第14期103卷 144105-144105页

作者： Yang-Shun Lan Zhao-Qi Wang Lei Liu Guo-Jun Li Hua-Yang Sun Zhi-Jian Fu Yun-Jun Gu Guang Yang Lu-Ning Li Zhi-Guo Li Qi-Feng Chen Xiang-Rong Chen College of Physics Sichuan University Chengdu 610064 People's Republic of China National Key Laboratory for Shock Wave and Detonation Physics Research Institute of Fluid Physics Chinese Academy of Engineering Physics Mianyang 621900 People's Republic of China Northwest Institute of Nuclear Technology Xi'an 710024 People's Republic of China School of Electronic Information and Electrical Engineering Chongqing University of Arts and Sciences Chongqing 402160 People's Republic of China Science and Technology on Space Physics Laboratory China Academy of Launch Vehicle Technology Beijing 100076 People's Republic of China

The first-order liquid-liquid phase transition (LLPT) describes the counterintuitive nature between two distinct liquids in a single system. However, the physical understanding of LLPT in simple liquid mixtures has remained elusive. Here, a first-order LLPT for nitrogen-oxygen (N-O) mixtures is investigated via extensive ab initio molecular dynamics simulations. The first-order LLPT is characterized by discontinuities of a short-range order and transport properties, occurring at the transition pressures identified by looking at isotherms. The LLPT in N-O mixtures is dominated primarily by the molecular-to-polymeric transformation. The resulting phase boundaries and further structural analysis show the crucial influence of oxygen on weakening the LLPT of N-O mixtures by promoting chemical reactions with nitrogen and crippling polymerizations. Furthermore, noncovalent interactions of short- to long-range van der Waals have evident impacts on the LLPT boundary. The introduction of the strongly constrained and appropriately normed functional with revised Vydrov–van Voorhis nonlocal correlation (SCAN-rVV10) functional to describe the phase-transition behaviors improves the agreement with experimental data. The results highlight the characteristic features of the complex interplay in binary mixtures and revisit the first-order phase transition of dense nitrogen.

关键词： Electrical conductivity First order phase transitions Liquid-liquid phase transition Phase diagrams Phase transitions First-principles calculations Meta-GGA Molecular dynamics

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Terrestrial Water Storage Changes of Qinghai Lake on the Tibetan Plateau From Joint Inversion of GNSS and InSAR Data

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Water Resources Research 2025年第6期61卷

作者： Hai Zhu Kejie Chen Mingjia Li Shunqiang Hu Guoqing Zhang Xingxing Kuang Wenfeng Cui Shengpeng Zhang Junguo Liu Department of Earth and Space Sciences Southern University of Science and Technology Shenzhen China Guangdong Provincial Key Laboratory of Geophysical High-resolution Imaging Technology Southern University of Science and Technology Shenzhen China Key Laboratory of Poyang Lake Wetland and Watershed Research Ministry of Education Jiangxi Normal University Nanchang China State Key Laboratory of Tibetan Plateau Earth System Science Environment and Resources (TPESER) Institute of Tibetan Plateau Research Chinese Academy of Sciences Beijing China Guangdong-Hong Kong Joint Laboratory for Soil and Groundwater Pollution Control School of Environmental Science and Engineering Southern University of Science and Technology Shenzhen China Qinghai Provincial Key Laboratory of Geomatics Technology and Application Xining China Qinghai Provincial Basic Surveying and Mapping Institute Xining China Henan Provincial Key Lab of Hydrosphere and Watershed Water Security North China University of Water Resources and Electric Power Zhengzhou China

Although geodetic techniques like Gravity Recovery and Climate Experiment have been widely applied to investigate terrestrial water storage (TWS) variations at regional or basin scales on the Tibetan Plateau (TP) caused by global warming, their coarse spatial has limited the study of individual lakes. In this study, we overcome this limitation by jointly using Global Navigation Satellite System (GNSS) and Interferometric Synthetic Aperture Radar (InSAR) data to generate a high-precision, high-resolution surface deformation field, enabling the quantitative assessment of TWS changes for Qinghai Lake, from January 2016 to December 2022. By leveraging Independent Component analysis to extract surface deformation induced by lake hydrological loads, we find that the deformation caused by Qinghai Lake's hydrological changes is spatially limited to within approximately 25 km of the lake and is largely overshadowed by regional background loads of the TP. The region surrounding Qinghai Lake exhibited an overall trend of initial subsidence (from January 2016 to August 2019, −2.89 to −0.30 mm/yr) followed by uplift (from September 2019 to December 2022, 2.20 to 4.89 mm/yr), primarily driven by variations in precipitation patterns. Notably, we found that lake water volume increase accounts for up to 86% of the total TWS changes in Qinghai Lake, underscoring the relatively marginal role of groundwater compared to previous assessments in Inner TP where groundwater accounted for 34% of TWS changes. This study demonstrates the effectiveness of integrating GNSS and InSAR data to overcome spatial resolution limitations, providing detailed insights into the hydrological dynamics of individual lakes like Qinghai Lake, and contributes to a more comprehensive understanding of TP's hydrological changes under the influence of climate change. Integrated GNSS-InSAR reveals that Qinghai Lake hydrological changes influenced surface deformation within ∼25 km during 2011–2023 Deformation around Q

关键词： GNSS InSAR joint inversion loading deformation lake storage monitoring

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Can the nature of a0(980) be tested in the Ds+→π+π0η decay?

