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| 1 | Cold-chain food contamination as the possible origin of COVID-19 resurgence in Beijing显示文摘COVID-19,caused by SARS-CoV-2[1,2],has been contained in China through stringent non-pharmaceutical interventions.Border control and quarantine have effectively prevented the virus from being spread by infected travellers,but the risk of resurgence caused by other routes of introduction and transmission remains unclear,and current strategies to prevent resurgence could be flawed.Since July,SARS-CoV-2 RNA contaminations in frozen food imported from countries with ongoing epidemics have been reported in nine provinces in China[3,4].However,there is no robust evidence of COVID-19 outbreaks initiated by environmentto-human transmission.Here we add to evidence of such transmission by investigating the recent COVID-19 resurgence in Beijing. | Xinghuo Pang Lili Ren Shuangsheng Wu Wentai Ma Jian Yang Lin Di Jie Li Yan Xiao Lu Kang Shichang Du Jing Du Jing Wang Gang Li Shuguang Zhai Lijuan Chen Wenxiong Zhou Shengjie Lai Lei Gao Yang Pan Quanyi Wang Mingkun Li Jianbin Wang Yanyi Huang Jianwei Wang COVID-19 Field Response Group COVID-19 Laboratory Testing Group | 2020 | National Science Review2020，7，12： | 51 |
| 2 | Q-switched fiber laser based on saturable absorption of ferroferric-oxide nanoparticles显示文摘We demonstrate that ferroferric-oxide(Fe_3O_4) nanoparticles exhibit nonlinear saturable absorption property at1.55 μm, and fabricate two filmy saturable absorbers by embedding the nanoparticles into a polyvinyl alcohol(PVA) film or polyimide(PI) film separately. In the Fe_3O_4-PVA(Fe_3O_4-PI) Q-switched fiber laser, the pulse repetition rate increases from 8.5 kHz(5.5 kHz) to 28 kHz(49 kHz) and the pulse duration decreases from 23.5 μs(47 μs) to 6 μs(3.5 μs) by varying the pump power from 25 m W(23 mW) to 150 m W(650 mW). Experiment results indicate that PI-based saturable absorbers can afford larger powers than PVA-based saturable absorbers, which can be attributed to the higher fusion point of the PI film. The Fe_3O_4-PI saturable absorber exhibits features of high damage threshold, low cost, and good flexibility, which could be applied in fields of near-infrared pulse generation and frequency conversions. | Dong Mao Xiaoqi Cui Wending Zhang Mingkun Li Tianxian Feng Bobo Du Hua Lu Jianlin Zhao | 2017 | Photonics Research2017，5，1： | 3 |
| 3 | Genomes of major fishes in world fisheries and aquaculture: Status, application and perspective显示文摘Capture fisheries and aquaculture provide a significant amount of high-quality protein to human beings and thus play an essential role in ending global hunger and malnutrition.The availability of tens of hundreds of fish genomes and the advances of genomics have allowed addressing many challenging issues such as overfishing and germplasm degradation faced by fisheries and aquaculture.In this review,we describe the current status of genomics in fisheries and aquaculture,with an emphasis on 14 species of fish that are considerably important to global fisheries and aquaculture,in the context of genome sequencing and assembly,annotation,GC contents,and repeats.The majority of these genomes are assembled at the chromosome level and annotated with proteins and pathways,with functional relevance to fisheries and aquaculture,such as environmental adaptation and phenotypic variation.We summarize potential genomic applications in fisheries and aquaculture that are related to assessment and use of genetic resources,disease resistance,growth and development,sexual determination,and fisheries management.Although much progress has been achieved in genomic application to fisheries and aquaculture,the full potential remains to be explored and reaped.We discuss the challenges and perspectives of genomics in translational aquaculture and fisheries,which include genome assembly and annotation,genomic selection and breeding,genomics in fisheries management,and integrated artificial intelligence systems.In the coming decades,we anticipate the applications of genomic techniques such as genome editing and genomic selection,along with the use of emerging intelligence systems,in aquaculture and fisheries will contribute significantly to genetic improvements of farmed fish and sustainable exploitation of fishery resources,which consequently lead to eradicating global poverty by 2030,an ambitious goal set by the United Nations. | Guoqing Lu Mingkun Luo | 2020 | Aquaculture and Fisheries2020，5，4： | 2 |