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Physical Review D 2021年第11期103卷 116016-116016页

作者： Xi-Zhe Ling Ming-Zhu Liu Jun-Xu Lu Li-Sheng Geng Ju-Jun Xie School of Physics Beihang University Beijing 100191 China School of Space and Environment Beihang University Beijing 100191 China Beijing Key Laboratory of Advanced Nuclear Materials and Physics Beihang University Beijing 100191 China School of Physics and Microelectronics Zhengzhou University Zhengzhou Henan 450001 China Institute of Modern Physics Chinese Academy of Sciences Lanzhou 730000 China School of Nuclear Science and Technology University of Chinese Academy of Sciences Beijing 101408 China

From the amplitude analysis of the Ds+→π+π0η decay, the BESIII Collaboration first observed the Ds+→a0(980)+π0 and Ds+→a0(980)0π+ decay modes, which are expected to occur through the pure W-annihilation processes. The measured branching fraction B[Ds+→a0(980)+(0)π0(+),a0(980)+(0)→π+(0)η] is, however, found to be larger than those of known W-annihilation decays by 1 order of magnitude. This apparent contradiction can be reconciled if the two decays are induced by internal W-conversion or external W-emission mechanisms instead of a W-annihilation mechanism. In this work, we propose that the Ds+ decay proceeds via both the external and internal W-emission instead of W-annihilation mechanisms. In such a scenario, we perform a study of the Ds+→π+π0η decay by taking into account the contributions from the tree diagram Ds+→ρ+η→π+π0η and the intermediate ρ+η and K*K¯/KK¯* triangle diagrams. The intermediate a0(980) state can be dynamically generated from the final state interactions of coupled KK¯ and πη channels, and it is shown that the experimental data can be described fairly well, which supports the interpretation of a0(980) as a molecular state.

关键词： Chiral perturbation theory Hadron-hadron interactions Hadronic decays Quark model

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21-cm foreground removal using AI and frequency-difference technique

arXiv

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arXiv 2023年

作者： Shi, Feng Chang, Haoxiang Zhang, Le Shan, Huanyuan Zhang, Jiajun Zhou, Suiping Jiang, Ming Wang, Zitong School of Aerospace Science And Technology Xidian University Xi’an710126 China Peng Cheng Laboratory No.2 Xingke 1st Street Shenzhen518000 China School of Physics and Astronomy Sun Yat-sen University 2 Daxue Road Tangjia Zhuhai519082 China CSST Science Center for the Guangdong-Hong Kong-Macau Greater Bay Area Zhuhai519082 China Nandan Road 80 Shanghai200030 China University of Chinese Academy of Sciences Beijing100049 China National Key Laboratory of Radar Signal Processing Xidian University Xi’an710126 China

The deep learning technique has been employed in removing foreground contaminants from 21-cm intensity mapping, but its effectiveness is limited by the large dynamic range of the foreground amplitude. In this study, we develop a novel foreground removal technique grounded in U-Net networks. The essence of this technique lies in introducing an innovative data preprocessing step specifically, utilizing the temperature difference between neighboring frequency bands as input. Combining with the frequency difference, we refer to our method as the UNet-fd (UNet frequency-difference), where the U-Net structure is the same as that in deep21. Based on our tests, we demonstrate that this frequency-difference preprocessing technique can substantially reduce the dynamic range of foreground amplitudes by approximately two orders of magnitude. This reduction proves to be highly advantageous for the U-Net foreground removal. We observe that the HI signal can be reliably recovered, as indicated by the cross-correlation power spectra showing unity agreement at the scale of k 0.3 hMpc−1 in the absence of instrumental effects. Moreover, accounting for the systematic beam effects, our reconstruction displays consistent auto-correlation and cross-correlation power spectrum ratios at the 1σ level across scales k 0.1 hMpc−1, with only a 10% reduction observed in the cross-correlation power spectrum at k 0.2 hMpc−1. The effects of redshift-space distortion are also reconstructed successfully, as evidenced by the quadrupole power spectra matching with the target truth. In order to test how thermal noise affects the performance of our method, we simulated various white noise levels in the map. This shows the mean cross-correlation ratio R¯cross 0.8 when the level of the thermal noise is smaller than or equal to that of the HI signal. In comparison, our method outperforms the traditional Principal Component analysis (PCA) method. The PCA-derived cross-correlation ratios are underestimated by

关键词： Power spectrum

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