| 4 | Artificial Intelligence in Pharmaceutical Sciences显示文摘Drug discovery and development affects various aspects of human health and dramatically impacts the pharmaceutical market.However,investments in a new drug often go unrewarded due to the long and complex process of drug research and development(R&D).With the advancement of experimental technology and computer hardware,artificial intelligence(AI)has recently emerged as a leading tool in analyzing abundant and high-dimensional data.Explosive growth in the size of biomedical data provides advantages in applying AI in all stages of drug R&D.Driven by big data in biomedicine,AI has led to a revolution in drug R&D,due to its ability to discover new drugs more efficiently and at lower cost.This review begins with a brief overview of common AI models in the field of drug discovery;then,it summarizes and discusses in depth their specific applications in various stages of drug R&D,such as target discovery,drug discovery and design,preclinical research,automated drug synthesis,and influences in the pharmaceutical market.Finally,the major limitations of AI in drug R&D are fully discussed and possible solutions are proposed. | Mingkun Lu Jiayi Yin Qi Zhu Gaole Lin Minjie Mou Fuyao Liu Ziqi Pan Nanxin You Xichen Lian Fengcheng Li Hongning Zhang Lingyan Zheng Wei Zhang Hanyu Zhang Zihao Shen Zhen Gu Honglin Li Feng Zhu | 2023 | Engineering2023，，8： | 1 |
| 5 | On the origin of SARS-CoV-2——The blind watchmaker argument显示文摘In the comparison with SARS-CoVof 2003,SARS-CoV-2 is extremely well adapted to the human populations and its adaptive shift from the animal host to humans must have been even more extensive.By the blind watchmaker argument,such an adaptive shift can only happen prior to the onset of the current pandemic and with the aid of step-by-step selection. | Chung-I Wu Haijun Wen Jian Lu Xiao-dong Su Alice CHughes Weiwei Zhai Chen Chen Hua Chen Mingkun Li Shuhui Song Zhaohui Qian Qihui Wang Bingjie Chen Zixiao Guo Yongsen Ruan Xuemei Lu Fuwen Wei Li Jin Le Kang Yongbiao Xue Guoping Zhao Ya-Ping Zhang | 2021 | Science China(Life Sciences)2021，64，9： | 1 |
| 6 | CRISPR-Cas9 sgRNA design and outcome assessment: Bioinformatics tools and aquaculture applications显示文摘The CRISPR-Cas9 genome editing has many advantages over its counterparts and could ultimately assist in disease control and molecular breeding in aquaculture.Single-guide RNA(sgRNA)design is presumably the most crucial task in a typical CRISPR-Cas9 experiment;an understanding of algorithms behind sgRNA design programs is thus essential for improved efficacy and specificity.We focus this review on the bioinformatics aspects in genome editing experiments and describe commonly used computational approaches and tools of sgRNA design and outcome assessment.We show an example of sgRNA design with optimal parameter settings and appropriate interpretation of results and present a brief overview of CRISPR-Cas9 applications,such as genetic improvement and sustainability in aquaculture.We discuss challenging issues,particularly in the context of computational biology,in the use of computational tools in CRISPR-based genome editing.This review provides a synthesis of bioinformatics tools used for CRISPR-Cas9 sgRNA design and outcome assessment and offers a general view of CRISPR-based applications in farmed fish,which are expected to facilitate genome editing programs and hence improve aquaculture breeding,production,and sustainability. | Mingkun Luo Jun Wang Zaijie Dong Chenghui Wang Guoqing Lu | 2022 | Aquaculture and Fisheries2022，7，2： | 0 |
| 7 | Health benefits from the rapid reduction in ambient exposure to air pollutants after China’s clean air actions:progress in efficacy and geographic equality显示文摘Clean air actions(CAAs)in China have been linked to considerable benefits in public health.However,whether the beneficial effects of CAAs are equally distributed geographically is unknown.Using high-resolution maps of the distributions of major air pollutants(fine particulate matter[PM_(2.5)]and ozone[O_(3)])and population,we aimed to track spatiotemporal changes in health impacts from,and geographic inequality embedded in,the reduced exposures to PM_(2.5)and O_(3)from 2013 to 2020.We used a method established by the Global Burden of Diseases Study.By analyzing the changes in loss of life expectancy(LLE)attributable to PM_(2.5)and O_(3),we calculated the gain of life expectancy(GLE)to quantify the health benefits of the air-quality improvement.Finally,we assessed the geographic inequality embedded in the GLE using the Gini index(GI).Based on risk assessments of PM_(2.5)and O_(3),during the first stage of CAAs(2013 to 2017),the mean GLE was 1.87 months.Half of the sum of the GLE was disproportionally distributed in about one quarter of the population exposed(GI 0.44).During the second stage of CAAs(2017 to 2020),the mean GLE increased to 3.94 months and geographic inequality decreased(GI 0.18).According to our assessments,CAAs were enhanced,from the first to second stages,in terms of not only preventing premature mortality but also ameliorating health inequalities.The enhancements were related to increased sensitivity to the health effects of air pollution and synergic control of PM_(2.5)and O_(3)levels.Our findings will contribute to optimizing future CAAs. | Tao Xue Ruohan Wang Meng Wang Yanying Wang Dan Tong Xia Meng Conghong Huang Siqi Ai Fangzhou Li Jingyuan Cao Mingkun Tong Xueqiu Ni Hengyi Liu Jianyu Deng Hong Lu Wei Wan Jicheng Gong Shiqiu Zhang Tong Zhu | 2024 | National Science Review2024，11，2： | 0 |
| 8 | Geochemical modeling to aid experimental design for multiple isotope tracer studies of coupled dissolution and precipitation reaction kinetics显示文摘It is a challenge to make thorough but efficient experimental designs for the coupled mineral dissolution and precipitation studies in a multi-mineral system, because it is difficult to speculate the best experimental duration, optimal sampling schedule, effects of different experimental conditions, and how to maximize the experimental outputs prior to the actual experiments. Geochemical modeling is an efficient and effective tool to assist the experimental design by virtually running all scenarios of interest for the studied system and predicting the experimental outcomes. Here we demonstrated an example of geochemical modeling assisted experimental design of coupled labradorite dissolution and calcite and clayey mineral precipitation using multiple isotope tracers. In this study, labradorite(plagioclase) was chosen as the reactant because it is both a major component and one of the most reactive minerals in basalt. Following our isotope doping studies of single minerals in the last ten years, initial solutions in the simulations were doped withmultiple isotopes(e.g., Ca and Si). Geochemical modeling results show that the use of isotope tracers gives us orders of magnitude more sensitivity than the conventional method based on concentrations and allows us to decouple dissolution and precipitation reactions at near-equilibrium condition. The simulations suggest that the precise unidirectional dissolution rates can inform us which rate laws plagioclase dissolution has followed. Calcite precipitation occurred at near-equilibrium and the multiple isotope tracer experiments would provide near-equilibrium precipitation rates, which was a challenge for the conventional concentration-based experiments. In addition, whether the precipitation of clayey phases is the rate-limiting step in some multi-mineral systems will be revealed. Overall, the modeling results of multimineral reaction kinetics will improve the understanding of the coupled dissolution–precipitation in the multi-mineral systems and the quality of geochemical modeling prediction of CO_(2) removal and storage efficacy in the basalt systems. | Mingkun Chen Peng Lu Yongchen Song Chen Zhu | 2024 | Acta Geochimica2024，43，1： | 0 |
| 9 | Potential Secretory Transporters and Biosynthetic Precursors of Biological Nitrification Inhibitor 1,9-Decanediol in Rice as Revealed by Transcriptome and Metabolome Analyses显示文摘Biological nitrification inhibitors(BNIs)are released from plant roots and inhibit the nitrification activity of microorganisms in soils,reducing NO_(3)^(‒)leaching and N2O emissions,and increasing nitrogenuse efficiency(NUE).Several recent studies have focused on the identification of new BNIs,yet little is known about the genetic loci that govern their biosynthesis and secretion.We applied a combined transcriptomic and metabolomic analysis to investigate possible biosynthetic pathways and transporters involved in the biosynthesis and release of BNI 1,9-decanediol(1,9-D),which was previously identified in rice root exudates.Our results linked four fatty acids,icosapentaenoic acid,linoleate,norlinolenic acid,and polyhydroxy-α,ω-divarboxylic acid,with 1,9-D biosynthesis and three transporter families,namely the ATP-binding cassette protein family,the multidrug and toxic compound extrusion family,and the major facilitator superfamily,with 1,9-D release from roots into the soil medium.Our finding provided candidates for further work on the genes implicated in the biosynthesis and secretion of 1,9-D and pinpoint genetic loci for crop breeding to improve NUE by enhancing 1,9-D secretion,with the potential to reduce NO_(3)^(‒)leaching and N2O emissions from agricultural soils. | DI Dongwei MA Mingkun ZHANG Xiaoyang LU Yufang Herbert J.KRONZUCKER SHI Weiming | 2024 | Rice science2024，31，1： | 0 |
| 10 | Back to Science in Searching for SARS-CoV-2 Origins显示文摘In recent decades,emerging and re-emerging human-infecting pathogens have been represented as huge threats to public health and have become a global concern(1).After outbreaks of two coronaviruses(CoVs),severe acute respiratory syndrome coronavirus(SARS-CoV)and Middle East respiratory syndrome coronavirus(MERS-CoV),severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)became the first-known pandemic hastening CoV with tremendous wrecking to the world(2).The origin tracing of these emerging pathogens is of great significance in infectious disease prevention and control(3–4).The origin of SARS-CoV-2 remains elusive after the more than 3-year pandemic,though scientists around the world are making great efforts.From the experience of studying many other infectious pathogens,origin tracing is systematic and time-consuming work.The supposed origins of many infectious pathogens are still in debate,including SARS-CoV and human immunodeficiency virus,etc(5). | William J Liu Wenwen Lei Xiaozhou He Peipei Liu Qihui Wang Zhiqiang Wu Yun Tan Shuhui Song Gary Wong Jian Lu Jingkun Jiang Qiang Wei Mingkun Li Juncai Ma Xiaozhong Peng Yixue Li Baoxu Huang Yigang Tong Jun Han Guizhen Wu | 2023 | China CDC weekly2023，5，14： | 0 |
| 11 | Genomic Epidemiology of SARS-CoV-2 in Pakistan显示文摘COVID-19 has swept globally and Pakistan is no exception.To investigate the initial introductions and transmissions of the SARS-CoV-2 in Pakistan,we performed the largest genomic epidemiology study of COVID-19 in Pakistan and generated 150 complete SARS-CoV-2 genome sequences from samples collected from March 16 to June 1,2020.We identified a total of 347 mutated positions,31 of which were over-represented in Pakistan.Meanwhile,we found over 1000 intra-host single-nucleotide variants(iSNVs).Several of them occurred concurrently,indicating possible interactions among them or coevolution.Some of the high-frequency iSNVs in Pakistan were not observed in the global population,suggesting strong purifying selections.The genomic epidemiology revealed five distinctive spreading clusters.The largest cluster consisted of 74 viruses which were derived from different geographic locations of Pakistan and formed a deep hierarchical structure,indicating an extensive and persistent nation-wide transmission of the virus that was probably attributed to a signature mutation(G8371T in ORF1ab)of this cluster.Furthermore,28 putative international introductions were identified,several of which are consistent with the epidemiological investigations.In all,this study has inferred the possible pathways of introductions and transmissions of SARS-CoV-2 in Pakistan,which could aid ongoing and future viral surveillance and COVID-19 control. | Shuhui Song Cuiping Li Lu Kang Dongmei Tian Nazish Badar Wentai Ma Shilei Zhao Xuan Jiang Chun Wang Yongqiao Sun Wenjie Li Meng Lei Shuangli Li Qiuhui Qi Aamer Ikram Muhammad Salman Massab Umair Huma Shireen Fatima Batool Bing Zhang Hua Chen Yun-Gui Yang Amir Ali Abbasi Mingkun Li Yongbiao Xue Yiming Bao | 2021 | Genomics, Proteomics & Bioinformatics2021，19，5： | 0 |
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